WO2019079706A1 - Aminoglycoside antibiotics - Google Patents

Aminoglycoside antibiotics Download PDF

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Publication number
WO2019079706A1
WO2019079706A1 PCT/US2018/056686 US2018056686W WO2019079706A1 WO 2019079706 A1 WO2019079706 A1 WO 2019079706A1 US 2018056686 W US2018056686 W US 2018056686W WO 2019079706 A1 WO2019079706 A1 WO 2019079706A1
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alkyl
cyclic
acyclic
linear
hydrogen
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PCT/US2018/056686
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French (fr)
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Fan Liu
Andrew G. Myers
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President And Fellows Of Harvard College
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H15/00—Compounds containing hydrocarbon or substituted hydrocarbon radicals directly attached to hetero atoms of saccharide radicals
    • C07H15/20—Carbocyclic rings
    • C07H15/22—Cyclohexane rings, substituted by nitrogen atoms
    • C07H15/222—Cyclohexane rings substituted by at least two nitrogen atoms
    • C07H15/226—Cyclohexane rings substituted by at least two nitrogen atoms with at least two saccharide radicals directly attached to the cyclohexane rings
    • C07H15/234—Cyclohexane rings substituted by at least two nitrogen atoms with at least two saccharide radicals directly attached to the cyclohexane rings attached to non-adjacent ring carbon atoms of the cyclohexane rings, e.g. kanamycins, tobramycin, nebramycin, gentamicin A2
    • C07H15/236—Cyclohexane rings substituted by at least two nitrogen atoms with at least two saccharide radicals directly attached to the cyclohexane rings attached to non-adjacent ring carbon atoms of the cyclohexane rings, e.g. kanamycins, tobramycin, nebramycin, gentamicin A2 a saccharide radical being substituted by an alkylamino radical in position 3 and by two substituents different from hydrogen in position 4, e.g. gentamicin complex, sisomicin, verdamycin

Definitions

  • Aminoglycoside antibiotics have been in continuous clinical use for more than seven decades.
  • the first member of the aminoglycoside antibiotic family, streptomycin was isolated in 1943 by the Nobel laureate Selman Waksman. Streptomycin exhibited activity against strains of mycobacteria and became the first effective treatment for tuberculosis. Following the success of streptomycin, numerous other aminoglycoside antibiotics were identified, including neomycin, paromomycin, kanamycin, gentamicin, and sisomicin. However, the use of aminoglycosides has steadily declined over the past decades due to a rise in bacterial resistance.
  • gentamicin is the most commonly prescribed aminoglycoside antibiotic and is used as a mixture of three components (gentamicin Ci, C la , and C 2 ).
  • the aminoglycosides exhibit broad-spectrum antibiotic activities and cause minimal allergic responses, which make them ideal for use in emergencies.
  • the main drawbacks of aminoglycoside therapy are nephrotoxic and ototoxic side effects. All current aminoglycoside antibiotics in use in the clinic are associated with similar adverse effects. Despite these side effects and widespread resistance, they are the drugs of choice in inhalation therapy to suppress lung infections in cystic fibrosis patients. They are also part of the drug cocktail used for the treatment of multi drug-resistant tuberculosis.
  • New and improved aminoglycoside antibiotics have come exclusively from semi- synthesis, the process of chemically converting natural fermentation products into drugs. Since the initial isolation of streptomycin, six semi-synthetic derivatives, prepared in 1-6 steps from naturally occurring aminoglycosides, have been approved by the FDA for the treatment of bacterial infections. In 2016, plazomicin, a third-generation aminoglycoside which showed both improved antibiotic and safety profiles, completed Phase III clinical trials (see Figure 1; positions that have been modified by semi-synthesis are indicated with arrows and brackets).
  • R.2b is halogen, hydroxy!, protected hydroxy!, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl or heteroaryl;
  • R 3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • R.3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group; or
  • R.3c and R 3 a together form a ring
  • R 4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or
  • R-ta and R 3c are combined to form a five or six-membered ring, or
  • R 4 a and R 3 d are combined to form a five or six-membered ring
  • R 4 is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or
  • R.4a and Rsc are combined to form a five or six-membered ring, or
  • R 4 a and R 3 d are combined to form a five or six-membered ring
  • Rvd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl ;
  • R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl , or a nitrogen protecting group
  • Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Risb i hydrogen, halogen, hydroxyl, protected hydroxyl , cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Ri6a is hydrogen, halogen, hydroxyl , protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Risa, Risb, and Risd independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or two of Riga, Risb, and Ri8d are combined to form a ring.
  • the compound of Formula (I) is of Formula ( ⁇ ):
  • composition comprising a compound of Formula (I),
  • a method of treating or preventing a bacterial infection in a subject in need thereof comprising administering to the subject a compound of Formula (I).
  • kits comprising an aminoglycoside of Formula (I) and a container.
  • Figure 1 shows a summary of semi-synthetic aminoglycoside derivatives. The positions that have been modified by semi-synthesis are indicated with arrows and brackets.
  • Figure 2 shows the biosynthesis of 2-deoxy streptamine and streptidine from glucose.
  • Figure 3 shows the biosynthetic pathway to 2-deoxystreptamine aminoglycoside antibiotics.
  • Figure 4 shows the hydrogenation of streptomycin produced dihydrostreptomycin, a compound of similar antibacterial properties but improved chemical stability.
  • Figure 5 shows the synthesis of dibekacin from kanamycin B.
  • Figure 6 shows the synthesis of amikacin from kanamycin A. Amikacin shows improved antibacterial and pharmacokinetic properties
  • Figure 7 shows the synthesis of arbekacin in 5 steps from dibekacin, a semi-synthetic derivative of kanamycin B.
  • Figure 8 shows the synthesis of isepamicin from gentamicin B. Isepamicin is a derivative of gentamicin and was first reported in 1978
  • Figure 9 shows the synthesis of netilmicin in one step from sisomicin in 25% yield (top).
  • An improved procedure involves the initial formation of a cobalt-chelation complex and provides netilmicin in 3 steps and 60% yield (bottom),
  • Figure 10 shows the synthesis of piazomicin, a next-generation aminoglycoside, from sisomicin in 7 steps with an overall yield of 0.1.6%.
  • Figure 11 shows the synthesis of 2-hydroxyarbekacin, a new aminoglycoside antibiotic with improved activity against MRSA.
  • Figure 12 shows a semi-synthetic derivative of tobramycin, SPX2523.
  • Figure 13 shows the chemical synthesis of 5 -epi sisomicin (SCH 22591).
  • FIG. 14 shows 5-episisomicin derivatives prepared from sisomicin.
  • AAC Aminoglycoside N-Acetyltransferase.
  • Figure 15 shows the synthesis of TS2037 from arbekacin in 1 1 steps.
  • the novel arbekacin derivative shows improved activity against MRSA and P. aeruginosa.
  • Figure 16 shows a summary of clinically approved semisynthetic aminoglycosides
  • Figure 17 shows the structural relationship of aminoglycosides and their semisynthetic derivatives. Semisynthetic antibiotics are linked to their natural product starting material through dotted lines.
  • Figure 18 shows a fully synthetic approach to assemble the aminoglycoside scaffold from three components (2-4).
  • the aminoglycoside, 1 -HABA-gentamicin Cia (1) is used as a representative example.
  • Figure 19 shows the coupling of the purpurosamine glycosyl donor 3 with the differentially protected 2-deoxystreptamine derivative 4 to afford the glycoside 140.
  • Figure 20 shows the introduction of the HABA sidechain to the C I amine of the glycoside 140 in two steps and 62% yield.
  • the dioi 144 is prepared in 61% yield from 140.
  • Figure 21 shows the synthesis of gentamicin Cia from components 3, 118, and 50 based on the fully synthetic route described herein. Late-stage derivatization of the Co' nitro group produces three novel aminoglycoside antibiotics that are inaccessible through semi- synthesis.
  • Figure 22 shows structures of gentamicin and sisomicin.
  • Figure 23 shows a convergent synthesis of the glycosyl donor 2, allowing late-stage diversification of the C3 " amino group.
  • Figure 24 shows diastereoselective nitroaldol coupling conditions.
  • Figure 25 shows practical and large-scale syntheses of building blocks 6 and 7.
  • Figure 26 shows structures of two representative 4, 6-di substituted aminoglycoside antibiotics, kanamycin and gentamicin.
  • the purpurosamines A-C are found in gentamicin C complex and are biosynthetically related to other carbohydrates that make up the ring I of aminoglycosides.
  • Figure 27 shows the synthesis of compound 3, which proceeds in 6 steps from D- glutamic acid.
  • Figure 28 shows representative aminoglycoside antibiotics.
  • Figure 29 shows the synthesis of compound 4 from the protected dimethyl tartrate 8.
  • Figure 30 shows the synthesis of the activated HABA sidechain 5.
  • Figure 31 shows the synthesis of the 2-deoxystreptamine glycosyl acceptor 137.
  • Figure 32 shows the synthesis of gentamicin Cia (FSA-3821 ) proceeded in five steps from the purpurosamine component 3 and the semisynthetic 2-deoxystreptamine glycosyl acceptor 118.
  • Figure 33 shows the synthesis of C6 -modified gentamicin derivatives FSA-38240, FSA-38255, and FSA-38252.
  • Figure 34 shows the bacterial ribosome carries out the production of proteins. Gentamicin, a representative aminoglycoside antibiotic, interferes with several stages of bacterial protein synthesis.
  • Figure 35 shows the resistance rate to gentamicin in four geographic regions between 1998 and 2007.
  • Figure 36 shows aminoglycosides are inactivated through modifications of polar functional groups by aminoglycoside modifying enzymes (AMEs).
  • AMEs aminoglycoside modifying enzymes
  • the AMEs found only in Gram-negative bacteria are ANT(2") and AAC(3).
  • Figure 37 shows overlapping binding sites of gentamicin and paromomycin in the 30S subunit of the ribosome.
  • the nucleobases, G1405 and A1408, which are substrates of rRNA methyltransferases ArmA and NmpA, respectively, are colored in blue.
  • the universally conserved nucleobases A1942 and A1943 adopt an extra-helical conformation upon aminoglycoside binding.
  • Figure 38 shows the minimum inhibitory concentrations ( , ug/mL) of synthetic gentamicin C ia and C6 -modified gentamicin analogs against two Gram-positive and five Gram- negative bacterial strains.
  • cErm :: constitutive eiythromycin ribosome methyl ase
  • FQ-R :: fluoroquinolone resistant
  • cErmB constitutive eiythromycin ribosome methylase B.
  • Figure 39 shows the preparation of a 2-deoxystreptamine glycosyl acceptor by semi synthesis.
  • Figure 40 shows exemplar ⁇ ' aminoglycoside modifications targeting resistance phenotypes.
  • Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various stereoi somen c forms, e.g. , enantiomers and/or diastereomers.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses.
  • HPLC high pressure liquid chromatography
  • structures depicted herein are al so meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
  • compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, replacement of 19 F with 18 F, or the replacement of a carbon by a 1 C- or 1 C-enriched carbon are within the scope of the disclosure.
  • Such compounds are useful, for example, as analytical tools or probes in biological assays.
  • Ci-6 alky is intended to encompass, Ci, Ci, C 3 , C 4 , Cs, Ce, Ci-6, Ci-5, Ci-4, Ci-3, Ci-2, C2--6, C2-5, C2--4, C2-3, C3-6, C3--5, C3-4, C4--6, C4-5, and C5--6 aikyi.
  • aliphatic refers to alk l, alkenyl, alkynyl, and carbocyclic groups.
  • heteroaliphatic refers to heteroalkyl, heteroalkenyl, heteroalkynyl, and heterocyclic groups.
  • alkyl refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms (“Ci-io alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“Ci-9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms ("Ci-s alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“Ci-7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“Ci-6 alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“Ci-s alkyl”).
  • an alkyl group has 1 to 4 carbon atoms ("Ci-4 alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms ("Ci-3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms ("C1-2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“Ci alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C2-6 alkyl”).
  • Ci-6 alkyl groups include methyl (Ci), ethyl (C2), propyl (C 3 ) (e.g., n-propyl, isopropyl), butyl (C4) (e.g., n-butyi, tert-butyl, sec-butyl, iso-butyl), pentyl (Cs) (e.g., n-pentyl, 3-pentanyi, amy], neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (Ce) (e.g., 2-methylpentyl, 3- methylpentyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, and n-hexyl).
  • Cs e.g., 2-methylpentyl, 3- methylpentyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, and n-hex
  • alkyl groups include n-heptyl (C?), n-octyl (Cs), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an "unsubstituted alkyl") or substituted (a "substituted alkyl") with one or more substituents (e.g., halogen, such as F).
  • substituents e.g., halogen, such as F
  • the alkyl group is an unsubstituted €1-10 alkyl (such as unsubstituted Ci-e alkyl, e.g., -CH3 (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n- propyl (n-Pr), unsubstituted isopropyl (/-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (w-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu or s-Bu), unsubstituted isobutyl (/-Bu)).
  • the alkyl group is a substituted Ci-10 alkyl (such as substituted Ci-e alkyl, e
  • haloalkyl is a substituted alkyl group, wherein one or more of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo.
  • a halogen e.g., fluoro, bromo, chloro, or iodo.
  • Perhaloalkyl is a subset of haloalkyl, and refers to an alkyl group wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo.
  • the haloalkyl moiety has 1 to 8 carbon atoms ("Ci-s haloalkyl").
  • the haloalkyl moiety has 1 to 6 carbon atoms ("Ci- ⁇ haloalkyl”). In some embodiments, the haloalkyl moiety has 1 to 4 carbon atoms ("C1-4 haloalkyl”). In some embodiments, the haloalkyl moiety has 1 to 3 carbon atoms ("C1-3 haloalkyl”). In some embodiments, the haloalkyl moiety has 1 to 2 carbon atoms ("C1--2 haloalkyl”). In some embodiments, all of the haloalkyl hydrogen atoms are replaced with fluoro to provide a perfluoroalkyl group.
  • haloalkyl hydrogen atoms are replaced with chloro to provide a "perchloroalkyl" group.
  • haloalkyl groups include -CF 3 , - CF2CF3, --CF2CF2CF3, -CCI3, -CFCI2, -CF2CI, and the like.
  • heteroalkyl refers to an alkyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCj-io alkyl").
  • a heteroalkyl group is a saturated group having 1 to 9 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCi-9 alkyl").
  • a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi-s alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and J or more heteroatoms within the parent chain ("heteroCi-7 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCi-6 alkyl").
  • a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroCt-s alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and l or 2 heteroatoms within the parent chain ("heteroCi-4 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having J to 3 carbon atoms and 1 heteroatom within the parent chain (“heteroCi-3 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 2 carbon atoms and 1 heteroatom within the parent chain (“heteroCi-2 alkyl").
  • a heteroalkyl group is a saturated group having 1 carbon atom and 1 heteroatom ("heteroCi alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroC 2 -6 alkyl"). Unless otherwise specified, each instance of a heteroalkyl group is independently unsubstituted (an "unsubstituted heteroalkyl") or substituted (a "substituted heteroalkyl”) with one or more substituents. In certain embodiments, the heteroalkyl group is an unsubstituted heterod-io alkyl . In certain embodiments, the heteroalkyl group is a substituted heteroCi-io alkyl.
  • Carboxyalkyl refers to an alkyl ester of the formula -CQ2(aikyi), wherein the alkyl moiety i s as defined above.
  • alkenyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3, or 4 double bonds).
  • an alkenyl group has 2 to 9 carbon atoms ("C2-9 alkenyl”).
  • an alkenyl group has 2 to 8 carbon atoms ("C2--8 alkenyl”).
  • an alkenyl group has 2 to 7 carbon atoms (“C2-7 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C2--6 alkenyl”).
  • an alkenyl group has 2 to 5 carbon atoms (" €2-5 alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms ("C2--4 alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (" €2-3 alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms ("C 2 alkenyl”).
  • the one or more carbon-carbon double bonds can be internal (such as in 2- butenyl) or terminal (such as in 1-butenyl).
  • Examples of C2-- alkenyl groups include ethenyl (C2), 1-propenyl (C3), 2-propenyl (C3), 1-butenyl (C 4 ), 2-butenyl (C 4 ), butadienyl (C 4 ), and the like.
  • Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkenyl groups as well as pentenyl (C?), pentadienyl (C5), hexenyl ⁇ ( . ' ⁇ . ⁇ . and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (Cs), octatrienyl (Cs), and the like.
  • each instance of an alkenyl group is independently unsubstituted (an "unsubstituted alkenyl") or substituted (a "substituted alkenyl") with one or more substituents.
  • the alkenyl group is an unsubstituted C2-10 alkenyl.
  • the al kenyl group is a substituted C 2 - 10 alkenyl.
  • heteroalkenyl refers to an alkenyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkenyl group refers to a group having from 2 to 10 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 - 10 alkenyl").
  • a heteroalkenyl group has 2 to 9
  • heteroalkenyi group has 2 to 8 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroCVs alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 7 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -7 alkenyl").
  • a heteroalkenyi group has 2 to 6 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -6 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heteroC 2 -5 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 4 carbon atoms, at least one double bond, and l or 2 heteroatoms within the parent chain (“heteroC 2 -4 alkenyl").
  • a heteroalkenyi group has 2 to 3 carbon atoms, at least one double bond, and 1 heteroatom within the parent chain ("heteroC 2 - 3 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heterod-s alkenyl"). Unless otherwise specified, each instance of a heteroalkenyi group is independently unsubstituted (an "unsubstituted heteroalkenyi") or substituted (a "substituted heteroalkenyi") with one or more substituents. In certain embodiments, the heteroalkenyi group is an unsubstituted heteroCi-io alkenyl. In certain embodiments, the heteroalkenyi group is a substituted heteroC 2 - 10 alkenyl,
  • alkynvl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon triple bonds (e.g., 1 , 2, 3, or 4 triple bonds) ("C2-10 alkynyl").
  • an alkynyl group has 2 to 9 carbon atoms ⁇ " ( ' .: ' alkynyl”).
  • an alkynyl group has 2 to 8 carbon atoms ("C2-8 alkynyl”).
  • an alkynyl group has 2 to 7 carbon atoms (“C2-7 alkynyl”).
  • an alkynyl group has 2 to 6 carbon atoms ("C2-6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms ("C2--5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms ("C2-4 alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms ("C2--3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms ("C2 alkynyl”).
  • the one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in l-butynyi).
  • Examples of C2-4 alkynyl groups include, without limitation, ethynyl (C 2 ), 1-propynyl (C 3 ), 2-propynyl (C 3 ), 1-butynyl (C 4 ), 2-butynyl (C 4 ), and the like.
  • Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkynyl groups as well as pentynyl (C?), hexynyl (C&), and the like. Additional examples of alkynyi include heptvnyl (C?), octynyl (Cs), and the like.
  • each instance of an alkynyi group is independently unsubstituted (an "un substituted alkynyi") or substituted (a "substituted alkynyi") with one or more substituents.
  • the alkynyi group is an unsubstituted €2-10 alkynyi.
  • the alkynyi group is a substituted €2-10 alkynyi.
  • heteroal kynyl refers to an alkynyi group, which further includes at least one heteroatom (e.g., I , 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkynyl group refers to a group having from 2 to 10 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -io alkynyi").
