WO2022035997A1 - In vivo assembly of asgpr binding therapeutics - Google Patents

In vivo assembly of asgpr binding therapeutics Download PDF

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WO2022035997A1
WO2022035997A1 PCT/US2021/045602 US2021045602W WO2022035997A1 WO 2022035997 A1 WO2022035997 A1 WO 2022035997A1 US 2021045602 W US2021045602 W US 2021045602W WO 2022035997 A1 WO2022035997 A1 WO 2022035997A1
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compound
alkyl
moiety
pharmaceutically acceptable
selective moiety
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PCT/US2021/045602
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WO2022035997A9 (en
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Milind Deshpande
Mark George Saulnier
Kevin Tyler SPROTT
Jesse Jingyang CHEN
Soumya Ray
Jason Allan Wiles
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Avilar Therapeutics, Inc.
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Publication of WO2022035997A1 publication Critical patent/WO2022035997A1/en
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    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
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    • C07H9/06—Compounds containing a hetero ring sharing at least two hetero atoms with a saccharide radical the hetero ring containing nitrogen as ring hetero atoms

Definitions

  • This invention provides compounds that assemble together in vivo to form an ASGPR- binding compound that has an asialoglycoprotein receptor (ASGPR) binding ligand bound to an extracellular protein binding ligand for the selective degradation of the target extracellular protein in vivo to treat disorders mediated by the extracellular protein.
  • ASGPR asialoglycoprotein receptor
  • Intracellular protein degradation is a natural and highly regulated, essential process that maintains cellular homeostasis.
  • the selective identification and removal of damaged, misfolded, or excess proteins within the cell is achieved via the ubiquitin-proteasome pathway (UPP).
  • UPP ubiquitin-proteasome pathway
  • the UPP is central to the regulation of almost all intracellular processes.
  • a number of companies and institutions have designed intracellular protein degrading molecules that take advantage of this natural process to degrade disease-mediating proteins intracellularly by linking a ligand to the protein to be degraded by a protein in the UPP. Examples are found in U.S. 2014/0356322 assigned to Yale University, GlaxoSmithKline, and Cambridge Enterprise Limited University of Cambridge; Buckley et al. (J. Am. Chem. Soc.
  • Nonlimiting examples of extracellular proteins include immunoglobulins and cytokines, which can play a strong role in creating or exacerbating serious diseases.
  • Immunoglobulins include IgA, IgG, IgD, IgE, and IgM.
  • Cytokines are cell signaling peptides secreted into the bloodstream which cannot cross the lipid bilayer of cells to enter the cytoplasm, for example, interferons, interleukins, chemokines, lymphokines, MIP, and tumor necrosis factors. Cytokines are involved in autocrine, paracrine, and endocrine signaling. They mediate immunity, inflammation, and hematopoiesis. Cytokines are produced by immune cells (macrophages, B-cells, T-cells, and mast cells), endothelial cells, fibroblasts and stromal cells.
  • the asialoglycoprotein receptor is a Ca 2+ -dependent lectin that is primarily expressed in parenchymal hepatocyte cells.
  • the main role of ASGPRs is to help regulate serum glycoprotein levels by mediating endocytosis of desialylated glycoproteins (as depicted below).
  • the receptor binds ligands with a terminal galactose or N-acetylgalactosamine.
  • the C 3 - and C 4 - hydroxyl groups bind to Ca 2+ .
  • the C 2 N-acetyl position has also been considered important to binding activity.
  • N-acetyl galactosamine Asialoglycoproteins bind to ASGPRs and are then cleared by receptor-mediated endocytosis.
  • the receptor and the protein are dissociated in the acidic endosomal compartment and the protein is eventually degraded by lysosomes.
  • the receptor is endocytosed and recycled constitutively from the endosome back to the plasma membrane about every 15 minutes regardless of whether or not a glycoprotein is bound.
  • the internalization rate of the receptor is dependent on the presence of ligand. In a 1998 study, the internalization rate of the protein without ligand was less than one-third of the rate of internalization of the ligandreceptor complex (Bider et al. FEBS Letters, 1998, 434, 37).
  • the ASGPR is comprised of two homologous subunits with 58% sequence identity known as Hl and H2. Various ratios of Hl and H2 form functional homo- and hetero-oligomers with different conformations, but the most abundant conformation is a trimer composed of two Hl and one H2 subunits.
  • the ASGPR is composed of a cytoplasmic domain, a transmembrane domain, a stalk region, and a carbohydrate recognition domain (CRD). Both the Hl and H2 subunit are required to form the CRD, and therefore, co-expression of both subunits is a requirement for endocytosis of asialoglycoproteins.
  • the crystal structure of the CRD region was published, revealing three Ca 2+ binding sites (Meier et al. J. Mol. Biol. 2000, 300, 857).
  • the receptor affinity for a ligand may be influenced by the ligand’s valency.
  • Lee et al. J. Biol. Chem., 1983, 258, 199
  • the ICso ranged from approximately 1 mM for monoantennary oligosaccharides to approximately 1 nM for triantennary oligosaccharides in an assay studying the binding ability of certain analogs to rabbit hepatocytes.
  • ASGPRs are primarily expressed on hepatocytes and are minimally found on cells outside of the liver. Hepatocytes exhibit a high exposition of ASGPR binding cites (approximately 100,000 - 500,000 binding sites per cell).
  • U.S. Patent 5,985,826 to NeoRx Corporation describes the use of hepatic-directed systems that include a therapeutic agent with activity against a liver disease or disorder that is bound to a director moiety.
  • the director moiety which in one embodiment is a galactose or galactose derivative, directs the active agent to the liver, where the active agent acts as a therapeutic agent that is then removed from circulation with assistance from the director moiety.
  • U.S. Patent Nos. 9,340,553; 9,617,293; 10,039,778; and 10,376,531 and U.S. Application US2019/0321382 assigned to Pfizer Inc. describe certain bicyclic, bridged ketal derivatives of GabVAc as targeting agents for the ASGPR receptor that in one embodiment are bound to a linker and/or a therapeutic agent such as a small molecule, an amino acid sequence, a nucleic acid sequence, an antibody, or a fluorescent probe.
  • the linker of the drug delivery system can be monovalent, divalent, or trivalent.
  • the disclosure also includes a method for the treatment of a liver disease or condition comprising administering the targeted drug delivery system.
  • Pfizer also developed PK2, a targeted drug delivery system wherein doxorubicin is linked via a lysosomally degradable tetrapeptide sequence to N-(2-hydroxypropyl)methacrylamide copolymers bearing galactosamine as the targeting agent.
  • PK2 a targeted drug delivery system wherein doxorubicin is linked via a lysosomally degradable tetrapeptide sequence to N-(2-hydroxypropyl)methacrylamide copolymers bearing galactosamine as the targeting agent.
  • Conjugates of paclitaxel covalently bound to one, two, or three units of GabVAc via a short linker are described in Petrov et al. (Bioorganic and Medicinal Chemistry Letters, 2018, 28, 382). The analogs were cytotoxic against human hepatocellular carcinoma cells and showed high affinity for ASGPR via surface plasmon resonance.
  • Avilar Therapeutics has filed a PCT Application WO2021/155317 describing the use of ASGPR ligands attached to Extracellular Protein Targeting Ligands for the degradation of the target extracellular protein.
  • Pfizer Inc. and Wave Life Sciences Ltd. jointly disclosed the use of selected ASGPR ligands attached to oligonucleotides in PCT Applications WO 2018/223073 and WO2018/223081.
  • the ‘ 073 application describes the use of APOC3 oligonucleotides attached to an ASGPR targeting ligand for selective delivery to the liver and the ‘081 application describes the use of PNPLA3 oligonucleotides attached to an ASGPR targeting ligand.
  • PCT Application WO 2018/223056 assigned to Wave Sciences Ltd. describes compositions comprising oligonucleotides for RNA interference and in one embodiment, the oligonucleotide is attached to an ASGPR targeting ligand.
  • ASGPR-targeted therapy using modified glycoproteins as the target agenting are reviewed in Huang etal. (Bioconjugate Chem. 2017, 28, 283).
  • a number of multivalent ligands that have been developed are discussed in addition to the relevant properties for drug delivery, including linker length and spatial geometry of the scaffold.
  • WO 2019/199621 and WO 2019/199634 which describe the use of certain ASGPR targeting ligands covalently bound to a circulating protein binding moiety. Once the circulating protein binding moiety binds the circulating protein, the complex passes to the liver where it is recognized by ASGPR and degraded via the endo- lysosomal pathway.
  • the ‘621 application describes circulating protein binding moieties that are capable of targeting macrophage migration inhibitory factor (MIF) and/or immunoglobulin G (IgG).
  • MIF macrophage migration inhibitory factor
  • IgG immunoglobulin G
  • the ‘634 application describes the targeting of numerous circulating proteins including CD40L, TNF-a, PCSK9, VEGF, TGF-p, uPAR, PSMA, IL-2, GP120, TSP-1, and CXCL-2 using a drug delivery system comprising a circulating protein binding moiety covalently bound to a targeting ligand, which is a ASGPR targeting ligand. Additional publications describing the use of ASGPR ligand containing heterobifunctional compounds include W02020/132100 and WO2021/142377.
  • the compound pair includes a compound with novel modifications of the exposition of the ASGPR binding ligand, referred to herein as R 2 or R 200 .
  • the invention provides an ASGPR binding ligand. In another aspect the invention provides an ASGPR binding ligands and an Extracellular Protein Targeting Ligand which when administered to a patient combine in vivo to create a therapeutic compound. In certain aspects the invention is the produced therapeutic compound itself.
  • the invention also includes a method to treat a patient in need thereof, comprising administering an effective amount of the component compounds as well as the method to treat the patient with the therapeutic compound produced in vivo.
  • the ASGPR binding ligands used in the present invention include derivatives of six-carbon pyranose moieties, specifically galactose and talose. These two sugars, shown below, differ only in the stereochemistry of the C 2 substituent.
  • the “down” C 2 configuration corresponds to the stereochemistry of galactose, while the C 2 substituent in the “up” configuration corresponds to the stereochemistry of talose. It has been discovered that certain substituents at the C 2 position of these two sugars improves the binding of the ligand ASGPR.
  • ASGPR binding ligands have been modified to present a selective moiety that in the body will react with the complementary selective moiety that has been installed on an Extracellular Protein Targeting Ligand.
  • selective linker moiety that the ASGPR ligand presents is “Selective Moiety A ” and the selective moiety that the Extracellular Targeting Ligand presents is “Selective Moiety B .”
  • Extracellular proteins that can be targeted according to the present invention include but are not limited to immunoglobulins such as IgA, IgG, IgD, IgE, and IgM, and derivatives thereof which retain the same basic function, and cytokines such as interferons, interleukins, chemokines, lymphokines, MIP, and tumor necrosis factors.
  • the extracellular protein is selected from IgA, IgG, IgE, TNF (a or p), IL-lb, IL-2, IFN-y, IL-6, VGEF, TGF-bl and PCSK-9.
  • Galactose-Based Molecules It has been discovered that sugars in the galactose stereochemistry with certain C 2 substituents are useful ligands for ASGPR. These molecules can react in vivo with an extracellular protein targeting ligand compound that has been modified to present a selective linking moiety, and resultant molecule can be used to recruit extracellular protein and degrade it in the liver.
  • X 1 is 1 to 5 contiguous atoms independently selected from O, S, N(R 6 ), and C(R 4 )(R 4 ), wherein if X 1 is 1 atom then X 1 is O, S, N(R 6 ), or C(R 4 )(R 4 ), if X 1 is 2 atoms then no more than 1 atom of X 1 is O, S, or N(R 6 ), if X 1 is 3, 4, or 5 atoms then no more than 2 atoms of X 1 are O, S, or N(R 6 );
  • R 2 is selected from
  • R 10 is selected from alkenyl, allyl, alkynyl, -NR 6 -alkenyl, -O-alkenyl, -NR 6 -alkynyl, -O-alkynyl, -NR 6 -heteroaryl, -NR 6 -aryl, -O-heteroaryl, -O-aryl, and -O-alkynyl, each of which R 10 is optionally substituted with 1, 2, 3, or 4 substituents;
  • R 1 and R 5 are independently selected from hydrogen, heteroalkyl, C 0 -C 6 alkyl-cyano, alkyl, alkenyl, alkynyl, haloalkyl, F, Cl, Br, I, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycle, heterocycloalkyl, haloalkoxy, -O-alkenyl, -O-alkynyl, C 0 -C 6 alkyl- OR 6 , C 0 -C 6 alkyl-SR 6 , C 0 -C 6 alkyl-NR 6 R 7 , C 0 -C 6 alkyl-C(0)R 3 , C 0 -C 6 alkyl-S(0)R 3 , C 0 -C 6 alkyl- C(S)R 3 , C 0 -C 6 alkyl-S(0) 2 R 3 , C 0 -C 6 alkyl-N(R 8 )-
  • R 3 at each occurrence is independently selected from hydrogen, alkyl, heteroalkyl, haloalkyl (including -CF 3 , -CHF2, -CH2F, -CH2CF 3 , -CH2CH2F, and -CF2CF 3 ), arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR 8 , and -NR 8 R 9 ;
  • R 4 is independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, haloalkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR 6 , -NR 6 R 7 , C(O)R 3 , S(O)R 3 , C(S)R 3 , and S(O) 2 R 3 ;
  • R 6 and R 7 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, haloalkyl, heteroaryl, heterocycle, -alkyl-OR 8 , - alkyl-NR 8 R 9 , C(O)R 3 , S(O)R 3 , C(S)R 3 , and S(O) 2 R 3 ;
  • R 8 and R 9 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocycle;
  • Cycle is a 3-8 membered fused cyclic group optionally substituted with 1, 2, 3, or 4 substituents; exemplary Cycle groups include carbocycle (e.g. cyclopropane, cyclohexane, or cyclohexene), heterocycle (e.g. oxetane, of piperazine), aryl (e.g. phenyl), or a heteroaryl group
  • carbocycle e.g. cyclopropane, cyclohexane, or cyclohexene
  • heterocycle e.g. oxetane, of piperazine
  • aryl e.g. phenyl
  • heteroaryl group e.g. phenyl
  • each Linked is a bond or a chemical moiety that covalently links the ASGPR ligand to Selective Moiety A , or Linker 17 , or Linker 19 ;
  • Selective Moiety A is selected from
  • cyclic group is a cycloalkyl, heterocycle, aryl, or heteroaryl group; each R 23 is independently alkyl or hydrogen; or two R 23 groups combine together to form a cycle;
  • R 24 , R 25 , and R 26 are independently selected at each instance from hydrogen, alkyl, aryl, heteroaryl, heterocycle, and halogen, each of which R 24 , R 25 , and R 26 groups other than hydrogen are optionally substituted with 1, 2, 3, or 4 substituents; or R 24 and R 25 together form a double bond; y is 0, 1, 2, 3, 4, 5, 6, 7, or 8; when compounds are “optionally substituted” they may be substituted as allowed by valence by groups selected from alkyl (including Ci-C4alkyl), alkenyl (including C2-C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR 6 , F, Cl, Br, I,
  • the optional substituents are independently selected from R 100 wherein R 100 is selected at each instance from alkyl (including Ci-C4alkyl), alkenyl (including C2- C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR 6 , F, Cl,
  • the compounds of Formula I, II, III, IV, V, VI, and VI can react in vivo with a compound of Formula VII, wherein the compound of Formula VII is: or a pharmaceutically acceptable salt thereof; wherein:
  • Linker® is a bond or a chemical moiety that covalently links Selective Moiety® to an Extracellular Protein Targeting Ligand;
  • Extracellular Protein Targeting Ligand is a chemical moiety that binds to the targeted extracellular protein;
  • Selective Moiety B is selected from each of which Selective Moi ety B groups is optionally substituted with 1, 2, 3, or 4 substituents. or Selective Moiety B is selected from each of which Selective Moiety B group is optionally substituted with 1, 2, 3, or 4 substituents;
  • non-limiting pairs of selective moieties include:
  • Non-limiting examples of Connecting Moiety groups that results from combination i) or ii) above include:
  • Non-limiting examples of Connecting Moiety groups that results from combination iii) or iv) above include:
  • Non-limiting examples of Connecting Moiety groups that results from combination v) or vi) above include:
  • Non-limiting examples of Connecting Moiety groups that results from combination vii) or viii) above include:
  • Non-limiting examples of Connecting Moiety groups that results from combination ix) or x) above include:
  • a compound of Formula I-Bi, Formula II-Bi, Formula III-Bi, Formula IV-Bi, Formula V-Bi, or Formula VI-Bi is also provided:
  • Linker C is a chemical moiety that links each Linker A to Selective Moiety A ; and all other variables are as defined herein.
  • a compound of Formula I-Tri, Formula II-Tri, Formula III-Tri, Formula IV-Tri, Formula V-Tri, or Formula VI-Tri is also provided:
  • Linker D is a chemical moiety that links each Linker A to Selective Moiety A ; and all other variables are as defined herein.
  • a compound of the present invention of Formula I, II, III, IV, V, or VI or the bis version (Formula Bi, II-Bi, III-Bi, IV-Bi, V-Bi, or VLBi), or the tris version (Formula LTri, II-Tri, III- Tri, IV-Tri, V-Tri, VI-Tri) can react in vivo with a compound of Formula VII as described herein to deliver an ASGPR-binding Extracellular Protein degrader that binds to the Extracellular Protein, typically in the blood stream, and carries it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation.
  • Examples of methods to deliver the degraders of the present invention include, but are not limited to, oral, intravenous, buccal, sublingual, subcutaneous and transnasal.
  • Extracellular Protein Targeting Ligand binds the protein after reacting with the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version, according to the invention described herein
  • Extracellular Protein Targeting Ligand binds the protein before reacting with the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version, according to the invention described herein.
  • the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version binds to ASGPR after reacting with the Extracellular Protein Targeting Ligand according to the invention described herein.
  • the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version binds to ASGPR before reacting with the Extracellular Protein Targeting Ligand, according to the invention described herein.
  • sugars in the talose stereochemistry with specific C 2 substituents are useful ligands for ASGPR. These molecules can be used as ASGPR ligands or linked to an extracellular protein targeting ligand to recruit extracellular protein and degrade it in the liver.
  • the compounds of Formula I-d, Il-d, Ill-d, and IV-d can react in vivo with a compound of Formula VII, wherein the compound of Formula VII is: or a pharmaceutically acceptable salt thereof; wherein:
  • Linker® is a bond or a chemical moiety that covalently links Selective Moiety® to an Extracellular Protein Targeting Ligand
  • Extracellular Protein Targeting Ligand is a chemical moiety that binds to the targeted extracellular protein
  • Selective Moiety® is as defined herein.
  • the invention also provides a method of treating a patient comprising administering a compound of Formula I-d, ILd, IILd, IV-d, V-d, or Vl-d in combination with a compound of Formula VII, wherein:
  • a compound of Formula I-d-Bi, Formula II-d-Bi, Formula III-d-Bi, or Formula IV-d-Bi is also provided:
  • the Extracellular Protein Targeting Ligand is a small organic molecule (i.e., a non-biologic) or a peptide, protein or biologic or a binding fragment thereof, that does not comprise an oligonucleotide or aptamer.
  • a small organic molecule i.e., a non-biologic
  • a peptide, protein or biologic or a binding fragment thereof that does not comprise an oligonucleotide or aptamer.
  • extracellular protein targeting ligands is provided in Fig. 1.
  • the present invention focuses on the degradation of circulating extracellular proteins that mediate diseases involving immunity, inflammation, hematopoiesis/blood disorders (including those caused or exacerbated by blood vessel formation) and abnormal cellular proliferation such as tumors and cancer.
  • neither the Extracellular Protein nor the Extracellular Protein Targeting Ligand directly mediates intracellular gene editing such as CRISPR.
  • Extracellular Protein Targeting Ligand does not comprise an oligonucleotide or aptamer.
  • a compound of the present invention of Formula Ld, ILd, IILd, or IV-d or the bis version (Formula Ld-Bi, ILd-Bi, III-d-Bi, or IV-d-Bi), or the tris version (Formula I-d-Tri, ILd-Tri, IILd- Tri, or IV-d-Tri) can react in vivo with a compound of Formula VII as described herein to deliver an ASGPR-binding Extracellular Protein degrader that binds to the Extracellular Protein, typically in the blood stream, and carry it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation.
  • Examples of methods to deliver the degraders of the present invention include, but are not limited to, oral, parenteral, topical, systemic, intraaortal, intravenous, buccal, sublingual, subcutaneous and transnasal.
  • a method of treating a disorder mediated by an Extracellular Protein comprises administering (i) an effective dose of a compound or pharmaceutical composition of Formula I, II, III, IV, V, VI, Ld, ILd, IILd, or IV-d or its respective bi- and tri-version or a pharmaceutically acceptable salt thereof to a patient in combination with (ii) an effective dose of a compound or pharmaceutical composition of Formula VII or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein.
  • step (i) and step (ii) are carried out within a sufficient temporal proximity that allows the selected compound of Formula I, II, III, IV, V, VI, Ld, ILd, IILd, or IV-d or its respective bi- and tri- version or a pharmaceutically acceptable salt thereof to react with the selected compound of Formula VII.
  • Step (i) can be carried out before or after step (ii) as long as the two steps are sufficiently close in time that the compounds are able to assemble in vivo.
  • the Extracellular Protein Targeting Ligand binds the protein after reacting with the compound of Formula Ld, ILd, IILd, or IV-d, or the bis or tris version.
  • the Extracellular Protein Targeting Ligand binds the protein before reacting with the compound of Formula I-d, ILd, IILd, or IV-d, or the bis or tris version.
  • the compound of Formula I-d, ILd, IILd, or IV-d, or the bis or tris version binds to ASGPR after reacting with the Extracellular Protein Targeting Ligand.
  • the compound of Formula Ld, ILd, IILd, or IV-d, or the bis or tris version binds to ASGPR before reacting with the Extracellular Protein Targeting Ligand.
  • FIG. 1 A provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin A (IgA).
  • FIG. IB provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin G (IgG).
  • FIG. 1C-1G provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin E (IgE).
  • FIG. 1H-1M provides a non-limiting list of Extracellular Protein Targeting Ligands that target Tumor Necrosis Factor alpha (TNF-a).
  • FIG. IN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin- 1 (IL-1).
  • FIG.10- IS provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-2 (IL-2).
  • FIG.1T-1W provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-6 (IL-6).
  • IL-6 Interleukin-6
  • FIG. 1X-1AA provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interferon gamma (IFN-y).
  • FIG. 1BB-1KK provides a non-limiting list of Extracellular Protein Targeting Ligands that target Vascular endothelial growth factor (VEGF).
  • FIG. ILL provides a non-limiting list of Extracellular Protein Targeting Ligands that target Transforming growth factor beta (TGF- ⁇ 1).
  • FIG. 1MM-1PP provides a non-limiting list of Extracellular Protein Targeting Ligands that target proprotein convertase subtilisin kexin 9 (PCSK-9).
  • FIG. 1QQ-1SS provides a non-limiting list of Extracellular Protein Targeting Ligands that target Carboxypeptidase B2 (CPB2).
  • FIG. 1TT-1UU provides a non-limiting list of Extracellular Protein Targeting Ligands that target Cholinesterase (ChE).
  • FIG. 1VV-1WW provides a non-limiting list of Extracellular Protein Targeting Ligands that target C-C Motif Chemokine Ligand 2 (CCL2).
  • FIG. 1XX-1BBB provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor VII (Factor VII).
  • FIG. 1CCC-1FFF provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor IX (Factor IX).
  • FIG. 1GGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target CD40 Ligand (CD40L).
  • FIG. 1HHH-1JJJ provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor Xa (Factor Xa).
  • FIG. 1KKK-1MMM provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XI (Factor XI).
  • FIG. INNN and 1OOO provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XII (Factor XII).
  • FIG. 1PPP and 1QQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XIII (Factor XIII).
  • FIG. 1RRR-1UUU provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibroblast growth factor 1 (FGF1).
  • FGF1 fibroblast growth factor 1
  • FIG. 1 VVV-1XXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibroblast growth factor 2 (FGF2).
  • FGF2 fibroblast growth factor 2
  • FIG. 1YYY and 1ZZZ provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibronectin (FN1).
  • FIG. 1AAAA and 1BBBB provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-5 (IL-5).
  • FIG. 1CCCC provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-8 (IL-8).
  • FIG. 1DDDD and 1EEEE provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin- 10 (IL-10).
  • IL-10 Interleukin- 10
  • FIG. 1FFFF and 1GGGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-21 (IL-21).
  • FIG. 1HHHH and 1IIII provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-22 (IL-22).
  • FIG. 1 JJJJ- 1NNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Kallikrein 1.
  • FIG. 1OOOO provides a non-limiting list of Extracellular Protein Targeting Ligands that target lipoprotein lipase (LPL).
  • FIG. 1PPPP and 1QQQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target matrix metalloproteinase- 1 (MMP1).
  • MMP1 matrix metalloproteinase- 1
  • FIG. 1RRRR-1DDDDD provides a non-limiting list of Extracellular Protein Targeting Ligands that target Macrophage migration inhibitory factor (MIF), also known as glycosylationinhibiting factor (GIF), L-dopachrome isomerase, or phenylpyruvate tautomerase.
  • MIF Macrophage migration inhibitory factor
  • GAF glycosylationinhibiting factor
  • L-dopachrome isomerase phenylpyruvate tautomerase.
  • FIG. 1EEEEE-1GGGGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target neutrophil elastase (NE).
  • FIG. 1HHHHH and 1IIIII provides a non-limiting list of Extracellular Protein Targeting Ligands that target Prothrombin.
  • FIG. 1JJJJJ-1NNNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Plasma kallikrein (KLKB1).
  • FIG. 1OOOOO-1 SSSSS provides a non-limiting list of Extracellular Protein Targeting Ligands that target plasminogen (PLG).
  • FIG. 1TTTTT-1XXXXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target Plasminogen activator inhibitor- 1 (PALI), endothelial plasminogen activator inhibitor or serpin EL
  • FIG. 1 YYYY-1 AAAAAA provides a non-limiting list of Extracellular Protein Targeting Ligands that target phospholipases A2, for example type IB or group IB (PLA2, PA21B, PLA2G1B, PLA2-IB).
  • FIG. 1BBBBBB-1DDDDDD provides a non-limiting list of Extracellular Protein Targeting Ligands that target phospholipases A2, for example type IIA or group IIA (PLA2, PLA2A, PA2IIA, PLA2G2A, PLA2-IIA).
  • PHA2A type IIA or group IIA
  • PA2IIA PA2IIA
  • PLA2G2A PLA2-IIA
  • FIG. 1EEEEEE-1NNNNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target placental growth factor (PGF).
  • PPF placental growth factor
  • FIG. 1 OOOOOO- 1QQQQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target plasminogen activator, tissue type (tPA, PLAT).
  • FIG. 1RRRRRR provides a non-limiting list of Extracellular Protein Targeting Ligands that target Transforming growth factor beta 2 (TGF- ⁇ 2, TGFB2).
  • FIG. 1SSSSSS provides a non-limiting list of Extracellular Protein Targeting Ligands that target thrombospondin 1 (TSP1, TSP-1, THBS1).
  • FIG. 1TTTTTT-1XXXXXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target Urokinase or Urokinase-type plasminogen activator (UP A, uPA).
  • FIG. 2 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor B.
  • FIG. 3 A and 3B provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor D.
  • FIG. 4 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor H.
  • FIG. 5 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement component 5.
  • FIG. 6 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target TNF-alpha.
  • FIG. 7 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target factor XI.
  • FIG. 8 provides non-limiting examples of Formulas of the present invention. DETAILED DESCRIPTION OF THE INVENTION
  • the compound pair includes a compound with novel modifications of the exposition of the ASGPR ligand, referred to herein as R 2 or R 200 .
  • the invention thus includes each of the compounds individually that are administered to the patient which combined in vivo to create the therapeutic compound as well as the in vivo produced therapeutic compound itself.
  • the invention also includes a method to treat a patient in need thereof, comprising administering an effective amount of the component compounds as well as the method to treat the patient with the therapeutic compound produced in vivo.
  • novel compounds and their pharmaceutically acceptable salts and compositions that degrade disease-mediating extracellular proteins, as well as starting materials and intermediates for such compounds and their methods of use and processes of manufacture are provided.
  • This invention focuses on novel modifications of the C 2 -position of the ASGPR ligand, referred to herein as R 2 .
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from and
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from:
  • a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from: In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: or a pharmaceutically acceptable salt thereof.
  • a compound of the present invention is selected from: In certain embodiments, a compound of the present invention is selected from:
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from
  • a compound of the present invention is selected from In certain embodiments, a compound of the present invention is selected from
  • Selective Moiety A is: In certain embodiments Selective Moiety A is:
  • Selective Moiety 1 is: In certain embodiments Selective Moiety B is:
  • Selective Moiety B is In certain embodiments Selective Moiety A is a heterocycle substituted with two vicinal hydroxyl groups in a cis fashion and optionally substituted with 1, 2, 3, or 4 additional substituents for example,
  • Selective Moiety A is an aryl group substituted with two vicinal hydroxyl groups and optionally substituted with 1, 2, 3, or 4 additional substituents, for example
  • Selective Moiety A is wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the heterocycle.
  • Selective Moiety A is wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the bicycle.
  • Selective Moiety A is wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the aryl.
  • Selective Moiety A is wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the carbocycle.
  • Selective Moiety B is a heterocycle substituted with two geminal hydroxyl groups in a cis fashion and optionally substituted with 1, 2, 3, or 4 additional substituents for example,
  • Selective Moiety B is an aryl group substituted with two geminal hydroxyl groups and optionally substituted with 1, 2, 3, or 4 additional substituents, for example
  • the Selective Moiety A is selected from
  • the Selective Moiety A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the Selective Moiety A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the Selective Moiety A is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Selective Moiety A is n certain embodiments, the Selective Moiety B is selected from
  • the Selective Moiety B is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the Selective Moiety B is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the Selective Moiety B is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • Selective Moiety A is each of which Selective Moiety A group is optionally substituted with 1, 2, 3, or 4 substituents.
  • Selective Moiety A is optionally substituted with 1, 2, 3, or 4 substituents.
  • Selective Moiety B is optionally substituted with 1, 2, 3, or 4 substituents.
  • R 2 is selected from 5 and
  • R 2 is selected from:
  • R 2 is selected from wherein R is an optional substituent as defined herein.
  • R 2 is selected from wherein R is an optional substituent as defined herein.
  • R 2A is selected from
  • R 2 is selected from
  • R 2 is selected from Embodiments of Cycle
  • R 200 is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • R 200 is
  • R 200 is
  • R 200 is
  • R 200 is
  • R 200 is
  • R 200 is
  • R 200 is
  • R 200 is In certain embodiments R 200 is
  • R 200 is V.
  • Linker A and Linker® are independently selected from: wherein:
  • R 11 , R 12 , R 13 , R 14 , R 15 , R 16 , R 17 , R 18 , R 19 , and R 20 are independently at each occurrence selected from the group consisting of a bond, alkyl, -C(O)-, -C(O)O-, -OC(O)-, -SO2-, -S(O)-, -C(S)-, -C(O)NR 6 -, -NR 6 C(O)-, -O-, -S-, -NR 6 -, -C(R 21 R 21 )-, -P(O)(R 3 )O-, -P(O)(R 3 )-, a divalent residue of a natural or unnatural amino acid, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, heterocycle, heteroaryl, -CH 2 CH2-[O-(CH 2 )2]n-O-, -
  • R 21 is independently at each occurrence selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, F, Cl, Br, I, hydroxyl, alkoxy, azide, amino, cyano, -NR 6 R 7 , -NR 8 SO 2 R 3 , -NR 8 S(O)R 3 , haloalkyl, heteroalkyl, aryl, heteroaryl, and heterocycle; and the remaining variables are as defined herein.
  • Linker A is bond and Linker® is
  • Linker® is bond and Linker A is
  • a divalent residue of an amino acid is selected from
  • a divalent residue of a dicarboxylic acid is generated from a nucleophilic addition reaction:
  • a divalent residue of a dicarboxylic acid is generated from a condensation reaction:
  • Non-limiting embodiments of a divalent residue of a saturated dicarboxylic acid include: Non-limiting embodiments of a divalent residue of a saturated monocarboxylic acid is selected from butyric acid (-OC(O)(CH2)2CH2-), caproic acid (-OC(O)(CH2)4CH2-), caprylic acid (-OC(O)(CH2)SCH2-), capric acid (-OC(O)(CH2)sCH2-), lauric acid (-OC(0)(CH2)IOCH2-), myristic acid (-OC(O)(CH2)i2CH2-), pentadecanoic acid (-OC(O)(CH 2 )i3CH 2 -), palmitic acid (-OC(O)(CH 2 )i4CH 2 -), stearic acid (-OC(O)(CH 2 )i6CH 2 -), behenic acid (-OC(0)(CH2)2oCH2-), and lignoceric acid (-OC(O)(CH2)22CH2-);
  • Non-limiting embodiments of a divalent residue of a fatty acid include residues selected from linoleic acid, palmitoleic acid, vaccenic acid, paullinic acid, oleic acid, elaidic acid, gondoic acid, gadoleic acid, nervonic acid, myristoleic acid, and erucic acid:
  • Non-limiting embodiments of a divalent residue of a fatty acid is selected from linoleic acid (-C(O)(CH 2 ) 7 (CH) 2 CH 2 (CH) 2 (CH 2 ) 4 CH 2 -), docosahexaenoic acid (-C(O)(CH 2 ) 2 (CHCHCH 2 ) 6 CH 2 -), eicosapentaenoic acid (-C(O)(CH 2 ) 3 (CHCHCH 2 ) 5 CH 2 -), alpha-linolenic acid (-C(O)(CH 2 )7(CHCHCH 2 ) 3 CH 2 -) stearidonic acid (-C(O)(CH 2 ) 4 (CHCHCH 2 ) 4 CH 2 -), y-linolenic acid (-C(O)(CH 2 ) 4 (CHCHCH 2 ) 3 (CH 2 ) 3 CH 2 -), arachidonic acid (-C(O)(CH 2 )
  • Linker C is selected from: wherein:
  • R 22 is independently at each occurrence selected from the group consisting of alkyl, -C(O)N-, -NC(O)-, -N-, -C(R 21 )-, -P(O)O-, -P(O)-, -P(O)(NR 6 R 7 )N-, alkenyl, haloalkyl, aryl, heterocycle, and heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R 21 ; and the remaining variables are as defined herein.
  • Linker D is selected from: wherein:
  • R 32 is independently at each occurrence selected from the group consisting of alkyl, N + X", -C-, alkenyl, haloalkyl, aryl, heterocycle, and heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R 21 ;
  • X" is an anionic group, for example Br" or Cl' ; and all other variables are as defined herein.
  • Linker 13 is selected from:
  • Linker A is selected from: In certain embodiments Linker A is selected from:
  • Linker A is selected from: In certain embodiments Linker A is selected from:
  • Linker® is selected from:
  • Linker® is selected from:
  • Linker® is selected from:
  • Linker® is selected from:
  • Linker® is selected from:
  • Linker® -Linker A is selected from:
  • Linker® -Linker A is selected from: In certain embodiments Linker C is selected from:
  • Linker C is selected from: In certain embodiments Linker C is selected from:
  • Linker c -(Linker A )2 is selected from:
  • Linker c -(Linker A )2 is selected from:
  • Linker c -(Linker A )2 is selected from:
  • Linker c -(Linker A )2 is selected from:
  • the present invention includes compounds with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e., enriched.
  • isotopes examples include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, and chlorine, such as 2 H, 3 H, 11 C, 13 C, 14 C, 15 N, 17 O, 18 O, 18 F 31 P, 32 P, 35 S, 36 CI, and 125 I respectively.
  • isotopically labelled compounds can be used in metabolic studies (with, for example 14 C), reaction kinetic studies (with, for example 2 H or 3 H), detection or imaging techniques, such as positron emission tomography (PET) or single-photon emission computed tomography (SPECT) including drug or substrate tissue distribution assays, or in radioactive treatment of patients.
  • PET positron emission tomography
  • SPECT single-photon emission computed tomography
  • a 18 F labeled compound may be desirable for PET or SPECT studies.
  • Isotopically labeled compounds of this invention and prodrugs thereof can generally be prepared by carrying out the procedures disclosed in the schemes or in the examples and preparations described below by substituting a readily available isotopically labeled reagent for a non-isotopically labeled reagent.
  • isotopes of hydrogen for example, deuterium ( 2 H) and tritium ( 3 H) may optionally be used anywhere in described structures that achieves the desired result.
  • isotopes of carbon e.g., 13 C and 14 C, may be used.
  • the isotopic substitution is replacing hydrogen with a deuterium at one or more locations on the molecule to improve the performance of the drug, for example, the pharmacodynamics, pharmacokinetics, biodistribution, half-life, stability, AUC, Tmax, Cmax, etc.
  • the deuterium can be bound to carbon in a location of bond breakage during metabolism (an a-deuterium kinetic isotope effect) or next to or near the site of bond breakage (a P-deuterium kinetic isotope effect).
  • Isotopic substitutions for example deuterium substitutions, can be partial or complete. Partial deuterium substitution means that at least one hydrogen is substituted with deuterium.
  • the isotope is 80, 85, 90, 95 or 99% or more enriched in an isotope at any location of interest.
  • deuterium is 80, 85, 90, 95 or 99% enriched at a desired location. Unless otherwise stated, the enrichment at any point is above natural abundance, and in an embodiment is enough to alter a detectable property of the drug in a human.
  • the substitution of a hydrogen atom for a deuterium atom occurs within any variable group.
  • the alkyl residue may be deuterated (in nonlimiting embodiments, CDH 2 , CD 2 H, CD 3 , CD 2 CD 3 , CHDCHzD, CH 2 CD 3 , CHDCHD 2 , OCDH 2 , OCD 2 H, or OCD 3 etc.).
  • a variable group has a “ ‘ “ or an “a” designation, which in one embodiment can be deuterated.
  • the unsubstituted methylene carbon may be deuterated.
  • the compound of the present invention may form a solvate with solvents (including water). Therefore, in one embodiment, the invention includes a solvated form of the active compound.
  • solvate refers to a molecular complex of a compound of the present invention (including a salt thereof) with one or more solvent molecules.
  • solvents are water, ethanol, dimethyl sulfoxide, acetone and other common organic solvents.
  • hydrate refers to a molecular complex comprising a compound of the invention and water.
  • Pharmaceutically acceptable solvates in accordance with the invention include those wherein the solvent of crystallization may be isotopically substituted, e.g. D 2 O, de-acetone, de-DMSO.
  • a solvate can be in a liquid or solid form.
  • a dash that is not between two letters or symbols is used to indicate a point of attachment for a substituent.
  • substituted means that any one or more hydrogens on the designated atom or group is replaced with a moiety selected from the indicated group, provided that the designated atom's normal valence is not exceeded and the resulting compound is stable.
  • a pyridyl group substituted by oxo is a pyridone.
  • Alkyl is a branched, straight chain, or cyclic saturated aliphatic hydrocarbon group. In one embodiment, the alkyl contains from 1 to about 12 carbon atoms, more generally from 1 to about 6 carbon atoms, from 1 to about 4 carbon atoms, or from 1 to 3 carbon atoms. In one embodiment, the alkyl contains from 1 to about 8 carbon atoms. In certain embodiments, the alkyl is C 1 -C 2 , C 1 -C 3 , C 1 -C 4 , C 1 -C 5 or C 1 -C 6 .
  • the specified ranges as used herein indicate an alkyl group which is considered to explicitly disclose as individual species each member of the range described as a unique species.
  • C 1 -C 6 alkyl indicates a straight or branched alkyl group having from 1, 2, 3, 4, 5, or 6 carbon atoms and also a carbocyclic alkyl group of 3, 4, 5, or 6 carbon atoms and is intended to mean that each of these is described as an independent species.
  • Ci-C4alkyl indicates a straight or branched alkyl group having from 1, 2, 3, or 4 carbon atoms and is intended to mean that each of these is described as an independent species.
  • Co-Cn alkyl is used herein in conjunction with another group, for example, (C 3 -C 7 cycloalkyl)C 0 -C 4 alkyl, or -C 0 -C 4 alkyl(C 3 -C 7 cycloalkyl), the indicated group, in this case cycloalkyl, is either directly bound by a single covalent bond (Coalkyl), or attached by an alkyl chain in this case 1, 2, 3, or 4 carbon atoms.
  • Alkyls can also be attached via other groups such as heteroatoms as in -0-C 0 -C 4 alkyl(C 3 -C 7 cycloalkyl).
  • alkyl examples include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, n-pentyl, isopentyl, tert-pentyl, neopentyl, n-hexyl, 2-methylpentane, 3 -methylpentane, 2,2-dimethylbutane, 2, 3 -dimethylbutane, and hexyl.
  • alk When a term is used that includes “alk” it should be understood that “cycloalkyl” or “carbocyclic” can be considered part of the definition, unless unambiguously excluded by the context.
  • alkyl, alkenyl, alkynyl, alkoxy, alkanoyl, alkenloxy, haloalkyl, etc. can all be considered to include the cyclic forms of alkyl, unless unambiguously excluded by context.
  • Alkenyl is a branched or straight chain aliphatic hydrocarbon group having one or more carbon-carbon double bonds that may occur at a stable point along the chain. Nonlimiting examples are C 2 -C 8 alkenyl, C 2 -C 7 alkenyl, C 2 -C 6 alkenyl, C 2 -C 5 alkenyl and C 2 -C 4 alkenyl.
  • the specified ranges as used herein indicate an alkenyl group having each member of the range described as an independent species, as described above for the alkyl moiety. Examples of alkenyl include, but are not limited to, ethenyl and propenyl.
  • Alkynyl is a branched or straight chain aliphatic hydrocarbon group having one or more carbon-carbon triple bonds that may occur at any stable point along the chain, for example, C 2 - C 8 alkynyl or C 2 -C 6 alkynyl.
  • the specified ranges as used herein indicate an alkynyl group having each member of the range described as an independent species, as described above for the alkyl moiety.
  • alkynyl examples include, but are not limited to, ethynyl, propynyl, 1-butynyl, 2- butynyl, 3-butynyl, 1-pentynyl, 2-pentynyl, 3-pentynyl, 4-pentynyl, 1-hexynyl, 2-hexynyl, 3- hexynyl, 4-hexynyl and 5-hexynyl.
  • Alkoxy is an alkyl group as defined above covalently bound through an oxygen bridge (-O-).
  • alkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, 2-butoxy, t-butoxy, n-pentoxy, 2-pentoxy, 3 -pentoxy, isopentoxy, neopentoxy, n- hexoxy, 2-hexoxy, 3-hexoxy, and 3 -methylpentoxy.
  • an “alkylthio” or a “thioalkyl” group is an alkyl group as defined above with the indicated number of carbon atoms covalently bound through a sulfur bridge (-S-). In one embodiment, the alkoxy group is optionally substituted as described above.
  • Haloalkyl indicates both branched and straight-chain alkyl groups substituted with 1 or more halogen atoms, up to the maximum allowable number of halogen atoms.
  • Examples of haloalkyl include, but are not limited to, trifluoromethyl, monofluoromethyl, difluoromethyl, 2- fluoroethyl, and penta-fluoroethyl.
  • Aryl indicates an aromatic group containing only carbon in the aromatic ring or rings.
  • the aryl group contains 1 to 3 separate or fused rings and is 6 to 14 or 18 ring atoms, without heteroatoms as ring members.
  • the term “aryl” includes groups where a saturated or partially unsaturated carbocycle group is fused with an aromatic ring.
  • the term “aryl” also includes groups where a saturated or partially unsaturated heterocycle group is fused with an aromatic ring so long as the attachment point is the aromatic ring.
  • Such compounds may include aryl rings fused to a 4 to 7 or a 5 to 7-membered saturated or partially unsaturated cyclic group that optionally contains 1, 2 or 3 heteroatoms independently selected from N, O, B, P, Si and S, to form, for example, a 3, 4-methylenedi oxyphenyl group.
  • Aryl groups include, for example, phenyl and naphthyl, including 1 -naphthyl and 2-naphthyl.
  • aryl groups are pendant.
  • An example of a pendant ring is a phenyl group substituted with a phenyl group.
  • bicycle refers to a ring system wherein two rings are fused together and each ring is independently selected from carbocycle, heterocycle, aryl, and heteroaryl.
  • Non-limiting examples of bicycle groups include:
  • bivalent bicycle groups include:
  • heterocycle refers to saturated and partially saturated heteroatom-containing ring radicals, where the heteroatoms may be selected from N, S, and O.
  • heterocycle includes monocyclic 3-12 membered rings, as well as bicyclic 5-16 membered ring systems (which can include fused, bridged, or spiro, bicyclic ring systems). It does not include rings containing - O-O- or -S-S- portions.
  • saturated heterocycle groups include saturated 4- to 7- membered monocyclic groups containing 1 to 4 nitrogen atoms [e.g., pyrrolidinyl, imidazolidinyl, piperidinyl, pyrrolinyl, azetidinyl, piperazinyl, and pyrazolidinyl]; saturated 4 to 6-membered monocyclic groups containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms [e.g., morpholinyl]; saturated 3 to 6-membered heteromonocyclic group containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms [e.g., thiazolidinyl].
  • nitrogen atoms e.g., pyrrolidinyl, imidazolidinyl, piperidinyl, pyrrolinyl, azetidinyl, piperazinyl, and pyrazolidinyl
  • partially saturated heterocycle radicals include but are not limited to, dihydrothienyl, dihydropyranyl, dihydrofuryl, and dihydrothiazolyl.
  • partially saturated and saturated heterocycle groups include but are not limited to, pyrrolidinyl, imidazolidinyl, piperidinyl, pyrrolinyl, pyrazolidinyl, piperazinyl, morpholinyl, tetrahydropyranyl, thiazolidinyl, dihydrothienyl, 2,3 -dihydro-benzofl, 4]dioxanyl, indolinyl, isoindolinyl, dihydrobenzothienyl, dihydrobenzofuryl, isochromanyl, chromanyl, 1,2- dihydroquinolyl, 1,2, 3, 4- tetrahydro-isoquinolyl, 1 ,2,3,4-tetrahydro-quinolyl, 2, 3, 4, 4a, 9,9a
  • “Bicyclic heterocycle” includes groups wherein the heterocyclic radical is fused with an aryl radical wherein the point of attachment is the heterocycle ring. “Bicyclic heterocycle” also includes heterocyclic radicals that are fused or bridged with a carbocycle radical. For example partially unsaturated condensed heterocyclic group containing 1 to 5 nitrogen atoms, for example, indoline, isoindoline, partially unsaturated condensed heterocyclic group containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms, partially unsaturated condensed heterocyclic group containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms, and saturated condensed heterocyclic group containing 1 to 2 oxygen or sulfur atoms.
  • bicyclic heterocycles include:
  • bicyclic heterocycle includes cis and trans diastereomers.
  • Non-limiting examples of chiral bicyclic heterocycles include:
  • Heteroaryl refers to a stable monocyclic, bicyclic, or multicyclic aromatic ring which contains from 1 to 3, or in some embodiments from 1, 2, or 3 heteroatoms selected from N, O, S, B, and P (and typically selected from N, O, and S) with remaining ring atoms being carbon, or a stable bicyclic or tricyclic system containing at least one 5, 6, or 7 membered aromatic ring which contains from 1 to 3, or in some embodiments from 1 to 2, heteroatoms selected from N, O, S, B or P with remaining ring atoms being carbon.
  • the only heteroatom is nitrogen.
  • the only heteroatom is oxygen.
  • the only heteroatom is sulfur.
  • Monocyclic heteroaryl groups typically have from 5 or 6 ring atoms.
  • bicyclic heteroaryl groups are 8- to 10-membered heteroaryl groups, that is, groups containing 8 or 10 ring atoms in which one 5, 6, or 7-member aromatic ring is fused to a second aromatic or non-aromatic ring wherein the point of attachment is the aromatic ring.
  • the total number of S and O atoms in the heteroaryl group exceeds 1, these heteroatoms are not adjacent to one another.
  • the total number of S and O atoms in the heteroaryl group is not more than 2.
  • the total number of S and O atoms in the aromatic heterocycle is not more than 1.
  • heteroaryl groups include, but are not limited to, pyridinyl (including, for example, 2-hydroxypyridinyl), imidazolyl, imidazopyridinyl, pyrimidinyl (including, for example, 4-hydroxypyrimidinyl), pyrazolyl, triazolyl, pyrazinyl, furyl, thienyl, isoxazolyl, thiazolyl, oxadiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, tetrahydroisoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazoly
  • Heteroarylalkyl is an alkyl group as described herein substituted with a heteroaryl group as described herein.
  • Arylalkyl is an alkyl group as described herein substituted with an aryl group as described herein.
  • Heterocycloalkyl is an alkyl group as described herein substituted with a heterocyclo group as described herein.
  • heteroalkyl refers to an alkyl, alkenyl, alkynyl, or haloalkyl moiety as defined herein wherein a CH2 group is either replaced by a heteroatom or a carbon atom is substituted with a heteroatom for example, an amine, carbonyl, carboxy, oxo, thio, phosphate, phosphonate, nitrogen, phosphorus, silicon, or boron.
  • the only heteroatom is nitrogen.
  • the only heteroatom is oxygen.
  • the only heteroatom is sulfur.
  • heteroalkyl is used to indicate a heteroaliphatic group (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-20 carbon atoms.
  • heteroalkyl moieties include polyethylene glycol, polyalkylene glycol, amide, polyamide, polylactide, polyglycolide, thioether, ether, alkyl-heterocycle-alkyl, -O-alkyl-O-alkyl, alkyl-O-haloalkyl, etc.
  • compounds When compounds are “optionally substituted” they may be substituted as allowed by valence by groups selected from alkyl (including Ci-C4alkyl), alkenyl (including C2-C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR 6 , F, Cl, Br, I, substituent is selected such that a stable compound results.
  • alkyl including Ci-C4alkyl
  • alkenyl including C2-C4alkenyl
  • alkynyl including C2-C4alkynyl
  • haloalkyl including Ci-C4haloalkyl
  • Non-limiting examples of optionally substituted CH2 groups include:
  • Non-limiting examples of optionally substituted -S- groups include:
  • a “dosage form” means a unit of administration of an active agent.
  • dosage forms include tablets, capsules, injections, suspensions, liquids, emulsions, implants, particles, spheres, creams, ointments, suppositories, inhalable forms, transdermal forms, buccal, sublingual, topical, gel, mucosal, and the like.
  • a “dosage form” can also include an implant, for example an optical implant.
  • “Pharmaceutical compositions” are compositions comprising at least one active agent, and at least one other substance, such as a carrier.
  • the present invention includes pharmaceutical compositions of the described compounds.
  • “Pharmaceutical combinations” are combinations of at least two active agents which may be combined in a single dosage form or provided together in separate dosage forms with instructions that the active agents are to be used together to treat any disorder described herein.
  • a “pharmaceutically acceptable salt” is a derivative of the disclosed compound in which the parent compound is modified by making inorganic and organic, pharmaceutically acceptable, acid or base addition salts thereof.
  • the salts of the present compounds can be synthesized from a parent compound that contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting free acid forms of these compounds with a stoichiometric amount of the appropriate base (such as Na, Ca, Mg, or K hydroxide, carbonate, bicarbonate, or the like), or by reacting free base forms of these compounds with a stoichiometric amount of the appropriate acid. Such reactions are typically carried out in water or in an organic solvent, or in a mixture of the two.
  • Salts of the present compounds further include solvates of the compounds and of the compound salts.
  • pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like.
  • the pharmaceutically acceptable salts include salts which are acceptable for human consumption and the quaternary ammonium salts of the parent compound formed, for example, from inorganic or organic acids.
  • salts examples include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, mesylic, esylic, besylic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, HOOC-(CH 2 )I-4- COOH, and the like, or using a different acid that produces the same counterion.
  • inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic
  • carrier applied to pharmaceutical compositions/combinations of the invention refers to a diluent, excipient, or vehicle with which an active compound is provided.
  • a “pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition/combination that is generally safe, acceptable for human consumption, and neither biologically nor otherwise inappropriate for administration to a host, typically a human. In one embodiment, an excipient is used that is acceptable for veterinary use.
  • a “patient” or “host” or “subject” is a human or non-human animal in need of treatment or prevention of any of the disorders as specifically described herein. Typically the host is a human.
  • a “patient” or “host” or “subject” also refers to for example, a mammal, primate (e.g., human), cow, sheep, goat, horse, dog, cat, rabbit, rat, mice, bird and the like.
  • a “therapeutically effective amount” of a compound, pharmaceutical composition, or combination of this invention means an amount effective, when administered to a host, provides a therapeutic benefit such as an amelioration of symptoms or reduction or dimunition of the disease itself.
  • alkyl is a Ci-Cioalkyl, C 1 -C 9 alkyl, C 1 -C 8 alkyl, C 1 -C 7 alkyl, C 1 -C 6 alkyl, C 1 -C 5 alkyl, C 1 -C 4 alkyl, C 1 -C 3 alkyl, or C 1 -C 2 alkyl. In one embodiment “alkyl” has one carbon.
  • alkyl has two carbons.
  • alkyl has three carbons.
  • alkyl has four carbons.
  • alkyl has five carbons.
  • alkyl has six carbons.
  • alkyl include: methyl, ethyl, propyl, butyl, pentyl, and hexyl.
  • alkyl examples include: isopropyl, isobutyl, isopentyl, and isohexyl.
  • alkyl examples include: ec-butyl, sec-pentyl, and sec-hexyl.
  • alkyl examples include: tert-butyl, tert-pentyl, and tert-hexyl.
  • alkyl include: neopentyl, 3 -pentyl, and active pentyl.
  • the “alkyl” group is optionally substituted.
  • haloalkyl is a C 1 -C 10 haloalkyl, C 1 -C 9 haloalkyl, C 1 -C 8 haloalkyl, C 1 - C 7 haloalkyl, C 1 -C 6 haloalkyl, C 1 -C 5 haloalkyl, C 1 -C 4 haloalkyl, C 1 -C 3 haloalkyl, and C 1 - C 2 haloalkyl.
  • haloalkyl has one carbon
  • haloalkyl has one carbon and one halogen.
  • haloalkyl has one carbon and two halogens.
  • haloalkyl has one carbon and three halogens.
  • haloalkyl has two carbons.
  • haloalkyl has three carbons.
  • haloalkyl has four carbons.
  • haloalkyl has five carbons. In one embodiment “haloalkyl” has six carbons.
  • haloalkyl include:
  • haloalkyl include:
  • haloalkyl include:
  • Non-limiting examples of 5 membered “heteroaryl” groups include pyrrole, furan, thiophene, pyrazole, imidazole, triazole, isoxazole, oxazole, oxadiazole, oxatriazole, isothiazole, thiazole, thiadiazole, and thiatriazole.
  • heteroaryl is a 6 membered aromatic group containing 1, 2, or 3 nitrogen atoms (i.e. pyridinyl, pyridazinyl, triazinyl, pyrimidinyl, and pyrazinyl).
  • Non-limiting examples of 6 membered “heteroaryl” groups with 1 or 2 nitrogen atoms include:
  • heteroaryl is a 9 membered bicyclic aromatic group containing 1 or
  • heteroaryl groups that are bicyclic include indole, benzofuran, isoindole, indazole, benzimidazole, azaindole, azaindazole, purine, isobenzofuran, benzothiophene, benzoisoxazole, benzoisothiazole, benzooxazole, and benzothiazole.
  • heteroaryl groups that are bicyclic include:
  • heteroaryl groups that are bicyclic include:
  • heteroaryl groups that are bicyclic include:
  • heteroaryl is a 10 membered bicyclic aromatic group containing 1 or 2 atoms selected from nitrogen, oxygen, and sulfur.
  • heteroaryl groups that are bicyclic include quinoline, isoquinoline, quinoxaline, phthalazine, quinazoline, cinnoline, and naphthyridine.
  • heteroaryl groups that are bicyclic include: Embodiments of “heterocycle”
  • heterocycle refers to a cyclic ring with one nitrogen and 3, 4, 5, 6, 7, or 8 carbon atoms.
  • heterocycle refers to a cyclic ring with one nitrogen and one oxygen and 3, 4, 5, 6, 7, or 8 carbon atoms.
  • heterocycle refers to a cyclic ring with two nitrogens and 3, 4, 5, 6, 7, or 8 carbon atoms.
  • heterocycle refers to a cyclic ring with one oxygen and 3, 4, 5, 6, 7, or 8 carbon atoms.
  • heterocycle refers to a cyclic ring with one sulfur and 3, 4, 5, 6, 7, or 8 carbon atoms.
  • heterocycle examples include aziridine, oxirane, thiirane, azetidine, 1,3- diazetidine, oxetane, and thietane.
  • heterocycle examples include pyrrolidine, 3 -pyrroline, 2- pyrroline, pyrazolidine, and imidazolidine.
  • heterocycle examples include tetrahydrofuran, 1,3 -di oxolane, tetrahydrothiophene, 1,2-oxathiolane, and 1,3 -oxathiolane.
  • heterocycle examples include piperidine, piperazine, tetrahydropyran, 1,4-dioxane, thiane, 1,3-dithiane, 1,4-dithiane, morpholine, and thiomorpholine.
  • heterocycle examples include indoline, tetrahydroquinoline, tetrahydroisoquinoline, and dihydrobenzofuran wherein the point of attachment for each group is on the heterocyclic ring.
  • heterocycle is a “heterocycle” group.
  • heterocycle also include:
  • heterocycle also include:
  • heterocycle also include:
  • heterocycle includes:
  • heterocycle includes:
  • aryl is a 6 carbon aromatic group (phenyl).
  • aryl is a 10 carbon aromatic group (naphthyl). In one embodiment “aryl” is a 6 carbon aromatic group fused to a heterocycle wherein the point of attachment is the aryl ring.
  • Non-limiting examples of “aryl” include indoline, tetrahydroquinoline, tetrahydroisoquinoline, and dihydrobenzofuran wherein the point of attachment for each group is on the aromatic ring.
  • arylalkyl include:
  • arylalkyl refers to a 2 carbon alkyl group substituted with an aryl group.
  • arylalkyl include:
  • extracellular proteins can cause, modulate, or amplify diseases in vivo, such as abnormal cellular proliferation such as tumors and cancer, autoimmune disorders, inflammation, and aging-related diseases.
  • extracellular proteins such as growth factors, cytokines, and chemokines bind to cell surface receptors, often initiating aberrant signaling in multiple diseases such as cancer and inflammation.
  • the Extracellular Protein of interest binds to a compound of Formula VII:
  • the compound of Formula VII can react in vivo with a compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d, or a bis or tris version thereof with the appropriate Selective Moiety A to form an extracellular protein degrading molecule, wherein the extracellular protein that is degraded is the protein that binds the Extracellular Protein Targeting Ligand.
  • the extracellular protein degraders described herein or their pharmaceutically acceptable salt and/or its pharmaceutically acceptable compositions can be used to treat a disorder which is mediated by the selected Target Protein that binds to the Extracellular Targeting Ligand.
  • the described degraders are capable of targeting specific extracellular Target Proteins that mediate pathological disorders for lysosomal degradation.
  • the selected extracellular Target Proteins may modulate a disorder in a human via a mechanism of action such as modification of a biological pathway, pathogenic signaling, or modulation of a signal cascade or cellular entry.
  • the Target Protein is a protein that is not druggable in the classic sense in that it does not have a binding pocket or an active site that can be inhibited or otherwise bound, and cannot be easily allosterically controlled.
  • the Target Protein is a protein that is drugable in the classic sense, yet for therapeutic purposes, degradation of the protein is preferred to inhibition.
  • the extracellular Target Protein is recruited with a Targeting Ligand, which is a ligand for the extracellular Target Protein.
  • the Targeting Ligand binds the Target Protein in a non-covalent fashion.
  • the Target Protein is covalently bound to the Targeting Ligand in a manner that can be irreversible or reversible.
  • a method to treat a host with a disorder mediated by an extracellular Target Protein includes administering an effective amount of a degrader targeting an extracellular protein or its pharmaceutically acceptable salt described herein to the host, typically a human, optionally in a pharmaceutically acceptable composition.
  • the extracellular Target Protein can be any amino acid sequence to which the degrader comprising a Targeting Ligand can be bound which through degradation thereof, results in a beneficial therapeutic effect.
  • the Target Protein is a non-endogenous peptide such as that from a pathogen or toxin.
  • the Target Protein can be an endogenous protein that mediates a disorder.
  • the endogenous protein can be either the normal form of the protein or an aberrant form.
  • the Target Protein can be an extracellular mutant protein, or a protein, for example, where a partial, or full, gain-of-function or loss-of- function is encoded by nucleotide polymorphisms.
  • the degrader targets the aberrant form of the protein and not the normal form of the protein.
  • the Targeting Ligand is a ligand which covalently or non-covalently binds to a Target Protein which has been selected for lysosomal degradation.
  • a Targeting Ligand is a small molecule or moiety (for example a peptide, nucleotide, antibody fragment, aptamer, biomolecule, or other chemical structure) that binds to a Target Protein, and wherein the Target Protein is a mediator of disease in a host as described in detail below.
  • Exemplary Target Ligands are provided in Fig. 1.
  • Extracellular Protein Targeting Ligand is not an oligomer.
  • neither the Extracellular Protein nor the Extracellular Protein Targeting Ligand directly mediates intracellular gene editing such as CRISPR.
  • the Extracellular Protein Target Ligand is covalently bound to Linker® in the compounds of Formula VII through the Anchor Bond (which is the chemical bond between the Extracellular Protein Target Ligand and Linker B). This bond can be placed at any location on the ligand that does not unacceptably disrupt the ability of the Extracellular Protein Target Ligand to bind to the Extracellular Protein Target.
  • the Anchor Bond is depicted on the nonlimiting examples of Extracellular Protein Target Ligands in Figure 1 as:
  • the exemplary extracellular proteins targeted for medical therapy described below have characterizing structural information in the well-known Protein Data Bank (“PDB”), which is a database for the three-dimensional structural information for large biological molecules such as proteins and nucleic acids.
  • PDB includes x-ray crystallography and other information submitted by scientists around the world, and is freely accessible. See for example www.rcsb.or ; www.wwpdb.org and www.uniprot.org.
  • PDB codes for example provided in Section ** or in the Data Bank itself, and technical references provided herein or otherwise publicly available, the skilled artisan can determine appropriate locations where the Extracellular Protein Target Ligand can be linked through an Anchor Bond to Linker B.
  • published references describe how a range of ligands bind to the target proteins, and from this information, one can determine reasonable Anchor Bond locations.
  • the skilled artisan can use available visualization tools, including those available on the PDB website, to determine where the Extracellular Protein Targeting Ligand docks into to the Extracellular Protein.
  • the skilled artisan can also import the crystal structure and the selected Extracellular Protein Targeting Ligand of interest into modeling software (including for example PyMOL, Glide, Maestro, RasMol, Visual Molecular Dynamics, Jmol, and AutoDock) to determine what portion of the Extracellular Protein Targeting Ligand is bound to the Extracellular Protein.
  • the ASGPR ligand is then bound through the Linker and the Anchor Bond at a point that does not unduly adversely affect binding to the extracellular protein.
  • Immunoglobulin A (IgA)
  • the Target Protein is human immunoglobulin A (IgA).
  • IgA is an antibody that plays a crucial role in the immune function of mucous membranes. The amount of IgA produced in association with mucosal membranes is greater than all other types of antibody combined.
  • IgA has two subclasses (IgAl and IgA2) and can be produced as a monomeric as well as a dimeric form. The IgA dimeric form is the most prevalent. In the blood, IgA interacts with an Fc receptor called FcaRI (or CD89), which is expressed on immune effector cells, to initiate inflammatory reactions.
  • FcaRI or CD89
  • IgA containing immune complexes causes antibody-dependent cell-mediated cytotoxicity (ADCC), degranulation of eosinophils and basophils, phagocytosis by monocytes, macrophages, and neutrophils, and triggering of respiratory burst activity by polymorphonuclear leukocytes.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • eosinophils and basophils degranulation of eosinophils and basophils
  • phagocytosis by monocytes
  • macrophages macrophages
  • neutrophils triggering of respiratory burst activity by polymorphonuclear leukocytes.
  • Aberrant IgA expression has been implicated in a number of autoimmune and immune-mediated disorders, including IgA nephropathy, celiac disease, Henoch-Sconiein purpura (HSP), liner IgA bullous dermatosis, and IgA pemphigus.
  • the Protein Data Bank website provides the crystal structure of IgA, as well as the crystal structure of IgA bound to various compounds searchable by 5E8E (Baglin, T.P., et al., J. Thromb. Haemost., 2016, 14: 137-142), and 2QTJ (Bonner, A., et al., J. Immunol., 2008, 180: 1008-1018). Additionally, Hatanaka T. et al., provides great insight into the specificity and high binding affinity of IgA to OPT-1 peptides (J Biol Chem., 2012, 287(51), 43126-43136.).
  • IgA Targeting Ligands are provided in Fig. 1.
  • Immunoglobulin G (IgG)
  • the Target Protein is a human immunoglobulin G (IgG).
  • IgG represents approximately 75% of serum antibodies in humans.
  • IgG is the most common type of antibody found in blood circulation.
  • IgG antibodies are large globular proteins with a molecular weight of about 150 kDa made of four peptide chains. It contains two identical y (gamma) heavy chains of about 50 kDa and two identical light chains of about 25 kDa, thus a tetrameric quaternary structure. The two heavy chains are linked to each other and to a light chain each by disulfide bonds. The resulting tetramer has two identical halves, which together form the Y-like shape. Each end of the fork contains an identical antigen binding site.
  • the various regions and domains of a typical IgG are depicted in the figure to the left.
  • the Fc regions of IgGs bear a highly conserved N-glycosylation site at asparagine 297 in the constant region of the heavy chain.
  • the N-glycans attached to this site are predominantly core-fucosylated biantennary structures of the complex type.
  • small amounts of these N-glycans also bear bisecting GlcNAc and a-2,6-linked sialic acid residues.
  • the N-glycan composition in IgG has been linked to several autoimmune, infectious and metabolic diseases.
  • IgG4-related diseases which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nephritis, Riedel's thyroiditis, Mikulicz's disease, Kuttner's tumor, inflammatory pseudotumors (in various sites of the body), mediastinal fibrosis and some cases of retroperitoneal fibrosis, aortitis, retroperitoneal fibrosis, proximal biliary strictures, tubulointerstitial nephritis, pachymeningitis, pancreatic enlargement and pericarditis.
  • IG4-related diseases which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nephritis, Riedel's thyroiditis, Mikulicz's disease, Kuttner's tumor, inflammatory pseudotumors (in various sites of the body), mediastinal fibrosis and some cases of retroperitoneal fibro
  • the Protein Data Bank website provides the crystal structure of IgG searchable by 1H3X (Krapp, S., et al., J. Mol. Biol., 2003, 325: 979); and 5V43 (Lee, C.H., et al., Nat. Immunol., 2017, 18: 889-898); as well as the crystal structure of IgG bound to various compounds searchable by 5YC5 (Kiyoshi M., et al., Sci. Rep., 2018, 8: 3955-3955); 5XJE (Sakae Y., et al., Sci. Rep., 2017, 7: 13780-13780); 5GSQ (Chen, C. L., et al., ACS Chem.
  • Kiyoshi, M., et al. provides insight into the structural basis for binding of human IgGl to its high-affinity human receptor FcyRI. (Kiyosi M., et al., Nat Commun., 2015, 6, 6866).
  • IgG Targeting Ligands are provided in Fig. 1.
  • Immunoglobulin E (IgE)
  • the Target Protein is human immunoglobulin E (IgE).
  • IgE is a type of immunoglobulin that plays an essential role in type I hypersensitivity, which can manifest into various allergic diseases, such as allergic asthma, most types of sinusitis, allergic rhinitis, food allergies, and specific types of chronic urticaria and atopic dermatitis.
  • IgE also plays a pivotal role in responses to allergens, such as: anaphylactic drugs, bee stings, and antigen preparations used in desensitization immunotherapy.
  • the Protein Data Bank website provides the crystal structure of IgE searchable by 1F2Q (Garman, S.C., Kinet, J.P., Jardetzky, T.S., Cell, 1998, 95: 951-961); as well as the crystal structure of IgE bound to various compounds searchable by 1F6A (Garman, S.C., et al., Nature, 2000, 406 259-266); 1RPQ (Stamos, J., et al., Structure, 2004, 12 1289-1301); 2Y7Q (Holdom, M.D., et al., Nat. Struct. Mol.
  • the Target Protein is human TNF-a (UniProtKB - P01375 (TNFA HU MAN)).
  • TNF-a is a pro-inflammatory cytokine active in the bodily immune response and serious inflammatory diseases.
  • TNF-a has been implicated in a number of disorders, including but not limited to rheumatoid arthritis, inflammatory bowel disease, graft-vs-host disease, ankylosing spondylitis, psoriasis, hidradenitis suppurativa, refractory asthma, systemic lupis erthyematosus, diabetes, and the induction of cachexia.
  • the Protein Data Bank website provides the crystal structure of TNF-a searchable by 6RMJ (Valentinis, B., et al., Int. J. Mol. Sci., 2019, 20); 5UUI (Carrington et al., Biophys J., 2017, 113 371-380); 6OOY, 6OOZ and 6OPO (O’Connell, J., et al., Nat. Commun, 2019, 10 5795- 5795); and 5TSW (Cha, S.
  • TNF-a Targeting Ligands are provided in Fig. 1. Additional TNF-a Targeting Ligands can be found in, for example, US Patent 8541572; J Chem Inf Model. 2017 May 22; 57(5): 1101-1111; each of which is incorporated by reference herein.
  • the Target Protein is human interleukin-1 (IL-1) (UniProtKB - P01584 (ILIB HUMAN)).
  • IL-1 is a potent proinflammatory cytokine. Initially discovered as the major endogenous pyrogen, induces prostaglandin synthesis, neutrophil influx and activation, T- cell activation and cytokine production, B-cell activation and antibody production, and fibroblast proliferation and collagen production.
  • IL-1 promotes Thl7 differentiation of T-cells, and Synergizes with IL12/interleukin-12 to induce IFNG synthesis from T-helper 1 (Thl) cells.
  • IL-1 has been implicated in a number of auto-inflammatory and autoimmune disorders, including, but not limited to, Blau syndrome, cryopyrin-associated periodic syndromes, familial Mediterranean fever, Majeed syndrome; mevalonate kinase deficiency syndrome, pyogenic arthritis-pyoderma gangrenosum-acne syndrome, tumor necrosis factor receptor-associated periodic syndrome, Behçet’s Disease, Sjogren’s Syndrome, gout and chondrocalcinosis, periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (or PFAPA) syndrome, rheumatoid arthritis, Type 2 diabetes mellitus, acute pericarditis, Chronic interstitial lung diseases (ILDs), Still’s Disease,
  • Blau syndrome cryopyrin-associated periodic syndromes
  • familial Mediterranean fever Majeed syndrome
  • mevalonate kinase deficiency syndrome pyogenic arthritis-pyoderma
  • the Protein Data Bank website provides the crystal structure of IL-1 searchable by 9ILB (Yu, B., et al., Proc Natl Acad Sci U S A, 1999, 96 103-108); H1B (Finzel, B. C., et al., J Mol Biol., 1989, 209 779-791); and 3040 (Wang et al., Nat.Immunol., 2010, 11 : 905-911); as well as the crystal structure of IL-1 bound to various compounds searchable by 4G6J (Blech, M., et al., J Mol Biol., 2013, 425 94-111); 5BVP (Rondeau e al., MAbs, 2015, 7 1151-1160); and 3LTQ (Barthelmes, K., et al., J Am Chem.
  • Guy et al. provides insight into the crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1 (Guy et al., The Journal of Biological Chemistry, 2000, 275, 36927-36933).
  • Additional IL-1 Targeting Ligands can be found in, for example, US Patent 9694015, each of which is incorporated herein by reference. Additional binding ligands include rilanocept or a binding fragment thereof (J Rheumatol. 2012;39:720-727 (2012); and Canakinumab, or a binding fragment thereof (J Rheumatol. 2004:31 : 1103-1111).
  • the Target Protein is human interleukin-2 (IL-2) (UniProtKB - P60568 (IL2 HUMAN)).
  • IL-2 is a potent pro-inflammatory cytokine. IL-2 has been implicated in host versus graft rejection and other autoimmune disorders.
  • the Protein Data Bank website provides the crystal structure of IL-2 searchable by 1M4C and 1M47 (Arkin, M. R., et al., Proc.Natl.Acad.Sci.USA, 2003, 100: 1603-1608); as well as the crystal structure of IL-2 bound to various compounds searchable by 4NEJ and 4NEM (Brenke, R., et al.); 1QVN (Thanos, C. D., et al., Proc Natl Acad Sci U S A, 2006, 103 15422-15427); 1PW6 and 1PY2 (Thanos, C.
  • IL-2 Targeting Ligands are provided in Fig. 1. Additional IL-2 Targeting Ligands can be found in, for example, US Patent 8802721; US Patent 9682976, US Patent 9708268; Eur J Med Chem 83: 294-306 (2014), J Med Chem 60: 6249-6272 (2017); Nature 450: 1001-1009 (2007); each of which is incorporated by reference herein.
  • the Target Protein is human inteleukin-6 (IL-6) (UniProtKB - P05231 (IL6 HUMAN)).
  • IL-6 is a cytokine with a wide variety of biological functions. It is a potent inducer of the acute phase response and plays an essential role in the final differentiation of B-cells into Ig-secreting cells. It is also involved in lymphocyte and monocyte differentiation. It also acts on B-cells, T-cells, hepatocytes, hematopoietic progenitor cells and cells of the CNS, and is required for the generation of T(H)17 cells.
  • IL-6 is a cytokine with a wide variety of biological functions. It is a potent inducer of the acute phase response and plays an essential role in the final differentiation of B-cells into Ig-secreting cells. It is also involved in lymphocyte and monocyte differentiation. It also acts on B-cells, T-cells, hepatocytes, hematopoietic progenitor
  • IL-6 has been implicated in a number of inflammatory diseases and cancers, including, but not limited to, Castleman’s disease, metastatic castration-associated prostate cancer, renal cell carcinoma, large-cell lung carcinoma, ovarian cancer, rheumatoid arthritis, asthma.
  • the Protein Data Bank website provides the crystal structure of IL-6 searchable by 1P9M (Boulanger, M. J., et al., Science, 2003, 300: 2101-2104); 1ALU (Somers et al., EMBO J., 1997, 16, 989-997); 1IL6 and 2IL6 (Xu, G.
  • IL-6 direct or indirect inhibitors are provided in Fig. 1. Additional potential IL- 6 direct or indirect inhibitors can be found in, for example, US Patent 8901310; US Patent 10189796; US Patent 9694015; each incorporated herein by reference.