  • a heteroal kynyl group has 2 to 9 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -9 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -s alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroCz-? alkynyi").
  • a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-6 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and I or 2 heteroatoms within the parent chain ("heteroC 2 -5 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and lor 2 heteroatoms within the parent chain ("heteroC 2 -4 alkynyi").
  • a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and 1 heteroatom within the parent chain ("heteroC 2 - 3 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and I or 2 heteroatoms within the parent chain ("heteroC 2 -6 alkynyi"). Unless otherwise specified, each instance of a heteroalkynyl group is independently unsubstituted (an "unsubstituted heteroalkynyl") or substituted (a "substituted heteroalkynyl") with one or more substituents.
  • the heteroalkynyl group is an unsubstituted heteroC 2 - 10 alkynyi. In certain embodiments, the heteroalkynyl group is a substituted heteroC 2 - 10 alkynyi .
  • "carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 14 ring carbon atoms ("C3-14 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 10 ring carbon atoms (" €3-10 cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms ("C3-8 cycloalkyl").
  • a cycloalkyl group has 3 to 6 ring carbon atoms ("C3-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 4 to 6 ring carbon atoms ⁇ "' ( ' ⁇ . ⁇ . cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms ("C5-6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C5-10 cycloalkyl”). Examples of C5-6 cycloalkyl groups include cyclopentyl (Cs) and cyclohexyl (Cs).
  • C3-6 cycloalkyl groups include the aforementioned Cs-e cycloalkyl groups as well as cyciopropyl (C3) and cyclobutyl (C 4 ).
  • C ; ⁇ cycloalkyl groups include the aforementioned C3--0 cycloalkyl groups as well as cycloheptyl (C?) and cyclooctyl (Cs).
  • each instance of a cycloalkyl group is independently unsubstituted (an "unsubstituted cycloalkyl") or substituted (a "substituted cycloal kyl") with one or more substituents.
  • heterocyclyl refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("3-14 membered heterocyclyl").
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”) or tricyclic system (“tricyclic heterocyclyl”)), and can be saturated or can contain one or more carbon-carbon double or triple bonds.
  • Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings
  • Heterocyclyl also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system.
  • each instance of heterocyclyl is independently unsubstituted (an "unsubstituted heterocyclyl") or substituted (a "substituted heterocyclyl") with one or more substituents.
  • the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl.
  • the heterocyclyl group is a substituted 3-14 membered heterocyclyl.
  • the heterocyclyl is substituted or unsubstituted, 3- to 7-membered, monocyclic heterocyclyl, wherein 1, 2, or 3 atoms in the heterocyclic ring system are independently oxygen, nitrogen, or sulfur, as valency permits.
  • a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heterocyclyl").
  • a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heterocyclyl").
  • a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heterocyclyl").
  • the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur,
  • Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azirdinyl, oxiranyl, and thiiranyl.
  • Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyi, and thietanyi.
  • Exemplary 5-membered heterocyclyl groups containing I heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione.
  • Exemplar ⁇ ' 5-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl.
  • Exemplar ⁇ ' 5-membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplar ⁇ ' 6-membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyi, tetrahydropvranyl, dihydropyridinyl, and thianyl.
  • Exemplary 6-membered heterocvclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl.
  • Exemplar ⁇ - 6-membered heterocvclyl groups containing 3 heteroatoms include, without limitation, triazinyl.
  • Exemplary 7-membered heterocyclyi groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl.
  • Exemplary 8- membered heterocyclyi groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
  • Exemplary bicyclic heterocvclyl groups include, without limitation, indolinyl, isoindoiinyl, dihydrobenzofuranyi, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyi, decahydronaphthyridinyl, decahydro-l,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyi, l H-benzo[
  • aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having 6- 14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system ("C6-- I4 aryl").
  • an aryl group has 6 ring carbon atoms ("Ce aryl”; e.g., phenyl).
  • an aryl group has 10 ring carbon atoms ("Cio aryl”; e.g., naphthyl such as 1-naphthyi and 2-naphthyl).
  • an aryl group has 14 ring carbon atoms ("CM aryl”, e.g., anthracyl).
  • CM aryl e.g., anthracyl
  • Aryl also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocvclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system.
  • each instance of an aryl group is independently unsubstituted (an "un substituted aryl") or substituted (a "substituted aryl") with one or more substituents.
  • the aryl group is an unsubstituted C 6 -i4 aryl.
  • the aryl group is a substituted Ce-i4 aryl .
  • “Aralkyl” is a subset of “alkyl” and refers to an alkyl group substituted by an aryl group, wherein the point of attachment is on the alkyl moiety.
  • heteroaryi refers to a radical of a 5-14 membered monocyclic or poly cyclic (e.g., bicyclic, tricyclic) 4n 2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-14 membered heteroaryi").
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryi polycyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heteroaryi includes ring systems wherein the heteroaryi ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryi ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryi ring system.
  • Heteroaryi also includes ring systems wherein the heteroaryi ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryi ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system.
  • polycyclic heteroaryi groups wherein one ring does not contain a heteroatom e.g., indolyi, quinolinyi, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indoiyl).
  • the heteroaryi is substituted or unsubstituted, 5- or 6-membered, monocyclic heteroaryi, wherein I, 2, 3, or 4 atoms in the heteroaryi ring system are independently oxygen, nitrogen, or sulfur.
  • the heteroaryi is substituted or unsubstituted, 9- or 10-membered, bicyclic heteroaryi, wherein 1, 2, 3, or 4 atoms in the heteroaryi ring system are independently oxygen, nitrogen, or sulfur,
  • a heteroaryi group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryi").
  • a heteroaryi group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heteroaryi").
  • a heteroaryi group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heteroaryl' '1 ).
  • the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has I ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • each instance of a heteroaryl group is independently unsubstituted (an "unsubstituted heteroaryl") or substituted (a "substituted heteroaryl") with one or more substituents.
  • the heteroaryl group is an unsubstituted 5-14 membered heteroaryl.
  • the heteroaryl group is a substituted 5-14 membered heteroaryl.
  • Exemplary 5-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyrroiyl, furanyl, and thiophenyl.
  • Exemplar ⁇ ' 5-membered heteroaryl groups containing 2 heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyi.
  • Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolvl.
  • Exemplary 5-membered heteroaryl groups containing 4 heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6- membered heteroaryl groups containing I heteroatom include, without limitation, pyridinyl.
  • Exemplar ⁇ - 6-membered heteroaryl groups containing 2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • Exemplary 6-membered heteroaryl groups containing 3 or 4 heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively,
  • Exemplar ⁇ ' 7- membered heteroaryl groups containing 1 heteroatom include, without limitation, azepinyi, oxepinyl, and thiepinyl.
  • Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyi, isoindolyi, indazolyl, benzotriazolyi, benzothiophenyl, isobenzothiophenyi, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
  • Exemplar ⁇ ' 6,6- bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Exemplar ⁇ ' tricyclic heteroaryl groups include, without limitation, phenanthridinyi, dibenzofuranyl, carbazolyi, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.
  • the term “unsaturated bond” refers to a double or triple bond.
  • the term “unsaturated” or “partially unsaturated” refers to a moiety that includes at least one double or triple bond,
  • saturated refers to a moiety that does not contain a double or triple bond, i.e., the moiety only contains single bonds.
  • alkylene is the divalent moiety of alkyl
  • alkenyiene is the divalent moiety of alkenyl
  • alkynylene is the divalent moiety of alkynyl
  • heteroalkylene is the divalent moiety of heteroalkyl
  • heteroalkenylene is the divalent moiety of heteroalkenyl
  • heteroalkynylene is the divalent moiety of heteroalkynvl
  • carbocyclylene is the divalent moiety of carbocyclvl
  • heterocyclvlene is the divalent moiety of heterocyclyl
  • aryl ene is the divalent moiety of aryl
  • heteroarylene is the divalent moiety of heteroaryl.
  • Optionally substituted refers to a group which may be substituted or unsubstituted (e.g., “substituted” or “unsubstituted” aliphatic, “substituted” or “un substituted” alkyl, “substituted” or “unsubstituted” alkenyl, "substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” heteroaliphatic, "substituted” or “unsubstituted” heteroalkyl, “substituted” or “unsubstituted” heteroalkenyl, "substituted” or “unsubstituted” heteroaikynyl, "substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, "substituted” or "unsubsti
  • substituted means that at least one hydrogen present on a group is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a "substituted" group has a substituent at one or more substitutable positions of the group, and when more than one position in any given staicture is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, and includes any of the substituents described herein that results in the formation of a stable compound.
  • the present invention contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • the invention is not intended to be limited in any manner by the exemplary substituents described herein.
  • Exemplar ⁇ ' carbon atom substituents include, but are not limited to, halogen, -CN, - () 2 , -N 3 , -SO2H, SO L -OH, -OR 33 , -ON(R bb )2, -N(R bb ) 2 , Ni !,!
  • Ci-io alkyl Ci-io perhaloaikyi, C?.-io alkenyl, C 2 -io alkynyl, heteroCi-io alkyl, heteroC 2 -io alkenyl, heteroC2-io alkynyl, C3-10 carbocyclyl, 3—14 membered heterocyclyl, Ce- i4 aiyl, and 5- 14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is
  • each instance of R aa is, independently, selected from Ci-io alkyl, Ci-io perhaloaikyi, C2- 10 alkenyl, C2--10 alkynyl, heteroCi -10 alkyl, heteroC 2 - 10 alkenyl, heteroC 2 - 10 alkynyl, C3-- 10 carbocyclyl, 3- 14 membered heterocyclyl, Ce-i4 aryl, and 5-14 membered heteroaryl, or two R aa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups; each instance of R b is, independently, selected from hydrogen, -OH, -OR 33 , -
  • each instance of R dd is, independently, selected from halogen, -CN, -N0 2 , -N3, -SO2H, - SO3H, -OH, -OR ee , -ON(R ff ) 2 , -N(R ff )2, N( R X . -N(OR ee )R ff , -SH, -SR ee , -SSR ee , - - NR ff C(-0)R ee , -NR ff C0 2 R ee , 0 . -
  • each instance of R ee is, independently, selected from Ci-6 alkyl, Ci-6 perhaloalkyl, C2-6 alkenyi, C2-6 alkynyl, heteroCi-e alkyl, heteroC 2 -6alkenyl, heteroC 2 -6 alkynyl, C3-10 carbocyclyl, C6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyi , alkynyl, heteroalkyi, heteroaikenyl, heteroalkynyl, carbocyclyl , heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups; each instance of R is, independently, selected from hydrogen, Ci-e alkyl, Ci-6 perhaloalkyl, C2-6 alkenyl, C2-0 alkynyi, heteroCi-ealkyl, heteroC 2 -6alkenyl, heteroCi-e
  • each instance of R gg is, independently, halogen, -CN, -NO2, -N3, -SO2H, -SO3H, -OH, -OCi-6 alkyl, -ON(Ci-6 alkyl) 2 , -N(Ci-6 alkyl) 2 , -N(Ci-6 alkyl)3 + X ⁇ , -NH(Ci-6 aiks i ) - X . - NH?.(Ci-6 alkyl) + X " , M h X .
  • alkyl (Ci-& alkyl), -N(OH)(Ci-6 alkyl), -NH(OH), - SI L -SCi-6 alkyl, -SS(Ci-6 alkyl), C( ( ) ⁇ (C ; ⁇ . alkyl), -CO2H, -C0 2 (Ci-6 alkyl),
  • the carbon atom substituents are independently halogen, substituted or unsubstituted Ci-e alkyl, -OR aa , ⁇ SR aa -N(R bb ) 2 , -CN, - [0082]
  • halo or "halogen” refers to fluorine (fluoro, -F), chlorine (chloro, -CI), bromine (bromo, -Br), or iodine (iodo, -I),
  • -hydroxyl refers to the group -OH.
  • amino refers to the group - H 2 .
  • substituted amino by extension, refers to a rnonosubstituted amino, a disubstituted amino, or a tri substituted amino. In certain embodiments, the "substituted amino” is a rnonosubstituted amino or a disubstituted amino group.
  • tri substituted amino refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with three groups, and includes groups selected from -N(R DD ) 3 and -N(R )3 ⁇ X ⁇ , wherein R and X ⁇ are as defined herein.
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quaternary nitrogen atoms.
  • the substituent present on the nitrogen atom is an nitrogen protecting group (also referred to herein as an "amine protecting group” or an “amino protecting group”).
  • the protecting group may be represented as "-PG”.
  • An amine group bearing a nitrogen protecting group, or two nitrogen protecting groups, may be referred to as a "protected amine.”
  • Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W . Greene and P. G. M. Wuts, 3 rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • Nitrogen protecting groups such as carbamate groups include, but are not limited to, methyl carbamate, ethyl carbamante, 9-fiuorenylmethyl carbamate (Fmoc), 9- (2-suifo)fluorenylmethyi carbamate, 9-(2,7-dibromo)fluoroenyir ethyl carbamate, 2,7-di-t- buty l-[9-( 10, 10-dio o- 10, 10, 10, 10-tetrahy drothioxanthy ] )]methyl carbamate (DBD-Tmoc), 4- methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyi carbamate (Troc), 2- trimethylsiiylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ),
  • Nitrogen protecting groups such as sulfonamide groups include, but are not limited to, jo-toluenesulfonamide (Ts), benzenesultonarnide, 2,3,6,-tiimethyl-4- methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-
  • Ts jo-toluenesulfonamide
  • Mtr 2,3,6,-tiimethyl-4- methoxybenzenesulfonamide
  • Mtb 2,4,6-trimethoxybenzenesulfonamide
  • nitrogen protecting groups include, but are not limited to, phenothiazinyi-(lO)- acyl derivative, /V ' -p-toluenesulfonylaminoacyl derivative, N -phenylaminothioacyl derivative, ⁇ -benzoylphenyialanyl derivative, ⁇ -acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2- one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, A-2,5- dimethylpyrrole, N-l ,l,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5- substituted l,3-dimethyl-l,3,5-triazacyclohexan-2-one, 5-substituted l,3-dibenzyl-l,3,5- triazacyclohe
  • the substituent present on an oxygen atom is an oxygen protecting group (also referred to herein as an "hydroxy! protecting group").
  • the protecting group may be represented as "-PG".
  • a hydroxyl group bearing an oxygen protecting group may be referred to as a "protected hydroxyl.”
  • oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyl oxymethyl (BOM), p - methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-
  • the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a "thiol protecting group”).
  • the protecting group may be represented as " ⁇ PG".
  • a thiol group bearing a sulfur protecting group may be referred to as a "protected thiol.”
  • leaving group is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile.
  • suitable leaving groups include, but are not limited to, halogen (such as F, CI, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O- dimethyihydroxylamino, pixyl, and haloformates.
  • the leaving group is a brosylate, such as />-bromobenzenesulfonyloxy.
  • the leaving group is a nosylate, such as 2- nitrobenzenesulfonyloxy. In some embodiments, the leaving group is a sulfonate-containing group. In some embodiments, the leaving group is a tosylate group.
  • the leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. In certain embodiments, the leaving group is of the formula SR ;ia . - S(0)R aa , S(0). ⁇ R ;i .
  • R aa is as defined herein.
  • Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
  • oxidizing agent refers to a substance that has the ability to oxidize another substance (i.e., cause the other substance to lose electrons).
  • exemplary oxidizing agents include acyl sulfoxide reagents, halides, hypervalent halide reagents, hexavalent chromium reagents, permanganate reagents, and peroxide reagents.
  • reducing agent refers to a substance that has the ability to reduce another substance (i.e., cause the other substance to gain electrons).
  • exemplary reducing agents include elemental hydrogen (e.g., in the presence of a transition metal catalyst such as palladium, platinum, rhodium, iridium or nickel), reducing metals (e.g., lithium, sodium, iron, aluminum, tin, and the like), borane reagents (e.g., diborane), metal hydride reagents (e.g., sodium borohydride, sodium triacetoxyborohydride, lithium aluminum hydride, diisobutyl aluminum hydride, and the like), and phosphorous reagents (e.g., ph ophites, phosphines such as triphenylphosphine, and the like).
  • a transition metal catalyst such as palladium, platinum, rhodium, iridium or nickel
  • reducing metals e.g.,
  • pharmaceutically acceptable salt refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, Berge et at describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1 -19, incorporated herein by reference.
  • Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases.
  • Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids, such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids, such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid
  • organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange.
  • Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium, and NP(Ci-4 alkyl) 4 " salts.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quateraary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxyiate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
  • composition and “formulation” are used interchangeably.
  • a "subject" to which administration is contemplated refers to a human ⁇ i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal.
  • pediatric subject e.g., infant, child, or adolescent
  • adult subject e.g., young adult, middle-aged adult, or senior adult
  • the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, cows, pig, horse, sheep, goat, cat, or dog), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey)).
  • the non-human animal is a fish, reptile, or amphibian.
  • the non-human animal may be a male or female at any stage of development.
  • the non-human animal may be a transgenic animal or genetically engineered animal.
  • a "patient" refers to a human subject in need of treatment of a disease.
  • the subject may also be a plant.
  • the plant is a land plant. In certain embodiments, the plant is a non-vascular land plant. In certain embodiments, the plant is a vascular land plant. In certain embodiments, the plant is a seed plant. In certain embodiments, the plant is a cultivated plant. In certain embodiments, the plant is a dicot. In certain embodiments, the plant is a monocot. In certain embodiments, the plant is a flowering plant. In some embodiments, the plant is a cereal plant, e.g., maize, corn, wheat, rice, oat, barley, rye, or millet. In some embodiments, the plant is a legume, e.g., a bean plant, e.g., soybean plant. In some embodiments, the plant produces fruit. In some embodiments, the plant is a tree or shrub.
  • administer refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound described herein, or a composition thereof, in or on a subject
  • treatment refers to reversing, alleviating, delaying the onset of, or inhibiting the progress of a disease (e.g., a bacterial infection) described herein.
  • treatment may be administered after one or more signs or symptoms of the disease have developed or have been observed.
  • treatment may be administered in the absence of signs or symptoms of the disease.
  • treatment may be administered to a susceptible subject prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of exposure to a pathogen). Treatment may also be continued after symptoms have resolved, for example, to delay and/or prevent recurrence.
  • prevent refers to a prophylactic treatment of a subject who is not and was not with a disease (e.g., a bacterial infection) but is at risk of developing the disease or who was with a disease, is not with the disease, but is at risk of regression of the disease.
  • the subject is at a higher risk of developing the disease or at a higher risk of regression of the disease than an average healthy member of a population of subjects.
  • the first semisynthetic aminoglycoside came as early as 1946, when hydrogenation of streptomycin in the presence of a platinum catalyst yielded dihydrostreptomycin, a compound with equipotent antibiotic properties but greatly improved chemical stability (Figure 4). It was shown much later that the ototoxic symptoms of dihydrostreptomycin differ from those of streptomycin. By 1950, the annual production of streptomycin and dihydrostreptomycin reached almost 100 tons. Both antibiotics found widespread clinical applications and continue to be used in veterinary medicine.