  • the IL-6 Extracellular Targeting Ligand is AvimarC326 or a binding fragment thereof which is described in Nat Biotechnol 23, 1556-1561 (2005).
  • the Target Protein is human interferon-y (IFN-y) (UniProtKB - Q14609 (Q14609_HUMAN)).
  • IFN-y is a immunoregulatory cytokine. IFN-y has been implicated in a number of autoimmune disorders, including, but not limited to rheumatoid arthritis, multiple sclerosis (MS), corneal transplant rejection, and various autoimmune skin diseases such as psoriasis, alopecia areata, vitiligo, acne vulgaris, and others.
  • the Protein Data Bank website provides the crystal structure of IFN-y searchable by 1HIG (Ealick, S. E., et al., Science 252, 1991, 698-702); as well as the crystal structure of IFN-y bound to various compounds searchable by 6E3K and 6E3L (Mendoza, J. L., et al., Nature, 2019, 567 56-60). Additionally, Randal et al., provides insight into the structure and activity of a monomeric interferon-y: a-chain receptor signaling complex (Randal, M., et al., Structure, 2001, 9(2), 155- 163).
  • IFN-y Targeting Ligands are described in Fig. 1. Additional IFN-y Targeting Ligands can be found in, for example, J Med Chem 57: 4511-20 (2014); which is incorporated by reference herein.
  • VEGF Vascular Epithelial Growth Factor
  • the Target Protein is human vascular epithelial growth factor (VEGF) (UniProtKB - Pl 5692 (VEGFA HUMAN)).
  • VEGF is a growth factor active in angiogenesis, vasculogenesis, and endothelial cell growth.
  • VEGF induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels.
  • VEGF has been implicated in the vascularization and angiogenesis of tumors.
  • the Protein Data Bank website provides the crystal structure of VEGF searchable by 3QTK (Mandal, K., et al., Angew Chem Int Ed Engl., 2011, 50 8029-8033); and 4KZN (Shen et al.); as well as the crystal structure of VEGF bound to various compounds searchable by 5O4E (Lobner, E., et al., MAbs, 2017, 9 1088-1104); 4QAF (Giese, T., et al.,); 5DN2 (Tsai, Y.C.I., et al., FEBS, 2017, J 283 1921-1934); 4GLS (Mandal, K., et al., Proc Natl Acad Sci U S A, 2012, 109 14779- 14784); and 1KMX (Stauffer, M.
  • Additional VEGF Targeting Ligands include, but are not limited to, (all cited referenced incorporated herein by reference) the peptide VEPNCDIHVMWEWECFERL-NH2 (Biochemistry 1998, 37, 17754- 177764). Additional VEGF Targeting Ligands are provided in, for example, J Med Chem 57: 3011-29 (2014), US Patent 9884843, US Patent 9446026, J Med Chem 53: 1686-99 (2010), J Med Chem 48: 8229-36 (2005), J Nat Prod 76: 29-35 (2013), each of which is incorporated herein by reference. Transforming Growth Factor- ⁇ 1 (TGF- ⁇ 1)
  • the Target Protein is human transforming growth factor-pi (TGF- ⁇ 1) (UniProtKB - P01137 (TGFB1 HUMAN)).
  • TGF- ⁇ 1 is a multifunctional protein that regulates the growth and differentiation of various cell types and is involved in various processes, such as normal development, immune function, microglia function and responses to neurodegeneration.
  • TGF- ⁇ 1 can promote either T-helper 17 cells (Thl7) or regulatory T-cells (Treg) lineage differentiation in a concentration-dependent manner.
  • TGF- ⁇ 1 expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF- ⁇ 1 mediated tumor suppression via T-cell exclusion. TGF- ⁇ 1 expression has also been implicated in hematological malignancies and fibrosis.
  • the Protein Data Bank website provides the crystal structure of TGF- ⁇ 1 searchable by 5E8S, 5E8T, and 5E8U (Tebben, A. J., et al., Acta Crystallogr D Struct Biol., 2016, 72 658-674); 2L5S (Zuniga, J.
  • Hinck et al. provides insight into the structural studies of the TGF- ps and their receptors and further insight into evolution of the TGF-P superfamily (Hinck, A., FEBS, 2012, 586(14), 1860-1870).
  • TGF- ⁇ 1 Targeting Ligands are provided in Fig. 1.
  • the TGF- ⁇ 1 Targeting Ligand is the peptide KRFK peptide (J. Biol. Chem. Vol. 274 (No.19) pp. 13586-13593 (1999)(incorporated herein by reference). Additional TGF- ⁇ 1 Targeting Ligands are provided in, for example, Bioorg Med Chem Lett 21 : 5642-5 (2011), which is incorporated herein by reference.
  • PCSK-9 Proprotein Convertase Subtilisin/Kexin Type 9
  • the Target Protein is human proprotein convertase subtilisin/kexin type 9 (PCSK-9) (UniProtKB - Q8NBP7 (PCSK9 HUMAN)).
  • PCSK-9 is a crucial player in the regulation of plasma cholesterol homeostasis.
  • PCSK-9 binds to low-density lipid receptor family members: low density lipoprotein receptor (LDLR), very low-density lipoprotein receptor (VLDLR), apolipoprotein E receptor (LRP1/APOER) and apolipoprotein receptor 2 (LRP8/APOER2), and promotes their degradation in intracellular acidic compartments.
  • LDLR low density lipoprotein receptor
  • VLDLR very low-density lipoprotein receptor
  • LRP1/APOER apolipoprotein E receptor
  • LRP8/APOER2 apolipoprotein receptor 2
  • PCSK-9 has been implicated in high blood cholesterol and the development of cardiovascular disease.
  • the Protein Data Bank website provides the crystal structure of PCSK-9 searchable by 2P4E (Cunningham, D., et al., Nat Struct Mol Biol., 2007, 14 413-419); as well as the crystal structure of PCSK-9 bound to various compounds searchable by 3BPS (Kwon, H. J., et al., Proc Natl Acad Sci U S A, 2008, 105 1820-1825); 6U26, 6U2N, 6U2P, 6U36, 6U38, and 6U3X (Petrilli, W. L., et al., Cell Chem Biol., 2019, 27 32-40.
  • PCSK-9 Targeting Ligands are provided in Fig. 1.
  • the PCSK-9 Targeting Ligand is the peptide TVFTSWEEYLDWV (J. Bio. Chem. 2014 Jan; 289(2):942-955, incorporated herein by reference).
  • Additional PCSK-9 Targeting Ligands are provided in, for example, US Patent 9227956, J Biol Chem 289: 942-55 (2014), each of which is incorporated by reference herein.
  • the Target Protein is human interleukin-21 (IL-21) (UniProtKB - Q9HBE4 (IL21 HUMAN)).
  • IL-21 is an immunoregulatory cytokine.
  • IL-21 has been implicated in a number of autoimmune disorders, including Sjogren’s syndrome, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease.
  • the Protein Data Bank website provides the crystal structure of IL-21 searchable by 2OQP (Bondensgaard, K., et al., J Biol Chem., 2007, 282 23326-23336); and 4NZD (Hamming et al.); as well as the crystal structure of IL-21 bound to various compounds searchable by 3TGX (Hamming, O. J., et al., J Biol Chem., 2012, 287(12), 9454-9460).
  • IL-21 Targeting Ligands are described in Fig. 1. Additional IL-21 Targeting Ligands can be found in, for example, US Patent 9701663, which is incorporated herein by reference.
  • the Target Protein is human interleukin-22 (IL-22) (UniProtKB - Q9GZX6 (IL22 HUMAN)).
  • IL-22 is a member of IL- 10 family cytokines that is produced by many different types of lymphocytes including both those of the innate and adaptive immune system.
  • IL-22 has been implicated in a number of autoimmune disorders, including, but not limited to, graft versus host disease (GVHD), psoriasis, rheumatoid arthritis, atopic dermatitis, and asthma.
  • GVHD graft versus host disease
  • psoriasis psoriasis
  • rheumatoid arthritis atopic dermatitis
  • asthma atopic dermatitis
  • the Protein Data Bank website provides the crystal structure of IL-22 searchable by 1M4R (Nagem, R.A.P., et al., Structure, 2002, 10 1051-1062); as well as the crystal structure of IL-22 bound to various compounds searchable by 3DGC (Jones, B. C. et al., Structure, 2008, 16 1333- 1344).
  • IL-22 Targeting Ligands are described in Fig. 1. Additional IL-22 Targeting Ligands can be found in, for example, US Patent 9,701,663, which is incorporated herein by reference.
  • the Target Protein is human interleukin- 10 (IL-10) (UniProtKB - P22301 (IL10 HUMAN)).
  • IL-10 is an inflammatory cytokine. IL-10 has been implicated in tumor survival and protection against cytotoxic chemotherapeutic drugs.
  • the Protein Data Bank website provides the crystal structure of IL-10 searchable by 2ILK (Zdanov, A et al., Protein Sci., 1996, 5 1955-1962); HLK (Zdanov, A. et al., Structure, 1995, 3 591-601); 2H24 (Yoon, S. I., et al., J Biol Chem., 2006, 281 35088-35096) and 3LQM (Yoon, S. I., et al., Structure, 2010, 18 638-648). Additionally, Zdanov, A., et al, provides insight into crystal structure of IL-10 (Zdanov A., Current Pharmaceutical design, 2004, 10, 3873-3884).
  • IL- 10 Targeting Ligands are provided in Fig. 1. Additional IL- 10 Targeting Ligands can be found, for example, in ACS Chem Biol 11 : 2105-11 (2016), which is incorporated herein by reference.
  • the Target Protein is human interleukin-5 (IL-5) (UniProtKB - P05113 (ILS HUMAN)).
  • IL-5 is a cytokine that regulates eosinophil maturation, recruitment, and survival.
  • IL-5 has been implicated in a number of allergic disorders, including, but not limited to, asthma, nasal polyposis, atopic dermatitis, eosinophilic esophagitis, hypereosinophilic syndrome, and Churg-Strauss syndrome.
  • the Protein Data Bank website provides the crystal structure of IL-5 searchable by 1HUL (Milburn, M. V., Nature, 1993, 363, 172-176) and 3VA2 (Kusano et al., Protein Sci., 2012, 21(6), 850-864); as well as the crystal structure of IL-5 bound to various compounds searchable by 1OBX and 1OBZ (Kang, B. S., et al., Structure, 2003, 11, 845).
  • IL-5 Targeting Ligands are provided in Fig. 1. Additional IL-5 Targeting Ligands can be found, for example, in Bioorg Med Chem 18: 4441-5 (2010); Bioorg Med Chem 18: 4625-9 (2011); Bioorg Med Chem 21 : 2543-50 (2013); Eur J Med Chem 59: 31-8 (2013); Bioorg Med Chem 23: 2498-504 (2015); Bioorg Med Chem 20: 5757-62 (2012); each of which is incorporated by reference herein.
  • the Target Protein is human interleukin-8 (IL-8) (UniProtKB - P10145 (IL8 HUMAN)).
  • IL-8 is a chemotactic factor that attracts neutrophils, basophils, and T- cells, but not monocytes. It is also involved in neutrophil activation. It is released from several cell types in response to an inflammatory stimulus. IL-8 has been implicated in the promotion of tumor progression, immune escape, epithelial-mesenchymal transition, and recruitment of myeloid-derived suppressor cells. Studies have demonstrated that high serum IL-8 levels correlate with poor prognosis in many malignant tumors.
  • IL-8 blockade may reduce mesenchymal features in tumor cells, making them less resistant to treatment.
  • the Protein Data Bank website provides the crystal structure of IL-8 searchable by 3IL8 (Baldwin, E. T., et al., Proc Natl Acad Sci U S A, 1991, 88, 502-506); and 1IL8 and 2IL8 (Clore, G.
  • IL-8 Targeting Ligands are provided in Fig. 1. Additional IL-8 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 19: 4026-30 (2009), which is incorporated by reference herein.
  • the Target Protein is human cholinesterase (UniProtKB - P06276 (CHLE HUMAN)). Cholinesterase contributes to the inactivation of the neurotransmitter acetylcholine. Inhibition of cholinesterase results in increased levels of acetylcholine in the synaptic cleft (the space between two nerve endings).
  • the main use of cholinesterase inhibitors is for the treatment of dementia in patients with Alzheimer's disease. People with Alzheimer's disease have reduced levels of acetylcholine in the brain. Cholinesterase inhibitors have been shown to have an effect on dementia symptoms such as cognition.
  • the Protein Data Bank website provides the crystal structure of cholinesterase searchable by 1P0I and 1P0Q (Nicolet, Y., et al., J Biol Chem., 2003, 278, 41141-41147); as well as the crystal structure of cholinesterase bound to various compounds searchable by 1P0M and 1P0P (Nicolet, Y., et al., J Biol Chem., 2003, 278, 41141-41147); 2J4C (Frasco, M.
  • Ahmad et al. provides insight into the isolation, crystal structure determination and cholinesterase inhibitory potential of isotalatizidine hydrate from delphinium denudatum (Ahmad H., et al., Journal Pharmaceutical Biology, 2016, 55(1), 680-686).
  • Fig. 1 Representative cholinesterase Targeting Ligands are provided in Fig. 1. Additional Targeting Ligands can be found in, for example, ACS Med Chem Lett 4: 1178-82 (2013); J Med Chem 49: 3421-5 (2006); Eur J Med Chem 55: 23-31 (2012); J Med Chem 51 : 3154-70 (2008); J Med Chem 46: 1-4 (2002); Eur J Med Chem 126: 652-668 (2017); Biochemistry 52: 7486-99 (2013); Bioorg Med Chem 23: 1321-40 (2015); which are each incorporated herein by reference.
  • CCL2 C-C motif chemokine ligand 2
  • Grygiel et al. provides insight into the synthesis by native chemical ligation and crystal structure of human CCL2 (Grygiel, T.L., et al., Biopolymers, 2010, 94(3), 350-9).
  • the Target Protein is human C-C motif chemokine ligand 2 (CCL2) (UniProtKB - P13500 (CCL2 HUMAN)).
  • CCL2 acts as a ligand for C-C chemokine receptor CCR2.
  • CCL2 signals through binding and activation of CCR2 and induces a strong chemotactic response and mobilization of intracellular calcium ions.
  • CCL2 exhibits a chemotactic activity for monocytes and basophils but not neutrophils or eosinophils.
  • CCL2 has been implicated in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis.
  • CCL2 Targeting Ligands are provided in Fig. 1. Additional CCL2 Targeting Ligands can be found in, for example, J Med Chem 56: 7706-14 (2013), which is incorporated herein by reference.
  • the Target Protein is human carboxypeptidase B2 (UniProtKB - Q96IY4 (CBPB2 HUMAN)).
  • Carboxypeptidase B2 also known as thrombin activatable fibrinolysis inhibitor (TAFIa) cleaves C-terminal arginine or lysine residues from biologically active peptides such as kinins or anaphylatoxins in the circulation thereby regulating their activities. It down-regulates fibrinolysis by removing C-terminal lysine residues from fibrin that has already been partially degraded by plasmin.
  • Carboxypeptidase B2 has been implicated and targeted to inhibit thrombosis.
  • the Protein Data Bank website provides the crystal structure of carboxypeptidase B2 (also known as thrombin-activatable fibrinolysis inhibitor (TAFI)) searchable by 3D66 (Marx, P. F., et al., Blood, 2008, 112, 2803-2809); 3DGV (Anand, K., et al., JBC, 2008, 283, 29416-29423); and 1KWM (Barbosa Pereira, P.J., et al., J Mol Biol., 2002, 321, 537-547); as well as the crystal structure of TAFI bound to various compounds searchable by 3D67 (Marx, P.
  • TAFI thrombin-activatable fibrinolysis inhibitor
  • carboxypeptidase B2 Targeting Ligands are provided in Fig. 1. Additional carboxypeptidase B2 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 20: 92-6 (2010), J Med Chem 50: 6095-103 (2007), Bioorg Med Chem Lett 14: 2141-5 (2004), J Med Chem 58: 4839-44 (2015), J Med Chem 55: 7696-705 (2012), J Med Chem 59: 9567-9573 (2016), Bioorg Med Chem Lett 17: 1349-54 (2007), US Patent 9662310, US Patent 8609710, US Patent 9688645, J Med Chem 46: 5294-7 (2003), each of which is incorporated herein by reference.
  • the Target Protein is human neutrophil elastase (UniProtKB - P08246 (ELNE HUMAN)).
  • Neutrophil elastase modifies the functions of natural killer cells, monocytes and granulocytes. Inhibits C5a-dependent neutrophil enzyme release and chemotaxis.
  • Neutrophil elastase has been implicated in a number of disorders, including lung disease, chronic obstructive pulmonary disease, pneumonia, respiratory distress, and acute lung injury (ALI), and cystic fibrosis, as well as chronic kidney disease.
  • the Protein Data Bank website provides the crystal structure of human neutrophil elastase bound to various compounds searchable by 3Q76 and 3Q77 (Hansen, G., et al., J.Mol.Biol., 2011, 409, 681-691); 5ABW (Von Nussbaum, et al., Bioorg Med Chem Lett., 2015, 25, 4370-4381); 1B0F (Cregge, R.
  • neutrophil elastase Targeting Ligands are provided in Fig. 1. Additional neutrophil elastase Targeting Ligands can be found in, for example, J Med Chem 53: 241-53 (2010), J Med Chem 38: 739-44 (1995), J Med Chem 37: 2623-6 (1994), J Med Chem 38: 4687- 92 (1995), J Med Chem 45: 3878-90 (2002), Bioorg Med Chem Lett 5: 105-109 (1995), Bioorg Med Chem Lett 11 : 243-6 (2001), J Med Chem 40: 1906-18 (1997), Bioorg Med Chem Lett 25: 4370-81 (2015), US Patent 8569314, US Patent 9174997, US Patent 9290457, each of which is incorporated herein by reference.
  • the Target Protein is human Factor Xa (UniProtKB - P00742 (FA10 HUMAN)).
  • Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.
  • Factor X has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of Factor Xa bound to various compounds searchable by 1G2L and 1G2M (Nar, H., et al., Structure, 2001, 9, 29-38); 2PR3 (Nan huis, C. A., et al., Chem Biol Drug Des., 2007, 69, 444-450); 2UWP (Young, R. J., et al., Bioorg Med Chem Lett., 2007, 17, 2927); 2VVC, 2VVV, 2VVU, 2VWL, 2VWM, 2VWN and 2VW0 (Zbinden, K.
  • Factor Xa Targeting Ligands are provided in Fig. 1. Additional Factor Xa Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 20: 5313-9 (2010), Bioorg Med Chem Lett 13: 679-83 (2003), J Med Chem 44: 566-78 (2001), J Med Chem 50: 2967-80 (2007), J Med Chem 38: 1511-22 (1995), Bioorg Med Chem Lett 18: 2845-9 (2008), J Med Chem 53: 6243-74 (2010), Bioorg Med Chem Lett 18: 2845-9 (2008), Bioorg Med Chem 16: 1562-95 (2008), each of which is incorporated herein by reference.
  • the Target Protein is human Factor XI UniProtKB - P03951 (FA11 HUMAN).
  • Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.
  • Factor XI has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of Factor XI bound to various compounds searchable by 1ZSL, 1ZTJ, 1ZTK, and 1ZTL (Nagafuji, P., et al.,); 1Z0M (Lin, J., et al., J Med Chem., 2006, 49, 7781-7791); 5EOK and 5EOD (Wong, S.S., et al., Blood, 2016, 127, 2915-2923 ); 1ZHM, 1ZHP and 1ZHR (Jin, L., et al., Acta Crystallogr D Biol Crystallogr., 2005, 61, 1418-1425 ); 1ZMJ, 1ZLR, 1ZML and 1ZMN (Lazarova, T.I., Bioorg Med Chem Lett., 2006, 16, 5022-5027); 1ZRK, 1ZSJ and 1ZSK (Guo, Z., et al); 4CRA, 4CRB, 4CRC, 4
  • Factor XI Targeting Ligands are provided in Fig. 1. Additional Factor XI Targeting Ligands can be found in, for example, US Patent 9783530, US Patent 10143681, US Patent 10214512, ACS Med Chem Lett 6: 590-5 (2015), J Med Chem 60: 9703-9723 (2017), J Med Chem 60: 9703-9723 (2017), US Patent 9453018 (2016), J Med Chem 60: 1060-1075 (2017), J Med Chem 57: 955-69 (2014), each of which is incorporated herein by reference.
  • the Target Protein is human Factor XII (UniProtKB - P00748 (FA12 HUMAN)).
  • Factor XII is a serum glycoprotein that participates in the initiation of blood coagulation, fibrinolysis, and the generation of bradykinin and angiotensin.
  • Prekallikrein is cleaved by factor XII to form kallikrein, which then cleaves factor XII first to alpha-factor Xlla and then trypsin cleaves it to beta-factor Xlla.
  • Alpha-factor Xlla activates factor XI to factor Xia.
  • Factor XII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of factor XII bound to various compounds searchable by 4XDE and 4XE4 (Pathak, M., et al., J Thromb Haemost., 2015, 13(4), 580-591); 6GT6 and 6QF7 (Pathak, M., et al., Acta Crystallogr D Struct Biol., 2019, 75, 578-591); and 6B74 and 6B77 (Dementiev, A.A., et al., Blood Adv., 2018, 2, 549-558). Additionally, Pathak et al., provides insight into the crystal structure of factor XII (Pathak, M., et al., J Thromb Haemost., 2015, 13(4), 580-591).
  • Factor XII Targeting Ligands are provided in Fig. 1. Additional Factor XII Targeting Ligands can be found in, for example, J Med Chem 60: 1151-1158 (2017), J Med Chem 48: 2906-15 (2005), J Med Chem 50: 5727-34 (2007), J Med Chem 50: 1876-85 (2007), Chembiochem 18: 387-395 (2017), each of which is incorporated herein by reference.
  • the Target Protein is human Factor XIII UniProtKB - P00488 (F13A HUMAN)).
  • Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl-epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin.
  • Factor XIII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of factor XIII searchable by 1FIE (Yee, V.C., et al., Thromb Res., 1995, 78, 389-397); and 1F13 (Weiss, M.S., et al., FEBS Lett., 1998, 423, 291-296); as well as the crystal structure of factor XIII bound to various compounds searchable by 1DE7 (Sadasivan, C., et al., J Biol Chem., 2000, 275, 36942-36948); and 5MHL, 5MHM, 5MHN, and 5MH0 (Stieler, M., et al., ).
  • Gupta et al. provides insight into the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective (Gupta, S., et al., Sci Rep., 2016; 6, 30105); and Komaromi et al., provides insight into the novel structural and functional aspect of factor XIII ( Komaromi, Z., et al., . J Thromb Haemost 2011, 9, 9-20).
  • Factor XIII Targeting Ligands are provided in Fig. 1. Additional Factor XIII Targeting Ligands can be found in, for example, Eur J Med Chem 98: 49-53 (2015), J Med Chem 55: 1021-46 (2012), J Med Chem 48: 2266-9 (2005), each of which is incorporated herein by reference.
  • the Target Protein is human Prothrombin (UniProtKB - P00734 (THRB HUMAN)).
  • Thrombin which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.
  • Thrombin is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of prothrombin searchable by 3NXP (Chen, Z.
  • Pozzi et al. provides insight into the mechanism and conformational flexibility for the crystal structure of prothrombin (Pozzi, N. et al., J Biol Chem.,
  • Prothrombin is converted to thrombin, as such the Protein Data Bank website provides the crystal structure of thrombin bound to compounds searchable by 1XMN (Carter, W.J. et al., J.Biol.Chem., 2005, 280, 2745-2749); 4CH2 and 4CH8 (Lechtenberg, B.C. et al., J Mol Biol.,
  • prothrombin Targeting Ligands are provided in Fig. 1. Additional prothrombin Targeting Ligands can be found in, for example, J Med Chem 46: 3612-22 (2003), Bioorg Med Chem Lett 12: 1017-22 (2002), J Med Chem 40: 830-2 (1997), Bioorg Med Chem Lett 15: 2771-5 (2005), J Med Chem 42: 3109-15 (1999), J Med Chem 47: 2995-3008 (2004), Bioorg Med Chem 16: 1562-95 (2008), J Med Chem 42: 3109-15 (1999), each of which is incorporated herein by reference. Coagulation Factor VII
  • the Target Protein is human coagulation Factor VII (UniProtKB - P08709 (FA7 HUMAN)).
  • Factor VII initiates the extrinsic pathway of blood coagulation. It is a serine protease that circulates in the blood in a zymogen form. Factor VII is converted to Factor Vila by Factor Xa, Factor Xlla, Factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, Factor Vila then converts Factor X to Factor Xa by limited proteolysis. Factor Vila will also convert Factor IX to Factor IXa in the presence of tissue factor and calcium.
  • Factor VII is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of factor VII bound to various compounds searchable by 2F9B (Rai, R., et al., Bioorg Med Chem Lett., 2006, 16, 2270-2273); 5U6J (Wurtz, N.R., et al., Bioorg Med Chem Lett., 2017, 27, 2650-2654); 5L2Y, 5L2Z, and 5L30 (Ladziata, .U., et al., Bioorg Med Chem Lett., 2016, 26, 5051-5057); 5146 (Glunz, P.
  • Kemball-Cook, et al. provides insight into the crystal structure of active site-inhibited factor Vila (Kemball-Cook, G., et al., J Struct Biol., 1999, 127(3), 213-23).
  • Factor VII Targeting Ligands are provided in Fig. 1. Additional Factor VII Targeting Ligands can be found in, for example, US Patent 9174974, Bioorg Med Chem Lett 26: 5051-5057 (2016), Bioorg Med Chem Lett 11 : 2253-6 (2001), Bioorg Med Chem Lett 15: 3006- 11 (2005), Bioorg Med Chem Lett 12: 2883-6 (2002), each of which is incorporated herein by reference.
  • the Target Protein is human coagulation Factor IX (UniProtKB - P00740 (FA9 HUMAN)).
  • Factor IX Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca2+ ions, phospholipids, and factor Villa.
  • Factor IX is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • the Protein Data Bank website provides the crystal structure of factor IX bound to various compounds searchable by 6MV4 (Vadivel, K., et al., J Thromb Haemost., 2019, 17, 574-584); 4ZAE (Zhang, T., et al., Bioorg Med Chem Lett., 2015, 25, 4945-4949); 4YZU and 4Z0K (Parker, D.L., et al., Bioorg Med Chem Lett., 2015, 25, 2321-2325); 5TNO and 5TNT (Sakurada, I., et al., Bioorg Med Chem Lett., 2017, 27, 2622-2628); 5JB8, 5JB9, 5JBA, 5JBB and 5JBC (Kristensen, L.H., et al., Biochem J., 2016, 473, 2395-2411); 3LC3 (Wang, S., et al., J Med Chem., 2010, 53, 1465-1472); 3LC5
  • Factor IX Targeting Ligands are provided in Fig. 1. Additional Factor IX Targeting Ligands can be found in, for example, US Patent 9409908, Bioorg Med Chem Lett 25: 5437-43 (2015), US Patent 10189819, each of which is incorporated herein by reference.
  • FGF1 Fibroblast Growth Factor 1
  • the Target Protein is human fibroblast growth factor 1 (FGF1) (UniProtKB - P05230 (F GF 1 HUMAN)).
  • FGF1 plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation and cell migration.
  • FGF1 acts as a ligand for FGFR1 and integrins, and binds to FGFR1 in the presence of heparin leading to FGFR1 dimerization and activation via sequential autophosphorylation on tyrosine residues which act as docking sites for interacting proteins, leading to the activation of several signaling cascades.
  • FGF 1 induces the phosphorylation and activation of FGFR1, FRS2, MAPK3/ERK1, MAPK1/ERK2 and AKT1.
  • FGF1 can induce angiogenesis.
  • FGF1 has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
  • the Protein Data Bank website provides the crystal structure of FGF 1 searchable by 2AFG (Blaber, M., et al., Biochemistry, 1996, 35, 2086-2094); and 1BAR (Zhu, X. et al., Science, 1991, 251, 90-93); as well as the crystal structure of FGF1 bound to various compounds searchable by 1AFC (Zhu, X., et al., Structure, 1993, 1, 27-34); 1AXM and 2AXM (DiGabriele, A.
  • FGF1 Targeting Ligands are provided in Fig. 1. Additional FGF1 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 18: 344-9 (2008), Chembiochem 6: 1882-90 (2005), J Med Chem 55: 3804-13 (2012), J Med Chem 47: 1683-93 (2004), J Med Chem 53: 1686-99 (2010, )each of which is incorporated herein by reference.
  • FGF2 Fibroblast Growth Factor 2
  • the Target Protein is human fibroblast growth factor 2 (FGF2) (UniProtKB - P09038 (FGF2 HUMAN)).
  • FGF2 acts as a ligand for FGFR1, FGFR2, FGFR3 and FGFR4.
  • FGF2 also acts as an integrin ligand which is required for FGF2 signaling, and plays an important role in the regulation of cell survival, cell division, cell differentiation and cell migration.
  • FGF2 also induces angiogenesis.
  • FGF2 has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
  • the Protein Data Bank website provides the crystal structure of FGF2 bound to various compounds searchable by 4OEE, 4OEF, and 4OEG (Li, Y.C., et al., ACS Chem Biol., 2014, 9, 1712-1717); 1EV2 (Plotnikov, A.N., et al., Cell, 2000, 101, 413-424); and 5X1O (Tsao, Y.H.).
  • FGF2 Targeting Ligands are provided in Fig. 1. Additional FGF2 Targeting Ligands can be found in, for example, US Patent 8933099, Bioorg Med Chem Lett 12: 3287-90 (2002), Chem Biol Drug Des 86: 1323-9 (2015), Bioorg Med Chem Lett 25: 1552-5 (2015), each of which is incorporated herein by reference.
  • the Target Protein is human fibronectin 1 (FN1) (UniProtKB - P02751 (FINC_HUMAN)). Fibronectin (FN) polymerization is necessary for collagen matrix deposition and is a key contributor to increased abundance of cardiac myofibroblasts (MFs) after cardiac injury. Interfering with FN polymerization may attenuate MF and fibrosis and improve cardiac function after ischemia/reperfusion (I/R) injury.
  • FN1 human fibronectin 1
  • MFs myofibroblasts
  • the Protein Data Bank website provides the crystal structure of fibronectin- 1 bound to various compounds searchable by 3M7P (Graille, M., et al., Structure, 2010, 18, 710-718); 3MQL (Erat, M.C., et al., J Biol Chem., 2010, 285, 33764-33770); and 3EJH (Erat, M.C., et al., Proc Natl Acad Sci U S A, 2009, 106, 4195-4200).
  • FN Targeting Ligands are provided in Fig. 1. Additional FN Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 18: 2499-504 (2008), which is incorporated herein by reference.
  • the Target Protein is human kallikrein-1 (UniProtKB - P06870 (KLK1 HUMAN)). Glandular kallikreins cleave Met-Lys and Arg-Ser bonds in kininogen to release Lys-bradykinin. Kallikrein has been implicated in adverse reactions in hereditary angioedema (HAE).
  • HAE hereditary angioedema
  • the Protein Data Bank website provides the crystal structure of KLK1 searchable by 1 SPJ (Laxmikanthan, G., et al., Proteins, 2005, 58, 802-814); as well as the crystal structure of KLK1 bound to various compounds searchable by 5F8Z, 5F8T, 5F8X, (Xu, M., et al.,); and 6A8O (Xu, M., et al., FEBS Lett., 2018, 592, 2658-2667). Additionally, Katz et al., provides insight into the crystal structure of kallikrein (Katz, B.A., et al., Protein Sci., 1998, 7(4), 875-85).
  • kallikrein Targeting Ligands are provided in Fig. 1. Additional kallikrein Targeting Ligands can be found in, for example, US Patent 9783530, J Med Chem 38: 2521-3 (1995), US Patent 9234000, US Patent 10221161, US Patent 9687479, US Patent 9670157, US Patent 9834513, J Med Chem 38: 1511-22 (1995), US Patent 10214512, each of which is incorporated herein by reference.
  • the Target Protein is human plasma kallikrein (UniProtKB - P03952 (KLKB1 HUMAN)). Plasma kallikrein cleaves Lys-Arg and Arg-Ser bonds. It activates, in a reciprocal reaction, factor XII after its binding to a negatively charged surface. It also releases bradykinin from HMW kininogen and may also play a role in the renin-angiotensin system by converting prorenin into renin. Plasma kallikrein has been implicated in retinal dysfunction, the development of diabetic macular edema and hereditary angioedema (HAE).
  • HAE hereditary angioedema
  • the Protein Data Bank website provides the crystal structure of plasma kallikrein bound to various compounds searchable by 5TJX (Li, Z., et al., ACS Med Chem Lett., 2017, 8, 185-190); 6O1G and 6O1S (Patridge, J. R., et al., J Struct Biol., 2019, 206, 170-182); 4OGX and 4OGY (Kenniston, J. A., et al., J Biol Chem., 2014, 289, 23596-23608); and 5F8T, 5F8X, and 5F8Z (Xu, M., et al.,).
  • Fig. 1 Representative plasma kallikrein Targeting Ligands are provided in Fig. 1. Additional plasma kallikrein Targeting Ligands can be found in, for example, J Med Chem 61 : 2823-2836 (2016), J Med Chem 55: 1171-80 (2012), US Patent 8598206, US Patent 9738655, Bioorg Med Chem Lett 16: 2034-6 (2006), US Patent 9409908, US Patent 10144746, US Patent 9290485, each of which is incorporated herein by reference.
  • the Target Protein is human lipoprotein lipase (UniProtKB - P06858 (LIPL HUMAN)).
  • Lipoprotein lipase is a key enzyme in triglyceride metabolism. It catalyzes the hydrolysis of triglycerides from circulating chylomicrons and very low density lipoproteins (VLDL), and thereby plays an important role in lipid clearance from the blood stream, lipid utilization and storage.
  • VLDL very low density lipoproteins
  • Lipoprotein lipase mediates margination of triglyceride-rich lipoprotein particles in capillaries. Lipoprotein lipase has been implicated in the development of cardiovascular disease and obesity.
  • the Protein Data Bank website provides the crystal structure of lipoprotein lipase bound to various compounds searchable by 6E7K (Birrane, G., et al., Proc Natl Acad Sci U S A, 2018 116 1723-1732).
  • lipoprotein lipase Targeting Ligands are provided in Fig. 1. Additional lipoprotein lipase Targeting Ligands can be found in, for example, J Med Chem 47: 400-10 (2004), which is incorporated herein by reference.
  • MMP-1 Matrix Metallopeptidase 1
  • the Target Protein is human matrix metallopeptidase 1 (MMP-1) (UniProtKB - P03956 (MMP1 HUMAN)).
  • MMP-1 cleaves collagens of types I, II, and III at one site in the helical domain. It also cleaves collagens of types VII and X. MMP-1 has been implicated in cardiovascular disease.
  • the Protein Data Bank website provides the crystal structure of MMP-1 searchable by 3SHI (Bertini, I., et al., FEBS Lett., 2012, 586, 557-567); as well as the crystal structure of MMP- 1 bound to various compounds searchable by 4AU0 (Manka, S. W., et al., Proc Natl Acad Sci U S A, 2012, 109, 12461); 3MA2 (Grossman, M., et al., Biochemistry, 2010, 49, 6184-6192); and 2J0T (Iyer, S., et al., J.Biol.Chem., 2007, 282, 364 ).
  • Iyer et al. provides insight into the crystal structure of an active form of MMP-1 (Iyer, S., et al., J Mol Biol., 2006, 362(1), 78- 88); and Lovejoy et al., provides insight into the crystal structure of MMP1 and the selectivity of collagenase inhibitors (Lovejoy, B., et al., Nat Struct Mol Biol., 1999, 6, 217-221).
  • MMP-1 Targeting Ligands are provided in Fig. 1. Additional MMP-1 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 5: 1415-1420 (1995), Bioorg Med Chem Lett 16: 2632-6 (2006), Bioorg Med Chem Lett 8: 837-42 (1999), Eur J Med Chem 60: 89-100 (2013), J Med Chem 54: 4350-64 (2011), Bioorg Med Chem Lett 8: 3251-6 (1999), J Med Chem 42: 4547-62 (1999), J Med Chem 61 : 2166-2210 (2016), J Med Chem 41 : 1209-17 (1998), which is incorporated herein by reference. Macrophage Migration Inhibitory Factor (MIF)
  • MIF Macrophage Migration Inhibitory Factor
  • the Target Protein is human macrophage migration inhibitory factor (MIF) (UniProtKB - P14174 (MIF HUMAN)).
  • MIF is a pro-inflammatory cytokine involved in the innate immune response to bacterial pathogens. The expression of MIF at sites of inflammation suggests a role as mediator in regulating the function of macrophages in host defense. It counteracts the anti-inflammatory activity of glucocorticoids.
  • MIF has been implicated in tumor progression; systemic inflammation; atherosclerosis; rheumatoid arthritis; and systemic lupus erythematosus, among others.
  • the Protein Data Bank website provides the crystal structure of MIF searchable by 1MIF (Sun, H-W. et al., Proc Natl Acad Sci U S A, 1996, 93, 5191-5196); as well as the crystal structure of MIF bound to various compounds searchable by 6PEG (Cirillo, P.F.
  • 3SMB and 3SMC Crichlow, G.V. et al., Biochemistry, 2012, 51, 7506-7514); 3U18 (Bai, F., et al., J Biol Chem., 2012, 287, 30653-30663); 4F2K (Tyndall, J.D.A., et al., Acta Crystallogr Sect F Struct Biol Cryst Commun., 2012, 68, 999-1002); 3IJG and 3IJJ (Cho, Y., et al., Proc Natl Acad Sci U S A, 2010, 107, 11313-11318); 3L5P, 3L5R, 3L5S, 3L5T, 3L5U, and 3L5V (McLean, L.R.
  • MIF Targeting Ligands are provided in Fig. 1. Additional MIF Targeting Ligands can be found in, for example, ACS Med Chem Lett 8: 124-127 (2017), J Med Chem 44: 540-7 (2001), J Med Chem 52: 416-24 (2009), J Med Chem 50: 1993-7 (2007), which is incorporated herein by reference.
  • TGF- ⁇ 2 Transforming Growth Factor- ⁇ 2 (TGF- ⁇ 2)
  • the Target Protein is human transforming growth factor- ⁇ 2 (TGF- ⁇ 2) (UniProtKB - P61812 (TGFB2 HUMAN)).
  • TGF- ⁇ 2 is a multifunctional protein that regulates various processes such as angiogenesis and heart development. Once activated following release of LAP, TGF-beta-2 acts by binding to TGF-beta receptors (TGFBR1 and TGFBR2), which transduce signal.
  • TGFBR1 and TGFBR2 TGF-beta receptors
  • TGFBR1 and TGFBR2 TGF-beta receptors
  • TGFBR1 and TGFBR2 TGF-beta receptors
  • TGF- ⁇ 2 expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF- ⁇ 2 mediated tumor suppression via T-cell exclusion. TGF- ⁇ 2 expression has also been implicated in hematological malignancies and fibrosis.
  • the Protein Data Bank website provides the crystal structure of TGF- ⁇ 2 searchable by 6I9J (Del Amo-Maestro L. et al., Sci Rep. 2019, 9, 8660-8660); as well as the crystal structure of TGF- ⁇ 2 bound to various compounds searchable by 1M9Z (Boesen, C.C., et al. Structure, 2002, 10, 913-919); 5QIN (Zhang, Y. et al., ACS Med Chem Lett., 2018, 9, 1117-1122); 5E8V, 5E8Y, 5E91 and 5E92 (Tebben, A.J.
  • TGF- ⁇ 2 Targeting Ligands are provided in Fig. 1.
  • TSP-1 Thrombospondin-1
  • the Target Protein is human thrombospondin-1 (TSP-1) (UniProtKB - P61812 (TGFB2 HUMAN)).
  • TSP1 acts as an angiogenesis inhibitor by stimulating endothelial cell apoptosis, inhibiting endothelial cell migration and proliferation, and regulating vascular endothelial growth factor bioavailability and activity.
  • TSP1 affects tumor immune response, tumor cell behaviors including adhesion, invasion, migration, apoptosis, and proliferation.
  • TSP-1 expression has been implicated in a number of diseases, including in promoting certain cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
  • cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
  • the Protein Data Bank website provides the crystal structure of TSP -1 searchable by 1LSL (Tan, K. et al., J Cell Biol., 2002, 159, 373-382); 2ES3 (Tan, K., et al., J Biol Chem., 2008, 283, 3932-3941); 1Z78 and 2ERF (Tan, K., et al., Structure, 2006, 14, 33-42); and 3R6B (Klenotic, P.A., et al., Protein ExprPurif., 2011, 80, 253-259); as well as the crystal structure of TSP-1 bound to various compounds searchable by 20UH and 2OUJ (Tan, K., et al., J Biol Chem., 2008, 283, 3932-3941); and 1ZA4 (Tan, K., et al., Structure, 2006, 14, 33-42).
  • TSP-1 Targeting Ligands are provided in Fig. 1.
  • CD40 Ligand CD40L
  • the Target Protein is human CD40 ligand (CD40L) (UniProtKB - P29965 (CD40L HUMAN)).
  • CD40L is a cytokine that acts as a ligand to CD40/TNFRSF5. It costimulates T-cell proliferation and cytokine production. Its cross-linking on T-cells generates a costimulatory signal which enhances the production of IL4 and IL 10 in conjunction with the TCR/CD3 ligation and CD28 costimulation.
  • CD40L induces the activation of NF-kappa-B, as well as kinases MAPK8 and PAK2 in T-cells.
  • CD40L mediates B-cell proliferation in the absence of co-stimulus as well as IgE production in the presence of IL4, and is involved in immunoglobulin class switching.
  • the Protein Data Bank website provides the crystal structure of CD40L searchable by 1ALY (Karpusas, M., et al., Structure, 1995, 3, 1031-1039); as well as the crystal structure of CD40L bound to various compounds searchable by 3QD6 (An, H.J., et al., J Biol Chem., 2011, 286, 11226-11235); and 6BRB (Kamell, J.L., et al., Sci Transl Med., 2019, 11(489), 6584).
  • CD40L has been implicated in HIV-associated neurocognitive disorders and cardiovascular complications.
  • Representative CD40L Targeting Ligands are provided in Fig. 1.
  • the Target Protein is human urokinase-type plasminogen activator (UP A) (UniProtKB - P00749 (UROK HUMAN)).
  • Urokinase-type plasminogen activator (uPA) is a serine protease present in the blood and in the extracellular matrix of many tissues.
  • the primary physiological substrate of this enzyme is plasminogen, which is an inactive form (zymogen) of the serine protease plasmin.
  • plasminogen is an inactive form (zymogen) of the serine protease plasmin.
  • Activation of plasmin triggers a proteolytic cascade that, depending on the physiological environment, participates in thrombolysis or extracellular matrix degradation. This cascade had been involved in vascular diseases and cancer progression. Elevated expression levels of urokinase and several other components of the plasminogen activation system are found to be correlated with tumor malignancy.
  • the Protein Data Bank website provides the crystal structure of UPA bound to various compounds searchable by 5ZA7, 5ZAJ, 5ZA8, 5ZA9, 5ZAE, 5ZAF, 5ZAG, 5ZAH, and 5ZC5 (Buckley, B.J. et al., J Med Chem., 2018, 61, 8299-8320); 5LHP, 5LHQ, 5LHR, and 5LHS (Kromann-Hansen, T. et al., Sci Rep., 2017, 7, 3385-3385); 2VNT (Fish, P.V. et al. J Med Chem., 2007, 50, 2341); 10WD, 10WE, 10WH, 1OWI, 1OWJ, and 10WK (Wendt, M.D.
  • UPA Targeting Ligands are provided in Fig. 1. Additional UPA Targeting Ligands are provided in, for example, J Med Chem 38: 1511-22 (1995), Bioorg Med Chem Lett 11 : 2253-6 (2001), Bioorg Med Chem Lett 14: 3063-8 (2004), J Med Chem 52: 3159-65 (2009), CSAR 1 : (2012), Bioorg Med Chem 22: 3187-203 (2014), J Med Chem 50: 2341-51 (2007), J Mol Biol 329: 93-120 (2003), Bioorg Med Chem Lett2: 1399-1404 (1992), J Med Chem 35: 4297-305 (1992), J Med Chem 35: 4150-9 (1992), J Med Chem 49: 5785-93 (2006), Bioorg Med Chem 23: 3696-704 (2015), Bioorg Med Chem Lett 10: 983-7 (2000), JMed Chem 49: 5785-93 (2006), each of which is incorporated by reference herein.
  • the Target Protein is human plasminogen activator, tissue type (TP A) (UniProtKB - P00750 (TPA HUMAN)).
  • TP A converts the abundant, but inactive, zymogen plasminogen to plasmin by hydrolyzing a single Arg-Val bond in plasminogen.
  • TPA plays a direct role in facilitating neuronal migration.
  • PLA has been shown activated in various cancers including oral malignancy.
  • the Protein Data Bank website provides the crystal structure of TPA searchable by 1VR1 (Dekker, R.J. et al., J Mol Biol., 1999, 293, 613-627); as well as the crystal structure of TPA bound to various compounds searchable by 1RTF (Lamba, D. et al., J Mol Biol., 1996, 258, 117- 135); 1 A5H (Renatus, M. et al., J Biol Chem., 1997, 272, 21713-21719); and 1BDA (Renatus, M. et al., EMBO J., 1997, 16, 4797-4805).
  • Representative TPA Targeting Ligands are provided in Fig. 1.
  • TPA Targeting Ligands are provided in, for example, Bioorg Med Chem Lett 15: 4411-6 (2005), Bioorg Med Chem Lett 13: 2781-4 (2003), Bioorg Med Chem Lett 6: 2913-2918 (1996), JMed Chem 44: 2753- 71 (2001), J Med Chem 41 : 5445-56 (1999), Bioorg Med Chem Lett 12: 3183-6 (2002), US Patent 10118930, J Biol Chem 285: 7892-902 (2010), each of which is incorporated by reference herein.
  • the Target Protein is human plasminogen (PLG) (UniProtKB - P00747 (PLMN HUMAN)).
  • PLG dissolves the fibrin of blood clots and acts as a proteolytic factor in a variety of other processes including embryonic development, tissue remodeling, tumor invasion, and inflammation. It activates the urokinase-type plasminogen activator, collagenases and several complement zymogens, such as Cl and C5. Its role in tissue remodeling and tumor invasion may be modulated by CSPG4.
  • the Protein Data Bank website provides the crystal structure of PLG searchable by 1DDJ (Wang, X. et al., J.Mol.Biol., 2000, 295, 903-914); and 4DUR and 4DUU (Law, R.H.P., et al., Cell Rep., 2012, 1, 185-190).
  • PLG Targeting Ligands are provided in Fig. 1. Additional PLG Targeting Ligands are provided in, for example, J Med Chem 35: 4297-305 (1992), J Med Chem 38: 1511- 22 (1995), J Med Chem 56: 820-31 (2013), US Patent 8598206, US Patent 8921319, J Med Chem 55: 1171-80 (2012), Bioorg Med Chem Lett 12: 3183-6 (2002), Bioorg Med Chem 23: 3696-704 (2015), Bioorg Med Chem Lett 13: 723-8 (2003), Bioorg Med Chem Lett 7: 331-336 (1997), each of which is incorporated by reference herein.
  • Plasminogen Activator Inhibitor-1 (PAI-1)
  • the Target Protein is human plasminogen activator inhibitor 1 (PAL 1) (UniProtKB - P05121 (PAI 1 HUMAN)).
  • PALI is a serine protease inhibitor, and a primary inhibitor of tissue-type plasminogen activator (PLAT) and urokinase-type plasminogen activator (PLAU).
  • PLAT inhibitor it is required for fibrinolysis down-regulation and is responsible for the controlled degradation of blood clot.
  • PLAU inhibitor it is involved in the regulation of cell adhesion and spreading, and acts as a regulator of cell migration, independently of its role as protease inhibitor.
  • Overexpression of PAI- 1 favors angiogenesis, metastasis, and poor prognosis in tumors, including, but not limited to, oral cancers and breast cancers.
  • the Protein Data Bank website provides the crystal structure of PAI-1 searchable by 3Q02 and 3Q03 (Jensen, J.K. et al., J Biol Chem., 2011, 286, 29709-29717); 1B3K (Sharp, A.M. et al., Structure, 1999, 7, 111-118); 1C5G (Tucker, H.M. et al., Nat Struct Biol., 1995, 2, 442-445); 1DVM (Stout, T.J. et al., Biochemistry, 2000, 39, 8460-8469); and 3UT3 (Lin, Z.H.
  • PALI Targeting Ligands are provided in Fig. 1. Additional PALI Targeting Ligands are provided in, for example, J Biol Chem 285: 7892-902 (2010), US Patent 9120744, Bioorg Med Chem Lett 13: 3361-5 (2003), Bioorg Med Chem Lett 12: 1063-6 (2002), Bioorg Med Chem Lett 13: 1705-8 (2003), Bioorg Med Chem Lett 11 : 2589-92 (2001), US Patent 9718760, each of which is incorporated by reference herein.
  • PIGF Placenta Growth Factor
  • the Target Protein is human placental growth factor (PGF) (UniProtKB - P49763 (PLGF HUMAN)).
  • PGF is growth factor active in angiogenesis and endothelial cell growth, stimulating their proliferation and migration. It binds to the receptor FLT1/VEGFR-1.
  • Isoform P1GF-2 binds NRPl /neuropilin- 1 and NRP2/neuropilin-2 in a heparindependent manner.
  • PGF also promotes cell tumor growth, and has been implicated in age-related macular degeneration (AMD) and choroidal neovascularization (CNV).
  • AMD age-related macular degeneration
  • CNV choroidal neovascularization
  • the Protein Data Bank website provides the crystal structure of PIGF searchable by 1FZV (Iyer, S. et al., J Biol Chem., 2001, 276, 12153-12161 ); as well as the crystal structure of PIGF bound to various compounds searchable by 1RV6 (Christinger, H. W., J Biol Chem., 2004, 279, 10382-10388). Additionally, De Falco provides insight into the discovery and biological activity of placenta growth factor (De Falco, Exp Mol Med., 2012, 44, 1-9). Representative PGF Targeting Ligands are provided in Fig. 1. Additional PGF Targeting Ligands are provided in, for example, J Med Chem 54: 1256-65 (2011), J Nat Prod 76: 29-35 (2013), each of which is incorporated by reference herein.
  • Phospholipase A2 Group IB (PA21B)
  • the Target Protein is human phospholipase A2, Group IB (PA21B) (UniProtKB - P04054 (PA21B HUMAN)).
  • PA21B cleaves phospholipids preferentially at the sn-2 position, liberating free fatty acids and lysophospholipids.
  • PA21B has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders and cancer.
  • the Protein Data Bank website provides the crystal structure of PA21B searchable by 3FVJ and 3FVI (Pan, Y.H. et al., Biochim.Biophys.Acta., 2010, 1804, 1443-1448).
  • PA21B Targeting Ligands are provided in Fig. 1. Additional PA21B Targeting Ligands are provided in, for example, J Med Chem 39: 3636-58 (1996), Chembiochem 4: 181-5 (2003), J Med Chem 39: 5159-75 (1997), J Med Chem 51 : 4708-14 (2008), each of which is incorporated by reference herein.
  • Phospholipase A2, Group IIA PA2GA
  • the Target Protein is human phospholipase A2, Group IIA (PA2GA) (UniProtKB - P04054 (PA21B HUMAN)).
  • PA2GA catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. It is thought to participate in the regulation of phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Independent of its catalytic activity, it also acts as a ligand for integrins. PA2GA Induces cell proliferation in an integrin-dependent manner. PA2GA has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders, and cancer.
  • the Protein Data Bank website provides the crystal structure of PA2GA bound to various compounds searchable by 2ARM and 1SV3 (Singh, N. et al., Proteins, 2006, 64, 89-100); 5G3M and 5G3N (Giordanetto, F., et al. ACS Med Chem Lett., 2016, 7, 884); 1KQU (Jansford, K.A., et al., Chembiochem., 2003, 4 ,181-185); and 1ZYX (Singh, N. et al.,).
  • Singh et al. provides insight into the crystal structure of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding (Singh, N. et al., Proteins, 2006, 64(l):89-100); and Kitadokoro et al also provides insight into the crystal structure of human secretory phospholipase A2-IIA complex with the potent indolizine inhibitor 120-1032 (Kitadokoro, K. et al., J Biochem., 1998, 123(4), 619-23).
  • PA2GA Targeting Ligands are provided in Fig. 1. Additional PA2GA Targeting Ligands are provided in, for example, J Med Chem 48: 893-6 (2005), J Med Chem 39: 5159-75 (1997), each of which is incorporated by reference herein.
  • the Extracellular Protein Targeting Ligand is OPT-3.
  • OPT-3 has the following structure.
  • OPT-3 is attached to the linker through the primary amine of histidine as shown below.
  • the Extracellular Protein Targeting Ligand is OPT-2.
  • OPT-2 has the following structure.
  • OPT-2 is attached to the linker through the primary amine of histidine as shown below.
  • the Extracellular Protein Targeting Ligand is OPT-1.
  • OPT-1 has the following structure.
  • OPT-1 is attached to the linker through the primary amine of histidine as shown below.
  • the present invention also provides a method of treating a patient in need thereof wherein an effective amount of a compound of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or a bi- or tri-version thereof is administered to a patient either before, concurrently, or after administration of a compound of Formula VII.
  • an effective amount of a compound of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or a bi- or tri-version thereof is administered to a patient either before, concurrently, or after administration of a compound of Formula VII.
  • a method of treating a disorder mediated by an Extracellular Protein comprises administering (i) an effective dose of a compound or pharmaceutical composition of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or its respective bi- and tri-version or a pharmaceutically acceptable salt thereof to a patient in combination with (ii) an effective dose of a compound or pharmaceutical composition of Formula VII or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein.
  • step (i) and step (ii) are carried out within a sufficient temporal proximity that allows the selected compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or its respective bi- and triversion or a pharmaceutically acceptable salt thereof to react with the selected compound of Formula VII.
  • Step (i) can be carried out before or after step (ii) as long as the two steps are sufficiently close in time that the compounds are able to assemble in vivo.
  • the compound of Formula VII is administered first.
  • the compound of Formula VII is administered in excess on a per molecule basis to the compound of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or their respective bi- and tri-versions.
  • the two compounds combine faster in human plasma than they would in an organic solvent such as methanol.
  • an organic solvent such as methanol.
  • bi- and tri-versions of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, and IV-d can be administered to the patient in need thereof and combined in vivo to form bi- and tri-versions of the Extracellular Protein Degrader.
  • a compound of Formula I-Bi is combined with a compound of Formula
  • the Target Proteins of the current invention may include, but are not limited to, immunoglobulins, cytokines, chemokines, growth factors, coagulation factors, extracellular matrix proteins and proteins involved in formation and/or degradation of the extracellular matrix, esterases, lipases, peptidases, convertases, among others. These proteins mediate a range of diseases that can be treated with an effective amount ASGPR Ligand and Extracellular Protein Targeting Ligand described herein.
  • Immunoglobulin A (IgA) aberrant expression mediates a range of autoimmune and immune-mediated disorders, including IgA nephropathy (also known as Berger’s disease), celiac disease, Crohn’s disease, Henoch-Sconiein purpura (HSP) (also known as IgA vasculitis), liner IgA bullous dermatosis, IgA pemphigus, dermatitis herpetiformis, inflammatory bowel disease (IBD), Sjogren's syndrome, ankylosing spondylitis, alcoholic liver cirrhosis, acquired immunodeficiency syndrome, IgA multiple myeloma, a-chain disease, IgA monoclonal gammopathy, monoclonal gammopathy of undetermined significance (MGUS), and linear IgA bullous dermatosis, among others.
  • IgA nephropathy also known as Berger’s disease
  • celiac disease Crohn’s disease
  • IgG Immunoglobulin G
  • IgG4-related diseases which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nephritis, Riedel's thyroiditis, storiform fibrosis, Mikulicz's disease, Kiittner's tumor, inflammatory pseudotumors (in various sites of the body), mediastinal fibrosis, retroperitoneal fibrosis (Ormond’s disease), aortitis and periaortitis, proximal biliary strictures, idiopathic hypocomplementic tubulointerstitial nephritis, multifocal fibrosclerosis, pachymeningitis, pancreatic enlargement, tumefactive lesions, pericarditis, rheumatoid arthritis (RA),
  • IgG4-related diseases which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nep
  • Immunoglobulin E (IgE) - IgE is a strong mediator of allergic disease, including but not limited to, atopic asthma, allergic rhinitis, atopic dermatitis, IgE-mediated food allergy, IgE-mediated animal allergies, allergic conjunctivitis, allergic urticaria, anaphylactic shock, nasal polyposis, keratoconjunctivitis, mastocytosis, and eosinophilic gastrointestinal disease, bullous pemphigoid, chemotherapy induced hypersensitivity reaction, seasonal allergic rhinitis, interstitial cystitis, eosinophilic esophagitis, angioedema, acute interstitial nephritis, atopic eczema, eosinophilic bronchitis, chronic obstructive pulmonary disease, gastroenteritis, hyper-IgE syndrome (Job's Syndrome), IgE monoclonal gammopathy, and monoclonal
  • TNF- ⁇ mediates a number of disorders, including but not limited to rheumatoid arthritis, inflammatory bowel disease, graft-vs-host disease, ankylosing spondylitis, psoriasis, hidradenitis suppurativa, refractory asthma, systemic lupis erthyematosus, diabetes, and the induction of cachexia.
  • IL-2 mediates host versus graft rejection in transplants and autoimmune disorders, including, but not limited to, multiple sclerosis, idiopathic arthritis, ulcerative colitis, IL-2 induced hypotension, psoriasis, and other autoimmune disorders
  • IL-1 mediates a number of auto-inflammatory and autoimmune disorders, including, but not limited to, Blau syndrome, cryopyrin-associated periodic syndromes, familial Mediterranean fever, Majeed syndrome; mevalonate kinase deficiency syndrome, pyogenic arthritis-pyoderma gangrenosum-acne syndrome, tumor necrosis factor receptor- associated periodic syndrome, Behçet’s Disease, Sjogren’s Syndrome, gout and chondrocalcinosis, periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (or PFAPA) syndrome, rheumatoid arthritis, Type 2 diabetes mellitus, acute pericarditis, Chronic interstitial lung diseases (ILDs), and Still’s disease amongst others.
  • Blau syndrome cryopyrin-associated periodic syndromes
  • familial Mediterranean fever Majeed syndrome
  • mevalonate kinase deficiency syndrome pyogenic arthritis-py
  • IFN-y mediates a wide range of autoimmune disorders, including, but not limited to rheumatoid arthritis, multiple sclerosis (MS), corneal transplant rejection, and various autoimmune skin diseases such as psoriasis, alopecia areata, vitiligo, acne vulgaris, and others.
  • MS multiple sclerosis
  • autoimmune skin diseases such as psoriasis, alopecia areata, vitiligo, acne vulgaris, and others.
  • IL-21 mediates a number of autoimmune disorders, including Sjogren’s syndrome, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease.
  • IL-22 mediates a number of autoimmune disorders, including, but not limited to, graft versus host disease (GVHD), psoriasis, rheumatoid arthritis, atopic dermatitis, and asthma.
  • GVHD graft versus host disease
  • psoriasis rheumatoid arthritis
  • atopic dermatitis and asthma.
  • IL- 10 has been implicated in tumor survival and protection against cytotoxic chemotherapeutic drugs.
  • IL-5 has been implicated in a number of allergic disorders, including, but not limited to, asthma, nasal polyposis, atopic dermatitis, eosinophilic esophagitis, hypereosinophilic syndrome, and Churg-Strauss syndrome.
  • IL-6 has been implicated in a number of inflammatory diseases and cancers, including, but not limited to, Castleman’s disease, metastatic castration-associated prostate cancer, renal cell carcinoma, large-cell lung carcinoma, ovarian cancer, rheumatoid arthritis, asthma.
  • IL-8 has been implicated in the promotion of tumor progression, immune escape, epithelial-mesenchymal transition, and recruitment of myeloid-derived suppressor cells. Studies have demonstrated that high serum IL-8 levels correlate with poor prognosis in many malignant tumors. Preclinical studies have shown that IL-8 blockade may reduce mesenchymal features in tumor cells, making them less resistant to treatment.
  • CCL2 C-C motif chemokine ligand 2
  • Macrophage Migration Inhibitory Factor is a mediator of tumor progression; systemic inflammation; atherosclerosis; rheumatoid arthritis; and systemic lupus erythematosus, among others.
  • FGF1 Fibroblast Growth Factor 1
  • FGF1 Fibroblast Growth Factor 1
  • FGF2 Fibroblast Growth Factor 2
  • VEGF-A Vascular Epithelial Growth Factor
  • TGF- ⁇ 1 Transforming Growth Factor- ⁇ 1 (TGF- ⁇ 1) expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF- ⁇ 1 mediated tumor suppression via T-cell exclusion. TGF- ⁇ 1 expression has also been implicated in hematological malignancies and fibrosis.
  • TGF- ⁇ 2 Transforming Growth Factor- ⁇ 2 (TGF- ⁇ 2) expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF- ⁇ 2 mediated tumor suppression via T-cell exclusion. TGF- ⁇ 2 expression has also been implicated in hematological malignancies and fibrosis.
  • Placental Growth Factor promotes cell tumor growth, and has been implicated in age-related macular degeneration (AMD) and choroidal neovascularization (CNV).
  • Cholinesterase has been implicated in cognitive disorders such as dementia and Alzheimer’s disease.
  • Carboxypeptidase B2 has been implicated and targeted to inhibit thrombosis.
  • Coagulation Factor Xa is a mediator in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • Coagulation Factor XI is a mediator in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • Coagulation Factor XII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • Coagulation Factor XIII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
  • Prothrombin is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • Coagulation Factor VII is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • Coagulation Factor IX is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
  • Neutrophil Elastase - Neutrophil elastase has been implicated in a number of disorders, including lung disease, chronic obstructive pulmonary disease, pneumonia, respiratory distress, and acute lung injury (ALI), and cystic fibrosis, as well as chronic kidney disease.
  • Fibronectin-1 - Interfering with FN polymerization may attenuate myofibroblasts and fibrosis and improve cardiac function after ischemia/reperfusion (I/R) injury.
  • I/R ischemia/reperfusion
  • Thrombospondin- 1- TSP-1 has been implicated in a number of diseases, including in promoting certain cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
  • cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
  • Urokinase-type Plasminogen Activator (UP A) - UPA has been implicated in vascular diseases and cancer progression. Elevated expression levels of urokinase and several other components of the plasminogen activation system are found to be correlated with tumor malignancy.
  • Plasminogen Activator, Tissue Type (TP A) - PLA has been shown activated in various cancers including oral malignancy.
  • Plasminogen (PLG) - PLG has been implicated in tumor invasion and inflammation.
  • Plasminogen Activator Inhibitor-1 (PAI-1) - PAI-1 has been implicated in angiogenesis, metastasis, and poor prognosis in tumors, including, but not limited to, oral cancers and breast cancers.
  • Kallikrein-1 - Kallikrein has been implicated in adverse reactions in hereditary angioedema (HAE).
  • Plasma Kallikrein - Plasma kallikrein has been implicated in retinal dysfunction, the development of diabetic macular edema and hereditary angioedema (HAE).
  • HAE hereditary angioedema
  • Matrix Metallopeptidase - 1 - MMP-1 has been implicated in cardiovascular disease, development of fibrosis, and growth of certain cancers such as bladder cancer.
  • Phospholipase A2, Group IIA (PA2GA) - PA2GA has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders, and cancer.
  • Lipoprotein Lipase - Lipoprotein lipase has been implicated in the development of cardiovascular disease and obesity.
  • PA21B Phospholipase A2
  • PA21B Group IB - PA21B has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders and cancer.
  • PCSK-9 Proprotein Convertase Subtilisin/Kexin Type 9
  • a third agent is administered to the patient in need thereof to treat a patient such as a human with a disorder as described herein that mediated by the targeted extracellular protein.
  • bioactive agent is used to describe this an agent, other than the two selected compounds according to the present invention, which can be used in combination or alternation with the compounds of the present invention to achieve a desired result of therapy.
  • the compounds of the present invention and the bioactive agent are administered in a manner that they are active in vivo during overlapping time periods, for example, have timeperiod overlapping Cmax, Tmax, AUC or other pharmacokinetic parameter.
  • the compounds of the present invention and the bioactive agent are administered to a patient in need thereof that do not have overlapping pharmacokinetic parameter, however, one has a therapeutic impact on the therapeutic efficacy of the other.
  • the bioactive agent is an immune modulator, including but not limited to a checkpoint inhibitor, including as non-limiting examples, a PD-1 inhibitor, PD-L1 inhibitor, PD-L2 inhibitor, CTLA-4 inhibitor, LAG-3 inhibitor, TIM-3 inhibitor, V-domain Ig suppressor of T-cell activation (VISTA) inhibitors, small molecule, peptide, nucleotide, or other inhibitor.
  • a checkpoint inhibitor including as non-limiting examples, a PD-1 inhibitor, PD-L1 inhibitor, PD-L2 inhibitor, CTLA-4 inhibitor, LAG-3 inhibitor, TIM-3 inhibitor, V-domain Ig suppressor of T-cell activation (VISTA) inhibitors, small molecule, peptide, nucleotide, or other inhibitor.
  • VISTA V-domain Ig suppressor of T-cell activation
  • the immune modulator is an antibody, such as a monoclonal antibody.
  • PD-L1 inhibitors that block the interaction of PD-1 and PD-L1 by binding to the PD-L1 receptor, and in turn inhibits immune suppression, include for example, atezolizumab (Tecentriq), durvalumab (AstraZeneca and Medlmmune), KN035 (Alphamab), and BMS-936559 (Bristol-Myers Squibb).
  • CTLA-4 checkpoint inhibitors that bind to CTLA-4 and inhibits immune suppression include, but are not limited to, ipilimumab, tremelimumab (AstraZeneca and Medlmmune), AGEN1884 and AGEN2041 (Agenus).
  • LAG-3 checkpoint inhibitors include, but are not limited to, BMS-986016 (Bristol-Myers Squibb), GSK2831781 (GlaxoSmithKline), IMP321 (Prima BioMed), LAG525 (Novartis), and the dual PD-1 and LAG-3 inhibitor MGD013 (MacroGenics).
  • BMS-986016 Bristol-Myers Squibb
  • GSK2831781 GaxoSmithKline
  • IMP321 Primary BioMed
  • LAG525 Novartis
  • MGD013 Non-Genics
  • An example of a TIM-3 inhibitor is TSR- 022 (Tesaro).
  • the checkpoint inhibitor is selected from nivolumab/OPDIVO®; pembrolizumab/KEYTRUDA®; and pidilizumab/CT-011, MPDL3280A/RG7446; MEDI4736; MSB0010718C; BMS 936559, a PDL2/lg fusion protein such as AMP 224 or an inhibitor of B7- H3 (e g., MGA271 ), B7-H4, BTLA, HVEM, TIM3, GAL9, LAG 3, VISTA, KIR, 2B4, CD 160, CGEN- 15049, CHK 1 , CHK2, A2aR, B-7 family ligands, or a combination thereof.
  • B7- H3 e g., MGA271
  • B7-H4 BTLA
  • HVEM TIM3, GAL9, LAG 3, VISTA, KIR, 2B4, CD 160, CGEN- 15049, CHK 1 , CHK2, A2a
  • the bioactive agent is an ALK inhibitor.
  • ALK inhibitors include but are not limited to Crizotinib, Alectinib, ceritinib, TAE684 (NVP-TAE684), GSK1838705A, AZD3463, ASP3026, PF-06463922, entrectinib (RXDX-101), and AP26113.
  • the bioactive agent is an EGFR inhibitor.
  • EGFR inhibitors include erlotinib (Tarceva), gefitinib (Iressa), afatinib (Gilotrif), rociletinib (CO- 1686), osimertinib (Tagrisso), olmutinib (Olita), naquotinib (ASP8273), soloartinib (EGF816), PF- 06747775 (Pfizer), icotinib (BPL2009), neratinib (HKL272; PB272); avitinib (AC0010), EAI045, tarloxotinib (TH-4000; PR-610), PF-06459988 (Pfizer), tesevatinib (XL647; EXEL-7647; KD- 019), transtinib, WZ-3146, WZ8040, CNX-2006, and
  • the bioactive agent is a CD20 inhibitor.
  • CD20 inhibitors include obinutuzumab, rituximab, fatumumab, ibritumomab, tositumomab, and ocrelizumab.
  • the bioactive agent is a JAK3 inhibitor.
  • JAK3 inhibitors include tasocitinib.
  • the bioactive agent is a BCL-2 inhibitor.
  • BCL-2 inhibitors include venetoclax, ABT-199 (4-[4-[[2-(4-Chlorophenyl)-4,4-dimethylcyclohex-l-en- l-yl]methyl]piperazin-l-yl]-N-[[3-nitro-4-[[(tetrahydro-2H-pyran-4- yl)methyl]amino]phenyl]sulfonyl]-2-[(lH- pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide), ABT-737 (4-[4-[[2-(4-chlorophenyl)phenyl]methyl]piperazin-l-yl]-N-[4- [[(2R)-4-(dimethylamino)-l- phenylsulfanylbutan-2-yl] amino]-3- nitrophenyl] sulfonyl
  • the bioactive agent is a kinase inhibitor.
  • the kinase inhibitor is selected from a phosphoinositide 3-kinase (PI3K) inhibitor, a Bruton’s tyrosine kinase (BTK) inhibitor, or a spleen tyrosine kinase (Syk) inhibitor, or a combination thereof.
  • PI3K phosphoinositide 3-kinase
  • BTK Bruton’s tyrosine kinase
  • Syk spleen tyrosine kinase
  • PI3 kinase inhibitors include, but are not limited to, Wortmannin, demethoxyviridin, perifosine, idelalisib, Pictilisib , Palomid 529, ZSTK474, PWT33597, CUDC- 907, and AEZS-136, duvelisib, GS-9820, BKM120, GDC-0032 (Taselisib) (2-[4-[2-(2-Isopropyl- 5-methyl-l,2,4-triazol-3-yl)-5,6-dihydroimidazo[l,2-d][l,4]benzoxazepin-9-yl]pyrazol-l-yl]-2- methylpropanamide), MLN-1117 ((2R)-l-Phenoxy-2-butanyl hydrogen (S)-methylphosphonate; or Methyl (oxo) ⁇ [(2R)-l-phenoxy-2-buty
  • BTK inhibitors examples include ibrutinib (also known as PCI-32765)(ImbruvicaTM)(l- [(3R)-3-[4-amino-3-(4-phenoxy-phenyl)pyrazolo[3,4-d]pyrimidin-l-yl]piperidin-l-yl]prop-2-en-
  • dianilinopyrimidine-based inhibitors such as AVL-101 and AVL-291/292 (N-(3-((5- fluoro-2-((4-(2-methoxyethoxy)phenyl)amino)pyrimidin-4-yl)amino)phenyl)acrylamide) (Avila Therapeutics) (see US Patent Publication No 2011/0117073, incorporated herein in its entirety), Dasatinib ([N-(2-chloro-6-methylphenyl)-2-(6-(4-(2-hydroxyethyl)piperazin- 1 -yl)-2- methylpyrimidin-4-ylamino)thiazole-5-carboxamide], LFM-A13 (alpha-cyano-beta-hydroxy - beta-methyl-N-(2,5-ibromophenyl) propenamide), GDC-0834 ([R-N-(3-(6-(4-(l,4-dimethyl-3-
  • Syk inhibitors include, but are not limited to, Cerdulatinib (4-(cyclopropylamino)-2-((4- (4-(ethylsulfonyl)piperazin-l-yl)phenyl)amino)pyrimidine-5-carboxamide), entospletinib (6-(lH- indazol-6-yl)-N-(4-morpholinophenyl)imidazo[l,2-a]pyrazin-8-amine), fostamatinib ([6-( ⁇ 5- Fluoro-2-[(3,4,5-trimethoxyphenyl)amino]-4-pyrimidinyl ⁇ amino)-2,2-dimethyl-3-oxo-2,3- dihydro-4H-pyrido[3,2-b][l,4]oxazin-4-yl]methyl dihydrogen phosphate), fostamatinib disodium salt (sodium (6-((5-fluoro-2-((
  • the bioactive agent is a MEK inhibitor.
  • MEK inhibitors are well known, and include, for example, trametinib/GSK1120212 (N-(3- ⁇ 3-Cyclopropyl-5-[(2-fluoro-4- iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin-l(2H- yl ⁇ phenyl)acetamide), selumetinib (6-(4-bromo-2-chloroanilino)-7-fluoro-N-(2 -hydroxy ethoxy)- 3-methylbenzimidazole-5-carboxamide), pimasertib/AS703026/MSC 1935369 ((S)-N-(2,3- dihydroxypropyl)-3-((2-fluoro-4- iodophenyl)amino)isonicot
  • the bioactive agent is a Raf inhibitor.
  • Raf inhibitors include, for example, Vemurafinib (N-[3-[[5-(4-Chlorophenyl)-lH-pyrrolo[2,3-b]pyridin-3- yl]carbonyl]-2,4-difluorophenyl]-l -propanesulfonamide), sorafenib tosylate (4-[4-[[4-chloro-3- (trifluoromethyl)phenyl]carbamoylamino]phenoxy]-N-methylpyridine-2-carboxamide;4- m ethylbenzenesulfonate), AZ628 (3-(2-cyanopropan-2-yl)-N-(4-methyl-3-(3-methyl-4-oxo-3,4- dihydroquinazolin-6-ylamino)phenyl)benzamide), NVP-BHG712 (4-methyl-3-(
  • the bioactive agent is an AKT inhibitor, including, but not limited to, MK-2206, GSK690693, Perifosine, (KRX-0401), GDC-0068, Triciribine, AZD5363, Honokiol, PF-04691502, and Miltefosine, a FLT-3 inhibitor, including, but not limited to, P406, Dovitinib, Quizartinib (AC220), Amuvatinib (MP-470), Tandutinib (MLN518), ENMD-2076, and KW- 2449, or a combination thereof.
  • AKT inhibitor including, but not limited to, MK-2206, GSK690693, Perifosine, (KRX-0401), GDC-0068, Triciribine, AZD5363, Honokiol, PF-04691502, and Miltefosine
  • a FLT-3 inhibitor including, but not limited to, P406, Dovitinib, Quizart
  • the bioactive agent is an mTOR inhibitor.
  • mTOR inhibitors include, but are not limited to, rapamycin and its analogs, everolimus (Afinitor), temsirolimus, ridaforolimus, sirolimus, and deforolimus.