  • Dibekacin was prepared in 6 steps from kanamycin B and developed by Meiji Seika in Japan ( Figure 5). Deoxygenation of the €3 ' and €4' positions overcame modifications by APH(3 ) and ANT(4 I ) enzymes, but at the same time increased the toxicity level. Dibekacin was active against resistant strains of Staphlococci and Pseudomonas and has been marketed worldwide, except in the United States, since 1975.
  • a common strategy for the generation of new aminoglycoside analogs is glyxodi versification, in which selective hydrolysis of the more labile ring III (and IV) of a naturally occurring aminoglycoside provides a neamine or paromomine derivative, which, after protection of the polar functional groups, is coupled with carbohydrate building blocks to generate a library of new aminoglycoside analogs.
  • the advantage of such an approach is that the 2-deoxystreptamine-glucosamine motif, which is important for ribosome recognition, is conserved while diversity is introduced to the substituent at the C5 ⁇ or C6-hydroxyl groups of 2- deoxystreptamine.
  • 2-hydroxyarbekacin a novel aminoglycoside antibiotic ( Figure 1 1), from 2-hydroxygentamicin.
  • 2-Hydroxygentamicin is produced by a mutant strain of M. purpurea, the producer of gentamicin. Hydrolysis of 2-hydroxygentamicin yielded 3',4'-dideoxyneamine, which was processed in 6 steps to provide a substrate for the introduction of the HABA sidechain. Subsequent glycosylation and deprotection furnished 2-hydroxyarbekacin in a total of 1 1 steps.
  • Introduction of a hydroxy! group at C2 provided a 4-fold to 64-fold improvement against MRS A clinical isolates resistant to arbekacin and led to a reduction in nephrotoxicity.
  • the present disclosure provides compounds of Formulae (I) and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopicallv labeled derivatives, and prodrugs thereof, collectively referred to as compounds of the invention.
  • rovided herein is a compound of Formula (I):
  • R.2b is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • R.3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Rsd is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group; or
  • R.3c and R 3 a together form a ring
  • R 4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
  • R 4a and R 3c are combined to form a five or six-membered ring, or
  • R 4a and R 3 d are combined to form a five or six-membered ring;
  • R b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
  • R 4a and The are combined to form a five or six-membered ring;
  • R 4a and R 3 d are combined to form a five or six-membered ring
  • R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Rub is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Rjsb is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Riea is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Riga, Risb, and Risd independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or two of Risa, Ri8b, and Risd are combined to form a ring.
  • any formulae described herein are also meant to include salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, and isotopically labeled derivatives thereof.
  • the provided compound is a salt of any of the formulae described herein.
  • the provided compound is a pharmaceutically acceptable salt of any of the formulae described herein.
  • the provided compound is a solvate of any of the formulae described herein .
  • the provided compound is a hydrate of any of the formulae described herein.
  • the provided compound is a polymorph of any of the formulae described herein.
  • the provided compound is a co-crystal of any of the formulae described herein. In certain embodiments, the provided compound is a tautomer of any of the formulae described herein. In certain embodiments, the provided compound is a stereoisomer of any of the formulae described herein. In certain embodiments, the provided compound is of an isotopicallv labeled form of any of the formulae described herein. For example, compounds having the present stmctures except for the replacement of hydrogen by deuterium or tritium, replacement of i 9 F with lS F, or the replacement of a f 2 C by a 1 C or 14 C are within the scope of the disclosure. In certain embodiments, the provided compound is a deuterated form of any of the formulae or compounds described herein.
  • Rib is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary] or heteroaryl .
  • Ra is fluorine, chlorine, bromine or iodine.
  • Rib is hydroxyl.
  • Ri i s protected hydroxyl.
  • Rib is amino (e.g., -NH 2 , - H(alkyl) or -N(alkyl) 2 ).
  • ib is protected amino.
  • i is cyano.
  • Rib is unsubstituted aliphatic (e.g. , unsubstituted 0-6 akyl).
  • Rib is substituted aliphatic (e.g., substituted Ci-6 akyl).
  • R i s unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyi).
  • Rib is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyi).
  • Rib is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-e heteroakyl).
  • Rib is substituted heteroaliphatic (e.g. , substituted Ci-6 heteroakyl).
  • Rib is unsubstituted cyclic heteroaliphatic (e.g.
  • ib is substituted cyclic heteroaliphatic (e.g., substituted C2-0 heterocyclyl).
  • Rib is unsubstituted Ce-io aryl.
  • Rib is substituted Ce-io aryl.
  • Rib is unsubstituted C3-10 heteroaryl.
  • Rib is substituted C3- 10 heteroaryl.
  • Rib is hydroxyl.
  • Group Rsc is a group consisting of:
  • Bee is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group.
  • R 3c is hydrogen. In certain embodiments, R 3c i s a nitrogen protecting group. In certain embodiments, R.3 ⁇ 4 is unsubstituted aliphatic ⁇ e.g. , unsubstituted Ci-e akyl). In certain embodiments, R 3c i s substituted aliphatic e.g. , substituted Ci-e. akyl). In certain embodiments, R 3 c is unsubstituted cyclic aliphatic ⁇ e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R.3c is substituted cyclic aliphatic ⁇ e.g.
  • R 3c is unsubstituted heteroaliphatic ⁇ e.g. , unsubstituted Ci-6 heteroakyl).
  • Bee is substituted heteroaliphatyl ⁇ e.g., substituted Ci-6 heteroakyl).
  • Rsc is unsubstituted cyclic heteroaliphatic ⁇ e.g. , unsubstituted C2-6 heterocyclyl).
  • R 3c is substituted cyclic heteroaliphatic (e.g. , substituted C2-0 heterocyclyl).
  • R 3c is unsubstituted Ce-io aryl .
  • R3c is substituted Ce-io aryl.
  • Bee is unsubstituted C3-10 heteroaryl.
  • R 3c is substituted €3-10 heteroaryl,
  • sc is hydrogen. In certain particular embodiments,
  • modification of R 3c is used to overcome ArmA-medidated resistance.
  • R 3 d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • B d is a nitrogen protecting group.
  • R3d is unsubstituted aliphatic (e.g. , unsubstituted Ci-e. akyl ).
  • R 3 d is substituted aliphatic (e.g., substituted Ci-& akyl).
  • Rsd is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl).
  • R 3 d is substituted cyclic aliphatic (e.g., subsituted C3-0 cycloakyl).
  • R 3 d is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-e heteroakyl). In certain embodiments, R 3 d is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl). In certain embodiments, RM is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-6 heterocyclyi). In certain embodiments, R 3 d is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyi). In certain embodiments, ad is unsubstituted C 6 -io aryl. In certain embodiments, R 3 d is substituted Ce-io aryl. In certain embodiments, R 3 d is unsubstituted C3-10 heteroaryl. In certain embodiments, Rsdis substituted C 3 - 10 heteroaryl.
  • R 3 d is methyl.
  • modification of R 3 d is used to overcome ArmA-medidated resistance
  • R 3 c and R 3 d are optionally combined to form a ring.
  • the ring is optionally substituted heterocyclyi (e.g., oxiranyl, butyrolactonyl, aziridinyl, azetidinyl, and the like).
  • the ring is a 3, 4, 5, 6 or 7 membered ring.
  • R3 ⁇ 4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl .
  • R 4A is fluorine, chlorine, bromine or iodine. In certain embodiments, R 4A is hydroxyl. In certain embodiments, R 4A is protected hydroxyl. In certain embodiments, R 4a is cyano. In certain embodiments, R 4a is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl). In certain embodiments, R 4a is substituted aliphatic (e.g., substituted Ci- 6 akyl). In certain embodiments, R 4a is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl).
  • R 4a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R 4a is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-e heteroakyl). In certain embodiments, R 4a is substituted heteroaliphatyl (e.g. , substituted Ci-6 heteroakyl). In certain embodiments, R 4a is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R 4a is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl).
  • R 4a is unsubstituted Ce-io aryl . In certain embodiments, R 4a is substituted Ce-io aryl. In certain embodiments, R a is unsubstituted C3-10 heteroaryl. In certain embodiments, R 4a is substituted C3-10 heteroaryl.
  • R 4a is hydroxyl
  • R 4 b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaiyl.
  • R 4 b is fluorine, chlorine, bromine or iodine. In certain embodiments, R 4 b is hydroxyl. In certain embodiments, R 4 b is protected hydroxyl. In certain embodiments, R 4 b i s cyano. In certain embodiments, R 4 b is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl). In certain embodiments, R 4 b is substituted aliphatic (e.g. , substituted Ci- 6 akyl). In certain embodiments, R 4 b is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl).
  • R 4a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl).
  • R 4 b is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl).
  • R 4 b is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl).
  • R 4 b is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl).
  • R*b is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl).
  • R 4 b is unsubstituted Ce-io aryl. In certain embodiments, R 4 b is substituted Ce.-io aryl. In certain embodiments, R 4 b is unsubstituted C3-10 heteroaiyl. In certain embodiments, R 4 b is substituted C3-10 heteroaiyl.
  • R 4 b is methyl .
  • R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaiyl, or a nitrogen protecting group.
  • R?d is hydrogen. In certain embodiments, R?d is a nitrogen protecting group. In certain embodiments, R:?d is unsubstituted aliphatic (e.g., unsubstituted d-6 akyl). In certain embodiments, R?d i s substituted aliphatic (e.g. , substituted Ci-e akyl). In certain embodiments, R?d is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R.?d is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl).
  • R?d is unsubstituted heteroaliphatic (e.g. , unsubstituted d-6 heteroakyl). In certain embodiments, R?d is substituted heteroaliphatyl (e.g. , substituted d-6 heteroakyl). In certain embodiments, R?d is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C 2 -6 heterocyclyl). In certain embodiments, R?d is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, R?d is unsubstituted C6-10 aryl .
  • R-'d is substituted Ce-io aryl.
  • R?d is unsubstituted C3-10 heteroaiyl.
  • R?d is substituted C3-10 heteroaiyl .
  • R?d has the structure:
  • R 7 f is alkyl or heteroalkyl.
  • R?f is halogenated.
  • R?f is d-6 alkyl or d-6 heteroalkyl.
  • R?f is substituted.
  • R?f is unsubstituted.
  • R?d has the structure: 00151 In certain embodiments, R?d has the structure:
  • R?d has the structure:
  • R 7g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acyclic, linear or branched aliphatic (e.g. , alkyl or cycloalkyl), cyclic or acyclic, linear or branched heteroaliphatic (e.g. , heteroalkvl or heterocyclvl), arvl or heteroaryl, or R 7g and R/h are combined to form a ring.
  • R 7 and R7 are independently substituted.
  • R? g and R?h are unsubstituted.
  • R? g and R?h are unsubstituted.
  • R 7g and R?h are combined to form an optionally substituted 5- or 6-membered ring (e.g. , pyrrolidinyi, piperidinyl, morpholinyl, and the like).
  • an optionally substituted 5- or 6-membered ring e.g. , pyrrolidinyi, piperidinyl, morpholinyl, and the like.
  • R?d is hydrogen.
  • R?d has the structure:
  • R?d has the structure:
  • modification of R?d is used to overcome A T(2")-medi dated resistance and/or AAC(3)-mediated resistance.
  • ja is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, arvl, or heteroaryl.
  • l a is hydrogen.
  • R9?. is a nitrogen protecting group.
  • R.9a is unsubstituted aliphatic (e.g. , unsubstituted d-6 akyl).
  • ⁇ 1 ⁇ 2 ⁇ is substituted aliphatic (e.g. , substituted Ci-e akyl).
  • R9a is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R.9a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R9a is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, I3 ⁇ 4 a is substituted heteroaliphatyl (e.g., substituted Ci-6 heteroakyl). In certain embodiments, R a is unsubstituted cyclic heteroaliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R.9a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R9a is unsubstituted heteroaliphatic
  • Rg a is substituted cyclic heteroaliphatic (e.g. , substituted C2-0 heterocyclyl).
  • Rsa is unsubstituted C0-10 aryl .
  • R.9a is substituted Ce-io aryl.
  • R3 ⁇ 4 is unsubstituted C 3 - 10 heteroaryl.
  • l3 ⁇ 4a is substituted C3-10 heteroaryl.
  • g a is an aldehyde (e.g., -CHO), a carboxylic acid (e.g., CO2H), a carboxyalkyl (e.g., -C0 2 (alkyl), or an amide (e.g., --CONH2, -CONH(alkyl) or -CON(alkyl) 2 ).
  • aldehyde e.g., -CHO
  • a carboxylic acid e.g., CO2H
  • a carboxyalkyl e.g., -C0 2 (alkyl)
  • an amide e.g., --CONH2, -CONH(alkyl) or -CON(alkyl) 2 .
  • R9a is hydroxymethyl.
  • R ⁇ : is cycloproyl.
  • R.9a is -CHO, In certain particular embodiments, R9a is -CO2CH3. In certain particular embodiments, R9a is hydrogen.
  • modification of R9a is used to overcome AAC(3)-mediated resistance.
  • R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • 9d is hydrogen.
  • R9d is a nitrogen protecting group.
  • R9d is unsubstituted aliphatic (e.g. , unsubstituted C i-e akyl).
  • R9d is substituted aliphatic (e.g. , substituted Ci-e akyl).
  • R3 ⁇ 4i is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl).
  • R ⁇ M is substituted cyclic aliphatic (e.g. , subsituted C3-0 cycloakyl).
  • R.9d is unsubstituted heteroaliphatic (e.g. , unsubstituted d-6 heteroakyl). In certain embodiments, 9d is substituted heteroaliphatyl (e.g. , substituted C1-0 heteroakyl). In certain embodiments, Rad is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyelyi). In certain embodiments, R.9d is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyelyi). In certain embodiments, 9d is unsubstituted Ce-io aryl. In certain embodiments, R d is substituted C 6 -i 0 aryl. In certain embodiments, d is unsubstituted C io heteroaryl. In certain embodiments, R9d is substituted C3-10 heteroaryl.
  • R9d is hydrogen
  • 9 d is CI ID, -C( ))R m , -CChR 83 , -C( ))SR aa , - ⁇
  • each instance of R aa independently is as defined herein, and wherein each instance of R bb independently is as defined herein.
  • R is halogen, hvdroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
  • Rub is fluorine, chlorine, bromine or iodine. In certain embodiments, Rub is hydroxyl. In certain embodiments, Rub i s protected hydroxyl . In certain embodiments, Rub is cyano. In certain embodiments, Rub is unsubstituted aliphatic (e.g. , unsubstituted Ci-& akyl). In certain embodiments, Rub is substituted aliphatic (e.g. , substituted Ci-6 akyl). In certain embodiments, Rub is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl).
  • Rub i s substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl).
  • Rub is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl).
  • Rub is substituted heteroaliphatic (e.g. , substituted Ci-6 heteroakyl).
  • Rub is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyelyi).
  • Ra is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyelyi).
  • Rub is unsubstituted Ce-io aryl. In certain embodiments, Rub is substituted Ce-io aryl. In certain embodiments, R» is unsubstituted C3-10 heteroaryl. In certain embodiments, Rub is substituted C3-10 heteroaryl.
  • Rub is hydroxyl.
  • Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary], heteroaryl, or a nitrogen protecting group.
  • Ri4d is hydrogen. In certain embodiments, Rwd is a nitrogen protecting group. In certain embodiments, R 14 d is unsubstituted aliphatic (e.g., unsubstituted Ci-e akyl). In certain embodiments, R 14 d is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, Ri4d is unsubstituted cyclic aliphatic (e.g., unsubsituted C 3 -6 cycloakyl). In certain embodiments, Rj4d is substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyl).
  • Ri d is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, Ri4d is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl). In certain embodiments, R i . ⁇ .. ⁇ is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R 14 d is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Ri4d is unsubstituted C0-10 aryl. In certain embodiments, R 14 d is substituted Ce-io aryl. In certain embodiments, Ri4d is unsubstituted C3-10 heteroaryl. In certain embodiments, Ri4d is substituted C3-10 heteroaryl.
  • Rnd is hydrogen
  • Risb is hydrogen, halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary! or heteroaryl.
  • Ri.3 ⁇ 4 is hydrogen.
  • Risb is fluorine, chlorine, bromine or iodine.
  • Ru is hydroxy!.
  • Risb is protected hydroxyl.
  • Ri.3 ⁇ 4 is cyano.
  • Risb is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl).
  • Risb is substituted aliphatic (e.g., substituted Ci-6 akyl).
  • Ri?b is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyi ). In certain embodiments, Risb i s substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyi). In certain embodiments, Risb is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, Risb is substituted heteroaiiphatic (e.g., substituted Ci-e heteroakyl).
  • Risb is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, Risb is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Risb is unsubstituted Ce.-io aryl. In certain embodiments, Risb is substituted Ce-io aryl. In certain embodiments, RL3 ⁇ 4 is unsubstituted C3-10 heteroaryi. In certain embodiments, Risb is substituted C3-10 heteroaryi .
  • RL3 ⁇ 4 is hydrogen
  • R 16 a is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryi.
  • Riea is hydrogen. In certain embodiments, Ri6a is fluorine, chlorine, bromine or iodine. In certain embodiments, Ri6a is hydroxyl. In certain embodiments, Ri6a is protected hydroxyl. In certain embodiments, R1 ⁇ 2a is cyano. In certain embodiments, Riea is unsubstituted aliphatic (e.g., unsubstituted Ci-e akyl). In certain embodiments, Ri6a is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, Ri6a is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyi).
  • Ri6a is substituted cyclic aliphatic (e.g., subsituted C3-0 cycloakyi).
  • Riea is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-6 heteroakyl).
  • Rie a is substituted heteroaiiphatic (e.g., substituted Ci-6 heteroakyl).
  • Riea is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-0 heterocyclyl).
  • Riea is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyl).
  • Ri6a is unsubstituted Ce-io aryl. In certain embodiments, Riea is substituted Ce-io aryl. In certain embodiments, Ri6a is unsubstituted C3-10 heteroaryi. In certain embodiments, Riea is substituted C3-10 heteroaryi.
  • Riea is hydrogen.
  • Riga is halogen, hydroxvl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl .
  • Riga is fluorine, chlorine, bromine or iodine.
  • Ri8a is hydroxyl.
  • Riga is protected hydroxy!.
  • Riga is cyano.
  • Ri8a i unsubstituted aliphatic (e.g., unsubstituted C i-e akyl).
  • Ri8a i s substituted aliphatic (e.g. , substituted Ci-6 akyl).
  • Risa is unsubstituted cyclic aiiphatic (e.g. , unsubsituted C3-6 cycloakyl).
  • Risa is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloaky!).
  • Riga is unsubstituted heteroaliphatic (e.g. , unsubstituted Cw heteroakyl).
  • Risa is substituted heteroaliphatic (e.g. , substituted Ci-e heteroakyl).
  • Rixa is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl).
  • Riga is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl).
  • Risa is unsubstituted Cr io aryl. In certain embodiments, Risa is substituted Ce-io aryl. In certain embodiments, Riga is unsubstituted C3-10 heteroaryl. In certain embodiments, Risa is substituted C3-10 heteroaryl.
  • Risa is hydrogen. In certain particular embodiments, Risa is hydroxy methyl. In certain particular embodiments, Risa is -CH(OH)CH 3 hydroxyeth-l-yl (e.g., the (S) stereoisomer of -CH(OH)CH 3 or the (R) stereoisomer of - CH(OH)CH 3 ). In certain particular embodiments, Risa is -CH 2 NHCH(CH 2 ) 2 .