  • MEK inhibitors include but are not limited to tametinib/GSK1120212 (N-(3- ⁇ 3-Cyclopropyl-5-[(2-fluoro-4- iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin-l(2H- yl ⁇ phenyl)acetamide), selumetinob (6-(4-bromo-2-chl oroanilino)-7-fluoro-N-(2 -hydroxy ethoxy)-
  • the bioactive agent is a RAS inhibitor.
  • RAS inhibitors include but are not limited to Reolysin and siG12D LODER.
  • the bioactive agent is a HSP inhibitor.
  • HSP inhibitors include but are not limited to Geldanamycin or 17-N-Allylamino-17-demethoxygeldanamycin (17AAG), and Radicicol.
  • Additional bioactive compounds include, for example, everolimus, trabectedin, abraxane, TLK 286, AV-299, DN-101, pazopanib, GSK690693, RTA 744, ON O91O.Na, AZD 6244 (ARRY- 142886), AMN-107, TKL258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197, MK- 0457, MLN8054, PHA-739358, R-763, AT-9263, aFLT-3 inhibitor, a VEGFR inhibitor, an aurora kinase inhibitor, a PIK-1 modulator, an HD AC inhbitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a focal adhesion kinase inhibitor, a Map kinase kinase (mek) inhibitor,
  • the compounds are administered in combination with ifosfamide.
  • the bioactive agent is selected from, but are not limited to, Imatinib mesylate (Gleevac®), Dasatinib (Sprycel®), Nilotinib (Tasigna®), Bosutinib (Bosulif®), Trastuzumab (Herceptin®), trastuzumab-DMl, Pertuzumab (PerjetaTM), Lapatinib (Tykerb®), Gefitinib (Iressa®), Erlotinib (Tarceva®), Cetuximab (Erbitux®), Panitumumab (Vectibix®), Vandetanib (Caprelsa®), Vemurafenib (Zelboraf®), Vorinostat (Zolinza®), Romidepsin (Istodax®), Bexarotene (Tagretin®), Alitretinoin (Panretin®), Tretinoin (Vesa
  • the bioactive agent is an anti-inflammatory agent, a chemotherapeutic agent, a radiotherapeutic, an additional therapeutic agent, or an immunosuppressive agent.
  • Suitable chemotherapeutic bioactive agents include, but are not limited to, a radioactive molecule, a toxin, also referred to as cytotoxin or cytotoxic agent, which includes any agent that is detrimental to the viability of cells, and liposomes or other vesicles containing chemotherapeutic compounds.
  • General anticancer pharmaceutical agents include: Vincristine (Oncovin®) or liposomal vincristine (Marqibo®), Daunorubicin (daunomycin or Cerubidine®) or doxorubicin (Adriamycin®), Cytarabine (cytosine arabinoside, ara-C, or Cytosar®), L-asparaginase (Elspar®) or PEG-L-asparaginase (pegaspargase or Oncaspar®), Etoposide (VP-16), Teniposide (Vumon®), 6-mercaptopurine (6-MP or Purinethol®), Methotrexate, Cyclophosphamide (Cytoxan®), Prednisone, Dexamethasone (Decadron), imatinib (Gleevec®), dasatinib (Sprycel®), nilotinib (Tasigna®), bosutinib (Bosul
  • chemotherapeutic agents include, but are not limited to 1- dehydrotestosterone, 5 -fluorouracil decarbazine, 6-mercaptopurine, 6-thioguanine, actinomycin D, adriamycin, aldesleukin, an alkylating agent, allopurinol sodium, altretamine, amifostine, anastrozole, anthramycin (AMC)), an anti-mitotic agent, cis-dichlorodiamine platinum (II) (DDP) cisplatin), diamino dichloro platinum, anthracycline, an antibiotic, an antimetabolite, asparaginase, BCG live (intravesical), betamethasone sodium phosphate and betamethasone acetate, bicalutamide, bleomycin sulfate, busulfan, calcium leucouorin, calicheamicin, capecitabine, carboplatin, lomustine (CCNU), carmustine
  • the compounds of the present invention are administered in combination with a chemotherapeutic agent (e.g., a cytotoxic agent or other chemical compound useful in the treatment of cancer).
  • chemotherapeutic agents include alkylating agents, antimetabolites, folic acid analogs, pyrimidine analogs, purine analogs and related inhibitors, vinca alkaloids, epipodopyyllotoxins, antibiotics, L-Asparaginase, topoisomerase inhibitors, interferons, platinum coordination complexes, anthracenedione substituted urea, methyl hydrazine derivatives, adrenocortical suppressant, adrenocorticosteroides, progestins, estrogens, antiestrogen, androgens, antiandrogen, and gonadotropin-releasing hormone analog.
  • 5 -fluorouracil 5 -fluorouracil
  • chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; cally statin; CC-1065
  • dynemicin including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo- 5-oxo-L-norleucine, ADRIAMYCIN® (doxorubicin, including morpholino-doxorubicin, cyanomorpholino- doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epi
  • Two or more chemotherapeutic agents can be used in a cocktail to be administered in combination with the compounds of the present invention.
  • Suitable dosing regimens of combination chemotherapies are known in the ar. For example combination dosing regimes are described in Saltz et al., Proc. Am. Soc. Clin. Oncol. 18:233a (1999) and Douillard et al., Lancet 355(9209): 1041 -1047 (2000).
  • Additional therapeutic agents that can be administered in combination with a Compound disclosed herein can include bevacizumab, sutinib, sorafenib, 2-methoxyestradiol or 2ME2, finasunate, vatalanib, vandetanib, aflibercept, volociximab, etaracizumab (MEDL522), cilengitide, erlotinib, cetuximab, panitumumab, gefitinib, trastuzumab, dovitinib, figitumumab, atacicept, rituximab, alemtuzumab, aldesleukine, atlizumab, tocilizumab, temsirolimus, everolimus, lucatumumab, dacetuzumab, HLL1, huN901-DMl, atiprimod, natalizumab, bortezomib, carfilzomi
  • the additional therapy is a monoclonal antibody (MAb).
  • MAbs stimulate an immune response that destroys cancer cells. Similar to the antibodies produced naturally by B cells, these MAbs may “coat” the cancer cell surface, triggering its destruction by the immune system.
  • bevacizumab targets vascular endothelial growth factor (VEGF), a protein secreted by tumor cells and other cells in the tumor’s microenvironment that promotes the development of tumor blood vessels. When bound to bevacizumab, VEGF cannot interact with its cellular receptor, preventing the signaling that leads to the growth of new blood vessels.
  • VEGF vascular endothelial growth factor
  • cetuximab and panitumumab target the epidermal growth factor receptor (EGFR), and trastuzumab targets the human epidermal growth factor receptor 2 (HER-2).
  • MAbs that bind to cell surface growth factor receptors prevent the targeted receptors from sending their normal growth-promoting signals. They may also trigger apoptosis and activate the immune system to destroy tumor cells.
  • the bioactive agent is an immunosuppressive agent.
  • the immunosuppressive agent can be a calcineurin inhibitor, e.g. a cyclosporin or an ascomycin, e.g. Cyclosporin A (NEORAL®), FK506 (tacrolimus), pimecrolimus, a mTOR inhibitor, e.g. rapamycin or a derivative thereof, e.g.
  • Sirolimus (RAPAMUNE®), Everolimus (Certican®), temsirolimus, zotarolimus, biolimus-7, biolimus-9, a rapalog, e.g.ridaforolimus, azathioprine, campath 1H, a SIP receptor modulator, e.g. fmgolimod or an analogue thereof, an anti IL-8 antibody, mycophenolic acid or a salt thereof, e.g. sodium salt, or a prodrug thereof, e.g.
  • Mycophenolate Mofetil (CELLCEPT®), OKT3 (ORTHOCLONE OKT3®), Prednisone, ATGAM®, THYMOGLOBULIN®, Brequinar Sodium, OKT4, T10B9.A-3A, 33B3.1, 15- deoxyspergualin, tresperimus, Leflunomide ARAVA®, CTLALIg, anti-CD25, anti-IL2R, Basiliximab (SIMULECT®), Daclizumab (ZENAPAX®), mizorbine, methotrexate, dexamethasone, ISAtx-247, SDZ ASM 981 (pimecrolimus, Elidel®), CTLA41g (Abatacept), belatacept, LFA31g courts etanercept (sold as Enbrel® by Immunex), adalimumab (Humira®), infliximab (Remicade®), an anti-LFA-1 antibody, natalizum
  • the bioactive agent is a therapeutic agent which is a biologic such a cytokine (e.g., interferon or an interleukin (e.g., IL-2)) used in cancer treatment.
  • a biologic such as a cytokine (e.g., interferon or an interleukin (e.g., IL-2)) used in cancer treatment.
  • the biologic is an anti -angiogenic agent, such as an anti-VEGF agent, e.g., bevacizumab (AVASTIN®).
  • the biologic is an immunoglobulin-based biologic, e.g., a monoclonal antibody (e.g., a humanized antibody, a fully human antibody, an Fc fusion protein or a functional fragment thereof) that agonizes a target to stimulate an anti-cancer response, or antagonizes an antigen important for cancer.
  • Such agents include RITUXAN® (rituximab); ZENAPAX® (daclizumab); SIMULECT® (basiliximab); SYNAGIS® (palivizumab); REMICADE® (infliximab); HERCEPTIN® (trastuzumab); MYLOTARG® (gemtuzumab ozogamicin); CAMPATH® (alemtuzumab); ZEVALIN® (ibritumomab tiuxetan); HUMIRA® (adalimumab); XOLAIR® (omalizumab); BEXXAR® (tositumomab-1- 131 ); RAPTIVA® (efalizumab); ERBITUX® (cetuximab); AVASTIN® (bevacizumab); TYSABRI® (natalizumab); ACTEMRA® (tocilizumab); VECTIBIX® (panit
  • the combination therapy may include a therapeutic agent which is a non-drug treatment.
  • the compound could be administered in addition to radiation therapy, cryotherapy, hyperthermia, and/or surgical excision of tumor tissue.
  • the compounds of the present invention assemble in vivo to afford an extracellular protein degrading compound.
  • this in vivo assembly is advantageous as compared to making the degrader in vitro because the individual components may have better pharmacokinetic or physical properties than the full molecule.
  • a compound of the present invention or a pharmaceutically acceptable salt, solvate or prodrug thereof as disclosed herein can be administered as a neat chemical, but is more typically administered as a pharmaceutical composition that includes an effective amount for a host, typically a human, in need of such treatment to treat a disorder mediated by the target extracellular protein, as described herein or otherwise well-known for that extracellular protein.
  • the two compounds of the present invention that form the ASGPR-binding Extracellular Protein degrader of the present invention can be administered in any manner that allows the degrader to bind to the Extracellular Protein, typically in the blood stream, and carry it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation.
  • methods to deliver the degraders of the present invention include, but are not limited to, oral, intravenous, sublingual, subcutaneous, parenteral, buccal, rectal, intra-aortal, intracranial, subdermal or transnasal, or by other means, in dosage unit formulations containing one or more conventional pharmaceutically acceptable carriers, as appropriate.
  • the compound of Formula VII is administered by a different route of administration from the compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, IV-d, V-d, Vl-d, or the bis or tris version.
  • compositions comprising an effective amount of the compound of the present invention or its pharmaceutically acceptable salt together with at least one pharmaceutically acceptable carrier for any appropriate use thereof.
  • the pharmaceutical composition may contain a compound or salt as the only active agent, or, in an alternative embodiment, the compound and at least one additional active agent.
  • pharmaceutically acceptable salt refers to a salt of the described compound which is, within the scope of sound medical judgment, suitable for administration to a host such as a human without undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for its intended use.
  • pharmaceutically acceptable salt refers to the relatively non-toxic, inorganic and organic acid addition salts of the presently disclosed compounds. These salts can be prepared during the final isolation and purification of the compounds or by separately reacting the purified compound in its free form with a suitable organic or inorganic acid and then isolating the salt thus formed.
  • Basic compounds are capable of forming a wide variety of different salts with various inorganic and organic acids.
  • Acid addition salts of the basic compounds are prepared by contacting the free base form with a sufficient amount of the desired acid to produce the salt in the conventional manner.
  • the free base form can be regenerated by contacting the salt form with a base and isolating the free base in the conventional manner.
  • the free base forms may differ from their respective salt forms in certain physical properties such as solubility in polar solvents.
  • Pharmaceutically acceptable base addition salts may be formed with metals or amines, such as alkali and alkaline earth metal hydroxides, or of organic amines. Examples of metals used as cations, include, but are not limited to, sodium, potassium, magnesium, calcium, and the like.
  • Suitable amines include, but are not limited to, N,N'-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, N-methylglucamine, and procaine.
  • the base addition salts of acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner.
  • the free acid form can be regenerated by contacting the salt form with an acid and isolating the free acid in a conventional manner.
  • the free acid forms may differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents.
  • Salts can be prepared from inorganic acids sulfate, pyrosulfate, bisulfate, sulfite, bisulfite, nitrate, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, nitric, phosphoric, sulfuric, hydrobromic, hydriodic, phosphorus, and the like.
  • Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfate, nitrate, acetate, oxalate, valerate, oleate, palmitate, stearate, laurate, borate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, naphthylate mesylate, glucoheptonate, lactobionate, laurylsulphonate and isethionate salts, and the like.
  • Salts can also be prepared from organic acids, such as aliphatic mono- and dicarboxylic acids, phenyl -substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and aromatic sulfonic acids, etc. and the like.
  • organic acids such as aliphatic mono- and dicarboxylic acids, phenyl -substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and aromatic sulfonic acids, etc. and the like.
  • Representative salts include acetate, propionate, caprylate, isobutyrate, oxalate, malonate, succinate, suberate, sebacate, fumarate, maleate, mandelate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, phthalate, benzenesulfonate, toluenesulfonate, phenyl acetate, citrate, lactate, maleate, tartrate, methanesulfonate, and the like.
  • Pharmaceutically acceptable salts can include cations based on the alkali and alkaline earth metals, such as sodium, lithium, potassium, calcium, magnesium and the like, as well as non-toxic ammonium, quaternary ammonium, and amine cations including, but not limited to, ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like. Also contemplated are the salts of amino acids such as arginate, gluconate, galacturonate, and the like. See, for example, Berge et al., J. Pharm. Sci., 1977, 66, 1-19, which is incorporated herein by reference.
  • the pharmaceutical composition is in a dosage form that contains from about 0.1 mg to about 1500 mg, from about 10 mg to about 1000 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of the active compound and optionally from about 0.1 mg to about 1500 mg, from about 10 mg to about 1000 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of an additional active agent in a unit dosage form.
  • dosage forms with at least 0.1, 1, 5, 10, 25, 50, 100, 200, 250, 300, 400, 500, 600, 700, or 750 mg of active compound, or its salt.
  • the dose ranges from about 0.01-100 mg/kg of patient body weight, for example about 0.01 mg/kg, about 0.05 mg/kg, about 0.1 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, about 2.5 mg/kg, about 3 mg/kg, about 3.5 mg/kg, about 4 mg/kg, about 4.5 mg/kg, about 5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, about 30 mg/kg, about 35 mg/kg, about 40 mg/kg, about 45 mg/kg, about 50 mg/kg, about 55 mg/kg, about 60 mg/kg, about 65 mg/kg, about 70 mg/kg, about 75 mg/kg, about 80 mg/kg, about 85 mg/kg, about 90 mg/kg, about 95 mg/kg, or about 100 mg/kg.
  • compounds disclosed herein or used as described are administered once a day (QD), twice a day (BID), or three times a day (TID).
  • compounds disclosed herein or used as described are administered at least once a day for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, at least 8 days, at least 9 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days, at least 21 days, at least 22 days, at least 23 days, at least 24 days, at least 25 days, at least 26 days, at least 27 days, at least 28 days, at least 29 days, at least 30 days, at least 31 days, at least 35 days, at least 45 days, at least 60 days, at least 75 days, at least 90 days, at least 120 days, at least 150 days, at least
  • the compound of the present invention is administered once a day, twice a day, three times a day, or four times a day.
  • the pharmaceutical composition may be formulated as any pharmaceutically useful form, e.g., a pill, capsule, tablet, an injection or infusion solution, a syrup, an inhalation formulation, a suppository, a buccal or sublingual formulation, a parenteral formulation, or in a medical device.
  • Some dosage forms, such as tablets and capsules, can be subdivided into suitably sized unit doses containing appropriate quantities of the active components, e.g., an effective amount to achieve the desired purpose.
  • Carriers include excipients and diluents and must be of sufficiently high purity and sufficiently low toxicity to render them suitable for administration to the patient being treated.
  • the carrier can be inert or it can possess pharmaceutical benefits of its own.
  • the amount of carrier employed in conjunction with the compound is sufficient to provide a practical quantity of material for administration per unit dose of the compound. If provided as in a liquid, it can be a solution or a suspension.
  • Representative carriers include phosphate buffered saline, water, solvent(s), diluents, pH modifying agents, preservatives, antioxidants, suspending agents, wetting agent, viscosity agents, tonicity agents, stabilizing agents, and combinations thereof.
  • the carrier is an aqueous carrier.
  • aqueous carries include, but are not limited to, an aqueous solution or suspension, such as saline, plasma, bone marrow aspirate, buffers, such as Hank’ s Buffered Salt Solution (HBSS), HEPES (4-(2-hy droxy ethyl)- 1 -piperazineethanesulfonic acid), Ringers buffer, ProVisc®, diluted Pro Vise®, Proviso® diluted with PBS, Krebs buffer, Dulbecco’s PBS, normal PBS, sodium hyaluronate solution (HA, 5 mg/mL in PBS), citrate buffer, simulated body fluids, plasma platelet concentrate and tissue culture medium or an aqueous solution or suspension comprising an organic solvent.
  • HBSS Hank’ s Buffered Salt Solution
  • HEPES 4-(2-hy droxy ethyl)- 1 -piperazineethanesulfonic acid
  • Ringers buffer such as Hank’ s
  • Acceptable solutions include, for example, water, Ringer’s solution and isotonic sodium chloride solutions.
  • the formulation may also be a sterile solution, suspension, or emulsion in a non-toxic diluent or solvent such as 1,3 -butanediol.
  • Viscosity agents may be added to the pharmaceutical composition to increase the viscosity of the composition as desired.
  • useful viscosity agents include, but are not limited to, hyaluronic acid, sodium hyaluronate, carbomers, polyacrylic acid, cellulosic derivatives, polycarbophil, polyvinylpyrrolidone, gelatin, dextin, polysaccharides, polyacrylamide, polyvinyl alcohol (including partially hydrolyzed polyvinyl acetate), polyvinyl acetate, derivatives thereof and mixtures thereof.
  • Solutions, suspensions, or emulsions for administration may be buffered with an effective amount necessary to maintain a pH suitable for the selected administration.
  • Suitable buffers are well known by those skilled in the art. Some examples of useful buffers are acetate, borate, carbonate, citrate, and phosphate buffers.
  • Solutions, suspensions, or emulsions for topical, for example, ocular administration may also contain one or more tonicity agents to adjust the isotonic range of the formulation. Suitable tonicity agents are well known in the art. Some examples include glycerin, mannitol, sorbitol, sodium chloride, and other electrolytes.
  • Classes of carriers include, but are not limited to binders, buffering agents, coloring agents, diluents, disintegrants, emulsifiers, flavorants, glidents, lubricants, preservatives, stabilizers, surfactants, tableting agents, and wetting agents.
  • Some carriers may be listed in more than one class, for example vegetable oil may be used as a lubricant in some formulations and a diluent in others.
  • Exemplary pharmaceutically acceptable carriers include sugars, starches, celluloses, powdered tragacanth, malt, gelatin; talc, and vegetable oils.
  • Optional active agents may be included in a pharmaceutical composition, which do not substantially interfere with the activity of the compound of the present invention.
  • compositions/combinations can be formulated for oral administration.
  • These compositions can contain any amount of active compound that achieves the desired result, for example between 0.1 and 99 weight % (wt.%) of the compound and usually at least about 5 wt.% of the compound. Some embodiments contain from about 25 wt.% to about 50 wt. % or from about 5 wt.% to about 75 wt.% of the compound.
  • Enteric coated oral tablets may also be used to enhance bioavailability of the compounds for an oral route of administration.
  • Formulations suitable for rectal administration are typically presented as unit dose suppositories. These may be prepared by admixing the active compound with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture. Processes of Manufacture
  • the compounds of the present invention can be manufactured according to routes described in the Working Examples below or as otherwise known in the patent or scientific literature and if appropriate supported by the knowledge of the ordinary worker or common general knowledge.
  • Some of the carbons in the compounds described herein are drawn with designated stereochemistry. Other carbons are drawn without stereochemical designation. When drawn without designated stereochemistry, that carbon can be in any desired stereochemical configuration that achieves the desired purpose.
  • One skilled in the art will recognize that pure enantiomers, enantiomerically enriched compounds, racemates and diastereomers can be prepared by methods known in the art as guided by the information provided herein. Examples of methods to obtain optically active materials include at least the following: i) chiral liquid chromatography - a technique whereby diastereomers are separated in a liquid mobile phase by virtue of their differing interactions with a stationary phase (including vial chiral HPLC).
  • the stationary phase can be made of chiral material or the mobile phase can contain an additional chiral material to provoke the differing interactions; ii) non-chiral chromatography of diastereomers-Often diastereomers can be separated using normal non-chiral column conditions; iii) chiral gas chromatography - a technique whereby the racemate is volatilized and enantiomers are separated by virtue of their differing interactions in the gaseous mobile phase with a column containing a fixed non-racemic chiral adsorbent phase; iv) simultaneous crystallization - a technique whereby the individual diastereomers are separately crystallized from a solution; v) enzymatic resolutions - a technique whereby partial or complete separation of diastereomers are separated by virtue of differing rates of reaction with an enzyme; vi) chemical asymmetric synthesis - a synthetic technique whereby the desired diastereomer is synthesized from an achiral precursor under conditions that produce asymmetry (i.e
  • diastereomer separations - a technique whereby a racemic compound is reaction with an enantiomerically pure reagent (the chiral auxiliary) that converts the individual enantiomers to diastereomers.
  • the resulting diastereomers are then separated by chromatography or crystallization by virtue of their now more distinct structural differences the chiral auxiliary later removed to obtain the desired enantiomer;
  • Reactions were monitored via TLC on silica gel 60 HSGF254 percolated plates (0.15-0.2 mm SiCh) and visualized using UV light (254 nm or 365 nm) and/or staining with phosphomolybdic acid ethanol solution (10 g in 100 mL ethanol) and subsequent heating or monitored via LCMS.
  • Example 1 and 2 above can react with the compounds of Example 3 in the body to form the following non-limiting extracellular degrading compounds:
  • Step 2 To a solution of (2R,3R,4R,5R,6R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6- methoxy-5-nitrotetrahydro-2H-pyran (535 mg, 1.09 mmol) in MeOH (10 mL) was added Raney Ni (50 mg). The mixture was charged with H2 for three times and stirred at rt for 12 h under a H2 balloon.
  • Step 1 To a solution of (2R,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (1.5 g, 3.24 mmol) in DCM (15 mL) was added AcCI (508 mg, 6.48 mmol) and TEA (3 mL). The mixture was stirred at rt for 2 h.
  • Step 2 To a solution of N-((2R,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-yl)acetamide (1.6 g, 3.17 mmol) inMeOH (15 mL) was added Pd/C (100 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon.
  • Step 3 To a solution of N-((2S,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)acetamide (670 mg, 2.85 mmol) in DMF (5 mL) and 2,2- dimethoxypropane (0.8 mL, 6.42 mmol) were added (+/-)-camphor-10-sulphonic acid (330 mg, 1.42 mmol). The reaction mixture was stirred at 70 °C for 24 h. Then it was cooled to room temperature and neutralized with triethylamine. The solvent was evaporated and the residue was co-evaporated 3 times with toluene.
  • Synthesis 5-6 and Synthesis 5-8 can be used to synthesize ligands with the following R 2 groups: wherein R is an optimal substituent has defined herein.
  • EDCI 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide Synthesis 5-11.
  • 3-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)oxazolidin-2-one (Compound A16) Synthesis 5-12.
  • Step 1 NaNs (4.3 g, 66 mmol) and CAN (87 g, 158 mmol) were added to a nitrogenflushed flask, and the mixture were stirred vigorously at -10°C. Then a solution of (2R,3R,4R)-2- (acetoxymethyl)-3,4-dihydro-2H-pyran-3,4-diyl diacetate (A90-1, 12 g, 44 mmol) in MeCN (250 mL) were added dropwise to the above mixture. The mixture was stirred at rt for 12 h. Then the reaction mixture was diluted with 500 mL EA.
  • Step 2 To a solution of (2R,3R,4R,5R)-2-(acetoxymethyl)-5-azido-6- (nitrooxy)tetrahydro-2H-pyran-3,4-diyl diacetate (A90-2, 15.0 g, 40.0 mmol) in anhydrous MeCN (120 mL) was added LiBr (34.6 g, 400 mmol) at room temperature under an argon atmosphere. The reaction was stirred at room temperature for 3 h. TLC indicated the starting material was consumed. EA (350 mL) was added to the reaction mixture.
  • Step 3 To a solution of (2R,3R,4R,5R,6R)-2-(acetoxymethyl)-5-azido-6- bromotetrahydro-2H-pyran-3,4-diyl diacetate (A90-3, 15.0 g, 38.1 mmol) in MeOH (100 mL) was added Ag2CO3 (15.7 g, 57.1 mmol) in portions at rt. The mixture was stirred at 60°C under N2 in the dark for 12 h. EA (350 mL) was added to the reaction mixture.
  • Step 4 To a solution of (2R,3R,4R,5R,6R)-2-(acetoxymethyl)-5-azido-6- methoxytetrahydro-2H-pyran-3,4-diyl diacetate (A90-4, 10.0 g, 29.0mmol) in MeOH (150 mL) was added NaOMe (23.2 mL, 5 M in MeOH) in portions at rt. The mixture was stirred at rt for 2 h. The reaction was neutralized by the addition of acidic Amberlite IR 120 (H + ) ion exchange resin. The solution was filtered through a glass fritted vacuum filter funnel equipped with a pad of Celite to remove the acidic resin.
  • Step 5 To a solution of (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A-89, 1.0 g, 4.57 mmol) in MeOH (20 mL) was added Pd/C (100 mg, 10% wt, 60% wet) under H2 atmosphere. The mixture was stirred at rt for 12 h under a H2 balloon.
  • Step 1 To a stirred solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- nitro-3,4-dihydro-2H-pyran (A91-1, 1.0 g, 2.17 mmol) in dry THF (10 ml) was added NaOMe (0.65 mL, 5 M in MeOH). After stirring at rt for 1 h, the reaction mixture was neutralized with Amberlite IR-120 resin (H + ).
  • Step 2 To a solution of (2R,3R,4R,5R,6S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6- methoxy-5-nitrotetrahydro-2H-pyran (A91-2, 425 mg, 0.86 mmol) in MeOH (10 mL) was added Raney Ni (50 mg). The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give (2S,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (A91-3, 473 mg, 72% yield). LC-MS (ESI) found: 464 [M+H] + .
  • Step 3 To a solution of (2S,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (A91-3, 200 mg, 0.431 mmol) in MeOH (10 mL) was added Pd/C (20 mg, 10% wt, 60% wet) and several drops of 1 N HCI. The mixture was stirred at rt for 12 h under a H2 balloon.
  • Step 1 To a mixture of (2S,3R,4R,5R,6R)-3-acetamido-6-(acetoxymethyl)tetrahydro-2H- pyran-2,4,5-triyl triacetate (A92-1, 20.0 g, 51.4 mmol) in DCM (200 mL) was added TiCh (61.6 mL, 1 M in DCM) at 0°C under N2.
  • Step 2 To a mixture of (2R,3R,4R,5R)-5-acetamido-2-(acetoxymethyl)-6- chlorotetrahydro-2H-pyran-3,4-diyl diacetate (A92-2, 8.5 g, 23.2 mmol) in toluene (85 mL) was added BusSnH (8.1 g, 27.9 mmol) and AIBN (0.08 g, 0.46 mmol) at rt under N2.
  • Step 3 To a mixture of (2R,3R,4R,5S)-5-acetamido-2-(acetoxymethyl)tetrahydro-2H- pyran-3,4-diyl diacetate (A92-3, 6.6 g, 19.9 mmol) in H2O (48 mL) was added HC1 (12 mL, 2.5 M in H2O) at rt under N2. After refluxing at 100°C for 2 h, the mixture was concentrated. EtOH (10 mL) and Et2O (10 mL) were added.
  • Step 2 To a mixture of N-((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro- 2H-pyran-3-yl)acetamide (A-94-2, 130 mg, 0.63 mmol) in DMF (5.0 mL) was added NaH (101 mg, 4.2 mmol) at 0°C under N2. After stirring at 0°C for 30 min, BnBr (0.07 mL, 0.63 mmol) was added slowly and the reaction was stirred for another 1 hour. The mixture was quenched with H2O and extracted with EA. The combined organic layers were washed with brine, dried over anhydrous Na2SO4.
  • Step 3 To a mixture of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A94-3, 1.2 g, 2.5 mmol) in THF (15 mL) was added Et 3 N (1.1 mL, 7.6 mmol), DMAP (30 mg, 0.25 mmol) and BOC2O (7.0 mL, 30.2 mmol) at 0°C under N2.
  • Step 4 To a mixture of tert-butyl acetyl((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A94-4, 860 mg, 1.5 mmol) in THF (10 mL) was added 2 mL NaOH (40 % aq) under N2. After refluxing at 60°C overnight, the mixture was diluted with H2O and extracted with EA. The combined organic layer was washed with brine, dried over Na2SO4, filtered.
  • Step 5 To a solution of tert-butyl ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A94-5, 450 mg, 0.84 mmol) in DCM (9.0 mL) was added TFA (3.0 mL) at rt under N2. After stirring for 2 h, the mixture was quenched with NaHCO 3 (aq) and extracted with EA. The combined organic layer was washed with brine, dried over anhydrous Na2SO4.
  • Step 2 To a solution of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)pyridin-2-amine (A96-1, 15 mg, 0.03 mmol) in MeOH (5 mL) was added Pd/C (2 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon.
  • Step 1 A solution of compound (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A89, 1 g, 4.6 mmol) in anhydrous pyridine (20 mL) was treated with trimethyl silyl chloride (3.5 mL, 27.8 mmol) and the mixture was stirred for 12 h at room temperature. The solvent was evaporated and the residue was diluted in ethyl acetate/ water. The organic layer was separated and further washed by water, brine, dried over anhydrous MgSCh, filtered, and concentrated to afford desired product as a yellow oil (1.6 g, 81% yield). LC-MS (ESI) found: 436 [M+H] + .
  • Step 2 To a solution of ((2R,3S,4R,5R,6R)-5-azido-6-methoxy-2- (((trimethylsilyl)oxy)methyl)tetrahydro-2H-pyran-3,4-diyl)bis(oxy))bis(trimethylsilane) (Al 18- 1, 1.0 g, 2.29 mmol) in MeOH (20 mL) was added Pd/C (100 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon.
  • Step 3 To a solution of ((2R,3S,4R,5R,6R)-5-amino-6-methoxy-3,4- bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-2-yl)methanol (Al 18-2, 150 mg, 0.444 mmol ) in MeOH (1 mL) H2O (1 mL) was added prop-2-enoyl chloride (0.04 mL, 0.533 mmol) and TEA (0.02 mL, 0.148 mmol). The mixture was stirred at 0°C for 4 h. The solvent was evaporated and the residue was diluted in DCM/water.
  • Step 4 To a solution of N-((2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2-methoxy-4,5- bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-3-yl)acrylamide (Al 18-3, 70 mg, 0.179 mmol) in THF (1 mL) was added TBAF (0.2 mL, 1 M in THF). The mixture was stirred at 0°C for 30 min.

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Abstract

Compounds are provided that assemble together in vivo to form an ASGPR-binding compound that has an asialoglycoprotein receptor (ASGPR) binding ligand bound to an extracellular protein binding ligand for the selective degradation of the target extracellular protein in vivo to treat disorders mediated by the extracellular protein.

Description

IN VIVO ASSEMBLY OF ASGPR BINDING THERAPEUTICS
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Patent Application 63/064,377 filed August 11, 2020, the entirety of which is incorporated by reference for all purposes.
FIELD OF THE INVENTION
This invention provides compounds that assemble together in vivo to form an ASGPR- binding compound that has an asialoglycoprotein receptor (ASGPR) binding ligand bound to an extracellular protein binding ligand for the selective degradation of the target extracellular protein in vivo to treat disorders mediated by the extracellular protein.
BACKGROUND OF THE INVENTION
Historically, therapeutic strategies for the inhibition of proteins employed small molecule inhibitors that bound in an enzymatic pocket or at an allosteric position. However, proteins that were not enzymes were difficult to control, and therefore some were considered “not druggable”.
Intracellular protein degradation is a natural and highly regulated, essential process that maintains cellular homeostasis. The selective identification and removal of damaged, misfolded, or excess proteins within the cell is achieved via the ubiquitin-proteasome pathway (UPP). The UPP is central to the regulation of almost all intracellular processes. A number of companies and institutions have designed intracellular protein degrading molecules that take advantage of this natural process to degrade disease-mediating proteins intracellularly by linking a ligand to the protein to be degraded by a protein in the UPP. Examples are found in U.S. 2014/0356322 assigned to Yale University, GlaxoSmithKline, and Cambridge Enterprise Limited University of Cambridge; Buckley et al. (J. Am. Chem. Soc. 2012, 134, 4465-4468) titled "Targeting the Von Hippel -Lindau E3 Ubiquitin Ligase Using Small Molecules to Disrupt the Vhl/Hif-1 alpha Interaction"; WO 2015/160845 assigned to Arvinas Inc. titled “Imide Based Modulators of Proteolysis and Associated Methods of Use”; Lu et al. (Chem. Biol. 2015, 22, 755-763) titled "Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target Brd4"; Bondeson et al. (Nat. Chem. Biol. 2015, 11, 611-617) titled "Catalytic in Vivo Protein Knockdown by Small-Molecule Protacs"; Gustafson et al. (Angewandte Chemie, International Edition in English 2015, 54, 9659- 9662) titled "Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging"; Lai et al. (Angewandte Chemie, International Edition in English 2016, 55, 807-810) titled "Modular Protac Design for the Degradation of Oncogenic Bcr-Abl"; Toure et al. (Angew. Chem. Int. Ed. 2016, 55, 1966-1973) titled "Small-Molecule Protacs: New Approaches to Protein Degradation"; Winter et al. (Science 2015, 348, 1376-1381) titled "Drug Development. Phthalimide Conjugation as a Strategy for in Vivo Targeted Protein Degradation"; U.S. 2016/0058872 assigned to Arvinas, Inc. titled “Imide Based Modulators of Proteolysis and Associated Methods of Use” and U.S. 2016/0045607 assigned to Arvinas Inc. titled “Estrogen- related Receptor Alpha Based PROTAC Compounds and Associated Methods of Use”.
The hijacking of the UPP intracellular process to degrade difficult or undruggable proteins, however, is not available to degrade extracellular proteins. Nonlimiting examples of extracellular proteins include immunoglobulins and cytokines, which can play a strong role in creating or exacerbating serious diseases. Immunoglobulins include IgA, IgG, IgD, IgE, and IgM. Cytokines are cell signaling peptides secreted into the bloodstream which cannot cross the lipid bilayer of cells to enter the cytoplasm, for example, interferons, interleukins, chemokines, lymphokines, MIP, and tumor necrosis factors. Cytokines are involved in autocrine, paracrine, and endocrine signaling. They mediate immunity, inflammation, and hematopoiesis. Cytokines are produced by immune cells (macrophages, B-cells, T-cells, and mast cells), endothelial cells, fibroblasts and stromal cells.
The asialoglycoprotein receptor (ASGPR) is a Ca2+-dependent lectin that is primarily expressed in parenchymal hepatocyte cells. The main role of ASGPRs is to help regulate serum glycoprotein levels by mediating endocytosis of desialylated glycoproteins (as depicted below). The receptor binds ligands with a terminal galactose or N-acetylgalactosamine. The C3- and C4- hydroxyl groups bind to Ca2+. The C2 N-acetyl position has also been considered important to binding activity.
Figure imgf000004_0001
N-acetyl galactosamine Asialoglycoproteins bind to ASGPRs and are then cleared by receptor-mediated endocytosis. The receptor and the protein are dissociated in the acidic endosomal compartment and the protein is eventually degraded by lysosomes. The receptor is endocytosed and recycled constitutively from the endosome back to the plasma membrane about every 15 minutes regardless of whether or not a glycoprotein is bound. However, it has been shown that the internalization rate of the receptor is dependent on the presence of ligand. In a 1998 study, the internalization rate of the protein without ligand was less than one-third of the rate of internalization of the ligandreceptor complex (Bider et al. FEBS Letters, 1998, 434, 37).
The ASGPR is comprised of two homologous subunits with 58% sequence identity known as Hl and H2. Various ratios of Hl and H2 form functional homo- and hetero-oligomers with different conformations, but the most abundant conformation is a trimer composed of two Hl and one H2 subunits. The ASGPR is composed of a cytoplasmic domain, a transmembrane domain, a stalk region, and a carbohydrate recognition domain (CRD). Both the Hl and H2 subunit are required to form the CRD, and therefore, co-expression of both subunits is a requirement for endocytosis of asialoglycoproteins. In 2000, the crystal structure of the CRD region was published, revealing three Ca2+ binding sites (Meier et al. J. Mol. Biol. 2000, 300, 857).
A number of publications describe ligands that are thought to bind to the CRD region of ASGPRs. For example, Stokmaier et al. (Bioorg. Med. Chem., 2009, 17, 7254) describes the synthesis of a series of D-GaWAc derivatives where the anomeric OH group is removed and the acetamido group is replaced with a 4-substituted 1,2, 3 -triazole moiety. The most potent compound is twice as potent as D-GaWAc in competitive NMR binding experiments. Mamidyala etal. (JACS, 2012, 134, 1978) describes compounds derived from 2-azidogalactosyl analogs where the anomeric position is occupied by either a P-methyl or a P-4-methoxy-phenyl group and the azide group is replaced with an amide or a triazole. The ligands were tested for binding activity by surface plasmon resonance, and many exhibited more potent Kd values than that of the parent N- acetylgalactosamine.
Studies have also shown that the receptor affinity for a ligand may be influenced by the ligand’s valency. For example, Lee et al. (J. Biol. Chem., 1983, 258, 199) showed that the ICso ranged from approximately 1 mM for monoantennary oligosaccharides to approximately 1 nM for triantennary oligosaccharides in an assay studying the binding ability of certain analogs to rabbit hepatocytes. ASGPRs are primarily expressed on hepatocytes and are minimally found on cells outside of the liver. Hepatocytes exhibit a high exposition of ASGPR binding cites (approximately 100,000 - 500,000 binding sites per cell).
U.S. Patent 5,985,826 to NeoRx Corporation describes the use of hepatic-directed systems that include a therapeutic agent with activity against a liver disease or disorder that is bound to a director moiety. The director moiety, which in one embodiment is a galactose or galactose derivative, directs the active agent to the liver, where the active agent acts as a therapeutic agent that is then removed from circulation with assistance from the director moiety.
U.S. Patent Nos. 9,340,553; 9,617,293; 10,039,778; and 10,376,531 and U.S. Application US2019/0321382 assigned to Pfizer Inc. describe certain bicyclic, bridged ketal derivatives of GabVAc as targeting agents for the ASGPR receptor that in one embodiment are bound to a linker and/or a therapeutic agent such as a small molecule, an amino acid sequence, a nucleic acid sequence, an antibody, or a fluorescent probe. The linker of the drug delivery system can be monovalent, divalent, or trivalent. The disclosure also includes a method for the treatment of a liver disease or condition comprising administering the targeted drug delivery system. Several monovalent, divalent, and trivalent bicyclic bridged GaWAc-derived ASGPR targeting agents linked to fluorescence probes are disclosed in Sanhueza et al. (JACS, 2017, 139, 3528). One trivalent conjugate in particular exhibited selective hepatocyte targeting in an in vivo biodistribution study in mice.
Pfizer Inc. and the Regents of the University of California jointly disclosed the use of targeted drug delivery systems comprising certain ASPGR targeting ligands covalently bound to a ribonucleoprotein or an endonuclease in US 2017/0137801 for use in CRISPR gene editing.
Pfizer also developed PK2, a targeted drug delivery system wherein doxorubicin is linked via a lysosomally degradable tetrapeptide sequence to N-(2-hydroxypropyl)methacrylamide copolymers bearing galactosamine as the targeting agent. In a Phase 1 clinical trial to determine the selectivity, toxicity, and pharmacokinetic profile, it was demonstrated that the drug targeted primary hepatocellular tumors in patients with primary or metastatic liver cancer (Seymour et al. J. Clin. Oncol. 2009, 20, 1668).
Conjugates of paclitaxel covalently bound to one, two, or three units of GabVAc via a short linker are described in Petrov et al. (Bioorganic and Medicinal Chemistry Letters, 2018, 28, 382). The analogs were cytotoxic against human hepatocellular carcinoma cells and showed high affinity for ASGPR via surface plasmon resonance.
Avilar Therapeutics has filed a PCT Application WO2021/155317 describing the use of ASGPR ligands attached to Extracellular Protein Targeting Ligands for the degradation of the target extracellular protein.
Pfizer Inc. and Wave Life Sciences Ltd. jointly disclosed the use of selected ASGPR ligands attached to oligonucleotides in PCT Applications WO 2018/223073 and WO2018/223081. The ‘ 073 application describes the use of APOC3 oligonucleotides attached to an ASGPR targeting ligand for selective delivery to the liver and the ‘081 application describes the use of PNPLA3 oligonucleotides attached to an ASGPR targeting ligand. PCT Application WO 2018/223056 assigned to Wave Sciences Ltd. describes compositions comprising oligonucleotides for RNA interference and in one embodiment, the oligonucleotide is attached to an ASGPR targeting ligand.
The targeted delivery of antisense oligonucleotides, which bind and modulate complementary RNA, to hepatocytes via an ASGPR targeting ligand was studied in Schmidt et al. (Nucleic Acids Research, 2017, 45, 2294). Mono, di, and trivalent Gal NA c were conjugated to single stranded and duplexed ASOs and it was found that di- and trivalent GabVAc-conjugated ASO systems were bind to ASGPR with the strongest affinity.
Examples of ASGPR-targeted therapy using modified glycoproteins as the target agenting are reviewed in Huang etal. (Bioconjugate Chem. 2017, 28, 283). A number of multivalent ligands that have been developed are discussed in addition to the relevant properties for drug delivery, including linker length and spatial geometry of the scaffold.
Yale University has filed two PCT Applications, WO 2019/199621 and WO 2019/199634, which describe the use of certain ASGPR targeting ligands covalently bound to a circulating protein binding moiety. Once the circulating protein binding moiety binds the circulating protein, the complex passes to the liver where it is recognized by ASGPR and degraded via the endo- lysosomal pathway. The ‘621 application describes circulating protein binding moieties that are capable of targeting macrophage migration inhibitory factor (MIF) and/or immunoglobulin G (IgG). The ‘634 application describes the targeting of numerous circulating proteins including CD40L, TNF-a, PCSK9, VEGF, TGF-p, uPAR, PSMA, IL-2, GP120, TSP-1, and CXCL-2 using a drug delivery system comprising a circulating protein binding moiety covalently bound to a targeting ligand, which is a ASGPR targeting ligand. Additional publications describing the use of ASGPR ligand containing heterobifunctional compounds include W02020/132100 and WO2021/142377.
While some progress has been made in the area of targeted degradation of diseasemediating extracellular proteins, there remains an unmet need for additional chemical compounds and approaches to treat such medical disorders.
SUMMARY OF THE INVENTION
Compounds that assemble in vivo and pharmaceutically acceptable salts and compositions thereof are provided that when assembled form therapeutic compounds that degrade diseasemediating extracellular proteins. The compound pair includes a compound with novel modifications of the exposition of the ASGPR binding ligand, referred to herein as R2 or R200.
In one aspect the invention provides an ASGPR binding ligand. In another aspect the invention provides an ASGPR binding ligands and an Extracellular Protein Targeting Ligand which when administered to a patient combine in vivo to create a therapeutic compound. In certain aspects the invention is the produced therapeutic compound itself. The invention also includes a method to treat a patient in need thereof, comprising administering an effective amount of the component compounds as well as the method to treat the patient with the therapeutic compound produced in vivo.
The ASGPR binding ligands used in the present invention include derivatives of six-carbon pyranose moieties, specifically galactose and talose. These two sugars, shown below, differ only in the stereochemistry of the C2 substituent. The “down” C2 configuration corresponds to the stereochemistry of galactose, while the C2 substituent in the “up” configuration corresponds to the stereochemistry of talose. It has been discovered that certain substituents at the C2 position of these two sugars improves the binding of the ligand ASGPR. β-D-Galactose β-D-Talose
Figure imgf000008_0001
These ASGPR binding ligands have been modified to present a selective moiety that in the body will react with the complementary selective moiety that has been installed on an Extracellular Protein Targeting Ligand.
Figure imgf000009_0004
Talose Stereochemistry
Figure imgf000009_0001
Talose Stereochemistry
As used herein the selective linker moiety that the ASGPR ligand presents is “Selective MoietyA” and the selective moiety that the Extracellular Targeting Ligand presents is “Selective MoietyB.”
Figure imgf000009_0002
In the body Selective MoietyA and Selective MoietyB react to form an Extracellular Protein degrading compound. For example, a compound of Formula:
Figure imgf000009_0003
Galactose Stereochemistry Qr
Figure imgf000010_0001
Talose Stereochemistry
The resulting extracellular protein degrading compounds that are formed in vivo from the compounds described herein can be used to degrade a selected extracellular protein. Extracellular proteins that can be targeted according to the present invention include but are not limited to immunoglobulins such as IgA, IgG, IgD, IgE, and IgM, and derivatives thereof which retain the same basic function, and cytokines such as interferons, interleukins, chemokines, lymphokines, MIP, and tumor necrosis factors. In certain embodiments, the extracellular protein is selected from IgA, IgG, IgE, TNF (a or p), IL-lb, IL-2, IFN-y, IL-6, VGEF, TGF-bl and PCSK-9.
Galactose-Based Molecules It has been discovered that sugars in the galactose stereochemistry with certain C2 substituents are useful ligands for ASGPR. These molecules can react in vivo with an extracellular protein targeting ligand compound that has been modified to present a selective linking moiety, and resultant molecule can be used to recruit extracellular protein and degrade it in the liver.
In particular, a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI is provided:
Figure imgf000010_0002
Figure imgf000011_0001
or a pharmaceutically acceptable salt thereof; wherein:
X1 is 1 to 5 contiguous atoms independently selected from O, S, N(R6), and C(R4)(R4), wherein if X1 is 1 atom then X1 is O, S, N(R6), or C(R4)(R4), if X1 is 2 atoms then no more than 1 atom of X1 is O, S, or N(R6), if X1 is 3, 4, or 5 atoms then no more than 2 atoms of X1 are O, S, or N(R6);
R2 is selected from
(i) aryl, heterocycle, and heteroaryl containing 1 or 2 heteroatoms independently selected from N, O, and S, each of which aryl, heterocycle, and heteroaryl is optionally substituted with 1, 2, 3, or 4 substituents;
Figure imgf000012_0001
(iii) -NR8-S(O)-R3, -NR8-C(S)-R3, -NR8-S(O)(NR6)-R3, -N=S(O)(R3)2,
-NR8C(O)NR9S(O)2R3, -NR8-S(O)2-R10, and -NR8-C(NR6)-R3 each of which is optionally substituted with 1, 2, 3, or 4 substituents; and
(iv) hydrogen, R10, alkyl-C(O)-R3, -C(O)-R3, alkyl, haloalkyl, -OC(O)R3, and
-NR8-C(O)R10;
R10 is selected from alkenyl, allyl, alkynyl, -NR6-alkenyl, -O-alkenyl, -NR6-alkynyl, -O-alkynyl, -NR6-heteroaryl, -NR6-aryl, -O-heteroaryl, -O-aryl, and -O-alkynyl, each of which R10 is optionally substituted with 1, 2, 3, or 4 substituents;
Figure imgf000012_0002
R1 and R5 are independently selected from hydrogen, heteroalkyl, C0-C6alkyl-cyano, alkyl, alkenyl, alkynyl, haloalkyl, F, Cl, Br, I, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycle, heterocycloalkyl, haloalkoxy, -O-alkenyl, -O-alkynyl, C0-C6alkyl- OR6, C0-C6alkyl-SR6, C0-C6alkyl-NR6R7, C0-C6alkyl-C(0)R3, C0-C6alkyl-S(0)R3, C0-C6alkyl- C(S)R3, C0-C6alkyl-S(0)2R3, C0-C6alkyl-N(R8)-C(0)R3, C0-C6alkyl-N(R8)-S(0)R3, C0-C6alkyl- N(R8)-C(S)R3, C0-C6alkyl-N(R8)-S(0)2R3 C0-C6alkyl-0-C(0)R3, C0-C6alkyl-0-S(0)R3, Co- C6alkyl-O-C(S)R3, -N=S(O)(R3)2, C0-C6alkyN3, and C0-C6alkyl-0-S(0)2R3, each of which is optionally substituted with 1, 2, 3, or 4 substituents;
R3 at each occurrence is independently selected from hydrogen, alkyl, heteroalkyl, haloalkyl (including -CF3, -CHF2, -CH2F, -CH2CF3, -CH2CH2F, and -CF2CF3), arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR8, and -NR8R9; R4 is independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, haloalkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR6, -NR6R7, C(O)R3, S(O)R3, C(S)R3, and S(O)2R3;
R6 and R7 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, haloalkyl, heteroaryl, heterocycle, -alkyl-OR8, - alkyl-NR8R9, C(O)R3, S(O)R3, C(S)R3, and S(O)2R3;
R8 and R9 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocycle;
Cycle is a 3-8 membered fused cyclic group optionally substituted with 1, 2, 3, or 4 substituents; exemplary Cycle groups include carbocycle (e.g. cyclopropane, cyclohexane, or cyclohexene), heterocycle (e.g. oxetane, of piperazine), aryl (e.g. phenyl), or a heteroaryl group
(e.g. pyridine, furan, or pyrrole) as appropriate and allowed by valence; and each Linked is a bond or a chemical moiety that covalently links the ASGPR ligand to Selective MoietyA, or Linker17, or Linker19; Selective MoietyA is selected from
Figure imgf000013_0001
Figure imgf000014_0001
5 each of which Selective MoietyA group is optionally substituted with 1, 2, 3, or 4 substituents; or Selective MoietyA is selected from
Figure imgf000014_0002
Figure imgf000015_0001
each of which Selective MoietyA group is optionally substituted with 1, 2, 3, or 4 substituents; cyclic group is a cycloalkyl, heterocycle, aryl, or heteroaryl group; each R23 is independently alkyl or hydrogen; or two R23 groups combine together to form a cycle;
R24, R25, and R26 are independently selected at each instance from hydrogen, alkyl, aryl, heteroaryl, heterocycle, and halogen, each of which R24, R25, and R26 groups other than hydrogen are optionally substituted with 1, 2, 3, or 4 substituents; or R24 and R25 together form a double bond; y is 0, 1, 2, 3, 4, 5, 6, 7, or 8; when compounds are “optionally substituted” they may be substituted as allowed by valence by groups selected from alkyl (including Ci-C4alkyl), alkenyl (including C2-C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR6, F, Cl, Br, I,
-NR6R7, heteroalkyl, cyano, nitro, C(O)R3, , wherein the optional
Figure imgf000016_0002
substituent is selected such that a stable compound results.
In certain embodiments the optional substituents are independently selected from R100 wherein R100 is selected at each instance from alkyl (including Ci-C4alkyl), alkenyl (including C2- C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR6, F, Cl,
Br, I, -NR6R7, heteroalkyl, cyano, nitro, C(O)R3,
Figure imgf000016_0001
optional substituent is selected such that a stable compound results.
The compounds of Formula I, II, III, IV, V, VI, and VI can react in vivo with a compound of Formula VII, wherein the compound of Formula VII is:
Figure imgf000016_0003
or a pharmaceutically acceptable salt thereof; wherein:
Linker® is a bond or a chemical moiety that covalently links Selective Moiety® to an Extracellular Protein Targeting Ligand; Extracellular Protein Targeting Ligand is a chemical moiety that binds to the targeted extracellular protein; and
Selective MoietyB is selected from
Figure imgf000017_0001
Figure imgf000018_0001
each of which Selective Moi etyB groups is optionally substituted with 1, 2, 3, or 4 substituents. or Selective MoietyB is selected from
Figure imgf000018_0002
Figure imgf000019_0001
each of which Selective MoietyB group is optionally substituted with 1, 2, 3, or 4 substituents;
According to the invention, non-limiting pairs of selective moieties include:
(i) if Selective MoietyA is selected from
Figure imgf000019_0002
Figure imgf000020_0001
then Selective MoietyB is selected from:
Figure imgf000020_0003
ii) if Selective MoietyA is selected from
Figure imgf000020_0004
then Selective MoietyB is selected from:
Figure imgf000020_0002
iii) if Selective MoietyA is selected from
Figure imgf000021_0001
then Selective MoietyB is selected from:
Figure imgf000021_0002
iv) if Selective MoietyA is selected from
Figure imgf000021_0003
then Selective MoietyB is selected from:
Figure imgf000021_0004
v) if Selective MoietyA is selected from
Figure imgf000021_0005
then Selective MoietyB is selected from:
Figure imgf000022_0004
then Selective MoietyB is selected from:
Figure imgf000022_0001
vii) if Selective MoietyA is selected from
Figure imgf000022_0002
then Selective MoietyB is selected from:
Figure imgf000022_0003
viii) if Selective MoietyA is selected from
Figure imgf000023_0001
then Selective MoietyB is selected from:
Figure imgf000023_0002
ix) if Selective MoietyA is selected from
Figure imgf000023_0006
then Selective MoietyB is selected from:
Figure imgf000023_0003
x) if Selective MoietyA is selected from
Figure imgf000023_0004
then Selective MoietyB is selected from:
Figure imgf000023_0005
A non-limiting example of the therapeutic compound resulting in vivo is a compound of
Formula:
Figure imgf000024_0001
Non-limiting examples of Connecting Moiety groups that results from combination i) or ii) above include:
Figure imgf000024_0002
Non-limiting examples of Connecting Moiety groups that results from combination iii) or iv) above include:
Figure imgf000024_0003
Non-limiting examples of Connecting Moiety groups that results from combination v) or vi) above include:
Figure imgf000024_0004
Figure imgf000025_0001
Non-limiting examples of Connecting Moiety groups that results from combination vii) or viii) above include:
Figure imgf000025_0002
Non-limiting examples of Connecting Moiety groups that results from combination ix) or x) above include:
Figure imgf000025_0003
A compound of Formula I-Bi, Formula II-Bi, Formula III-Bi, Formula IV-Bi, Formula V-Bi, or Formula VI-Bi, is also provided:
Figure imgf000025_0004
Figure imgf000026_0001
Figure imgf000027_0001
or a pharmaceutically acceptable salt thereof; wherein: LinkerC is a chemical moiety that links each LinkerA to Selective MoietyA; and all other variables are as defined herein.
A compound of Formula I-Tri, Formula II-Tri, Formula III-Tri, Formula IV-Tri, Formula V-Tri, or Formula VI-Tri, is also provided:
Figure imgf000028_0001
Figure imgf000029_0001
Figure imgf000030_0001
Figure imgf000030_0002
(VI-Tri), or a pharmaceutically acceptable salt thereof; wherein:
LinkerD is a chemical moiety that links each LinkerA to Selective MoietyA; and all other variables are as defined herein.
A compound of the present invention of Formula I, II, III, IV, V, or VI or the bis version (Formula Bi, II-Bi, III-Bi, IV-Bi, V-Bi, or VLBi), or the tris version (Formula LTri, II-Tri, III- Tri, IV-Tri, V-Tri, VI-Tri) can react in vivo with a compound of Formula VII as described herein to deliver an ASGPR-binding Extracellular Protein degrader that binds to the Extracellular Protein, typically in the blood stream, and carries it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation. Examples of methods to deliver the degraders of the present invention include, but are not limited to, oral, intravenous, buccal, sublingual, subcutaneous and transnasal.
In certain embodiments the Extracellular Protein Targeting Ligand binds the protein after reacting with the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version, according to the invention described herein
In certain embodiments the Extracellular Protein Targeting Ligand binds the protein before reacting with the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version, according to the invention described herein.
In certain embodiments the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version binds to ASGPR after reacting with the Extracellular Protein Targeting Ligand according to the invention described herein.
In certain embodiments the compound of Formula I, II, III, IV, V, or VI, or the bis or tris version binds to ASGPR before reacting with the Extracellular Protein Targeting Ligand, according to the invention described herein.
Talose-Based Molecules
It has been also discovered that sugars in the talose stereochemistry with specific C2 substituents are useful ligands for ASGPR. These molecules can be used as ASGPR ligands or linked to an extracellular protein targeting ligand to recruit extracellular protein and degrade it in the liver.
In particular, a compound of Formula I-d, Formula Il-d, Formula Ill-d, or Formula IV-d, is provided:
Figure imgf000031_0001
Figure imgf000032_0001
or a pharmaceutically acceptable salt thereof; wherein R200 is selected from:
(i) aryl, heterocycle, and heteroaryl containing 1 or 2 heteroatoms independently selected from N, O, and S, each of which aryl, heterocycle, and heteroaryl is optionally substituted with 1, 2, 3, or 4 substituents;
Figure imgf000032_0002
(iii) -NR8-S(O)-R3, -NR8-C(S)-R3, -NR8-S(O)(NR6)-R3, -N=S(O)(R3)2,
-NR8C(O)NR9S(O)2R3, -NR8-S(O)2-R10, and -NR8-C(NR6)-R3 each of which is optionally substituted with 1, 2, 3, or 4 substituents; and
(iv) hydrogen, R10, alkyl-C(O)-R3, -C(O)-R3, alkyl, haloalkyl, -OC(O)R3, and -NR8-C(O)R10; and
(v) -NR8-C(O)-R3; and all other variables are as defined herein.
The compounds of Formula I-d, Il-d, Ill-d, and IV-d can react in vivo with a compound of Formula VII, wherein the compound of Formula VII is:
Figure imgf000033_0001
or a pharmaceutically acceptable salt thereof; wherein:
Linker® is a bond or a chemical moiety that covalently links Selective Moiety® to an Extracellular Protein Targeting Ligand;
Extracellular Protein Targeting Ligand is a chemical moiety that binds to the targeted extracellular protein; and
Selective Moiety® is as defined herein.
The invention also provides a method of treating a patient comprising administering a compound of Formula I-d, ILd, IILd, IV-d, V-d, or Vl-d in combination with a compound of Formula VII, wherein:
(i) if Selective MoietyA is selected from
Figure imgf000033_0002
then Selective MoietyB is selected from:
Figure imgf000034_0001
ii) if Selective MoietyA is selected from
Figure imgf000034_0002
then Selective MoietyB is selected from:
Figure imgf000034_0003
, and
Figure imgf000034_0005
iii) if Selective MoietyA is selected from
Figure imgf000034_0004
then Selective MoietyB is selected from:
Figure imgf000035_0001
then Selective MoietyB is selected from:
Figure imgf000035_0002
v) if Selective MoietyA is selected from
Figure imgf000035_0003
then Selective MoietyB is selected from:
Figure imgf000035_0004
vi) if Selective MoietyA is selected from
Figure imgf000036_0001
then Selective MoietyB is selected from:
Figure imgf000036_0002
vii) if Selective MoietyA is selected from
Figure imgf000036_0003
then Selective MoietyB is selected from:
Figure imgf000036_0004
viii) if Selective MoietyA is selected from
Figure imgf000036_0005
then Selective MoietyB is selected from:
Figure imgf000037_0001
ix) if Selective MoietyA is selected from
Figure imgf000037_0002
then Selective MoietyB is selected from:
Figure imgf000037_0003
x) if Selective MoietyA is selected from
Figure imgf000037_0004
then Selective MoietyB is selected from:
Figure imgf000037_0006
A non-limiting example of the therapeutic compound produced in vivo according to the invention as described above is a compound of Formula:
Figure imgf000037_0005
Figure imgf000038_0001
A compound of Formula I-d-Bi, Formula II-d-Bi, Formula III-d-Bi, or Formula IV-d-Bi is also provided:
Figure imgf000038_0002
Figure imgf000039_0001
or a pharmaceutically acceptable salt thereof, wherein the variables are as defined herein.
A compound of Formula I-d-Tri, Formula II-d-Tri, Formula III-d-Tri, or Formula IV-d-
Tri, is also provided:
Figure imgf000040_0001
Figure imgf000041_0001
or a pharmaceutically acceptable salt thereof, wherein the variables are as defined herein. In an embodiment of the invention, the Extracellular Protein Targeting Ligand is a small organic molecule (i.e., a non-biologic) or a peptide, protein or biologic or a binding fragment thereof, that does not comprise an oligonucleotide or aptamer. A plethora of nonlimiting examples of extracellular protein targeting ligands is provided in Fig. 1. The present invention focuses on the degradation of circulating extracellular proteins that mediate diseases involving immunity, inflammation, hematopoiesis/blood disorders (including those caused or exacerbated by blood vessel formation) and abnormal cellular proliferation such as tumors and cancer. In one nonlimiting embodiment of the invention, neither the Extracellular Protein nor the Extracellular Protein Targeting Ligand directly mediates intracellular gene editing such as CRISPR.
In one embodiment of the invention, when R2 is NR6-alkenyl, -NR6-alkynyl,-NR8-C(O)R10, -NR8-S(O)2-alkenyl, -NR8-S(O)2-alkynyl, -NR6-heteroaryl, or -NR6-aryl, then Extracellular Protein Targeting Ligand does not comprise an oligonucleotide or aptamer.
A compound of the present invention of Formula Ld, ILd, IILd, or IV-d or the bis version (Formula Ld-Bi, ILd-Bi, III-d-Bi, or IV-d-Bi), or the tris version (Formula I-d-Tri, ILd-Tri, IILd- Tri, or IV-d-Tri) can react in vivo with a compound of Formula VII as described herein to deliver an ASGPR-binding Extracellular Protein degrader that binds to the Extracellular Protein, typically in the blood stream, and carry it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation. Examples of methods to deliver the degraders of the present invention include, but are not limited to, oral, parenteral, topical, systemic, intraaortal, intravenous, buccal, sublingual, subcutaneous and transnasal.
In certain embodiments a method of treating a disorder mediated by an Extracellular Protein is provided that comprises administering (i) an effective dose of a compound or pharmaceutical composition of Formula I, II, III, IV, V, VI, Ld, ILd, IILd, or IV-d or its respective bi- and tri-version or a pharmaceutically acceptable salt thereof to a patient in combination with (ii) an effective dose of a compound or pharmaceutical composition of Formula VII or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein. The term “combination” as used in this method means that step (i) and step (ii) are carried out within a sufficient temporal proximity that allows the selected compound of Formula I, II, III, IV, V, VI, Ld, ILd, IILd, or IV-d or its respective bi- and tri- version or a pharmaceutically acceptable salt thereof to react with the selected compound of Formula VII. Step (i) can be carried out before or after step (ii) as long as the two steps are sufficiently close in time that the compounds are able to assemble in vivo.
In certain embodiments the Extracellular Protein Targeting Ligand binds the protein after reacting with the compound of Formula Ld, ILd, IILd, or IV-d, or the bis or tris version.
In certain embodiments the Extracellular Protein Targeting Ligand binds the protein before reacting with the compound of Formula I-d, ILd, IILd, or IV-d, or the bis or tris version.
In certain embodiments the compound of Formula I-d, ILd, IILd, or IV-d, or the bis or tris version binds to ASGPR after reacting with the Extracellular Protein Targeting Ligand.
In certain embodiments the compound of Formula Ld, ILd, IILd, or IV-d, or the bis or tris version binds to ASGPR before reacting with the Extracellular Protein Targeting Ligand.
BRIEF DESCRIPTION OF FIGURES
FIG. 1 A provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin A (IgA).
FIG. IB provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin G (IgG).
FIG. 1C-1G provides a non-limiting list of Extracellular Protein Targeting Ligands that target Immunoglobulin E (IgE).
FIG. 1H-1M provides a non-limiting list of Extracellular Protein Targeting Ligands that target Tumor Necrosis Factor alpha (TNF-a).
FIG. IN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin- 1 (IL-1).
FIG.10- IS provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-2 (IL-2).
FIG.1T-1W provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-6 (IL-6).
FIG. 1X-1AA provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interferon gamma (IFN-y).
FIG. 1BB-1KK provides a non-limiting list of Extracellular Protein Targeting Ligands that target Vascular endothelial growth factor (VEGF). FIG. ILL provides a non-limiting list of Extracellular Protein Targeting Ligands that target Transforming growth factor beta (TGF-β1).
FIG. 1MM-1PP provides a non-limiting list of Extracellular Protein Targeting Ligands that target proprotein convertase subtilisin kexin 9 (PCSK-9).
FIG. 1QQ-1SS provides a non-limiting list of Extracellular Protein Targeting Ligands that target Carboxypeptidase B2 (CPB2).
FIG. 1TT-1UU provides a non-limiting list of Extracellular Protein Targeting Ligands that target Cholinesterase (ChE).
FIG. 1VV-1WW provides a non-limiting list of Extracellular Protein Targeting Ligands that target C-C Motif Chemokine Ligand 2 (CCL2).
FIG. 1XX-1BBB provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor VII (Factor VII).
FIG. 1CCC-1FFF provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor IX (Factor IX).
FIG. 1GGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target CD40 Ligand (CD40L).
FIG. 1HHH-1JJJ provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor Xa (Factor Xa).
FIG. 1KKK-1MMM provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XI (Factor XI).
FIG. INNN and 1OOO provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XII (Factor XII).
FIG. 1PPP and 1QQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target coagulation factor XIII (Factor XIII).
FIG. 1RRR-1UUU provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibroblast growth factor 1 (FGF1).
FIG. 1 VVV-1XXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibroblast growth factor 2 (FGF2).
FIG. 1YYY and 1ZZZ provides a non-limiting list of Extracellular Protein Targeting Ligands that target fibronectin (FN1). FIG. 1AAAA and 1BBBB provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-5 (IL-5).
FIG. 1CCCC provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-8 (IL-8).
FIG. 1DDDD and 1EEEE provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin- 10 (IL-10).
FIG. 1FFFF and 1GGGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-21 (IL-21).
FIG. 1HHHH and 1IIII provides a non-limiting list of Extracellular Protein Targeting Ligands that target Interleukin-22 (IL-22).
FIG. 1 JJJJ- 1NNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Kallikrein 1.
FIG. 1OOOO provides a non-limiting list of Extracellular Protein Targeting Ligands that target lipoprotein lipase (LPL).
FIG. 1PPPP and 1QQQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target matrix metalloproteinase- 1 (MMP1).
FIG. 1RRRR-1DDDDD provides a non-limiting list of Extracellular Protein Targeting Ligands that target Macrophage migration inhibitory factor (MIF), also known as glycosylationinhibiting factor (GIF), L-dopachrome isomerase, or phenylpyruvate tautomerase.
FIG. 1EEEEE-1GGGGG provides a non-limiting list of Extracellular Protein Targeting Ligands that target neutrophil elastase (NE).
FIG. 1HHHHH and 1IIIII provides a non-limiting list of Extracellular Protein Targeting Ligands that target Prothrombin.
FIG. 1JJJJJ-1NNNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target Plasma kallikrein (KLKB1).
FIG. 1OOOOO-1 SSSSS provides a non-limiting list of Extracellular Protein Targeting Ligands that target plasminogen (PLG).
FIG. 1TTTTT-1XXXXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target Plasminogen activator inhibitor- 1 (PALI), endothelial plasminogen activator inhibitor or serpin EL FIG. 1 YYYYY-1 AAAAAA provides a non-limiting list of Extracellular Protein Targeting Ligands that target phospholipases A2, for example type IB or group IB (PLA2, PA21B, PLA2G1B, PLA2-IB).
FIG. 1BBBBBB-1DDDDDD provides a non-limiting list of Extracellular Protein Targeting Ligands that target phospholipases A2, for example type IIA or group IIA (PLA2, PLA2A, PA2IIA, PLA2G2A, PLA2-IIA).
FIG. 1EEEEEE-1NNNNNN provides a non-limiting list of Extracellular Protein Targeting Ligands that target placental growth factor (PGF).
FIG. 1 OOOOOO- 1QQQQQQ provides a non-limiting list of Extracellular Protein Targeting Ligands that target plasminogen activator, tissue type (tPA, PLAT).
FIG. 1RRRRRR provides a non-limiting list of Extracellular Protein Targeting Ligands that target Transforming growth factor beta 2 (TGF-β2, TGFB2).
FIG. 1SSSSSS provides a non-limiting list of Extracellular Protein Targeting Ligands that target thrombospondin 1 (TSP1, TSP-1, THBS1).
FIG. 1TTTTTT-1XXXXXX provides a non-limiting list of Extracellular Protein Targeting Ligands that target Urokinase or Urokinase-type plasminogen activator (UP A, uPA).
FIG. 2 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor B.
FIG. 3 A and 3B provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor D.
FIG. 4 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement factor H.
FIG. 5 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target complement component 5.
FIG. 6 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target TNF-alpha.
FIG. 7 provides a non-limiting list of exemplary Extracellular Protein Targeting Ligands that target factor XI.
FIG. 8 provides non-limiting examples of Formulas of the present invention. DETAILED DESCRIPTION OF THE INVENTION
Compounds that assemble in vivo and pharmaceutically acceptable salts and compositions thereof are provided that, when assembled, form therapeutic compounds that degrade diseasemediating extracellular proteins. The compound pair includes a compound with novel modifications of the exposition of the ASGPR ligand, referred to herein as R2 or R200.
The invention thus includes each of the compounds individually that are administered to the patient which combined in vivo to create the therapeutic compound as well as the in vivo produced therapeutic compound itself. The invention also includes a method to treat a patient in need thereof, comprising administering an effective amount of the component compounds as well as the method to treat the patient with the therapeutic compound produced in vivo.
In particular, novel compounds and their pharmaceutically acceptable salts and compositions that degrade disease-mediating extracellular proteins, as well as starting materials and intermediates for such compounds and their methods of use and processes of manufacture are provided. This invention focuses on novel modifications of the C2-position of the ASGPR ligand, referred to herein as R2.
These modifications include molecules with the C2 substituent in the “down” configuration which correspond to the stereochemistry of galactose as well as molecules with the C2 substituent in the “up” configuration which corresponds to the stereochemistry of talose.
I. Galactose-Based ASGPR Ligands of the Present Invention
In certain embodiments a compound of the present invention is selected from:
Figure imgf000047_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000048_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000048_0002
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000048_0003
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000049_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000049_0002
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000049_0003
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000050_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000050_0002
Figure imgf000051_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000051_0002
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000052_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000052_0002
Figure imgf000053_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000053_0002
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000054_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000055_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000056_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000057_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000058_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000058_0002
Figure imgf000059_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000059_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000059_0003
In certain embodiments a compound of the present invention is selected from:
Figure imgf000060_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000060_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000061_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000061_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000061_0003
Figure imgf000062_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000062_0003
In certain embodiments a compound of the present invention is selected from:
Figure imgf000062_0001
Figure imgf000063_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000063_0002
Figure imgf000064_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000064_0002
Figure imgf000065_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000065_0002
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000068_0002
Figure imgf000069_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000069_0002
and
Figure imgf000070_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000070_0002
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000073_0002
Figure imgf000074_0001
Figure imgf000075_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000075_0002
Figure imgf000076_0001
Figure imgf000077_0001
II. Talose-Based ASGPR-Ligands of the Present Invention
In certain embodiments a compound of the present invention is selected from:
Figure imgf000077_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000077_0003
In certain embodiments a compound of the present invention is selected from:
Figure imgf000078_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000078_0003
In certain embodiments a compound of the present invention is selected from:
Figure imgf000078_0002
Figure imgf000079_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000079_0002
Figure imgf000080_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000080_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000081_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000082_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000083_0001
In certain embodiments a compound of the present invention is selected from:
Figure imgf000084_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000084_0002
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000084_0003
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000085_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000085_0002
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000085_0003
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000086_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000086_0002
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000087_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000087_0002
Figure imgf000088_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000088_0002
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000089_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000090_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000091_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000092_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000093_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000094_0001
or a pharmaceutically acceptable salt thereof. In certain embodiments a compound of the present invention is selected from:
Figure imgf000095_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000095_0002
Figure imgf000096_0001
or a pharmaceutically acceptable salt thereof.
In certain embodiments a compound of the present invention is selected from:
Figure imgf000096_0002
In certain embodiments a compound of the present invention is selected from:
Figure imgf000096_0003
In certain embodiments, a compound of the present invention is selected from
Figure imgf000097_0001
Figure imgf000098_0001
Figure imgf000099_0001
Figure imgf000100_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000100_0002
Figure imgf000101_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000101_0002
In certain embodiments, a compound of the present invention is selected from
Figure imgf000101_0003
Figure imgf000102_0001
Figure imgf000103_0001
Figure imgf000104_0001
Figure imgf000105_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000105_0002
Figure imgf000106_0001
In certain embodiments, a compound of the present invention is selected from
Figure imgf000107_0001
Figure imgf000108_0001
III. Selective Moiety Embodiments
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
Figure imgf000108_0002
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyA is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective Moiety1 is:
Figure imgf000109_0001
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyB is:
In certain embodiments Selective MoietyA is
In certain embodiments Selective MoietyB is
Figure imgf000110_0001
In certain embodiments Selective MoietyA is a heterocycle substituted with two vicinal hydroxyl groups in a cis fashion and optionally substituted with 1, 2, 3, or 4 additional substituents for example,
Figure imgf000111_0001
In certain embodiments Selective MoietyA is an aryl group substituted with two vicinal hydroxyl groups and optionally substituted with 1, 2, 3, or 4 additional substituents, for example
Figure imgf000111_0002
In certain embodiments Selective MoietyA is
Figure imgf000111_0003
wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the heterocycle.
In certain embodiments Selective MoietyA is
Figure imgf000111_0004
wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the bicycle.
In certain embodiments Selective MoietyA is
Figure imgf000111_0005
wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the aryl.
In certain embodiments Selective MoietyA is
Figure imgf000111_0006
wherein the two hydroxyl groups are connected to carbon atoms that are bound to each other in the carbocycle. In certain embodiments Selective MoietyB is a heterocycle substituted with two geminal hydroxyl groups in a cis fashion and optionally substituted with 1, 2, 3, or 4 additional substituents for example,
Figure imgf000112_0001
In certain embodiments Selective MoietyB is an aryl group substituted with two geminal hydroxyl groups and optionally substituted with 1, 2, 3, or 4 additional substituents, for example
Figure imgf000112_0002
In certain embodiments, the Selective MoietyA is selected from
Figure imgf000112_0003
In certain embodiments, the Selective MoietyA is
In certain embodiments, the Selective MoietyA is
In certain embodiments, the Selective MoietyA is
Figure imgf000112_0004
In certain embodiments Selective MoietyA is
Figure imgf000112_0005
In certain embodiments Selective MoietyA is
Figure imgf000112_0006
n certain embodiments, the Selective MoietyB is selected from
Figure imgf000113_0001
In certain embodiments, the Selective MoietyB is
In certain embodiments, the Selective MoietyB is
In certain embodiments, the Selective MoietyB is
Figure imgf000113_0002
In certain embodiments Selective MoietyB is
In certain embodiments Selective MoietyB is
Figure imgf000113_0003
In certain embodiments,
Figure imgf000113_0004
Figure imgf000113_0005
Figure imgf000114_0001
Figure imgf000115_0001
In certain embodiments Selective MoietyA is
Figure imgf000115_0002
each of which Selective MoietyAgroup is optionally substituted with 1, 2, 3, or 4 substituents.
In certain embodiments Selective MoietyA is
Figure imgf000115_0003
optionally substituted with 1, 2, 3, or 4 substituents.
In certain embodiments Selective MoietyB is
Figure imgf000115_0004
optionally substituted with 1, 2, 3, or 4 substituents.
IV. Embodiments of the ASGPR Ligand
Embodiments of R2
In certain embodiments R2 is selected from 5 and
Figure imgf000116_0001
Figure imgf000116_0002
In certain embodiments R2 is selected from:
Figure imgf000116_0003
In certain embodiments R2 is selected from
Figure imgf000116_0004
Figure imgf000117_0001
wherein R is an optional substituent as defined herein.
In certain embodiments R2 is selected from
Figure imgf000117_0002
wherein R is an optional substituent as defined herein. In certain embodiments R2A is selected from
Figure imgf000118_0001
In certain embodiments, R2 is selected from
Figure imgf000118_0002
Figure imgf000119_0001
In certain embodiments, R2 is selected from
Figure imgf000119_0002
Embodiments of Cycle
In certain embodiments Cycle is selected from
Figure imgf000120_0001
Embodiments of R200
Figure imgf000120_0002
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is
In certain embodiments R200 is In certain embodiments R200 is
In certain embodiments R200 is
Figure imgf000121_0001
V. Embodiments of the Linker
In non-limiting embodiments, LinkerA and Linker® are independently selected from:
Figure imgf000122_0001
wherein:
R11, R12, R13, R14, R15, R16, R17, R18, R19, and R20 are independently at each occurrence selected from the group consisting of a bond, alkyl, -C(O)-, -C(O)O-, -OC(O)-, -SO2-, -S(O)-, -C(S)-, -C(O)NR6-, -NR6C(O)-, -O-, -S-, -NR6-, -C(R21R21)-, -P(O)(R3)O-, -P(O)(R3)-, a divalent residue of a natural or unnatural amino acid, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, heterocycle, heteroaryl, -CH2CH2-[O-(CH2)2]n-O-, -CH2CH2-[O-(CH2)2]n-NR6-, -CH2CH2-[O- (CH2)2]n-, -[-(CH2)2-O-]n-, -[O-(CH2)2]n-, -[O-CH(CH3)C(O)]n-, -[C(O)-CH(CH3)-O]n-, -[O- CH2C(O)]n-, -[C(O)-CH2-O]n-, a divalent residue of a fatty acid, a divalent residue of an unsaturated or saturated mono- or di-carboxylic acid, or a bicycle, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R21; n is independently selected at each instance from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;
R21 is independently at each occurrence selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, F, Cl, Br, I, hydroxyl, alkoxy, azide, amino, cyano, -NR6R7, -NR8SO2R3, -NR8S(O)R3, haloalkyl, heteroalkyl, aryl, heteroaryl, and heterocycle; and the remaining variables are as defined herein.
In one embodiment LinkerA is bond and Linker® is
Figure imgf000122_0002
In one embodiment Linker® is bond and LinkerA is
Figure imgf000122_0003
In one embodiment, a divalent residue of an amino acid is selected from
Figure imgf000122_0004
Figure imgf000123_0001
wherein the amino acid can be oriented in either direction and wherein the amino acid can be in the L- or D-form. In one embodiment, a divalent residue of a dicarboxylic acid is generated from a nucleophilic addition reaction:
Figure imgf000124_0004
Non-limiting embodiments of a divalent residue of a dicarboxylic acid generated from a nucleophilic addition reaction include:
Figure imgf000124_0001
In one embodiment, a divalent residue of a dicarboxylic acid is generated from a condensation reaction:
Figure imgf000124_0002
Non-limiting embodiments of a divalent residue of a dicarboxylic acid generated from a condensation include:
Figure imgf000124_0003
Figure imgf000125_0001
Non-limiting embodiments of a divalent residue of a saturated dicarboxylic acid include:
Figure imgf000125_0002
Non-limiting embodiments of a divalent residue of a saturated monocarboxylic acid is selected from butyric acid (-OC(O)(CH2)2CH2-), caproic acid (-OC(O)(CH2)4CH2-), caprylic acid (-OC(O)(CH2)SCH2-), capric acid (-OC(O)(CH2)sCH2-), lauric acid (-OC(0)(CH2)IOCH2-), myristic acid (-OC(O)(CH2)i2CH2-), pentadecanoic acid (-OC(O)(CH2)i3CH2-), palmitic acid (-OC(O)(CH2)i4CH2-), stearic acid (-OC(O)(CH2)i6CH2-), behenic acid (-OC(0)(CH2)2oCH2-), and lignoceric acid (-OC(O)(CH2)22CH2-);
Non-limiting embodiments of a divalent residue of a fatty acid include residues selected from linoleic acid, palmitoleic acid, vaccenic acid, paullinic acid, oleic acid, elaidic acid, gondoic acid, gadoleic acid, nervonic acid, myristoleic acid, and erucic acid:
Figure imgf000125_0003
Figure imgf000126_0001
Non-limiting embodiments of a divalent residue of a fatty acid is selected from linoleic acid (-C(O)(CH2)7(CH)2CH2(CH)2(CH2)4CH2-), docosahexaenoic acid (-C(O)(CH2)2(CHCHCH2)6CH2-), eicosapentaenoic acid (-C(O)(CH2)3(CHCHCH2)5CH2-), alpha-linolenic acid (-C(O)(CH2)7(CHCHCH2)3CH2-) stearidonic acid (-C(O)(CH2)4(CHCHCH2)4CH2-), y-linolenic acid (-C(O)(CH2)4(CHCHCH2)3(CH2)3CH2-), arachidonic acid (-C(O)(CH2)3,(CHCHCH2)4(CH2)4CH2-), docosatetraenoic acid (-C(O)(CH2)5(CHCHCH2)4(CH2)4CH2-), palmitoleic acid (-C(O)(CH2)7CHCH(CH2)5CH2-), vaccenic acid (-C(O)(CH2)9CHCH(CH2)sCH2-), paullinic acid (-C(O)(CH2)nCHCH(CH2)5CH2-), oleic acid (-C(O)(CH2)7CHCH(CH2)7CH2-), elaidic acid (-C(O)(CH2)7CHCH(CH2)7CH2-), gondoic acid (-C(O)(CH2)9CHCH(CH2)7CH2-), gadoleic acid (-
C(O)(CH2)7CHCH(CH2)9CH2-), nervonic acid (-C(O)(CH2)I3CHCH(CH2)7CH2-), mead acid (- C(O)(CH2)3(CHCHCH2)3(CH2)6CH2-), myristoleic acid (-C(O)(CH2)7CHCH(CH2)3CH2-), and erucic acid (-C(O)(CH2)uCHCH(CH2)7CH2-). In certain embodiments LinkerC is selected from:
Figure imgf000127_0001
wherein:
R22 is independently at each occurrence selected from the group consisting of alkyl, -C(O)N-, -NC(O)-, -N-, -C(R21)-, -P(O)O-, -P(O)-, -P(O)(NR6R7)N-, alkenyl, haloalkyl, aryl, heterocycle, and heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R21; and the remaining variables are as defined herein.
In certain embodiments LinkerC is selected from:
Figure imgf000127_0002
In certain embodiments LinkerD is selected from:
Figure imgf000127_0003
wherein:
R32 is independently at each occurrence selected from the group consisting of alkyl, N+X", -C-, alkenyl, haloalkyl, aryl, heterocycle, and heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R21; X" is an anionic group, for example Br" or Cl'; and all other variables are as defined herein.
In certain embodiments Linker13 is selected from:
Figure imgf000128_0001
In certain embodiments LinkerA is selected from:
Figure imgf000128_0002
In certain embodiments LinkerA is selected from:
Figure imgf000128_0003
In certain embodiments LinkerA is selected from:
Figure imgf000129_0001
In certain embodiments LinkerA is selected from:
Figure imgf000129_0002
Figure imgf000130_0001
In certain embodiments LinkerA is selected from:
Figure imgf000131_0001
Figure imgf000132_0001
In certain embodiments LinkerA is selected from:
Figure imgf000132_0002
In certain embodiments LinkerA is selected from:
Figure imgf000132_0003
In certain embodiments LinkerA is selected from:
Figure imgf000132_0004
Figure imgf000133_0001
In certain embodiments LinkerA is selected from:
Figure imgf000133_0002
In certain embodiments LinkerA is selected from:
Figure imgf000133_0003
In certain embodiments Linker® is selected from:
Figure imgf000133_0004
Figure imgf000134_0001
In certain embodiments Linker® is selected from:
Figure imgf000134_0002
In certain embodiments Linker® is selected from:
Figure imgf000134_0003
In certain embodiments Linker® is selected from:
Figure imgf000134_0004
In certain embodiments Linker® is selected from:
Figure imgf000134_0005
Figure imgf000135_0001
Figure imgf000136_0001
In certain embodiments Linker® -LinkerA is selected from:
Figure imgf000136_0002
In certain embodiments Linker® -LinkerA is selected from:
Figure imgf000136_0003
In certain embodiments LinkerC is selected from:
Figure imgf000137_0001
In certain embodiments LinkerC is selected from:
Figure imgf000137_0002
In certain embodiments LinkerC is selected from:
Figure imgf000137_0003
In certain embodiments LinkerC is selected from:
Figure imgf000138_0001
In certain embodiments LinkerC is selected from:
Figure imgf000138_0002
Figure imgf000139_0001
In certain embodiments Linkerc-(LinkerA)2 is selected from:
Figure imgf000139_0002
In certain embodiments Linkerc-(LinkerA)2 is selected from:
Figure imgf000139_0003
Figure imgf000140_0001
In certain embodiments Linkerc-(LinkerA)2 is selected from:
Figure imgf000140_0002
In certain embodiments Linkerc-(LinkerA)2 is selected from:
Figure imgf000140_0003
Figure imgf000141_0001
VI. Compound Terminology
Compounds are described using standard nomenclature. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. The compounds in any of the Formulas described herein include enantiomers, mixtures of enantiomers, diastereomers, tautomers, racemates and other isomers, such as rotamers, as if each is specifically described, unless otherwise indicated or otherwise excluded by context.
The terms “a” and “an” do not denote a limitation of quantity, but rather denote the presence of at least one of the referenced item. The term “or” means “and/or”. Recitation of ranges of values are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. The endpoints of all ranges are included within the range and independently combinable. All methods described herein can be performed in a suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of examples, or exemplary language (e.g., “such as”), is intended merely to better illustrate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. Unless defined otherwise, technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs.
The present invention includes compounds with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e., enriched.
Examples of isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, and chlorine, such as 2H, 3H, 11C, 13C, 14C, 15N, 17O, 18O, 18F 31P, 32P, 35S, 36CI, and 125I respectively. In one embodiment, isotopically labelled compounds can be used in metabolic studies (with, for example 14C), reaction kinetic studies (with, for example 2H or 3H), detection or imaging techniques, such as positron emission tomography (PET) or single-photon emission computed tomography (SPECT) including drug or substrate tissue distribution assays, or in radioactive treatment of patients. For example, a 18F labeled compound may be desirable for PET or SPECT studies. Isotopically labeled compounds of this invention and prodrugs thereof can generally be prepared by carrying out the procedures disclosed in the schemes or in the examples and preparations described below by substituting a readily available isotopically labeled reagent for a non-isotopically labeled reagent.
By way of general example and without limitation, isotopes of hydrogen, for example, deuterium (2H) and tritium (3H) may optionally be used anywhere in described structures that achieves the desired result. Alternatively, or in addition, isotopes of carbon, e.g., 13C and 14C, may be used. In one embodiment, the isotopic substitution is replacing hydrogen with a deuterium at one or more locations on the molecule to improve the performance of the drug, for example, the pharmacodynamics, pharmacokinetics, biodistribution, half-life, stability, AUC, Tmax, Cmax, etc. For example, the deuterium can be bound to carbon in a location of bond breakage during metabolism (an a-deuterium kinetic isotope effect) or next to or near the site of bond breakage (a P-deuterium kinetic isotope effect).
Isotopic substitutions, for example deuterium substitutions, can be partial or complete. Partial deuterium substitution means that at least one hydrogen is substituted with deuterium. In certain embodiments, the isotope is 80, 85, 90, 95 or 99% or more enriched in an isotope at any location of interest. In certain embodiments deuterium is 80, 85, 90, 95 or 99% enriched at a desired location. Unless otherwise stated, the enrichment at any point is above natural abundance, and in an embodiment is enough to alter a detectable property of the drug in a human.
In one embodiment, the substitution of a hydrogen atom for a deuterium atom occurs within any variable group. For example, when any variable group is, or contain for example through substitution, methyl, ethyl, or methoxy, the alkyl residue may be deuterated (in nonlimiting embodiments, CDH2, CD2H, CD3, CD2CD3, CHDCHzD, CH2CD3, CHDCHD2, OCDH2, OCD2H, or OCD3 etc.). In certain other embodiments, a variable group has a “ ‘ “ or an “a” designation, which in one embodiment can be deuterated. In certain other embodiments, when two substituents of the central core ring are combined to form a cyclopropyl ring, the unsubstituted methylene carbon may be deuterated.
The compound of the present invention may form a solvate with solvents (including water). Therefore, in one embodiment, the invention includes a solvated form of the active compound. The term "solvate" refers to a molecular complex of a compound of the present invention (including a salt thereof) with one or more solvent molecules. Nonlimiting examples of solvents are water, ethanol, dimethyl sulfoxide, acetone and other common organic solvents. The term "hydrate" refers to a molecular complex comprising a compound of the invention and water. Pharmaceutically acceptable solvates in accordance with the invention include those wherein the solvent of crystallization may be isotopically substituted, e.g. D2O, de-acetone, de-DMSO. A solvate can be in a liquid or solid form. A dash that is not between two letters or symbols is used to indicate a point of attachment for a substituent. For example, -(C=O)NH2 is attached through carbon of the keto (C=O) group.
The term “substituted”, as used herein, means that any one or more hydrogens on the designated atom or group is replaced with a moiety selected from the indicated group, provided that the designated atom's normal valence is not exceeded and the resulting compound is stable. For example, when the substituent is oxo (i.e., =0) then two hydrogens on the atom are replaced. For example a pyridyl group substituted by oxo is a pyridone. Combinations of substituents and/or variables are permissible only if such combinations result in stable compounds or useful synthetic intermediates.
“Alkyl” is a branched, straight chain, or cyclic saturated aliphatic hydrocarbon group. In one embodiment, the alkyl contains from 1 to about 12 carbon atoms, more generally from 1 to about 6 carbon atoms, from 1 to about 4 carbon atoms, or from 1 to 3 carbon atoms. In one embodiment, the alkyl contains from 1 to about 8 carbon atoms. In certain embodiments, the alkyl is C1-C2, C1-C3, C1-C4, C1-C5 or C1-C6. The specified ranges as used herein indicate an alkyl group which is considered to explicitly disclose as individual species each member of the range described as a unique species. For example, the term C1-C6 alkyl as used herein indicates a straight or branched alkyl group having from 1, 2, 3, 4, 5, or 6 carbon atoms and also a carbocyclic alkyl group of 3, 4, 5, or 6 carbon atoms and is intended to mean that each of these is described as an independent species. For example, the term Ci-C4alkyl as used herein indicates a straight or branched alkyl group having from 1, 2, 3, or 4 carbon atoms and is intended to mean that each of these is described as an independent species. When Co-Cn alkyl is used herein in conjunction with another group, for example, (C3-C7cycloalkyl)C0-C4 alkyl, or -C0-C4alkyl(C3-C7cycloalkyl), the indicated group, in this case cycloalkyl, is either directly bound by a single covalent bond (Coalkyl), or attached by an alkyl chain in this case 1, 2, 3, or 4 carbon atoms. Alkyls can also be attached via other groups such as heteroatoms as in -0-C0-C4alkyl(C3-C7cycloalkyl). Examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, n-pentyl, isopentyl, tert-pentyl, neopentyl, n-hexyl, 2-methylpentane, 3 -methylpentane, 2,2-dimethylbutane, 2, 3 -dimethylbutane, and hexyl.
When a term is used that includes “alk” it should be understood that “cycloalkyl” or “carbocyclic” can be considered part of the definition, unless unambiguously excluded by the context. For example and without limitation, the terms alkyl, alkenyl, alkynyl, alkoxy, alkanoyl, alkenloxy, haloalkyl, etc. can all be considered to include the cyclic forms of alkyl, unless unambiguously excluded by context.
“Alkenyl” is a branched or straight chain aliphatic hydrocarbon group having one or more carbon-carbon double bonds that may occur at a stable point along the chain. Nonlimiting examples are C2-C8alkenyl, C2-C7alkenyl, C2-C6alkenyl, C2-C5alkenyl and C2-C4alkenyl. The specified ranges as used herein indicate an alkenyl group having each member of the range described as an independent species, as described above for the alkyl moiety. Examples of alkenyl include, but are not limited to, ethenyl and propenyl.
“Alkynyl” is a branched or straight chain aliphatic hydrocarbon group having one or more carbon-carbon triple bonds that may occur at any stable point along the chain, for example, C2- C8alkynyl or C2-C6alkynyl. The specified ranges as used herein indicate an alkynyl group having each member of the range described as an independent species, as described above for the alkyl moiety. Examples of alkynyl include, but are not limited to, ethynyl, propynyl, 1-butynyl, 2- butynyl, 3-butynyl, 1-pentynyl, 2-pentynyl, 3-pentynyl, 4-pentynyl, 1-hexynyl, 2-hexynyl, 3- hexynyl, 4-hexynyl and 5-hexynyl.
“Alkoxy” is an alkyl group as defined above covalently bound through an oxygen bridge (-O-). Examples of alkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, 2-butoxy, t-butoxy, n-pentoxy, 2-pentoxy, 3 -pentoxy, isopentoxy, neopentoxy, n- hexoxy, 2-hexoxy, 3-hexoxy, and 3 -methylpentoxy. Similarly an “alkylthio” or a “thioalkyl” group is an alkyl group as defined above with the indicated number of carbon atoms covalently bound through a sulfur bridge (-S-). In one embodiment, the alkoxy group is optionally substituted as described above.
“Haloalkyl” indicates both branched and straight-chain alkyl groups substituted with 1 or more halogen atoms, up to the maximum allowable number of halogen atoms. Examples of haloalkyl include, but are not limited to, trifluoromethyl, monofluoromethyl, difluoromethyl, 2- fluoroethyl, and penta-fluoroethyl.
“Aryl" indicates an aromatic group containing only carbon in the aromatic ring or rings. In one embodiment, the aryl group contains 1 to 3 separate or fused rings and is 6 to 14 or 18 ring atoms, without heteroatoms as ring members. The term “aryl” includes groups where a saturated or partially unsaturated carbocycle group is fused with an aromatic ring. The term “aryl” also includes groups where a saturated or partially unsaturated heterocycle group is fused with an aromatic ring so long as the attachment point is the aromatic ring. Such compounds may include aryl rings fused to a 4 to 7 or a 5 to 7-membered saturated or partially unsaturated cyclic group that optionally contains 1, 2 or 3 heteroatoms independently selected from N, O, B, P, Si and S, to form, for example, a 3, 4-methylenedi oxyphenyl group. Aryl groups include, for example, phenyl and naphthyl, including 1 -naphthyl and 2-naphthyl. In one embodiment, aryl groups are pendant. An example of a pendant ring is a phenyl group substituted with a phenyl group.
The term “bicycle” refers to a ring system wherein two rings are fused together and each ring is independently selected from carbocycle, heterocycle, aryl, and heteroaryl. Non-limiting examples of bicycle groups include:
Figure imgf000146_0001
When the term “bicycle” is used in the context of a bivalent residue such as LinkerA, Linker®, LinkerC , and LinkerD the attachment points can be on separate rings or on the same ring. In certain embodiments both attachment points are on the same ring. In certain embodiments both attachment points are on different rings. Non -limiting exmples of bivalent bicycle groups include:
Figure imgf000146_0002
The term “heterocycle” refers to saturated and partially saturated heteroatom-containing ring radicals, where the heteroatoms may be selected from N, S, and O. The term “heterocycle” includes monocyclic 3-12 membered rings, as well as bicyclic 5-16 membered ring systems (which can include fused, bridged, or spiro, bicyclic ring systems). It does not include rings containing - O-O- or -S-S- portions. Examples of saturated heterocycle groups include saturated 4- to 7- membered monocyclic groups containing 1 to 4 nitrogen atoms [e.g., pyrrolidinyl, imidazolidinyl, piperidinyl, pyrrolinyl, azetidinyl, piperazinyl, and pyrazolidinyl]; saturated 4 to 6-membered monocyclic groups containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms [e.g., morpholinyl]; saturated 3 to 6-membered heteromonocyclic group containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms [e.g., thiazolidinyl]. Examples of partially saturated heterocycle radicals include but are not limited to, dihydrothienyl, dihydropyranyl, dihydrofuryl, and dihydrothiazolyl. Examples of partially saturated and saturated heterocycle groups include but are not limited to, pyrrolidinyl, imidazolidinyl, piperidinyl, pyrrolinyl, pyrazolidinyl, piperazinyl, morpholinyl, tetrahydropyranyl, thiazolidinyl, dihydrothienyl, 2,3 -dihydro-benzofl, 4]dioxanyl, indolinyl, isoindolinyl, dihydrobenzothienyl, dihydrobenzofuryl, isochromanyl, chromanyl, 1,2- dihydroquinolyl, 1,2, 3, 4- tetrahydro-isoquinolyl, 1 ,2,3,4-tetrahydro-quinolyl, 2, 3, 4, 4a, 9,9a- hexahydro-lH-3-aza-fluorenyl, 5,6,7- trihydro-1, 2, 4-triazolo[3,4-a]isoquinolyl, 3,4-dihydro-2H- benzofl, 4]oxazinyl, benzofl, 4]dioxanyl, 2,3- dihydro-lH-lX’-benzo[d]isothiazol-6-yl, dihydropyranyl, dihydrofuryl and dihydrothiazolyl. “Bicyclic heterocycle” includes groups wherein the heterocyclic radical is fused with an aryl radical wherein the point of attachment is the heterocycle ring. “Bicyclic heterocycle” also includes heterocyclic radicals that are fused or bridged with a carbocycle radical. For example partially unsaturated condensed heterocyclic group containing 1 to 5 nitrogen atoms, for example, indoline, isoindoline, partially unsaturated condensed heterocyclic group containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms, partially unsaturated condensed heterocyclic group containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms, and saturated condensed heterocyclic group containing 1 to 2 oxygen or sulfur atoms.
Non-limiting examples of bicyclic heterocycles include:
Figure imgf000147_0001
Unless otherwise drawn or clear from the context, the term “bicyclic heterocycle” includes cis and trans diastereomers. Non-limiting examples of chiral bicyclic heterocycles include:
Figure imgf000148_0001
“Heteroaryl” refers to a stable monocyclic, bicyclic, or multicyclic aromatic ring which contains from 1 to 3, or in some embodiments from 1, 2, or 3 heteroatoms selected from N, O, S, B, and P (and typically selected from N, O, and S) with remaining ring atoms being carbon, or a stable bicyclic or tricyclic system containing at least one 5, 6, or 7 membered aromatic ring which contains from 1 to 3, or in some embodiments from 1 to 2, heteroatoms selected from N, O, S, B or P with remaining ring atoms being carbon. In one embodiment, the only heteroatom is nitrogen. In one embodiment, the only heteroatom is oxygen. In one embodiment, the only heteroatom is sulfur. Monocyclic heteroaryl groups typically have from 5 or 6 ring atoms. In some embodiments bicyclic heteroaryl groups are 8- to 10-membered heteroaryl groups, that is, groups containing 8 or 10 ring atoms in which one 5, 6, or 7-member aromatic ring is fused to a second aromatic or non-aromatic ring wherein the point of attachment is the aromatic ring. When the total number of S and O atoms in the heteroaryl group exceeds 1, these heteroatoms are not adjacent to one another. In one embodiment, the total number of S and O atoms in the heteroaryl group is not more than 2. In another embodiment, the total number of S and O atoms in the aromatic heterocycle is not more than 1. Examples of heteroaryl groups include, but are not limited to, pyridinyl (including, for example, 2-hydroxypyridinyl), imidazolyl, imidazopyridinyl, pyrimidinyl (including, for example, 4-hydroxypyrimidinyl), pyrazolyl, triazolyl, pyrazinyl, furyl, thienyl, isoxazolyl, thiazolyl, oxadiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, tetrahydroisoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, triazolyl, thiadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl, quinoxalinyl, naphthyridinyl, tetrahydrofuranyl, and furopyridinyl. Heteroaryl groups are optionally substituted independently with one or more substituents described herein. “Heteroaryl oxy” is a heteroaryl group as described bound to the group it substituted via an oxygen, -O-, linker.
“Heteroarylalkyl” is an alkyl group as described herein substituted with a heteroaryl group as described herein. “Arylalkyl” is an alkyl group as described herein substituted with an aryl group as described herein.
“Heterocycloalkyl” is an alkyl group as described herein substituted with a heterocyclo group as described herein.
The term "heteroalkyl" refers to an alkyl, alkenyl, alkynyl, or haloalkyl moiety as defined herein wherein a CH2 group is either replaced by a heteroatom or a carbon atom is substituted with a heteroatom for example, an amine, carbonyl, carboxy, oxo, thio, phosphate, phosphonate, nitrogen, phosphorus, silicon, or boron. In one embodiment, the only heteroatom is nitrogen. In one embodiment, the only heteroatom is oxygen. In one embodiment, the only heteroatom is sulfur. In one embodiment, "heteroalkyl" is used to indicate a heteroaliphatic group (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-20 carbon atoms. Nonlimiting examples of heteroalkyl moieties include polyethylene glycol, polyalkylene glycol, amide, polyamide, polylactide, polyglycolide, thioether, ether, alkyl-heterocycle-alkyl, -O-alkyl-O-alkyl, alkyl-O-haloalkyl, etc.
When compounds are “optionally substituted” they may be substituted as allowed by valence by groups selected from alkyl (including Ci-C4alkyl), alkenyl (including C2-C4alkenyl), alkynyl (including C2-C4alkynyl), haloalkyl (including Ci-C4haloalkyl), -OR6, F, Cl, Br, I,
Figure imgf000149_0001
substituent is selected such that a stable compound results. For example
Figure imgf000149_0002
could be substituted with 1 or 2 groups independently selected from alkyl, alkenyl, alkynyl, haloalkyl, -OR6, F, Cl, Br, I, -NR6R7, heteroalkyl, cyano, nitro, C(O)R3 so long as a stable compound results but only one group selected from
Figure imgf000149_0003
, so long as a stable compound results.
Figure imgf000149_0005
on the other hand could only be substituted with 1 or 2 groups selected from ,
Figure imgf000149_0004
Figure imgf000149_0006
Non-limiting examples of optionally substituted CH2 groups include:
Figure imgf000150_0001
Non-limiting examples of optionally substituted -S- groups include:
Figure imgf000150_0002
A “dosage form” means a unit of administration of an active agent. Examples of dosage forms include tablets, capsules, injections, suspensions, liquids, emulsions, implants, particles, spheres, creams, ointments, suppositories, inhalable forms, transdermal forms, buccal, sublingual, topical, gel, mucosal, and the like. A “dosage form” can also include an implant, for example an optical implant.
“Pharmaceutical compositions” are compositions comprising at least one active agent, and at least one other substance, such as a carrier. The present invention includes pharmaceutical compositions of the described compounds.
“Pharmaceutical combinations” are combinations of at least two active agents which may be combined in a single dosage form or provided together in separate dosage forms with instructions that the active agents are to be used together to treat any disorder described herein.
A “pharmaceutically acceptable salt” is a derivative of the disclosed compound in which the parent compound is modified by making inorganic and organic, pharmaceutically acceptable, acid or base addition salts thereof. The salts of the present compounds can be synthesized from a parent compound that contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting free acid forms of these compounds with a stoichiometric amount of the appropriate base (such as Na, Ca, Mg, or K hydroxide, carbonate, bicarbonate, or the like), or by reacting free base forms of these compounds with a stoichiometric amount of the appropriate acid. Such reactions are typically carried out in water or in an organic solvent, or in a mixture of the two. Salts of the present compounds further include solvates of the compounds and of the compound salts. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts include salts which are acceptable for human consumption and the quaternary ammonium salts of the parent compound formed, for example, from inorganic or organic acids. Examples, of such salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, mesylic, esylic, besylic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, HOOC-(CH2)I-4- COOH, and the like, or using a different acid that produces the same counterion. Lists of additional suitable salts may be found, e.g., in Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, Pa., p. 1418 (1985).
The term “carrier” applied to pharmaceutical compositions/combinations of the invention refers to a diluent, excipient, or vehicle with which an active compound is provided.
A “pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition/combination that is generally safe, acceptable for human consumption, and neither biologically nor otherwise inappropriate for administration to a host, typically a human. In one embodiment, an excipient is used that is acceptable for veterinary use.
A “patient” or “host” or “subject” is a human or non-human animal in need of treatment or prevention of any of the disorders as specifically described herein. Typically the host is a human. A “patient” or “host” or “subject” also refers to for example, a mammal, primate (e.g., human), cow, sheep, goat, horse, dog, cat, rabbit, rat, mice, bird and the like.
A “therapeutically effective amount” of a compound, pharmaceutical composition, or combination of this invention means an amount effective, when administered to a host, provides a therapeutic benefit such as an amelioration of symptoms or reduction or dimunition of the disease itself.
Embodiments of “alkyl”
In one embodiment “alkyl” is a Ci-Cioalkyl, C1-C9alkyl, C1-C8alkyl, C1-C7alkyl, C1-C6alkyl, C1-C5alkyl, C1-C4alkyl, C1-C3alkyl, or C1-C2alkyl. In one embodiment “alkyl” has one carbon.
In one embodiment “alkyl” has two carbons.
In one embodiment “alkyl” has three carbons.
In one embodiment “alkyl” has four carbons.
In one embodiment “alkyl” has five carbons.
In one embodiment “alkyl” has six carbons.
Non-limiting examples of “alkyl” include: methyl, ethyl, propyl, butyl, pentyl, and hexyl.
Additional non-limiting examples of “alkyl” include: isopropyl, isobutyl, isopentyl, and isohexyl.
Additional non-limiting examples of “alkyl” include: ec-butyl, sec-pentyl, and sec-hexyl.
Additional non-limiting examples of “alkyl” include: tert-butyl, tert-pentyl, and tert-hexyl.
Additional non-limiting examples of “alkyl” include: neopentyl, 3 -pentyl, and active pentyl.
In an alternative embodiment the “alkyl” group is optionally substituted.
In an alternative embodiment the “alkenyl” group is optionally substituted.
In an alternative embodiment the “alkynyl” group is optionally substituted.
Embodiments of “haloalkyl”
In one embodiment “haloalkyl” is a C1-C10haloalkyl, C1-C9haloalkyl, C1-C8haloalkyl, C1- C7haloalkyl, C1-C6haloalkyl, C1-C5haloalkyl, C1-C4haloalkyl, C1-C3haloalkyl, and C1- C2haloalkyl.
In one embodiment “haloalkyl” has one carbon.
In one embodiment “haloalkyl” has one carbon and one halogen.
In one embodiment “haloalkyl” has one carbon and two halogens.
In one embodiment “haloalkyl” has one carbon and three halogens.
In one embodiment “haloalkyl” has two carbons.
In one embodiment “haloalkyl” has three carbons.
In one embodiment “haloalkyl” has four carbons.
In one embodiment “haloalkyl” has five carbons. In one embodiment “haloalkyl” has six carbons.
Non-limiting examples of “haloalkyl” include:
Figure imgf000153_0001
Figure imgf000153_0005
Figure imgf000153_0006
Figure imgf000153_0002
Figure imgf000153_0003
Additional non-limiting examples of “haloalkyl” include:
Additional non-limiting examples of “haloalkyl” include:
Figure imgf000153_0004
Embodiments of “heteroaryl”
Non-limiting examples of 5 membered “heteroaryl” groups include pyrrole, furan, thiophene, pyrazole, imidazole, triazole, isoxazole, oxazole, oxadiazole, oxatriazole, isothiazole, thiazole, thiadiazole, and thiatriazole.
Additional non-limiting examples of 5 membered “heteroaryl” groups include:
Figure imgf000153_0007
In one embodiment “heteroaryl” is a 6 membered aromatic group containing 1, 2, or 3 nitrogen atoms (i.e. pyridinyl, pyridazinyl, triazinyl, pyrimidinyl, and pyrazinyl).
Non-limiting examples of 6 membered “heteroaryl” groups with 1 or 2 nitrogen atoms include:
Figure imgf000154_0001
In one embodiment “heteroaryl” is a 9 membered bicyclic aromatic group containing 1 or
2 atoms selected from nitrogen, oxygen, and sulfur.
Non-limiting examples of “heteroaryl” groups that are bicyclic include indole, benzofuran, isoindole, indazole, benzimidazole, azaindole, azaindazole, purine, isobenzofuran, benzothiophene, benzoisoxazole, benzoisothiazole, benzooxazole, and benzothiazole.
Additional non-limiting examples of “heteroaryl” groups that are bicyclic include:
Figure imgf000154_0002
Additional non-limiting examples of “heteroaryl” groups that are bicyclic include:
Figure imgf000154_0003
Additional non-limiting examples of “heteroaryl” groups that are bicyclic include:
Figure imgf000154_0004
In one embodiment “heteroaryl” is a 10 membered bicyclic aromatic group containing 1 or 2 atoms selected from nitrogen, oxygen, and sulfur.
Non-limiting examples of “heteroaryl” groups that are bicyclic include quinoline, isoquinoline, quinoxaline, phthalazine, quinazoline, cinnoline, and naphthyridine.
Additional non-limiting examples of “heteroaryl” groups that are bicyclic include:
Figure imgf000154_0005
Embodiments of “heterocycle”
In one embodiment “heterocycle” refers to a cyclic ring with one nitrogen and 3, 4, 5, 6, 7, or 8 carbon atoms.
In one embodiment “heterocycle” refers to a cyclic ring with one nitrogen and one oxygen and 3, 4, 5, 6, 7, or 8 carbon atoms.
In one embodiment “heterocycle” refers to a cyclic ring with two nitrogens and 3, 4, 5, 6, 7, or 8 carbon atoms.
In one embodiment “heterocycle” refers to a cyclic ring with one oxygen and 3, 4, 5, 6, 7, or 8 carbon atoms.
In one embodiment “heterocycle” refers to a cyclic ring with one sulfur and 3, 4, 5, 6, 7, or 8 carbon atoms.
Non-limiting examples of “heterocycle” include aziridine, oxirane, thiirane, azetidine, 1,3- diazetidine, oxetane, and thietane.
Additional non-limiting examples of “heterocycle” include pyrrolidine, 3 -pyrroline, 2- pyrroline, pyrazolidine, and imidazolidine.
Additional non-limiting examples of “heterocycle” include tetrahydrofuran, 1,3 -di oxolane, tetrahydrothiophene, 1,2-oxathiolane, and 1,3 -oxathiolane.
Additional non-limiting examples of “heterocycle” include piperidine, piperazine, tetrahydropyran, 1,4-dioxane, thiane, 1,3-dithiane, 1,4-dithiane, morpholine, and thiomorpholine.
Additional non-limiting examples of “heterocycle” include indoline, tetrahydroquinoline, tetrahydroisoquinoline, and dihydrobenzofuran wherein the point of attachment for each group is on the heterocyclic ring.
For example,
Figure imgf000155_0001
is a “heterocycle” group.
However,
Figure imgf000155_0002
is an “aryl” group. Non-limiting examples of “heterocycle” also include:
Figure imgf000156_0001
Non-limiting examples of “heterocycle” also include:
Figure imgf000156_0002
Non-limiting examples of “heterocycle” also include:
Figure imgf000156_0003
Additional non-limiting examples of “heterocycle” include:
Figure imgf000156_0004
Additional non-limiting examples of “heterocycle” include:
Figure imgf000156_0005
Aryl
In one embodiment “aryl” is a 6 carbon aromatic group (phenyl).
In one embodiment “aryl” is a 10 carbon aromatic group (naphthyl). In one embodiment “aryl” is a 6 carbon aromatic group fused to a heterocycle wherein the point of attachment is the aryl ring. Non-limiting examples of “aryl” include indoline, tetrahydroquinoline, tetrahydroisoquinoline, and dihydrobenzofuran wherein the point of attachment for each group is on the aromatic ring.
For example,
Figure imgf000157_0001
group.
However,
Figure imgf000157_0002
group.
Embodiments of “arylalkyl”
Non-limiting examples of “arylalkyl” include:
Figure imgf000157_0003
In one embodiment the “arylalkyl” refers to a 2 carbon alkyl group substituted with an aryl group.
Non-limiting examples of “arylalkyl” include:
Figure imgf000157_0004
VII. Extracellular Proteins and Targeting Ligands
A wide range of well-known and characterized extracellular proteins can cause, modulate, or amplify diseases in vivo, such as abnormal cellular proliferation such as tumors and cancer, autoimmune disorders, inflammation, and aging-related diseases. For example, extracellular proteins such as growth factors, cytokines, and chemokines bind to cell surface receptors, often initiating aberrant signaling in multiple diseases such as cancer and inflammation. According to the invention, the Extracellular Protein of interest binds to a compound of Formula VII:
Figure imgf000158_0001
The compound of Formula VII can react in vivo with a compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d, or a bis or tris version thereof with the appropriate Selective MoietyA to form an extracellular protein degrading molecule, wherein the extracellular protein that is degraded is the protein that binds the Extracellular Protein Targeting Ligand.
The extracellular protein degraders described herein or their pharmaceutically acceptable salt and/or its pharmaceutically acceptable compositions can be used to treat a disorder which is mediated by the selected Target Protein that binds to the Extracellular Targeting Ligand. The described degraders are capable of targeting specific extracellular Target Proteins that mediate pathological disorders for lysosomal degradation. The selected extracellular Target Proteins may modulate a disorder in a human via a mechanism of action such as modification of a biological pathway, pathogenic signaling, or modulation of a signal cascade or cellular entry. In one embodiment, the Target Protein is a protein that is not druggable in the classic sense in that it does not have a binding pocket or an active site that can be inhibited or otherwise bound, and cannot be easily allosterically controlled. In another embodiment, the Target Protein is a protein that is drugable in the classic sense, yet for therapeutic purposes, degradation of the protein is preferred to inhibition. The extracellular Target Protein is recruited with a Targeting Ligand, which is a ligand for the extracellular Target Protein. Typically, the Targeting Ligand binds the Target Protein in a non-covalent fashion. In an alternative embodiment, the Target Protein is covalently bound to the Targeting Ligand in a manner that can be irreversible or reversible.
Accordingly, in some embodiments, a method to treat a host with a disorder mediated by an extracellular Target Protein is provided that includes administering an effective amount of a degrader targeting an extracellular protein or its pharmaceutically acceptable salt described herein to the host, typically a human, optionally in a pharmaceutically acceptable composition.
The extracellular Target Protein can be any amino acid sequence to which the degrader comprising a Targeting Ligand can be bound which through degradation thereof, results in a beneficial therapeutic effect. In one embodiment, the Target Protein is a non-endogenous peptide such as that from a pathogen or toxin. In another embodiment, the Target Protein can be an endogenous protein that mediates a disorder. The endogenous protein can be either the normal form of the protein or an aberrant form. For example, the Target Protein can be an extracellular mutant protein, or a protein, for example, where a partial, or full, gain-of-function or loss-of- function is encoded by nucleotide polymorphisms. In some embodiments, the degrader targets the aberrant form of the protein and not the normal form of the protein.
The Targeting Ligand is a ligand which covalently or non-covalently binds to a Target Protein which has been selected for lysosomal degradation. A Targeting Ligand is a small molecule or moiety (for example a peptide, nucleotide, antibody fragment, aptamer, biomolecule, or other chemical structure) that binds to a Target Protein, and wherein the Target Protein is a mediator of disease in a host as described in detail below. Exemplary Target Ligands are provided in Fig. 1.
In one embodiment the Extracellular Protein Targeting Ligand is not an oligomer.
In another embodiment neither the Extracellular Protein nor the Extracellular Protein Targeting Ligand directly mediates intracellular gene editing such as CRISPR.
In an alternative embodiment of the invention, when R2 is NR6-alkenyl, -NR6-alkynyl,- NR8-C(O)R10, -NR8-S(O)2-alkenyl, -NR8-S(O)2-alkynyl, -NR6-heteroaryl, or -NR6-aryl, then Extracellular Protein Targeting Ligand does not comprise an oligonucleotide.
Anchor Bond
The Extracellular Protein Target Ligand is covalently bound to Linker® in the compounds of Formula VII through the Anchor Bond (which is the chemical bond between the Extracellular Protein Target Ligand and Linker B). This bond can be placed at any location on the ligand that does not unacceptably disrupt the ability of the Extracellular Protein Target Ligand to bind to the Extracellular Protein Target. The Anchor Bond is depicted on the nonlimiting examples of Extracellular Protein Target Ligands in Figure 1 as:
Figure imgf000159_0001
The exemplary extracellular proteins targeted for medical therapy described below have characterizing structural information in the well-known Protein Data Bank (“PDB”), which is a database for the three-dimensional structural information for large biological molecules such as proteins and nucleic acids. PDB includes x-ray crystallography and other information submitted by scientists around the world, and is freely accessible. See for example www.rcsb.or ; www.wwpdb.org and www.uniprot.org. Using the PDB codes for example provided in Section ** or in the Data Bank itself, and technical references provided herein or otherwise publicly available, the skilled artisan can determine appropriate locations where the Extracellular Protein Target Ligand can be linked through an Anchor Bond to Linker B. For many of these proteins, published references describe how a range of ligands bind to the target proteins, and from this information, one can determine reasonable Anchor Bond locations.
For example, the skilled artisan can use available visualization tools, including those available on the PDB website, to determine where the Extracellular Protein Targeting Ligand docks into to the Extracellular Protein. The skilled artisan can also import the crystal structure and the selected Extracellular Protein Targeting Ligand of interest into modeling software (including for example PyMOL, Glide, Maestro, RasMol, Visual Molecular Dynamics, Jmol, and AutoDock) to determine what portion of the Extracellular Protein Targeting Ligand is bound to the Extracellular Protein. The ASGPR ligand is then bound through the Linker and the Anchor Bond at a point that does not unduly adversely affect binding to the extracellular protein.
Non-Limiting Examples of Extracellular Target Proteins
Immunoglobulin A (IgA)
In some embodiments, the Target Protein is human immunoglobulin A (IgA). IgA is an antibody that plays a crucial role in the immune function of mucous membranes. The amount of IgA produced in association with mucosal membranes is greater than all other types of antibody combined. IgA has two subclasses (IgAl and IgA2) and can be produced as a monomeric as well as a dimeric form. The IgA dimeric form is the most prevalent. In the blood, IgA interacts with an Fc receptor called FcaRI (or CD89), which is expressed on immune effector cells, to initiate inflammatory reactions. Ligation of FcaRI by IgA containing immune complexes causes antibody-dependent cell-mediated cytotoxicity (ADCC), degranulation of eosinophils and basophils, phagocytosis by monocytes, macrophages, and neutrophils, and triggering of respiratory burst activity by polymorphonuclear leukocytes. Aberrant IgA expression has been implicated in a number of autoimmune and immune-mediated disorders, including IgA nephropathy, celiac disease, Henoch-Sconiein purpura (HSP), liner IgA bullous dermatosis, and IgA pemphigus. The Protein Data Bank website provides the crystal structure of IgA, as well as the crystal structure of IgA bound to various compounds searchable by 5E8E (Baglin, T.P., et al., J. Thromb. Haemost., 2016, 14: 137-142), and 2QTJ (Bonner, A., et al., J. Immunol., 2008, 180: 1008-1018). Additionally, Hatanaka T. et al., provides great insight into the specificity and high binding affinity of IgA to OPT-1 peptides (J Biol Chem., 2012, 287(51), 43126-43136.).
Representative IgA Targeting Ligands are provided in Fig. 1.
Immunoglobulin G (IgG)
In some embodiments, the Target Protein is a human immunoglobulin G (IgG). IgG represents approximately 75% of serum antibodies in humans. IgG is the most common type of antibody found in blood circulation. IgG antibodies are large globular proteins with a molecular weight of about 150 kDa made of four peptide chains. It contains two identical y (gamma) heavy chains of about 50 kDa and two identical light chains of about 25 kDa, thus a tetrameric quaternary structure. The two heavy chains are linked to each other and to a light chain each by disulfide bonds. The resulting tetramer has two identical halves, which together form the Y-like shape. Each end of the fork contains an identical antigen binding site. The various regions and domains of a typical IgG are depicted in the figure to the left. The Fc regions of IgGs bear a highly conserved N-glycosylation site at asparagine 297 in the constant region of the heavy chain. The N-glycans attached to this site are predominantly core-fucosylated biantennary structures of the complex type. In addition, small amounts of these N-glycans also bear bisecting GlcNAc and a-2,6-linked sialic acid residues. The N-glycan composition in IgG has been linked to several autoimmune, infectious and metabolic diseases. In addition, overexpression of IgG4 has been associated with IG4- related diseases, which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nephritis, Riedel's thyroiditis, Mikulicz's disease, Kuttner's tumor, inflammatory pseudotumors (in various sites of the body), mediastinal fibrosis and some cases of retroperitoneal fibrosis, aortitis, retroperitoneal fibrosis, proximal biliary strictures, tubulointerstitial nephritis, pachymeningitis, pancreatic enlargement and pericarditis.
The Protein Data Bank website provides the crystal structure of IgG searchable by 1H3X (Krapp, S., et al., J. Mol. Biol., 2003, 325: 979); and 5V43 (Lee, C.H., et al., Nat. Immunol., 2017, 18: 889-898); as well as the crystal structure of IgG bound to various compounds searchable by 5YC5 (Kiyoshi M., et al., Sci. Rep., 2018, 8: 3955-3955); 5XJE (Sakae Y., et al., Sci. Rep., 2017, 7: 13780-13780); 5GSQ (Chen, C. L., et al., ACS Chem. Biol., 2017, 12: 1335-1345); and 1HZH (Saphire E. O., et al., Science, 2001, 293: 1155-1159). Additionally, Kiyoshi, M., et al., provides insight into the structural basis for binding of human IgGl to its high-affinity human receptor FcyRI. (Kiyosi M., et al., Nat Commun., 2015, 6, 6866).
Representative IgG Targeting Ligands are provided in Fig. 1.
Immunoglobulin E (IgE)
In some embodiments, the Target Protein is human immunoglobulin E (IgE). IgE is a type of immunoglobulin that plays an essential role in type I hypersensitivity, which can manifest into various allergic diseases, such as allergic asthma, most types of sinusitis, allergic rhinitis, food allergies, and specific types of chronic urticaria and atopic dermatitis. IgE also plays a pivotal role in responses to allergens, such as: anaphylactic drugs, bee stings, and antigen preparations used in desensitization immunotherapy.
The Protein Data Bank website provides the crystal structure of IgE searchable by 1F2Q (Garman, S.C., Kinet, J.P., Jardetzky, T.S., Cell, 1998, 95: 951-961); as well as the crystal structure of IgE bound to various compounds searchable by 1F6A (Garman, S.C., et al., Nature, 2000, 406 259-266); 1RPQ (Stamos, J., et al., Structure, 2004, 12 1289-1301); 2Y7Q (Holdom, M.D., et al., Nat. Struct. Mol. Biol., 2011, 18 571); and 4GRG (Kim, B., et al., Nature, 2012, 491 : 613-617). Additionally, Wan et al., provides insight into the crystal structure of IgE Fc, revealing an asymmetrically bent conformation (Wan et al., Nat. Immunol., 2002, 3(7), 681-6); and Dhaliwal et al, provides insight into the crystal structure of IgE bound to its B-cell receptor CD23 reveals a mechanism of reciprocal allosteric inhibition with high affinity receptor FcsRI (Dhaliwal, B., et al., Proc Natl Acad Sci U S A., 2012, 109(31), 12686-91).
TNF-a
In some embodiments, the Target Protein is human TNF-a (UniProtKB - P01375 (TNFA HU MAN)). TNF-a is a pro-inflammatory cytokine active in the bodily immune response and serious inflammatory diseases. TNF-a has been implicated in a number of disorders, including but not limited to rheumatoid arthritis, inflammatory bowel disease, graft-vs-host disease, ankylosing spondylitis, psoriasis, hidradenitis suppurativa, refractory asthma, systemic lupis erthyematosus, diabetes, and the induction of cachexia. The Protein Data Bank website provides the crystal structure of TNF-a searchable by 6RMJ (Valentinis, B., et al., Int. J. Mol. Sci., 2019, 20); 5UUI (Carrington et al., Biophys J., 2017, 113 371-380); 6OOY, 6OOZ and 6OPO (O’Connell, J., et al., Nat. Commun, 2019, 10 5795- 5795); and 5TSW (Cha, S. S., J Biol Chem., 1998, 273 2153-2160); as well as the crystal structure of TNF-a bound to various compounds searchable by 5YOY (Ono et al., Protein Sci., 2018, 27 1038-1046 ); 2AZ5 (He., M. M., et al., Science, 2005, 310: 1022-1025); 5WUX (Lee, J. U., Int J Mol Sci., 2017, 18); 5MU8 (Blevitt et al., J Med Chem., 2017, 60 3511-3517); 4Y6O (Feldman J. L., et al., Biochemistry, 2015, 543037-3050); 3WD5 (Hu, S., et al., JBiol Chem, 2013, 28827059- 27067); and 4G3Y (Liang, S. Y., J Biol Chem., 2013, 288 13799-13807).
Representative TNF-a Targeting Ligands are provided in Fig. 1. Additional TNF-a Targeting Ligands can be found in, for example, US Patent 8541572; J Chem Inf Model. 2017 May 22; 57(5): 1101-1111; each of which is incorporated by reference herein.
IL-1
In some embodiments, the Target Protein is human interleukin-1 (IL-1) (UniProtKB - P01584 (ILIB HUMAN)). IL-1 is a potent proinflammatory cytokine. Initially discovered as the major endogenous pyrogen, induces prostaglandin synthesis, neutrophil influx and activation, T- cell activation and cytokine production, B-cell activation and antibody production, and fibroblast proliferation and collagen production. IL-1 promotes Thl7 differentiation of T-cells, and Synergizes with IL12/interleukin-12 to induce IFNG synthesis from T-helper 1 (Thl) cells. IL-1 has been implicated in a number of auto-inflammatory and autoimmune disorders, including, but not limited to, Blau syndrome, cryopyrin-associated periodic syndromes, familial Mediterranean fever, Majeed syndrome; mevalonate kinase deficiency syndrome, pyogenic arthritis-pyoderma gangrenosum-acne syndrome, tumor necrosis factor receptor-associated periodic syndrome, Behçet’s Disease, Sjogren’s Syndrome, gout and chondrocalcinosis, periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (or PFAPA) syndrome, rheumatoid arthritis, Type 2 diabetes mellitus, acute pericarditis, Chronic interstitial lung diseases (ILDs), Still’s Disease,
The Protein Data Bank website provides the crystal structure of IL-1 searchable by 9ILB (Yu, B., et al., Proc Natl Acad Sci U S A, 1999, 96 103-108); H1B (Finzel, B. C., et al., J Mol Biol., 1989, 209 779-791); and 3040 (Wang et al., Nat.Immunol., 2010, 11 : 905-911); as well as the crystal structure of IL-1 bound to various compounds searchable by 4G6J (Blech, M., et al., J Mol Biol., 2013, 425 94-111); 5BVP (Rondeau e al., MAbs, 2015, 7 1151-1160); and 3LTQ (Barthelmes, K., et al., J Am Chem. Soc., 2011, 133 808-819). Additionally, Guy et al., provides insight into the crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1 (Guy et al., The Journal of Biological Chemistry, 2000, 275, 36927-36933).
Potential IL-1 direct or indirect inhibitors are described in Fig. 1. Additional IL-1 Targeting Ligands can be found in, for example, US Patent 9694015, each of which is incorporated herein by reference. Additional binding ligands include rilanocept or a binding fragment thereof (J Rheumatol. 2012;39:720-727 (2012); and Canakinumab, or a binding fragment thereof (J Rheumatol. 2004:31 : 1103-1111).
IL-2
In some embodiments, the Target Protein is human interleukin-2 (IL-2) (UniProtKB - P60568 (IL2 HUMAN)). IL-2 is a potent pro-inflammatory cytokine. IL-2 has been implicated in host versus graft rejection and other autoimmune disorders.
The Protein Data Bank website provides the crystal structure of IL-2 searchable by 1M4C and 1M47 (Arkin, M. R., et al., Proc.Natl.Acad.Sci.USA, 2003, 100: 1603-1608); as well as the crystal structure of IL-2 bound to various compounds searchable by 4NEJ and 4NEM (Brenke, R., et al.); 1QVN (Thanos, C. D., et al., Proc Natl Acad Sci U S A, 2006, 103 15422-15427); 1PW6 and 1PY2 (Thanos, C. D., et al., J Am Chem Soc., 2003, 125 15280-15281); INBP (Hyde, J., et al., Biochemistry, 2003, 42 6475-6483); and 1M48, 1M49, 1M4A, 1M4B, and 1M4C (Arkin, M. R., et al., Proc Natl Acad Sci U S A, 2003, 100 1603-1608). Additionally, Stauber, D. J., et al, provides insight into the crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor (Stauber, D. J., et al., PNAS, 2006, 103(8), 2788-2793).
Representative IL-2 Targeting Ligands are provided in Fig. 1. Additional IL-2 Targeting Ligands can be found in, for example, US Patent 8802721; US Patent 9682976, US Patent 9708268; Eur J Med Chem 83: 294-306 (2014), J Med Chem 60: 6249-6272 (2017); Nature 450: 1001-1009 (2007); each of which is incorporated by reference herein.
IL-6
In some embodiments, the Target Protein is human inteleukin-6 (IL-6) (UniProtKB - P05231 (IL6 HUMAN)). IL-6 is a cytokine with a wide variety of biological functions. It is a potent inducer of the acute phase response and plays an essential role in the final differentiation of B-cells into Ig-secreting cells. It is also involved in lymphocyte and monocyte differentiation. It also acts on B-cells, T-cells, hepatocytes, hematopoietic progenitor cells and cells of the CNS, and is required for the generation of T(H)17 cells. IL-6 has been implicated in a number of inflammatory diseases and cancers, including, but not limited to, Castleman’s disease, metastatic castration-associated prostate cancer, renal cell carcinoma, large-cell lung carcinoma, ovarian cancer, rheumatoid arthritis, asthma.
The Protein Data Bank website provides the crystal structure of IL-6 searchable by 1P9M (Boulanger, M. J., et al., Science, 2003, 300: 2101-2104); 1ALU (Somers et al., EMBO J., 1997, 16, 989-997); 1IL6 and 2IL6 (Xu, G. Y., et al., J Mol Biol., 1997, 268 468-481) and 1N26 (Varghese et al., Proc Natl Acad Sci U S A., 2002, 99 15959-15964); as well as the crystal structure of IL-6 bound to various compounds searchable by 4CNI (Shaw, S., et al., Mabs, 2014, 6: 773); and 4NI7 and 4NI9 (Gelinas et al., J Biol Chem. 2014, 289(12), 8720-8734). Additionally, Gelinas et al., provides insight into the crystal structure of interleukin-6 in complex with a modified nucleic acid ligand (Gelinas, A. D., et al., J Biol Chem. 2014, 289(12), 8720-8734); and Somers et al., provides insight into the crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling.
Potential IL-6 direct or indirect inhibitors are provided in Fig. 1. Additional potential IL- 6 direct or indirect inhibitors can be found in, for example, US Patent 8901310; US Patent 10189796; US Patent 9694015; each incorporated herein by reference. In another embodiment the IL-6 Extracellular Targeting Ligand is AvimarC326 or a binding fragment thereof which is described in Nat Biotechnol 23, 1556-1561 (2005).
IFN-y
In some embodiments, the Target Protein is human interferon-y (IFN-y) (UniProtKB - Q14609 (Q14609_HUMAN)). IFN-y is a immunoregulatory cytokine. IFN-y has been implicated in a number of autoimmune disorders, including, but not limited to rheumatoid arthritis, multiple sclerosis (MS), corneal transplant rejection, and various autoimmune skin diseases such as psoriasis, alopecia areata, vitiligo, acne vulgaris, and others.
The Protein Data Bank website provides the crystal structure of IFN-y searchable by 1HIG (Ealick, S. E., et al., Science 252, 1991, 698-702); as well as the crystal structure of IFN-y bound to various compounds searchable by 6E3K and 6E3L (Mendoza, J. L., et al., Nature, 2019, 567 56-60). Additionally, Randal et al., provides insight into the structure and activity of a monomeric interferon-y: a-chain receptor signaling complex (Randal, M., et al., Structure, 2001, 9(2), 155- 163).
Representative IFN-y Targeting Ligands are described in Fig. 1. Additional IFN-y Targeting Ligands can be found in, for example, J Med Chem 57: 4511-20 (2014); which is incorporated by reference herein.
Vascular Epithelial Growth Factor (VEGF)
In some embodiments, the Target Protein is human vascular epithelial growth factor (VEGF) (UniProtKB - Pl 5692 (VEGFA HUMAN)). VEGF is a growth factor active in angiogenesis, vasculogenesis, and endothelial cell growth. VEGF induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. VEGF has been implicated in the vascularization and angiogenesis of tumors.
The Protein Data Bank website provides the crystal structure of VEGF searchable by 3QTK (Mandal, K., et al., Angew Chem Int Ed Engl., 2011, 50 8029-8033); and 4KZN (Shen et al.); as well as the crystal structure of VEGF bound to various compounds searchable by 5O4E (Lobner, E., et al., MAbs, 2017, 9 1088-1104); 4QAF (Giese, T., et al.,); 5DN2 (Tsai, Y.C.I., et al., FEBS, 2017, J 283 1921-1934); 4GLS (Mandal, K., et al., Proc Natl Acad Sci U S A, 2012, 109 14779- 14784); and 1KMX (Stauffer, M. E. et al., J Biomol NMR, 2002, 23 57-61). Additionally, Mueller, Y. A., et al, provides insight into the Crystal structure and functional mapping of the kinase domain receptor binding site of VEGF (Mueller, Y. A., et al., Proc Natl Acad Sci U S A., 1997 Jul 8; 94(14): 7192-7197).
Representative VEGF Targeting Ligands are provided in Fig. 1. Additional VEGF Targeting Ligands include, but are not limited to, (all cited referenced incorporated herein by reference) the peptide VEPNCDIHVMWEWECFERL-NH2 (Biochemistry 1998, 37, 17754- 177764). Additional VEGF Targeting Ligands are provided in, for example, J Med Chem 57: 3011-29 (2014), US Patent 9884843, US Patent 9446026, J Med Chem 53: 1686-99 (2010), J Med Chem 48: 8229-36 (2005), J Nat Prod 76: 29-35 (2013), each of which is incorporated herein by reference. Transforming Growth Factor-β1 (TGF-β1)
In some embodiments, the Target Protein is human transforming growth factor-pi (TGF- β1) (UniProtKB - P01137 (TGFB1 HUMAN)). TGF-β1 is a multifunctional protein that regulates the growth and differentiation of various cell types and is involved in various processes, such as normal development, immune function, microglia function and responses to neurodegeneration. TGF-β1 can promote either T-helper 17 cells (Thl7) or regulatory T-cells (Treg) lineage differentiation in a concentration-dependent manner. TGF-β1 expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF-β1 mediated tumor suppression via T-cell exclusion. TGF-β1 expression has also been implicated in hematological malignancies and fibrosis.
The Protein Data Bank website provides the crystal structure of TGF-β1 searchable by 5E8S, 5E8T, and 5E8U (Tebben, A. J., et al., Acta Crystallogr D Struct Biol., 2016, 72 658-674); 2L5S (Zuniga, J. E., et al, J Mol Biol., 2011, 412 601-618); and 2PJY (Groppe, J., et al., Mol Cell, 2008, 29 157-168); as well as the crystal structure of TGF-β1 bound to various compounds searchable by 5QIK, 5QIL and 5QIM, (Zhang, Y., et al., ACS Med Chem Lett., 2018, 9 1117- 1122); 6B8Y (Harikrishnan, L. S., et al., Bioorg Med Chem., 2018, 26 1026-1034); 5E8W, 5E8X, 5E8Z, and 5E90 (Tebben, A. J., et al., Acta Crystallogr D Struct Biol., 2016, 72 658-674); 3TZM (Ogunjimi, A.A. et al., Cell Signal, 2012, 24 476-483); 2X70 (Roth, G. J., et al., J Med Chem., 2010, 53 7287); 3KCF (Guckian, K., et al., Bioorg Med Chem Lett., 2010, 20 326-329); 3FAA (Bonafoux, D., et al., Bioorg Med Chem Lett., 2009, 19 912-916); 1VJY (Gellibert, F, J., et al., J Med Chem., 2004 47 4494-4506); and 1PY5 (Sawyer, J. S., et al., Bioorg Med Chem Lett., 2004, 14 3581-3584). Additionally, Hinck et al., provides insight into the structural studies of the TGF- ps and their receptors and further insight into evolution of the TGF-P superfamily (Hinck, A., FEBS, 2012, 586(14), 1860-1870).
Representative TGF-β1 Targeting Ligands are provided in Fig. 1. In some embodiments, the TGF-β1 Targeting Ligand is the peptide KRFK peptide (J. Biol. Chem. Vol. 274 (No.19) pp. 13586-13593 (1999)(incorporated herein by reference). Additional TGF-β1 Targeting Ligands are provided in, for example, Bioorg Med Chem Lett 21 : 5642-5 (2011), which is incorporated herein by reference. Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK-9)
In some embodiments, the Target Protein is human proprotein convertase subtilisin/kexin type 9 (PCSK-9) (UniProtKB - Q8NBP7 (PCSK9 HUMAN)). PCSK-9 is a crucial player in the regulation of plasma cholesterol homeostasis. PCSK-9 binds to low-density lipid receptor family members: low density lipoprotein receptor (LDLR), very low-density lipoprotein receptor (VLDLR), apolipoprotein E receptor (LRP1/APOER) and apolipoprotein receptor 2 (LRP8/APOER2), and promotes their degradation in intracellular acidic compartments. It acts via a non-proteolytic mechanism to enhance the degradation of the hepatic LDLR through a clathrin LDLRAPl/ARH-mediated pathway, and may prevent the recycling of LDLR from endosomes to the cell surface or direct it to lysosomes for degradation. PCSK-9 has been implicated in high blood cholesterol and the development of cardiovascular disease.
The Protein Data Bank website provides the crystal structure of PCSK-9 searchable by 2P4E (Cunningham, D., et al., Nat Struct Mol Biol., 2007, 14 413-419); as well as the crystal structure of PCSK-9 bound to various compounds searchable by 3BPS (Kwon, H. J., et al., Proc Natl Acad Sci U S A, 2008, 105 1820-1825); 6U26, 6U2N, 6U2P, 6U36, 6U38, and 6U3X (Petrilli, W. L., et al., Cell Chem Biol., 2019, 27 32-40. e3); 5OCA (Gustafsen, C., et al., Nat Commun., 2017, 8 503-503); 4NE9 (Schroeder, C. I., et al., Chem Biol., 2014, 21 284-294); 4OV6 (Mitchell, T., et al., J Pharmacol Exp Ther., 2014, 350412-424); and 4NMX (Zhang, Y., et al., J Biol Chem., 2014, 289 942-955). Additionally, Piper et al., provides insight into the crystal structure of PCSK9 (Piper, D. E., et al., Structure, 2007, 15(5), 545-52).
Representative PCSK-9 Targeting Ligands are provided in Fig. 1. In some embodiments, the PCSK-9 Targeting Ligand is the peptide TVFTSWEEYLDWV (J. Bio. Chem. 2014 Jan; 289(2):942-955, incorporated herein by reference). Additional PCSK-9 Targeting Ligands are provided in, for example, US Patent 9227956, J Biol Chem 289: 942-55 (2014), each of which is incorporated by reference herein.
IL-21
In some embodiments, the Target Protein is human interleukin-21 (IL-21) (UniProtKB - Q9HBE4 (IL21 HUMAN)). IL-21 is an immunoregulatory cytokine. IL-21 has been implicated in a number of autoimmune disorders, including Sjogren’s syndrome, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease.
The Protein Data Bank website provides the crystal structure of IL-21 searchable by 2OQP (Bondensgaard, K., et al., J Biol Chem., 2007, 282 23326-23336); and 4NZD (Hamming et al.); as well as the crystal structure of IL-21 bound to various compounds searchable by 3TGX (Hamming, O. J., et al., J Biol Chem., 2012, 287(12), 9454-9460).
Representative IL-21 Targeting Ligands are described in Fig. 1. Additional IL-21 Targeting Ligands can be found in, for example, US Patent 9701663, which is incorporated herein by reference.
IL-22
In some embodiments, the Target Protein is human interleukin-22 (IL-22) (UniProtKB - Q9GZX6 (IL22 HUMAN)). IL-22 is a member of IL- 10 family cytokines that is produced by many different types of lymphocytes including both those of the innate and adaptive immune system. IL-22 has been implicated in a number of autoimmune disorders, including, but not limited to, graft versus host disease (GVHD), psoriasis, rheumatoid arthritis, atopic dermatitis, and asthma.
The Protein Data Bank website provides the crystal structure of IL-22 searchable by 1M4R (Nagem, R.A.P., et al., Structure, 2002, 10 1051-1062); as well as the crystal structure of IL-22 bound to various compounds searchable by 3DGC (Jones, B. C. et al., Structure, 2008, 16 1333- 1344).
Representative IL-22 Targeting Ligands are described in Fig. 1. Additional IL-22 Targeting Ligands can be found in, for example, US Patent 9,701,663, which is incorporated herein by reference.
IL-10
In some embodiments, the Target Protein is human interleukin- 10 (IL-10) (UniProtKB - P22301 (IL10 HUMAN)). IL-10 is an inflammatory cytokine. IL-10 has been implicated in tumor survival and protection against cytotoxic chemotherapeutic drugs.
The Protein Data Bank website provides the crystal structure of IL-10 searchable by 2ILK (Zdanov, A et al., Protein Sci., 1996, 5 1955-1962); HLK (Zdanov, A. et al., Structure, 1995, 3 591-601); 2H24 (Yoon, S. I., et al., J Biol Chem., 2006, 281 35088-35096) and 3LQM (Yoon, S. I., et al., Structure, 2010, 18 638-648). Additionally, Zdanov, A., et al, provides insight into crystal structure of IL-10 (Zdanov A., Current Pharmaceutical design, 2004, 10, 3873-3884).
Representative IL- 10 Targeting Ligands are provided in Fig. 1. Additional IL- 10 Targeting Ligands can be found, for example, in ACS Chem Biol 11 : 2105-11 (2016), which is incorporated herein by reference.
IL-5
In some embodiments, the Target Protein is human interleukin-5 (IL-5) (UniProtKB - P05113 (ILS HUMAN)). IL-5 is a cytokine that regulates eosinophil maturation, recruitment, and survival. IL-5 has been implicated in a number of allergic disorders, including, but not limited to, asthma, nasal polyposis, atopic dermatitis, eosinophilic esophagitis, hypereosinophilic syndrome, and Churg-Strauss syndrome.
The Protein Data Bank website provides the crystal structure of IL-5 searchable by 1HUL (Milburn, M. V., Nature, 1993, 363, 172-176) and 3VA2 (Kusano et al., Protein Sci., 2012, 21(6), 850-864); as well as the crystal structure of IL-5 bound to various compounds searchable by 1OBX and 1OBZ (Kang, B. S., et al., Structure, 2003, 11, 845).
Representative IL-5 Targeting Ligands are provided in Fig. 1. Additional IL-5 Targeting Ligands can be found, for example, in Bioorg Med Chem 18: 4441-5 (2010); Bioorg Med Chem 18: 4625-9 (2011); Bioorg Med Chem 21 : 2543-50 (2013); Eur J Med Chem 59: 31-8 (2013); Bioorg Med Chem 23: 2498-504 (2015); Bioorg Med Chem 20: 5757-62 (2012); each of which is incorporated by reference herein.
IL8
In some embodiments, the Target Protein is human interleukin-8 (IL-8) (UniProtKB - P10145 (IL8 HUMAN)). IL-8 is a chemotactic factor that attracts neutrophils, basophils, and T- cells, but not monocytes. It is also involved in neutrophil activation. It is released from several cell types in response to an inflammatory stimulus. IL-8 has been implicated in the promotion of tumor progression, immune escape, epithelial-mesenchymal transition, and recruitment of myeloid-derived suppressor cells. Studies have demonstrated that high serum IL-8 levels correlate with poor prognosis in many malignant tumors. Preclinical studies have shown that IL-8 blockade may reduce mesenchymal features in tumor cells, making them less resistant to treatment. The Protein Data Bank website provides the crystal structure of IL-8 searchable by 3IL8 (Baldwin, E. T., et al., Proc Natl Acad Sci U S A, 1991, 88, 502-506); and 1IL8 and 2IL8 (Clore, G. M., et al., Biochemistry, 1990, 29, 1689-1696); as well as the crystal structure of IL-8 bound to various compounds searchable by 1ILP and 1ILQ (Skelton, N, J., et al., Structure, 1999, 7, 157- 168); and 1ROD (Sticht, H., et al., Eur J Biochem., 1996, 235, 26-35); 4XDX (Ostrov et al.,) and 5WDZ (Beckamp, S., J Biomol NMR, 2017, 69, 111-121).
Representative IL-8 Targeting Ligands are provided in Fig. 1. Additional IL-8 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 19: 4026-30 (2009), which is incorporated by reference herein.
Cholinesterase
In some embodiments, the Target Protein is human cholinesterase (UniProtKB - P06276 (CHLE HUMAN)). Cholinesterase contributes to the inactivation of the neurotransmitter acetylcholine. Inhibition of cholinesterase results in increased levels of acetylcholine in the synaptic cleft (the space between two nerve endings). The main use of cholinesterase inhibitors is for the treatment of dementia in patients with Alzheimer's disease. People with Alzheimer's disease have reduced levels of acetylcholine in the brain. Cholinesterase inhibitors have been shown to have an effect on dementia symptoms such as cognition.
The Protein Data Bank website provides the crystal structure of cholinesterase searchable by 1P0I and 1P0Q (Nicolet, Y., et al., J Biol Chem., 2003, 278, 41141-41147); as well as the crystal structure of cholinesterase bound to various compounds searchable by 1P0M and 1P0P (Nicolet, Y., et al., J Biol Chem., 2003, 278, 41141-41147); 2J4C (Frasco, M. F., et al., FEBS J., 2007, 274 1849); 4BDT, 4BDS (Nachon, F., et al., Biochem J, 2013, 453, 393-399); 1GQR and 1GQS (Bar-on, P., et al., Biochemistry, 2002, 41, 3555); 3DJY and 3DKK (Carletti, E., et al., J Am Chem Soc., 2008, 130, 16011-16020); 4AXB, 4BOO, 4B0P, and 4BBZ (Wandhammer, M., et al., Chem Biol Interact., 2013, 203, 19); 1DX6 (Greenblatt, H. M., et al., FEBS Lett., 1999, 463 321); 1GPK and 1GPN (Dvir, H., et al., Biochemistry, 2002, 41, 10810); 6CQY (Bester, S. M., et al., Chem Res Toxicol., 2018, 31, 1405-1417 ); 1XLV and 1XLW (Nachon, F., et al., Biochemistry, 2005, 44, 1154-1162); 2Y1K (Carletti, E., et al., Chem Res Toxicol., 2011, 24, 797); and 2WIG, 2WIJ, 2WIK, 2WIL, and 2WSL (Carletti, E., et al., Biochem J., 2009, 421, 97-106). Additionally, Ahmad et al., provides insight into the isolation, crystal structure determination and cholinesterase inhibitory potential of isotalatizidine hydrate from delphinium denudatum (Ahmad H., et al., Journal Pharmaceutical Biology, 2016, 55(1), 680-686).
Representative cholinesterase Targeting Ligands are provided in Fig. 1. Additional Targeting Ligands can be found in, for example, ACS Med Chem Lett 4: 1178-82 (2013); J Med Chem 49: 3421-5 (2006); Eur J Med Chem 55: 23-31 (2012); J Med Chem 51 : 3154-70 (2008); J Med Chem 46: 1-4 (2002); Eur J Med Chem 126: 652-668 (2017); Biochemistry 52: 7486-99 (2013); Bioorg Med Chem 23: 1321-40 (2015); which are each incorporated herein by reference.
C-C motif chemokine ligand 2 (CCL2)
Grygiel et al., provides insight into the synthesis by native chemical ligation and crystal structure of human CCL2 (Grygiel, T.L., et al., Biopolymers, 2010, 94(3), 350-9).
In some embodiments, the Target Protein is human C-C motif chemokine ligand 2 (CCL2) (UniProtKB - P13500 (CCL2 HUMAN)). CCL2 acts as a ligand for C-C chemokine receptor CCR2. CCL2 signals through binding and activation of CCR2 and induces a strong chemotactic response and mobilization of intracellular calcium ions. CCL2 exhibits a chemotactic activity for monocytes and basophils but not neutrophils or eosinophils.
CCL2 has been implicated in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis.
Representative CCL2 Targeting Ligands are provided in Fig. 1. Additional CCL2 Targeting Ligands can be found in, for example, J Med Chem 56: 7706-14 (2013), which is incorporated herein by reference.