  • modification of Risa is used to overcome NpmA-medidated resistance and/or AAC(6')-mediated resistance.
  • Risb is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
  • Risb is fluorine, chlorine, bromine or iodine. In certain embodiments, Risb is hydroxyl. In certain embodiments, Risb is protected hydroxy!. In certain embodiments, Risb is cyano. In certain embodiments, Risb i s unsubstituted aliphatic (e.g. , unsubstituted Ci-& akyl). In certain embodiments, Risa is substituted aliphatic (e.g. , substituted Ci-6 akyl). In certain embodiments, Risb is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl).
  • R i substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl).
  • Risb is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl).
  • Risb is substituted heteroaliphatic (e.g. , substituted Ci-e heteroakyl).
  • Risb is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl).
  • Risb is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl).
  • Risb is unsubstituted Ce-io aryl. In certain embodiments, Risb is substituted Ce-io aryl . In certain embodiments, Rm is unsubstituted C3-10 heteroaryl. In certain embodiments, Ri8b is substituted C3-10 heteroaryl.
  • Risb is hydrogen. In certain particular embodiments, Risb is hydroxy methyl. In certain particular embodiments, Risb is -CH(OH)CH 3 hydroxyeth-l-yl (e.g., the (S) stereoisomer of -CH(OH)CH 3 or the (R) stereoisomer of - CH(OH)CH 3 ). In certain particular embodiments, isb is -CH2 HC (CH2)2.
  • Risd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • Risd is hydrogen. In certain embodiments, Risd is a nitrogen protecting group. In certain embodiments, Risd is unsubstituted aliphatic (e.g. , unsubstituted Ci-6 akyl). In certain embodiments, Risd is substituted aliphatic (e.g. , substituted Ci-& akyl). In certain embodiments, Risd is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-0 cycloakyl). In certain embodiments, Risd is substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyl).
  • Ri8d is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl). In certain embodiments, Risd is substituted heteroaliphatyl (e.g., substituted Ci-6 heteroakyl). In certain embodiments, Risd is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl).
  • Risd is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl). In certain embodiments, Risd is unsubstituted Ce-io aryl. In certain embodiments, Ri8d is substituted Ce-io aryl. In certain embodiments, Ri»d is unsubstituted C3-10 heteroaryl. In certain embodiments, Risd is substituted C3-10 heteroaryl.
  • Risd is hydrogen
  • any two of R 18a , Risb and Risd are optionally combined to form a ring.
  • Rj.8a and Ri8b are combined to form a ring.
  • R 18a and Risd are combined to form a ring.
  • Risb and Risd are combined to form a ring.
  • the ring is optionally substituted carbocyclyl (e.g., C3-10 cycloalkyl, or C3-10 cycloalkenyl, or C3-10 cycloalkynyl).
  • the ring is optionally substituted C2-10 heterocvclyl (e.g., oxiranyl, butyrolactonyl, aziridinyl, azetidinyl, and the like). In certain embodiments, the ring is a 3, 4, 5, 6, 7, 8, 9 or 10 membered ring.
  • C2-10 heterocvclyl e.g., oxiranyl, butyrolactonyl, aziridinyl, azetidinyl, and the like.
  • the ring is a 3, 4, 5, 6, 7, 8, 9 or 10 membered ring.
  • R 2 b is halogen, -OH, -G(aikyi), -OC(0)alkyl, -NH2, -NHC(0)alkyl, or heteroaryl;
  • ic is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • R d is alkyl, cycloalkyl, heteroalkyl or heterocyclyl
  • RJC and R 3 d together form a ring
  • R 4a is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
  • Ri is alkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • R?d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • R9a is hydrogen, alkyl, carboxyalkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • R.9d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • Rub is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
  • Ri4d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl
  • Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, - HC(0)alkyl, alkyl heteroalkyl,
  • Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
  • Risa, Risb, and Ri8d independently are hydrogen, alkyl, cycloalkyl, heteroalkyl heterocyclyl, or two of Risa, Ri8t>, and Risd are combined to form a ring,
  • the compound of Formula (I) is of Formula (II):
  • Rib, R:3 ⁇ 4, 4a, Rib, R?d, 9a, R9d, Rub, Ri4d, Risb, Riea, Risa, Risb, and isa are as defined herein.
  • the compound of Formula (II) is of Formula (II- 1):
  • the compound of Formula (II) is of Formula (II ⁇ 2):
  • R 3c i, R4b, R?d, R d, Ri4d, Ri8a, Ri8 and Ri8d are as defined herein.
  • the compound of Fonnuia (II) is of Formula (11-3):
  • the compound of Formula (II) is of Formula ( ⁇ -4):
  • R 3 d, R-4 , R?d, Rsd, Ri4d, Risb, and Ri8d are as defined herein.
  • the compound of Formula (II) is of Formula ( ⁇ -6):
  • R ⁇ d, d, Rsa, Risb, Ri6a, Ri8a, Ris and Ri8d are as defined herein.
  • the compound of Formula (I) is selected from the following compounds:
  • X is a leaving group
  • Ri5b is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl,
  • Riea is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Ri8a and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
  • Risa and Risb are combined to form a ring.
  • Ri5b is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
  • Ri6a is hydrogen, halogen, ⁇ OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
  • Risa and Rssb are hydrogen, alkyl, cycloalkyl, heteroalkyl or heterocyclyi; or
  • Ri8a and Risb are combined to form a ring.
  • X is - SPh, -S(0)Ph or -S(0) 2 Ph.
  • Fommla (I-a) is of Formulae (I-al)-(I-a4):
  • R?e is -N3 or -N(R?c)(R7d), wherein:
  • R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Ri2a is an oxygen protecting group
  • Rub and R 12a are combined to form a five or six-membered ring.
  • R? e is a radical of the formula: wherein R?f is Ci-e alkyl or C1-0 heteroalkyl.
  • R?c is hydrogen or a nitrogen protecting group
  • R?d is hydrogen or a nitrogen protecting group
  • R9a is hydrogen, alkyl, carboxyalkyl, cycloalkyl, heteroalkyl or heterocyclyl
  • Riib is halogen, protected hydroxy!, -O(alkyl), -OC(0)alkyl, ⁇ HC(0)alkyl, or heteroaryl;
  • Ri2a is an oxygen protecting group
  • Rub and R 12a are combined to form a five or six-membered ring.
  • R9a is hydrogen
  • Riib is protected hydroxyl; and Ri2a is an oxygen protecting group.
  • R9a is hydrogen
  • Riib and R 12a are combined to form a five or six-membered ring.
  • Formula (I-b) is of Formulae (I ⁇ bl)-(l-b8):
  • R?e is -N3 or -N(R?c)(R7d), wherein:
  • R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Rvd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
  • Rsa is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl ;
  • Riib is halogen, hydroxvl, protected hvdroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Ri2a is an oxygen protecting group
  • Riib and R 12a are combined to form a five or six-membered ring
  • Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
  • Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
  • Risa and Risb are hydrogen, alkyl, cycloalkyl, heteroalkyl or heterocyclyl; or
  • Risa and Rss are combined to form a ring.
  • R?e is a radical of the formula:
  • R?f is Ci- ⁇ alkyl or Ci-e heteroalkyl.
  • R ⁇ is -N3 or ⁇ ( ! ⁇ ,)(! ⁇ .: ⁇ :
  • R?c is hydrogen or a nitrogen protecting group
  • R?d is hydrogen or a nitrogen protecting group
  • R9a is hydrogen, alkyl, carboxvalkyl, cycloalkyl, heteroalkyl or heterocyclyl;
  • Rub is halogen, protected hydroxyl, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, heteroaryl;
  • Ri2a is an oxygen protecting group
  • Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
  • Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
  • Risa and Rssb independently are hydrogen, alkyl, cycloalkyl, or cyclic or acyclic heteroalkyl.
  • R9a is hydrogen
  • Ri2a is an oxygen protecting group
  • Risb and R 16a are hydrogen;
  • Risa and Ri8b independently are hydrogen, alkyl, or heteroalkyl. [00211] In certain embodiments Formula (I-c):
  • R-9a is hydrogen
  • Riib is protected hydroxy]
  • R 12a is an oxygen protecting group
  • R9a is hydrogen
  • Riib and R 12a are combined to form a five or six-membered ring.
  • Formula (I-c) is of Formulae (I-cl)-(I-c6):
  • X is a leaving group
  • R2 is halogen, hydroxy!, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Rsc is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • '3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group, or
  • R a is halogen, hydroxy!, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • R 4 b is halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • R 4a and R 3c are combined to form a five or six-membered ring;
  • R 3 d are combined to form a five or six-membered ring.
  • X is a leaving group
  • Ra is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -TMH 2 , protected amino, -NHC(0)a!ky!, or heteroaryl;
  • R 3c is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
  • Rsd is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group
  • R a is halogen, -Oil protected hydroxyl, -O(alkyl), -OC(0)alkyl, alkyl, cycioalkyl heteroaikyi, or heterocyciyl;
  • i is alkyl, cycioalkyl, heteroaikyi or heterocyciyl; or
  • R4a and R 3c are combined to form a five or six-membered ring;
  • R4a and R 3 d are combined to form a five or six-membered ring
  • X is -SPh, -S(0)Ph or -S(0) 2 Ph
  • Ri is protected hydroxyl
  • R d is alkyl or benzyl
  • R 4a is protected hydroxyl; and b is alkyl .
  • a and R.3c are combined to form a five or six-membered ring; or Ua and R.3d are combined to form a five or six-membered ring.
  • Formula (I-d) is of Formulae (I-dl)-(I-d6)
  • R.2b is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Rsc is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • '3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group, or
  • R a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • R 4 b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • R?e is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
  • R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
  • Ri5b is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Ri6a is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
  • Ri8a and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
  • Ra> is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -TMH 2 , protected amino, -NHC(0)alkyl, or heteroaryl;
  • R 3c is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
  • R'3d is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group
  • R 4a is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, alkyl, cycioalkyl heteroaikyi, or heterocyciyl; and P b is alkyl, cycioalkyl, heteroalkyl or heterocyclyl; or
  • R4a and R 3c are combined to form a five or six-membered ring;
  • R 4 a and R 3 d are combined to form a five or six-membered ring
  • R-/e is -N3 or ⁇ N(R7c)(R7d);
  • R?c is hydrogen or a nitrogen protecting group
  • R'?d is hydrogen or a nitrogen protecting group
  • R9a is hydrogen, alkyl, cycioalkyl, heteroalkyl or heterocyclyl,
  • Rub is halogen, protected hydroxyl, -OH, -O(alkyl), -QC(0)alkyl, -NHC(0)alkyl, heteroaryl;
  • Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
  • Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroaikvi;
  • Ri8a and Risb independently are hydrogen, alkyl, cycioalkyl, or cyclic or acyclic heteroalkyl.
  • Ra> is protected hydroxyl
  • 3d is alkyl
  • R 4 a is protected hydroxyl
  • Rtb is alkyl or benzyl
  • R a and Rsc are combined to form a five-membered ring
  • e is -N3 or -N(R7c)(R7d);
  • R?c is hydrogen or a nitrogen protecting group
  • R is hydrogen or a nitrogen protecting group
  • R9a is hydrogen
  • Risb and Rie a are hydrogen;
  • Risa and Risb independently are hydrogen, alkyl, or heteroalkyl.
  • Formula (I-e) is of Formulae (I-el)-(I-e6):
  • the method further comprises contacting the compound of Formula (I-e), or a salt thereof wherein R 18a and Risb are hydrogen, with a base and an electrophile to produce a compound of Formula (I-e), or a salt thereof, wherein one or both of Ri8a and Risb are not hydrogen.
  • R 18a and Ri8b are independently alky] .
  • the base is selected from a carbonate (e.g., sodium carbonate, potassium carbonate, and the like), a tertiary amine (e.g., trimethylamme, diisopropylethylamine, l ,8-diazabicyclo[5.4.0]undec-7-ene, and the like), a hydride (e.g., sodium hydride, potassium hydride, and the like), and an amide (lithium diisopropyl amide, sodium hexamethyidisilazide, potassium hexamethyidisilazide, and the like).
  • a carbonate e.g., sodium carbonate, potassium carbonate, and the like
  • a tertiary amine e.g., trimethylamme, diisopropylethylamine, l ,8-diazabicyclo[5.4.0]undec-7-ene, and the like
  • a hydride
  • the electrophile has the structure of R 18 a-X or Rssb-X, wherein Risa and Risb are not hydrogen, and wherein X is a leaving group as defined herein.
  • the electrophile is an aldehyde (e.g., formaldehyde), an activated carboxylic acid derivative (e.g., an acid chloride, carboxylic acid anhydride, or the like), an activated carbonate acid derivative (e.g., an alkoxy carbonyl chloride), a halogen or haiogenating agent (e.g., bromine, N-bromosuccinimide, or the like), or a Schiff base (e.g., a formal dimine).
  • an aldehyde e.g., formaldehyde
  • an activated carboxylic acid derivative e.g., an acid chloride, carboxylic acid anhydride, or the like
  • an activated carbonate acid derivative e.g., an alkoxy carbonyl chloride
  • said reducing a compound of Formula (I-e), or a salt thereof comprises:
  • the first reducing agent and the second reducing agent are the same, and the nitro group and azide groups are reduced simultaneously. In certain embodiments, the first reducing agent and the second reducing agent are different.
  • the method further comprises coupling a comp nd of Formula (I-c):
  • the suitable conditions comprise an oxidizing agent.
  • said coupling a compound of Formula (I-c), or a salt thereof, with a compound of Formula (I-d), or a salt thereof comprises:
  • R?e has a structure selected from:
  • PG is a protecting group
  • R?g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acy devis, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl, or vg and R?h are combined to form a ring.
  • the suitable conditions of (a) comprise an oxidizing agent.
  • the suitable conditions of (b) comprise an oxidizing agent, hydrogenolysis, acid hydrolysis, or base hydrolysi s.
  • the method further comprises coupling a compound of Formula (I-a):
  • the suitable conditions comprise an oxidizing agent.
  • said coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof comprises: (a) coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof, under suitable conditions to produce a compound of Formula (I-c), wherein R 12a is an oxygen protecting group; and
  • the suitable conditions of (a) comprise an oxidizing agent.
  • the suitable conditions of (b) comprise hydrogenolysis, acid hydrolysis or base hydrolysis.
  • R2 , Rsc, Rsd, R.4a, R.4b, Rvd, R9a, 9d, Rub, Ri4d, Ri 5b, Ri&a, Risa, Ri»b, and i8d are as defined above, comprising:
  • step (i) comprises:
  • step (i-b) removing the oxygen protecting group under suitable conditions to produce a compound of Formula (I-c), wherein R 12a is hydrogen.
  • R? e is N(R.7c)(R7d), wherein R?c and R?d are nitrogen protecting groups, and step (ii) comprises:
  • step (ii-c) acylating the product of step (ii-b) with a compound having the formula: , wherein
  • X is a leaving group and R?f is Ci-6 alkyl or Ci-e heteroalkyl,
  • R?e has the structure:
  • R?e has the structure:
  • R 7g and R?h are as defined herein.
  • R?d is hydrogen. In certain particular embodiments, R?d has the structure:
  • the method of making Formula (I) further comprises contacting the compound of Formula (I-e), or a salt thereof wherein Riga and i8 are hydrogen, with a base and an electrophile to produce a compound of Formula (I-e), or a salt thereof, wherein one or both of Risa and Risb are not hydrogen.
  • Riga and Ri8b are independently alkyl.
  • the base is selected from carbonate (e.g., sodium carbonate, potassium carbonate, and the li ke), tertiary amine (e.g., trimethylamine, diisopropyl ethyl amine, l,8-diazabicyclo[5.4.0]undec-7-ene, and the like), hydride (e.g., sodium hydride, potassium hydride, and the like), and amide (lithium diisopropyl amide, sodium hexamethyldisilazide, potassium hexamethyldisilazide, and the like).
  • carbonate e.g., sodium carbonate, potassium carbonate, and the li ke
  • tertiary amine e.g., trimethylamine, diisopropyl ethyl amine, l,8-diazabicyclo[5.4.0]undec-7-ene, and the like
  • hydride e.g., sodium hydride
  • the electrophile has the structure of Risa-X or Ri8b-X, wherein Riga and Risb are not hydrogen, and wherein X is a leaving group as defined herein.
  • the electrophile is an aldehyde (e.g., formaldehyde), an activated carboxylic acid derivative (e.g., an acid chloride, carboxylic acid anhydride, or the like), an activated carbonate acid derivative (e.g., an alkoxy carbonyl chloride), a halogen or haiogenating agent (e.g., bromine, N-bromosuccinimide, or the li ke), or a Schiff base (e.g., a formal dimine).
  • an aldehyde e.g., formaldehyde
  • an activated carboxylic acid derivative e.g., an acid chloride, carboxylic acid anhydride, or the like
  • an activated carbonate acid derivative e.g., an alkoxy carbonyl chlor
  • step (iii) comprises reducing both the azido and nitro groups of the compound of Formula (I-e) with the same reducing agent. In certain embodiments, step (iii) comprises orthogonal reduction of the azido and nitro groups with different reducing agents.
  • step (iii) comprises:
  • (iii-d) optionally, alkylating or acylating the primary amines of (iii-c).
  • the suitable conditions of steps (i) and (i-a) independently comprise an oxidizing agent.
  • Exemplary conditions are disclosed herein, for example, in Figure 8 and Figure 21.
  • the suitable conditions of steps (ii) and (ii-a) independently comprise an oxidizing agent.
  • the suitable conditions of step (ii-b) comprises acid hydrolysis (e.g., aqueous hydrochloric acid) or hydrogenolysis (e.g., catalytic hydrogenation), or oxidation (e.g., eerie ammonium nitrate).
  • acid hydrolysis e.g., aqueous hydrochloric acid
  • hydrogenolysis e.g., catalytic hydrogenation
  • oxidation e.g., eerie ammonium nitrate
  • a method of making a compound of Formula (1- c), comprising coupling a compound of Formula (I-a) with a compound of Formula (I-b) under suitable conditions, wherein the compounds of Formulae (I-a), (I-b) and (I-e) have structures as described herein.
  • the suitable conditions comprise an oxidizing agent. Exemplary conditions are disclosed herein, for example, in Figure 18 and Figure 21.
  • a method of making a compound of Formula (I- e), comprising coupling the compound of Formula (I-c) with a compound of Formula (I-d) wherein the compounds of Formulae (I ⁇ d) and ( ⁇ - ⁇ ) have structures as described herein.
  • the suitable conditions comprise an oxidizing agent. Exemplar ⁇ ' conditions are disclosed herein, for example, in Figure 18 and Figure 21 ,
  • compositions comprising an aminoglycoside compound as described herein (e.g., a compound of Formulae (I), (II), (II-l), ( ⁇ -2), ( ⁇ -3), ( ⁇ -4), ( ⁇ -5), ( ⁇ -6), FSA-38240, FSA-38252, FSA-382SS, FSA-392S4
  • an aminoglycoside compound as described herein (e.g., a compound of Formulae (I), (II), (II-l), ( ⁇ -2), ( ⁇ -3), ( ⁇ -4), ( ⁇ -5), ( ⁇ -6), FSA-38240, FSA-38252, FSA-382SS, FSA-392S4
  • compositions agents include any and all solvents, diluents, or other liquid vehicles, dispersions, suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • General considerations in formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).
  • compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the aminoglycoside of the present invention into association with a carrier and/or one or more other accessor ⁇ ' ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
  • compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, ami/or as a plurality of single unit doses.
  • a "unit dose" is discrete amount of the pharmaceutical composition comprising a predetermined amount of the aminoglycoside of the present invention.
  • the amount of the aminoglycoside is generally equal to the dosage of the aminoglycoside which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
  • Relative amounts of the aminoglycoside, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between 0.1% and 100% (w/w) aminoglycoside.
  • compositions used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
  • Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, soiubilizing agents, and emulsifiers, and mixtures thereof.
  • the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
  • the conjugates of the invention are mixed with soiubilizing agents, and mixtures thereof.
  • Injectable preparations for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the aminoglycoside is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or di calcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitoi, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol
  • Dosage forms for topical and/or transdermal administration of an aminoglycoside of this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches.
  • the aminoglycoside is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any needed preservatives and/or buffers as can be required.
  • compositions are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
  • Aminoglycosides provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily amount of the aminoglycoside will be decided by the attending physician within the scope of sound medical judgment.
  • the specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific aminoglycoside employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject, the time of administration, route of administration, and rate of excretion of the specific aminoglycoside employed; the duration of the treatment; drugs used in combination or coincidental with the specific aminoglycoside employed; and like factors well known in the medical arts.
  • aminoglycosides and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation, and/or as an oral spray, nasal spray, and/or aerosol.
  • enteral e.g., oral
  • parenteral intravenous, intramuscular, intra-arterial, intramedullary
  • intrathecal subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal
  • topical as by powders, ointments, creams, and/or drops
  • Oral administration is the preferred mode of administration.
  • the subject may not be in a condition to tolerate oral administration, and thus intravenous, intramuscular, and/or rectal administration are also preferred altermative modes of administration.
  • An effective amount may be included in a single dose (e.g., single oral dose) or multiple doses (e.g., multiple oral doses).
  • a single dose e.g., single oral dose
  • multiple doses e.g., multiple oral doses
  • any two doses of the multiple doses include different or substantially the same amounts of a compound described herein.
  • the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks.
  • a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 g and 1 ug, between 0.001 nig and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1 ,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein.
  • an aminoglycoside or composition can be administered in combination with one or more additional therapeutically active agents.
  • the aminoglycoside or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents.
  • each agent will be administered at a dose and/or on a time schedule determined for that agent.
  • the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions.
  • the particular combination to employ in a regimen will take into account compatibility of the inventive aminoglycoside with the additional therapeutical ly active agent and/or the desired therapeutic effect to be achieved.
  • additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
  • Exemplary additional therapeutically active agents include, but are not limited to, antibiotics, anti-viral agents, anesthetics, anti-coagulants, inhibitors of an enzyme, steroidal agents, steroidal or non-steroidal anti-inflammatory agents, antihistamine, immunosuppressant agents, antigens, vaccines, antibodies, decongestant, sedatives, opioids, pain-relieving agents, analgesics, anti-pyretics, hormones, and prostaglandins.
  • Therapeutical ly active agents include small organic molecules such as drug compounds (e.g., compounds approved by the US Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucieoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells.
  • drug compounds e.g., compounds approved by the US Food and Drug Administration as provided in the Code of Federal Regulations (CFR)
  • CFR Code of Federal Regulations
  • the additional therapeutically active agent is an antibiotic.
  • antibiotics include, but are not limited to, penicillins (e.g., penicillin, amoxicillin), cephalosporins (e.g., cephalexin), macrolides (e.g., erythromycin, clarithormycin, azithromycin, troieandomycin), fluoroquinolones (e.g., ciprofloxacin, levofloxacin, ofloxacin), sulfonamides (e.g., co-trimoxazole, trimethoprim), tetracyclines (e.g., tetracycline, chlortetracyciine, oxytetracycline, demeclocycline, methacycline, sancycline, doxycline, aureomycin, terramycin, minocycline, 6-deoxytetracycline, iymecycline, meclocycline, meclocycline, meclocycline, me
  • kits e.g., pharmaceutical packs
  • the kits provided may comprise an inventive pharmaceutical composition or aminoglycoside and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container).
  • a container e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container.
  • provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or aminoglycoside.
  • the inventive pharmaceutical composition or aminoglycoside provided in the container and the second container are combined to form one unit dosage form.
  • kits e.g., pharmaceutical packs
  • the kits provided may comprise an inventive pharmaceutical composition or aminoglycoside and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container).
  • a container e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container.
  • provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or aminoglycoside.
  • the inventive kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or aminoglycoside.
  • compositions or aminoglycoside provided in the container and the second container are combined to form one unit dosage form.
  • the bacterial ribosome is composed of ribosomal RNA (rRNA) and proteins, which are organized into two subu its, the 30S and the 50S ( Figure 34). There are three sites on the ribosome that allow tRNA binding: the A site, P site, and E site. Prior to the formation of a peptide bond, an aminoacyl-tRNA, which carries the correct amino acid for the codon displayed by the mRNA, is selected by the A site. The P site is bound to the peptidyi-tRNA, which carries the nascent peptide. The E site houses uncharged tRNA, which is subject to ejection from the ribosome.
  • rRNA ribosomal RNA
  • the process of protein synthesis can be divided into four phases: initiation, elongation, termination, and recycling ( Figure 34),
  • the 2-deoxystreptamine class of aminoglycosides (for example, compounds of Formula (I)), exert their antibacterial action by binding to the bacterial ribosome, which affects protein synthesis in multiple stages.
  • AMEs Aminoglycoside Modifying Enzymes
  • AMEs aminoglycoside modifying enzymes
  • AMEs can occur alone or in combination in both Gram-positive and Gram- negative pathogens, and exhibit a high level of substrate promiscuity.
  • Most are encoded on mobile elements such as plasmids, transposons, and integrons, which facilitate rapid dissemination of resistance.
  • AAC aminoglycoside JV-acetyltransf erase
  • APH aminoglycoside ⁇ -phosphotransferase
  • ANT aminoglycoside ⁇ -nucleotidyltransferase or O-adenyltransferase
  • AAC(6')-Ia and AAC(6')-Ib both acetylate the 6 -amino group of aminoglycosides and have identical resistance profiles. But they are two unique proteins encoded by two different genes.
  • RMTs rRNA methyltransferases
  • This class of RMTs is related to ones found in the gentamicin producing-producing strain Micromonospora purpurea, and methylates the N7 position of G1405, which is located in close proximity to the 3 "-amino group on ring III of 4,6-disubstituted aminoglycosides. Methylation results in the introduction of a positive charge on the nucleotide and, together with increased steric bulk, disfavors aminoglycoside binding and confers high-level resistance to all 4,6-disubstituted 2-deoxystreptamine aminoglycosides.
  • NmpA A second class of RMT, NmpA, was found in a clinical isolate of E. coli in Japan in 2007, which methylates Nl of AMOS, Strains carrying the nmpA gene exhibited resistance to all aminoglycosides, including the 4, 5 -di substituted aminoglycoside neomycin and the atypical aminoglycoside apramycin.
  • Efflux Pumps and Change in Membrane Permeability Resistance to aminoglycosides in P, aeruginosa is associated with changes to the outer membrane lipopolysaccharides. Structural changes to the outer membrane composition is partly regulated by the two-component regulatory system, PhoP-PhoQ, which reduces permeability of the outer membrane to aminoglycosides under Mg 2 ⁇ starvation or in the presence of polyamines. Additionally, both mutations to the electron-transport chain and nitric oxide-mediated repression of respiratory activity result in inhibition of the energy-dependent phase of aminoglycoside uptake. This attenuates the threshold buildup of aminoglycosides that is necessary for cell death and confers antibiotic resistance.
  • aminoglycoside efflux systems are named AcrAD-TolC in E. coli, AdeAB-AdeC in A. baumannii, and MexXY-OprM in P. aeruginosa. They are distinct from RND pumps used for the active export of other classes of antibiotics, which have hydrophobic binding pockets that make aminoglycosides poor substrates. Overexpression of efflux pumps, often induced by exposure to aminoglycosides, are well correlated with multidrug resistance in clinical isolates.
  • the resistance mechanisms outlined above can occur alone or in combination. Because of difference in usage pattern, the frequency of resistance mechanisms also differs depending on geographical location. Each pathogenic strain of bacteria expresses different levels of resistance, with pan-resistance observed in some species that cany clusters of resistance genes. The occurrence of aminoglycoside resistance mechanism in ESKAPE pathogens is shown in the following table:
  • the present disclosure contemplates the use of the aminoglycosides as described herein as antibacterial agents.
  • a method of treating a bacterial infection comprising administering an effective amount of an aminoglycoside of the present invention (e.g., a compound of Formulae (1), (II), (H-l), (0-2), (II-3), (0-4), (H-5), (II-6), FSA-38240, FSA-38252, FSA-38255, FSA-39254 (compound 1), or a pharmaceutically acceptable salt thereof) to a subject in need thereof.
  • an aminoglycoside of the present invention e.g., a compound of Formulae (1), (II), (H-l), (0-2), (II-3), (0-4), (H-5), (II-6), FSA-38240, FSA-38252, FSA-38255, FSA-39254 (compound 1), or a pharmaceutically acceptable salt thereof
  • Such a method can be conducted in vivo (i.e., by administration to a subject) or in vitro (e.g. , upon contact with the pathogen, biological sample,
  • the effective amount is a therapeutically effective amount.
  • administering an effective amount of an aminoglycoside kills or stops the growth of the bacteria.
  • administering an effective amount of an aminoglycoside slows the progress of a bacterial infection in the subject.
  • administering an effective amount of an aminoglycoside improves the condition of the subject suffering from a bacterial infection.
  • the subject has a suspected or confirmed bacterial infection.
  • the effective amount is a prophylatically effective amount.
  • the method prevents or reduces the likelihood of a bacterial infection, e.g., in certain embodiments, the method comprises administering an aminoglycoside of the present invention to a subject in need thereof in an amount sufficient to prevent or reduce the likelihood of a bacterial infection.
  • the subject is at risk of a bacterial infection (e.g. , has been exposed to another subject who has a suspected or confirmed bacterial infection or has been exposed or thought to be exposed to a bacterium).
  • a method of inhibiting bacterial growth comprising contacting an effective amount of the aminoglycoside of the present invention with a bacterium.
  • the method is in vitro. In certain embodiments, the method is in vivo.
  • bacterial infection refers to an infection with a bacterium, such as a gram-negative or a gram-positive bacterium.
  • the bacterial infection is caused by a bacterium resistant to other treatments.
  • the bacterial infection is caused by a bacterium that is multi-drag tolerant or resistant, e.g., the bacterial infection is caused by a bacterium that neither grows nor dies in the presence of or as a result of other treatments.
  • the aminoglycoside of the present invention has a mean inhibitory concentration (MIC), with respect to a particular bacteria, of less than 50 ⁇ ,, less than 25 ⁇ g/mL, less than 20 ⁇ ⁇ , less than 10 ,ug/mL, less than 5 ug/mL, or less than 1 ⁇ ig/mL.
  • MIC mean inhibitory concentration
  • the bacteria is susceptible (e.g., responds to) or resistant to known commercial aminoglycosides, such as plazomicin, kanamycin A, amikacin, tobramycin, dibekacin, gentamicin, sisomicin, netilmicin, neomycins B, C, and E, streptomycin, and the like.
  • the bactera is resistant to a known aminoglycoside.
  • the bacterial infection is resistant to other antibiotics therapy.
  • the bacteria is vancomycin resistant (VR).
  • the bacteria is methicillin-resistant (MR), e.g., in certain embodiments, the bacterial infection is a methicillin-resistant S. aureus infection (a MRS A infection).
  • the bacteria is quinolone resistant (QR).
  • the pathogen is fluoroquinolone resistant (FR)
  • the bacteria is selected from Enterococcus faecium, Staphlococcus aureus, Klebsiella pneumonia, Acinetohacter haumannu, Pseudomonas aeruginosa, and Enter obacteria.
  • the bacteria has an efflux ⁇ e.g., mef, msr) genotype. In certain embodiments, the bacteria has a methylase ⁇ e.g., erm) genotype. In a particular embodiment, the bacteria has an ArmA genotype. In a particular embodiment, the bacterial infection is associated with bacteria expressing ribosomal methylase ArmA, In certain embodiments, the bacteria has a constitutive genotype. In certain embodiments, the bacteria has an inducible genotype.
  • Exemplary bacterial infections include, but are not limited to, infections with a Gram positive bacteria ⁇ e.g., of the phylum Actinobacteria, phylum Firmicutes, or phylum Tenericutes); Gram negative bacteria ⁇ e.g., of the phylum Aquifieae, phylum Deinococcus- Thermus, phylum Fibrobacteres/Chlorobi/Bacteroidetes (FCB), phyium Fusobacteria, phyium Gemraatimonadest, phylum Ntrospirae, phylum Planctomycetes/Verrucomicrobia/Chlamydiae (PVC), phylum Proteobacteria, phylum Spirochaetes, or phylum Synergistetes); or other bacteria ⁇ e.g., of the phyium Acidobacteria, phylum Chlroflexi, phylum Chrystiogenetes, phylum Cy
  • the bacterial infection is an infection with a Gram positive bacteria.
  • the Gram positive bacteria is a bacteria of the phylum Firmicutes,
  • the bacteria is a member of the phylum Firmicutes and the genus Enterococcus, i.e., the bacterial infection is an Enterococcus infection.
  • Exemplary Enter ococci bacteria include, but are not limited to, E. avium, E. durans, E. fa.eca.lis, E. faecium, E. gallinarum, E. solitarius, / ⁇ instruct ' . casseliflavus, and /. ' . raffmosus.
  • the bacteria is a member of the phylum Firmicutes and the genus Staphylococcus, i.e., the bacterial infection is a Staphylococcus infection.
  • Exemplary Staphylococci bacteria include, but are not limited to, . arlettae, S. aureus, S. auricularis, S. capitis, S. caprae, S. carnous, S. chromogenes, S. cohii, S. condimenti, S. croceolyticus, S. delphini, S. devriesei, S. epidermis, S. equorum, S. felis, S. fluroettii, S.
  • gallinarum. S. haemolyticus, S. hominis, S. hyicus, S. intermedins, S. kloosii, S. leei, S. lenus, S. lugdunesis, S. lutrae, S. lyticcms, S. massiliensis, S. microti, S. muscae, S. nepalensis, S. pasteuri, S. pentlenkoferi, S. piscifermentans, S. psuedointermedius, S. psudolugdensis, S. pulvereri, S. rosiri, S. saccharolyticus, S. saprophytics, S.
  • the Siaphylococcus infection is an S. aureus infection.
  • the S. aureus has an efflux (e.g., mef, msr) genotype.
  • the S. aureus has a methylase (e.g., erm) genotype.
  • the bacteria is a member of the phylum Firmicutes and the genus Bacillus, i.e., the bacterial infection is a Bacillus infection.
  • Bacillus bacteria include, but are not limited to, B. alcalophilus, B. alvei, B. aminovorans, B. amyloliquefaciens, B. aneurinolyticus, B. anihracis, B. aquaemaris, B. atrophaeus, B. horoniphilus, B. brevis, B. caldolyticus, B. cenirosporus, B. cereus, B. circulans, B. coagulans, B. firmus, B. flavothermus, B.
  • fusiformis B. glohigii, B. infernus, B. larvae, B. laterosporus, B. lentiis, B. licheniformis, B. megaterium, B. mesentericus, B. mucilaginosus, B. mycoides, B. natto, B. pantothenticus, B. polymyxa, B. pseudoanihracis, B. pumilus, B. schlegelii, B. sphaericus, B. sporothermodurans, B. stearothermophilus, B. suhtilis, B. thermoglucosidasius, B. thuringiensis, B. vulgatis, and B.
  • the Bacillus infection is a B. subtilis infection.
  • the B. subtilis has an efflux (e.g., mef, msr) genotype.
  • the B. subtilis has a methylase (e.g., erm) genotype.
  • the bacteria is a member of the phylum Firmicutes and the genus Streptococcus, i.e., the bacterial infection is a Strepococctis infection.
  • exemplary Streptococcus bacteria include, but are not limited to, S. agalactiae, S. anginosus, S. bovis, S. can is, S. constellatus, S. dysgalactiae , S. equinus, S. iniae, S. intermedins, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. per or is, S. pneumoniae, S. pyogenes, S.
  • the Strepococcus infection is an S. pyogenes infection. In certain embodiments, the Strepococcus infection is an .V. pneumoniae infection. In certain embodiments, the S. pneumoniae has an efflux (e.g., mef, msr) genotype. In certain embodiments, the S. pneumoniae has a methylase (e.g. , erm) genotype.
  • the bacterial infection is an infection with a Gram negative bacteria.
  • the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Escherichia, i.e., the bacterial infection is an Escherichia infection.
  • Exemplary Escherichia bacteria include, but are not limited to, E. alhertii, E. blattae, E. coli, E. fergusonii, E. hermannii, and E. vulneris.
  • the Escherichia infection is an E. coli infection.
  • the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Haemophilus, i.e., the bacterial infection is an Haemophilus infection.
  • Exemplary Haemophilus bacteria include, but are not limited to, H. aegyptius, H. aphrophilus, H. avium, //. ducreyi, //. felis, //. haemoiyticus, H. influenzae, H. parainfluenzae, H. paracuniculus, H. parahaemolyticus, H. pittmaniae, Haemophilus segnis, and / . so nus.
  • the Haemophilus infection is an //, influenzae infection.
  • the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Acinetobacter .
  • the bacterial infection is an Acinetobacter infection.
  • Exemplary Acinetobacter bacteria include, but are not limited to, A. haurnanii, A. haemoiyticus, and A. Iwoffii.
  • the Acinetobacter infection is an A. haurnanii infection.
  • the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Klebsiella, i.e., the bacterial infection is a Klebsiella infection.
  • Exemplar ⁇ - Klebsiella bacteria include, but are not limited to, K granulomatis, K, oxytoca, K. michiganensis, K. pneumoniae, K. quasi pneumoniae, and K. variicola.
  • the Klebsiella infection is a K. pneumoniae infection.
  • the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Pseudomonas. i.e., the bacterial infection is a Pseudomonas infection.
  • Exemplary Pseudomonas bacteria include, but are not limited to, P. aeruginosa, P. oryzihabitans, P. plecoglissicida, P. syringae, P. putida, and P. fluoroscen .
  • the Pseudomonas infection is a P. aeruginosa infection.
  • the bacteria is an atypical bacteria, i.e., are neither Gram positive nor Gram negative.
  • TLC plates were visualized by exposure to ultraviolet light, then were stained with an aqueous sulfuric acid solution of eerie ammonium molybdate (CAM), or an aqueous sodium carbonate solution of potassium permanganate ( Mn0 4 ), then briefly heated on a hot plate. Flash-column chromatography was performed as described by Still et ai., employing silica gel (60 A, 32-63 uM, standard grade, Dynamic Adsorbents, Inc.).