Carboxypeptidase B2
In some embodiments, the Target Protein is human carboxypeptidase B2 (UniProtKB - Q96IY4 (CBPB2 HUMAN)). Carboxypeptidase B2, also known as thrombin activatable fibrinolysis inhibitor (TAFIa), cleaves C-terminal arginine or lysine residues from biologically active peptides such as kinins or anaphylatoxins in the circulation thereby regulating their activities. It down-regulates fibrinolysis by removing C-terminal lysine residues from fibrin that has already been partially degraded by plasmin. Carboxypeptidase B2 has been implicated and targeted to inhibit thrombosis. The Protein Data Bank website provides the crystal structure of carboxypeptidase B2 (also known as thrombin-activatable fibrinolysis inhibitor (TAFI)) searchable by 3D66 (Marx, P. F., et al., Blood, 2008, 112, 2803-2809); 3DGV (Anand, K., et al., JBC, 2008, 283, 29416-29423); and 1KWM (Barbosa Pereira, P.J., et al., J Mol Biol., 2002, 321, 537-547); as well as the crystal structure of TAFI bound to various compounds searchable by 3D67 (Marx, P. F., et al., Blood, 2008, 112, 2803-2809); 5HVF, 5HVG, 5HVH (Zhou, X., et al., J Thromb Haemost., 2016, 14, 1629-1638); and 3LMS (Sanglas, L., et al., J Thromb Haemost., 2010, 8, 1056-1065). Additionally, Schreuder et al., provides insight into the interaction of TAFI and anabaenopeptin, a highly potent inhibitor of TAFI (Schreuder, H., et al., Sci Rep., 2016, 6, 32958).
Representative carboxypeptidase B2 Targeting Ligands are provided in Fig. 1. Additional carboxypeptidase B2 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 20: 92-6 (2010), J Med Chem 50: 6095-103 (2007), Bioorg Med Chem Lett 14: 2141-5 (2004), J Med Chem 58: 4839-44 (2015), J Med Chem 55: 7696-705 (2012), J Med Chem 59: 9567-9573 (2016), Bioorg Med Chem Lett 17: 1349-54 (2007), US Patent 9662310, US Patent 8609710, US Patent 9688645, J Med Chem 46: 5294-7 (2003), each of which is incorporated herein by reference.
Neutrophil Elastase
In some embodiments, the Target Protein is human neutrophil elastase (UniProtKB - P08246 (ELNE HUMAN)). Neutrophil elastase modifies the functions of natural killer cells, monocytes and granulocytes. Inhibits C5a-dependent neutrophil enzyme release and chemotaxis.
Neutrophil elastase has been implicated in a number of disorders, including lung disease, chronic obstructive pulmonary disease, pneumonia, respiratory distress, and acute lung injury (ALI), and cystic fibrosis, as well as chronic kidney disease.
The Protein Data Bank website provides the crystal structure of human neutrophil elastase bound to various compounds searchable by 3Q76 and 3Q77 (Hansen, G., et al., J.Mol.Biol., 2011, 409, 681-691); 5ABW (Von Nussbaum, et al., Bioorg Med Chem Lett., 2015, 25, 4370-4381); 1B0F (Cregge, R. J., et al., J Med Chem., 1998, 41, 2461-2480); 1H1B (Macdonald, S.J.F., et al., J Med Chem., 2002, 45, 3878); 2Z7F (Koizumi, M., et al., J Synchrotron Radiat., 2008, 15 308- 311); 5A09, 5A0A, 5A0B, and 5A0C (Von Nussbaum, F., et al., Chem Med Chem., 2015, 10, 1163-1173); 5A8X, 5A8Y and 5A8Z (Von Nussbaum, F., et al., ChemMedChem., 2016, 11, 199- 206); 1HNE (Navia, M. A., et al., Proc Natl Acad Sci U S A, 1989, 86, 7-11); 6F5M (Hochscherf, J., et al., Acta Crystallogr F Struct Biol Commun., 2018, 74, 480-489); and 4WVP (Lechtenberg, B. C., et al., ACS Chem Biol., 2015, 10, 945-951).
Representative neutrophil elastase Targeting Ligands are provided in Fig. 1. Additional neutrophil elastase Targeting Ligands can be found in, for example, J Med Chem 53: 241-53 (2010), J Med Chem 38: 739-44 (1995), J Med Chem 37: 2623-6 (1994), J Med Chem 38: 4687- 92 (1995), J Med Chem 45: 3878-90 (2002), Bioorg Med Chem Lett 5: 105-109 (1995), Bioorg Med Chem Lett 11 : 243-6 (2001), J Med Chem 40: 1906-18 (1997), Bioorg Med Chem Lett 25: 4370-81 (2015), US Patent 8569314, US Patent 9174997, US Patent 9290457, each of which is incorporated herein by reference.
Factor Xa
In some embodiments, the Target Protein is human Factor Xa (UniProtKB - P00742 (FA10 HUMAN)). Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.
Factor X has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
The Protein Data Bank website provides the crystal structure of Factor Xa bound to various compounds searchable by 1G2L and 1G2M (Nar, H., et al., Structure, 2001, 9, 29-38); 2PR3 (Nan huis, C. A., et al., Chem Biol Drug Des., 2007, 69, 444-450); 2UWP (Young, R. J., et al., Bioorg Med Chem Lett., 2007, 17, 2927); 2VVC, 2VVV, 2VVU, 2VWL, 2VWM, 2VWN and 2VW0 (Zbinden, K. G., et al., Eur J Med Chem., 2009, 44, 2787); 4Y6D, 4Y71, 4Y7A, 4Y7B, 4zh8, 4ZHA (Convery, M.A. et al.); 4Y76, 4Y79, 2J94 and 2J95 (Chan, C., et al., J Med Chem., 2007, 50 1546-1557); 1FAX (Brandstetter, H., et al., J Biol Chem., 1996, 271, 29988-29992 ); 2JKH (Salonen, L. M., et al., Angew Chem Int Ed Engl., 2009, 48, 811); 2PHB (Kohrt, J. T., et al., Chem Biol Drug Des., 2007, 70, 100-112); 2W26 (Roehrig, S., et al., J Med Chem., 2005, 48, 5900); 2Y5F, 2Y5G and 2Y5H (Salonen, L.M., et al., Chemistry, 2012, 18, 213); 3Q3K (Yoshikawa, K., et al., Bioorg Med Chem Lett., 2011, 21, 2133-2140); 2BMG (Matter, K., et al., J Med Chem., 2005, 48, 3290); 2BOH, 2BQ6 2BQ7, and 2BQW (Nazare, M., et al., J Med Chem., 2005, 48, 4511); 2CJI (Watson, N.S., et al, Bioorg Med Chem Lett., 2006, 16, 3784); 2J2U, 2J34, 2J38, 2J41 (Senger, S., et al., Bioorg Med Chem Lett., 2006, 16 5731); 3IIT (Yoshikawa, K., et al., Bioorg Med Chem., 2009, 17 8221-8233); 1EZQ, IFOR and 1F0S (Maignan, S., et al., J Med Chem., 2000, 43, 3226-3232); 1FJS (Adler, M., et al., Biochemistry, 2000, 39, 12534-12542 ); 1KSN (Guertin, K. R., et al., Bioorg Med Chem Lett., 2002, 12, 1671-1674); 1NFU, 1NFW, 1NFX and 1NFY (Maignan, S., et al., J Med Chem., 2003, 46, 685-690); 2XBV, 2XBW, 2XBX, 2XBY, 2XC0, 2XC4 and 2XC5 (Anselm, L., et al., Bioorg Med Chem Lett., 2010, 20, 5313); 4A7I (Nazare, M., et al., Angew Chem Int Ed Engl., 2012, 51, 905); 4BTI, 4BTT and 4BTU (Meneyrol,
L., et al., J Med Chem., 2013, 56, 9441); 3FFG, 3KQB, 3KQC, 3KQD and 3KQE (Quan, M. L., et al., Bioorg Med Chem Lett., 2010, 20, 1373-1377); 2P93, 2P94 and 2P95 (Qiao, J. X., et al., Bioorg Med Chem Lett., 2007, 17, 4419-4427); 1V3X (Haginoya, N., et al., J Med Chem., 2004, 47, 5167-5182); 2P16 (Pinto, D.J.P., et al., J Med Chem., 2007, 50, 5339-5356); 2RA0 (Lee, Y.K., et al., J Med Chem., 2008, 51, 282-297 ); 3SW2 (Shi, Y., et al., Bioorg Med Chem Lett., 2011, 21, 7516-7521); 2VH6 (Young, R.J., et al., Bioorg Med Chem Lett., 2008, 18, 23); 2WYG and 2WYJ (Kleanthous, S., et al., Bioorg Med Chem Lett., 2010, 20, 618); 2Y7X (Watson, N.S., et al., Bioorg Med Chem Lett., 2011, 21, 1588); 2Y7Z, 2Y80, 2Y81 and 2Y82 (Young, R.J., et al., Bioorg Med Chem Lett., 2011, 21, 1582); 3KL6 (Fujimoto, T., et al., J Med Chem., 2010, 53, 3517-3531); 3LIW (Meuller, M.M., et al., Biol.Chem., 2003, 383, 1185); 5K0H (Schweinitz, A., et al., Med Chem., 2006, 2, 349-361); 1XKA and 1XKB (Kamata, K., et al., Proc Natl Acad Sci U S A, 1998, 95, 6630-6635); 2EI6 and 2EI7 (Nagata, T., et al., Bioorg Med Chem Lett., 2007, 17, 4683-4688); 2P3T (Ye, B., et al., J Med Chem., 2007, 50, 2967-2980); 1MQ5 and 1MQ6 (Adler, M., et al., Biochemistry, 2002, 41, 15514-15523); 3K9X and 3HPT (Shi, Y., et al., Bioorg Med Chem Lett., 2009, 19, 6882-6889); 3CEN (Corte, J.R., et al., Bioorg Med Chem Lett., 2008, 18, 2845-2849); 2W3I and 2W3K (Van Huis, C.A., et al., Bioorg Med Chem., 2009, 17, 2501); 2H9E (Murakami,
M.T., et al., J Mol Biol., 2007, 366, 602-610); 1WU1 and 2D1J (Komoriya, S., et al., Bioorg Med Chem., 2005, 13, 3927-3954); 2G00 (Pinto, D.J.P., et al., Bioorg Med Chem Lett., 2006, 16, 5584- 5589); 3M36 and 3M37 (Pruitt, J.R. et al., J Med Chem., 2003, 46, 5298-5315); 3CS7 (Qiao, J.X., et al., Bioorg Med Chem Lett., 2008, 18, 4118-4123); 1Z6E (Quan, M.L., et al., J Med Chem., 2005, 48, 1729-1744); 2FZZ (Pinto, D.J.P., et al., Bioorg Med Chem Lett., 2006, 16, 4141-4147); and 3ENS (Shi, Y., et al., J Med Chem., 2008, 51, 7541-7551).
Representative Factor Xa Targeting Ligands are provided in Fig. 1. Additional Factor Xa Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 20: 5313-9 (2010), Bioorg Med Chem Lett 13: 679-83 (2003), J Med Chem 44: 566-78 (2001), J Med Chem 50: 2967-80 (2007), J Med Chem 38: 1511-22 (1995), Bioorg Med Chem Lett 18: 2845-9 (2008), J Med Chem 53: 6243-74 (2010), Bioorg Med Chem Lett 18: 2845-9 (2008), Bioorg Med Chem 16: 1562-95 (2008), each of which is incorporated herein by reference.
Factor XI
In some embodiments, the Target Protein is human Factor XI UniProtKB - P03951 (FA11 HUMAN). Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.
Factor XI has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
The Protein Data Bank website provides the crystal structure of Factor XI bound to various compounds searchable by 1ZSL, 1ZTJ, 1ZTK, and 1ZTL (Nagafuji, P., et al.,); 1Z0M (Lin, J., et al., J Med Chem., 2006, 49, 7781-7791); 5EOK and 5EOD (Wong, S.S., et al., Blood, 2016, 127, 2915-2923 ); 1ZHM, 1ZHP and 1ZHR (Jin, L., et al., Acta Crystallogr D Biol Crystallogr., 2005, 61, 1418-1425 ); 1ZMJ, 1ZLR, 1ZML and 1ZMN (Lazarova, T.I., Bioorg Med Chem Lett., 2006, 16, 5022-5027); 1ZRK, 1ZSJ and 1ZSK (Guo, Z., et al); 4CRA, 4CRB, 4CRC, 4CRD, 4CRE, 4CRF and 4CRG (Fjellstrom, O., et al., PLoS One, 2015, 10, 13705); 3SOR and 3S0S (Fradera, X., et al., Acta Crystallogr Sect F Struct Biol Cryst Commun., 2012, 68, 404-408); 1ZPB, 1ZPC, 2FDA (Deng, H., et. al., Bioorg Med Chem Lett., 2006, 16, 3049-3054); 5WB6 (Wang, C., et al., Bioorg Med Chem Lett., 2017, 27, 4056-4060); 4NA7 and 4NA8 (Quan, M.L., et al., J Med Chem., 2014, 57, 955-969); 4WXI (Corte, J.R., et al., Bioorg Med Chem Lett., 2015, 25, 925-930); 5QTV, 5QTW, 5QTX and 5QTY (Fang, T., et al., Bioorg Med Chem Lett., 2020, 126949-126949); 6C0S (Hu, Z., et al., Bioorg Med Chem Lett., 28, 987-992); 5QQP and 5QQO (Clark, C.G., et al., Bioorg Med Chem Lett., 2019, 29, 126604-126604); 5Q0D, 5Q0E, 5Q0F, 5Q0G, and 5Q0H (Corte, J.R., et al., Bioorg Med Chem Lett., 2017, 27, 3833-3839); 5QCK, 5QCL, 5QCM, and 5QCN (Pinto, D.J.P., et al., J Med Chem., 2017, 60, 9703-9723); 5TKS and 5TKU (Corte, J.R., et al., J Med Chem., 2017, 60, 1060-1075); 1XXD and 1XX9 (Jin, L., et al., J Biol Chem., 2005, 280, 4704- 4712); 5QTT and 5QTU (Corte, J. R., et al., J Med Chem., 2019, 63, 784-803); 4TY6, 4TY7 (Hangeland, J.J., et al., J Med Chem., 2014, 57, 9915-9932); 4X6M, 4X6N, 4X60, and 4X6P (Pinto, D.J.P., et al., Bioorg Med Chem Lett., 2015, 25, 1635-1642); and 5EXM (Corte, J.R., et al., Bioorg Med Chem., 2016, 24, 2257-2272). Additionally, Al-Horani et al., provides insight into a review of patent literature regarding Factor Xia inhibitors (Al-Horani et al., Expert Opin Ther Pat. 2016; 26(3), 323-345).
Representative Factor XI Targeting Ligands are provided in Fig. 1. Additional Factor XI Targeting Ligands can be found in, for example, US Patent 9783530, US Patent 10143681, US Patent 10214512, ACS Med Chem Lett 6: 590-5 (2015), J Med Chem 60: 9703-9723 (2017), J Med Chem 60: 9703-9723 (2017), US Patent 9453018 (2016), J Med Chem 60: 1060-1075 (2017), J Med Chem 57: 955-69 (2014), each of which is incorporated herein by reference.
Factor XII
In some embodiments, the Target Protein is human Factor XII (UniProtKB - P00748 (FA12 HUMAN)). Factor XII is a serum glycoprotein that participates in the initiation of blood coagulation, fibrinolysis, and the generation of bradykinin and angiotensin. Prekallikrein is cleaved by factor XII to form kallikrein, which then cleaves factor XII first to alpha-factor Xlla and then trypsin cleaves it to beta-factor Xlla. Alpha-factor Xlla activates factor XI to factor Xia.
Factor XII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
The Protein Data Bank website provides the crystal structure of factor XII bound to various compounds searchable by 4XDE and 4XE4 (Pathak, M., et al., J Thromb Haemost., 2015, 13(4), 580-591); 6GT6 and 6QF7 (Pathak, M., et al., Acta Crystallogr D Struct Biol., 2019, 75, 578-591); and 6B74 and 6B77 (Dementiev, A.A., et al., Blood Adv., 2018, 2, 549-558). Additionally, Pathak et al., provides insight into the crystal structure of factor XII (Pathak, M., et al., J Thromb Haemost., 2015, 13(4), 580-591).
Representative Factor XII Targeting Ligands are provided in Fig. 1. Additional Factor XII Targeting Ligands can be found in, for example, J Med Chem 60: 1151-1158 (2017), J Med Chem 48: 2906-15 (2005), J Med Chem 50: 5727-34 (2007), J Med Chem 50: 1876-85 (2007), Chembiochem 18: 387-395 (2017), each of which is incorporated herein by reference. Factor XIII
In some embodiments, the Target Protein is human Factor XIII UniProtKB - P00488 (F13A HUMAN)). Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl-epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin.
Factor XIII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
The Protein Data Bank website provides the crystal structure of factor XIII searchable by 1FIE (Yee, V.C., et al., Thromb Res., 1995, 78, 389-397); and 1F13 (Weiss, M.S., et al., FEBS Lett., 1998, 423, 291-296); as well as the crystal structure of factor XIII bound to various compounds searchable by 1DE7 (Sadasivan, C., et al., J Biol Chem., 2000, 275, 36942-36948); and 5MHL, 5MHM, 5MHN, and 5MH0 (Stieler, M., et al., ). Additionally, Gupta et al., provides insight into the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective (Gupta, S., et al., Sci Rep., 2016; 6, 30105); and Komaromi et al., provides insight into the novel structural and functional aspect of factor XIII (Komaromi, Z., et al., . J Thromb Haemost 2011, 9, 9-20).
Representative Factor XIII Targeting Ligands are provided in Fig. 1. Additional Factor XIII Targeting Ligands can be found in, for example, Eur J Med Chem 98: 49-53 (2015), J Med Chem 55: 1021-46 (2012), J Med Chem 48: 2266-9 (2005), each of which is incorporated herein by reference.
Prothrombin
In some embodiments, the Target Protein is human Prothrombin (UniProtKB - P00734 (THRB HUMAN)). Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.
Thrombin is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation. The Protein Data Bank website provides the crystal structure of prothrombin searchable by 3NXP (Chen, Z. et al., Proc Natl Acad Sci U S A, 2010, 107, 19278-19283); as well as the crystal structure of prothrombin bound to various compounds searchable by 2HPP and 2HPQ (Arni, R.K., et al., Biochemistry, 1993, 32, 4727-4737); 6BJR, 6C2W (Chinnaraj, M., et al., Sci Rep., 2018, 8, 2945-2945); 5EDK, 5EDM (Pozzi, N., et al., J Biol Chem., 2016, 291, 6071-6082); 3K65 (Adams, T.E., et al., Biochimie, 2016, 122, 235-242); and 6BJR and 6C2W (Chinnaraj, M. et al., Sci Rep., 2018, 8, 2945-2945). Additionally, Pozzi et al., provides insight into the mechanism and conformational flexibility for the crystal structure of prothrombin (Pozzi, N. et al., J Biol Chem.,
2013, 288(31), 22734-22744); and Zhiwei et al., provides insight into the crystal structure of prothrombin-1 (Zhiwei, C. et al., PNAS, 2010, 107(45), 19278-19283).
Prothrombin is converted to thrombin, as such the Protein Data Bank website provides the crystal structure of thrombin bound to compounds searchable by 1XMN (Carter, W.J. et al., J.Biol.Chem., 2005, 280, 2745-2749); 4CH2 and 4CH8 (Lechtenberg, B.C. et al., J Mol Biol.,
2014, 426, 881); 3PO1 (Karie, M. et al., Bioorg Med Chem Lett., 2012, 22, 4839-4843); 3DA9 (Nilsson, M. et al., J Med Chem., 2009, 52, 2708-2715); 2H9T and 3BF6 (Lima, L.M.T.R. et al., Biochim Biophys Acta., 2009, 1794, 873-881); 3BEF and 3BEI (Gandhi, P.S. et al., Proc Natl Acad Sci U S A, 2008, 105, 1832-1837); 3BV9 (Nieman, M.T. et al., J Thromb Haemost., 2008, 6, 837-845); 2HWL (Pineda, A.O. et al., Biophys Chem., 2007, 125, 556-559); 2AFQ (Johnson, D.J.D. et al., Biochem J., 2005, 392, 21-28); 1SHH (Pineda, A.O. et al., J Biol Chem., 2004, 279, 31842-31853); 1JWT (Levesque, S. et al., Bioorg Med Chem Lett., 2001, 11, 3161-3164); 1G37 (Bachand, B. et al., Bioorg Med Chem Lett., 2001, 11, 287-290); 1EOJ and 1EOL (Slon- Usakiewicz, J.J. et al., Biochemistry, 2000, 39, 2384-2391); 1AWH (Weir, M.P. et al., Biochemistry, 1998, 37, 6645-6657); 1DIT (Krishnan, R. et al., Protein Sci., 1996, 5, 422-433); 1HAO and 1HAP (Padmanabhan, K. et al., Acta Crystallogr D Biol Crystallogr., 1996, 52, 272- 282); and 1HBT (Rehse, P.H. et al., Biochemistry, 1995, 34, 11537-11544).
Representative prothrombin Targeting Ligands are provided in Fig. 1. Additional prothrombin Targeting Ligands can be found in, for example, J Med Chem 46: 3612-22 (2003), Bioorg Med Chem Lett 12: 1017-22 (2002), J Med Chem 40: 830-2 (1997), Bioorg Med Chem Lett 15: 2771-5 (2005), J Med Chem 42: 3109-15 (1999), J Med Chem 47: 2995-3008 (2004), Bioorg Med Chem 16: 1562-95 (2008), J Med Chem 42: 3109-15 (1999), each of which is incorporated herein by reference. Coagulation Factor VII
In some embodiments, the Target Protein is human coagulation Factor VII (UniProtKB - P08709 (FA7 HUMAN)). Factor VII initiates the extrinsic pathway of blood coagulation. It is a serine protease that circulates in the blood in a zymogen form. Factor VII is converted to Factor Vila by Factor Xa, Factor Xlla, Factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, Factor Vila then converts Factor X to Factor Xa by limited proteolysis. Factor Vila will also convert Factor IX to Factor IXa in the presence of tissue factor and calcium.
Factor VII is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
The Protein Data Bank website provides the crystal structure of factor VII bound to various compounds searchable by 2F9B (Rai, R., et al., Bioorg Med Chem Lett., 2006, 16, 2270-2273); 5U6J (Wurtz, N.R., et al., Bioorg Med Chem Lett., 2017, 27, 2650-2654); 5L2Y, 5L2Z, and 5L30 (Ladziata, .U., et al., Bioorg Med Chem Lett., 2016, 26, 5051-5057); 5146 (Glunz, P. W., et al., J Med Chem., 2016, 59, 4007-4018); 4YLQ, 4Z6A, and 4ZMA (Sorensen, A.B., et al., J Biol Chem., 2016, 291, 4671-4683); 4YT6 and 4YT7 (Glunz, P.W., et al., Bioorg Med Chem Lett, 2015, 25, 2169-2173); 4NA9 (Quan, M.L., et al., J Med Chem., 2014, 57, 955-969); 4NG9 (hang, X., et al., ACS Med Chem Lett., 2014, 5, 188-192); 4JZD, 4JZE and 4JZF (Bolton, S. A., et al., Bioorg Med Chem Lett., 2013, 23, 5239-5243); 4JYU and 4JYV (Glunz, P.W., et al., Bioorg Med Chem Lett., 2013, 23, 5244-5248); 4ISH (Priestley, E.S., et al., Bioorg Med Chem Lett., 2013, 23, 2432-2435); 4ISI (Zhang, X., et al., Bioorg Med Chem Lett., 2013, 23, 1604-1607); 2ZZU (Shiraishi, T., et al., Chem Pharm Bull (Tokyo), 2010, 58, 38-44); 1WV7 and 1WUN (Kadono, S., et al., Biochem Biophys Res Commun, 2005, 327, 589-596); 2ZWL, 2ZP0, (Kadono, S., et al.); 2EC9 (Krishan, R., et al., Acta Crystallogr D Biol Crystallogr., 2007, 63, 689-697); 2PUQ (Larsen, K. S., et al., Biochem J., 2007, 405, 429-438); 2FLR (Riggs, J. R., et al., Bioorg Med Chem Lett., 2006, 16, 3197-3200); 2C4F (Kohrt, J.T., et al., Bioorg Med Chem Lett., 2006, 16, 1060); 2AEI (Kohrt, J.T. et al., Bioorg Med Chem Lett., 2005, 15, 4752-4756); 1WTG (Kadono, S., et al., Biochem Biophys Res Commun., 2005, 326, 859-865); 1WSS (Kadono, S., et al., Acta Crystallogr Sect F Struct Biol Cryst Commun., 2005, 61, 169-173); 1W7X and 1W8B (Zbinden, K.G., et al., Bioorg Med Chem Lett., 2005, 15, 5344); 1WQV (Kadono, S., et al., Biochem Biophys Res Commun., 2004, 324, 1227-1233); 1Z6J (Schweitzer, B. A., et al., Bioorg Med Chem Lett., 2005, 15, 3006-3011); 1YGC (Olivero, A. G., et al., J Biol Chem., 2005, 280, 9160-9169); 6R2W (Sorensen, A.B., et al., J Biol Chem., 2019, 295, 517-528); 5PA8, 5PA9, 5PAA, 5PAB, 5PAC, 5PAE, 5PAF, 5PAG, 5PAI, 5PAJ, 5PAK, 5PAM, 5PAN, 5PAO, 5PAQ, 5PAR, 5PAS, 5PAT, 5PAU, 5PABV, 5PAW, 5PAX, 5PAY, 5PB0, 5PB1, 5PB2, 5PB3, 5PB4, 5PB5, and 5PB6 (Mayweg, A.V., et al.,); and 5L0S (Li, Z., et al., Nat Commun., 2017, 8, 185-185). Additionally, Kemball-Cook, et al., provides insight into the crystal structure of active site-inhibited factor Vila (Kemball-Cook, G., et al., J Struct Biol., 1999, 127(3), 213-23).
Representative Factor VII Targeting Ligands are provided in Fig. 1. Additional Factor VII Targeting Ligands can be found in, for example, US Patent 9174974, Bioorg Med Chem Lett 26: 5051-5057 (2016), Bioorg Med Chem Lett 11 : 2253-6 (2001), Bioorg Med Chem Lett 15: 3006- 11 (2005), Bioorg Med Chem Lett 12: 2883-6 (2002), each of which is incorporated herein by reference.
Coagulation Factor IX
In some embodiments, the Target Protein is human coagulation Factor IX (UniProtKB - P00740 (FA9 HUMAN)). Factor IX Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca2+ ions, phospholipids, and factor Villa.
Factor IX is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
The Protein Data Bank website provides the crystal structure of factor IX bound to various compounds searchable by 6MV4 (Vadivel, K., et al., J Thromb Haemost., 2019, 17, 574-584); 4ZAE (Zhang, T., et al., Bioorg Med Chem Lett., 2015, 25, 4945-4949); 4YZU and 4Z0K (Parker, D.L., et al., Bioorg Med Chem Lett., 2015, 25, 2321-2325); 5TNO and 5TNT (Sakurada, I., et al., Bioorg Med Chem Lett., 2017, 27, 2622-2628); 5JB8, 5JB9, 5JBA, 5JBB and 5JBC (Kristensen, L.H., et al., Biochem J., 2016, 473, 2395-2411); 3LC3 (Wang, S., et al., J Med Chem., 2010, 53, 1465-1472); 3LC5 (Wang, S., et al., J Med Chem., 2010, 53, 1473-1482); 3KCG (Johnson, D.J.D., et al., Proc Natl Acad Sci U S A, 2010, 107, 645-650); 1NL0 (Huang, M., et al., J Biol Chem., 2004, 279, 14338-14346); 1RFN (Hopfner, K.P., et al., Structure, 1999, 7, 989-996); and 6RFK (Sendall, T.J., et al.,). Representative Factor IX Targeting Ligands are provided in Fig. 1. Additional Factor IX Targeting Ligands can be found in, for example, US Patent 9409908, Bioorg Med Chem Lett 25: 5437-43 (2015), US Patent 10189819, each of which is incorporated herein by reference.
Fibroblast Growth Factor 1 (FGF1)
In some embodiments, the Target Protein is human fibroblast growth factor 1 (FGF1) (UniProtKB - P05230 (F GF 1 HUMAN)). FGF1 plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation and cell migration. FGF1 acts as a ligand for FGFR1 and integrins, and binds to FGFR1 in the presence of heparin leading to FGFR1 dimerization and activation via sequential autophosphorylation on tyrosine residues which act as docking sites for interacting proteins, leading to the activation of several signaling cascades. FGF 1 induces the phosphorylation and activation of FGFR1, FRS2, MAPK3/ERK1, MAPK1/ERK2 and AKT1. FGF1 can induce angiogenesis. FGF1 has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
The Protein Data Bank website provides the crystal structure of FGF 1 searchable by 2AFG (Blaber, M., et al., Biochemistry, 1996, 35, 2086-2094); and 1BAR (Zhu, X. et al., Science, 1991, 251, 90-93); as well as the crystal structure of FGF1 bound to various compounds searchable by 1AFC (Zhu, X., et al., Structure, 1993, 1, 27-34); 1AXM and 2AXM (DiGabriele, A. D., et al., Nature, 1998, 393, 812-817); 1EVT (Plotnikov, A.N., et al., Cell, 2000, 101, 413-424); 1E0O (Pellegrini, L., et al., Nature, 2000, 407, 1029); and 2ERM (Canales, A., et al., FEBS J, 2006, 273, 4716-4727).
Representative FGF1 Targeting Ligands are provided in Fig. 1. Additional FGF1 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 18: 344-9 (2008), Chembiochem 6: 1882-90 (2005), J Med Chem 55: 3804-13 (2012), J Med Chem 47: 1683-93 (2004), J Med Chem 53: 1686-99 (2010, )each of which is incorporated herein by reference.
Fibroblast Growth Factor 2 (FGF2)
In some embodiments, the Target Protein is human fibroblast growth factor 2 (FGF2) (UniProtKB - P09038 (FGF2 HUMAN)). FGF2 acts as a ligand for FGFR1, FGFR2, FGFR3 and FGFR4. FGF2 also acts as an integrin ligand which is required for FGF2 signaling, and plays an important role in the regulation of cell survival, cell division, cell differentiation and cell migration. FGF2 also induces angiogenesis. FGF2 has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
The Protein Data Bank website provides the crystal structure of FGF2 bound to various compounds searchable by 4OEE, 4OEF, and 4OEG (Li, Y.C., et al., ACS Chem Biol., 2014, 9, 1712-1717); 1EV2 (Plotnikov, A.N., et al., Cell, 2000, 101, 413-424); and 5X1O (Tsao, Y.H.).
Representative FGF2 Targeting Ligands are provided in Fig. 1. Additional FGF2 Targeting Ligands can be found in, for example, US Patent 8933099, Bioorg Med Chem Lett 12: 3287-90 (2002), Chem Biol Drug Des 86: 1323-9 (2015), Bioorg Med Chem Lett 25: 1552-5 (2015), each of which is incorporated herein by reference.
Fibronectin-1
In some embodiments, the Target Protein is human fibronectin 1 (FN1) (UniProtKB - P02751 (FINC_HUMAN)). Fibronectin (FN) polymerization is necessary for collagen matrix deposition and is a key contributor to increased abundance of cardiac myofibroblasts (MFs) after cardiac injury. Interfering with FN polymerization may attenuate MF and fibrosis and improve cardiac function after ischemia/reperfusion (I/R) injury.
The Protein Data Bank website provides the crystal structure of fibronectin- 1 bound to various compounds searchable by 3M7P (Graille, M., et al., Structure, 2010, 18, 710-718); 3MQL (Erat, M.C., et al., J Biol Chem., 2010, 285, 33764-33770); and 3EJH (Erat, M.C., et al., Proc Natl Acad Sci U S A, 2009, 106, 4195-4200).
Representative FN Targeting Ligands are provided in Fig. 1. Additional FN Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 18: 2499-504 (2008), which is incorporated herein by reference.
Kallikrein-1 (KLK1)
In some embodiments, the Target Protein is human kallikrein-1 (UniProtKB - P06870 (KLK1 HUMAN)). Glandular kallikreins cleave Met-Lys and Arg-Ser bonds in kininogen to release Lys-bradykinin. Kallikrein has been implicated in adverse reactions in hereditary angioedema (HAE).
The Protein Data Bank website provides the crystal structure of KLK1 searchable by 1 SPJ (Laxmikanthan, G., et al., Proteins, 2005, 58, 802-814); as well as the crystal structure of KLK1 bound to various compounds searchable by 5F8Z, 5F8T, 5F8X, (Xu, M., et al.,); and 6A8O (Xu, M., et al., FEBS Lett., 2018, 592, 2658-2667). Additionally, Katz et al., provides insight into the crystal structure of kallikrein (Katz, B.A., et al., Protein Sci., 1998, 7(4), 875-85).
Representative kallikrein Targeting Ligands are provided in Fig. 1. Additional kallikrein Targeting Ligands can be found in, for example, US Patent 9783530, J Med Chem 38: 2521-3 (1995), US Patent 9234000, US Patent 10221161, US Patent 9687479, US Patent 9670157, US Patent 9834513, J Med Chem 38: 1511-22 (1995), US Patent 10214512, each of which is incorporated herein by reference.
Plasma Kallikrein
In some embodiments, the Target Protein is human plasma kallikrein (UniProtKB - P03952 (KLKB1 HUMAN)). Plasma kallikrein cleaves Lys-Arg and Arg-Ser bonds. It activates, in a reciprocal reaction, factor XII after its binding to a negatively charged surface. It also releases bradykinin from HMW kininogen and may also play a role in the renin-angiotensin system by converting prorenin into renin. Plasma kallikrein has been implicated in retinal dysfunction, the development of diabetic macular edema and hereditary angioedema (HAE).
The Protein Data Bank website provides the crystal structure of plasma kallikrein bound to various compounds searchable by 5TJX (Li, Z., et al., ACS Med Chem Lett., 2017, 8, 185-190); 6O1G and 6O1S (Patridge, J. R., et al., J Struct Biol., 2019, 206, 170-182); 4OGX and 4OGY (Kenniston, J. A., et al., J Biol Chem., 2014, 289, 23596-23608); and 5F8T, 5F8X, and 5F8Z (Xu, M., et al.,).
Representative plasma kallikrein Targeting Ligands are provided in Fig. 1. Additional plasma kallikrein Targeting Ligands can be found in, for example, J Med Chem 61 : 2823-2836 (2018), J Med Chem 55: 1171-80 (2012), US Patent 8598206, US Patent 9738655, Bioorg Med Chem Lett 16: 2034-6 (2006), US Patent 9409908, US Patent 10144746, US Patent 9290485, each of which is incorporated herein by reference.
Lipoprotein Lipase
In some embodiments, the Target Protein is human lipoprotein lipase (UniProtKB - P06858 (LIPL HUMAN)). Lipoprotein lipase is a key enzyme in triglyceride metabolism. It catalyzes the hydrolysis of triglycerides from circulating chylomicrons and very low density lipoproteins (VLDL), and thereby plays an important role in lipid clearance from the blood stream, lipid utilization and storage. Lipoprotein lipase mediates margination of triglyceride-rich lipoprotein particles in capillaries. Lipoprotein lipase has been implicated in the development of cardiovascular disease and obesity.
The Protein Data Bank website provides the crystal structure of lipoprotein lipase bound to various compounds searchable by 6E7K (Birrane, G., et al., Proc Natl Acad Sci U S A, 2018 116 1723-1732).
Representative lipoprotein lipase Targeting Ligands are provided in Fig. 1. Additional lipoprotein lipase Targeting Ligands can be found in, for example, J Med Chem 47: 400-10 (2004), which is incorporated herein by reference.
Matrix Metallopeptidase 1 (MMP-1)
In some embodiments, the Target Protein is human matrix metallopeptidase 1 (MMP-1) (UniProtKB - P03956 (MMP1 HUMAN)). MMP-1 cleaves collagens of types I, II, and III at one site in the helical domain. It also cleaves collagens of types VII and X. MMP-1 has been implicated in cardiovascular disease.
The Protein Data Bank website provides the crystal structure of MMP-1 searchable by 3SHI (Bertini, I., et al., FEBS Lett., 2012, 586, 557-567); as well as the crystal structure of MMP- 1 bound to various compounds searchable by 4AU0 (Manka, S. W., et al., Proc Natl Acad Sci U S A, 2012, 109, 12461); 3MA2 (Grossman, M., et al., Biochemistry, 2010, 49, 6184-6192); and 2J0T (Iyer, S., et al., J.Biol.Chem., 2007, 282, 364 ). Additionally, Iyer et al., provides insight into the crystal structure of an active form of MMP-1 (Iyer, S., et al., J Mol Biol., 2006, 362(1), 78- 88); and Lovejoy et al., provides insight into the crystal structure of MMP1 and the selectivity of collagenase inhibitors (Lovejoy, B., et al., Nat Struct Mol Biol., 1999, 6, 217-221).
Representative MMP-1 Targeting Ligands are provided in Fig. 1. Additional MMP-1 Targeting Ligands can be found in, for example, Bioorg Med Chem Lett 5: 1415-1420 (1995), Bioorg Med Chem Lett 16: 2632-6 (2006), Bioorg Med Chem Lett 8: 837-42 (1999), Eur J Med Chem 60: 89-100 (2013), J Med Chem 54: 4350-64 (2011), Bioorg Med Chem Lett 8: 3251-6 (1999), J Med Chem 42: 4547-62 (1999), J Med Chem 61 : 2166-2210 (2018), J Med Chem 41 : 1209-17 (1998), which is incorporated herein by reference. Macrophage Migration Inhibitory Factor (MIF)
In some embodiments, the Target Protein is human macrophage migration inhibitory factor (MIF) (UniProtKB - P14174 (MIF HUMAN)). MIF is a pro-inflammatory cytokine involved in the innate immune response to bacterial pathogens. The expression of MIF at sites of inflammation suggests a role as mediator in regulating the function of macrophages in host defense. It counteracts the anti-inflammatory activity of glucocorticoids.
MIF has been implicated in tumor progression; systemic inflammation; atherosclerosis; rheumatoid arthritis; and systemic lupus erythematosus, among others.
The Protein Data Bank website provides the crystal structure of MIF searchable by 1MIF (Sun, H-W. et al., Proc Natl Acad Sci U S A, 1996, 93, 5191-5196); as well as the crystal structure of MIF bound to various compounds searchable by 6PEG (Cirillo, P.F. et al.,); 5XEJ (Fukushima, K); 6FVE and 6FVH (Sokolov, A.V., et al., Biochemistry (Mose), 2018, 83, 701-707); 6CB5, 6CBF, 6CBG, and 6CBH (Trivedi-Parmar, V., et al., ChemMedChem., 2018, 13, 1092-1097); 6B1C, 6B1K, 6B2C, (Dawson, T.K., et al., ACS Med Chem Lett., 2017, 8, 1287-1291); 4Z15, 4Z1T and 4Z1U (Singh, A.K., et al, J Cell Mol Med., 2017, 21, 142-153); 5HVS and 5HVT (Cisneros, J.A., et al., J Am Chem Soc., 2016, 138, 8630-8638); 4PKK (Pantouris, G., et al.,); 5J7P and 5J7Q (Cisneros, J. A., et al., Bioorg Med Chem Lett., 2016, 26, 2764-2767); 5B4O (Kimura, H., et al., Chem Biol., 2010, 17, 1282-1294 ); 4PLU, 4TRF, 4P0H, and 4P01 (Pantouris, G., et al., Chem Biol., 2015, 22, 1197-1205); 4WR8 and 4WRB (Dziedzic, P., et al., J Am Chem Soc., 2015, 137 2996-3003); 4K9G (loannou, K., etal., Int J Oncol., 2014, 45, 1457-1468); 4OSF, 3WNR, 3WNS and 3WNT (Spencer, E.S., et al., Eur J Med Chem., 2015, 93, 501-510); 4OYQ (Spencer, E.S. et al.,); 3SMB and 3SMC (Crichlow, G.V. et al., Biochemistry, 2012, 51, 7506-7514); 3U18 (Bai, F., et al., J Biol Chem., 2012, 287, 30653-30663); 4F2K (Tyndall, J.D.A., et al., Acta Crystallogr Sect F Struct Biol Cryst Commun., 2012, 68, 999-1002); 3IJG and 3IJJ (Cho, Y., et al., Proc Natl Acad Sci U S A, 2010, 107, 11313-11318); 3L5P, 3L5R, 3L5S, 3L5T, 3L5U, and 3L5V (McLean, L.R. et al., Bioorg Med Chem Lett., 2010, 20, 1821-1824); 3JSF, 3JSG and 3JTU (McLean, L.R., et al., Bioorg Med Chem Lett., 2009, 19, 6717); 3HOF (Crawley, L., et al.); 3CE4 and 3DJI (Crichlow G.V., et al., Biochemistry, 2009, 48, 132-139); 3B9S (Winner, M. et al., Cancer Res., 2008, 68, 7253-7257 ); 2OOH, 2OOW and 2OOZ (Crichlow, G.V. et al., J Biol Chem., 2007, 282, 23089-23095); 1GCZ and 1GD0 (Orita, M. et al., J Med Chem., 2001, 44, 540- 547); and 1CA7, 1CGQ and 1P1G (Lubetsky, J.B. et al., Biochemistry, 1999, 38, 7346-7354). Additionally, Sun et al., provides insight into the crystal structure of MIF (Proc Natl Acad Sci U S A., 1996, 28;93(11), 5191-6).
Representative MIF Targeting Ligands are provided in Fig. 1. Additional MIF Targeting Ligands can be found in, for example, ACS Med Chem Lett 8: 124-127 (2017), J Med Chem 44: 540-7 (2001), J Med Chem 52: 416-24 (2009), J Med Chem 50: 1993-7 (2007), which is incorporated herein by reference.
Transforming Growth Factor-β2 (TGF-β2)
In some embodiments, the Target Protein is human transforming growth factor- β2 (TGF- β2) (UniProtKB - P61812 (TGFB2 HUMAN)). TGF- β2 is a multifunctional protein that regulates various processes such as angiogenesis and heart development. Once activated following release of LAP, TGF-beta-2 acts by binding to TGF-beta receptors (TGFBR1 and TGFBR2), which transduce signal. TGF- β2 expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF-β2 mediated tumor suppression via T-cell exclusion. TGF- β2 expression has also been implicated in hematological malignancies and fibrosis.
The Protein Data Bank website provides the crystal structure of TGF-β2 searchable by 6I9J (Del Amo-Maestro L. et al., Sci Rep. 2019, 9, 8660-8660); as well as the crystal structure of TGF- β2 bound to various compounds searchable by 1M9Z (Boesen, C.C., et al. Structure, 2002, 10, 913-919); 5QIN (Zhang, Y. et al., ACS Med Chem Lett., 2018, 9, 1117-1122); 5E8V, 5E8Y, 5E91 and 5E92 (Tebben, A.J. et al., Acta Crystallogr D Struct Biol., 2016, 72, 658-674); 4P7U (Wangkanont, K. et al., Protein Expr Purif., 2015, 115, 19-25); 4XJJ (Wangkanont et al.); and 1KTZ (Hart, P.J., et al., Nat Struct Biol., 2002, 9, 203-208).
Representative TGF-β 2 Targeting Ligands are provided in Fig. 1.
Thrombospondin-1 (TSP-1)
In some embodiments, the Target Protein is human thrombospondin-1 (TSP-1) (UniProtKB - P61812 (TGFB2 HUMAN)). TSP1 acts as an angiogenesis inhibitor by stimulating endothelial cell apoptosis, inhibiting endothelial cell migration and proliferation, and regulating vascular endothelial growth factor bioavailability and activity. TSP1 affects tumor immune response, tumor cell behaviors including adhesion, invasion, migration, apoptosis, and proliferation.
TSP-1 expression has been implicated in a number of diseases, including in promoting certain cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
The Protein Data Bank website provides the crystal structure of TSP -1 searchable by 1LSL (Tan, K. et al., J Cell Biol., 2002, 159, 373-382); 2ES3 (Tan, K., et al., J Biol Chem., 2008, 283, 3932-3941); 1Z78 and 2ERF (Tan, K., et al., Structure, 2006, 14, 33-42); and 3R6B (Klenotic, P.A., et al., Protein ExprPurif., 2011, 80, 253-259); as well as the crystal structure of TSP-1 bound to various compounds searchable by 20UH and 2OUJ (Tan, K., et al., J Biol Chem., 2008, 283, 3932-3941); and 1ZA4 (Tan, K., et al., Structure, 2006, 14, 33-42).
Representative TSP-1 Targeting Ligands are provided in Fig. 1.
CD40 Ligand (CD40L)
In some embodiments, the Target Protein is human CD40 ligand (CD40L) (UniProtKB - P29965 (CD40L HUMAN)). CD40L is a cytokine that acts as a ligand to CD40/TNFRSF5. It costimulates T-cell proliferation and cytokine production. Its cross-linking on T-cells generates a costimulatory signal which enhances the production of IL4 and IL 10 in conjunction with the TCR/CD3 ligation and CD28 costimulation. CD40L induces the activation of NF-kappa-B, as well as kinases MAPK8 and PAK2 in T-cells. It also induces tyrosine phosphorylation of isoform 3 of CD28. CD40L mediates B-cell proliferation in the absence of co-stimulus as well as IgE production in the presence of IL4, and is involved in immunoglobulin class switching.
The Protein Data Bank website provides the crystal structure of CD40L searchable by 1ALY (Karpusas, M., et al., Structure, 1995, 3, 1031-1039); as well as the crystal structure of CD40L bound to various compounds searchable by 3QD6 (An, H.J., et al., J Biol Chem., 2011, 286, 11226-11235); and 6BRB (Kamell, J.L., et al., Sci Transl Med., 2019, 11(489), 6584).
The expression of CD40L has been implicated in HIV-associated neurocognitive disorders and cardiovascular complications. Representative CD40L Targeting Ligands are provided in Fig. 1. Urokinase-type Plasminogen Activator (UP A)
In some embodiments, the Target Protein is human urokinase-type plasminogen activator (UP A) (UniProtKB - P00749 (UROK HUMAN)). Urokinase-type plasminogen activator (uPA), is a serine protease present in the blood and in the extracellular matrix of many tissues. The primary physiological substrate of this enzyme is plasminogen, which is an inactive form (zymogen) of the serine protease plasmin. Activation of plasmin triggers a proteolytic cascade that, depending on the physiological environment, participates in thrombolysis or extracellular matrix degradation. This cascade had been involved in vascular diseases and cancer progression. Elevated expression levels of urokinase and several other components of the plasminogen activation system are found to be correlated with tumor malignancy.
The Protein Data Bank website provides the crystal structure of UPA bound to various compounds searchable by 5ZA7, 5ZAJ, 5ZA8, 5ZA9, 5ZAE, 5ZAF, 5ZAG, 5ZAH, and 5ZC5 (Buckley, B.J. et al., J Med Chem., 2018, 61, 8299-8320); 5LHP, 5LHQ, 5LHR, and 5LHS (Kromann-Hansen, T. et al., Sci Rep., 2017, 7, 3385-3385); 2VNT (Fish, P.V. et al. J Med Chem., 2007, 50, 2341); 10WD, 10WE, 10WH, 1OWI, 1OWJ, and 10WK (Wendt, M.D. et al., J Med Chem., 2004, 47, 303-324); 1SQA, 1SQO, and 1SQT (Wendt, M.D., et al., Bioorg Med Chem Lett., 2004, 14, 3063-3068); 1U6Q (Bruncko, M. et al., Bioorg Med Chem Lett., 2005, 15, 93-98); 30X7, 3OY5 and 3OY6 (Jiang, L.G. et al., J Mol Biol., 2011, 412, 235-250); 4OS1, 4OS2, 4OS4, 4OS5, 4OS6 and 4OS7 (Chen, S. et al., Nat Chem., 2014, 6, 1009-1016); 3IG6 (West, C.W. et al., Bioorg Med Chem Lett., 2009, 19, 5712-5715); 4X0W and 4X1P (Jiang, L. et al., Int J Biochem Cell Biol., 2015, 62, 88-92); 4X1N, 4X1Q, 4XlR and 4XlS (Zhao, B. et al., PLoS One, 2014, 9, el 15872-el 15872); 5WX0 and 5WXP (Jiang, L. et al., Biochim Biophys Acta., 2018, 1862, 2017- 2023); 4MNV, 4MNW, 4MNX, and 4MNY (Chen, S., et al., Angew Chem Int Ed Engl., 2014, 53, 1602-1606); 4GLY (Chen, S., et al., J Am Chem Soc., 2013, 135, 6562-6569); 4JK5 and 4JK5 (Chen, S., et al., Chembiochem., 2013, 14, 1316-1322); 3QN7 (Angelini, A. et al., ACS Chem Biol., 2012, 7, 817-821); 2NWN (Zhao, G. et al., J Struct Biol., 2007, 160, 1-10); 6NMB (Wu, G. et al., Blood Adv., 2019, 3, 729-733); 1W0Z, 1W10, 1W11, 1W12, 1W13, and 1W14 (Zeslawska, E. et al., J Mol Biol., 2003, 328, 109); 4DVA (Jiang, L et al., Biochem J., 2013, 449, 161-166); 6A8G 6A8N (Wang, D. et al., J Med Chem., 2019, 62, 2172-2183); 2VIN, 2VIO, 2VIP, 2VIQ, 2VIV, and 2VIW (Frederickson, M. et al., J Med Chem., 2008, 51, 183); 1EJN (Speri, S., et al., Proc Natl Acad Sci U S A, 2000, 97, 5113-5118); 3PB1 (Lin, Z. et al., J Biol Chem., 2011, 286, 7027-7032); 3U73 (Xu, X. et al., J Mol Biol., 2012, 416, 629-641); 1C5W, 1C5X, lC5Y and IC5Z (Katz, B.A., et al., Chem Biol., 2000, 7, 299-312); 5XG4 (Xue, G. et al., Food Funct., 2017, 8, 2437-2443); 5WXF (Jiang, L. et al., Biochim Biophys Acta., 2018, 1862, 2017-2023); 5WXS, 4ZKS, 5WXQ, 5WXT, 5YC6, 5YC7, 5Z1C, (Jiang, L. et al.); 4H42 (Yu, H.Y. et al.,); 6AG3 and 6AG9 (Buckley, B. et al); 3KGP, 3KHV, 3KID, 3M61, 3MHW, and 3MWI (Jiang, L.G. et al.,); 4ZKN, 4ZKO and 4ZKR (Jiang, L. et al.); 2O8T, 2O8U, 2O8W (Zhao, G. et al.,); and 4FU7, 4FU8, 4FU9, 4FUB, 4FUC, 4FUD, 4FUE, 4FUF, 4FUG, 4FUH, 4FUI, and 4FUJ (Kang, Y.N. et al.).
Representative UPA Targeting Ligands are provided in Fig. 1. Additional UPA Targeting Ligands are provided in, for example, J Med Chem 38: 1511-22 (1995), Bioorg Med Chem Lett 11 : 2253-6 (2001), Bioorg Med Chem Lett 14: 3063-8 (2004), J Med Chem 52: 3159-65 (2009), CSAR 1 : (2012), Bioorg Med Chem 22: 3187-203 (2014), J Med Chem 50: 2341-51 (2007), J Mol Biol 329: 93-120 (2003), Bioorg Med Chem Lett2: 1399-1404 (1992), J Med Chem 35: 4297-305 (1992), J Med Chem 35: 4150-9 (1992), J Med Chem 49: 5785-93 (2006), Bioorg Med Chem 23: 3696-704 (2015), Bioorg Med Chem Lett 10: 983-7 (2000), JMed Chem 49: 5785-93 (2006), each of which is incorporated by reference herein.
Plasminogen Activator, Tissue Type (TP A)
In some embodiments, the Target Protein is human plasminogen activator, tissue type (TP A) (UniProtKB - P00750 (TPA HUMAN)). TP A converts the abundant, but inactive, zymogen plasminogen to plasmin by hydrolyzing a single Arg-Val bond in plasminogen. By controlling plasmin-mediated proteolysis, it plays an important role in tissue remodeling and degradation, in cell migration and many other physiopathological events. TPA plays a direct role in facilitating neuronal migration. PLA has been shown activated in various cancers including oral malignancy.
The Protein Data Bank website provides the crystal structure of TPA searchable by 1VR1 (Dekker, R.J. et al., J Mol Biol., 1999, 293, 613-627); as well as the crystal structure of TPA bound to various compounds searchable by 1RTF (Lamba, D. et al., J Mol Biol., 1996, 258, 117- 135); 1 A5H (Renatus, M. et al., J Biol Chem., 1997, 272, 21713-21719); and 1BDA (Renatus, M. et al., EMBO J., 1997, 16, 4797-4805). Representative TPA Targeting Ligands are provided in Fig. 1. Additional TPA Targeting Ligands are provided in, for example, Bioorg Med Chem Lett 15: 4411-6 (2005), Bioorg Med Chem Lett 13: 2781-4 (2003), Bioorg Med Chem Lett 6: 2913-2918 (1996), JMed Chem 44: 2753- 71 (2001), J Med Chem 41 : 5445-56 (1999), Bioorg Med Chem Lett 12: 3183-6 (2002), US Patent 10118930, J Biol Chem 285: 7892-902 (2010), each of which is incorporated by reference herein.
Plasminogen (PLG)
In some embodiments, the Target Protein is human plasminogen (PLG) (UniProtKB - P00747 (PLMN HUMAN)). PLG dissolves the fibrin of blood clots and acts as a proteolytic factor in a variety of other processes including embryonic development, tissue remodeling, tumor invasion, and inflammation. It activates the urokinase-type plasminogen activator, collagenases and several complement zymogens, such as Cl and C5. Its role in tissue remodeling and tumor invasion may be modulated by CSPG4.
The Protein Data Bank website provides the crystal structure of PLG searchable by 1DDJ (Wang, X. et al., J.Mol.Biol., 2000, 295, 903-914); and 4DUR and 4DUU (Law, R.H.P., et al., Cell Rep., 2012, 1, 185-190).
Representative PLG Targeting Ligands are provided in Fig. 1. Additional PLG Targeting Ligands are provided in, for example, J Med Chem 35: 4297-305 (1992), J Med Chem 38: 1511- 22 (1995), J Med Chem 56: 820-31 (2013), US Patent 8598206, US Patent 8921319, J Med Chem 55: 1171-80 (2012), Bioorg Med Chem Lett 12: 3183-6 (2002), Bioorg Med Chem 23: 3696-704 (2015), Bioorg Med Chem Lett 13: 723-8 (2003), Bioorg Med Chem Lett 7: 331-336 (1997), each of which is incorporated by reference herein.
Plasminogen Activator Inhibitor-1 (PAI-1)
In some embodiments, the Target Protein is human plasminogen activator inhibitor 1 (PAL 1) (UniProtKB - P05121 (PAI 1 HUMAN)). PALI is a serine protease inhibitor, and a primary inhibitor of tissue-type plasminogen activator (PLAT) and urokinase-type plasminogen activator (PLAU). As PLAT inhibitor, it is required for fibrinolysis down-regulation and is responsible for the controlled degradation of blood clot. As PLAU inhibitor, it is involved in the regulation of cell adhesion and spreading, and acts as a regulator of cell migration, independently of its role as protease inhibitor. Overexpression of PAI- 1 favors angiogenesis, metastasis, and poor prognosis in tumors, including, but not limited to, oral cancers and breast cancers.
The Protein Data Bank website provides the crystal structure of PAI-1 searchable by 3Q02 and 3Q03 (Jensen, J.K. et al., J Biol Chem., 2011, 286, 29709-29717); 1B3K (Sharp, A.M. et al., Structure, 1999, 7, 111-118); 1C5G (Tucker, H.M. et al., Nat Struct Biol., 1995, 2, 442-445); 1DVM (Stout, T.J. et al., Biochemistry, 2000, 39, 8460-8469); and 3UT3 (Lin, Z.H. et al.,); as well as the crystal structure of PALI bound to various compounds searchable by 4AQH (Fjellstrom, O. et al., J Biol Chem., 2013, 288, 873); 3R4L (Jankun, J. et al., Int J Mol Med., 2012, 29 61-64); 1A7C (Xue, Y., et al., Structure, 1998, 6, 627-636); 1OC0 (Zhou, A. et al., Nat Struct Biol., 2003, 10, 541); 6I8S (Vousden, K.A. et al., Sci Rep., 2019, 9, 1605-1605 ); 4G8O and 4G8R (Li, S.H. et al., Proc Natl Acad Sci U S A, 2013, 110, E4941-E4949); 6GWQ, 6GWN and 6GWP (Sillen, M. et al., J Thromb Haemost, 2019); and 4IC0 (Hong, Z.B. et al.,).
Representative PALI Targeting Ligands are provided in Fig. 1. Additional PALI Targeting Ligands are provided in, for example, J Biol Chem 285: 7892-902 (2010), US Patent 9120744, Bioorg Med Chem Lett 13: 3361-5 (2003), Bioorg Med Chem Lett 12: 1063-6 (2002), Bioorg Med Chem Lett 13: 1705-8 (2003), Bioorg Med Chem Lett 11 : 2589-92 (2001), US Patent 9718760, each of which is incorporated by reference herein.
Placenta Growth Factor (PIGF)
In some embodiments, the Target Protein is human placental growth factor (PGF) (UniProtKB - P49763 (PLGF HUMAN)). PGF is growth factor active in angiogenesis and endothelial cell growth, stimulating their proliferation and migration. It binds to the receptor FLT1/VEGFR-1. Isoform P1GF-2 binds NRPl /neuropilin- 1 and NRP2/neuropilin-2 in a heparindependent manner. PGF also promotes cell tumor growth, and has been implicated in age-related macular degeneration (AMD) and choroidal neovascularization (CNV).
The Protein Data Bank website provides the crystal structure of PIGF searchable by 1FZV (Iyer, S. et al., J Biol Chem., 2001, 276, 12153-12161 ); as well as the crystal structure of PIGF bound to various compounds searchable by 1RV6 (Christinger, H. W., J Biol Chem., 2004, 279, 10382-10388). Additionally, De Falco provides insight into the discovery and biological activity of placenta growth factor (De Falco, Exp Mol Med., 2012, 44, 1-9). Representative PGF Targeting Ligands are provided in Fig. 1. Additional PGF Targeting Ligands are provided in, for example, J Med Chem 54: 1256-65 (2011), J Nat Prod 76: 29-35 (2013), each of which is incorporated by reference herein.
Phospholipase A2, Group IB (PA21B)
In some embodiments, the Target Protein is human phospholipase A2, Group IB (PA21B) (UniProtKB - P04054 (PA21B HUMAN)). PA21B cleaves phospholipids preferentially at the sn-2 position, liberating free fatty acids and lysophospholipids. PA21B has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders and cancer.
The Protein Data Bank website provides the crystal structure of PA21B searchable by 3FVJ and 3FVI (Pan, Y.H. et al., Biochim.Biophys.Acta., 2010, 1804, 1443-1448).
Representative PA21B Targeting Ligands are provided in Fig. 1. Additional PA21B Targeting Ligands are provided in, for example, J Med Chem 39: 3636-58 (1996), Chembiochem 4: 181-5 (2003), J Med Chem 39: 5159-75 (1997), J Med Chem 51 : 4708-14 (2008), each of which is incorporated by reference herein.
Phospholipase A2, Group IIA (PA2GA)
In some embodiments, the Target Protein is human phospholipase A2, Group IIA (PA2GA) (UniProtKB - P04054 (PA21B HUMAN)). PA2GA catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. It is thought to participate in the regulation of phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Independent of its catalytic activity, it also acts as a ligand for integrins. PA2GA Induces cell proliferation in an integrin-dependent manner. PA2GA has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders, and cancer.
The Protein Data Bank website provides the crystal structure of PA2GA bound to various compounds searchable by 2ARM and 1SV3 (Singh, N. et al., Proteins, 2006, 64, 89-100); 5G3M and 5G3N (Giordanetto, F., et al. ACS Med Chem Lett., 2016, 7, 884); 1KQU (Jansford, K.A., et al., Chembiochem., 2003, 4 ,181-185); and 1ZYX (Singh, N. et al.,). Additionally, Singh et al., provides insight into the crystal structure of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding (Singh, N. et al., Proteins, 2006, 64(l):89-100); and Kitadokoro et al also provides insight into the crystal structure of human secretory phospholipase A2-IIA complex with the potent indolizine inhibitor 120-1032 (Kitadokoro, K. et al., J Biochem., 1998, 123(4), 619-23).
Representative PA2GA Targeting Ligands are provided in Fig. 1. Additional PA2GA Targeting Ligands are provided in, for example, J Med Chem 48: 893-6 (2005), J Med Chem 39: 5159-75 (1997), each of which is incorporated by reference herein.
In certain embodiments the Extracellular Protein Targeting Ligand is OPT-3. OPT-3 has the following structure.
Figure imgf000194_0001
In certain embodiments OPT-3 is attached to the linker through the primary amine of histidine as shown below.
Figure imgf000195_0001
In certain embodiments the Extracellular Protein Targeting Ligand is OPT-2. OPT-2 has the following structure.
Figure imgf000195_0002
In certain embodiments OPT-2 is attached to the linker through the primary amine of histidine as shown below.
Figure imgf000196_0001
In certain embodiments the Extracellular Protein Targeting Ligand is OPT-1. OPT-1 has the following structure.
Figure imgf000196_0002
In certain embodiments OPT-1 is attached to the linker through the primary amine of histidine as shown below.
Figure imgf000197_0001
VIII. Treatment of Diseases with the ASGPR-binding Extracellular Protein Degraders that are Formed In Vivo
In addition to compounds of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, and IV-d and their respective bi- and tri-versions, the present invention also provides a method of treating a patient in need thereof wherein an effective amount of a compound of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or a bi- or tri-version thereof is administered to a patient either before, concurrently, or after administration of a compound of Formula VII. These two compounds then combine for form an Extracellular Protein Degrading compound in vivo.
In certain embodiments a method of treating a disorder mediated by an Extracellular Protein is provided that comprises administering (i) an effective dose of a compound or pharmaceutical composition of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or its respective bi- and tri-version or a pharmaceutically acceptable salt thereof to a patient in combination with (ii) an effective dose of a compound or pharmaceutical composition of Formula VII or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein. The term “combination” as used in this method means that step (i) and step (ii) are carried out within a sufficient temporal proximity that allows the selected compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or its respective bi- and triversion or a pharmaceutically acceptable salt thereof to react with the selected compound of Formula VII. Step (i) can be carried out before or after step (ii) as long as the two steps are sufficiently close in time that the compounds are able to assemble in vivo.
In certain embodiments the compound of Formula VII is administered first.
In certain embodiments the compound of Formula VII is administered in excess on a per molecule basis to the compound of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, or IV-d or their respective bi- and tri-versions.
In certain embodiments the two compounds combine faster in human plasma than they would in an organic solvent such as methanol. For example, see the paper by Ursuequi, S. Et al., Nat. Commun. 2017, 8, 15242 and Warther, D., et al., Org. Biomol. Chem. 2021, 19, 5063-5067.
For example, when a compound of Formula I is combined with a compound of Formula VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000198_0001
Similarly, when a compound of Formula III is combined with a compound of Formula VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000198_0002
Similarly, when a compound of Formula I-d is combined with a compound of Formula VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000198_0003
Similarly, when a compound of Formula Ill-d is combined with a compound of Formula VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000199_0001
In a similar manner bi- and tri-versions of Formulas I, II, III, IV, V, VI, I-d, Il-d, Ill-d, and IV-d can be administered to the patient in need thereof and combined in vivo to form bi- and tri-versions of the Extracellular Protein Degrader. For example, when a compound of Formula I-Bi is combined with a compound of Formula
VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000199_0002
For example, when a compound of Formula I-Tri is combined with a compound of Formula VII with an appropriate Selective Moiety the resulting compound that forms in the body is:
Figure imgf000199_0003
The Target Proteins of the current invention may include, but are not limited to, immunoglobulins, cytokines, chemokines, growth factors, coagulation factors, extracellular matrix proteins and proteins involved in formation and/or degradation of the extracellular matrix, esterases, lipases, peptidases, convertases, among others. These proteins mediate a range of diseases that can be treated with an effective amount ASGPR Ligand and Extracellular Protein Targeting Ligand described herein.
Immunoglobulins
1) Immunoglobulin A (IgA) aberrant expression mediates a range of autoimmune and immune-mediated disorders, including IgA nephropathy (also known as Berger’s disease), celiac disease, Crohn’s disease, Henoch-Sconiein purpura (HSP) (also known as IgA vasculitis), liner IgA bullous dermatosis, IgA pemphigus, dermatitis herpetiformis, inflammatory bowel disease (IBD), Sjogren's syndrome, ankylosing spondylitis, alcoholic liver cirrhosis, acquired immunodeficiency syndrome, IgA multiple myeloma, a-chain disease, IgA monoclonal gammopathy, monoclonal gammopathy of undetermined significance (MGUS), and linear IgA bullous dermatosis, among others.
2) Immunoglobulin G (IgG) mediates a range of autoimmune, infectious and metabolic diseases, including systemic fibroinflammatory disease. In addition, overexpression of IgG4 is associated with IgG4-related diseases, which generally include multiple organs, and disorders include type 1 autoimmune pancreatitis, interstitial nephritis, Riedel's thyroiditis, storiform fibrosis, Mikulicz's disease, Kiittner's tumor, inflammatory pseudotumors (in various sites of the body), mediastinal fibrosis, retroperitoneal fibrosis (Ormond’s disease), aortitis and periaortitis, proximal biliary strictures, idiopathic hypocomplementic tubulointerstitial nephritis, multifocal fibrosclerosis, pachymeningitis, pancreatic enlargement, tumefactive lesions, pericarditis, rheumatoid arthritis (RA), inflammatory bowel disease, multiple sclerosis, myasthenic gravis, ankylosing spondylitis, primary Sjogren’s syndrome, psoriatic arthritis, and systemic lupus erythematosus (SLE), sclerosing cholangitis, and IgG monoclonal gammopathy, monoclonal gammopathy of undetermined significance (MGUS), among others.
3) Immunoglobulin E (IgE) - IgE is a strong mediator of allergic disease, including but not limited to, atopic asthma, allergic rhinitis, atopic dermatitis, IgE-mediated food allergy, IgE-mediated animal allergies, allergic conjunctivitis, allergic urticaria, anaphylactic shock, nasal polyposis, keratoconjunctivitis, mastocytosis, and eosinophilic gastrointestinal disease, bullous pemphigoid, chemotherapy induced hypersensitivity reaction, seasonal allergic rhinitis, interstitial cystitis, eosinophilic esophagitis, angioedema, acute interstitial nephritis, atopic eczema, eosinophilic bronchitis, chronic obstructive pulmonary disease, gastroenteritis, hyper-IgE syndrome (Job's Syndrome), IgE monoclonal gammopathy, and monoclonal gammopathy of undetermined significance (MGUS), among others.
Cytokines/Chemokines
1) TNF-α mediates a number of disorders, including but not limited to rheumatoid arthritis, inflammatory bowel disease, graft-vs-host disease, ankylosing spondylitis, psoriasis, hidradenitis suppurativa, refractory asthma, systemic lupis erthyematosus, diabetes, and the induction of cachexia.
2) IL-2 mediates host versus graft rejection in transplants and autoimmune disorders, including, but not limited to, multiple sclerosis, idiopathic arthritis, iritis, anterior uveitis, IL-2 induced hypotension, psoriasis, and other autoimmune disorders
3) IL-1 mediates a number of auto-inflammatory and autoimmune disorders, including, but not limited to, Blau syndrome, cryopyrin-associated periodic syndromes, familial Mediterranean fever, Majeed syndrome; mevalonate kinase deficiency syndrome, pyogenic arthritis-pyoderma gangrenosum-acne syndrome, tumor necrosis factor receptor- associated periodic syndrome, Behçet’s Disease, Sjogren’s Syndrome, gout and chondrocalcinosis, periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (or PFAPA) syndrome, rheumatoid arthritis, Type 2 diabetes mellitus, acute pericarditis, Chronic interstitial lung diseases (ILDs), and Still’s disease amongst others.
4) IFN-y mediates a wide range of autoimmune disorders, including, but not limited to rheumatoid arthritis, multiple sclerosis (MS), corneal transplant rejection, and various autoimmune skin diseases such as psoriasis, alopecia areata, vitiligo, acne vulgaris, and others.
5) IL-21 mediates a number of autoimmune disorders, including Sjogren’s syndrome, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease. 6) IL-22 mediates a number of autoimmune disorders, including, but not limited to, graft versus host disease (GVHD), psoriasis, rheumatoid arthritis, atopic dermatitis, and asthma.
7) IL- 10 has been implicated in tumor survival and protection against cytotoxic chemotherapeutic drugs.
8) IL-5 has been implicated in a number of allergic disorders, including, but not limited to, asthma, nasal polyposis, atopic dermatitis, eosinophilic esophagitis, hypereosinophilic syndrome, and Churg-Strauss syndrome.
9) IL-6 has been implicated in a number of inflammatory diseases and cancers, including, but not limited to, Castleman’s disease, metastatic castration-associated prostate cancer, renal cell carcinoma, large-cell lung carcinoma, ovarian cancer, rheumatoid arthritis, asthma.
10) IL-8 has been implicated in the promotion of tumor progression, immune escape, epithelial-mesenchymal transition, and recruitment of myeloid-derived suppressor cells. Studies have demonstrated that high serum IL-8 levels correlate with poor prognosis in many malignant tumors. Preclinical studies have shown that IL-8 blockade may reduce mesenchymal features in tumor cells, making them less resistant to treatment.
11) C-C motif chemokine ligand 2 (CCL2) has been implicated in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis.
12) Macrophage Migration Inhibitory Factor (MIF) is a mediator of tumor progression; systemic inflammation; atherosclerosis; rheumatoid arthritis; and systemic lupus erythematosus, among others.
Growth Factors
1) Fibroblast Growth Factor 1 (FGF1) can induce angiogenesis. FGF1 has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
2) Fibroblast Growth Factor 2 (FGF2) has been implicated in oncogenesis, cancer cell proliferation, resistance to anticancer therapies, and neoangiogenesis.
3) Vascular Epithelial Growth Factor (VEGF-A) has been implicated in the vascularization and angiogenesis of tumors.
4) Transforming Growth Factor-β1 (TGF-β1) expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF-β1 mediated tumor suppression via T-cell exclusion. TGF-β1 expression has also been implicated in hematological malignancies and fibrosis.
5) Transforming Growth Factor-β2 (TGF-β2) expression in the tumor microenvironment has been associated with a poor prognosis, and is implicated in TGF-β2 mediated tumor suppression via T-cell exclusion. TGF- β2 expression has also been implicated in hematological malignancies and fibrosis.
6) Placental Growth Factor (PGF) promotes cell tumor growth, and has been implicated in age-related macular degeneration (AMD) and choroidal neovascularization (CNV).
Esterase
1) Cholinesterase has been implicated in cognitive disorders such as dementia and Alzheimer’s disease.
Coagulation Factors
1) Carboxypeptidase B2 has been implicated and targeted to inhibit thrombosis.
2) Coagulation Factor Xa is a mediator in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
3) Coagulation Factor XI is a mediator in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
4) Coagulation Factor XII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
5) Coagulation Factor XIII has been implicated in the development of deep vein thrombosis and acute pulmonary embolism, and the risk of stroke and embolism in people with nonvalvular atrial fibrillation.
6) Prothrombin is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
7) Coagulation Factor VII is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation. 8) Coagulation Factor IX is involved in blood clot formation and arterial and venous thrombosis, and thromboembolism associated with atrial fibrillation.
Extracellular Matrix Proteins
1) Neutrophil Elastase - Neutrophil elastase has been implicated in a number of disorders, including lung disease, chronic obstructive pulmonary disease, pneumonia, respiratory distress, and acute lung injury (ALI), and cystic fibrosis, as well as chronic kidney disease.
2) Fibronectin-1 - Interfering with FN polymerization may attenuate myofibroblasts and fibrosis and improve cardiac function after ischemia/reperfusion (I/R) injury.
3) Thrombospondin- 1- TSP-1 has been implicated in a number of diseases, including in promoting certain cancers such as breast cancer, prostate cancer, melanoma, SCLC, osteosarcoma, cutaneous squamous cell carcinoma, oral squamous cell carcinoma, papillary thyroid carcinoma, thyroid cancer, medulloblastoma, and fibrotic disorders such as diabetes, liver fibrosis, and in multiple myeloma.
4) Urokinase-type Plasminogen Activator (UP A) - UPA has been implicated in vascular diseases and cancer progression. Elevated expression levels of urokinase and several other components of the plasminogen activation system are found to be correlated with tumor malignancy.
5) Plasminogen Activator, Tissue Type (TP A) - PLA has been shown activated in various cancers including oral malignancy.
6) Plasminogen (PLG) - PLG has been implicated in tumor invasion and inflammation.
7) Plasminogen Activator Inhibitor-1 (PAI-1) - PAI-1 has been implicated in angiogenesis, metastasis, and poor prognosis in tumors, including, but not limited to, oral cancers and breast cancers.
Peptidase
1) Kallikrein-1 - Kallikrein has been implicated in adverse reactions in hereditary angioedema (HAE).
2) Plasma Kallikrein - Plasma kallikrein has been implicated in retinal dysfunction, the development of diabetic macular edema and hereditary angioedema (HAE). 3) Matrix Metallopeptidase - 1 - MMP-1 has been implicated in cardiovascular disease, development of fibrosis, and growth of certain cancers such as bladder cancer.
4) Phospholipase A2, Group IIA (PA2GA) - PA2GA has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders, and cancer.
Lipase
1) Lipoprotein Lipase - Lipoprotein lipase has been implicated in the development of cardiovascular disease and obesity.
2) Phospholipase A2, Group IB (PA21B) - PA21B has been implicated in a number of diseases, including cardiovascular diseases, atherosclerosis, immune disorders and cancer.
Convertase
1) Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK-9) - PCSK-9 has been implicated in high blood cholesterol and the development of cardiovascular disease.
IX. Combination Therapy
In certain embodiments the in addition to a compound of Formula VII and a compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, IV-d, or a bi- or tri-version thereof, a third agent is administered to the patient in need thereof to treat a patient such as a human with a disorder as described herein that mediated by the targeted extracellular protein.
The term “bioactive agent” is used to describe this an agent, other than the two selected compounds according to the present invention, which can be used in combination or alternation with the compounds of the present invention to achieve a desired result of therapy. In one embodiment, the compounds of the present invention and the bioactive agent are administered in a manner that they are active in vivo during overlapping time periods, for example, have timeperiod overlapping Cmax, Tmax, AUC or other pharmacokinetic parameter. In another embodiment, the compounds of the present invention and the bioactive agent are administered to a patient in need thereof that do not have overlapping pharmacokinetic parameter, however, one has a therapeutic impact on the therapeutic efficacy of the other.