  • Dry solvents were purchased from the Aldrich Chemical Company in Sure/SealTM glass bottles and used without purification. All reagents were purchased and used without purification with the following exceptions: benzaldehyde, 3-methyl-2-butenal, trimethylsilyi chloride, trifluoromethanesulfonic anhydride, and trimethylsilyi trifluoromethanesulfonate were distilled under an atmosphere of argon. Benzyl bromide and methyl iodide were filtered neat through a column of oven-dried basic alumina immediately prior to use.
  • Proton magnetic resonance ( ! H NMR) spectra were recorded on Varian INOVA 500 (500 MHz) or 600 (600 MHz) NMR spectrometers at 23 °C.
  • the first glycosylation reaction forges the C4-C1' bond and affords the glycoside 140 in 43% yield.
  • Alternative conditions are shown in Figure 19.
  • the p-methoxybenzyl groups on the CI amine are then cleaved (CAN), and the resulting primary amine is coupled with the activated 4-amino-2- hydroxybutanoic acid (HABA) sidechain 5 to provide the glycoside 141 in 62% yield over two steps.
  • Unveiling the diol functional group in 141 (TFA, 83%) gives the glycosyl acceptor 139, which undergoes the second convergent coupling with the glycosyl donor 2 (a garosamine derivative) to furnish the fully protected aminoglycoside 138 in 37% yield.
  • a one-step hydrogenolytic deprotection in the presence of palladium hydroxide affords a fully synthetic aminoglycoside (1) in a total of six steps.
  • the gentamicin derivative FSA- 38252 is obtained in two steps from the diol 151, while deprotection of 149 provides gentamicin Cia (FSA-38219).
  • the synthesis of gentamicin C la proceeds in five steps and 16% yield from 3 and 118,
  • the structures of the three synthetic derivatives prepared herein deviate from the gentamicin Cia scaffold by the hydroxymethyl groups at the C6' position, which would be difficult to access via semisynthetic modifications of gentamicin itself.
  • Garosamme Compounds 2 and 50 Garosamine is an amino sugar that is biosynthetically derived from xylose ( Figure 3). It is a component of the gentamicin and sisomicin classes of aminoglycosides ( Figure 22), and its unique C- and N-methylation patterns improve the antibiotic activities of gentamicin and sisomicin, relative to kanamycin, against bacteria carrying aminoglycoside modifying enzymes (AMEs). Compared to ring I of the aminoglycosides, few medicinal chemical modifications have been made to the garosamine subunit (ring III).
  • the recently identified ribosome methyltransferase, ArmA selectively inactivates 4,6-disubsituted aminoglycosides by methylation of the N7 amine of G1405, which introduces steric and electronic repulsions with the garosamine sugar.
  • the efficient synthesis of garosamine described herein allows systematic investigations of the carbohydrate scaffold. Intermediates in the synthesis are amenable to late-stage diversification, particularly at the C3" ⁇ amino group, providing access to compounds capable of overcoming resistance to bacteria expressing ArmA, among other resistance phenotypes.
  • the protecting groups in 47 (Boc, acetonide, and the JV,O-acetal) are cleaved by heating in a solution of hydrochloric acid. Subsequent transformation to the phenyl thiogiycoside 48 proceeds in 77% yield over two steps.
  • the thiogiycoside 48 serves as a branching point for the syntheses of glycosyl donors 2 and 50.
  • the alternative glycosyl donor 50 is prepared by first treatment of 48 with phosgene (79%), followed by methylation of the carbamate in 86% yield (Mel, NaH).
  • the route to 2 and 50 proceeds in a total of seven steps, which is shorter and higher yielding than all previous syntheses of garosamine derivatives.
  • all prior syntheses of activated garosamine derivatives use carbohydrates as starting materials, which inherently limit the positions available for modification and do not offer any distinct advantage over semi synthesis.
  • the present approach allows flexible access to the entire scaffold of 2.
  • late-stage modifications of the C3 "-amino group provides access to analogs with activity against bacteria expressing the ribosomal methylase ArmA, which confers pan-resi stance to all aminoglycosides, including the next-generation aminoglycoside, plazomicin, by introducing steric and/or electrostatic repulsion near the C3 " amine binding site.
  • the aldehyde 7 can be obtained by the condensation of (l S,2R) ⁇ (+)-norephedrine with 3-methyl-2-butenal followed by treatment of the resulting imine (without purification) with di-tert-butyl di carbonate (92%). The olefin is then cleaved through ozonolysis to provide the norephedrine oxazoiine 7 in 76%> yield.
  • the coupling of 6 and 7 represents the first example of a diastereoselective intermolecular nitroaldol reaction using norephedrine as the auxiliary.
  • Purpurosamine Compound 3 Purpurosamines A-C are the ring-I amino sugars in gentamicin C complex, a clinically important antibiotic ( Figure 26). They are present in gentamicins Ci, i, and Cia, respectively, and differ in the methylation patterns at the C6' position and C6'-amino group (aminoglycoside numbering). As a part of a conserved 2- deoxystreptamine-glucosamine motif in aminoglycoside natural products, purpurosamine plays a key role in the recognition and binding of gentamicin to the bacterial ribosome.
  • ring I glucosamine components
  • APH(3') and ANT(4') enzymes which inactivate aminoglycosides by phosphorylation and adenylation of the C3' ⁇ and C4'-hydroxyl groups, has rendered aminoglycoside antibiotics such as kanamycin clinically obsolete.
  • Gentamicin is the most commonly prescribed aminoglycoside due to its inherent immunity to the actions of these two prevalent resistance mechanisms.
  • the building block azido aldehyde 24 is obtained in three steps from D-glutamic acid.
  • glutamic acid is converted to its dimethyl ester (TMSC1 in methanol), which is transformed to the azide 87 in 86% yield by the treatment of trifluoromethanesulfonyl azide.
  • TMSC1 dimethyl ester
  • DIBAL-FI less hindered methyl ester
  • Diastereoselectivity of the nitroaldol addition to set the C5' stereocenter is achieved through the use of the chirai diamine ligand 86.
  • Partial reduction of the methyl ester in 81 (D1BAL-H), followed by spontaneous intramolecular cyclization leads to the formation of the nitropurpurosamine derivative 80 in 88% yield.
  • the anomeric position of 80 was then activated by transformation to the corresponding phenyl thioglycoside 3, which is isolated in 94% yield.
  • the disclosed synthetic approach allows opportunities for modifications of the entire scaffold of component 3, i.e., through alkylations of the intermediate 87 at the C3' and C4' positions.
  • 2-Deoxystreptamine Compound 4 and Differentially Protected 2-Deoxystreptamines 2-Deoxystreptamine is a conserved structural motif in the 4,5- and 4,6-disubstituted aminoglycoside antibiotics ( Figure 28). Together with the ring I hexose, 2-deoxystreptamine engages in key stabilizing interactions with the RNA bases in the bacterial ribosome. Because of its relevance in ribosome recognition, minor perturbations to the 2-deoxystreptamine structure have been shown to greatly influence both the antibiotic property and the safety profile of the resulting analogs. [00330] Several resistance mechanisms target polar functional groups on 2- deoxystreptamine for enzymatic modification.
  • AAC(3) enzymes a family of aminoglycoside acetyltransferases, the AAC(3) enzymes, are widely found in Gram-negative bacteria, and inactivate all aminoglycosides currently in clinical use by acylating the C3 -amino group.
  • the most recently approved next-generation aminoglycoside, plazomicin, has only limited activity (MIC 8 ⁇ ig/niL) against P. aeruginosa carrying the aac(3) gene. Because the C3 amine plays an important role in the binding of aminoglycosides to the ribosome, attempts to overcome the action of the AAC(3) enzyme by derivatization of the C3 amine through semisynthesis have resulted in complete loss of antibiotic activity.
  • Compound 4 an orthogonally protected 2-deoxystreptamine, is a conserved structural motif in all clinically relevant aminoglycoside antibiotics.
  • the primary source of 2-deoxystreptamine for synthetic and biological studies is the degradation of naturally occurring aminoglycosides to give /Me.so-2-deoxystreptamine, which is enantiomerically enriched through enzymatic resolution.
  • the fully synthetic approach is depicted in Figure 29 and begins with the protected dimethyl tartrate 8. Desymmetrization of 8 is achieved by its convergent coupling with the lithiated ethyl vinyl ether (9) to give the vinyl ketone 121 in 73% yield.
  • the hvdroxyester 122 is obtained by Luche reduction of 122, which installs the C4 stereocenter in 60% yield and >20: 1 diastereoselectivity. Mitsunobu inversion of the C4 hydroxyl group proceeds in 78% yield with benzoic acid as the nucleophiie to afford the allylic benzoate 126.
  • Partial reduction of the methyl ester in 126 and cleavage of the benzoate ester occurs in one pot (DIBAL-H) and the resulting crude hydroxyaldehyde is treated with bis(p-methoxybenzyl)amine and ytterbium trifluoromethanesulfonate to provide the all trans-6,6-bicycie 119 (35%) as a single diastereomer.
  • the diethyl ketal 127 and the mixed benzyl ethyl ketal 128 are also isolated in 10% and 9% yield, respectively, which can be hvdrolyzed with hydrochloric acid in acetone to afford the amino ketone 119 in 68% yield.
  • the reduction-Mannich cyclization sequence from 126 provides the ketone 119 in two steps and 48% yield.
  • the C3 amine can be installed in a three-step sequence in 58% overall yield: Formation of the methyl oxime of 119, which is reduced in a mixture of lithium aluminum hydride and sodium methoxide (5: 1 dr), followed by transformation of the amine 36 to the corresponding azide 4.
  • the synthesis of component 4 described here is the shortest and most efficient synthesis of an orthogonally protected 2-deoxystreptamine.
  • a notable feature of the disclosed synthesis is the differentiation of the CI and the C3 amino groups, which allows regioselective introduction of the HABA sidechain at any stage of the disclosed synthetic route, a significant advantage over all prior syntheses of aminoglycoside antibiotics.
  • a two-step deprotection sequence which involved first hydrogenation of 149 followed by hydrolysis of the intermediate carbamate, completed the component-based approach to gentamicin Cia (FSA-38219).
  • the synthesis of gentamicin Cia proceeded in five steps and 16% yield from the glycosyl donor 3 and the semisynthetic glycosyl acceptor 118.
  • the gentamicin derivative FSA-38252 was obtained in two steps from the diol 151.
  • the structures of the three synthetic derivatives prepared herein deviate from the gentamicin Cia scaffold by the hydroxymethyl groups at the C6' position, which would be difficult to access via semisynthetic modifications of gentamicin itself.
  • ethyl pyruvate (70.0 mL, 627 mmol, I equiv) was added dropwise via a dropping funnel over 30 min while maintaining the internal temperature below -18 °C.
  • the addition was quantitated with dichloromethane (27.0 mL).
  • the resulting solution was stirred at -20 °C. After 2 h, white precipitate appeared.
  • the resulting heterogeneous mixture was stirred at -20 °C for an additional 12 h, at which point the reaction had become homogeneous and analysis by thin-layer chromatography indicated full consumption of the ethyl pyruvate starting material.
  • O2NCH2CCH3 1.42 (s, 3H, ⁇ ⁇ , 1.40 (s, 3H, OCiC ' f ! ; ⁇ ,: ⁇ .
  • the bright yellow solution was poured into a mixture of ethyl ether (300 mL) and half saturated aqueous sodium chloride solution (300 mL). The layers were separated and the aqueous layer was extracted with ethyl ether (3 x 200 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil.
  • the crude product was purified by flash-column chromatography (5% ethyl ether-hexanes initially, grading to 40% ethyl ether-hexanes) to give norephedrine oxazoline aldehyde 7 as a clear and colorless oil (3.98 g, 76%, 90% purity).
  • the aldehyde 7 was used in the subsequent coupling reaction without further purification.
  • Nitroacetonide 6 (1.20 g, 6.83 mmol, 1 equiv) and norephedrine oxazoline aldehyde 7 (3.98 g, 13.7 mmol 2.00 equiv) were dissolved in tetrahydrofuran (68.3 mL). The resulting solution was cooled to -20 °C. A solution of potassium ter -butoxide in tetrahydrofuran (1.0 M, 0.410 mL, 0.410 mmol, 0.06 equiv) was added dropwise by syringe. The resulting solution was stirred at - 20 °C for 30 min.
  • aqueous hydrogen chloride (2.00 M, 7,50 mL, 15.0 mmol, 7.0 equiv) was added to a solution of 42 (1.00 g, 2, 14 mmol, 1 equiv) in a mixture of dioxane (20.0 mL) and water (12.5 mL) at 23 °C.
  • the flask was then immersed in an oil bath preheated to 55 °C, After 15 h, the heating bath was removed and the solution was allowed to cool to 23 °C. The cooled solution was concentrated under reduced pressure.
  • the residue was purified by flash- column chromatography on silica gel (30% ethyl acetate-hexanes initially, then grading to 80% ethyl acetate-hexanes) to provide phenyl thioglycoside ⁇ -49 (189 mg, 54%) and a-49 (89.0 mg, 25%>) as white solids.
  • aminoalcohol 48 (53.9 mg, 0.156 mmol, 1 equiv) and acetic acid (89 ⁇ ]_, 1.56 mmol, 10.0 equiv) in dichloromethane (3 ,47 raL) and methanol (433 fiL) at 23 °C.
  • Sodium cyanoborohydride (32.4 mg, 0.515 mmol, 3.30 equiv) was then added in one portion.
  • the resulting solution was stirred for 1 h at 23 °C, at which point thin-layer chromatographic analysis indicated complete consumption of the starting aminoalcohol 48.
  • a solution of formaldehyde in water (37 wt%, 58.1 ⁇ , 0.780 mmol, 5,00 equiv) was then added, followed by another portion of sodium
  • 13 C MR (125 MHz, CDCb), ⁇ : 153.1, 140.5, 138.3, 135.4, 134.2, 131.2, 128.9, 128.8, 128.5, 128.3, 128,3, 128, 1, 128.0, 128.90, 127.7, 127,2, 126.7, 90.6, 86.1, 75.6, 73.5, 72.4, 70.9, 68.8, 18.4.
  • 13 C signals corresponding to NCHVPh and NCH3 were not visible due to broadening.
  • the crude reaction mixture was purified by flash-column chromatography on silica gel (10% ethyl acetate- hexanes initially, then grading to 30% ethyl acetate-hexanes) to afford the nitroglycoside 80 as a white solid (2:1 ratio of ⁇ : ⁇ anomers, 1.29 g, 88%).
  • purpurosamiiie phenyl thioglycosyl donor 3 as a colorless oil (2,5 : 1 ratio of ⁇ : ⁇ anomers, 1 .72 g, 94%).
  • the anomers could be partially separated by flash-column chromatography on silica gel (10% ethyl ether-hexanes initially, then grading to 50% ethyl ether-hexanes) to obtain small amounts of pure samples, which were used for characterization purposes.
  • (+)-dimethyl tartrate (8.00 g, 44.9 mmol, 1 equiv) in methanol (44.9 mL) was added sequentially 2,3-butanedione (4,73 mL, 53.9 mmol, 1.20 equiv), trimethylorthoformate (14.7 mL, 135 mmol, 3 ,00 equiv), and ( ⁇ )-camphorsulfonic acid (1.04 g, 4.49 mmol, 0.10 equiv).
  • the resulting light yel low solution was heated to 75 °C. After stirring for 21 hours at 75 °C, the dark brown reaction mixture was cooled to 23 °C.
  • the pH of the aqueous layer was adjusted to 7 by the addition of 1 M aqueous hydrochloric acid.
  • the layers were separated and the aqueous layer was extracted with ethyl ether (2 x 300 mL).
  • the organic layers were combined.
  • the combined organic layers were dried over sodium sulfate.
  • the dried solution was filtered and the filtrate was concentrated.
  • the residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 20% ethyl acetate-hexanes) to provide pure vinyl ketone 121 as a clear and colorless oil (2.49 g, 73%).
  • Vinyl ketone 1.21 (494 mg, 1 .49 mmol, 1 equiv) was dissolved in methanol (21.2 mL) and the resulting solution was cooled to -40 °C.
  • Cerium trichloride heptahydrate (609 mg, 1.64 mmol, 1.10 equiv) was added in one portion.
  • Sodium borohydride (67.5 mg, 1.78 mmol, 1.20 equiv) was then added as a solid, in two portions. The resulting solution was stirred at -40 °C for 30 min and then warmed to 23 °C.
  • azodicarboxylate (2.52 mL, 13.0 mmol, 3.50 equiv) was then added dropwise. The solution turned yellow and then white precipitate appeared.
  • a solution of benzoic acid (498 mg, 4.08 mmol, 1.10 equiv) in tetrahydrofuran (8.00 mL) was then added dropwise via syringe. The addition was quantitated with tetrahydrofuran (1.00 mL). The resulting heterogeneous mixture was stirred at 23 °C for 2 h. The reaction mixture was filtered, and the solids were washed with 50% ethyl ether-hexanes (200 mL).
  • the filtrate was poured into saturated aqueous sodium bicarbonate solution (200 mL). The layers were separated and the aqueous layer was extracted with ethyl ether (2 x 200 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated.
  • Step 1 reduction.
  • a solution of diisobutylaluminum hydride (1.0 M solution in dichlorom ethane, 547 .uL, 0.547 mmol, 6.00 equiv) was added dropwise to a solution of the benzoyl ester 126 (40.0 mg, 0.091 mmol, 1 equiv) in dichloromethane (1.82 mL) at -85 °C.
  • the resulting solution was stirred for 15 min, at which point propanal (39.2 iL, 0.547 mmol, 6.00 equiv) was then added.
  • the reaction mixture was stirred at -85 °C for another 5 min, at which point ethyl acetate (4 mL) was added.
  • the residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes + 1% tri ethyl amine initially, then grading to 50% ethyl acetate-hexanes + 1% tri ethyl amine) to provide aminoketone 119 (9: 1 mixture of 119 and bis(4- methoxybenzyl)amine, 17.3 mg, 35%), benzyl ethyl ketal 128 (impure, 5.60 mg, 9%), and diethyl ketal 127 (5.60 mg, 10%).
  • Step 3 ketal hydrolysis.
  • diethyl ketai 127 48.7 mg, 0.083 mmol, 1 equiv
  • benzyl ethyl ketal 128 43.1 mg, 0.066 mmol, 1 equiv
  • acetone 7.42 mL
  • hydrochloric acid 2.0 M in water, 744 jiL, 1 ,49 mmol, 10.0 equiv

Abstract

Provided herein are aminoglycosides for the treatment of infections, and pharmaceutical compositions, methods, kits, and uses thereof. Also provided are a methods of making aminoglycosides that enables late-stage derivatization of the C6' and C3 " amino groups, thereby allowing facile access to previously inaccessible aminoglycosides.

Description

[0001] This invention was made with government support under DGEl 144152 supported by the National Science Foundation. The government has certain rights in the invention.
BACKGROUND
[0002] Aminoglycoside antibiotics have been in continuous clinical use for more than seven decades. The first member of the aminoglycoside antibiotic family, streptomycin, was isolated in 1943 by the Nobel laureate Selman Waksman. Streptomycin exhibited activity against strains of mycobacteria and became the first effective treatment for tuberculosis. Following the success of streptomycin, numerous other aminoglycoside antibiotics were identified, including neomycin, paromomycin, kanamycin, gentamicin, and sisomicin. However, the use of aminoglycosides has steadily declined over the past decades due to a rise in bacterial resistance.
[0003] Today, gentamicin is the most commonly prescribed aminoglycoside antibiotic and is used as a mixture of three components (gentamicin Ci, Cla, and C2). As a class, the aminoglycosides exhibit broad-spectrum antibiotic activities and cause minimal allergic responses, which make them ideal for use in emergencies. The main drawbacks of aminoglycoside therapy are nephrotoxic and ototoxic side effects. All current aminoglycoside antibiotics in use in the clinic are associated with similar adverse effects. Despite these side effects and widespread resistance, they are the drugs of choice in inhalation therapy to suppress lung infections in cystic fibrosis patients. They are also part of the drug cocktail used for the treatment of multi drug-resistant tuberculosis.
[0004] New and improved aminoglycoside antibiotics have come exclusively from semi- synthesis, the process of chemically converting natural fermentation products into drugs. Since the initial isolation of streptomycin, six semi-synthetic derivatives, prepared in 1-6 steps from naturally occurring aminoglycosides, have been approved by the FDA for the treatment of bacterial infections. In 2016, plazomicin, a third-generation aminoglycoside which showed both improved antibiotic and safety profiles, completed Phase III clinical trials (see Figure 1; positions that have been modified by semi-synthesis are indicated with arrows and brackets). While it is clear that semi -synthesis has played a role in providing new medicines, it is also apparent from the progression of aminoglycoside drug discovery that the synthesis of next- generation aminoglycoside antibiotics against multidrug-resistant bacteria is comparably lengthier and less efficient. In addition, synthetic modifications of the aminoglycoside scaffold have been limited to heteroatom substitution and interconversion. Optimization of the core carbon scaffold has been inaccessible due to a lack of chemical enablement.
[0005] Semisynthesis has fueled the engineering of naturally occurring aminoglycosides and led to safer and more powerful antibiotic therapies, Glycodiversification, the strategy employed in the synthesis of 2-hydroxyarbekacin, has allowed the preparation of libraries of aminoglycoside analogs. The number of approved quinolones and lactams, which are prepared by diversifiabie synthetic methods, greatly exceeds the number of aminoglycosides in clinical use, which remain by far some of the most potent antibacterial agents. The prevalence of multidrug-resistant Gram-negative pathogens has highlighted the urgent need for new aminoglycoside antibiotics. There remains a need for a fully synthetic approach to creating new aminoglycoside antibiotics in the search for new antibiotics to combat resistance and/or decrease the side effects of known aminoglycoside antibiotics.
SUMMARY
[0006] Accordingly, described herein is the development of a practical, fully synthetic platform for the discovery of new aminoglycoside antibiotics for use in the treatment of bacterial infections. The synthetic route features two convergent coupling reactions of three diversifiabie components. Each component can be prepared by the union of two building blocks, which are obtained in three or fewer steps. Implementation of the disclosed method has led to the preparation of new aminoglycoside antibiotics from a common, late-stage intermediate. The novel structural modifications permitted by the disclosed component-based approach are inaccessible through semi syntheses. Antimicrobial testing reveals that the disclosed compounds exhibit antibacterial activities against a panel of Gram -positive and Gram-negative strains. Accordingly, in one aspect, provided herein is a compound of Formula (I):
Figure imgf000005_0001
or a pharmaceutically acceptable salt thereof, wherein:
R.2b is halogen, hydroxy!, protected hydroxy!, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl or heteroaryl;
R3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl, heteroaryl, or a nitrogen protecting group;
R.3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group; or
R.3c and R3a together form a ring,
R4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or
R-ta and R3c are combined to form a five or six-membered ring, or
R4a and R3d are combined to form a five or six-membered ring;
R4 is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or
R.4a and Rsc are combined to form a five or six-membered ring, or
R4a and R3d are combined to form a five or six-membered ring;
Rvd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group;
R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl ;
R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl , or a nitrogen protecting group, Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Risb i s hydrogen, halogen, hydroxyl, protected hydroxyl , cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Ri6a is hydrogen, halogen, hydroxyl , protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Risa, Risb, and Risd independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or two of Riga, Risb, and Ri8d are combined to form a ring.
[0008] In certain embodiments, the compound of Formula (I) is of Formula (Π):
Figure imgf000006_0001
In another aspect, provided herein is a pharmaceutical composition comprising a compound of Formula (I),
[0010] In another aspect, provided herein is a method of treating or preventing a bacterial infection in a subject in need thereof comprising administering to the subject a compound of Formula (I).
[0011] In another aspect, provided herein is a kit comprising an aminoglycoside of Formula (I) and a container.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] Figure 1 shows a summary of semi-synthetic aminoglycoside derivatives. The positions that have been modified by semi-synthesis are indicated with arrows and brackets.
[0013] Figure 2 shows the biosynthesis of 2-deoxy streptamine and streptidine from glucose.
[0014] Figure 3 shows the biosynthetic pathway to 2-deoxystreptamine aminoglycoside antibiotics. [0015] Figure 4 shows the hydrogenation of streptomycin produced dihydrostreptomycin, a compound of similar antibacterial properties but improved chemical stability.
[0016] Figure 5 shows the synthesis of dibekacin from kanamycin B.
[0017] Figure 6 shows the synthesis of amikacin from kanamycin A. Amikacin shows improved antibacterial and pharmacokinetic properties,
[0018] Figure 7 shows the synthesis of arbekacin in 5 steps from dibekacin, a semi-synthetic derivative of kanamycin B.
[0019] Figure 8 shows the synthesis of isepamicin from gentamicin B. Isepamicin is a derivative of gentamicin and was first reported in 1978
[0020] Figure 9 shows the synthesis of netilmicin in one step from sisomicin in 25% yield (top). An improved procedure involves the initial formation of a cobalt-chelation complex and provides netilmicin in 3 steps and 60% yield (bottom),
[0021] Figure 10 shows the synthesis of piazomicin, a next-generation aminoglycoside, from sisomicin in 7 steps with an overall yield of 0.1.6%.
[0022] Figure 11 shows the synthesis of 2-hydroxyarbekacin, a new aminoglycoside antibiotic with improved activity against MRSA.
[0023] Figure 12 shows a semi-synthetic derivative of tobramycin, SPX2523.
[0024] Figure 13 shows the chemical synthesis of 5 -epi sisomicin (SCH 22591).
[0025] Figure 14 shows 5-episisomicin derivatives prepared from sisomicin. ANT =
Aminoglycoside O-Nucleotidyltransferase. AAC = Aminoglycoside N-Acetyltransferase.
[0026] Figure 15 shows the synthesis of TS2037 from arbekacin in 1 1 steps. The novel arbekacin derivative shows improved activity against MRSA and P. aeruginosa.
[0027] Figure 16 shows a summary of clinically approved semisynthetic aminoglycosides
(top two rows) and several newly reported aminoglycoside analogs (bottom row), which have potent activities against resistant clinical isolates.
[0028] Figure 17 shows the structural relationship of aminoglycosides and their semisynthetic derivatives. Semisynthetic antibiotics are linked to their natural product starting material through dotted lines.
[0029] Figure 18 shows a fully synthetic approach to assemble the aminoglycoside scaffold from three components (2-4). The aminoglycoside, 1 -HABA-gentamicin Cia (1), is used as a representative example. [0030] Figure 19 shows the coupling of the purpurosamine glycosyl donor 3 with the differentially protected 2-deoxystreptamine derivative 4 to afford the glycoside 140.
[0031] Figure 20 shows the introduction of the HABA sidechain to the C I amine of the glycoside 140 in two steps and 62% yield. Alternatively, the dioi 144 is prepared in 61% yield from 140.
[0032] Figure 21 shows the synthesis of gentamicin Cia from components 3, 118, and 50 based on the fully synthetic route described herein. Late-stage derivatization of the Co' nitro group produces three novel aminoglycoside antibiotics that are inaccessible through semi- synthesis.
[0033] Figure 22 shows structures of gentamicin and sisomicin.
[0034] Figure 23 shows a convergent synthesis of the glycosyl donor 2, allowing late-stage diversification of the C3 " amino group.
[0035] Figure 24 shows diastereoselective nitroaldol coupling conditions.
[0036] Figure 25 shows practical and large-scale syntheses of building blocks 6 and 7.
[0037] Figure 26 shows structures of two representative 4, 6-di substituted aminoglycoside antibiotics, kanamycin and gentamicin. The purpurosamines A-C are found in gentamicin C complex and are biosynthetically related to other carbohydrates that make up the ring I of aminoglycosides.
[0038] Figure 27 shows the synthesis of compound 3, which proceeds in 6 steps from D- glutamic acid.
[0039] Figure 28 shows representative aminoglycoside antibiotics.
[0040] Figure 29 shows the synthesis of compound 4 from the protected dimethyl tartrate 8.
[0041] Figure 30 shows the synthesis of the activated HABA sidechain 5.
[0042] Figure 31 shows the synthesis of the 2-deoxystreptamine glycosyl acceptor 137.
[0043] Figure 32 shows the synthesis of gentamicin Cia (FSA-3821 ) proceeded in five steps from the purpurosamine component 3 and the semisynthetic 2-deoxystreptamine glycosyl acceptor 118.
[0044] Figure 33 shows the synthesis of C6 -modified gentamicin derivatives FSA-38240, FSA-38255, and FSA-38252. [0045] Figure 34 shows the bacterial ribosome carries out the production of proteins. Gentamicin, a representative aminoglycoside antibiotic, interferes with several stages of bacterial protein synthesis.
[0046] Figure 35 shows the resistance rate to gentamicin in four geographic regions between 1998 and 2007.
[0047] Figure 36 shows aminoglycosides are inactivated through modifications of polar functional groups by aminoglycoside modifying enzymes (AMEs). The AMEs found only in Gram-negative bacteria are ANT(2") and AAC(3).
[0048] Figure 37 shows overlapping binding sites of gentamicin and paromomycin in the 30S subunit of the ribosome. The nucleobases, G1405 and A1408, which are substrates of rRNA methyltransferases ArmA and NmpA, respectively, are colored in blue. The universally conserved nucleobases A1942 and A1943 adopt an extra-helical conformation upon aminoglycoside binding.
[0049] Figure 38 shows the minimum inhibitory concentrations (,ug/mL) of synthetic gentamicin C ia and C6 -modified gentamicin analogs against two Gram-positive and five Gram- negative bacterial strains. cErm =:: constitutive eiythromycin ribosome methyl ase; FQ-R =:: fluoroquinolone resistant; cErmB = constitutive eiythromycin ribosome methylase B.
[0050] Figure 39 shows the preparation of a 2-deoxystreptamine glycosyl acceptor by semi synthesis.
[0051] Figure 40 shows exemplar}' aminoglycoside modifications targeting resistance phenotypes.
DETAILED DESCRIPTION
Definitions
[0052] Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito, 1999; Smith and March March 's Advanced Organic Chemistry, 5* Edition, John Wiley & Sons, Inc., New York, 2001 ; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989, and Carruthers, Some Modern Methods of Organic Synthesis, 3rd Edition, Cambridge University Press, Cambridge, 1987.
[0053] Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various stereoi somen c forms, e.g. , enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Iiiterscience, New York, 1981); Wilen et al , Teirahedron 33 :2725 (1977); Eiiel, E.L. Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, S.H. Tables of Resolving Agents and Optical Resolutions p. 268 (E.L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, IN 1972). The invention additionally encompasses compounds as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.
[0054] In a formula, «« is a single bond where the stereochemistry of the moieties immediately attached thereto is not specified, — is absent or a single bond, and =-=-= or is a single or double bond,
[0055] Unless otherwise stated, structures depicted herein are al so meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, replacement of 19F with 18F, or the replacement of a carbon by a 1 C- or 1 C-enriched carbon are within the scope of the disclosure. Such compounds are useful, for example, as analytical tools or probes in biological assays.
[0056] When a range of values is listed, it is intended to encompass each value and subrange within the range. For example "Ci-6 alky!" is intended to encompass, Ci, Ci, C3, C4, Cs, Ce, Ci-6, Ci-5, Ci-4, Ci-3, Ci-2, C2--6, C2-5, C2--4, C2-3, C3-6, C3--5, C3-4, C4--6, C4-5, and C5--6 aikyi. [0057] The term "aliphatic" refers to alk l, alkenyl, alkynyl, and carbocyclic groups. Likewise, the term "heteroaliphatic" refers to heteroalkyl, heteroalkenyl, heteroalkynyl, and heterocyclic groups.
[0058] The term "alkyl" refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms ("Ci-io alkyl"). In some embodiments, an alkyl group has 1 to 9 carbon atoms ("Ci-9 alkyl"). In some embodiments, an alkyl group has 1 to 8 carbon atoms ("Ci-s alkyl"). In some embodiments, an alkyl group has 1 to 7 carbon atoms ("Ci-7 alkyl"). In some embodiments, an alkyl group has 1 to 6 carbon atoms ("Ci-6 alkyl"). In some embodiments, an alkyl group has 1 to 5 carbon atoms ("Ci-s alkyl"). In some embodiments, an alkyl group has 1 to 4 carbon atoms ("Ci-4 alkyl"). In some embodiments, an alkyl group has 1 to 3 carbon atoms ("Ci-3 alkyl"). In some embodiments, an alkyl group has 1 to 2 carbon atoms ("C1-2 alkyl"). In some embodiments, an alkyl group has 1 carbon atom ("Ci alkyl"). In some embodiments, an alkyl group has 2 to 6 carbon atoms ("C2-6 alkyl"). Examples of Ci-6 alkyl groups include methyl (Ci), ethyl (C2), propyl (C3) (e.g., n-propyl, isopropyl), butyl (C4) (e.g., n-butyi, tert-butyl, sec-butyl, iso-butyl), pentyl (Cs) (e.g., n-pentyl, 3-pentanyi, amy], neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (Ce) (e.g., 2-methylpentyl, 3- methylpentyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, and n-hexyl). Additional examples of alkyl groups include n-heptyl (C?), n-octyl (Cs), and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an "unsubstituted alkyl") or substituted (a "substituted alkyl") with one or more substituents (e.g., halogen, such as F). In certain embodiments, the alkyl group is an unsubstituted€1-10 alkyl (such as unsubstituted Ci-e alkyl, e.g., -CH3 (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstituted n- propyl (n-Pr), unsubstituted isopropyl (/-Pr)), unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (w-Bu), unsubstituted tert-butyl (tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu or s-Bu), unsubstituted isobutyl (/-Bu)). In certain embodiments, the alkyl group is a substituted Ci-10 alkyl (such as substituted Ci-e alkyl, e.g., -CH2F, -CHF2, -CF3 or benzyl (Bn)).
[0059] The term "haloalkyl" is a substituted alkyl group, wherein one or more of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. "Perhaloalkyl" is a subset of haloalkyl, and refers to an alkyl group wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the haloalkyl moiety has 1 to 8 carbon atoms ("Ci-s haloalkyl"). In some embodiments, the haloalkyl moiety has 1 to 6 carbon atoms ("Ci-ό haloalkyl"). In some embodiments, the haloalkyl moiety has 1 to 4 carbon atoms ("C1-4 haloalkyl"). In some embodiments, the haloalkyl moiety has 1 to 3 carbon atoms ("C1-3 haloalkyl"). In some embodiments, the haloalkyl moiety has 1 to 2 carbon atoms ("C1--2 haloalkyl"). In some embodiments, all of the haloalkyl hydrogen atoms are replaced with fluoro to provide a perfluoroalkyl group. In some embodiments, all of the haloalkyl hydrogen atoms are replaced with chloro to provide a "perchloroalkyl" group. Examples of haloalkyl groups include -CF3, - CF2CF3, --CF2CF2CF3, -CCI3, -CFCI2, -CF2CI, and the like.
[0060] The term "heteroalkyl" refers to an alkyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCj-io alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 9 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi-9 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi-s alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and J or more heteroatoms within the parent chain ("heteroCi-7 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi-6 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroCt-s alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and l or 2 heteroatoms within the parent chain ("heteroCi-4 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having J to 3 carbon atoms and 1 heteroatom within the parent chain ("heteroCi-3 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 2 carbon atoms and 1 heteroatom within the parent chain ("heteroCi-2 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and 1 heteroatom ("heteroCi alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroC2-6 alkyl"). Unless otherwise specified, each instance of a heteroalkyl group is independently unsubstituted (an "unsubstituted heteroalkyl") or substituted (a "substituted heteroalkyl") with one or more substituents. In certain embodiments, the heteroalkyl group is an unsubstituted heterod-io alkyl . In certain embodiments, the heteroalkyl group is a substituted heteroCi-io alkyl.
[0061] The term "carboxyalkyl" refers to an alkyl ester of the formula -CQ2(aikyi), wherein the alkyl moiety i s as defined above.
[0062] The term "alkenyl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3, or 4 double bonds). In some embodiments, an alkenyl group has 2 to 9 carbon atoms ("C2-9 alkenyl"). In some embodiments, an alkenyl group has 2 to 8 carbon atoms ("C2--8 alkenyl"). In some embodiments, an alkenyl group has 2 to 7 carbon atoms ("C2-7 alkenyl"). In some embodiments, an alkenyl group has 2 to 6 carbon atoms ("C2--6 alkenyl"). In some embodiments, an alkenyl group has 2 to 5 carbon atoms ("€2-5 alkenyl"). In some embodiments, an alkenyl group has 2 to 4 carbon atoms ("C2--4 alkenyl"). In some embodiments, an alkenyl group has 2 to 3 carbon atoms ("€2-3 alkenyl"). In some embodiments, an alkenyl group has 2 carbon atoms ("C2 alkenyl"). The one or more carbon-carbon double bonds can be internal (such as in 2- butenyl) or terminal (such as in 1-butenyl). Examples of C2-- alkenyl groups include ethenyl (C2), 1-propenyl (C3), 2-propenyl (C3), 1-butenyl (C4), 2-butenyl (C4), butadienyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkenyl groups as well as pentenyl (C?), pentadienyl (C5), hexenyl {(. '<■. }. and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (Cs), octatrienyl (Cs), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an "unsubstituted alkenyl") or substituted (a "substituted alkenyl") with one or more substituents. In certain embodiments, the alkenyl group is an unsubstituted C2-10 alkenyl. In certain embodiments, the al kenyl group is a substituted C2-10 alkenyl. In an alkenyl group, a C=C double bond for which the stereochemistry is not specified (e.g., Ci ! CHC! l ; or may be in the (£)- or (Z)-configuration.