In one aspect of this embodiment, the bioactive agent is an immune modulator, including but not limited to a checkpoint inhibitor, including as non-limiting examples, a PD-1 inhibitor, PD-L1 inhibitor, PD-L2 inhibitor, CTLA-4 inhibitor, LAG-3 inhibitor, TIM-3 inhibitor, V-domain Ig suppressor of T-cell activation (VISTA) inhibitors, small molecule, peptide, nucleotide, or other inhibitor. In certain aspects, the immune modulator is an antibody, such as a monoclonal antibody.
PD-1 inhibitors that blocks the interaction of PD-1 and PD-L1 by binding to the PD-1 receptor, and in turn inhibit immune suppression include, for example, nivolumab (Opdivo), pembrolizumab (Keytruda), pidilizumab, AMP-224 (AstraZeneca and Medlmmune), PF- 06801591 (Pfizer), MEDI0680 (AstraZeneca), PDR001 (Novartis), REGN2810 (Regeneron), SHR-12-1 (Jiangsu Hengrui Medicine Company and Incyte Corporation), TSR-042 (Tesaro), and the PD-L1/VISTA inhibitor CA-170 (Curis Inc.). PD-L1 inhibitors that block the interaction of PD-1 and PD-L1 by binding to the PD-L1 receptor, and in turn inhibits immune suppression, include for example, atezolizumab (Tecentriq), durvalumab (AstraZeneca and Medlmmune), KN035 (Alphamab), and BMS-936559 (Bristol-Myers Squibb). CTLA-4 checkpoint inhibitors that bind to CTLA-4 and inhibits immune suppression include, but are not limited to, ipilimumab, tremelimumab (AstraZeneca and Medlmmune), AGEN1884 and AGEN2041 (Agenus). LAG-3 checkpoint inhibitors include, but are not limited to, BMS-986016 (Bristol-Myers Squibb), GSK2831781 (GlaxoSmithKline), IMP321 (Prima BioMed), LAG525 (Novartis), and the dual PD-1 and LAG-3 inhibitor MGD013 (MacroGenics). An example of a TIM-3 inhibitor is TSR- 022 (Tesaro).
In certain embodiments the checkpoint inhibitor is selected from nivolumab/OPDIVO®; pembrolizumab/KEYTRUDA®; and pidilizumab/CT-011, MPDL3280A/RG7446; MEDI4736; MSB0010718C; BMS 936559, a PDL2/lg fusion protein such as AMP 224 or an inhibitor of B7- H3 (e g., MGA271 ), B7-H4, BTLA, HVEM, TIM3, GAL9, LAG 3, VISTA, KIR, 2B4, CD 160, CGEN- 15049, CHK 1 , CHK2, A2aR, B-7 family ligands, or a combination thereof.
In one embodiment, the bioactive agent is an ALK inhibitor. Examples of ALK inhibitors include but are not limited to Crizotinib, Alectinib, ceritinib, TAE684 (NVP-TAE684), GSK1838705A, AZD3463, ASP3026, PF-06463922, entrectinib (RXDX-101), and AP26113.
In one embodiment, the bioactive agent is an EGFR inhibitor. Examples of EGFR inhibitors include erlotinib (Tarceva), gefitinib (Iressa), afatinib (Gilotrif), rociletinib (CO- 1686), osimertinib (Tagrisso), olmutinib (Olita), naquotinib (ASP8273), nazartinib (EGF816), PF- 06747775 (Pfizer), icotinib (BPL2009), neratinib (HKL272; PB272); avitinib (AC0010), EAI045, tarloxotinib (TH-4000; PR-610), PF-06459988 (Pfizer), tesevatinib (XL647; EXEL-7647; KD- 019), transtinib, WZ-3146, WZ8040, CNX-2006, and dacomitinib (PF-00299804; Pfizer). In one embodiment, the bioactive agent is an HER-2 inhibitor. Examples of HER-2 inhibitors include trastuzumab, lapatinib, ado-trastuzumab emtansine, and pertuzumab.
In one embodiment, the bioactive agent is a CD20 inhibitor. Examples of CD20 inhibitors include obinutuzumab, rituximab, fatumumab, ibritumomab, tositumomab, and ocrelizumab.
In one embodiment, the bioactive agent is a JAK3 inhibitor. Examples of JAK3 inhibitors include tasocitinib.
In one embodiment, the bioactive agent is a BCL-2 inhibitor. Examples of BCL-2 inhibitors include venetoclax, ABT-199 (4-[4-[[2-(4-Chlorophenyl)-4,4-dimethylcyclohex-l-en- l-yl]methyl]piperazin-l-yl]-N-[[3-nitro-4-[[(tetrahydro-2H-pyran-4- yl)methyl]amino]phenyl]sulfonyl]-2-[(lH- pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide), ABT-737 (4-[4-[[2-(4-chlorophenyl)phenyl]methyl]piperazin-l-yl]-N-[4- [[(2R)-4-(dimethylamino)-l- phenylsulfanylbutan-2-yl] amino]-3- nitrophenyl] sulfonylbenzamide) (navitoclax), ABT-263 ((R)-4-(4-((4'-chloro-4,4-dimethyl-3,4,5,6-tetrahydro-[l, l'-biphenyl]-2-yl)methyl)piperazin-l-yl)- N-((4-((4-morpholino- 1 -(phenylthio)butan-2-yl)amino)- 3((trifluoromethyl)sulfonyl)phenyl)sulfonyl)benzamide), GX15-070 (obatoclax mesylate, (2Z)-2- [(5Z)-5-[(3,5- dimethyl -lH-pyrrol-2-yl)methylidene]-4-methoxypyrrol-2-ylidene]indole; methanesulfonic acid))), 2-methoxy-antimycin A3, YC137 (4-(4,9-dioxo-4,9- dihydronaphtho[2,3-d]thiazol-2-ylamino)-phenyl ester), pogosin, ethyl 2-amino-6-bromo-4-(l- cyano-2-ethoxy-2-oxoethyl)-4H-chromene-3-carboxylate, Nilotinib-d3, TW-37 (N-[4-[[2-(l , 1 - Dimethylethyl)phenyl]sulfonyl]phenyl]-2,3,4-trihydroxy-5-[[2-(l- methylethyl)phenyl]methyl]benzamide), Apogossypolone (ApoG2), HA14-1, AT101, sabutoclax, gambogic acid, or G3139 (Oblimersen).
In one embodiment, the bioactive agent is a kinase inhibitor. In one embodiment, the kinase inhibitor is selected from a phosphoinositide 3-kinase (PI3K) inhibitor, a Bruton’s tyrosine kinase (BTK) inhibitor, or a spleen tyrosine kinase (Syk) inhibitor, or a combination thereof.
Examples of PI3 kinase inhibitors include, but are not limited to, Wortmannin, demethoxyviridin, perifosine, idelalisib, Pictilisib , Palomid 529, ZSTK474, PWT33597, CUDC- 907, and AEZS-136, duvelisib, GS-9820, BKM120, GDC-0032 (Taselisib) (2-[4-[2-(2-Isopropyl- 5-methyl-l,2,4-triazol-3-yl)-5,6-dihydroimidazo[l,2-d][l,4]benzoxazepin-9-yl]pyrazol-l-yl]-2- methylpropanamide), MLN-1117 ((2R)-l-Phenoxy-2-butanyl hydrogen (S)-methylphosphonate; or Methyl (oxo) {[(2R)-l-phenoxy-2-butanyl]oxy}phosphonium)), BYL-719 ((2S)-Nl-[4-Methyl- 5-[2-(2,2,2-trifluoro-l,l-dimethylethyl)-4-pyridinyl]-2-thiazolyl]-l,2-pyrrolidinedicarboxamide), GSK2126458 (2,4-Difluoro-N-{2-(methyloxy)-5-[4-(4-pyridazinyl)-6-quinolinyl]-3- pyridinyl}benzenesulfonamide) (omipalisib), TGX-221 ((±)-7-Methyl-2-(morpholin-4-yl)-9-(l- phenylaminoethyl)-pyrido[l,2-a]-pyrimidin-4-one), GSK2636771 (2-Methyl-l-(2-methyl-3- (trifluoromethyl)benzyl)-6-morpholino-lH-benzo[d]imidazole-4-carboxylic acid dihydrochloride), KIN- 193 ((R)-2-((l-(7-methyl-2-morpholino-4-oxo-4H-pyrido[ 1 ,2-a]pyrimidin- 9-yl)ethyl)amino)benzoic acid), TGR-1202/RP5264, GS-9820 ((S)- l-(4-((2-(2-aminopyrimidin- 5-yl)-7-methyl-4-mohydroxypropan- 1 -one), GS-1101 (5-fluoro-3-phenyl-2-([S)]-l-[9H-purin-6- ylamino]-propyl)-3H-quinazolin-4-one), AMG-319, GSK-2269557, SAR245409 (N-(4-(N-(3- ((3,5-dimethoxyphenyl)amino)quinoxalin-2-yl)sulfamoyl)phenyl)-3-methoxy-4 methylbenzamide), BAY80-6946 (2-amino-N-(7-methoxy-8-(3-morpholinopropoxy)-2,3- dihydroimidazo[l,2-c]quinaz), AS 252424 (5-[l-[5-(4-Fluoro-2-hydroxy-phenyl)-furan-2-yl]- meth-(Z)-ylidene]-thiazolidine-2, 4-dione), CZ 24832 (5-(2-amino-8-fluoro-[l,2,4]triazolo[l,5- a]pyridin-6-yl)-N-tert-butylpyridine-3-sulfonamide), Buparlisib (5-[2,6-Di(4-morpholinyl)-4- pyrimidinyl]-4-(trifluoromethyl)-2-pyridinamine), GDC-0941 (2-(lH-Indazol-4-yl)-6-[[4-
(methylsulfonyl)-l-piperazinyl]methyl]-4-(4-morpholinyl)thieno[3,2-d]pyrimidine), GDC-0980 ((S)-l-(4-((2-(2-aminopyrimidin-5-yl)-7-methyl-4-morpholinothieno[3,2-d]pyrimidin-6 yl)methyl)piperazin-l-yl)-2-hydroxypropan-l-one (also known as RG7422)), SF1126
((8S,14S,17S)-14-(carboxymethyl)-8-(3-guanidinopropyl)-17-(hydroxymethyl)-3,6,9,12,15- pentaoxo- 1 -(4-(4-oxo-8-phenyl-4H-chromen-2-yl)morpholino-4-ium)-2-oxa-7, 10,13,16- tetraazaoctadecan- 18-oate), PF-05212384 (N-[4-[[4-(Dimethylamino)-l- piperidinyl]carbonyl]phenyl]-N'-[4-(4,6-di-4-morpholinyl-l,3,5-triazin-2-yl)phenyl]urea) (gedatolisib), LY3023414, BEZ235 (2-Methyl-2-{4-[3-methyl-2-oxo-8-(quinolin-3-yl)-2,3- dihydro-lH-imidazo[4,5-c]quinolin-l-yl]phenyl}propanenitrile) (dactolisib), XL-765 (N-(3-(N-(3- (3,5-dimethoxyphenylamino)quinoxalin-2-yl)sulfamoyl)phenyl)-3-methoxy-4- methylbenzamide), and GSK1059615 (5-[[4-(4-Pyridinyl)-6-quinolinyl]methylene]-2,4- thiazolidenedione), PX886 ([(3aR,6E,9S,9aR,10R,l laS)-6-[[bis(prop-2- enyl)amino]methylidene]-5-hydroxy-9-(methoxymethyl)-9a,l la-dimethyl-l,4,7-trioxo- 2,3,3a,9,10,ll-hexahydroindeno[4,5h]isochromen- 10-yl] acetate (also known as sonolisib)), LY294002, AZD8186, PF-4989216, pilaralisib, GNE-317, PI-3065, PI-103, NU7441 (KU- 57788), HS 173, VS-5584 (SB2343), CZC24832, TG100-115, A66, YM201636, CAY10505, PIK- 75, PIK-93, AS-605240, BGT226 (NVP-BGT226), AZD6482, voxtalisib, alpelisib, IC-87114, TGI100713, CH5132799, PKI402, copanlisib (BAY 80-6946), XL 147, PIK-90, PIK-293, PIK- 294, 3-MA (3 -methyladenine), AS-252424, AS-604850, apitolisib (GDC-0980; RG7422).
Examples of BTK inhibitors include ibrutinib (also known as PCI-32765)(Imbruvica™)(l- [(3R)-3-[4-amino-3-(4-phenoxy-phenyl)pyrazolo[3,4-d]pyrimidin-l-yl]piperidin-l-yl]prop-2-en-
1-one), dianilinopyrimidine-based inhibitors such as AVL-101 and AVL-291/292 (N-(3-((5- fluoro-2-((4-(2-methoxyethoxy)phenyl)amino)pyrimidin-4-yl)amino)phenyl)acrylamide) (Avila Therapeutics) (see US Patent Publication No 2011/0117073, incorporated herein in its entirety), Dasatinib ([N-(2-chloro-6-methylphenyl)-2-(6-(4-(2-hydroxyethyl)piperazin- 1 -yl)-2- methylpyrimidin-4-ylamino)thiazole-5-carboxamide], LFM-A13 (alpha-cyano-beta-hydroxy - beta-methyl-N-(2,5-ibromophenyl) propenamide), GDC-0834 ([R-N-(3-(6-(4-(l,4-dimethyl-3- oxopiperazin-2-yl)phenylamino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl)-2-methylphenyl)- 4,5,6,7-tetrahydrobenzo[b]thiophene-2-carboxamide], CGI-560 4-(tert-butyl)-N-(3-(8-
(phenylamino)imidazo[ 1 ,2-a]pyrazin-6-yl)phenyl)benzamide, CGI- 1746 (4-(tert-butyl)-N-(2- methyl-3-(4-methyl-6-((4-(morpholine-4-carbonyl)phenyl)amino)-5-oxo-4,5-dihydropyrazin-2- yl)phenyl)benzamide), CNX-774 (4-(4-((4-((3-acrylamidophenyl)amino)-5-fluoropyrimidin-2- yl)amino)phenoxy)-N-methylpicolinamide), CTA056 (7-benzyl-l-(3-(piperidin-l-yl)propyl)-2- (4-(pyridin-4-yl)phenyl)-lH-imidazo[4,5-g]quinoxalin-6(5H)-one), GDC-0834 ((R)-N-(3-(6-((4- (l,4-dimethyl-3-oxopiperazin-2-yl)phenyl)amino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl)-2- methylphenyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-2-carboxamide), GDC-0837 ((R)-N-(3-(6- ((4-(l,4-dimethyl-3-oxopiperazin-2-yl)phenyl)amino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl)-
2-methylphenyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-2-carboxamide), HM-71224, ACP-196, ONO-4059 (Ono Pharmaceuticals), PRT062607 (4-((3-(2H- 1,2,3 -triazol-2-yl)phenyl)amino)-2- (((lR,2S)-2-aminocyclohexyl)amino)pyrimidine-5-carboxamide hydrochloride), QL-47 (1-(1- acryloylindolin-6-yl)-9-(l -methyl- lH-pyrazol-4-yl)benzo[h][l,6]naphthyridin-2(lH)-one), and RN486 (6-cyclopropyl-8-fluoro-2-(2-hydroxymethyl-3-{l-methyl-5-[5-(4-methyl-piperazin-l- yl)-pyridin-2-ylamino]-6-oxo-l,6-dihydro-pyridin-3-yl}-phenyl)-2H-isoquinolin-l-one), and other molecules capable of inhibiting BTK activity, for example those BTK inhibitors disclosed in Akinleye et ah, Journal of Hematology & Oncology, 2013, 6:59, the entirety of which is incorporated herein by reference. Syk inhibitors include, but are not limited to, Cerdulatinib (4-(cyclopropylamino)-2-((4- (4-(ethylsulfonyl)piperazin-l-yl)phenyl)amino)pyrimidine-5-carboxamide), entospletinib (6-(lH- indazol-6-yl)-N-(4-morpholinophenyl)imidazo[l,2-a]pyrazin-8-amine), fostamatinib ([6-({5- Fluoro-2-[(3,4,5-trimethoxyphenyl)amino]-4-pyrimidinyl}amino)-2,2-dimethyl-3-oxo-2,3- dihydro-4H-pyrido[3,2-b][l,4]oxazin-4-yl]methyl dihydrogen phosphate), fostamatinib disodium salt (sodium (6-((5-fluoro-2-((3,4,5-trimethoxyphenyl)amino)pyrimidin-4-yl)amino)-2,2- dimethyl-3-oxo-2H-pyrido[3,2-b][l,4]oxazin-4(3H)-yl)methyl phosphate), BAY 61-3606 (2-(7- (3,4-Dimethoxyphenyl)-imidazo[l,2-c]pyrimidin-5-ylamino)-nicotinamide HC1), RO9021 (6- [(lR,2S)-2-Amino-cy cl ohexylamino]-4-(5,6-dimethyl-pyri din-2 -ylamino)-pyridazine-3- carboxylic acid amide), imatinib (Gleevac; 4-[(4-methylpiperazin-l-yl)methyl]-N-(4-methyl-3- {[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide), staurosporine, GSK143 (2- (((3R,4R)-3-aminotetrahydro-2H-pyran-4-yl)amino)-4-(p-tolylamino)pyrimidine-5- carboxamide), PP2 (l-(tert-butyl)-3-(4-chlorophenyl)-lH-pyrazolo[3,4-d]pyrimidin-4-amine), PRT-060318 (2-(((lR,2S)-2-aminocyclohexyl)amino)-4-(m-tolylamino)pyrimidine-5- carboxamide), PRT-062607 (4-((3-(2H-l,2,3-triazol-2-yl)phenyl)amino)-2-(((lR,2S)-2- aminocyclohexyl)amino)pyrimidine-5-carboxamide hydrochloride), R112 (3,3'-((5- fluoropyrimidine-2,4-diyl)bis(azanediyl))diphenol), R348 (3-Ethyl-4-methylpyridine), R406 (6- ((5-fluoro-2-((3,4,5-trimethoxyphenyl)amino)pyrimidin-4-yl)amino)-2,2-dimethyl-2H- pyrido[3,2-b][l,4]oxazin-3(4H)-one), piceatannol (3-Hydroxyresveratol), YM193306 (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643), 7-azaindole, piceatannol, ER-27319 (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), Compound D (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), PRT060318 (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), luteolin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), apigenin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), quercetin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), fisetin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), myricetin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein), morin (see Singh et al. Discovery and Development of Spleen Tyrosine Kinase (SYK) Inhibitors, J. Med. Chem. 2012, 55, 3614-3643 incorporated in its entirety herein).
In one embodiment, the bioactive agent is a MEK inhibitor. MEK inhibitors are well known, and include, for example, trametinib/GSK1120212 (N-(3-{3-Cyclopropyl-5-[(2-fluoro-4- iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin-l(2H- yl}phenyl)acetamide), selumetinib (6-(4-bromo-2-chloroanilino)-7-fluoro-N-(2 -hydroxy ethoxy)- 3-methylbenzimidazole-5-carboxamide), pimasertib/AS703026/MSC 1935369 ((S)-N-(2,3- dihydroxypropyl)-3-((2-fluoro-4- iodophenyl)amino)isonicotinamide), XL-518/GDC-0973 (1- ({3,4-difluoro-2-[(2-fluoro-4- iodophenyl)amino]phenyl}carbonyl)-3-[(2S)-piperidin-2- yl]azetidin-3-ol), refametinib/BAY869766/RDEAl 19 (N-(3,4-difluoro-2-(2-fluoro-4- iodophenylamino)-6-m ethoxyphenyl)- 1 -(2,3 -dihydroxypropyl)cyclopropane- 1 -sulfonamide), PD-0325901 (N- [(2R)-2, 3 -Dihy droxypropoxy ] -3 ,4-difluoro-2- [(2-fluoro-4-iodophenyl)amino] - benzamide), TAK733 ((R)-3-(2,3-Dihydroxypropyl)-6-fluoro-5-(2-fluoro-4-iodophenylamino)-8- methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione), MEK162/ARRY438162 (5-[(4-Bromo-2- fluorophenyl)amino]-4-fluoro-N-(2- hy droxy ethoxy)- 1 -methyl- lH-benzimidazole-6- carboxamide), R05126766 (3-[[3-Fluoro-2- (methylsulfamoylamino)-4-pyridyl]methyl]-4- methyl-7-pyrimidin-2-yloxychromen-2-one), WX-554, R04987655/CH4987655 (3,4-difluoro-2- ((2-fluoro-4-iodophenyl)amino)-N-(2-hydroxyethoxy)-5-((3-oxo-l,2-oxazinan- 2yl)methyl)benzamide), or AZD8330 (2-((2-fluoro-4-iodophenyl)amino)-N-(2 hy droxy ethoxy)- 1 ,5-dimethyl-6-oxo-l,6-dihydropyridine-3-carboxamide), U0126-EtOH, PD184352 (CI-1040), GDC-0623, BI-847325, cobimetinib, PD98059, BIX 02189, BIX 02188, binimetinib, SL-327, TAK-733, PD318088.
In one embodiment, the bioactive agent is a Raf inhibitor. Raf inhibitors are known and include, for example, Vemurafinib (N-[3-[[5-(4-Chlorophenyl)-lH-pyrrolo[2,3-b]pyridin-3- yl]carbonyl]-2,4-difluorophenyl]-l -propanesulfonamide), sorafenib tosylate (4-[4-[[4-chloro-3- (trifluoromethyl)phenyl]carbamoylamino]phenoxy]-N-methylpyridine-2-carboxamide;4- m ethylbenzenesulfonate), AZ628 (3-(2-cyanopropan-2-yl)-N-(4-methyl-3-(3-methyl-4-oxo-3,4- dihydroquinazolin-6-ylamino)phenyl)benzamide), NVP-BHG712 (4-methyl-3-(l-methyl-6- (pyridin-3-yl)-lH-pyrazolo[3,4-d]pyrimidin-4-ylamino)-N-(3-
(trifluoromethyl)phenyl)benzamide), RAF-265 (l-methyl-5-[2-[5-(trifluoromethyl)-lH-imidazol-
2-yl]pyridin-4-yl]oxy-N-[4-(trifluoromethyl)phenyl]benzimidazol-2-amine), 2 -Bromoal disine (2-Bromo-6,7-dihydro-lH,5H-pyrrolo[2,3-c]azepine-4, 8-dione), Raf Kinase Inhibitor IV (2- chloro-5-(2-phenyl-5-(pyridin-4-yl)-lH-imidazol-4-yl)phenol), Sorafenib N-Oxide (4-[4-[[[[4- Chloro-3(trifluoroMethyl)phenyl]aMino]carbonyl]aMino]phenoxy]-N-Methyl-
2pyridinecarboxaMide 1 -Oxide), PLX-4720, dabrafenib (GSK2118436), GDC-0879, RAF265, AZ 628, SB590885, ZM336372, GW5074, TAK-632, CEP-32496, LY3009120, and GX818 (Encorafenib).
In one embodiment, the bioactive agent is an AKT inhibitor, including, but not limited to, MK-2206, GSK690693, Perifosine, (KRX-0401), GDC-0068, Triciribine, AZD5363, Honokiol, PF-04691502, and Miltefosine, a FLT-3 inhibitor, including, but not limited to, P406, Dovitinib, Quizartinib (AC220), Amuvatinib (MP-470), Tandutinib (MLN518), ENMD-2076, and KW- 2449, or a combination thereof.
In one embodiment, the bioactive agent is an mTOR inhibitor. Examples of mTOR inhibitors include, but are not limited to, rapamycin and its analogs, everolimus (Afinitor), temsirolimus, ridaforolimus, sirolimus, and deforolimus. Examples of MEK inhibitors include but are not limited to tametinib/GSK1120212 (N-(3-{3-Cyclopropyl-5-[(2-fluoro-4- iodophenyl)amino]-6,8-dimethyl-2,4,7-trioxo-3,4,6,7-tetrahydropyrido[4,3-d]pyrimidin-l(2H- yl}phenyl)acetamide), selumetinob (6-(4-bromo-2-chl oroanilino)-7-fluoro-N-(2 -hydroxy ethoxy)-
3-methylbenzimidazole-5-carboxamide), pimasertib/AS703026/MSC 1935369 ((S)-N-(2,3- dihydroxypropyl)-3-((2-fluoro-4-iodophenyl)amino)isonicotinamide), XL-518/GDC-0973 (1- ({3,4-difluoro-2-[(2-fluoro-4- iodophenyl)amino]phenyl}carbonyl)-3-[(2S)-piperidin-2- yl]azetidin-3-ol) (cobimetinib), refametinib/BAY869766/RDEA119 (N-(3,4-difluoro-2-(2-fluoro-
4-iodophenylamino)-6-methoxyphenyl)-l-(2,3-dihydroxypropyl)cyclopropane-l-sulfonamide), PD-0325901 (N- [(2R)-2, 3 -Dihy droxypropoxy ] -3 ,4-difluoro-2- [(2-fluoro-4-iodophenyl)amino] - benzamide), TAK733 ((R)-3-(2,3-Dihydroxypropyl)-6-fluoro-5-(2-fluoro-4-iodophenylamino)-8- methylpyrido[2,3d]pyrimidine-4,7(3H,8H)-dione), MEK162/ARRY438162 (5-[(4-Bromo-2- fluorophenyl)amino]-4-fluoro-N-(2-hydroxyethoxy)-l-methyl-lH-benzimidazole-6 carboxamide), R05126766 (3-[[3-Fluoro-2-(methylsulfamoylamino)-4-pyridyl]methyl]-4- methyl-7-pyrimidin-2-yloxychromen-2-one), WX-554, R04987655/CH4987655 (3,4-difluoro-2- ((2-fluoro-4-iodophenyl)amino)-N-(2-hydroxyethoxy)-5-((3-oxo-l,2-oxazinan-2 yl)methyl)benzamide), or AZD8330 (2-((2-fluoro-4-iodophenyl)amino)-N-(2-hydroxyethoxy)- l,5-dimethyl-6-oxo-l,6-dihydropyridine-3-carboxamide).
In one embodiment, the bioactive agent is a RAS inhibitor. Examples of RAS inhibitors include but are not limited to Reolysin and siG12D LODER.
In one embodiment, the bioactive agent is a HSP inhibitor. HSP inhibitors include but are not limited to Geldanamycin or 17-N-Allylamino-17-demethoxygeldanamycin (17AAG), and Radicicol.
Additional bioactive compounds include, for example, everolimus, trabectedin, abraxane, TLK 286, AV-299, DN-101, pazopanib, GSK690693, RTA 744, ON O91O.Na, AZD 6244 (ARRY- 142886), AMN-107, TKL258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197, MK- 0457, MLN8054, PHA-739358, R-763, AT-9263, aFLT-3 inhibitor, a VEGFR inhibitor, an aurora kinase inhibitor, a PIK-1 modulator, an HD AC inhbitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a focal adhesion kinase inhibitor, a Map kinase kinase (mek) inhibitor, a VEGF trap antibody, pemetrexed, panitumumab, amrubicin, oregovomab, Lep-etu, nolatrexed, azd2171, batabulin, of atumumab, zanolimumab, edotecarin, tetrandrine, rubitecan, tesmilifene, oblimersen, ticilimumab, ipilimumab, gossypol, Bio 111, 131- I-TM-601, ALT-110, BIO 140, CC 8490, cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdRi KRX-0402, lucanthone, LY317615, neuradiab, vitespan, Rta 744, Sdx 102, talampanel, atrasentan, Xr 311, romidepsin, ADS-100380, sunitinib, 5-fluorouracil, vorinostat, etoposide, gemcitabine, doxorubicin, liposomal doxorubicin, 5'-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709, seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid, N- [4-[2-(2-amino-4,7-dihydro-4-oxo-lH-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt, heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen, toremifene citrate, anastrazole, exemestane, letrozole, DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen, bevacizumab, IMC-1C11, CHIR-258); 3-[5-(methylsulfonylpiperadinemethyl)-indolyl- quinolone, vatalanib, AG-013736, AVE-0005, goserelin acetate, leuprolide acetate, triptorelin pamoate, medroxyprogesterone acetate, hydroxyprogesterone caproate, megestrol acetate, raloxifene, bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714; TAK-165, HKI- 272, erlotinib, lapatanib, canertinib, ABX-EGF antibody, erbitux, EKB-569, PKL166, GW- 572016, lonafarnib, BMS-214662, tipifarnib; amifostine, NVP-LAQ824, suberoyl analide hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, adriamycin, bleomycin, buserelin, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine, clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, diethylstilbestrol, epirubicin, fludarabine, fludrocortisone, fluoxymesterone, flutamide, gleevec, gemcitabine, hydroxyurea, idarubicin, ifosfamide, imatinib, leuprolide, levamisole, lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna, methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin, porfimer, procarbazine, raltitrexed, rituximab, streptozocin, teniposide, testosterone, thalidomide, thioguanine, thiotepa, tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard, uracil mustard, estramustine, altretamine, floxuridine, 5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine, deoxycoformycin, calcitriol, valrubicin, mithramycin, vinblastine, vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat, BMS-275291, squalamine, endostatin, SU5416, SU6668, EMD121974, interleukin- 12, IM862, angiostatin, vitaxin, droloxifene, idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab, denileukin diftitox, gefitinib, bortezimib, paclitaxel, cremophor-free paclitaxel, docetaxel, epithilone B, BMS-247550, BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339, ZK186619, topotecan, PTK787/ZK 222584, VX-745, PD 184352, rapamycin, 40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001, ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646, wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin, erythropoietin, granulocyte colony-stimulating factor, zolendronate, prednisone, cetuximab, granulocyte macrophage colony-stimulating factor, histrelin, pegylated interferon alfa-2a, interferon alfa-2a, pegylated interferon alfa-2b, interferon alfa-2b, azacitidine, PEG-L- asparaginase, lenalidomide, gemtuzumab, hydrocortisone, interleukin-11, dexrazoxane, alemtuzumab, all-transretinoic acid, ketoconazole, interleukin-2, megestrol, immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene, tositumomab, arsenic trioxide, cortisone, editronate, mitotane, cyclosporine, liposomal daunorubicin, Edwina-asparaginase, strontium 89, casopitant, netupitant, an NK-1 receptor antagonist, palonosetron, aprepitant, diphenhydramine, hydroxyzine, metoclopramide, lorazepam, alprazolam, haloperidol, droperidol, dronabinol, dexamethasone, methylprednisolone, prochlorperazine, granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim, erythropoietin, epoetin alfa, darbepoetin alfa and mixtures thereof.
In certain embodiments the compounds are administered in combination with ifosfamide.
In one embodiment, the bioactive agent is selected from, but are not limited to, Imatinib mesylate (Gleevac®), Dasatinib (Sprycel®), Nilotinib (Tasigna®), Bosutinib (Bosulif®), Trastuzumab (Herceptin®), trastuzumab-DMl, Pertuzumab (PerjetaTM), Lapatinib (Tykerb®), Gefitinib (Iressa®), Erlotinib (Tarceva®), Cetuximab (Erbitux®), Panitumumab (Vectibix®), Vandetanib (Caprelsa®), Vemurafenib (Zelboraf®), Vorinostat (Zolinza®), Romidepsin (Istodax®), Bexarotene (Tagretin®), Alitretinoin (Panretin®), Tretinoin (Vesanoid®), Carfilizomib (KyprolisTM), Pralatrexate (Folotyn®), Bevacizumab (Avastin®), Ziv-afhbercept (Zaltrap®), Sorafenib (Nexavar®), Sunitinib (Sutent®), Pazopanib (Votrient®), Regorafenib (Stivarga®), and Cabozantinib (CometriqTM).
In certain aspects, the bioactive agent is an anti-inflammatory agent, a chemotherapeutic agent, a radiotherapeutic, an additional therapeutic agent, or an immunosuppressive agent.
Suitable chemotherapeutic bioactive agents include, but are not limited to, a radioactive molecule, a toxin, also referred to as cytotoxin or cytotoxic agent, which includes any agent that is detrimental to the viability of cells, and liposomes or other vesicles containing chemotherapeutic compounds. General anticancer pharmaceutical agents include: Vincristine (Oncovin®) or liposomal vincristine (Marqibo®), Daunorubicin (daunomycin or Cerubidine®) or doxorubicin (Adriamycin®), Cytarabine (cytosine arabinoside, ara-C, or Cytosar®), L-asparaginase (Elspar®) or PEG-L-asparaginase (pegaspargase or Oncaspar®), Etoposide (VP-16), Teniposide (Vumon®), 6-mercaptopurine (6-MP or Purinethol®), Methotrexate, Cyclophosphamide (Cytoxan®), Prednisone, Dexamethasone (Decadron), imatinib (Gleevec®), dasatinib (Sprycel®), nilotinib (Tasigna®), bosutinib (Bosulif®), and ponatinib (Iclusig™).
Examples of additional suitable chemotherapeutic agents include, but are not limited to 1- dehydrotestosterone, 5 -fluorouracil decarbazine, 6-mercaptopurine, 6-thioguanine, actinomycin D, adriamycin, aldesleukin, an alkylating agent, allopurinol sodium, altretamine, amifostine, anastrozole, anthramycin (AMC)), an anti-mitotic agent, cis-dichlorodiamine platinum (II) (DDP) cisplatin), diamino dichloro platinum, anthracycline, an antibiotic, an antimetabolite, asparaginase, BCG live (intravesical), betamethasone sodium phosphate and betamethasone acetate, bicalutamide, bleomycin sulfate, busulfan, calcium leucouorin, calicheamicin, capecitabine, carboplatin, lomustine (CCNU), carmustine (BSNU), Chlorambucil, Cisplatin, Cladribine, Colchicin, conjugated estrogens, Cyclophosphamide, Cyclothosphamide, Cytarabine, Cytarabine, cytochalasin B, Cytoxan, Dacarbazine, Dactinomycin, dactinomycin (formerly actinomycin), daunirubicin HCL, daunorucbicin citrate, denileukin diftitox, Dexrazoxane, Dibromomannitol, dihydroxy anthracin dione, Docetaxel, dolasetron mesylate, doxorubicin HCL, dronabinol, E. coll L-asparaginase, emetine, epoetin-a, Erwinia L-asparaginase, esterified estrogens, estradiol, estramustine phosphate sodium, ethidium bromide, ethinyl estradiol, etidronate, etoposide citrororum factor, etoposide phosphate, filgrastim, floxuridine, fluconazole, fludarabine phosphate, fluorouracil, flutamide, folinic acid, gemcitabine HCL, glucocorticoids, goserelin acetate, gramicidin D, granisetron HCL, hydroxyurea, idarubicin HCL, ifosfamide, interferon a- 2b, irinotecan HCL, letrozole, leucovorin calcium, leuprolide acetate, levamisole HCL, lidocaine, lomustine, maytansinoid, mechlorethamine HCL, medroxyprogesterone acetate, megestrol acetate, melphalan HCL, mercaptipurine, mesna, methotrexate, methyltestosterone, mithramycin, mitomycin C, mitotane, mitoxantrone, nilutamide, octreotide acetate, ondansetron HCL, paclitaxel, pamidronate disodium, pentostatin, pilocarpine HCL, plimycin, polifeprosan 20 with carmustine implant, porfimer sodium, procaine, procarbazine HCL, propranolol, rituximab, sargramostim, streptozotocin, tamoxifen, taxol, teniposide, tenoposide, testolactone, tetracaine, thioepa chlorambucil, thioguanine, thiotepa, topotecan HCL, toremifene citrate, trastuzumab, tretinoin, valrubicin, vinblastine sulfate, vincristine sulfate, and vinorelbine tartrate.
In some embodiments, the compounds of the present invention are administered in combination with a chemotherapeutic agent (e.g., a cytotoxic agent or other chemical compound useful in the treatment of cancer). Examples of chemotherapeutic agents include alkylating agents, antimetabolites, folic acid analogs, pyrimidine analogs, purine analogs and related inhibitors, vinca alkaloids, epipodopyyllotoxins, antibiotics, L-Asparaginase, topoisomerase inhibitors, interferons, platinum coordination complexes, anthracenedione substituted urea, methyl hydrazine derivatives, adrenocortical suppressant, adrenocorticosteroides, progestins, estrogens, antiestrogen, androgens, antiandrogen, and gonadotropin-releasing hormone analog. Also included is 5 -fluorouracil (5-FU), leucovorin (LV), irenotecan, oxaliplatin, capecitabine, paclitaxel, and doxetaxel. Non-limiting examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; cally statin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1 ); eleutherobin; pancrati statin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall (see, e.g., Agnew, Chem. Inti. Ed Engl. 33: 183- 186 (1994)); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo- 5-oxo-L-norleucine, ADRIAMYCIN® (doxorubicin, including morpholino-doxorubicin, cyanomorpholino- doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5 -fluorouracil (5- FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6- mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6- azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, OR); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2',2"-trichlorotriethylamine; trichothecenes (especially T- 2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (" Ara- C"); cyclophosphamide; thiotepa; taxoids, e.g., TAXOL® (paclitaxel; Bristol-Myers Squibb Oncology, Princeton, NJ), ABRAXANE®, cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, IL), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil; GEMZAR® gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP- 16); ifosfamide; mitoxantrone; vincristine; NAVELBINE® vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-1 1 ); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. Two or more chemotherapeutic agents can be used in a cocktail to be administered in combination with the compounds of the present invention. Suitable dosing regimens of combination chemotherapies are known in the ar. For example combination dosing regimes are described in Saltz et al., Proc. Am. Soc. Clin. Oncol. 18:233a (1999) and Douillard et al., Lancet 355(9209): 1041 -1047 (2000).
Additional therapeutic agents that can be administered in combination with a Compound disclosed herein can include bevacizumab, sutinib, sorafenib, 2-methoxyestradiol or 2ME2, finasunate, vatalanib, vandetanib, aflibercept, volociximab, etaracizumab (MEDL522), cilengitide, erlotinib, cetuximab, panitumumab, gefitinib, trastuzumab, dovitinib, figitumumab, atacicept, rituximab, alemtuzumab, aldesleukine, atlizumab, tocilizumab, temsirolimus, everolimus, lucatumumab, dacetuzumab, HLL1, huN901-DMl, atiprimod, natalizumab, bortezomib, carfilzomib, marizomib, tanespimycin, saquinavir mesylate, ritonavir, nelfinavir mesylate, indinavir sulfate, belinostat, panobinostat, mapatumumab, lexatumumab, dulanermin, ABT-737, oblimersen, plitidepsin, talmapimod, P276-00, enzastaurin, tipifamib, perifosine, imatinib, dasatinib, lenalidomide, thalidomide, simvastatin, celecoxib, bazedoxifene, AZD4547, rilotumumab, oxaliplatin (Eloxatin), PD0332991, ribociclib (LEE011), amebaciclib (LY2835219), HDM201, fulvestrant (Faslodex), exemestane (Aromasin), PIM447, ruxolitinib (INC424), BGJ398, necitumumab, pemetrexed (Alimta), and ramucirumab (IMC-1121B).
In one embodiment, the additional therapy is a monoclonal antibody (MAb). Some MAbs stimulate an immune response that destroys cancer cells. Similar to the antibodies produced naturally by B cells, these MAbs may “coat” the cancer cell surface, triggering its destruction by the immune system. For example, bevacizumab targets vascular endothelial growth factor (VEGF), a protein secreted by tumor cells and other cells in the tumor’s microenvironment that promotes the development of tumor blood vessels. When bound to bevacizumab, VEGF cannot interact with its cellular receptor, preventing the signaling that leads to the growth of new blood vessels. Similarly, cetuximab and panitumumab target the epidermal growth factor receptor (EGFR), and trastuzumab targets the human epidermal growth factor receptor 2 (HER-2). MAbs that bind to cell surface growth factor receptors prevent the targeted receptors from sending their normal growth-promoting signals. They may also trigger apoptosis and activate the immune system to destroy tumor cells.
In one aspect of the present invention, the bioactive agent is an immunosuppressive agent. The immunosuppressive agent can be a calcineurin inhibitor, e.g. a cyclosporin or an ascomycin, e.g. Cyclosporin A (NEORAL®), FK506 (tacrolimus), pimecrolimus, a mTOR inhibitor, e.g. rapamycin or a derivative thereof, e.g. Sirolimus (RAPAMUNE®), Everolimus (Certican®), temsirolimus, zotarolimus, biolimus-7, biolimus-9, a rapalog, e.g.ridaforolimus, azathioprine, campath 1H, a SIP receptor modulator, e.g. fmgolimod or an analogue thereof, an anti IL-8 antibody, mycophenolic acid or a salt thereof, e.g. sodium salt, or a prodrug thereof, e.g. Mycophenolate Mofetil (CELLCEPT®), OKT3 (ORTHOCLONE OKT3®), Prednisone, ATGAM®, THYMOGLOBULIN®, Brequinar Sodium, OKT4, T10B9.A-3A, 33B3.1, 15- deoxyspergualin, tresperimus, Leflunomide ARAVA®, CTLALIg, anti-CD25, anti-IL2R, Basiliximab (SIMULECT®), Daclizumab (ZENAPAX®), mizorbine, methotrexate, dexamethasone, ISAtx-247, SDZ ASM 981 (pimecrolimus, Elidel®), CTLA41g (Abatacept), belatacept, LFA31g„ etanercept (sold as Enbrel® by Immunex), adalimumab (Humira®), infliximab (Remicade®), an anti-LFA-1 antibody, natalizumab (Antegren®), Enlimomab, gavilimomab, antithymocyte immunoglobulin, siplizumab, Alefacept efalizumab, pentasa, mesalazine, asacol, codeine phosphate, benorylate, fenbufen, naprosyn, diclofenac, etodolac and indomethacin, aspirin and ibuprofen.
In some embodiments, the bioactive agent is a therapeutic agent which is a biologic such a cytokine (e.g., interferon or an interleukin (e.g., IL-2)) used in cancer treatment. In some embodiments the biologic is an anti -angiogenic agent, such as an anti-VEGF agent, e.g., bevacizumab (AVASTIN®). In some embodiments the biologic is an immunoglobulin-based biologic, e.g., a monoclonal antibody (e.g., a humanized antibody, a fully human antibody, an Fc fusion protein or a functional fragment thereof) that agonizes a target to stimulate an anti-cancer response, or antagonizes an antigen important for cancer. Such agents include RITUXAN® (rituximab); ZENAPAX® (daclizumab); SIMULECT® (basiliximab); SYNAGIS® (palivizumab); REMICADE® (infliximab); HERCEPTIN® (trastuzumab); MYLOTARG® (gemtuzumab ozogamicin); CAMPATH® (alemtuzumab); ZEVALIN® (ibritumomab tiuxetan); HUMIRA® (adalimumab); XOLAIR® (omalizumab); BEXXAR® (tositumomab-1- 131 ); RAPTIVA® (efalizumab); ERBITUX® (cetuximab); AVASTIN® (bevacizumab); TYSABRI® (natalizumab); ACTEMRA® (tocilizumab); VECTIBIX® (panitumumab); LUCENTIS® (ranibizumab); SOURIS® (eculizumab); CIMZIA® (certolizumab pegol); SIMPONI® (golimumab); ILARIS® (canakinumab); STELARA® (ustekinumab); ARZERRA® (ofatumumab); PROLIA® (denosumab); NUMAX® (motavizumab); ABTHRAX® (raxibacumab); BENLYSTA® (belimumab); YERVOY® (ipilimumab); ADCETRIS® (brentuximab vedotin); PERJETA® (pertuzumab); KADCYLA® (ado- trastuzumab emtansine); and GAZYVA® (obinutuzumab). Also included are antibody-drug conjugates.
The combination therapy may include a therapeutic agent which is a non-drug treatment. For example, the compound could be administered in addition to radiation therapy, cryotherapy, hyperthermia, and/or surgical excision of tumor tissue.
X. Pharmaceutical Compositions and Dosage Forms
The compounds of the present invention assemble in vivo to afford an extracellular protein degrading compound.
In certain embodiments this in vivo assembly is advantageous as compared to making the degrader in vitro because the individual components may have better pharmacokinetic or physical properties than the full molecule.
A compound of the present invention or a pharmaceutically acceptable salt, solvate or prodrug thereof as disclosed herein can be administered as a neat chemical, but is more typically administered as a pharmaceutical composition that includes an effective amount for a host, typically a human, in need of such treatment to treat a disorder mediated by the target extracellular protein, as described herein or otherwise well-known for that extracellular protein.
The two compounds of the present invention that form the ASGPR-binding Extracellular Protein degrader of the present invention can be administered in any manner that allows the degrader to bind to the Extracellular Protein, typically in the blood stream, and carry it to the ASGPR-bearing hepatocyte cells on the liver for endocytosis and degradation. As such, examples of methods to deliver the degraders of the present invention include, but are not limited to, oral, intravenous, sublingual, subcutaneous, parenteral, buccal, rectal, intra-aortal, intracranial, subdermal or transnasal, or by other means, in dosage unit formulations containing one or more conventional pharmaceutically acceptable carriers, as appropriate. In certain embodiments, the compound of Formula VII is administered by a different route of administration from the compound of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, IV-d, V-d, Vl-d, or the bis or tris version.
Therefore, the disclosure provides pharmaceutical compositions comprising an effective amount of the compound of the present invention or its pharmaceutically acceptable salt together with at least one pharmaceutically acceptable carrier for any appropriate use thereof. The pharmaceutical composition may contain a compound or salt as the only active agent, or, in an alternative embodiment, the compound and at least one additional active agent.
The term "pharmaceutically acceptable salt" as used herein refers to a salt of the described compound which is, within the scope of sound medical judgment, suitable for administration to a host such as a human without undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for its intended use. Thus, the term "pharmaceutically acceptable salt" refers to the relatively non-toxic, inorganic and organic acid addition salts of the presently disclosed compounds. These salts can be prepared during the final isolation and purification of the compounds or by separately reacting the purified compound in its free form with a suitable organic or inorganic acid and then isolating the salt thus formed. Basic compounds are capable of forming a wide variety of different salts with various inorganic and organic acids. Acid addition salts of the basic compounds are prepared by contacting the free base form with a sufficient amount of the desired acid to produce the salt in the conventional manner. The free base form can be regenerated by contacting the salt form with a base and isolating the free base in the conventional manner. The free base forms may differ from their respective salt forms in certain physical properties such as solubility in polar solvents. Pharmaceutically acceptable base addition salts may be formed with metals or amines, such as alkali and alkaline earth metal hydroxides, or of organic amines. Examples of metals used as cations, include, but are not limited to, sodium, potassium, magnesium, calcium, and the like. Examples of suitable amines include, but are not limited to, N,N'-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, N-methylglucamine, and procaine. The base addition salts of acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner. The free acid form can be regenerated by contacting the salt form with an acid and isolating the free acid in a conventional manner. The free acid forms may differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents.
Salts can be prepared from inorganic acids sulfate, pyrosulfate, bisulfate, sulfite, bisulfite, nitrate, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, nitric, phosphoric, sulfuric, hydrobromic, hydriodic, phosphorus, and the like. Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfate, nitrate, acetate, oxalate, valerate, oleate, palmitate, stearate, laurate, borate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, naphthylate mesylate, glucoheptonate, lactobionate, laurylsulphonate and isethionate salts, and the like. Salts can also be prepared from organic acids, such as aliphatic mono- and dicarboxylic acids, phenyl -substituted alkanoic acids, hydroxy alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and aromatic sulfonic acids, etc. and the like. Representative salts include acetate, propionate, caprylate, isobutyrate, oxalate, malonate, succinate, suberate, sebacate, fumarate, maleate, mandelate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, phthalate, benzenesulfonate, toluenesulfonate, phenyl acetate, citrate, lactate, maleate, tartrate, methanesulfonate, and the like. Pharmaceutically acceptable salts can include cations based on the alkali and alkaline earth metals, such as sodium, lithium, potassium, calcium, magnesium and the like, as well as non-toxic ammonium, quaternary ammonium, and amine cations including, but not limited to, ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like. Also contemplated are the salts of amino acids such as arginate, gluconate, galacturonate, and the like. See, for example, Berge et al., J. Pharm. Sci., 1977, 66, 1-19, which is incorporated herein by reference.
In certain embodiments the pharmaceutical composition is in a dosage form that contains from about 0.1 mg to about 1500 mg, from about 10 mg to about 1000 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of the active compound and optionally from about 0.1 mg to about 1500 mg, from about 10 mg to about 1000 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of an additional active agent in a unit dosage form. Examples are dosage forms with at least 0.1, 1, 5, 10, 25, 50, 100, 200, 250, 300, 400, 500, 600, 700, or 750 mg of active compound, or its salt.
In certain embodiments the dose ranges from about 0.01-100 mg/kg of patient body weight, for example about 0.01 mg/kg, about 0.05 mg/kg, about 0.1 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, about 2.5 mg/kg, about 3 mg/kg, about 3.5 mg/kg, about 4 mg/kg, about 4.5 mg/kg, about 5 mg/kg, about 10 mg/kg, about 15 mg/kg, about 20 mg/kg, about 25 mg/kg, about 30 mg/kg, about 35 mg/kg, about 40 mg/kg, about 45 mg/kg, about 50 mg/kg, about 55 mg/kg, about 60 mg/kg, about 65 mg/kg, about 70 mg/kg, about 75 mg/kg, about 80 mg/kg, about 85 mg/kg, about 90 mg/kg, about 95 mg/kg, or about 100 mg/kg.
In some embodiments, compounds disclosed herein or used as described are administered once a day (QD), twice a day (BID), or three times a day (TID). In some embodiments, compounds disclosed herein or used as described are administered at least once a day for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, at least 8 days, at least 9 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days, at least 21 days, at least 22 days, at least 23 days, at least 24 days, at least 25 days, at least 26 days, at least 27 days, at least 28 days, at least 29 days, at least 30 days, at least 31 days, at least 35 days, at least 45 days, at least 60 days, at least 75 days, at least 90 days, at least 120 days, at least 150 days, at least 180 days, or longer.
In certain embodiments the compound of the present invention is administered once a day, twice a day, three times a day, or four times a day.
The pharmaceutical composition may be formulated as any pharmaceutically useful form, e.g., a pill, capsule, tablet, an injection or infusion solution, a syrup, an inhalation formulation, a suppository, a buccal or sublingual formulation, a parenteral formulation, or in a medical device. Some dosage forms, such as tablets and capsules, can be subdivided into suitably sized unit doses containing appropriate quantities of the active components, e.g., an effective amount to achieve the desired purpose.
Carriers include excipients and diluents and must be of sufficiently high purity and sufficiently low toxicity to render them suitable for administration to the patient being treated. The carrier can be inert or it can possess pharmaceutical benefits of its own. The amount of carrier employed in conjunction with the compound is sufficient to provide a practical quantity of material for administration per unit dose of the compound. If provided as in a liquid, it can be a solution or a suspension.
Representative carriers include phosphate buffered saline, water, solvent(s), diluents, pH modifying agents, preservatives, antioxidants, suspending agents, wetting agent, viscosity agents, tonicity agents, stabilizing agents, and combinations thereof. In some embodiments, the carrier is an aqueous carrier. Examples of aqueous carries include, but are not limited to, an aqueous solution or suspension, such as saline, plasma, bone marrow aspirate, buffers, such as Hank’ s Buffered Salt Solution (HBSS), HEPES (4-(2-hy droxy ethyl)- 1 -piperazineethanesulfonic acid), Ringers buffer, ProVisc®, diluted Pro Vise®, Proviso® diluted with PBS, Krebs buffer, Dulbecco’s PBS, normal PBS, sodium hyaluronate solution (HA, 5 mg/mL in PBS), citrate buffer, simulated body fluids, plasma platelet concentrate and tissue culture medium or an aqueous solution or suspension comprising an organic solvent. Acceptable solutions include, for example, water, Ringer’s solution and isotonic sodium chloride solutions. The formulation may also be a sterile solution, suspension, or emulsion in a non-toxic diluent or solvent such as 1,3 -butanediol.
Viscosity agents may be added to the pharmaceutical composition to increase the viscosity of the composition as desired. Examples of useful viscosity agents include, but are not limited to, hyaluronic acid, sodium hyaluronate, carbomers, polyacrylic acid, cellulosic derivatives, polycarbophil, polyvinylpyrrolidone, gelatin, dextin, polysaccharides, polyacrylamide, polyvinyl alcohol (including partially hydrolyzed polyvinyl acetate), polyvinyl acetate, derivatives thereof and mixtures thereof.
Solutions, suspensions, or emulsions for administration may be buffered with an effective amount necessary to maintain a pH suitable for the selected administration. Suitable buffers are well known by those skilled in the art. Some examples of useful buffers are acetate, borate, carbonate, citrate, and phosphate buffers. Solutions, suspensions, or emulsions for topical, for example, ocular administration may also contain one or more tonicity agents to adjust the isotonic range of the formulation. Suitable tonicity agents are well known in the art. Some examples include glycerin, mannitol, sorbitol, sodium chloride, and other electrolytes.
Classes of carriers include, but are not limited to binders, buffering agents, coloring agents, diluents, disintegrants, emulsifiers, flavorants, glidents, lubricants, preservatives, stabilizers, surfactants, tableting agents, and wetting agents. Some carriers may be listed in more than one class, for example vegetable oil may be used as a lubricant in some formulations and a diluent in others. Exemplary pharmaceutically acceptable carriers include sugars, starches, celluloses, powdered tragacanth, malt, gelatin; talc, and vegetable oils. Optional active agents may be included in a pharmaceutical composition, which do not substantially interfere with the activity of the compound of the present invention.
The pharmaceutical compositions/combinations can be formulated for oral administration. These compositions can contain any amount of active compound that achieves the desired result, for example between 0.1 and 99 weight % (wt.%) of the compound and usually at least about 5 wt.% of the compound. Some embodiments contain from about 25 wt.% to about 50 wt. % or from about 5 wt.% to about 75 wt.% of the compound. Enteric coated oral tablets may also be used to enhance bioavailability of the compounds for an oral route of administration.
Formulations suitable for rectal administration are typically presented as unit dose suppositories. These may be prepared by admixing the active compound with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture. Processes of Manufacture
The compounds of the present invention can be manufactured according to routes described in the Working Examples below or as otherwise known in the patent or scientific literature and if appropriate supported by the knowledge of the ordinary worker or common general knowledge.
Some of the carbons in the compounds described herein are drawn with designated stereochemistry. Other carbons are drawn without stereochemical designation. When drawn without designated stereochemistry, that carbon can be in any desired stereochemical configuration that achieves the desired purpose. One skilled in the art will recognize that pure enantiomers, enantiomerically enriched compounds, racemates and diastereomers can be prepared by methods known in the art as guided by the information provided herein. Examples of methods to obtain optically active materials include at least the following: i) chiral liquid chromatography - a technique whereby diastereomers are separated in a liquid mobile phase by virtue of their differing interactions with a stationary phase (including vial chiral HPLC). The stationary phase can be made of chiral material or the mobile phase can contain an additional chiral material to provoke the differing interactions; ii) non-chiral chromatography of diastereomers-Often diastereomers can be separated using normal non-chiral column conditions; iii) chiral gas chromatography - a technique whereby the racemate is volatilized and enantiomers are separated by virtue of their differing interactions in the gaseous mobile phase with a column containing a fixed non-racemic chiral adsorbent phase; iv) simultaneous crystallization - a technique whereby the individual diastereomers are separately crystallized from a solution; v) enzymatic resolutions - a technique whereby partial or complete separation of diastereomers are separated by virtue of differing rates of reaction with an enzyme; vi) chemical asymmetric synthesis - a synthetic technique whereby the desired diastereomer is synthesized from an achiral precursor under conditions that produce asymmetry (i.e. chirality) in the product, which may be achieved by chiral catalysts or chiral auxiliaries; vii) diastereomer separations - a technique whereby a racemic compound is reaction with an enantiomerically pure reagent (the chiral auxiliary) that converts the individual enantiomers to diastereomers. The resulting diastereomers are then separated by chromatography or crystallization by virtue of their now more distinct structural differences the chiral auxiliary later removed to obtain the desired enantiomer; and viii) extraction with chiral solvents - a technique whereby diastereomers are separated by virtue of preferential dissolution of one over the others in a particular chiral solvent.
General Procedures applied to the working examples of synthesis:
All reagents were purchased from commercial suppliers (Sigma-Aldrich, Alfa, Across etc.) and used without further purification unless otherwise stated. THF was continuously refluxed and freshly distilled from sodium and benzophenone under nitrogen, dichloromethane was continuously refluxed and freshly distilled from CaHz under nitrogen.
Reactions were monitored via TLC on silica gel 60 HSGF254 percolated plates (0.15-0.2 mm SiCh) and visualized using UV light (254 nm or 365 nm) and/or staining with phosphomolybdic acid ethanol solution (10 g in 100 mL ethanol) and subsequent heating or monitored via LCMS.
LCMS were performed on SHIMADZU LCMS-2010EV (Chromolith SpeedROD, RP-18e, 50x4.6 mm, mobile phase: Solvent A: CH3CN/H2O /HCOOH=10/90/0.05, Solvent B: CH3CN/H2O /HCOOH=90/10/0.05, 0.8min@ 10% B, 2.7min gradient (10-95% B), then 0.8min@95%B, Flow rate: 3mL/min, temperature: 40°C).
Preparative HPLC were performed either on Method A: SHIMADZU LC-8A (Column: YMC Pack ODS-A (150*30mm, 10pm)) or Method B: LC-6AD (Column: Shim=Pack PREP-ODS-H (250*20mm, 10pm)) with UV detection which were controlled by LC solution Chemstation software. H2O (0.1% HCOOH) and MeOH (MeCN) as mobile phase at the indicated flow rate.
Analytical HPLC were performed on SHIMADZU LC-2010A (Chromolith SpeedROD, RP-18e, 50×4.6 mm, mobile phase: Solvent A: CH3CN/H2O /HCOOH=10/90/0.05, Solvent B: CH3CN/H2O /HCOOH=90/10/0.05, 0.8min@ 10% B, 2.7min gradient (10-95% B), then 0.8min@95%B, Flow rate: 3mL/min, temperature: 40°C). Chiral HPLC were performed on SHIMADZU LC-2010A (Chiral column, mobile phase: Solvent A: hexane (or contained 0.1% diethylamine), Solvent B: Ethanol or Isopropanol; Flow rate: 0.8 mL/min, temperature: 30°C). 1H spectra were recorded on Bruker Avance II 400MHz, Chemical shifts (δ) were reported in ppm relative to tetramethylsilane (δ = 0.000 ppm) and the spectra were calibrated to the residual solvent signal of chloroform (δ = 7.26), Dimethyl sulfoxide (δ = 2.50), methanol (δ = 3.30). Data for 1H NMR spectra were reported as following: chemical shift (multiplicity, number of hydrogens). Abbreviations were described as following: s (singlet), d (doublet), t (triplet), q (quartet), quant (quintet), m (multiple), br (broad).
IV. Working Examples
Example 1. Synthesis of Compounds of Formula I, II, III, IV, V, VI and bi- and tri-versions thereof
Synthesis 1-1. Preparation of an exemplary compound of Formula III
Figure imgf000228_0001
Synthesis 1-2. Preparation of an exemplary compound of Formula III-Bi
Figure imgf000229_0001
Synthesis 1-3. Preparation of an exemplary compound of Formula III
Figure imgf000229_0002
Synthesis 1-4. Preparation of an exemplary compound of Formula III-Bi
Figure imgf000230_0001
Example 2. Synthesis of Compounds of Formula I-d, Il-d, Ill-d, IV-d, and bi- and tri-versions thereof Synthesis 2-1. Preparation of an exemplary compound of N-(l-((lS,2R,3R,4S,5S)-2,3- dihydroxy-4-(2,2,2-trifluoroacetamido)-6,8-dioxabicyclo[3.2.1]octan-l-yl)-2,5,8,ll- tetrao atridecan-13-yl)-3-(2-((3S,4R)-3,4-dihydro ypyrrolidin-l-yl)etho y)propanamide
Figure imgf000231_0001
Synthesis 2-2. Preparation of 3,3'-((2-((3S,4R)-3,4-dihydroxypyrrolidin-l-yl)propane-l,3- diyl)bis(oxy))bis(N-(l-((lS,2R,3R,4S,5S)-2,3-dihydroxy-4-(2,2,2-trifluoroacetamido)-6,8- dioxabicyclo[3.2.1]octan-l-yl)-2,5,8,ll-tetraoxatridecan-13-yl)propanamide)
Figure imgf000231_0002
Figure imgf000232_0001
Synthesis 2-3. Preparation of 2-amino-N-(l-((lS,2R,3R,4S,5S)-2,3-dihydroxy-4-(2,2,2- trifluoroacetamido)-6,8-dioxabicyclo[3.2.1]octan-l-yl)-15-oxo-2,5,8,ll,18-pentaoxa-14- azaicosan-20-yl)-3-mercaptopropanamide
Figure imgf000232_0002
Synthesis 2-4. Preparation of 3,3'-((2-(2-amino-3-mercaptopropanamido)propane-l,3- diyl)bis(oxy))bis(N-(l-((lS,2R,3R,4S,5S)-2,3-dihydroxy-4-(2,2,2-trifluoroacetamido)-6,8- dioxabicyclo[3.2.1]octan-l-yl)-2,5,8,ll-tetraoxatridecan-13-yl)propanamide)
Figure imgf000233_0001
Example 3. Synthesis of Compounds of Formula VII
Synthesis 3-1. General synthesis of exemplary boron containing selectivity moieties
Figure imgf000234_0001
Synthesis 3-2. General synthesis of exemplary cyano containing selectivity moieties
Figure imgf000234_0002
Compounds of Formula I, II, III, IV, V, VI, I-d, Il-d, Ill-d, and IV-d react with compounds of Formula VII in vivo to form an extracellular degrading compound. For example, the compounds
of Example 1 and 2 above can react with the compounds of Example 3 in the body to form the following non-limiting extracellular degrading compounds:
Figure imgf000235_0001
Figure imgf000236_0001
Example 4. Synthesis of Boc-protected and Bn-protected Intermediates
Synthesis 4-1. Preparation of tert-Butyl (((3aR,4S,8R,8aR)-8-amino-2,2- dimethyltetrahydro-4,7-epoxy[l,3]dioxolo[4,5-d]oxepin-4(5H)-yl)methyl)carbamate
(Intermediate 1)
Figure imgf000237_0001
Synthesis 4-2. Preparation of tert-Butyl (((3aS,4R,7R,7aR)-7-amino-6-hydroxy-2,2- dimethyltetr ahydro-4H- [1,3] dioxolo [4,5-c] pyran-4-yl)methyl)carbamate (Intermediate 2)
Figure imgf000237_0002
Synthesis 4-3: Preparation of (2R,3R,4R,5R,6R)-4,5-Bis(benzyloxy)-6-((benzyloxy)methyl)-
2-methoxytetrahydro-2H-pyran-3-amine (Intermediate 3)
Figure imgf000237_0003
Step 1: To a stirred mixture of 1 mL methanol (24.5 mmol) and TEA (5 mL) was added a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-nitro-3,4-dihydro-2H-pyran (1.0 g, 2.17 mmol) in dry THF (5 mL) dropwise under argon. After stirring for 5 h at rt, the volatiles were removed in vacuo. The resulting crude material was purified by column to give (2R,3R,4R,5R,6R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6-methoxy-5-nitrotetrahydro-2H- pyran (535 mg, 50%) and (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-nitro-3,4- dihydro-2H-pyran (65 mg, 6%). LC-MS (ESI) of both found: 494 [M+H]+.
Step 2: To a solution of (2R,3R,4R,5R,6R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6- methoxy-5-nitrotetrahydro-2H-pyran (535 mg, 1.09 mmol) in MeOH (10 mL) was added Raney Ni (50 mg). The mixture was charged with H2 for three times and stirred at rt for 12 h under a H2 balloon. The mixture was filtered and the filtrate was concentrated to give (2R,3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-amine (300 mg, 59% yield) as white solid. LC-MS (ESI) found: 464 [M+H]+.
Synthesis 4-4: Preparation of N-((3aR,4R,6R,7R,7aR)-4-(Hydroxymethyl)-6-methoxy-2,2- dimethyltetr ahydro-4H- [1,3] dioxolo [4,5-c] pyran-7-yl)acetamide (Intermediate 4)
Figure imgf000238_0001
Intermediate 4
Step 1: To a solution of (2R,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (1.5 g, 3.24 mmol) in DCM (15 mL) was added AcCI (508 mg, 6.48 mmol) and TEA (3 mL). The mixture was stirred at rt for 2 h. The mixture was concentrated and purified by silica column to give N-((2R,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-yl)acetamide (1.6 g, 98%) as white solid. LC-MS (ESI) found: 506 [M+H]+.
Step 2: To a solution of N-((2R,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-yl)acetamide (1.6 g, 3.17 mmol) inMeOH (15 mL) was added Pd/C (100 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give N-((2R,3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)-2-methoxytetrahydro-2H-pyran-3-yl)acetamide (670 mg, 90% yield). LC-MS (ESI) found: 236 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.68 (d, J = 3.7 Hz, 1H), 4.27 (dd, J = 10.9, 3.6 Hz, 1H), 3.87 (d, J = 3.1 Hz, 1H), 3.79 - 3.69 (m, 3H), 3.37 (d, J = 5.6 Hz, 3H), 2.02 - 1.93 (m, 3H).
Step 3: To a solution of N-((2S,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)acetamide (670 mg, 2.85 mmol) in DMF (5 mL) and 2,2- dimethoxypropane (0.8 mL, 6.42 mmol) were added (+/-)-camphor-10-sulphonic acid (330 mg, 1.42 mmol). The reaction mixture was stirred at 70 °C for 24 h. Then it was cooled to room temperature and neutralized with triethylamine. The solvent was evaporated and the residue was co-evaporated 3 times with toluene. The resulting crude material was purified by column to give N-((3aR,4R,6S,7R,7aR)-4-(hydroxymethyl)-6-methoxy-2,2-dimethyltetrahydro-4H- [l,3]dioxolo[4,5-c]pyran-7-yl)acetamide (392 mg, 50%) as white solid. LC-MS (ESI) found: 276 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.30 (dd, J = 8.6, 5.5 Hz, 1H), 4.16 (ddd, J = 13.6, 6.8, 3.5 Hz, 2H), 3.88 - 3.71 (m, 3H), 3.48 - 3.41 (m, 3H), 3.34 (s, 1H), 2.01 - 1.90 (m, 3H), 1.53 - 1.44 (m, 3H), 1.32 (d, J = 11.4 Hz, 3H).
Example 5. Synthesis of ASGPR Ligands
Synthesis 5-1. General Synthesis of Sulfonamide-containing Ligands
Figure imgf000239_0001
Synthesis 5-2. General Synthesis of Sulfonimidamide-containing Ligands
Figure imgf000240_0001
Compound A2
Synthesis 5-3. General Synthesis of Sulfonyl Urea-Containing Compounds
Figure imgf000240_0003
Synthesis 5-4: Alternative General Synthesis of Sulfonyl Urea-Containing Compounds
Figure imgf000240_0002
Org. BiomoL Chem., 2017,15, 4992-4999 Synthesis 5-5. General Synthesis of Sulfonimidamide-containing Ligands
Figure imgf000241_0001
Synthesis 5-6. General Synthesis of ASGPR Ligands
Figure imgf000241_0002
Synthesis 5-7. General Synthesis of ASGPR Ligands
Figure imgf000242_0001
Figure imgf000242_0004
Compound A6
Figure imgf000242_0002
Synthesis 5-6 and Synthesis 5-8 can be used to synthesize ligands with the following R2 groups:
Figure imgf000242_0003
Figure imgf000243_0001
wherein R is an optimal substituent has defined herein.
Synthesis 5-8. Preparation of N-(((3R,4R,5R,6R)-2,4,5-Trihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)methyl)acetamide (Compound A9) and N-
(((3R,4R,5R,6R)-6-(aminomethyl)-2,4,5-trihydroxytetrahydro-2H-pyran-3- yl)methyl)acetamide (Compound A10)
Figure imgf000243_0003
Figure imgf000243_0002
Synthesis 5-9. General Synthesis of Amide-Containing Ligands
Figure imgf000244_0001
Compound A14
Synthesis 5-10. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)pyrrolidin-2-one (Compound A15)
Figure imgf000244_0002
EDCI = 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide Synthesis 5-11. Preparation of 3-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)oxazolidin-2-one (Compound A16)
Figure imgf000245_0001
Synthesis 5-12. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)imidazolidin-2-one (Compound A17)
Figure imgf000245_0002
Synthesis 5-13. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)imidazolidine-2-thione (Compound A18)
Figure imgf000246_0001
Synthesis 5-14. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)pyrrolidine-2, 5-dione (Compound A19)
Figure imgf000246_0002
Synthesis 5-15. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)-lH-pyrrole-2, 5-dione (Compound A20)
Figure imgf000246_0003
Synthesis 5-16. Preparation of 3-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)thiazolidine-2, 4-dione (Compound A21)
Figure imgf000247_0001
A21-2 Compound A21
Synthesis 5-17. Preparation of 3-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)oxazolidine-2, 4-dione (Compound A22)
Figure imgf000247_0002
Compound A22
Synthesis 5-18. Preparation of 2-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)isoindoline-l, 3-dione (Compound A23)
Figure imgf000247_0003
Figure imgf000248_0001
Compound A-23
Synthesis 5-19. Preparation of 2-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)isoindolin-l-one (Compound A24)
Figure imgf000248_0002
Compound A24
Synthesis 5-20. Preparation of (lS,2R,3R,4R)-l-(Aminomethyl)-4-(lH-imidazol-l-yl)-6,8- dioxabicyclo[3.2.1]octane-2,3-diol (Compound A25)
Figure imgf000248_0003
Synthesis 5-21. Preparation of (lS,2R,3R,4R)-l-(Aminomethyl)-4-(lH-pyrrol-l-yl)-6,8- dioxabicyclo[3.2.1]octane-2,3-diol (Compound A26)
Figure imgf000249_0001
Synthesis 5-22. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)pyridin-2(lH)-one (Compound A27)
Figure imgf000249_0002
Synthesis 5-23. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)pyrimidin-2(lH)-one (Compound A28)
Figure imgf000250_0001
Compound A28 Synthesis 5-24. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)pyridin-4(lH)-one (Compound A29)
Figure imgf000250_0002
Compound A29 Synthesis 5-25. Preparation of (3R,4R,5R,6R)-6-(Aminomethyl)-3-(piperidin-l- yl)tetrahydro-2H-pyran-2,4,5-triol (Compound A30)
Figure imgf000251_0001
Synthesis 5-26. Preparation of (3R,4R,5R,6R)-6-(Aminomethyl)-3-morpholinotetrahydro-
2H-pyran-2,4,5-triol (Compound A31)
Figure imgf000251_0002
Synthesis 5-27. Preparation of (3R,4R,5R,6R)-6-(Aminomethyl)-3- thiomorpholinotetrahydro-2H-pyran-2,4,5-triol (Compound A32)
Figure imgf000252_0001
Synthesis 5-28. Preparation of l-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)azetidin-2-one (Compound A33)
Figure imgf000252_0002
Synthesis 5-29. Preparation of (4R,5R,6R)-6-(Aminomethyl)tetrahydro-2H-pyran-2,4,5-triol
(Compound A34) and (4R,5R,6R)-6-(hydroxymethyl)tetrahydro-2H-pyran-2,4,5-triol
(Compound A35)
Figure imgf000253_0001
Synthesis 5-30. Preparation of l-((3R,4R,5R,6R)-6-(Aminomethyl)-2,4,5- trihydroxytetrahydro-2H-pyran-3-yl)tetrahydropyrimidin-2(lH)-one (Compound A36)
Figure imgf000253_0002
Synthesis 5-31. Preparation of N-((lS,2R,3R,4R)-l-(Aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)methanesulfinamide (Compound A37) and N-((1S,2R,3R,4R)- l-(aminomethyl)-2,3-dihydroxy-6,8-dioxabicyclo[3.2.1]octan-4-yl)-l,l,l- trifluoromethanesulfinamide (Compound A38)
Figure imgf000254_0001
Synthesis 5-32. Preparation of (4aR,6R,7R,8R,8aR)-6-(Aminomethyl)-7,8- dihydroxyhexahydro-lH,3H-pyrano[3,2-c][l,2,6]thiadiazine 2,2-dioxide (Compound A39), (4aR,6R,7R,8R,8aR)-6-(aminomethyl)-7,8-dihydroxyhexahydro-lH-pyrano[3,2- d]pyrimidin-2(3H)-one (Compound A40), and (4aS,6R,7R,8R,8aR)-6-(aminomethyl)-7,8- dihydroxyhexahydropyrano[3,2-d][l,3]oxazin-2(lH)-one (Compound A41)
Figure imgf000255_0001
Synthesis 5-33. Alternative Preparation of (4aS,6R,7R,8R,8aR)-6-(Aminomethyl)-7,8- dihydroxytetrahydro-lH,6H-pyrano[2,3-b] [l,4]oxazin-2(3H)-one (Compound A41)
Figure imgf000256_0001
Synthesis 5-34. Preparation of (3aR,5R,6R,7R,7aR)-7-Amino-5-(hydroxymethyl)-2-methyl- 3a,6,7,7a-tetrahydro-5H-pyrano[3,2-d]oxazol-6-ol (Compound A43) and (3aR,5R,6R,7R,7aR)-7-amino-5-(hydroxymethyl)-2-(trifluoromethyl)-3a,6,7,7a-tetrahydro- 5H-pyrano[3,2-d]oxazol-6-ol (Compound A44)
Figure imgf000256_0002
Synthesis 5-35. Preparation of (5R,6R,7R)-5-(Hydroxymethyl)-2-methyl-6,7-dihydro-5H- pyrano[3,2-d]oxazole-6,7-diol (Compound A45) and (5R,6R,7R)-5-(hydroxymethyl)-2- (trifluoromethyl)-6,7-dihydro-5H-pyrano[3,2-d]oxazole-6,7-diol (Compound A46)
Figure imgf000256_0003
Synthesis 5-36. Preparation of (3aS,5R,6R,7R,7aR)-7-Amino-5-(hydroxymethyl)-2-methyl- 3,3a,5,6,7,7a-hexahydropyrano[2,3-d]imidazol-6-ol (Compound A47) and (3aS,5R,6R,7R,7aR)-7-amino-5-(hydroxymethyl)-2-(trifluoromethyl)-3,3a,5,6,7,7a- hexahydropyrano[2,3-d]imidazol-6-ol (Compound A48)
Figure imgf000257_0001
Synthesis 5-37. Preparation of (5R,6R,7R)-5-(Hydroxymethyl)-2-methyl-3,5,6,7- tetrahydropyrano[2,3-d]imidazole-6,7-diol (Compound A49) and (5R,6R,7R)-5- (hydroxymethyl)-2-(trifluoromethyl)-3,5,6,7-tetrahydropyrano[2,3-d]imidazole-6,7-diol (Compound A50)
Figure imgf000257_0002
Synthesis 5-38. Preparation of !-((3aR,5R,6R,7R,7aR)-5-(Aminomethyl)-6,7- dihydroxyhexahydropyrano[3,2-b]pyrrol-l(2H)-yl)-2,2,2-trifluoroethan-l-one (Compound A51) and l-((5R,6R,7R)-5-(aminomethyl)-6,7-dihydroxy-6,7-dihydropyrano[3,2-b]pyrrol- l(5H)-yl)-2,2,2-trifluoroethan-l-one (Compound A52)
Figure imgf000258_0001
Synthesis 5-39. Preparation of !-((4aS,6R,7R,8R,8aR)-6-(Aminomethyl)-7,8- dihydroxyhexahydro-lH,6H-pyrano[2,3-b][l,4]oxazin-l-yl)ethan-l-one (Compound A53) and !-((4aS,6R,7R,8R,8aR)-6-(aminomethyl)-7,8-dihydroxyhexahydro-lH,6H-pyrano[2,3- b][l,4]oxazin-l-yl)-2,2,2-trifluoroethan-l-one (Compound A54)
Figure imgf000258_0002
Synthesis 5-40. Preparation of !-((3aS,4R,5aS,9aR,9bR)-4-(Aminomethyl)-2,2,7- trimethylhexahydro-4H,9H- [1,3] dioxolo [4', 5' : 4,5] pyrano [2,3-b] [1,4] oxazin-9-yl)ethan-l-one (Compound A55) and !-((3aS,4R,5aS,9aR,9bR)-4-(Aminomethyl)-2,2,7- trimethylhexahydr o-4H,9H- [1,3] dioxolo [4' ,5' : 4,5] pyrano [2,3-b] [1,4] oxazin-9-yl)-2,2,2- trifluoroethan-l-one (Compound A56)
Figure imgf000259_0001
Synthesis 5-41. Preparation of l-((3aS,4R,5aS,llaR,llbR)-4-(Aminomethyl)-2,2- dimethyloctahydro-4H,llH-[l,3]dioxolo[4',5':4,5]pyrano[2,3-b][l,4]oxazocin-ll-yl)ethan-l- one (Compound A57) and l-((3aS,4R,5aS,llaR,llbR)-4-(Aminomethyl)-2,2- dimethyloctahydro-4H,llH-[l,3]dioxolo[4',5':4,5]pyrano[2,3-b][l,4]oxazocin-ll-yl)-2,2,2- trifluoroethan-l-one (Compound A58)
Figure imgf000259_0002
Synthesis 5-42. Preparation of !-((3aR,5R,6R,7R,7aR)-6,7-Dihydroxy-5- (hydroxymethyl)hexahydropyrano[3,2-b]pyrrol-l(2H)-yl)ethan-l-one (Compound A59) and (2R,3R,4R,4aR,8aR)-2-(Hydroxymethyl)octahydro-2H-pyrano[3,2-b]pyridine-3,4-diol
(Compound A60)
Figure imgf000260_0001
Synthesis 5-43. Preparation of !-((2R,3R,4R,4aR,9aR)-3,4-Dihydroxy-2-
(hydroxymethyl)octahydropyrano[3,2-b]azepin-5(2H)-yl)ethan-l-one (Compound A61)
Figure imgf000260_0002
Synthesis 5-44. Preparation of ((3aR,4R,5aR,9aS,9bR)-2,2-Dimethyl-8-oxooctahydro-4H- [l,3]dioxolo[4',5':4,5]pyrano[3,2-b]pyridin-4-yl)methyl acetate (Compound A62)
Figure imgf000261_0001
Synthesis 5-45. Preparation of (2R,3R,4R)-2-(Hydroxymethyl)-3,4-dihydro-2H-pyrano[3,2- b]pyridine-3,4-diol (Compound A63) and ((3aR,4R,9bR)-2,2-dimethyl-8-oxooctahydro-4H- [l,3]dioxolo[4',5':4,5]pyrano[3,2-b]pyridin-4-yl)methyl acetate (Compound A64)
Figure imgf000261_0002
Compound A64 Synthesis 5-46. Preparation of N-((3aR,8R,8aR)-4-(Hydroxymethyl)-2,2- dimethylhexahydro-4H-4,7-epoxy[l,3]dioxolo[4,5-d]azepin-8-yl)acetamide (Compound A65)
Figure imgf000262_0001
Synthesis 5-47. Preparation of N-((3aR,4R,9R,9aR)-9-(Hydroxymethyl)-2,2- dimethyloctahydro-5, 9-epoxy[l,3]dioxolo[4,5-d]azocin-4-yl)acetamide (Compound A66)
Figure imgf000262_0002
Synthesis 5-48. Preparation of N-((3aR,4R,9R,9aR)-9-(Hydroxymethyl)-2,2- dimethylhexahydro-5H-5,9-epoxy[l,3]dioxolo[4,5-d]oxocin-4-yl)acetamide (Compound A67)
Figure imgf000263_0001
Compound A68, Compound A69, and Compound A70 can also be synthesized using Synthesis
5-46, 5-47, and 5-48.
Figure imgf000263_0002
Synthesis 5-49. Preparation of (3R,4R,5R,6R)-6-(Aminomethyl)-3-
(trifluoromethyl)tetrahydro-2H-pyran-2,4,5-triol (Compound A71)
Figure imgf000264_0001
Synthesis 5-50. Preparation of General Synthesis to install R2
Figure imgf000264_0002
Synthesis 5-51. Preparation of Alternative General Synthesis to install R2
Figure imgf000264_0003
Synthesis 5-52. Preparation of (lS,2R,3R,4R)-l-(Aminomethyl)-4-(isoxazol-5-ylamino)-6,8- dioxabicyclo[3.2.1]octane-2,3-diol (Compound A73)
Figure imgf000264_0004
Synthesis 5-53. Preparation of (lS,2R,3R,4R)-l-(Aminomethyl)-4-((4,6-dichloro-l,3,5- triazin-2-yl)amino)-6,8-dioxabicyclo[3.2.1]octane-2,3-diol (Compound A74)
Figure imgf000265_0001
Synthesis 5-54. Preparation of (3R,4R,5R,6R)-6-(Aminomethyl)-3-(thiazol-2- ylamino)tetrahydro-2H-pyran-2,4,5-triol (Compound A75)
Figure imgf000265_0002
Synthesis 5-55. Preparation of (2R,3R,4R,5S)-2-(Hydroxymethyl)-5-((3- (trifluoromethyl)pyridin-2-yl)amino)tetrahydro-2H-pyran-3,4-diol (Compound A76)
Figure imgf000265_0003
Synthesis 5-56. Preparation of (3aR,4R,8S,8aR)-8-Azido-4-(azidomethyl)-2,2- dimethylhexahydro-4H-4,7-epoxycyclohepta[d] [l,3]dioxole (Compound A78)
Figure imgf000266_0001
Synthesis 5-57. Preparation of (3R,4S,5R,6R)-6-(aminomethyl)-3-(oxazol-2- yloxy)tetrahydro-2H-pyran-2,4,5-triol (Compound A79)
Figure imgf000266_0002
Synthesis 5-58. Preparation of (3R,4S,5R,6R)-6-(aminomethyl)-2,4,5-trihydroxytetrahydro- 2H-pyran-3-yl acetate (Compound A80)
1 mCPBA
Figure imgf000266_0003
Figure imgf000267_0001
Synthesis 5-59. Preparation of l-((3R,4R,5R,6R)-6-(aminomethyl)-2,4,5- trihydroxytetrahydro-2H-pyran-3-yl)guanidine (Compound A81) and (Compound A82)
Figure imgf000267_0002
Synthesis 5-60. Preparation of Compound A83 and Compound A84
Figure imgf000268_0001
Alternatively, Compound A85 can be synthesized if is used instead of
Figure imgf000268_0002
Figure imgf000268_0003
the Schotten Bauman reaction step.
Figure imgf000268_0004
Synthesis 5-61. Preparation of Compound A88
Figure imgf000269_0001
Org. Biomol. Chem., 2017,15, 4992-4999
Synthesis 5-62: Preparation of (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (Compound A89) and (2R,3R,4R,5R,6R)-5-amino-2- (hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (Compound A90)
Figure imgf000269_0002
Step 1: NaNs (4.3 g, 66 mmol) and CAN (87 g, 158 mmol) were added to a nitrogenflushed flask, and the mixture were stirred vigorously at -10°C. Then a solution of (2R,3R,4R)-2- (acetoxymethyl)-3,4-dihydro-2H-pyran-3,4-diyl diacetate (A90-1, 12 g, 44 mmol) in MeCN (250 mL) were added dropwise to the above mixture. The mixture was stirred at rt for 12 h. Then the reaction mixture was diluted with 500 mL EA. The organic phase was washed with H2O (400mL x 3) and brine, filtered and concentrated to give a yellow oil, which was purified by column chromatography to give (2R,3R,4R,5R)-2-(acetoxymethyl)-5-azido-6-(nitrooxy)tetrahydro-2H- pyran-3,4-diyl diacetate (A90-2, 7.5 g, 45% yield) as white solid. LC-MS (ESI) found: 377 [M+H]+.
Step 2: To a solution of (2R,3R,4R,5R)-2-(acetoxymethyl)-5-azido-6- (nitrooxy)tetrahydro-2H-pyran-3,4-diyl diacetate (A90-2, 15.0 g, 40.0 mmol) in anhydrous MeCN (120 mL) was added LiBr (34.6 g, 400 mmol) at room temperature under an argon atmosphere. The reaction was stirred at room temperature for 3 h. TLC indicated the starting material was consumed. EA (350 mL) was added to the reaction mixture. The organic phase was washed with water (50 mL x2), saturated NaHCO3 (60 mL x2), water (50 mLx2), brine (50 mL), dried (Na2SO4), filtered. The filtrate was concentrated to give a crude (2R,3R,4R,5R,6R)-2- (acetoxymethyl)-5-azido-6-bromotetrahydro-2H-pyran-3,4-diyl diacetate (A90-3, 15.0 g, 96%) as white foam. LC-MS (ESI) found: 394 [M+H]+.
Step 3: To a solution of (2R,3R,4R,5R,6R)-2-(acetoxymethyl)-5-azido-6- bromotetrahydro-2H-pyran-3,4-diyl diacetate (A90-3, 15.0 g, 38.1 mmol) in MeOH (100 mL) was added Ag2CO3 (15.7 g, 57.1 mmol) in portions at rt. The mixture was stirred at 60°C under N2 in the dark for 12 h. EA (350 mL) was added to the reaction mixture. The organic phase was washed with water (50 mL x 2), saturated NaHCO3 (60 mL x2), water (50 mL x2), brine (50 mL), dried (Na2SO4), filtered. The filtrate was concentrated to give a crude product, which was purified by column chromatography to give (2R,3R,4R,5R,6R)-2-(acetoxymethyl)-5-azido-6- methoxytetrahydro-2H-pyran-3,4-diyl diacetate (A90-4, 10.0 g, 76%) as colorless oil. LC-MS (ESI) found: 346 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 5.33 - 5.29 (m, 1H), 4.91 - 4.86 (m, 1H), 4.43 (d, J = 8.0 Hz, 1H), 4.16 - 4.10 (m, 2H), 4.07 - 4.00 (m, 1H), 3.63 - 3.59 (m, 1H), 3.57 (d, J = 3.7 Hz, 3H), 2.15 - 2.13 (m, 3H), 2.03 - 1.97 (m, 6H).
Step 4: To a solution of (2R,3R,4R,5R,6R)-2-(acetoxymethyl)-5-azido-6- methoxytetrahydro-2H-pyran-3,4-diyl diacetate (A90-4, 10.0 g, 29.0mmol) in MeOH (150 mL) was added NaOMe (23.2 mL, 5 M in MeOH) in portions at rt. The mixture was stirred at rt for 2 h. The reaction was neutralized by the addition of acidic Amberlite IR 120 (H+) ion exchange resin. The solution was filtered through a glass fritted vacuum filter funnel equipped with a pad of Celite to remove the acidic resin. The filtrate was concentrated and purified by column to give (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A89, 5.5 g, 78%) as white solid. LC-MS (ESI) found: 220 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.21 - 4.15 (m, 1H), 3.79 (t, J = 3.5 Hz, 1H), 3.76 - 3.70 (m, 2H), 3.54 (s, 3H), 3.49-3.42 (m, 1H), 3.41 (dd, J = 4.0, 2.6 Hz, 2H).
Step 5: To a solution of (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A-89, 1.0 g, 4.57 mmol) in MeOH (20 mL) was added Pd/C (100 mg, 10% wt, 60% wet) under H2 atmosphere. The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give (2R,3R,4R,5R,6R)-5-amino- 2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A90, 749 mg, 85% yield) as white solid. LC-MS (ESI) found: 194 [M+H]+.
Synthesis 5-63: Preparation of (2R,3R,4R,5R,6S)-5-amino-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (Compound A91)
Figure imgf000271_0001
A91-3 A91
Step 1: To a stirred solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- nitro-3,4-dihydro-2H-pyran (A91-1, 1.0 g, 2.17 mmol) in dry THF (10 ml) was added NaOMe (0.65 mL, 5 M in MeOH). After stirring at rt for 1 h, the reaction mixture was neutralized with Amberlite IR-120 resin (H+). The reaction mixture was filtered, the filtrate was concentrated to give a crude product, which was purified by column to get ((2R,3R,4R,5R,6S)-3,4-bis(benzyloxy)- 2-((benzyloxy)methyl)-6-methoxy-5-nitrotetrahydro-2H-pyran (A91-2, 425 mg, 39% yield) and (2R,3R,4R,5R,6R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6-methoxy-5-nitrotetrahydro-2H- pyran (52 mg, 5%). LC-MS (ESI) of both found: 494 [M+H]+.
Step 2: To a solution of (2R,3R,4R,5R,6S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-6- methoxy-5-nitrotetrahydro-2H-pyran (A91-2, 425 mg, 0.86 mmol) in MeOH (10 mL) was added Raney Ni (50 mg). The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give (2S,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (A91-3, 473 mg, 72% yield). LC-MS (ESI) found: 464 [M+H]+.
Step 3: To a solution of (2S,3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (A91-3, 200 mg, 0.431 mmol) in MeOH (10 mL) was added Pd/C (20 mg, 10% wt, 60% wet) and several drops of 1 N HCI. The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give (2R,3R,4R,5R,6S)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A91, 452 mg, 62% yield) as colorless oil. LC-MS (ESI) found: 194 [M+H]+.
Synthesis 5-64: Preparation of (2R,3R,4R,5S)-5-amino-2-(hydroxymethyl)tetrahydro-2H- pyran-3,4-diol (Compound A92)
Figure imgf000272_0001
Step 1: To a mixture of (2S,3R,4R,5R,6R)-3-acetamido-6-(acetoxymethyl)tetrahydro-2H- pyran-2,4,5-triyl triacetate (A92-1, 20.0 g, 51.4 mmol) in DCM (200 mL) was added TiCh (61.6 mL, 1 M in DCM) at 0°C under N2. After refluxing at 50°C overnight, the mixture was concentrated and purified by chromatography (0-80% ethyl acetate in petroleum) to give (2R,3R,4R,5R)-5- acetamido-2-(acetoxymethyl)-6-chlorotetrahydro-2H-pyran-3,4-diyl diacetate (A92-2, 8.5 g, 45% yield) as white solid. LC-MS (ESI) found: 366 [M+l]+.
Step 2: To a mixture of (2R,3R,4R,5R)-5-acetamido-2-(acetoxymethyl)-6- chlorotetrahydro-2H-pyran-3,4-diyl diacetate (A92-2, 8.5 g, 23.2 mmol) in toluene (85 mL) was added BusSnH (8.1 g, 27.9 mmol) and AIBN (0.08 g, 0.46 mmol) at rt under N2. After refluxing at 110°C for 1.5 h, the mixture was concentrated and purified by chromatography on silica gel (70- 100% ethyl acetate in petroleum) to give (2R,3R,4R,5S)-5-acetamido-2- (acetoxymethyl)tetrahydro-2H-pyran-3,4-diyl diacetate (A92-3, 6.6 g, 86%) as white solid. LC- MS (ESI) found: 332 [M+l]+. Step 3: To a mixture of (2R,3R,4R,5S)-5-acetamido-2-(acetoxymethyl)tetrahydro-2H- pyran-3,4-diyl diacetate (A92-3, 6.6 g, 19.9 mmol) in H2O (48 mL) was added HC1 (12 mL, 2.5 M in H2O) at rt under N2. After refluxing at 100°C for 2 h, the mixture was concentrated. EtOH (10 mL) and Et2O (10 mL) were added. The solid formed was filtered to give (2R,3R,4R,5S)-5- amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol hydrochloride (A-92, 2.7 g, 68%) as white solid. LC-MS (ESI) found: 164 [M+H]+.
Synthesis 5-65: Preparation of (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (Compound A94)
Figure imgf000273_0001
Step 1: To a mixture of (2R,3R,4R,5S)-5-acetamido-2-(acetoxymethyl)tetrahydro-2H- pyran-3,4-diyl diacetate (A94-1, 1.5 g, 4.5 mmol) in MeOH (20 mL) was added NaOMe (2.7 mL, 5 M in MeOH) at 0°C under N2. After stirring at rt for 2 h, the mixture was neutralized with HC1 (2 M) and concentrated. Then the mixture was purified by chromatography on silica gel (0-20% methanol in DCM) to give N-((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-3-yl)acetamide (A94-2, 560 mg, 60%) as white solid. LC-MS (ESI) found: 206 [M+H]+.
Step 2: To a mixture of N-((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro- 2H-pyran-3-yl)acetamide (A-94-2, 130 mg, 0.63 mmol) in DMF (5.0 mL) was added NaH (101 mg, 4.2 mmol) at 0°C under N2. After stirring at 0°C for 30 min, BnBr (0.07 mL, 0.63 mmol) was added slowly and the reaction was stirred for another 1 hour. The mixture was quenched with H2O and extracted with EA. The combined organic layers were washed with brine, dried over anhydrous Na2SO4. The residue was concentrated and purified by chromatography on silica gel (0-20% methanol in DCM) to give N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A94-3, 130 mg, 43%) as white solid. LC-MS (ESI) found: 476 [M+H]+.
Step 3: To a mixture of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A94-3, 1.2 g, 2.5 mmol) in THF (15 mL) was added Et3N (1.1 mL, 7.6 mmol), DMAP (30 mg, 0.25 mmol) and BOC2O (7.0 mL, 30.2 mmol) at 0°C under N2. After stirring at rt overnight, the mixture was concentrated and purified by chromatography on silica gel (0-10% methanol in DCM) to give tert-butyl acetyl((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3- yl)carbamate (A94-4, 860 mg, 60%) as colorless oil. LC-MS (ESI) found: 576 [M+l]+.
Step 4: To a mixture of tert-butyl acetyl((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A94-4, 860 mg, 1.5 mmol) in THF (10 mL) was added 2 mL NaOH (40 % aq) under N2. After refluxing at 60°C overnight, the mixture was diluted with H2O and extracted with EA. The combined organic layer was washed with brine, dried over Na2SO4, filtered. The filtrate was concentrated and purified by chromatography on silica gel (0-70% ethyl acetate in petroleum) to give tert-butyl ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A94-5, 450 mg, 56%) as a white solid. LC-MS (ESI) found: 534 [M+l]+.
Step 5: To a solution of tert-butyl ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A94-5, 450 mg, 0.84 mmol) in DCM (9.0 mL) was added TFA (3.0 mL) at rt under N2. After stirring for 2 h, the mixture was quenched with NaHCO3(aq) and extracted with EA. The combined organic layer was washed with brine, dried over anhydrous Na2SO4. The residue was concentrated and purified by chromatography on silica gel (0-50% ethyl acetate in petroleum) to give (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A94, 280 mg, 77%) as colorless oil. LC-MS (ESI) found: 434 [M+l]+. Synthesis 5-66: Preparation of 4-chloro-2-(((3S,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)amino)thiazole-5-carbonitrile (Compound A95)
Figure imgf000275_0001
To a mixture of (2R,3R,4R,5S)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol hydrochloride (A92, 50 mg, 0.25 mmol) in NMP (2.0 mL) was added 2,4-dichlorothiazole-5- carbonitrile (135 mg, 0.75 mmol) and DIPEA (0.17 mL, 1.0 mmol) at rt under N2. After stirring at 120°C overnight, the mixture was concentrated and purified by prep-TLC to give 4-chloro-2- (((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)amino)thiazole-5- carbonitrile (A95, 6.3 mg, 8% yield) as brown solid. LC-MS (ESI) found: 306 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.12 - 4.00 (m, 2H), 3.90 (d, J = 2.5 Hz, 1H), 3.77 - 3.65 (m, 2H), 3.58 (dd, J = 10.1, 3.2 Hz, 1H), 3.46 - 3.41 (m, 1H), 3.16 (t, J = 10.5 Hz, 1H).
Synthesis 5-67: Preparation of (2R,3R,4R,5S)-2-(hydroxymethyl)-5-(pyridin-2- ylamino)tetrahydro-2H-pyran-3,4-diol (Compound A96)
Figure imgf000276_0001
Step 1: To a solution of (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A-94, 40.0 mg, 0.092 mmol) in toluene (4 mL) was added 2-bromopyridine (21.9 mg, 0.139 mmol), Pd(OAc)2 (2.07 mg, 0.009 mmol), BINAP (5.75 mg, 0.009 mmol), and NaOt-Bu (26.6 mg, 0.277 mmol). The mixture was stirred under N2 at 100°C for 24 h. The reaction mixture was concentrated and purified by prep-HPLC (Method A) to give N-((3 S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3- yl)pyridin-2-amine (A96-1, 15 mg, 32% ) as white solid. LC-MS (ESI) found: 511 [M+H]+.
Step 2: To a solution of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)pyridin-2-amine (A96-1, 15 mg, 0.03 mmol) in MeOH (5 mL) was added Pd/C (2 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and the filtrate was concentrated to give (2R,3R,4R,5S)-2-(hydroxymethyl)-5-(pyridin-2-ylamino)tetrahydro-2H-pyran-3,4-diol (A96, 0.6 mg, 9% yield) as white solid. LC-MS (ESI) found: 241 [M+H]+. 1H NMR (400 MHz, Methanol - d4): 6 8.03 - 7.81 (m, 1H), 7.42 (ddd, J = 8.8, 7.0, 2.0 Hz, 1H), 6.67 - 6.38 (m, 2H), 4.67 - 4.37 (m, 1H), 4.16 - 3.96 (m, 1H), 3.89 (d, J = 3.1 Hz, 1H), 3.79 - 3.58 (m, 2H), 3.54 (dd, J = 9.9, 3.0 Hz, 1H), 3.44 (t, J = 6.0 Hz, 1H), 3.21 - 2.99 (m, 1H). The following compounds below were made using the method described in Synthesis 5-66 or Synthesis 5-67:
Figure imgf000277_0001
Figure imgf000277_0002
δ δ δ δ δ δ
Figure imgf000278_0002
Synthesis 5-68: Preparation of (2R,3R,4R,5R,6S)-5-((3-chloro-l,2,4-thiadiazol-5-yl)amino)- 2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (Compound A105) and (2R,3R,4R,5R,6R)-5-((3-chloro-l,2,4-thiadiazol-5-yl)amino)-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (Compound A106)
Figure imgf000278_0001
A solution of (2R,3R,4R,5R,6R)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran- 3,4-diol (A90, 224.0 mg, 1.2 mmol), 3,5-dichloro-l,2,4-thiadiazole (372.0 mg, 2.4 mmol) and DIEA (464.4 mg, 3.6 mmol) in i-PrOH (10 mL) was stirred at rt overnight. The mixture was concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-10% MeOH in DCM) and pre-HPLC (Method B) to give (2R,3R,4R,5R,6S)-5-((3-chloro-l,2,4- thiadiazol-5-yl)amino)-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (0.8 mg, 0.2% yield) as a white solid and (2R,3R,4R,5R,6R)-5-((3-chloro-l,2,4-thiadiazol-5-yl)amino)-2- (hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (3.7 mg, 1% yield) as white solid. Compound A105: LC-MS (ESI) found: 312 [M+H]+. 1H NMR (400 MHz, Methanol-d4): 6 4.85 - 4.80 (m, 1H), 4.23 - 4.11 (m, 1H), 3.91 (d, J = 3.1 Hz, 1H), 3.85 - 3.77 (m, 2H), 3.76 - 3.69 (m, 2H), 3.40 (s, 3H). Compound A106: LC-MS (ESI) found: 312 [M+H]+. 1H NMR (400 MHz, Methanol-d4): 3 4.33 (d, J = 8.1 Hz, 1H), 3.87 (d, J = 3.2 Hz, 1H), 3.84 - 3.70 (m, 2H), 3.68 (dd, J = 10.4, 3.3 Hz, 1H), 3.53 (ddd, J = 6.7, 5.4, 1.1 Hz, 1H), 3.48 (s, 3H), 3.46 - 3.40 (m, 1H).
Synthesis 5-69: Preparation of (2R,3R,4R,5R,6R)-5-((6-fluoropyridin-2-yl)amino)-2-
(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (Compound A107)
Figure imgf000279_0001
To a solution of (2R,3R,4R,5R,6R)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran- 3,4-diol (A90, 50.0 mg, 0.259 mmol) in NMP (2 mL) was added 2,6-difluoropyridine (89.0 mg, 0.777 mmol) and DIPEA (101 mg, 0.777 mmol). The mixture was stirred at 180°C for 1 h under microwave. The reaction mixture was lyophilized and purified by prep-HPLC (Method A) to give (2R,3R,4R,5R,6R)-5-((6-fluoropyridin-2-yl)amino)-2-(hydroxymethyl)-6-methoxytetrahydro- 2H-pyran-3,4-diol (A107, 1.4 mg, 2% yield) as white solid. LC-MS (ESI) found: 289 [M+H]+. The following compounds below were made using the method described in Synthesis 5-68 or Synthesis 5-69:
Figure imgf000280_0001
Figure imgf000280_0002
Synthesis 5-70: Preparation of 6-(((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)amino)-l,3,5-triazine-2,4(lH,3H)-dione (Compound A112)
Figure imgf000281_0001
To a solution of 2,4,6-trichloro-l,3,5-triazine (187 mg 1.03 mmol) in THF (5 mL) was added DIPEA (200 mg, 1.55 mmol) at -78°C. (2R,3R,4R,5R,6R)-5-amino-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A90, 100 mg, 0.51 mmol) was then added at -78°C. The mixture was further stirred for 2 h at -78°C. Then it was quenched by adding H2O (5 mL). The mixture was warmed to rt and stirred for another 2 h. The solvent was evaporated and the residual was purified by prep-HPLC (Method A) to give 6-(((2R,3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)-2-methoxytetrahydro-2H-pyran-3-yl)amino)-l,3,5-triazine-2,4(lH,3H)-dione (Al 12, 6.1 mg, 4% yield) as white solid. LC-MS (ESI) found: 305 [M+H]+. 1H NMR (400 MHz, D2O): δ 4.39 (d, J = 8.4 Hz, 1H), 4.02 (dd, J = 10.7, 8.5 Hz, 1H), 3.88 (d, J = 3.2 Hz, 1H), 3.81 - 3.67 (m, 3H), 3.63 (dd, J = 7.8, 4.3 Hz, 1H).
The following compound below was made using the method described in Synthesis 5-70 with (2R,3R,4R,5R,6S)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol instead of A90:
Figure imgf000282_0001
Figure imgf000282_0003
Synthesis 5-71: Preparation of (2R,3R,4R,5R,6S)-5-((3-(dimethylamino)-l,2,4-thiadiazol-5- yl)amino)-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (Compound Al 14)
Figure imgf000282_0002
A solution of (2R,3R,4R,5R,6S)-5-((3-chloro-l,2,4-thiadiazol-5-yl)amino)-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A105, 10.0 mg, 0.03 mmol), dimethylamine (0.1 mL, 0.1 mmol, 1 M in THF) and DIEA (11.6 mg, 0.09 mmol) in NMP (4 mL) was stirred at 120°C overnight. The mixture was concentrated in vacuo. The crude product was purified by pre-HPLC (Method B) to give (2R,3R,4R,5R,6S)-5-((3-(dimethylamino)-l,2,4-thiadiazol-5-yl)amino)-2- (hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (Al 14, 0.8 mg, 8.3% yield) as white solid. LC-MS (ESI) found: 321 [M+H]+. 1H NMR (400 MHz, Methanol-d4): 64.85 - 4.81 (m, 1H), 4.12 (d, J = 13.7 Hz, 1H), 3.90 (d, J = 3.2 Hz, 1H), 3.81 (ddd, J = 11.4, 7.8, 3.3 Hz, 2H), 3.77 - 3.67 (m, 2H), 3.39 (s, 3H), 3.04 (s, 6H). The following compounds below were made using the method described in Synthesis 5-71 with the appropriate amine and, A106 instead of A105:
Figure imgf000283_0001
Figure imgf000283_0002
Synthesis 5-72: Preparation of N-((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)acrylamide (Compound Al 18)
Figure imgf000284_0001
Step 1: A solution of compound (2R,3R,4R,5R,6R)-5-azido-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (A89, 1 g, 4.6 mmol) in anhydrous pyridine (20 mL) was treated with trimethyl silyl chloride (3.5 mL, 27.8 mmol) and the mixture was stirred for 12 h at room temperature. The solvent was evaporated and the residue was diluted in ethyl acetate/ water. The organic layer was separated and further washed by water, brine, dried over anhydrous MgSCh, filtered, and concentrated to afford desired product as a yellow oil (1.6 g, 81% yield). LC-MS (ESI) found: 436 [M+H]+.
Step 2: To a solution of (((2R,3S,4R,5R,6R)-5-azido-6-methoxy-2- (((trimethylsilyl)oxy)methyl)tetrahydro-2H-pyran-3,4-diyl)bis(oxy))bis(trimethylsilane) (Al 18- 1, 1.0 g, 2.29 mmol) in MeOH (20 mL) was added Pd/C (100 mg, 10% wt, 60% wet). The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to give ((2R,3S,4R,5R,6R)-5-amino-6-methoxy-3,4-bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-2- yl)methanol (Al 18-2, 401 mg, 52% yield). LC-MS (ESI) found: 338 [M+H]+.
Step 3: To a solution of ((2R,3S,4R,5R,6R)-5-amino-6-methoxy-3,4- bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-2-yl)methanol (Al 18-2, 150 mg, 0.444 mmol ) in MeOH (1 mL) H2O (1 mL) was added prop-2-enoyl chloride (0.04 mL, 0.533 mmol) and TEA (0.02 mL, 0.148 mmol). The mixture was stirred at 0°C for 4 h. The solvent was evaporated and the residue was diluted in DCM/water. The organic layer was separated and further washed by water, brine, dried over anhydrous MgSO4, filtered, and concentrated to afford a crude product, which was purified by silica gel column to give N-((2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2- methoxy-4,5-bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-3-yl)acrylamide (Al 18-3, 70 mg, 40%). LC-MS (ESI) found: 392 [M+H]+.
Step 4: To a solution of N-((2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2-methoxy-4,5- bis((trimethylsilyl)oxy)tetrahydro-2H-pyran-3-yl)acrylamide (Al 18-3, 70 mg, 0.179 mmol) in THF (1 mL) was added TBAF (0.2 mL, 1 M in THF). The mixture was stirred at 0°C for 30 min. The solvent was evaporated and the residual was purified by prep-HPLC (Method A) to give N- ((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-methoxytetrahydro-2H-pyran-3- yl)acrylamide (Al 18, 17 mg, 38%) as white solid. LC-MS (ESI) found: 248 [M+H]+. 1H NMR (400 MHz, Methanol-d4): 6 6.04-6.17 (m, 2H), 5.63-5.66 (m, 1H), 4.29 (d, J = 8.4 Hz, 1H), 3.79- 3.83 (m, 2H), 3.55-3.65 (m, 4H), 3.35 (s, 3H).
Synthesis 5-73: Preparation of l-((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)pyridin-4(lH)-one (Compound Al 19)
Figure imgf000285_0001
To a solution of 4H-pyran-4-one (9.6 mg, 0.100 mmol) in MeOH (3 mL) was added NaOH (8 mg, 0.2 mmol) in H2O (2 mL) to adjust pH to 11, then (2R,3R,4R,5R,6R)-5-amino-2-(hydroxymethyl)- 6-methoxytetrahydro-2H-pyran-3,4-diol (A90, 20 mg, 0.1 mmol) was added to the mixture. The mixture was stirred at 60 °C for 3 h. Then the solvent was evaporated and the residual was purified by prep-HPLC (Method A) to give l-((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)pyridin-4(lH)-one (Al 19, 2.1 mg, 7.7%) as white solid. LC- MS (ESI) found: 272 [M+H]+. 1H NMR (400 MHz, Methanol-d4): 6 8.49 (s, 1H), 7.86 (d, J = 7.6 Hz, 2H), 6.46 (d, J = 7.6 Hz, 2H), 4.65 (d, J = 8.3 Hz, 1H), 4.08 (dd, J = 10.9, 3.3 Hz, 1H), 3.98 - 3.89 (m, 2H), 3.85 - 3.75 (m, 2H), 3.68 (t, J = 6.1 Hz, 1H), 3.42 (s, 3H). Synthesis 5-74: Preparation of N-((2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)-4-methylbenzenesulfonamide (Compound A120)
Figure imgf000286_0002
A solution of (2R,3R,4R,5R,6R)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran- 3,4-diol (A90, 50 mg, 0.26 mmol) in MeOH (0.5 mL) and H2O(0.5 mL) was added DIPEA (0.92 mL, 5.2 mmol) and 4-methylbenzene-l -sulfonyl chloride (0.25 mL, 1.3 mmol). After stirring under N2 at rt overnight, the mixture was concentrated to give crude product which was further purified by prep-HPLC (Method B) to afford N-((2R,3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)-2-methoxytetrahydro-2H-pyran-3-yl)-4-methylbenzenesulfonamide (A120, 7.0 mg, 15%) as white solid. LC-MS (ESI) found: 348 [M+l]+. 1H NMR (400 MHz, DMSO ): 6 7.64 (d, J= 8.3 Hz, 2H), 7.48 (s, 1H), 7.31 (d, J= 8.0 Hz, 2H), 4.55 (dd, J= 7.7, 3.6 Hz, 2H), 4.50 (d, J = 6.6 Hz, 1H), 3.88 (d, J = 8.1 Hz, 1H), 3.63 (t, J= 3.6 Hz, 1H), 3.53 - 3.40 (m, 2H), 3.30 (dd, J= 6.7, 3.2 Hz, 1H), 3.22 (dd, J= 8.0, 4.2 Hz, 2H), 2.85 (s, 3H), 2.36 (s, 3H).
Synthesis 5-75: Preparation of N-((3S,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-4-methylbenzenesulfonamide (Compound A121)
Figure imgf000286_0001
Step 1: To a mixture of (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A94, 50 mg, 0.12 mmol) in MeOH (1.0 mL) and H2O (1.0 mL) was added TsCI (219 mg, 1.2 mmol) and TEA (175 mg, 1.7 mmol) at 0°C under N2. After string for 2 h, the mixture was concentrated and purified by prep-HPLC (Method A) to give N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-4- methylbenzenesulfonamide (A121-1, 30 mg, 44%) as a white solid. LC-MS (ESI) found: 588 [M+l]+. Step 2: To a mixture of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-4-methylbenzenesulfonamide (A121-1, 30 mg, 0.051 mmol) in MeOH (3.0 mL) was added Pd/C (10 mg, 10% wt, 60% wet) at rt. The mixture was stirred at rt for 12 h under a H2 balloon. The mixture was filtered and concentrated to afford N-((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-4- methylbenzenesulfonamide (A121, 10 mg, 62%) as white solid. LC-MS (ESI) found: 318 [M+l]+. 1H NMR (400 MHz, CD3OD): δ 7.78 (d, J= 8.3 Hz, 2H), 7.36 (d, J= 8.0 Hz, 2H), 3.80 (dd, J = 2.9, 0.8 Hz, 1H), 3.75 (dd, J = 11.2, 4.8 Hz, 1H), 3.62 (ddd, J = 16.4, 11.4, 6.0 Hz, 2H), 3.45 - 3.31 (m, 3H), 3.08 - 3.00 (m, 1H), 2.42 (s, 3H).
Synthesis 5-76: Preparation of (3R,4R,5R,6R)-3-(4-fluorophenyl)-6-
(hydroxymethyl)tetrahydro-2H-pyran-2,4,5-triol (Compound A122)
Figure imgf000287_0001
Step 1: To a solution of (2R,3S,4S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- iodo-3,4-dihydro-2H-pyran (Al 22-1, 100 mg, 0.184 mmol) in DME (10 mL) was added Pd(PPh3)4 (21 mg, 0.018 mmol), K2CO3 (76 mg, 0.552 mmol) and (4-fluorophenyl)boronic acid (34 mg, 0.239 mmol). The mixture was charged with N2 for three times and stirred at 90°C under N2 for 16 h. The mixture was filtered, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by flash chromatography (silica gel, 5-10% EtOAc in PE) to give (2R,3R,4R)-4-(benzyloxy)-2-((benzyloxy)methyl)-5-(4-fluorophenyl)-3,4-dihydro-2H-pyran-3- ol (A122-2, 25 mg, 31 % yield) as colorless oil. LC-MS (ESI) found: 533 [M+23]+. (2R,3R,4R,5R)-5-(2,4-difluorophenyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A122a), (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(lH-pyrazol-3-yl)tetrahydro-2H- pyran-3,4-diol (Compound A122b) and (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(lH-pyrazol-4- yl)tetrahydro-2H-pyran-3,4-diol (Compound A122c) were prepared using the procedure shown in Synthesis 5-7
Figure imgf000288_0001
Example 6. Synthesis of Talose-Based ASGPR ligands
Synthesis 6-1. Preparation of Bicyclic Talose amine Compound A123, Compound A124, and Compound A125:
Figure imgf000288_0002
Figure imgf000289_0001
Synthesis 6-2. Preparation of tert-Butyl (((3aR,4S,8S,8aR)-8-amino-2,2-dimethyltetrahydro- 4,7-epoxy[l,3]dioxolo[4,5-d]oxepin-4(5H)-yl)methyl)carbamate (Intermediate lb):
Figure imgf000289_0002
Synthesis 6-3. Preparation of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran (Compound A126)
Figure imgf000289_0003
Step 1: To a solution of (2R,3R,4R)-2-(acetoxymethyl)-3,4-dihydro-2H-pyran-3,4-diyl diacetate (A126-1, 30.0 g, 55.1 mmol) in MeOH (300 mL) was added NaOMe (31.0 mL, 165.3 mmol, 5.4 M in MeOH) at room temperature. The mixture was stirred at room temperature for 2 hours. The reaction was neutralized by the addition of Amberlite IR 120 (H+) ion exchange resin. The solution was filtered through a glass fritted funnel with a pad of Celite to remove the resin. The filtrate was concentrated to dryness to give a crude triol. The crude material was passed through a plug of silica (70:30 to 85: 15 EtOAc/hexanes) to give D-galactal triol (A126-2, 15.0 g 93%) as white solid. LC-MS (ESI) found: 147 [M+H]+.
Step 2: To a solution of (2R,3R,4R)-2-(hydroxymethyl)-3,4-dihydro-2H-pyran-3,4-diol (A126-2, 15.0 g, 51.3 mmol) in DMF (200 mL) was added NaH (8.2 g, 205.3 mmol, 60% in mineral oil) at 0 °C in portions. The mixture was stirred at 0 °C for 0.5 hours. Benzyl bromide (49.0 mL, 205.3 mmol) was added at 0°C in portions. The mixture was stirred at room temperature for 2 hours. The mixture was quenched with H2O, extracted with ethyl acetate, washed with H2O, and concentrated and purified by column to give (2R,3R,4R)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)-3,4-dihydro-2H-pyran (A126, 29.0 g, 68%) as white oil. LC-MS (ESI) found: 417 [M+H]+.
Synthesis 6-4. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)acetamide (Compound A127)
Figure imgf000290_0001
Figure imgf000291_0001
Step 1: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran from Synthesis 6-3 (A126, 6.6 g, 15.8 mmol) and n-Bu4NNO3 (5.3 g, 17.4 mmol) in dry DCM (70 mL) was added dropwise TFAA (3.7 g, 17.430 mmol) at 0°C under N2 atmosphere. After the addition was complete, the reaction was stirred at room temperature for 1 hour. Once the starting material was consumed (TLC monitoring), the reaction vessel was again cooled to 0°C, TEA (2.4 mL, 17.4 mmol) was slowly added and the reaction mixture was stirred for another 15 minutes. The reaction mixture was quenched with 10 mL ice water. Extraction was done with DCM (50 mL x 3), and the combined organic extracts were washed with water (50 mL x 3) and brine (150 mL), dried over Na2SO4. The mixture was concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-20% EtOAc in PE) to give (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-nitro-3,4-dihydro-2H-pyran (A126-1, 4 g, 8.7 mmol, 54.7% yield) as a yellow oil. 1H NMR (400 MHz, CDCh): 6 8.09 (s, 1H), 7.36 - 7.29 (m, 15H), 4.90 (dd, J = 3.7, 1.3 Hz, 1H), 4.86 (d, J = 10.8 Hz, 1H), 4.79 (d, J = 10.8 Hz, 1H), 4.70 (dd, J = 13.4, 8.5 Hz, 2H), 4.62 (d, J = 11.9 Hz, 1H), 4.56 (d, J = 11.9 Hz, 1H), 4.47 (d, J = 11.9 Hz, 1H), 3.96 - 3.90 (m, 3H).
Step 2: To a solution of LiAlH4 (0.66 g, 17.3 mmol) in dry THF (40 mL) was added (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-nitro-3,4-dihydro-2H-pyran (A126-1, 4 g, 8.7 mmol) in THF (10 mL) dropwise at 0°C under N2 atmosphere. The reaction mixture was stirred at rt for 1 h. The reaction was cooled to 0°C and quenched with water (0.66 g), NaOH (0.66 g, 15% (w/w) in water), water (1.98 g). The mixture was filtered and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-90% EtOAc in PE) to give (4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A126-2, 1 g, 2.307 mmol, 26.6% yield) as a colorless oil, as approximate 4: 1 mixture of 3R/3S epimers. 1H NMR (400 MHz, CDCh): 6 7.39 - 7.27 (m, 15H), 4.90 (dd, J = 22.9, 11.5 Hz, 1H), 4.74 - 4.68 (m, 1H), 4.67 - 4.60 (m, 1H), 4.58 - 4.50 (m, 2H), 4.44 (d, J = 11.9 Hz, 1H), 4.05 (dd, J = 12.0, 2.0 Hz, 1H), 3.92 - 3.85 (m, 1H), 3.73 - 3.66 (m, 1H), 3.59 - 3.51 (m, 3H), 3.48 (dd, J = 8.4, 5.0 Hz, 1H), 3.15 - 3.07 (m, 1H).
Step 3: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro- 2H-pyran-3 -amine (A 126-2. 7.4 g, 17.1 mmol) and DIPEA (8.5 mL, 51.2 mmol) in DCM (80 mL) was added acetyl chloride (2.4 mL, 34.1 mmol) dropwise at 0°C. The reaction mixture was stirred at rt for 1.5 h. The resulting mixture was diluted with DCM (100 mL), washed with H2O (80 mL x 2) and brine (80 mL), dried over Na2SO4, filtered. The organic layer was separated and concentrated in vacuo to give a crude product, which was purified by flash chromatography (silica gel, 0-80% EA in PE) to give N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A127-3, 4.0 g, 8.4 mmol, 49.3%) as a colorless oil and N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H- pyran-3-yl)acetamide (A127-4, 1.0 g, 2.1 mmol, 12.3% yield) as white solid. N-((3R,4R,5R,6R)- 4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A127-3): LC- MS (ESI) found: 476 [M+H]+. 1H NMR (400 MHz, CDCh): 6 7.38 - 7.28 (m, 15H), 7.20 (d, J = 8.5 Hz, 1H), 4.88 (d, J = 10.3 Hz, 1H), 4.74 (d, J = 11.8 Hz, 1H), 4.58 (d, J = 11.8 Hz, 1H), 4.55 - 4.50 (m, 2H), 4.48 (d, J = 10.9 Hz, 2H), 4.01 (dd, J = 12.2, 1.8 Hz, 1H), 3.95 - 3.92 (m, 1H), 3.63 (d, J = 6.4 Hz, 2H), 3.59 (dd, J = 4.4, 2.9 Hz, 1H), 3.55 - 3.50 (m, 1H), 3.46 (dd, J = 12.2, 1.7 Hz, 1H), 1.77 (s, 3H). N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H- pyran-3-yl)acetamide (127-4): LC-MS (ESI) found: 476 [M+H]+. 1H NMR (400 MHz, CDCh): 3 7.39 - 7.28 (m, 15H), 5.05 (s, 1H), 4.88 (d, J = 11.5 Hz, 1H), 4.73 (d, J = 12.2 Hz, 1H), 4.60 (d, J = 11.6 Hz, 1H), 4.51 (d, J = 11.9 Hz, 1H), 4.42 (dd, J = 14.7, 12.0 Hz, 2H), 4.24 - 4.16 (m, 2H), 4.00 (d, J = 1.8 Hz, 1H), 3.66 - 3.60 (m, 1H), 3.58 - 3.49 (m, 3H), 3.15 (t, J = 11.9 Hz, 1H), 1.85 (s, 3H).
Step 4: To a solution of N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetamide (A127-3, 100 mg, 0.2 mmol) in dry DCM (5 mL) was added BCl3 (2.1 mL, 2.1 mmol, 1 M in DCM) dropwise at -10°C under N2 atmosphere. The reaction mixture was stirred at rt for 0.5 h. Then the reaction was cooled to 0°C and quenched with saturated sodium bicarbonate solution. The mixture was filtered and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-40% MeOH in DCM) to give N-((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-3-yl)acetamide (A127, 20 mg, 0.1 mmol, 46.4% yield) as a colorless oil. LC-MS (ESI) found: 206[M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.08 (d, J = 3.3 Hz, 1H), 3.93 - 3.86 (m, 2H), 3.79 - 3.73 (m, 2H), 3.67 (dd, J = 11.5, 4.8 Hz, 1H), 3.53 (dd, J = 12.0, 1.7 Hz, 1H), 3.44 - 3.37 (m, 1H).
Synthesis 6-5. Preparation of N-((3aR,4R,7R,7aR)-4-(hydroxymethyl)-2,2- dimethyltetrahydro-4H-[l,3]dioxolo[4,5-c]pyran-7-yl)acetamide (Intermediate 5) and N- ((4aR,7R,8R,8aR)-8-hydroxy-2,2-dimethylhexahydropyrano[3,2-d][l,3]dioxin-7- yl)acetamide
Figure imgf000293_0001
A127 Intermediate 5
To a solution of N-((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3- yl)acetamide from Synthesis 6-4 (A127, 100 mg, 0.49 mmol) in 2,2-dimethoxypropane (2 mL) was added CSA (16.7 mg, 0.1 mmol) at room temperature under N2.The reaction was stirred at room temperature overnight. The crude product was purified by prep-HPLC (Method A) to give N-((3aR,4R,7R,7aR)-4-(hydroxymethyl)-2,2-dimethyltetrahydro-3aH-[l,3]dioxolo[4,5-c]pyran- 7-yl)acetamide (Intermediate 5).
Synthesis 6-6. Preparation of (2R,3R,4R,5R)-5-amino-2-(hydroxymethyl)tetrahydro-2H- pyran-3,4-diol (Compound A128)
Figure imgf000293_0002
To a solution of N-((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3- yl)acetamide from Synthesis 6-4 (A127, 20.0 mg, 0.09 mmol) in H2O (2 mL) was added Ba(OH)2 (166.0 mg, 0.97 mmol) at rt under N2.The reaction mixture was stirred at 100°C overnight. The resulting mixture was filtered and concentrated in vacuo. The crude product was purified by SCX cartridges to give (2R,3R,4R,5R)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A128, 4.5 mg, 28%) as colorless oil. LC-MS (ESI) found: 164 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 3.96 (dd, J= 12.1, 1.9 Hz, 1H), 3.82 - 3.80 (m, 1H), 3.76 (dd, J= 11.4, 7.2 Hz, 1H), 3.68 - 3.64 (m, 1H), 3.62 - 3.58 (m, 2H), 3.38 - 3.35 (m, 1H), 2.97 (dd, J= 3.8, 1.8 Hz, 1H).
Synthesis 6-7. Preparation of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (Compound A127-2a) and (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (Compound A127-2b)
Figure imgf000294_0001
75 mg of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A127-2a) and 20 mg of (3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H- pyran-3-amine (A127-2b) were obtained by SFC separation from 100 mg of (3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A127-2 from Synthesis 6- 4). The SFC was performed on Waters Thar 80 preparative SFC (ChiralPak IC, 250x21.2mm I.D., 5pm; mobile phase: A for CO2 and B for MeOH + 0.1% NH3H2O, gradient (40% B); Flow rate: 50 mL/min, temperature: 35°C).
Synthesis 6-8. Preparation of tert-butyl ((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)carbamate (Compound A129)
Figure imgf000294_0002
Step 1: To a solution of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-amine (A127-2a, 60 mg, 0.14 mmol) from Synthesis 6-7 in DCM (3 mL) was added (Boc)2O (60 mg, 0.28 mmol) at rt. After stirring at rt for 2 h, the mixture was concentrated. Then the residue was purified by flash chromatography (silica gel, 0- 20% EtOAc in PE) to give tert-butyl ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A129-1, 65 mg, 0.12 mmol, 88 %) as a colorless oil. LC-MS (ESI) found: 556 [M+Na]+. 1H NMR (400 MHz, CDCh): 6 7.41 - 7.27 (m, 15H), 6.25 (d, J = 9.1 Hz, 1H), 4.97 (d, J = 10.7 Hz, 1H), 4.79 (d, J = 11.8 Hz, 1H), 4.50-4.46 (m, 4H), 4.20 (dd, J = 9.0, 2.8 Hz, 1H), 4.04 (dd, J = 12.1, 1.8 Hz, 1H), 3.87 (t, J = 7.0 Hz, 1H), 3.60- 3.56 (m, 3H), 3.47 (dd, J = 12.1, 1.8 Hz, 1H), 1.57 (s, 9H).
Step 2: To a solution of tert-butyl ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A129-1, 60 mg, 0.11 mmol) in MeOH (2 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The reaction was charged with H2 for three time and stirred at rt for 16 h. The mixture was filtered through a Celite pad, and the filtrate was concentrated. The residue was purified by prep-HPLC (Column YMC Triart C18 250*20mm, I.D: 5 urn. A: H2O (0.1% FA), B: ACN, A% from 95 to 55) to give tert-butyl ((3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)carbamate (A129, 20 mg, 0.076 mmol, 67.5%) as a colorless oil. LC-MS (ESI) found: 264 [M+H]+. 1H NMR (400 MHz, CD3OD): 3 δ.89 (dd, J = 11.9, 1.4 Hz, 1H), 3.85 - 3.82 (m, 1H), 3.75 (dd, J = 11.4, 7.1 Hz, 2H), 3.72 - 3.69 (m, 1H), 3.64 (dd, J = 11.5, 4.8 Hz, 1H), 3.48 (dt, J = 8.4, 4.2 Hz, 1H), 3.39 - 3.34 (m, 1H), 1.44 (s, 9H).
Synthesis 6-9. Alternative Preparation of (2R,3R,4R,5R)-5-amino-2- (hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A128)
Figure imgf000295_0001
A129 A128
A solution of tert-butyl ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran- 3-yl)carbamate from Synthesis 6-8 (A129, 10 mg, 0.04 mmol) in DCM(1 mL) was treated with HCl/dioxane (1 mL). The reaction mixture was stirred at rt for 3 h and then evaporated to give (2R,3R,4R,5R)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A130, 3.5 mg, 0.021 mmol, 56.5%) as a colorless oil. LC-MS (ESI) found: 164 [M+H]+.
Synthesis 6-10. Preparation of N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanesulfonamide (Compound A130)
Figure imgf000296_0003
Synthesis 6-11. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)methanesulfonamide (Compound A131)
Figure imgf000296_0001
Synthesis 6-12. Preparation of N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-l,l,l-trifluoromethanesulfonamide
(Compound A132)
Figure imgf000296_0002
Synthesis 6-13. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-l,l,l-trifluoromethanesulfonamide
(Compound A133)
Figure imgf000297_0001
Synthesis 6-14. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-2,2,2-trifluoroacetamide (Compound A134) and N-((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-2,2,2- trifluoroacetamide (Compound A135)
Figure imgf000297_0002
Step 1: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro- 2H-pyran-3 -amine from Synthesis 6-7 (Al 27-2, 1.0 g, 2.3 mmol) and TEA (0.8 mL, 5.8 mmol) in MeOH (5 mL) was added dropwise CFsCOOEt (0.41 mL, 3.46 mmol) at 0°C and the reaction was stirred at rt for 1.5 h. The resulting mixture was diluted with DCM (50 mL), washed with H2O (15 mL x 2) and brine (20 mL), dried over Na2SO4, filtered. The organic layer was concentrated in vacuo to get a crude product, which was purified by flash chromatography (silica gel, 0-80% EA in PE) to give the mixture (1.0 g) as a colorless oil. The mixture (100 mg) was then separated by SFC (OJ-H 4.6*250 mm, MeOH + 0.05% DEA, 40%, 8 min) to give N-((3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-2, 2, 2-tri fluoroacetamide (A134-1, 50.0 mg) and N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro- 2H-pyran-3-yl)-2,2,2-trifhioroacetamide (A135-1, 15.0 mg). N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-2,2,2- trifluoroacetamide (A134-1): LC-MS (ESI) found: 530 [M+H]+. 1H NMR (400 MHz, CDCh): 3 7.40 - 7.29 (m, 15H), 6.09 (d, J = 5.9 Hz, 1H), 4.90 (d, J = 11.5 Hz, 1H), 4.71 (d, J = 12.1 Hz, 1H), 4.62 (d, J = 11.5 Hz, 1H), 4.54 - 4.44 (m, 2H), 4.39 (d, J = 12.1 Hz, 1H), 4.36 - 4.27 (m, 1H), 4.25
- 4.18 (m, 1H), 4.06 (d, J = 2.2 Hz, 1H), 3.64 - 3.48 (m, 4H), 3.21 (t, J = 10.8 Hz, 1H). N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-2,2,2- trifluoroacetamide (A-135-1): LC-MS (ESI) found: 530 [M+H]+.1H NMR (400 MHz, CDCh): 3 8.26 (d, J = 8.3 Hz, 1H), 7.41 - 7.24 (m, 15H), 4.86 (d, J = 10.6 Hz, 1H), 4.72 (d, J = 11.8 Hz, 1H), 4.57 - 4.44 (m, 5H), 4.04 (dd, J = 12.5, 1.6 Hz, 1H), 3.96 (s, 1H), 3.65 - 3.49 (m, 5H).
Step 2A: To a solution of N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-2,2,2-trifluoroacetamide (A134-1, 35 mg, 0.07 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated in vacuo. The crude product was purified by prep-HPLC (Method A) to give N-((3R,4R,5R,6R)- 4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-2,2,2-trifluoroacetamide (Al 34, 6.6 mg, 39%) as a white solid. LC-MS (ESI) found: 258 [M-H]'. 1 H NMR (400 MHz, CD3OD): 84.28
- 4.15 (m, 1H), 3.95 - 3.86 (m, 2H), 3.76 - 3.61 (m, 3H), 3.44 - 3.39 (m, 1H), 3.20 (t, J = 11.0 Hz, 1H). 19F NMR (377 MHz, CD3OD): δ -77.23 (s).
Step 2B: To a solution of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-2,2,2-trifluoroacetamide (A135-1, 15 mg, 0.03 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated in vacuo. The crude product was purified by (Method B) to give N-((3 S,4R,5R,6R)-4,5-dihydroxy- 6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-2,2,2-trifluoroacetamide (A135, 4.9 mg, 66%) as a colorless oil. LC-MS (ESI) found: 258 [M-H]'. 1H NMR (400 MHz, MeOD): δ 4.12 (d, J = 2.3 Hz, 1H), 3.97 - 3.89 (m, 2H), 3.83 - 3.74 (m, 2H), 3.70 - 3.57 (m, 2H), 3.45 - 3.39 (m, 1H). 19F NMR (377 MHz, MeOD): δ -78.03 (s).
Synthesis 6-15. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)benzamide (Compound A136) and N- ((3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)benzamide
(Compound A137)
Figure imgf000299_0001
Step 1: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro- 2H-pyran-3 -amine from Synthesis 6-7 (A127-2, 0.74 g, 1.7 mmol) and DIPEA (0.85 mL, 5.1 mmol) in DCM (8.0 mL) was added benzoyl chloride (0.48 g, 3.4 mmol) dropwise at 0°C. The reaction mixture was stirred at rt for 1.5 h. The resulting mixture was diluted with DCM (10 mL), washed with H2O (10 mL x 2) and brine (10 mL), dried over Na2SO4, filtered. The organic layer was concentrated in vacuo to give a crude product, which was purified by flash chromatography (silica gel, 0-80% EA in PE) to give N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)benzamide (A136-l)and N-((3S,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)benzamide (A137-1). LC-MS (ESI) of both found: 538 [M+H]+.
Step 2A: To a solution of N-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)benzamide (A136-1, 35 mg, 0.065 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10% wt, 60% wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated in vacuo. The crude product was purified by prep-HPLC (Method A) to give N-((3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)benzamide (A136). LC-MS (ESI) of found: 268 [M+H]+.
Step 2B: To a solution of N-((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)benzamide (A137-1, 35 mg, 0.065 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated in vacuo. The crude product was purified by prep-HPLC (Method A) to give N-((3S,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)benzamide (A136). LC-MS (ESI) of found: 268 [M+H]+.
Synthesis 6-16. Alternative Preparation of (2R,3R,4R,5R)-5-amino-2-
(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A128) and (2R,3R,4R,5S)-5- amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A92)
Figure imgf000300_0001
Step 1: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro- 2H-pyran-3 -amine from Synthesis 6-7 (A127-2, 0.74 g, 1.7 mmol) and DIPEA (0.85 mL, 5.1 mmol) in DCM (8.0 mL) was added CbzCl (0.58 g, 3.4 mmol) dropwise at 0°C. The reaction mixture was stirred at rt for 1.5 h. The resulting mixture was diluted with DCM (10 mL), washed with H2O (10 mL x 2) and brine (10 mL), dried over Na2SO4, filtered. The organic layer was concentrated in vacuo to give a crude product, which was purified by flash chromatography (silica gel, 0-80% EA in PE) to give benzyl ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A128-1) and benzyl ((3S,4R,5R,6R)- 4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A92-4). LC-MS (ESI) of both found: 568 [M+H]+.
Step 2A: To a solution of benzyl ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A128-1, 35 mg, 0.06 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10% wt, 60% wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated to give (2R,3R,4R,5R)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A128). LC-MS (ESI) of both found: 164 [M+H]+.
Step 2B: To a solution of benzyl ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)carbamate (A92-4, 35 mg, 0.06 mmol ) in MeOH (3 mL) was added Pd/C (5 mg, 10% wt, 60% wet) at rt under EE. The reaction was stirred at rt under Eb atmosphere for 3 h. The resulting mixture was filtered and concentrated to give (2R,3R,4R,5S)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A92). LC-MS (ESI) of both found: 164 [M+H]+.
Synthesis 6-17. Preparation of (2R,3R,4R,5R)-5-((5-chloro-3-fluoropyridin-2-yl)amino)-2- (hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A138)
Figure imgf000301_0001
A solution of (2R,3R,4R,5R)-5-amino-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A128, 3.5 mg, 0.02 mmol), 5-chloro-2,3-difluoropyridine (8.9 mg, 0.06 mmol) and DIPEA (11.6 mg, 0.09 mmol) in z-PrOH (4 mL) was stirred at 120°C overnight. The mixture was concentrated in vacuo. The crude product was purified by pre-HPLC (Method A) to give (2R,3R,4R,5R)-5-((5- chloro-3-fluoropyridin-2-yl)amino)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A138) as a white solid (1.0 mg, 16%). LC-MS (ESI) found: 293 [M+H]+.
The following compounds are prepared by the SNAr reaction in a method similar to that of Synthesis 6-17 using either heating in isopropanol or NMP with Hunig’s base and the corresponding commercially available chloro or fluoro heterocycle.
Figure imgf000302_0001
Synthesis 6-18. Preparation of (2R,3R,4R,5R)-5-((3-(dimethylamino)-l,2,4-thiadiazol-5- yl)amino)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A151)
Figure imgf000302_0002
Synthesis 6-19. General Synthesis of Amine-containing Compounds
Figure imgf000303_0001
Synthesis 6-20. Preparation of N-((3S,4R,5R,6R)-6-(aminomethyl)-4,5-dihydroxy-2- methoxytetrahydro-2H-pyran-3-yl)acetamide (Compound A53) and N-((3S,4R,5R,6R)-6- (aminomethyl)-4,5-dihydroxy-2-methoxytetrahydro-2H-pyran-3-yl)-2,2,2- trifluoroacetamide (Compound A154)
Figure imgf000303_0002
Example 7. Synthesis of ASGPR Ligands Synthesis 7-1. General Synthesis of Sulfonamide-containing Ligands
Figure imgf000303_0003
Synthesis 7-2. General Synthesis of Sulfonyl Urea-Containing Compounds
Figure imgf000304_0001
Org. Biomol. Chem., 2017,15, 4992-4999
Synthesis 7-3. Preparation of N-(((3S,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)carbamoyl)methanesulfonamide (Compound A157)
Figure imgf000304_0002
Synthesis 7-4. General Synthesis of Sulfonimidamide-containing Ligands
Figure imgf000304_0003
A158 Synthesis 7-5. Alternative General Synthesis of Sulfonimidamide-containing Ligands
Figure imgf000305_0001
Synthesis 7-6. General Synthesis of ASGPR Ligands
Figure imgf000305_0002
Synthesis 7-7. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-phenethyltetrahydro-2H- pyran-3,4-diol (Compound A161)
Figure imgf000305_0003
Step 1: A solution of (2R,3R)-3,4-bis(benzyloxy)-2-[(benzyloxy)methyl]-3,4-dihydro-2H- pyran (A126, 6.0 g, 14.4 mmol), NIS (3.8 g, 17.3 mmol) and AgNCh (0.5 g, 2.9 mmol) in CH3CN (100 mL) was stirred at 80°C for 30 min. The mixture was filtered and concentrated to give a yellow solid, which was purified by column chromatography on silica gel to give (2R,3S,4S)-3,4- bis(benzyloxy)-2-((benzyloxy)methyl)-5-iodo-3,4-dihydro-2H-pyran (A122-1, 3.4 g, 44%) as a white solid. LC-MS (ESI) found: 543 [M+H]+. H NMR (400 MHz, CD3OD): δ 7.45 - 7.22 (m, 15H), 6.63 (d, J = 1.2 Hz, 1H), 4.81 - 4.67 (m, 3H), 4.60 - 4.38 (m, 3H), 4.34 (t, J = 7.0 Hz, 1H), 4.20 (t, J = 5.5 Hz, 1H), 4.13 (dt, J = 12.2, 6.1 Hz, 1H), 3.76 - 3.60 (m, 2H).
Step 2: To a solution of (2R,3S,4S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-iodo- 3,4-dihydro-2H-pyran (A122-1, 400 mg, 0.74 mmol) in THF (3 mL) was added Cui (14 mg, 0.074 mmol), TEA (223.45 mg, 2.212 mmol), Pd(PPh3)2C12 (85 mg, 0.074 mmol) and ethynylbenzene (0.12 mL, 1.106 mmol). The mixture was charged with N2 for three times and stirred at 60°C under N2 atmosphere overnight. The mixture was concentrated and purified by flash eluting with PEZEA (from 95/5 to 50/50) to give desired product (A160-1, 360 mg, 95%) as off-white solid. LC-MS (ESI) found: 517 [M+H]+.
Step 3: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- (phenylethynyl)-3,4-dihydro-2H-pyran (160-1, 25 mg, 0.048 mmol) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The mixture was stirred at rt under H2 atmosphere for 12 h. The mixture was filtered and concentrated to give 4.1 mg of (2R,3R,4R,5R)-2-(hydroxymethyl)-5- phenethyltetrahydro-2H-pyran-3,4-diol (A160). LC-MS (ESI) found: 253 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 7.55 - 6.74 (m, 5H), 3.95 - 3.84 (m, 2H), 3.83 - 3.77 (m, 1H), 3.74 (t, J= 3.1 Hz, 1H), 3.66 (dd, J= 11.8, 4.0 Hz, 1H), 3.51 (dt, 7.3, 3.6 Hz, 1H), 3.43 (dd, J= 11.7, 3.0 Hz, 1H), 2.70 (ddd, J= 13.6, 10.3, 5.8 Hz, 1H), 2.54 (ddd, J= 13.6, 9.8, 6.4 Hz, 1H), 2.05 - 1.76 (m, 2H), 1.70 (dt, J = 9.2, 4.5 Hz, 1H). nOe experiment was consistent with the indicated stereochemistry of the product. Using the procedure shown in Synthesis 7-7, (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(3- hydroxypropyl)tetrahydro-2H-pyran-3,4-diol (Compound A162) and N-(3-((3R,4R,5R,6R)- 4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)propyl)acetamide (Compound A163) were prepared
Figure imgf000307_0001
Synthesis 7-8. Preparation of (2R,3R,4R,5R)-5-(4-fluorophenyl)-2-
(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A164):
Figure imgf000307_0002
Step 1: To a solution of (2R,3S,4S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- iodo-3,4-dihydro-2H-pyran from Synthesis 7-7 (A122-1, 100 mg, 0.184 mmol) in DME (10 mL) was added Pd(PPh3)4 (21 mg, 0.018 mmol), K2CO3 (76 mg, 0.552 mmol) and (4- fluorophenyl)boronic acid (34 mg, 0.239 mmol). The mixture was charged with N2 for three times and stirred at 90°C under N2 for 16 h. The mixture was filtered, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by flash chromatography (silica gel, 5-10% EtOAc in PE) to give (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-(4- fluorophenyl)-3,4-dihydro-2H-pyran (A164-1, 25 mg, 31 % yield) as colorless oil. LC-MS (ESI) found: 533 [M+23]+. Step 2: To a solution of 3-((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-yl)prop-2-yn-l-ol (A164-1, 20 mg, 0.039 mmol) in MeOH (5 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under Hz atmosphere. The mixture was filtered and concentrated to give (2R,3R,4R,5R)-5-(4-fluorophenyl)-2- (hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A164, 5.0 mg, 53% yield). LC-MS (ESI) found: 243 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 7.56 - 7.42 (m, 2H), 7.04 - 6.88 (m, 2H), 4.23 (dd, J = 11.7, 7.1 Hz, 1H), 4.09 (td, J = 9.0, 2.8 Hz, 1H), 4.01 - 3.95 (m, 1H), 3.92 - 3.85 (m, 1H), 3.76 (ddd, J = 13.7, 7.4, 3.6 Hz, 2H), 3.71 - 3.62 (m, 1H), 3.02 - 2.91 (m, 1H). Using the procedures shown in Synthesis 7-8, (2R,3R,4R,5R)-5-(2,4-difluorophenyl)-2- (hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A165), (2R,3R,4R,5R)-2-
(hydroxymethyl)-5-(lH-pyrazol-3-yl)tetrahydro-2H-pyran-3,4-diol (Compound A166) and (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(lH-pyrazol-4-yl)tetrahydro-2H-pyran-3,4-diol (Compound A167) were prepared
Figure imgf000308_0002
Synthesis 7-9. Alternative General Synthesis of ASGPR Ligands:
Figure imgf000308_0001
Synthesis 7-6 and Synthesis 7-9 can be used to synthesize ligands with the following R2 groups:
Figure imgf000309_0001
wherein R is an optimal substituent has defined herein.
Synthesis 7-10: Preparation of (3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-N,N- dimethyltetrahydro-2H-pyran-3-carboxamide (Compound A169) and (3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-carboxylic acid (Compound A170)
Figure imgf000309_0002
Step 1: A solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanol (A170-1, 500 mg, 1.115 mmol), NalOi (978 mg, 4.570 mmol) and RuCh (0.002 mL, 0.028 mmol) in CCh (10 mL), H2O (15 mL), and MeCN (10 mL) was stirred at rt for 2 h. The mixture was extracted with DCM (10 mLx3). The combined organic phase was washed with brine, dried over Na2SO4, filtered and concentrated in vacuo to give a crude product, which was purified by column to give (3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-carboxylic acid (A169-1, 400 mg, 78%) as white solid. LC-MS (ESI) found: 463 [M+H]+. 1H NMR (400 MHz, MeOD): δ 7.35 - 7.19 (m, 15H), 4.75 - 4.62 (m, 3H), 4.59 - 4.39 (m, 3H), 4.28 - 4.22 (m, 1H), 4.05 (dd, J = 12.0, 7.8 Hz, 1H), 3.93 (ddd, J = 22.1, 13.1, 5.9 Hz, 2H), 3.81 (dd, J = 4.0, 2.6 Hz, 1H), 3.66 - 3.57 (m, 2H), 2.84 (dt, J = 8.0, 4.2 Hz, 1H).
Step 2: To a solution of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-carboxylic acid (A169-1, 60 mg, 0.13 mmol) in THF (5 mL) was added EDCI (30 mg, 0.16 mmol), HOBT (26 mg, 0.19 mmol), and dimethylamine (0.13 mmol, 1 M in THF). The mixture was stirred at rt for 12 h. The mixture was extracted by DCM (10 mLx3). The combined organic phase was washed with brine, dried over Na2SO4, filtered and concentrated in vacuo to give a crude product, which was purified by silica gel column to give desired product (Al 70-2). LC-MS (ESI) found: 490 [M+H]+. Need to add amounts and data later Step 3A: To a solution of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-carboxylic acid (A169-1, 30 mg, 0.065 mmol) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under H2 atmosphere. The mixture was filtered and concentrated to give (3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-carboxylic acid (A169), 3.0 mg. LC-MS (ESI) found: 193 [M+H]+.
Step 3B: To a solution of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-N,N- dimethyltetrahydro-2H-pyran-3-carboxamide (A170-2, 30 mg, 0.061 mmol) in MeOH (3 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under H2 atmosphere. The mixture was filtered and concentrated to give 2 mg of (3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)-N,N-dimethyltetrahydro-2H-pyran-3-carboxamide (A170). LC-MS (ESI) found: 220 [M+H]+. Using the procedure shown in Synthesis 7-10, l-(4-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-carbonyl)piperazin-l-yl)ethan-l-one (Compound A171), ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)(4- methylpiperazin-l-yl)methanone (Compound A172), ((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)(piperidin-l-yl)methanone (Compound A173), and (3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-carboxamide (Compound A174) were prepared
Figure imgf000311_0001
Synthesis 7-11. Preparation of (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-N'- (2,2,2-trifluoroacetyl)tetrahydro-2H-pyran-3-carbohydrazide (Compound A175)
Figure imgf000311_0002
Synthesis 7-12. Preparation of 2-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-5-(trifluoromethyl)-l,3,4-oxadiazole (Compound A176)
Figure imgf000312_0001
Synthesis 7-13. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(5-(trifluoromethyl)- l,3,4-oxadiazol-2-yl)tetrahydro-2H-pyran-3,4-diol (Compound A177)
Figure imgf000312_0002
Synthesis 7-14. Preparation of (3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-N-
(methylsulfonyl)tetrahydro-2H-pyran-3-carboxamide (Compound A178)
Figure imgf000312_0003
Synthesis 7-15. General Synthesis of Amide-Containing Ligands
Figure imgf000313_0001
Synthesis 7-16: Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyrrolidin-2-one (Compound A180)
Figure imgf000313_0002
Step 1: To a solution of (2R,3S,4S)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5-iodo- 3,4-dihydro-2H-pyran (A122-1, 100 mg, 0.184 mmol) in DMF (3 mL) was added Cui (3.4 mg, 0.018 mmol), CS2CO3 (120 mg, 0.368 mmol), pyrrolidin-2-one (43 mg, 0.552 mmol). The mixture was stirred at 160°C under microwave for 1 h. The mixture was filtered, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by flash chromatography to give l-((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro- 2H-pyran-5-yl)pyrrolidin-2-one (A180-1, 27 mg, 30% yield) as colorless oil. LC-MS (ESI) found: 500 [M+l]+. Step 2: To a solution of l-((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-yl)pyrrolidin-2-one (Al 80-1, 20 mg, 0.04 mmol) in MeOH (5 mL) was added Pd/C (5 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under H2 atmosphere. The mixture was filtered and concentrated to give 3 mg of l-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyrrolidin-2-one (Al 80). LC-MS (ESI) found: 232 [M+H]+.
Synthesis 7-17: Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-methyltetrahydro-2H- pyran-3,4-diol (Compound A181) and (2R,3R,4R,5R)-2,5-bis(hydroxymethyl)tetrahydro-
2H-pyran-3,4-diol (Compound Al-182)
Figure imgf000314_0001
Step 1: To a solution of DMF (50 mL) was added POCh (6.2 mL, 66.3 mmol) at 0°C in portions. The mixture was stirred at 0°C for 0.5 h. (2R,3R,4R)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)-3,4-dihydro-2H-pyran from Synthesis 6-3 (A126, 9.2 g, 22.1 mmol) in DMF (20 mL) was added at 0°C in portions. The mixture was stirred at rt for 5 h. The mixture was quenched with H2O, extracted with EA, washed with H2O and brine, and concentrated and purified by silica gel column to give (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro- 2H-pyran-5-carbaldehyde (A182-1, 6.0 g, 61%) as yellow oil. LC-MS (ESI) found: 445 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 9.29 (s, 1H), 7.40 - 7.14 (m, 15H), 4.76 - 4.64 (m, 4H), 4.62 - 4.54 (m, 2H), 4.48 (q, J = 12.0 Hz, 2H), 4.00 - 3.80 (m, 3H). Step 2: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-carbaldehyde (A182-1, 10.0 g, 22.4 mmol) in MeOH (50 mL) was added NaBH4 (17.0 g, 45.0 mmol) at 0°C in portions. The mixture was stirred at rt for 12 h. The mixture was quenched with H2O, extracted with EA, and concentrated to give crude ((2R,3R,4R)-3,4- bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro-2H-pyran-5-yl)methanol (A182-2, 9.5 g, 95% yield) as yellow oil. LC-MS (ESI) found: 469 [M+Na]+. 1H NMR (400 MHz, CD3OD); δ 7.38 - 7.21 (m, 15H), 6.37 (s, 1H), 4.78 (t, J = 10.9 Hz, 2H), 4.63 (dd, J = 20.6, 11.4 Hz, 2H), 4.54 - 4.37 (m, 3H), 4.28 - 4.14 (m, 2H), 4.08 - 4.02 (m, 1H), 3.89 (d, J = 11.9 Hz, 1H), 3.75-3.65 (m, 2H).
Step 3: To a solution of ((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-yl)methanol (A182-2, 6.0 g, 13.4 mmol) in MeOH (2 mL) was added Pd/C (1.2 g, 10 % wt, 60 % wet) in portions. The mixture was stirred at rt under H2 for 2 h. The mixture was filtered, concentrated, and purified by silica column to give ((3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanol (A170-1, 0.49 g, 8% yield), LC-MS (ESI) found: 449 [M+H]+, and (2R,3R,4R,5R)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)-5-methyltetrahydro-2H-pyran (A182-3, 1.1 g, 19% yield) as colorless oil, LC-MS (ESI) found: 433 [M+H]+.
Step 4A: To a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanol (A170-1, 60.0 mg, 0.134 mmol) in MeOH(2 mL) was added Pd/C (30 mg, 10 % wt, 60 % wet). The mixture was stirred at rt under H2 for 12 h. The mixture was filtered and concentrated to give (2R,3R,4R,5R)-2,5- bis(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A181, 6.3 mg, 26%) as brown oil. LC-MS (ESI) found: 179 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 4.08 (dd, J = 11.8, 2.0 Hz, 1H), 3.89 (ddd, J = 9.1, 8.4, 5.5 Hz, 2H), 3.81 (dd, J = 11.0, 4.0 Hz, 1H), 3.75 (dt, J = 11.3, 5.6 Hz, 2H), 3.64 (dd, J = 11.5, 4.6 Hz, 1H), 3.50 (dd, J = 11.8, 2.7 Hz, 1H), 3.37 (ddd, J = 13.0, 7.4, 5.1 Hz, 1H), 1.88 (d, J = 2.9 Hz, 1H).
Step 4B: To a solution of (2R,3R,4R,5R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- methyltetrahydro-2H-pyran (A182-3, 50 mg, 0.11 mmol) in MeOH (2 mL) was added Pd/C (10 mg, 10 % wt, 60 % wet). The mixture was stirred at rt under H2 for 2 h. Then the reaction mixture was filtered and concentrated to give (2R,3R,4R)-2,5-bis(hydroxymethyl)oxane-3,4-diol (Al 82, 8 mg, 40%) as a white solid. LC-MS (ESI) found: 185 [M+Na]+. 1H NMR (400 MHz, CD3OD): δ 3.85 (dd, J = 11.7, 7.6 Hz, 1H), 3.79 - 3.62 (m, 4H), 3.55-3.42 (m, 2H), 1.93 - 1.79 (m, 1H), 1.11 (d, J = 7.2 Hz, 3H).
Synthesis 7-18. Preparation of ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl 4-methylbenzenesulfonate
(Compound A183)
Figure imgf000316_0001
Step 1: To a solution of ((4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanol from Synthesis 7-17 (A170-1, 350 mg, 0.78 mmol) and TEA (394 mg, 3.90 mmol) in DCM (10 mL) was added T sCl (446 mg, 2.34 mmol) slowly at 0°C. The reaction mixture was stirred at rt overnight. The resulting mixture was extracted with EA (50 mL), washed with H2O (40 mL x 2) and brine (40 mL), dried over Na2SO4, filtered. The organic layer was separated and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-50% EA in PE) to give ((4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl 4-methylbenzenesulfonate (A183-1, 180 mg, 38%) as a yellow oil. LC-MS (ESI) found: 603 [M+H]+.
Step 2: To a solution of (2R,3R,4R)-5-(azidomethyl)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)tetrahydro-2H-pyran (A183-1, 185 mg, 0.31 mmol) in dry DMF (10 mL) was added NaNs (180 mg, 3.10 mmol). The reaction mixture was stirred at 80°C overnight. The mixture was extracted with EA (20 mL), washed with H2O (20 mL x 2) and brine (20 mL), dried over Na2SO4, filtered. The organic layer was separated and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-50% EA in PE) to give (2R,3R,4R)-5- (azidomethyl)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)tetrahydro-2H-pyran (Al 83-2, 65 mg, 45% yield) as a colorless oil. LC-MS (ESI) found: 496[M+Na]+.
Step 3: To a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanamine (Al 83-3, 65 mg, 0.14 mmol) in THF (5 mL) was added PPI13 (72 mg, 0.27 mmol) and water (5 mL). The reaction mixture was stirred at rt overnight. The mixture was concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-10% MeOH in DCM) to give ((3R,4R,5R,6R)-4,5-bis(benzyloxy)- 6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanamine (Al 83-3, 60 mg, 98% yield) as a colorless oil. LC-MS (ESI) found: 448[M+H]+.
Step 4: To a solution of N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)acetamide (Al 83-3, 30 mg, 0.067 mmol) in dry DCM (5 mL) was added DIPEA (30 mg, 0.07 mmol) and acetyl chloride (11 mg, 0.14 mmol) dropwise at 0°C under N2 atmosphere. The reaction mixture was stirred at rt for 8 h. The reaction was cooled to 0°C and quenched with saturated sodium bicarbonate solution. The mixture was extracted with EA (10 mL), washed with H2O (10 mL x 2) and brine (10 mL), dried over Na2SO4, filtered. The organic layer was separated and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-50% EA in PE) to give N-(((3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)acetamide (Al 83-4, 14 mg, 44% yield) as a colorless oil. LC-MS (ESI) found: 490[M+H]+.
Step 5: To a solution of N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)acetamide (Al 83-4, 14 mg, 0.03 mmol) in dry MeOH (5 mL) was added Pd/C (10 mg, 10 % wt, 60 % wet). The reaction mixture was charged with H2 and stirred at rt for 3 days under H2 atmosphere. The mixture was filtered and concentrated in vacuo to give N-(((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3- yl)methyl)acetamide (A183, 1 mg, 16% yield) as a colorless oil. LC-MS (ESI) found: 220[M+H]+. 1H NMR (400 MHz, CD3OD): δ 3.91 (dd, J = 11.9, 2.8 Hz, 1H), 3.85 - 3.72 (m, 3H), 3.66 (dd, J = 11.7, 4.3 Hz, 1H), 3.58 (dd, J = 13.9, 4.3 Hz, 1H), 3.48 - 3.40 (m, 3H), 1.93 (s, 3H), 1.92 - 1.84 (m, 1H).
Synthesis 7-19. Preparation of (2R,3R,4R)-5-(azidomethyl)-2-(hydroxymethyl)tetrahydro-
2H-pyran-3,4-diol (Compound Al 84)
Figure imgf000318_0002
To a solution of (2R,3R,4R)-5-(azidomethyl)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)tetrahydro-2H-pyran from Synthesis 7-18 (A183-2, 20 mg, 0.04 mmol) in dry DCM (5 mL) at -78 °C under N2 atmosphere was added BCl3 (0.4 mL, 0.04 mmol, 1 M in DCM) slowly. After the addition was complete, the reaction was stirred at 0°C for 45 min. On consumption of starting material (TLC monitoring), the reaction mixture was quenched with 1 mL MeOH. The mixture was concentrated in vacuo. The crude product was purified by pre-HPLC (Method A) to give (2R,3R,4R)-5-(azidomethyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Al 84, 0.7 mg, 8% yield) as a colorless oil. LC-MS (ESI) found: 226 [M+Na]+. 1H NMR (400 MHz, CD3OD): δ 3.99 (dd, J = 11.9, 2.0 Hz, 1H), 3.82 (dd, J = 5.4, 3.3 Hz, 1H), 3.79 - 3.74 (m, 2H), 3.73 - 3.67 (m, 2H), 3.64 (dd, J = 11.5, 4.5 Hz, 1H), 3.48 - 3.44 (m, 1H), 3.40 - 3.36 (m, 1H), 1.97 - 1.84 (m, 1H).
Synthesis 7-20. Preparation of (2R,3R,4R,5R)-5-(aminomethyl)-2-
(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A185)
Figure imgf000318_0001
To a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran- 3 -yl)m ethanamine from Synthesis 7-18 (Al 83-3, 20 mg, 0.044 mmol) in dry MeOH (5 mL) was added Pd/C (5 mg, 10% wt, 60% wet). The reaction mixture was charged with H2 and stirred at rt for 3 days under H2 atmosphere. Then the mixture was filtered and concentrated in vacuo to give (2R,3R,4R,5R)-5-(aminomethyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Al 85) as a colorless oil. LC-MS (ESI) found: 178 [M+H]+.
Synthesis 7-21. Preparation of N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-2,2,2-trifluoroacetamide
(Compound A186)
Figure imgf000319_0001
Step 1: To a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanamine from Synthesis 7-18 (A183-3, 30 mg, 0.067 mmol) in dry MeOH (5 mL) was added ethyl 2,2,2-trifluoroacetate (19 mg, 0.134 mmol) and tri ethylamine (26 mg, 0.201 mmol) at rt. The reaction mixture was stirred at rt overnight. The resulting mixture was diluted with EA (10 mL), washed with H2O (10 mL x 2) and brine (10 mL), dried over Na2SO4, filtered. The organic layer was concentrated in vacuo to get a crude product, which was purified by flash chromatography (silica gel, 0-50% EA in PE) to give N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3- yl)methyl)-2,2,2-trifluoroacetamide (A186-1, 16 mg, 44%) as a yellow oil. LC-MS (ESI) found: 566 [M+Na]+.
Step 2: To a solution of N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-2,2,2-trifluoroacetamide (A186-1, 16 mg, 0.029 mmol) in dry MeOH (5 mL) was added Pd/C (3 mg, 10% wt, 60% wet). The reaction mixture was charged with H2 for three times and stirred at rt for 3 days under H2 atmosphere. The mixture was filtered and concentrated in vacuo to give 3 mg of N-(((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)methyl)-2,2,2-trifluoroacetamide (Al 86) as colorless oil. LC-MS (ESI) found: 274 / 296 [M+H]+ / [M+Na]+.
Synthesis 7-22. Preparation of N-((l-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-lH-l,2,3-triazol-4- yl)methyl)acetamide (Compound A187)
Figure imgf000320_0001
Step 1: A solution of THPTA (0.32 mg, 0.001 mmol) and Q1SO4 (2.4 mg, 0.02 mmol) in H2O (0.5 mL) was added to a solution of (2R,3R,4R)-5-(azidomethyl)-3,4-bis(benzyloxy)-2- ((benzyloxy)methyl)tetrahydro-2H-pyran from Synthesis 7-18 (A183-2, 32.0 mg, 0.07 mmol) and N-(prop-2-yn-l-yl)acetamide (8.6 mg, 0.09 mmol) in MeOH (2 mL). A freshly-prepared solution of sodium ascorbate (5.9 mg, 0.03 mmol) in H2O (0.5 mL) was added and the reaction mixture was stirred at room temperature for 24 h. Then the mixture was concentrated and the residual was purified by flash chromatography (0-5% methanol in di chloromethane) to give N-((l- (((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)- lH-l,2,3-triazol-4-yl)methyl)acetamide (A187-1, 33 mg, 78%) as oil. LC-MS (ESI) found: 571 [M+H]+.
Step 2: To a solution of N-((l-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-lH-l,2,3-triazol-4-yl)methyl)acetamide (Al 87-1, 16 mg, 0.03 mmol) in MeOH (3 mL) was added Pd/C (2 mg, 10 %wt, 60% wet), the mixture was charged with H2 for three times and stirred at the room temperature under H2 atmosphere overnight. The mixture was filtered, the filtrate was concentrated under reduced pressure to give a crude product, which was purified by flash chromatography (0-50% ethyl acetate in petroleum ether) to give N-((l-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-lH-l,2,3-triazol-4-yl)methyl)acetamide (A187, 2 mg, 24%). LC-MS (ESI) found: 301 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 7.85 (s, 1H), 4.83 (s, 1H), 4.68 (dd, J= 14.1, 1.9 Hz, 1H), 4.42 (s, 2H), 3.91 (dd, J= 5.3, 3.2 Hz, 1H), 3.82 (dd, J= 11.5, 7.1 Hz, 2H), 3.75 - 3.68 (m, 2H), 3.49 - 3.40 (m, 2H), 2.33 - 2.23 (m, 1H), 1.98 (s, 3H).
Synthesis 7-23. Preparation of (2R,3R,4R,5R)-5-(((3-chloro-l,2,4-thiadiazol-5- yl)amino)methyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A188)
Figure imgf000321_0001
1: A solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanamine from Synthesis 7-18 (A183-3, 50 mg, 0.112 mmol), 5-chloro-2,3-difluoropyridine (51 mg, 0.336 mmol) and DIPEA (44 mg, 0.336 mmol) in z-PrOH (5 mL) was stirred at rt overnight. The mixture was concentrated in vacuo. The crude product was purified by pre-HPLC (Method A) to give N-(((3R,4R,5R,6R)-4,5- bis(benzyl oxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-3-chl oro-1, 2,4- thiadiazol-5-amine (Al 88-1, 25 mg, 40%). LC-MS (ESI) found: 566 [M+H]+
Step 2: To a solution of N-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)-3-chloro-l,2,4-thiadiazol-5-amine (Al 88- 1, 25 mg, 0.044 mmol) in dry DCM (5 mL) was added BCl3 (0.44 mL, 1 M in DCM) dropwise at -10°C under N2 atmosphere. The reaction mixture was stirred at rt for 0.5 h. Then the reaction was cooled to 0°C and quenched with saturated sodium bicarbonate solution. The mixture was filtered and concentrated in vacuo. The crude product was purified by prep-HPLC (Method A) to give 7 mg of (2R,3R,4R,5R)-5-(((3-chloro-l,2,4-thiadiazol-5-yl)amino)methyl)-2-
(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Al 88). LC-MS (ESI) found: 296 [M+H]+. Synthesis 7-24. Preparation of (E)-2-((((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)methyl)amino)ethene-l-sulfonyl fluoride
(Compound A189)
Figure imgf000322_0001
Organic Letters 202022 (11), 4316-4321
Synthesis 7-25. Preparation of 2-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)acetonitrile (Compound A190)
Figure imgf000322_0002
Step 1: To a solution of ((3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)m ethyl 4-methylbenzenesulfonate from Synthesis 7-18 (A183-1, 200 mg, 0.46 mmol) in DMSO (5 mL) was added NaCN (68 mg, 1.39 mmol) at room temperature. The mixture was stirred at rt overnight. Then the mixture was extracted by
DCM (10 mL * 3) and the organic phase was concentrated. The residual was then purified by silica gel column (0-22% ethyl acetate in petroleum ether) to give 2-((3R,4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetonitrile (A190-1, 80 mg, 38%) as an oil. LC-MS (ESI) found: 458 [M+H]+.
Step 2: To a solution of 2-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetonitrile (A190-1. 15 mg, 0.03 mmol) in dry DCM (3 mL) was added BCl3 (0.33 mL, 0.33 mmol, 1 M in DCM) dropwise at -10°C under N2 atmosphere. The reaction mixture was stirred at rt for 0.5 h. Then the reaction was cooled to 0°C and quenched with saturated sodium bicarbonate solution. The mixture was filtered and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel, 0-40% MeOH in DCM) to give 2-((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-3-yl)acetonitrile (A190, 2 mg, 33%) as a colorless oil. LC-MS (ESI) found: 188 [M+H]+. 1H NMR (400 MHz, MeOD): δ 4.05 (dd, J = 12.3, 1.8 Hz, 1H), 3.80 (ddd, J = 16.3, 8.4, 4.5 Hz, 3H), 3.68 (d, J = 4.3 Hz, 1H), 3.66 - 3.58 (m, 2H), 3.42 (ddd, J = 7.2, 4.5, 1.6 Hz, 1H), 2.98 (dd, J
= 17.4, 11.3 Hz, 1H), 2.85 (ddd, J = 17.4, 3.8, 1.3 Hz, 1H).
Synthesis 7-26. Preparation of (2R,3R,4R,5S,6S)-2-(hydroxymethyl)-5-methyl-6- phenoxytetrahydro-2H-pyran-3,4-diol (Compound A191), (2R,3R,4R,5S,6R)-2- (hydroxymethyl)-5-methyl-6-phenoxytetrahydro-2H-pyran-3,4-diol (Compound A192), and (2R,3R,4R,5S)-2-(hydroxymethyl)-5-(phenoxymethyl)tetrahydro-2H-pyran-3,4-diol
Figure imgf000323_0001
Step 1: To a solution of ((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-yl)methanol from Synthesis 7-17 (Al 82-2, 100 mg, 0.224 mmol, 1.0 eq), PPh3 (88 mg, 0.336 mmol, 1.5 eq) and nucleophiles (1.0 eq) in dry DCM (1.1 mL) was added DIAD (0.053 mL, 0.269 mmol, 1.2 eq) dropwise at ice-bath under N2 atmosphere. Then the reaction was allowed to warm to rt. The resulting reaction mixture was stirred at the same temperature for another 40 min, at which time TLC showed the disappearance of all starting material. The mixture was evaporated. The crude product was further purified by silica gel column chromatography to give desired products. Yield (A192-1): 30 mg, 26%. LC-MS (ESI) found: 545 [M+Na]+. Yield (A193-1): 70 mg, 60%. LC-MS (ESI) found: 545 [M+Na]+.
Step 2A: A suspension of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- methylene-6-phenoxytetrahydro-2H-pyran (Al 92-1, 100 mg, 1.0 eq) and Pd/C (0.2 eq, 10 % wt, 60 % wet) in MeOH was charged with H2 and stirred under H2 atmosphere. The reaction was stirred at rt and monitored by TLC. When TLC showed the disappearance of all starting material, the mixture was filtered and evaporated. The crude product was further purified by silica gel column chromatography to give desired products. Yield (A192): 0.5 mg, 2%. Yield (A191): 7 mg, 14%. LC-MS (ESI) found: 277 [M+Na]+. 1H NMR (400 MHz, CD3OD) δ 7.30 - 7.22 (m, 2H), 7.13 - 7.06 (m, 2H), 6.96 (tt, J= 7.4, 1.1 Hz, 1H), 5.44 (d, J= 1.8 Hz, 1H), 4.11 (dd, J= 5.5, 3.5 Hz, 1H), 3.89 (d, J= 2.2 Hz, 2H), 3.75 - 3.68 (m, 2H), 2.20 (ddd, J= 7.4, 5.3, 1.8 Hz, 1H), 1.23 (d, J = 7.4 Hz, 3H).
Step 2B: (2R,3R,4R,5S)-2-(hydroxymethyl)-5-(phenoxymethyl)tetrahydro-2H-pyran-3,4- diol) (Al 93) was synthesized according to the hydrogenation procedure described for Step 2A above. Yield: 9.8 mg, 20%. LC-MS (ESI) found: 277 [M+Na]+. 1H NMR (400 MHz, Methanol- d 4): δ 7.30 - 7.19 (m, 2H), 6.95 - 6.84 (m, 3H), 4.37 (t, J= 10.0 Hz, 1H), 4.24 (ddd, J= 9.7, 3.0, 1.4 Hz, 1H), 4.14 (dd, J= 11.7, 1.9 Hz, 1H), 3.91 (dd, J= 5.6, 3.2 Hz, 1H), 3.81 - 3.74 (m, 2H), 3.66 (dd, J= 11.5, 4.6 Hz, 1H), 3.51 (ddd, J= 11.7, 2.6, 1.4 Hz, 1H), 3.41 (ddd, J= 7.2, 4.6, 1.7 Hz, 1H), 2.22 (ddd, J= 10.2, 5.4, 2.7 Hz, 1H). Synthes 5-27. Preparation of (2R,3R,4R,5S,6S)-2-(hydroxymethyl)-5-methyl-6-(lH-tetrazol- l-yl)tetrahydro-2H-pyran-3,4-diol (Compound A194), (2R,3R,4R,5S,6R)-2-
(hydroxymethyl)-5-methyl-6-(lH-tetrazol-l-yl)tetrahydro-2H-pyran-3,4-diol (Compound
A195), and (2R,3R,4R,5R)-5-((lH-tetrazol-l-yl)methyl)-2-(hydroxymethyl)tetrahydro-2H- pyran-3,4-diol (Compound A196)
Figure imgf000325_0001
Step 1: l-((4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-3- methylenetetrahydro-2H-pyran-2-yl)-lH-tetrazole (A195-1) and l-(((2R,3R,4R)-3,4- bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro-2H-pyran-5-yl)methyl)-lH-tetrazole (Al 96- 1) were synthesized according to the Mitsunobu procedure described in Synthesis 7-26 using 500 mg of ((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro-2H-pyran-5- yl)methanol (A182-2) from Synthesis 7-17. l-((4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-3-methylenetetrahydro-2H-pyran-2-yl)-lH-tetrazole (A195-1) Yield: 50 mg, 9%. LC-MS (ESI) found: 521 [M+Na]+. l-(((2R,3R,4R)-3,4-bis(benzyloxy)-2-
((benzyloxy)methyl)-3,4-dihydro-2H-pyran-5-yl)methyl)-lH-tetrazole (A196-1) Yield: 15 mg, 5%. LC-MS (ESI) found: 521 [M+Na]+.
Step 2A: (2R,3R,4R,5S,6R)-2-(hydroxymethyl)-5-methyl-6-(lH-tetrazol-l-yl)tetrahydro- 2H-pyran-3,4-diol (A195) and (2R,3R,4R,5S,6S)-2-(hydroxymethyl)-5-methyl-6-(lH-tetrazol-l- yl)tetrahydro-2H-pyran-3,4-diol (A194) were synthesized according to the hydrogenation procedure described in Synthesis 7-26 using 65 mg of l-((4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-3-methylenetetrahydro-2H-pyran-2-yl)-lH-tetrazole (Al 95-1): Yield
((2R,3R,4R,5S,6R)-2-(hydroxymethyl)-5-methyl-6-(lH-tetrazol-l-yl)tetrahydro-2H-pyran-3,4- diol) (A195): 3 mg, 10%. LC-MS (ESI) found: 253 [M+Na]+. Yield ((2R,3R,4R,5S,6S)-2- (hydroxymethyl)-5-methyl-6-(lH-tetrazol-l-yl)tetrahydro-2H-pyran-3,4-diol) (A194): 1 mg, 3%. LC-MS (ESI) found: 253 [M+Na]+.
Step 2B: (2R,3R,4R,5R)-5-((lH-tetrazol-l-yl)methyl)-2-(hydroxymethyl)tetrahydro-2H- pyran-3,4-diol (A196)was synthesized according to the hydrogenation procedure described in Synthesis 7-26 using 14.4 mg of l-(((2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4- dihydro-2H-pyran-5-yl)methyl)-lH-tetrazole (A196-1):. Yield ((2R,3R,4R,5R)-5-((lH-tetrazol- l-yl)methyl)-2-(hydroxym ethyl )tetrahydro-2H-pyran-3,4-diol) (A196): 2 mg, 30%. LC-MS (ESI) found: 231 [M+H]+. 1H NMR (400 MHz, MeOD): 6 8.68 (s, 1H), 5.20 (dd, J = 14.0, 11.0 Hz, 1H), 5.05 - 4.93 (m, 1H), 3.93 (dd, J = 5.5, 3.2 Hz, 1H), 3.87 - 3.76 (m, 3H), 3.70 (dd, J = 11.5, 4.6 Hz, 1H), 3.50 - 3.38 (m, 2H), 2.54 - 2.22 (m, 1H).
Synthesis 7-28. (2R,3R,4R,5R)-2-(hydroxymethyl)-5-((4-(trifluoromethyl)-lH-pyrazol-l- yl)methyl)tetrahydro-2H-pyran-3,4-diol (Compound A197), l-(((3R,4R,5R,6R)-4,5- dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)methyl)-lH-pyrazole-4- carbonitrile (Compound A198), (2R,3R,4R,5R)-5-((4-chloro-lH-pyrazol-l-yl)methyl)-2- (hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A199), and (2R,3R,4R,5R)-5- ((lH-pyrazolo[3,4-b]pyridin-l-yl)methyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A200) were prepared using the procedure shown in Synthesis 7-26
Figure imgf000327_0001
Synthesis 7-29. Preparation of (2R,3R,4R,5S,6S)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-6- phenoxytetrahydro-2H-pyran-3,4-diol (Compound A200) and (2R,3R,4R,5S,6R)-5-(2- hydroxyethyl)-2-(hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4-diol (Compound
Figure imgf000327_0002
Step 1: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- methylene-6-phenoxytetrahydro-2H-pyran from Synthesis 7-26 (A192-1, 100 mg, 0.19 mmol) in DCM (10 mL) was added prop-2-en-l-ol (110 mg, 1.9 mmol) and Grubbs catalyst 2nd generation (16 mg, 0.019 mmol). The reaction was charged with N2 for three time and stirred at 40°C for 16 h. LCMS showed the desired product was detected. The solvent was concentrated in vacuo to get a crude product, which was purified by column to afford (Z)-2-((4R,5R,6R)-4,5-bis(benzyloxy)- 6-((benzyloxy)methyl)-2-phenoxydihydro-2H-pyran-3(4H)-ylidene)ethan-l-ol (A200-1) as yellow oil. LC-MS (ESI) found: 553 [M+H]+. Reference: Journal of the American Chemical Society, 123(42), 10417-10418; 2001.
Step 2: A solution of (Z)-2-((4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- phenoxydihydro-2H-pyran-3(4H)-ylidene)ethan-l-ol (A200-1, 50 mg, 0.09 mmol) and Pd/C (5 mg, 10 % wt, 60 % wet) in MeOH was stirred under H2 atmosphere. The reaction was stirred at r.t overnight Then the mixture was filtered and evaporated. The crude product was further purified by silica gel column chromatography to give (2R,3R,4R,5S,6S)-5-(2-hydroxyethyl)-2- (hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4-diol (A200) and (2R,3R,4R,5S,6R)-5-(2- hydroxyethyl)-2-(hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4-diol (A201). LC-MS (ESI): 285 [M+H]+.
Synthesis 7-30. Preparation of (2R,3R,4R,5S,6S)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-6- phenoxytetrahydro-2H-pyran-3,4-diol (Compound A202) and (2R,3R,4R,5S,6R)-5-(2- hydroxyethyl)-2-(hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4-diol (Compound A203)
Figure imgf000328_0001
Step 1: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- methylene-6-phenoxytetrahydro-2H-pyran from Synthesis 7-26 (A192-1, 100 mg, 0.19 mmol) in DCM ( 10 mL was added N-allylacetamide (188 mg, 1.9 mmol) and Grubbs catalyst 2nd generation (16 mg, 0.019 mmol). The reaction was charged with N2 for three time and stirred at 40°C for 16 h. LCMS showed the desired product was detected. The solvent was concentrated in vacuo to get a crude product, which was purified by column to afford N-((Z)-2-((4R,5R,6R)-4,5- bis(benzyloxy)-6-((benzyloxy)methyl)-2-phenoxydihydro-2H-pyran-3(4H)- ylidene)ethyl)acetamide (A202-1). LC-MS (ESI) found: 594 [M+H]+. Reference: Journal of the American Chemical Society, 123(42), 10417-10418; 2001.
Step 2: A solution of (Z)-2-((4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- phenoxydihydro-2H-pyran-3(4H)-ylidene)ethan-l-ol (A202-1, 50 mg, 0.08 mmol) and Pd/C (5 mg, 10 % wt, 60 % wet) in MeOH was stirred under Hz atmosphere. The reaction was stirred at r.t overnight Then the mixture was filtered and evaporated. The crude product was further purified by silica gel column chromatography to give (2R,3R,4R,5S,6S)-5-(2-hydroxyethyl)-2- (hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4-diol (Compound A202) and (2R,3R,4R,5S,6R)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-6-phenoxytetrahydro-2H-pyran-3,4- diol (Compound A203). LC-MS (ESI): 326 [M+H]+.
Synthesis 7-31. Preparation of di-tert-butyl 2-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)malonate (Compound A204)
Figure imgf000329_0001
Synthesis 7-32. Preparation of 3-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)propanoic acid (Compound A205)
Figure imgf000329_0002
A204 A205
Synthesis 7.33. Preparation of N-(2-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)ethyl)acetamide (Compound A206) and N-(2- ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)ethyl)-2,2,2- trifluoroacetamide (Compound A207)
Figure imgf000330_0001
Step 1: A solution of 2-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)acetonitrile (A190-1, 100 mg, 0.22 mmol) and Raney Ni (15 mg) in MeOH was charged with H2 for three times and stirred under H2 atmosphere overnight Then the mixture was filtered and evaporated. The crude product was further purified by silica gel column chromatography to give 2-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)ethan-l -amine (A206-1). LC-MS (ESI): 462 [M+H]+.
Step 2: To a solution of 2-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)ethan-l -amine (A206-1, 80 mg, 0.17 mmol) in MeOH (5 mL) was added Pd/C (10 mg, 10 % wt, 60 % wet). The reaction was charged with H2 for three time and stirred under H2 atmosphere overnight. The crude product was obtained by filtration and concentration. LC-MS (ESI) found for both targets: 192 [M+H]+.
Step 3A: To a solution of (2R,3R,4R,5R)-5-(2-aminoethyl)-2-(hydroxymethyl)tetrahydro- 2H-pyran-3,4-diol (A206-2, 15 mg, 0.078 mmol) in THF (2 mL) was added AcCl (9.1 mg, 0.118 mmol) and TEA (23.6 mg, 0.234 mmol) at rt. The mixture was stirred at rt for 2 h. The mixture was concentrated and the crude material was purified by silica gel column to give N-(2- ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)ethyl)acetamide (A206). LC-MS (ESI) found: 234 [M+H]+. Step 3B: To a solution of (2R,3R,4R,5R)-5-(2-aminoethyl)-2-(hydroxymethyl)tetrahydro- 2H-pyran-3,4-diol (A206-2, 15 mg, 0.078 mmol) in MeOH (2 mL) was added CFsCOOEt (16.7 mg, 0.118 mmol) and TEA (23.6 mg, 0.234 mmol) at rt. The mixture was stirred at rt for 2 h. The mixture was concentrated and the crude material was purified by silica gel column to give N-(2- ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)ethyl)-2,2,2- trifluoroacetamide (A207). LC-MS (ESI) found: 288 [M+H]+.
Synthesis 7-34. Preparation of 4-nitrophenyl 3-(((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)methyl)-l,l-dimethylurea (Compound A208)
Figure imgf000331_0001
To a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanamine from Synthesis 7-18 (A183-3, 100 mg, 0.224 mmol) in DCM (5 mL) was added 4-nitrophenyl carb onochlori date (67.4 mg, 0.336 mmol) and DIPEA (87.0 mg, 0.672 mmol) at rt. The mixture was stirred at rt overnight. The mixture was concentrated and used directly for next step. LC-MS (ESI) found: 613 [M+H]+.
Step 2: To a solution of 4-nitrophenyl (((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)carbamate (A208-1, 137 mg, 0.224 mmol) in DCM (5 mL) was added dimethylamine (0.448 mmol, 1 M in THF) and DIPEA (87.0 mg, 0.672 mmol) at rt. The mixture was stirred at rt overnight. The mixture was concentrated and purified by silica gel column to give 30 mg of the desired product (A208-2). LC-MS (ESI) found: 519 [M+H]+.
Step 3: To a solution of 3-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)m ethyl)- 1,1 -dimethylurea (A208-2, 30 mg, 0.058 mmol) in MeOH (3 mL) was added Pd/C (6 mg, 10 % wt, 60 % wet). The reaction was charged with H2 for three times and stirred under H2 atmosphere overnight. The crude product was obtained by filtration and concentration. LC-MS (ESI): 249 [M+H]+.
Synthesis 7-35. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-
(morpholinomethyl)tetrahydro-2H-pyran-3,4-diol (Compound A209)
Figure imgf000332_0001
Step 1: a solution of ((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methanol from Synthesis 7-17 (A192-2, 500.0 mg, 1.11 mmol) in DCM (5 mL) was added DMP (945.5 mg, 2.22 mmol) at 0°C in portions. The mixture was stirred at rt for 5 h. The mixture was quenched with aqueous NaHCO3. The two phases were separated and the organic phase was dried over Na2SO4, filtered and concentrated to give a crude product, which was purified by column to give (3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-carbaldehyde (A209-1, 350.2 mg, 70%) as yellow oil. LC-MS (ESI) found: 447 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 9.93 (s, 1H), 7.47 - 7.14 (m, 15H), 4.81 - 4.37 (m, 8H), 4.17 - 3.95 (m, 2H), 3.79 - 3.62 (m, 1H), 3.59 - 3.41 (m, 2H), 2.70 (s, 1H).
Step 2: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-[(benzyloxy)methyl]oxane-3- carbaldehyde (A209-2, 60.0 mg, 0.134 mmol) and morpholine(0.024 mL, 0.269 mmol) in DCM (2 mL) was added NaBH(OAc)3 (170 mg, 0.269 mmol) at 0°C in portions. The mixture was stirred at rt for 2 h. The mixture was quenched with H2O and concentrated in vacuo to give a crude product, which was purified by prep-HPLC to give 4-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)morpholine (A209-2, 62 mg, 89%) as colorless oil. LC-MS (ESI) found: 518 [M+H]+.
Step 3: To a solution of 4-(((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)methyl)morpholine (A290-2, 60.0 mg, 0.116 mmol) in MeOH (2 mL) was added Pd/C (30 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under H2 atmosphere. The mixture was filtered and concentrated to give (2R,3R,4R,5R)- 2-(hydroxymethyl)-5-(morpholinomethyl)tetrahydro-2H-pyran-3,4-diol (A209, 4.2 mg, 15%) as yellow oil. LC-MS (ESI) found: 248 [M+H]+. 1H NMR (400 MHz, MeOD); 53.87 - 3.81 (m, 2H), 3.76 (dd, J = 6.8, 4.7 Hz, 2H), 3.68 (ddd, J = 13.9, 9.3, 4.4 Hz, 6H), 3.56 (dd, J = 12.1, 3.2 Hz, 1H), 3.37 (ddd, J = 7.2, 4.5, 1.5 Hz, 1H), 3.23 (dd, J = 12.8, 9.4 Hz, 1H), 2.68 - 2.52 (m, 4H), 2.14 (d, J = 4.5 Hz, 1H).
Synthesis 7-36. Preparation of l-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-
((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-N,N-dimethylmethanamine (Compound
A2010)
Figure imgf000333_0001
Step 1: To a solution of (4R,5R,6R)-4,5-bis(benzyloxy)-6-[(benzyloxy)methyl]oxane-3- carbaldehyde from Synthesis 7-35 (A209-1, 60 mg, 0.134 mmol) and dimethylamine hydrochloride (33 mg, 0.403 mmol) in DCM (2 mL) was added NaBH(OAc)3 (170 mg, 0.134 mmol) at 0°C in portions. The mixture was stirred at rt for 2 h. The mixture was quenched with H2O and concentrated to give a crude product, which was purified by prep-HPLC (Method A) to give l-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)- N,N-dimethylmethanamine (A210-1, 60 mg, 94%) as colorless oil. LC-MS (ESI) found: 476 [M+H]+. 1H NMR (400 MHz, CD3OD): δ 7.42 - 7.20 (m, 15H), 4.79 (d, J = 11.2 Hz, 1H), 4.66 (d, J = 12.4 Hz, 2H), 4.56 - 4.41 (m, 3H), 3.94 (dd, J = 11.9, 2.7 Hz, 1H), 3.89 - 3.80 (m, 2H), 3.70 - 3.61 (m, 2H), 3.52 (ddd, J = 13.9, 12.7, 6.0 Hz, 2H), 2.98 - 2.86 (m, 1H), 2.76 (s, 1H), 2.29 (s, 6H), 2.16 (d, J = 7.2 Hz, 1H).
Step 2: To a solution of l-((3R,4R,5R,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)tetrahydro-2H-pyran-3-yl)-N,N-dimethylmethanamine (A210-1, 60 mg, 0.126 mmol) in MeOH (3 mL) was added Pd/C (10 mg, 10 % wt, 60 % wet). The mixture was stirred at rt for 12 h under H2 atmosphere. The mixture was filtered and concentrated to give (2R,3R,4R,5R)-5-((dimethylamino)methyl)-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (A210) as yellow oil. LC-MS (ESI) found: 206 [M+H]+.
Synthesis 7-37. l-(4-(((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-3-yl)methyl)piperazin-l-yl)ethan-l-one (Compound A211), (2R,3R,4R,5R)-2-
(hydroxymethyl)-5-((4-methylpiperazin-l-yl)methyl)tetrahydro-2H-pyran-3,4-diol
(Compound A212), and (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(piperidin-l- ylmethyl)tetrahydro-2H-pyran-3,4-diol (Compound A213) were prepared using the procedure of Synthesis 7-36.
Figure imgf000334_0001
Synthesis 7-38. Preparation of (2R,3R,4R,5S,6R)-5-amino-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (Compound A214)
Figure imgf000335_0001
Step 1: To a mixture of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro- 2H-pyran from Synthesis 6-3 (A126, 6.5 g, 15.6 mmol) and l-dodecyl-3-methylImidazolium tetrafluoroborate (1.06 g, 3.1 mmol) in DCM (65 mL) was added acetone (26 mL) and NaHCCh (49 mL). Then oxone (19.5 g, mmol) in H2O (81 mL) was added dropwise to the stirring reaction at 0°C. After 2 hours, the mixture was quenched with H2O and extracted with EA. The combined organic layer was washed with brine, dried over anhydrous Na2SO4, filtered. The filtrate was concentrated to give (lS,3R,4S,5S,6R)-4,5-bis(benzyloxy)-3-((benzyloxy)methyl)-2,7- dioxabicyclo[4.1.0]heptane (A214-1, 6.0 g, 89%) as a colorless oil. LC-MS (ESI) found: 433 [M+H]+.
Step 2: A solution of (lS,3R,4S,5S,6R)-4,5-bis(benzyloxy)-3-((benzyloxy)methyl)-2,7- dioxabicyclo[4.1.0]heptane (A214-1, 6.0 g, 13.9 mmol) in MeOH (0.6 mL, 13.9 mmol) was stirred at rt overnight. The mixture was concentrated and purified by chromatography on (silical gel, 0- 50% ethyl acetate in petroleum ether) to give (2R,3R,4R,5S,6R)-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-ol (A214-2, 4.5 g, 70%) as a white solid. LC-MS (ESI) found: 465 [M+H]+.
Step 3: To a mixture of (2R,3R,4R,5S,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-ol (A214-2, 200 mg, 0.43 mmol) in dry DCM (5.0 mL) was added dry pyridine (0.53 mL) and Tf20 (705 mg, 0.43 mmol) at 0°C under N2. After stirring for 2 h, the mixture was concentrated and purified by chromatography on (0-30% ethyl acetate in petroleum) to give (2R,3R,4S,5S,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxytetrahydro-2H- pyran-3-yl trifluoromethanesulfonate (A214-3, 137 mg, 53.3%) as a yellow oil. LC-MS (ESI) found: 597 [M+H]+. 1H NMR (400 MHz, CDCh) 6 7.37 - 7.25 (m, 15H), 5.23 (dd, J= 9.8, 3.7 Hz, 1H), 4.96 (d, J= 3.7 Hz, 1H), 4.89 (d, J= 11.2 Hz, 1H), 4.74 - 4.62 (m, 2H), 4.51 - 4.39 (m, 3H), 4.05 - 3.98 (m, 2H), 3.92 (t, J= 6.5 Hz, 1H), 3.53 (t, J= 5.2 Hz, 2H), 3.43 (d, J= 10.1 Hz, 3H).
Step 4: A solution of (2R,3R,4S,5S,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-yl trifluoromethanesulfonate (A214-3, 200 mg, 0.336 mmol) and benzyl amine (360 mg, 3.36 mmol) in dry THF (2 mL) was heated to 80°C in seal tube. The resulting reaction mixture was monitored by TLC. When TLC showed the disappearance of all starting material, the mixture was evaporated. The crude product was further purified by silica gel column chromatography (PEZEA = 1 : 1) to give desired product (A214-4, 250 mg, 67% yield) as yellow oil. LC-MS (ESI) found: 554[M+H]+.
Step 5: To a solution of (2R,3S,4R,5R,6R)-N-benzyl-4,5-bis(benzyloxy)-6- ((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-amine (A214-4, 35 mg, 0.063 mmol ) in MeOH (3 mL) was added Pd/C (10 mg, 10% wt, 60% wet) at rt under H2. The reaction was stirred at rt under H2 atmosphere for 3 h. The resulting mixture was filtered and concentrated in vacuo to give (2R,3R,4R,5S,6R)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A214) as a white solid. LC-MS (ESI) found: 194[M+H]+.
Synthesis 7-39. Preparation of N-((2R,3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)acetamide (Compound A215)
Figure imgf000336_0001
Synthesis 7-40. Alternative Preparation of (2R,3R,4R,5S,6R)-5-amino-2-(hydroxymethyl)-6- methoxytetrahydro-2H-pyran-3,4-diol (Compound A214)
Figure imgf000337_0001
Step 1: (2R,3S,4R,5R,6R)-3-azido-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran (A215-2) was prepared following a similar procedure for (2R,3S,4R,5R,6R)-N-benzyl-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxytetrahydro- 2H-pyran-3 -amine (A214-4) in Synthesis 7-38. Yield: 300 mg, 73%. LC-MS (ESI) found: 512 [M+Na]+.
Synthesis 7-41: Preparation of (2R,3R,4R,5S,6R)-2-(hydroxymethyl)-6-methoxy-5- (methylamino)tetrahydro-2H-pyran-3,4-diol (Compound A216)
Figure imgf000337_0002
Step 1: (2R,3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxy-N- methyltetrahydro-2H-pyran-3 -amine (A216-1) was prepared following a similar procedure for (2R,3S,4R,5R,6R)-N-benzyl-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxytetrahydro- 2H-pyran-3 -amine (A214-4) in Synthesis 7-38. LC-MS (ESI) found: 478 [M+H]+.
Step 2: (2R,3R,4R,5S,6R)-2-(hydroxymethyl)-6-methoxy-5-(methylamino)tetrahydro- 2H-pyran-3,4-diol (A216) was prepared following a similar procedure for (2R,3R,4R,5S,6R)-5- amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A214) in Synthesis 7-38. LC-MS (ESI) found: 208 [M+H]+. Synthesis 7-42. Preparation of (2R,3R,4S,5S,6R)-2-(hydroxymethyl)-5,6- dimethoxytetrahydro-2H-pyran-3,4-diol (Compound A217)
Figure imgf000338_0001
Step 1: (2R,3S,4S,5S,6R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5,6- dimethoxytetrahydro-2H-pyran (A217-1) was prepared following a similar procedure for (2R,3S,4R,5R,6R)-N-benzyl-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2-methoxytetrahydro- 2H-pyran-3 -amine (A214-4) in Synthesis 7-38. Yield: 170 mg, 83%. LC-MS (ESI) found: 501 [M+Na]+.
Step 2: (2R,3R,4S,5S,6R)-2-(hydroxymethyl)-5,6-dimethoxytetrahydro-2H-pyran-3,4- diol (A217) was prepared following a similar procedure for (2R,3R,4R,5S,6R)-5-amino-2- (hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A214) in Synthesis 7-38. Yield: 15 mg, 55%. LC-MS (ESI) found: 231 [M+Na]+. 1H NMR (400 MHz, Methanol-^) 64.33 (d, J= 4.6 Hz, 1H), 4.17 (p, J = 5.0 Hz, 2H), 4.03 - 3.97 (m, 1H), 3.89 (t, J = 4.9 Hz, 1H), 3.79 - 3.68 (m, 2H), 3.44 (s, 3H), 3.43 (s, 3H).
Synthesis 7-43. Preparation of (2R,3R,4R,5S,6R)-2-(hydroxymethyl)-6-methoxy-5- morpholinotetrahydro-2H-pyran-3,4-diol (Compound A218)
Figure imgf000338_0002
Step 1 4-((2R,3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-yl)morpholine (A218-1) was prepared following a similar procedure for (2R,3 S,4R,5R,6R)-N-benzyl-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxytetrahydro-2H-pyran-3-amine (A214-4) in Synthesis 7-38. Yield: 550 mg, 62%. LC-MS (ESI) found: 534 [M+H]+.
Step 2: (2R,3R,4R,5S,6R)-2-(hydroxymethyl)-6-methoxy-5-morpholinotetrahydro-2H- pyran-3,4-diol (A218) was prepared following a similar procedure for (2R,3R,4R,5S,6R)-5- amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A214) in Synthesis 7-38. Yield: 6 mg, 30%. LC-MS (ESI) found: 264 [M+H]+.
Synthesis 7-44: Preparation of N-((2R,3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2- methoxytetrahydro-2H-pyran-3-yl)-N-methylacetamide (Compound A219)
Figure imgf000339_0001
A219
Step 1: To a solution of (2R,3S,4R,5R,6R)-4,5-bis(benzyloxy)-6-((benzyloxy)methyl)-2- methoxy-N-methyltetrahydro-2H-pyran-3-amine from Synthesis 7-41 (A216-1, 100 mg, 0.210 mmol) and TEA (64 mg, 0.630 mmol) in DCM (5 mL) was added AcCl (25 mg, 0.315 mmol) dropwise at 0°C. The reaction mixture was stirred at rt for 1.5 h. The resulting mixture was diluted with DCM (10 mL), washed with H2O (10 mL x 2) and brine (10 mL), dried over Na2SO4, filtered. The organic layer was concentrated in vacuo to give a crude product, which was purified by flash chromatography (silica gel, 0-80% EA in PE) to give N-((2R,3S,4R,5R,6R)-4,5-bis(benzyloxy)- 6-((benzyloxy)methyl)-2-methoxytetrahydro-2H-pyran-3-yl)-N-methylacetamide (A219-1). LC- MS (ESI) of both found: 520 [M+H]+.
Step 2: N-((2R,3 S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-methoxytetrahydro- 2H-pyran-3-yl)-N-m ethyl acetamide (A219) was prepared following a similar procedure for (2R,3R,4R,5S,6R)-5-amino-2-(hydroxymethyl)-6-methoxytetrahydro-2H-pyran-3,4-diol (A214) in Synthesis 7-38. Yield: 7 mg, 32%. LC-MS (ESI) found: 250 [M+H]+.
Synthesis 7-46. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-
(trifluoromethyl)tetrahydro-2H-pyran-3,4-diol (Compound A221)
Figure imgf000340_0001
Step 1: A 10 mL flame-dried round bottom flask was charged with 5-(trifluoromethyl)- 5H-dibenzo[b,d]thiophen-5-ium trifluoromethanesulfonate (A126, 1.0 g, 2.49 mmol) and fac- Ir(ppy)3 (8 mg, 1.5 mol%). Then the flask was degassed and filled with argon for three times. (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-3,4-dihydro-2H-pyran (345 mg, 0.83 mmol) in DMA (10 mL) was added and the flask was sealed. The reaction mixture was stirred upon irradiation with blue bulbs (12 W *2; kmax = 465 nm) at room temperature. After 12 h, the reaction mixture was poured into water (15 mL), and then extracted with ethyl acetate (10*3 mL). The combined organic phase was washed with brine, dried over Na2SO4, filtered and concentrated to give a crude product, which was purified by column chromatography (silica gel, 0-20% MeOH in DCM) to afford the product (A221-1, 100 mg, 25% yield). LC-MS (ESI) found: 507 [M+Na]+.
Step 2: To a solution of (2R,3R,4R)-3,4-bis(benzyloxy)-2-((benzyloxy)methyl)-5- (trifluoromethyl)-3,4-dihydro-2H-pyran (A221-1, 50 mg, 0.10 mmol) in dry DCM (5 mL) at -78 °C under N2 atmosphere was added BCI3 (1 mL, 1 M in DCM) slowly. After the addition, the reaction was stirred at room temperature for overnight. On consumption of starting material monitored by TLC, the reaction mixture was quenched with 1 mL MeOH. The mixture was concentrated in vacuo to give (2R,3R,4R)-2-(hydroxymethyl)-5-(trifluoromethyl)-3,4-dihydro- 2H-pyran-3,4-diol (A221-2). LC-MS (ESI) found: 213 [M-l]'.
Step 3: To a solution of (2R,3R,4R)-2-(hydroxymethyl)-5-(trifluoromethyl)-3,4-dihydro- 2H-pyran-3,4-diol (A221-2, 20 mg, 0.10 mmol) in MeOH (5 mL) was added Pd/C (3 mg, 10 % wt, 60 % wet). The reaction mixture was charged with H2 for three times and stirred at rt for 16 h under H2 atmosphere. The mixture was filtered and concentrated in vacuo to give product (A221). LC-MS (ESI) found: 239 [M+Na]+.
Synthesis 7-47. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-morpholinotetrahydro- 2H-pyran-3,4-diol (Compound A222)
Figure imgf000341_0001
Synthesis 7-48. Preparation of 3-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)oxazolidin-2-one (Compound A223)
Figure imgf000342_0001
Synthesis 7-49. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)imidazolidin-2-one (Compound A224)
Figure imgf000342_0002
Synthesis 7-50. Preparation of l-((lS,2R,3R,4S)-l-(aminomethyl)-2,3-dihydroxy-6,8- dioxabicyclo[3.2.1]octan-4-yl)imidazolidine-2-thione (Compound A225)
Figure imgf000342_0003
Figure imgf000343_0001
Compound A225
Synthesis 7-51. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyrrolidine-2, 5-dione (Compound A226)
Figure imgf000343_0002
Synthesis 7-52. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-lH-pyrrole-2, 5-dione (Compound A227)
Figure imgf000343_0003
Synthesis 7-53. Preparation of 3-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)thiazolidine-2, 4-dione (Compound A228)
S
Figure imgf000343_0004
Figure imgf000344_0001
Synthesis 7-54. Preparation of 3-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)oxazolidine-2, 4-dione (Compound A229)
Figure imgf000344_0002
Synthesis 7-55. Preparation of 2-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)isoindoline-l, 3-dione (Compound A230)
Figure imgf000344_0003
Synthesis 7-56. Preparation of 2-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)isoindolin-l-one (Compound A231)
Figure imgf000345_0001
Synthesis 7-57. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(lH-imidazol-l- yl)tetrahydro-2H-pyran-3,4-diol (Compound A232)
Figure imgf000345_0002
Synthesis 7-58. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(lH-pyrrol-l- yl)tetrahydro-2H-pyran-3,4-diol (Compound A234)
Figure imgf000345_0003
Synthesis 7-59. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyridin-2(lH)-one (Compound A235)
Figure imgf000346_0001
Synthesis 7-60. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyrimidin-2(lH)-one (Compound A236)
Figure imgf000346_0002
Synthesis 7-61. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)pyridin-4(lH)-one (Compound A237)
Figure imgf000346_0003
Synthesis 7-62. Preparation of (3S,4R,5R,6R)-6-(aminomethyl)-3-(piperidin-l- yl)tetrahydro-2H-pyran-2,4,5-triol (Compound A238)
Figure imgf000347_0001
Synthesis 7-63. Preparation of (3S,4R,5R,6R)-6-(aminomethyl)-3-morpholinotetrahydro-
2H-pyran-2,4,5-triol (Compound A239)
Figure imgf000347_0002
Synthesis 7-64. Preparation of (3S,4R,5R,6R)-6-(aminomethyl)-3- thiomorpholinotetrahydro-2H-pyran-2,4,5-triol (Compound A240)
Figure imgf000348_0001
Synthesis 7-65. Preparation of l-((3R,4R,5R,6R)-4,5-dihydroxy-6-
(hydroxymethyl)tetrahydro-2H-pyran-3-yl)azetidin-2-one (Compound A241)
Figure imgf000348_0002
Synthesis 7-66. Preparation of l-((3S,4R,5R,6R)-6-(aminomethyl)-2,4,5- trihydroxytetrahydro-2H-pyran-3-yl)tetrahydropyrimidin-2(lH)-one (Compound A242)
Figure imgf000348_0003
Figure imgf000349_0001
Synthesis 7-67. Preparation of N-((3R,4R,5R,6R)-4,5-dihydroxy-6- (hydroxymethyl)tetrahydro-2H-pyran-3-yl)methanesulfinamide (Compound A243) andN- ((3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)-l,l,l- trifluoromethanesulfinamide (Compound A244)
Figure imgf000349_0002
Synthesis 7-68. Alternative Preparation of (4aR,6R,7R,8R,8aS)-6-(aminomethyl)-7,8- dihydroxytetrahydro-lH,6H-pyrano[2,3-b] [l,4]oxazin-2(3H)-one (Compound A245)
Figure imgf000349_0003
Synthesis 7-69. Preparation of (4aS,6R,7R,8R,8aS)-6-(aminomethyl)-7,8- dihydroxyhexahydro-lH,3H-pyrano[3,2-c][l,2,6]thiadiazine 2,2-dioxide (Compound A246), (4aS,6R,7R,8R,8aS)-6-(aminomethyl)-7,8-dihydroxyhexahydro-lH-pyrano[3,2- d]pyrimidin-2(3H)-one (Compound A247), and (4aR,6R,7R,8R,8aS)-6-(aminomethyl)-7,8- dihydroxyhexahydropyrano[3,2-d][l,3]oxazin-2(lH)-one (Compound A248)
Figure imgf000350_0001
Synthesis 7-70. Preparation of ((3aS,5R,6R,7R,7aS)-7-amino-5-(hydroxymethyl)-2-methyl- 3a,6,7,7a-tetrahydro-5H-pyrano[3,2-d]oxazol-6-ol (Compound A249) and (3aS,5R,6R,7R,7aS)-7-amino-5-(hydroxymethyl)-2-(trifluoromethyl)-3a,6,7,7a-tetrahydro- 5H-pyrano[3,2-d]oxazol-6-ol (Compound A250)
Figure imgf000351_0001
Synthesis 7-71. Preparation of (3aR,5R,6R,7R,7aS)-7-amino-5-(hydroxymethyl)-2-methyl- 3,3a,5,6,7,7a-hexahydropyrano[2,3-d]imidazol-6-ol (Compound A251) and (3aR,5R,6R,7R,7aS)-7-amino-5-(hydroxymethyl)-2-(trifluoromethyl)-3,3a,5,6,7,7a- hexahydropyrano[2,3-d]imidazol-6-ol (Compound A252)
Figure imgf000351_0002
Synthesis 7-72. Preparation of l-((3aS,5R,6R,7R,7aS)-5-(aminomethyl)-6,7- dihydroxyhexahydropyrano[3,2-b]pyrrol-l(2H)-yl)-2,2,2-trifluoroethan-l-one (Compound
Figure imgf000352_0002
Synthesis 7-73. Preparation of !-((4aR,6R,7R,8R,8aS)-6-(aminomethyl)-7,8- dihydroxyhexahydro-lH,6H-pyrano[2,3-b][l,4]oxazin-l-yl)ethan-l-one (Compound A254) and l-((4aR,6R,7R,8R,8aS)-6-(aminomethyl)-7,8-dihydroxyhexahydro-lH,6H-pyrano[2,3- b][l,4]oxazin-l-yl)-2,2,2-trifluoroethan-l-one (Compound A255)
Figure imgf000352_0001
Synthesis 7-74. Preparation of !-((3aS,4R,5aR,9aS,9bR)-4-(aminomethyl)-2,2,7- trimethylhexahydro-4H,9H- [1,3] dioxolo [4 * ,5 4,5] pyrano [2,3-b] [1,4] oxazin-9-yl)ethan-l-one (Compound A256) and !-((3aS,4R,5aR,9aS,9bR)-4-(aminomethyl)-2,2,7- trimethylhexahydr o-4H,9H- [1,3] dioxolo [4' ,5' : 4,5] pyrano [2,3-b] [1,4] oxazin-9-yl)-2,2,2- trifluoroethan-l-one (Compound A257)
Figure imgf000353_0001
Synthesis 7-75. Preparation of l-((3aS,4R,5aR,llaR,llbR)-4-(aminomethyl)-2,2- dimethyloctahydro-4H,llH-[l,3]dioxolo[4',5':4,5]pyrano[2,3-b][l,4]oxazocin-ll-yl)ethan-l- one (Compound A258) and l-((3aS,4R,5aR,llaR,llbR)-4-(aminomethyl)-2,2- dimethyloctahydro-4H,llH-[l,3]dioxolo[4',5':4,5]pyrano[2,3-b][l,4]oxazocin-ll-yl)-2,2,2- trifluoroethan-l-one (Compound A259)
Figure imgf000353_0002
Synthesis 7-76. Preparation of !-((3aS,5R,6R,7R,7aR)-6,7-dihydroxy-5- (hydroxymethyl)hexahydropyrano[3,2-b]pyrrol-l(2H)-yl)ethan-l-one (Compound A260) and !-((2R,3R,4R,4aR,8aS)-3,4-dihydroxy-2-(hydroxymethyl)octahydro-5H-pyrano[3,2- b]pyridin-5-yl)ethan-l-one (Compound A261)
Figure imgf000354_0001
Synthesis 7-77. Preparation of !-((2R,3R,4R,4aR,9aS)-3,4-dihydroxy-2- (hydroxymethyl)octahydropyrano[3,2-b]azepin-5(2H)-yl)ethan-l-one (Compound A262)
Figure imgf000354_0002
Figure imgf000355_0001
Synthesis 7-78. Preparation of ((3aR,4R,5aS,9aR,9bR)-2,2-dimethyl-8-oxooctahydro-4H- [l,3]dioxolo[4',5':4,5]pyrano[3,2-b]pyridin-4-yl)methyl acetate (Compound A263)
Figure imgf000355_0002
Synthesis 7-79. Preparation of N-((3aR,8S,8aR)-4-(hydroxymethyl)-2,2-dimethylhexahydro- 4H-4,7-epoxy[l,3]dioxolo[4,5-d]azepin-8-yl)acetamide (Compound A264)
Figure imgf000355_0003
Synthesis 7-80. Preparation of N-((3aR,4S,9R,9aR)-9-(hydroxymethyl)-2,2- dimethyloctahydro-5,9-epoxy[l,3]dioxolo[4,5-d]azocin-4-yl)acetamide (Compound A265)
Figure imgf000356_0001
Synthesis 7-81. Preparation of N-((3aR,4S,9R,9aR)-9-(hydroxymethyl)-2,2- dimethylhexahydro-5H-5,9-epoxy[l,3]dioxolo[4,5-d]oxocin-4-yl)acetamide (Compound A266)
Figure imgf000356_0002
Synthesis 7-82. Compound A267, Compound A268, and Compound A269 can also be synthesized using Synthesis 7-79 - 7-81
Figure imgf000357_0001
Synthesis 7-82. General Synthesis to install R2
Figure imgf000357_0002
Synthesis 7-83. Alternative General Synthesis to install R2
Figure imgf000357_0003
Synthesis 7-84. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(isoxazol-5- ylamino)tetrahydro-2H-pyran-3,4-diol (Compound A272)
Figure imgf000357_0004
Synthesis 7-85. Preparation of (2R,3R,4R,5R)-5-((4,6-dichloro-l,3,5-triazin-2-yl)amino)-2-
(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (Compound A273)
Figure imgf000358_0001
Synthesis 7-86. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-(thiazol-2- ylamino)tetrahydro-2H-pyran-3,4-diol (Compound A274)
Figure imgf000358_0002
Synthesis 7-87. Preparation of (2R,3R,4R,5R)-2-(hydroxymethyl)-5-((3-
(trifluoromethyl)pyridin-2-yl)amino)tetrahydro-2H-pyran-3,4-diol. (Compound A275)
Figure imgf000358_0003
Synthesis 7-88. Preparation of (3aR,4R,8R,8aR)-8-azido-4-(azidomethyl)-2,2- dimethylhexahydro-4H-4,7-epoxycyclohepta[d] [l,3]dioxole (Compound A276)
Figure imgf000359_0001
Figure imgf000359_0002
Alternatively, Compound A279 can be synthesized if in
Figure imgf000360_0001
is used instead of
Figure imgf000360_0002
the Schotten Bauman reaction step.
Figure imgf000360_0003
Compound A279 Synthesis 7-90. Preparation of l-((3S,4R,5R,6R)-6-(aminomethyl)-2,4,5- trihydroxytetrahydro-2H-pyran-3-yl)guanidine (Compound A280) And (Compound A281)
Figure imgf000360_0004
Synthesis 7-91. Preparation of Compound A282
Figure imgf000361_0001
Table 1. Non-limiting examples of ASGPR Ligands for use in making compounds of Formula I- VI and Formula I-d - IV-d
Figure imgf000361_0002
Figure imgf000362_0001
Figure imgf000363_0001
Figure imgf000364_0001
Figure imgf000365_0001
Figure imgf000366_0001
Figure imgf000367_0001
Example 8. Affinity of compounds to ASGPR measured using Surface Plasmon Resonance (SPR)
The dissociation constants (KD) of compounds described herein to the ASGP receptor are measured in SPR experiments using a Biacore 8K instrument (GE Healthcare) at 25°C. Recombinant ASGPR protein is first biotinylated using Maleimide-PEG2 -biotin reagent (Pierce, 19-fold molar excess) in phosphate-buffered saline (PBS) solution overnight at 4°C. Excess amount of biotin in the reaction mixture is removed by Zeba desalting columns (Thermo). Biotinylation is confirmed by mass spectroscopic analysis of ASGPR. Biotinylated ASGPR is then immobilized on SA sensor chips (GE Healthcare) with an immobilization level ranging from 1500- 3000 resonance units (RU). The running buffer is 50mM Tris, pH7.5, 150mMNaCl, 50mM CaCh, 0.01%P20, 3%DMSO. The concentration of compounds sometimes vary from 2 mM to 50 pM depending on KD values. The compounds are diluted 3 folds with total 8 concentration points. Solutions containing serially diluted compounds are injected at a flow rate of 50 pL/min for 60 sec followed by a 180 sec dissociation phase for each concentration. Data is processed using the analysis software in Biacore 8K to perform background subtraction, double referencing and solvent correction. Values of affinity expressed as the dissociation constants (KD) were determined by fitting the steady state binding responses (RUss) as a function of the concentration ([Compound]) using the following equation: RUss= RUmax/(KD+[Compound]), where RUmax is the calculated maximal response.

Claims

Claims We Claim:
1. A compound of Formula:
Figure imgf000369_0001
367
Figure imgf000370_0001
368
Figure imgf000371_0001
Figure imgf000372_0001
Figure imgf000373_0001
371
Figure imgf000374_0001
Figure imgf000375_0001
Figure imgf000376_0001
Figure imgf000377_0001
Figure imgf000378_0001
or a pharmaceutically acceptable salt thereof; wherein:
X1 is 1 to 5 contiguous atoms independently selected from O, S, N(R6), and C(R4)(R4), wherein if X1 is 1 atom then X1 is O, S, N(R6), or C(R4)(R4), if X1 is 2 atoms then no more than 1 atom of X1 is O, S, or N(R6), if X1 is 3, 4, or 5 atoms then no more than 2 atoms of X1 are O, S, or N(R6);
R2 is selected from
(i) aryl, heterocycle, and heteroaryl containing 1 or 2 heteroatoms independently selected from N, O, and S, each of which aryl, heterocycle, and heteroaryl is optionally substituted with 1, 2, 3, or 4 substituents;
Figure imgf000378_0002
(iii) -NR8-S(O)-R3, -NR8-C(S)-R3, -NR8-S(O)(NR6)-R3, -N=S(O)(R3)2,
-NR8C(O)NR9S(O)2R3, -NR8-S(O)2-R10, and -NR8-C(NR6)-R3 each of which is optionally substituted with 1, 2, 3, or 4 substituents; and
(iv) hydrogen, R10, alkyl-C(O)-R3, -C(O)-R3, alkyl, haloalkyl, -OC(O)R3, and -NR8-C(O)R10;
R10 is selected from alkenyl, allyl, alkynyl, -NR6-alkenyl, -O-alkenyl, -NR6-alkynyl, -O-alkynyl, -NR6-heteroaryl, -NR6-aryl, -O-heteroaryl, -O-aryl, and -O-alkynyl, each of which R10 is optionally substituted with 1, 2, 3, or 4 substituents;
R1 and R5 are independently selected from hydrogen, heteroalkyl, C0-C6alkyl-cyano, alkyl, alkenyl, alkynyl, haloalkyl, F, Cl, Br, I, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycle, heterocycloalkyl, haloalkoxy, -O-alkenyl, -O-alkynyl, C0-C6alkyl- OR6, C0-C6alkyl-SR6, C0-C6alkyl-NR6R7, C0-C6alkyl-C(0)R3, C0-C6alkyl-S(0)R3, C0-C6alkyl- C(S)R3, C0-C6alkyl-S(0)2R3, C0-C6alkyl-N(R8)-C(0)R3, C0-C6alkyl-N(R8)-S(0)R3, C0-C6alkyl- N(R8)-C(S)R3, C0-C6alkyl-N(R8)-S(0)2R3 C0-C6alkyl-0-C(0)R3, C0-C6alkyl-0-S(0)R3, C0- C6alkyl-O-C(S)R3, -N=S(O)(R3)2, C0-C6alkyN3, and C0-C6alkyl-0-S(0)2R3, each of which is optionally substituted with 1, 2, 3, or 4 substituents;
R3 at each occurrence is independently selected from hydrogen, alkyl, heteroalkyl, haloalkyl, arylalkyl, heteroaryl alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR8, and -NR8R9;
R4 is independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, haloalkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocycle, -OR6, -NR6R7, C(O)R3, S(O)R3, C(S)R3, and S(O)2R3;
R6 and R7 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, haloalkyl, heteroaryl, heterocycle, -alkyl-OR8, -alkyl-NR8R9, C(O)R3, S(O)R3, C(S)R3, and S(O)2R3;
R8 and R9 are independently selected at each occurrence from hydrogen, heteroalkyl, alkyl, arylalkyl, heteroarylalkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocycle;
Cycle is a 3-8 membered fused cyclic group optionally substituted with 1, 2, 3, or 4 substituents as allowed by valence; each LinkeA is a bond or a chemical moiety that covalently links the ASGPR ligand to Selective MoietyA, or LinkerC , or LinkerD ; LinkerC is a chemical moiety that links each LinkerA to Selective MoietyA;
LinkerD is a chemical moiety that links each LinkerA to Selective MoietyA; Selective MoietyA is selected from
Figure imgf000380_0001
378 and j)
Figure imgf000381_0001
each of which Selective MoietyA group is optionally substituted with 1, 2, 3, or 4 substituents; each R23 is independently alkyl or hydrogen; or two R23 groups combine together to form a cycle;
R24, R25, and R26 are independently selected at each instance from hydrogen, alkyl, aryl, heteroaryl, heterocycle, and halogen, each of which R24, R25, and R26 groups other than hydrogen are optionally substituted with 1, 2, 3, or 4 substituents; or R24 and R25 together form a double bond; y is 0, 1, 2, 3, 4, 5, 6, 7, or 8;
379 R200 is selected from:
(i) aryl, heterocycle, and heteroaryl containing 1 or 2 heteroatoms independently selected from N, O, and S, each of which aryl, heterocycle, and heteroaryl is optionally substituted with 1, 2, 3, or 4 substituents;
Figure imgf000382_0001
(iii) -NR8-S(O)-R3, -NR8-C(S)-R3, -NR8-S(O)(NR6)-R3, -N=S(O)(R3)2,
-NR8C(O)NR9S(O)2R3, -NR8-S(O)2-R10, and -NR8-C(NR6)-R3 each of which is optionally substituted with 1, 2, 3, or 4 substituents; and (iv) hydrogen, R10, alkyl -C(O)-R3, -C(O)-R3, alkyl, haloalkyl, -OC(O)R3, and -NR8-C(O)R10; and
(v) -NR8-C(O)-R3; and when compounds are “optionally substituted” they may be substituted as allowed by valence by groups selected from alkyl, alkenyl, alkynyl, haloalkyl, -OR6, F, Cl, Br, I, -NR6R7, heteroalkyl, cyano, nitro, C(O)R3, wherein the optional
Figure imgf000382_0002
substituent is selected such that a stable compound results.
2. The compound od claim 1, wherein Selective MoietyA is selected from:
Figure imgf000383_0001
10 each of which Selective MoietyA group is optionally substituted with 1, 2, 3, or 4 substituents.
3. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000384_0001
or a pharmaceutically acceptable salt thereof.
4. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000384_0002
or a pharmaceutically acceptable salt thereof.
5. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000384_0003
Figure imgf000385_0001
or a pharmaceutically acceptable salt thereof.
6. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000385_0002
or a pharmaceutically acceptable salt thereof.
7. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000385_0003
or a pharmaceutically acceptable salt thereof.
8. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000386_0001
5 or a pharmaceutically acceptable salt thereof.
384
9. The compound of claim 1 or claim 2, wherein the compound is of Formula:
Figure imgf000387_0001
or a pharmaceutically acceptable salt thereof.
10. The compound of any one of claims 1-9, wherein R10 is selected from:
Figure imgf000387_0002
385
11. The compound of any one of claims 1-10, wherein LinkerA is of Formula:
Figure imgf000388_0001
wherein:
R11, R12, R13, R14, R15, R16, R17, R18, R19, and R20 are independently at each occurrence selected from the group consisting of a bond, alkyl, -C(O)-, -C(O)O-, -OC(O)-, -SO2-, -S(O)-, -C(S)-, -C(O)NR6-, -NR6C(O)-, -O-, -S-, -NR6-, -C(R21R21)-, -P(O)(R3)O-, -P(O)(R3)-, a divalent residue of a natural or unnatural amino acid, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, heterocycle, heteroaryl, -CH2CH2-[O-(CH2)2]n-O-, -CH2CH2-[O-(CH2)2]n-NR6-, -CH2CH2-[O- (CH2)2]n-, -[-(CH2)2-O-]n-, -[O-(CH2)2]n-, -[O-CH(CH3)C(O)]n-, -[C(O)-CH(CH3)-O]n-, -[O- CH2C(O)]n-, -[C(O)-CH2-O]n-, a divalent residue of a fatty acid, a divalent residue of an unsaturated or saturated mono- or di-carboxylic acid, or a bicycle, each of which is optionally substituted with 1, 2, 3, or 4 substituents independently selected from R21; n is independently selected at each instance from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and
R21 is independently at each occurrence selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, F, Cl, Br, I, hydroxyl, alkoxy, azide, amino, cyano, -NR6R7, -NR8SO2R3, -NR8S(O)R3, haloalkyl, heteroalkyl, aryl, heteroaryl, and heterocycle.
12. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000388_0002
, and
Figure imgf000388_0003
386
13. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000389_0001
14. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000389_0002
15. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000389_0003
16. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000389_0004
387
17. The compound of any one of claims 1-11, wherein Selective MoietyA is selected from:
Figure imgf000390_0001
18. A pharmaceutical composition comprising a compound of any one of claims 1-17 or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable excipient.
19. A compound of Formula
Figure imgf000390_0002
or a pharmaceutically acceptable salt thereof; wherein:
Linker® is a bond or a chemical moiety that covalently links Selective Moiety® to an Extracellular Protein Targeting Ligand;
Extracellular Protein Targeting Ligand is a chemical moiety that binds to the targeted extracellular protein; and Selective Moiety® is selected from
Figure imgf000390_0003
388
Figure imgf000391_0001

Figure imgf000392_0002
each of which Selective MoietyB groups is optionally substituted with 1, 2, 3, or 4 substituents selected from the group consisting of alkyl, alkenyl, alkynyl, haloalkyl, -OR6, F, Cl,
I,
-NR6R7, heteroalkyl, cyano, nitro, C(O)R3, wherein the optional
Figure imgf000392_0001
substituent is selected such that a stable compound results.
20. The compound of claim 19, wherein Selective MoietyB is selected from
Figure imgf000392_0003
Figure imgf000393_0002
each of which Selective Moi etyB groups is optionally substituted with 1, 2, 3, or 4 substituents selected from the group consisting of alkyl, alkenyl, alkynyl, haloalkyl, -OR6, F, Cl, Br, I,
-NR6R7, heteroalkyl, cyano, nitro, C(O)R3, wherein the optional
Figure imgf000393_0001
substituent is selected such that a stable compound results.
21. The compound of claim 19 or claim 20, wherein the Extracellular Protein Targeting Ligand is an IgG Targeting Ligand.
391
22. The compound of claim 19 or claim 20, wherein the Extracellular Protein Targeting Ligand is an IgA Targeting Ligand.
23. The compound of claim 19 or claim 20, wherein the Extracellular Protein Targeting Ligand is a Targeting Ligand selected from the Figures.
24. A pharmaceutical composition comprising a compound of any one of claims 19-23 or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable excipient.
25. A method of treating a disorder mediated by an Extracellular Protein comprising administering (i) an effective dose of a compound or pharmaceutical composition of any one of claims 1-18 or a pharmaceutically acceptable salt thereof to a patient in combination with (ii) an effective dose of a compound or pharmaceutical composition of any one of claims 19-24 or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein.
26. The method of claim 25, wherein
(i) if Selective MoietyA is selected from
Figure imgf000394_0001
then Selective MoietyB is selected from:
392
Figure imgf000395_0001
ii) if Selective MoietyA is selected from
Figure imgf000395_0002
then Selective MoietyB is selected from:
Figure imgf000395_0003
iii) if Selective MoietyA is selected from
Figure imgf000395_0004
then Selective MoietyB is selected from:
393
Figure imgf000396_0001
iv) if Selective MoietyA is selected from
Figure imgf000396_0002
then Selective MoietyB is selected from:
Figure imgf000396_0003
v) if Selective MoietyA is selected from
Figure imgf000396_0004
then Selective MoietyB is selected from:
Figure imgf000396_0005
394 vi) if Selective MoietyA is selected from
Figure imgf000397_0001
then Selective MoietyB is selected from:
Figure imgf000397_0002
vii) if Selective MoietyA is selected from
Figure imgf000397_0003
then Selective MoietyB is selected from:
Figure imgf000397_0004
viii) if Selective MoietyA is selected from
Figure imgf000397_0005
then Selective MoietyB is selected from:
395
Figure imgf000398_0001
ix) if Selective MoietyA is selected from
Figure imgf000398_0002
then Selective MoietyB is selected from:
Figure imgf000398_0003
x) if Selective MoietyA is selected from
Figure imgf000398_0004
then Selective MoietyB is selected from:
Figure imgf000398_0005
27. Use of a compound of any one of claims 1-18 or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutical composition, in the manufacture of a medicament for the treatment of a disorder mediated by an Extracellular Protein wherein the medicament will be administered in combination with an effective dose of a compound or pharmaceutical composition of any one of claims 19-24 or a pharmaceutically acceptable salt thereof, wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein. Use of a compound of any one of claims 1-18 or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutical composition, in the treatment of a disorder mediated by an Extracellular Protein wherein the compound is administered to a patient in combination with a compound or pharmaceutical composition of any one of claims 19-24 or a pharmaceutically acceptable salt thereof, and wherein the Extracellular
Protein Targeting Ligand targets the Extracellular Protein. A compound of any one of claims 1-18 or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutical composition, for use in the treatment of an Extracellular Protein mediated disorder, wherein the compound is administered in combination with a compound or pharmaceutical composition of any one of claims 19-24 or a pharmaceutically acceptable salt thereof, and wherein the Extracellular Protein Targeting Ligand targets the Extracellular Protein.
397
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WO2019199621A1 (en) * 2018-04-09 2019-10-17 Yale University Bi-functional molecules to degrade circulating proteins
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