[0063] The term "heteroalkenyl" refers to an alkenyl group, which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkenyl group refers to a group having from 2 to 10 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-10 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 9
I I carbon atoms at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-9 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 8 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroCVs alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 7 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-7 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 6 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-6 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heteroC2-5 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 4 carbon atoms, at least one double bond, and l or 2 heteroatoms within the parent chain ("heteroC2-4 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 3 carbon atoms, at least one double bond, and 1 heteroatom within the parent chain ("heteroC2-3 alkenyl"). In some embodiments, a heteroalkenyi group has 2 to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heterod-s alkenyl"). Unless otherwise specified, each instance of a heteroalkenyi group is independently unsubstituted (an "unsubstituted heteroalkenyi") or substituted (a "substituted heteroalkenyi") with one or more substituents. In certain embodiments, the heteroalkenyi group is an unsubstituted heteroCi-io alkenyl. In certain embodiments, the heteroalkenyi group is a substituted heteroC2-10 alkenyl,
[0064] The term "alkynvl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more carbon-carbon triple bonds (e.g., 1 , 2, 3, or 4 triple bonds) ("C2-10 alkynyl"). In some embodiments, an alkynyl group has 2 to 9 carbon atoms {"('.: ' alkynyl"). In some embodiments, an alkynyl group has 2 to 8 carbon atoms ("C2-8 alkynyl"). In some embodiments, an alkynyl group has 2 to 7 carbon atoms ("C2-7 alkynyl"). In some embodiments, an alkynyl group has 2 to 6 carbon atoms ("C2-6 alkynyl"). In some embodiments, an alkynyl group has 2 to 5 carbon atoms ("C2--5 alkynyl"). In some embodiments, an alkynyl group has 2 to 4 carbon atoms ("C2-4 alkynyl"). In some embodiments, an alkynyl group has 2 to 3 carbon atoms ("C2--3 alkynyl"). In some embodiments, an alkynyl group has 2 carbon atoms ("C2 alkynyl"). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in l-butynyi). Examples of C2-4 alkynyl groups include, without limitation, ethynyl (C2), 1-propynyl (C3), 2-propynyl (C3), 1-butynyl (C4), 2-butynyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2-4 alkynyl groups as well as pentynyl (C?), hexynyl (C&), and the like. Additional examples of alkynyi include heptvnyl (C?), octynyl (Cs), and the like. Unless otherwise specified, each instance of an alkynyi group is independently unsubstituted (an "un substituted alkynyi") or substituted (a "substituted alkynyi") with one or more substituents. In certain embodiments, the alkynyi group is an unsubstituted€2-10 alkynyi. In certain embodiments, the alkynyi group is a substituted€2-10 alkynyi.
[0065] The term "heteroal kynyl" refers to an alkynyi group, which further includes at least one heteroatom (e.g., I , 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkynyl group refers to a group having from 2 to 10 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-io alkynyi"). In some embodiments, a heteroal kynyl group has 2 to 9 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-9 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-s alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroCz-? alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-6 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and I or 2 heteroatoms within the parent chain ("heteroC2-5 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and lor 2 heteroatoms within the parent chain ("heteroC2-4 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and 1 heteroatom within the parent chain ("heteroC2-3 alkynyi"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and I or 2 heteroatoms within the parent chain ("heteroC2-6 alkynyi"). Unless otherwise specified, each instance of a heteroalkynyl group is independently unsubstituted (an "unsubstituted heteroalkynyl") or substituted (a "substituted heteroalkynyl") with one or more substituents. In certain embodiments, the heteroalkynyl group is an unsubstituted heteroC2-10 alkynyi. In certain embodiments, the heteroalkynyl group is a substituted heteroC2-10 alkynyi . [0066] In some embodiments, "carbocyclyl" is a monocyclic, saturated carbocyclyl group having from 3 to 14 ring carbon atoms ("C3-14 cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 10 ring carbon atoms ("€3-10 cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms ("C3-8 cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms ("C3-6 cycloalkyl"). In some embodiments, a cycloalkyl group has 4 to 6 ring carbon atoms {"'( ' < .·. cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms ("C5-6 cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms ("C5-10 cycloalkyl"). Examples of C5-6 cycloalkyl groups include cyclopentyl (Cs) and cyclohexyl (Cs). Examples of C3-6 cycloalkyl groups include the aforementioned Cs-e cycloalkyl groups as well as cyciopropyl (C3) and cyclobutyl (C4). Examples of C ; χ cycloalkyl groups include the aforementioned C3--0 cycloalkyl groups as well as cycloheptyl (C?) and cyclooctyl (Cs). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an "unsubstituted cycloalkyl") or substituted (a "substituted cycloal kyl") with one or more substituents. In certain embodiments, the cycloalkyl group is an unsubstituted C3-14 cycloalkyl. In certain embodiments, the cycloalkyl group is a substituted C3-14 cycloalkyl. In certain embodiments, the carbocyclyl includes 0, 1 , or 2 C=C double bonds in the carbocyclic ring system, as valency permits.
[0067] The term "heterocyclyl" or "heterocyclic" refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("3-14 membered heterocyclyl"). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic ("monocyclic heterocyclyl") or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system ("bicyclic heterocyclyl") or tricyclic system ("tricyclic heterocyclyl")), and can be saturated or can contain one or more carbon-carbon double or triple bonds. Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings, "Heterocyclyl" also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently unsubstituted (an "unsubstituted heterocyclyl") or substituted (a "substituted heterocyclyl") with one or more substituents. In certain embodiments, the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl group is a substituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl is substituted or unsubstituted, 3- to 7-membered, monocyclic heterocyclyl, wherein 1, 2, or 3 atoms in the heterocyclic ring system are independently oxygen, nitrogen, or sulfur, as valency permits.
[0068] In some embodiments, a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heterocyclyl"). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur,
[0069] Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azirdinyl, oxiranyl, and thiiranyl. Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyi, and thietanyi. Exemplary 5-membered heterocyclyl groups containing I heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione. Exemplar}' 5-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl. Exemplar}' 5-membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplar}' 6-membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyi, tetrahydropvranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocvclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplar}- 6-membered heterocvclyl groups containing 3 heteroatoms include, without limitation, triazinyl. Exemplary 7-membered heterocyclyi groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8- membered heterocyclyi groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary bicyclic heterocvclyl groups include, without limitation, indolinyl, isoindoiinyl, dihydrobenzofuranyi, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyi, decahydronaphthyridinyl, decahydro-l,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyi, l H-benzo[e][l ,4]diazepinyl, 1,4,5, 7-tetrahydropyrano[3,4-b]pyrrolyl, 5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro- 5 H-furo [3 , 2- b ] py an y 1 , 5 , 7-di hy dro-4H-thi en o [2 , 3 -c] py rany 1 , 2,3 -di by dro- 1 H-py rrol o [2 , 3 - bjpyridinyi, 2,3-dihydrofuro[2,3-b]pyridinyl, 4,5,6,7-tetrahydro-lH-pyrrolo[2,3-b]pyridinyl, 4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl, 4,5,6,7-tetrahydrothieno[3,2-b]pyridinyl, 1,2,3,4- tetrahydro-l,6-naphthyridinyl, and the like.
[0070] The term "aryl" refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having 6- 14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system ("C6-- I4 aryl"). In some embodiments, an aryl group has 6 ring carbon atoms ("Ce aryl"; e.g., phenyl). In some embodiments, an aryl group has 10 ring carbon atoms ("Cio aryl"; e.g., naphthyl such as 1-naphthyi and 2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms ("CM aryl", e.g., anthracyl). "Aryl" also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocvclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently unsubstituted (an "un substituted aryl") or substituted (a "substituted aryl") with one or more substituents. In certain embodiments, the aryl group is an unsubstituted C6-i4 aryl. In certain embodiments, the aryl group is a substituted Ce-i4 aryl . [0071] "Aralkyl" is a subset of "alkyl" and refers to an alkyl group substituted by an aryl group, wherein the point of attachment is on the alkyl moiety.
[0072] The term "heteroaryi" refers to a radical of a 5-14 membered monocyclic or poly cyclic (e.g., bicyclic, tricyclic) 4n 2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-14 membered heteroaryi"). In heteroaryi groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryi polycyclic ring systems can include one or more heteroatoms in one or both rings. "Heteroaryi" includes ring systems wherein the heteroaryi ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryi ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryi ring system. "Heteroaryi" also includes ring systems wherein the heteroaryi ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryi ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryi groups wherein one ring does not contain a heteroatom (e.g., indolyi, quinolinyi, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indoiyl). In certain embodiments, the heteroaryi is substituted or unsubstituted, 5- or 6-membered, monocyclic heteroaryi, wherein I, 2, 3, or 4 atoms in the heteroaryi ring system are independently oxygen, nitrogen, or sulfur. In certain embodiments, the heteroaryi is substituted or unsubstituted, 9- or 10-membered, bicyclic heteroaryi, wherein 1, 2, 3, or 4 atoms in the heteroaryi ring system are independently oxygen, nitrogen, or sulfur,
[0073] In some embodiments, a heteroaryi group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryi"). In some embodiments, a heteroaryi group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heteroaryi"). In some embodiments, a heteroaryi group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heteroaryl''1). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has I ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an "unsubstituted heteroaryl") or substituted (a "substituted heteroaryl") with one or more substituents. In certain embodiments, the heteroaryl group is an unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5-14 membered heteroaryl.
[0074] Exemplary 5-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyrroiyl, furanyl, and thiophenyl. Exemplar}' 5-membered heteroaryl groups containing 2 heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyi. Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolvl. Exemplary 5-membered heteroaryl groups containing 4 heteroatoms include, without limitation, tetrazolyl. Exemplary 6- membered heteroaryl groups containing I heteroatom include, without limitation, pyridinyl. Exemplar}- 6-membered heteroaryl groups containing 2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing 3 or 4 heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively, Exemplar}' 7- membered heteroaryl groups containing 1 heteroatom include, without limitation, azepinyi, oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyi, isoindolyi, indazolyl, benzotriazolyi, benzothiophenyl, isobenzothiophenyi, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplar}' 6,6- bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplar}' tricyclic heteroaryl groups include, without limitation, phenanthridinyi, dibenzofuranyl, carbazolyi, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.
[0075] The term "unsaturated bond" refers to a double or triple bond. [0076] The term "unsaturated" or "partially unsaturated" refers to a moiety that includes at least one double or triple bond,
[0077] The term "saturated" refers to a moiety that does not contain a double or triple bond, i.e., the moiety only contains single bonds.
[0078] Affixing the suffix "-ene" to a group indicates the group is a divalent moiety, e.g., alkylene is the divalent moiety of alkyl, alkenyiene is the divalent moiety of alkenyl, alkynylene is the divalent moiety of alkynyl, heteroalkylene is the divalent moiety of heteroalkyl, heteroalkenylene is the divalent moiety of heteroalkenyl, heteroalkynylene is the divalent moiety of heteroalkynvl, carbocyclylene is the divalent moiety of carbocyclvl, heterocyclvlene is the divalent moiety of heterocyclyl, aryl ene is the divalent moiety of aryl, and heteroarylene is the divalent moiety of heteroaryl.
[0079] Groups recited herein in variable definitions are optionally substituted unless expressly provided otherwise. The term "optionally substituted" refers to being substituted or un substituted. In certain embodiments, aliphatic, alkyl, alkenyl, alkynyl, heteroaliphatic, heteroalkyl, heteroalkenyl, heteroaikynyl, carbocyclvl, heterocyclyl, aryl, and heteroaryl groups are optionally substituted. "Optionally substituted" refers to a group which may be substituted or unsubstituted (e.g., "substituted" or "unsubstituted" aliphatic, "substituted" or "un substituted" alkyl, "substituted" or "unsubstituted" alkenyl, "substituted" or "unsubstituted" alkynyl, "substituted" or "unsubstituted" heteroaliphatic, "substituted" or "unsubstituted" heteroalkyl, "substituted" or "unsubstituted" heteroalkenyl, "substituted" or "unsubstituted" heteroaikynyl, "substituted" or "unsubstituted" carbocyclyl, "substituted" or "unsubstituted" heterocyclyl, "substituted" or "unsubstituted" aryl or "substituted" or "unsubstituted" heteroaryl group). In general, the term "substituted" means that at least one hydrogen present on a group is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a "substituted" group has a substituent at one or more substitutable positions of the group, and when more than one position in any given staicture is substituted, the substituent is either the same or different at each position. The term "substituted" is contemplated to include substitution with all permissible substituents of organic compounds, and includes any of the substituents described herein that results in the formation of a stable compound. The present invention contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety. The invention is not intended to be limited in any manner by the exemplary substituents described herein.
[0080] Exemplar}' carbon atom substituents include, but are not limited to, halogen, -CN, - ()2, -N3, -SO2H, SO L -OH, -OR33, -ON(Rbb)2, -N(Rbb)2, Ni !,!V X , -N(ORcc)R , Si L SR::\ -SSRCC, -C(=0)Raa, -CO2H, -CHO, -C(ORaa)2, -C02Raa, -OC(=0)Raa, --OC02Raa, -
Figure imgf000022_0001
-NRb C(-0)Raa, -NR bC02Raa, -NR bC(-0)N(Rbb)2, -
Figure imgf000022_0002
OC(-NR )N(R )2, -NRb C(-NR )N(R )2, -C(=O)NR S02Raa, -NR SQ2Raa, -S02N(R b)2, - S()2Raa, -S02()Raa, -OS02Raa, -S(===0)Raa, -OS( ))Raa, -Si(Raa)3, -OSi(Raa)3 -C(=S)N(Rbb)2, - C(=0)SRaa, -C(=S)SRaa, -SC(=S)SRaa, -SC(=0)SRaa, -OC(=0)SR¾s, -SC(=0)ORaa, -
Figure imgf000022_0003
Figure imgf000022_0004
-P(RCC , -P(RCC)3, -OP(Rcc)2, -OP(Rcc)3, -B(Raa)2, -B(ORcc)2, -BRaa(ORcc), Ci-io alkyl, Ci-io perhaloaikyi, C?.-io alkenyl, C2-io alkynyl, heteroCi-io alkyl, heteroC2-io alkenyl, heteroC2-io alkynyl, C3-10 carbocyclyl, 3—14 membered heterocyclyl, Ce- i4 aiyl, and 5- 14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 RQQ groups,
or two geminal hydrogens on a carbon atom are replaced with the group =0, =S, \N( R¾\).% \\ Rbi;C( ()}R a, ==NNRbbC(==0)ORaa, X\ Rbi;S( 0) -Ra;\ \ Ri;h, or X R -. each instance of Raa is, independently, selected from Ci-io alkyl, Ci-io perhaloaikyi, C2- 10 alkenyl, C2--10 alkynyl, heteroCi -10 alkyl, heteroC2-10alkenyl, heteroC2-10alkynyl, C3-- 10 carbocyclyl, 3- 14 membered heterocyclyl, Ce-i4 aryl, and 5-14 membered heteroaryl, or two Raa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each instance of R b is, independently, selected from hydrogen, -OH, -OR33, -N(RCC)2, -
Figure imgf000022_0005
S02N(RCC)2, SO 'R \ SO ) c- -SORaa, -C(=S) (RCC)2, -€(=0)SRcc, -C(=S)SRCC, - Pi 0)
Figure imgf000023_0001
Ci-io alkyl, Ci-io perhaloalkyl, C2-10 alkenyi, C2-10 alkynyl, heteroCi-ioalkyl, heteroCi-ioaikenyl, heteroCVioalkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, Ce-u aryl, and 5-14 membered heteroaryl, or two R b groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyi, alkynyl, heteroalkyi, heteroaikenyl, heteroalkynyl, carbocvclyi, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1 , 2, 3, 4, or 5 Rdd groups; each instance of Rcc is, independently, selected from hydrogen, Ci-10 alkyl, Ci-10 perhaloalkyl, C2-10 alkenyi, C2-10 alkynyl, heteroCi -io alkyl, heteroC2-10 alkenyi, heteroC2-io alkynyl, €3-10 carbocyclyl, 3- 14 membered heterocyclyl, C&-14 aryl, and 5-14 membered heteroaryl, or two Rcc groups are joined to form a 3—14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyi, alkynyl, heteroal kyi , heteroai kenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1 , 2, 3, 4, or 5 Rdd groups;
each instance of Rdd is, independently, selected from halogen, -CN, -N02, -N3, -SO2H, - SO3H, -OH, -ORee, -ON(Rff)2, -N(Rff)2, N( R X . -N(ORee)Rff, -SH, -SRee, -SSRee, -
Figure imgf000023_0002
- NRffC(-0)Ree, -NRffC02Ree,
Figure imgf000023_0003
0. -
Figure imgf000023_0004
S02N(Rff)2, -S02Ree, -S02ORee, -OS02Ree, S( 0 )RC\ -Si(Ree)3, -OSi(Ree)3, -C(-S)N(Rff)2, - C(-0)SRee,
Figure imgf000023_0005
-■
Figure imgf000023_0006
C J -6 alkyl, Ci-6 perhaloalkyl, C2-6 alkenyi, C2-6 alkynyl, heteroCi-ealkyi, heteroC2-6alkenyl, heteroC2-6alkynyl,€3-10 carbocyclyl , 3-10 membered heterocyclyl, Ce-io aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyi, alkynyl, heteroalkyi, heteroaikenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1 , 2, 3, 4, or 5 Rss groups, or two geminal Rdd substituents can be joined to form =0 or =S;
each instance of Ree is, independently, selected from Ci-6 alkyl, Ci-6 perhaloalkyl, C2-6 alkenyi, C2-6 alkynyl, heteroCi-e alkyl, heteroC2-6alkenyl, heteroC2-6 alkynyl, C3-10 carbocyclyl, C6-10 aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyi , alkynyl, heteroalkyi, heteroaikenyl, heteroalkynyl, carbocyclyl , heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; each instance of R is, independently, selected from hydrogen, Ci-e alkyl, Ci-6 perhaloalkyl, C2-6 alkenyl, C2-0 alkynyi, heteroCi-ealkyl, heteroC2-6alkenyl, heteroCi-ealkynyl, C3-10 carbocyclyi, 3-10 membered heterocyclyl, Ce-io aryl and 5- 10 membered heteroaryl, or two Rff groups are joined to form a 3-10 membered heterocyclyl or 5-10 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyi, heteroalkyl, heteroalkenyl, heteroalkynyi, carbocyclyi, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; and
each instance of Rgg is, independently, halogen, -CN, -NO2, -N3, -SO2H, -SO3H, -OH, -OCi-6 alkyl, -ON(Ci-6 alkyl)2, -N(Ci-6 alkyl)2, -N(Ci-6 alkyl)3+X~, -NH(Ci-6 aiks i ) - X . - NH?.(Ci-6 alkyl) +X", M h X . \{OC ; alkyl)(Ci-& alkyl), -N(OH)(Ci-6 alkyl), -NH(OH), - SI L -SCi-6 alkyl, -SS(Ci-6 alkyl), C( ( )}(C ; <. alkyl), -CO2H, -C02(Ci-6 alkyl),
Figure imgf000024_0001
alkyl), OC MC i <■ alkyl), C( OiXS h,
Figure imgf000024_0002
alkyl), - alkyl), -N(Ci~6 alkyl)C(=0)( C; .-. alkyl), -NHC02(Ci-6 al
Figure imgf000024_0003
6 alkyl)2, alkyl), N! !Ci 0)NH % -C(=NH)0(Ci-6
alkyl),
Figure imgf000024_0004
-.
()(·( Ni i iNiC i alkyi)2, -OC(NH)NH(Ci-6 alkyl),
Figure imgf000024_0005
-NHC(NH)N(C I-6 alkyl)., - NHC(=NH) H2, -NHS02(Ci-6 alkyl), S0 -\(O .-, alkyi)2, SO-M liC i alkyl), -SO2NH2,- S( );:C ; alkyl, -SO2OC1-6 alkyl, -OSO2C1-6 alkyl, -SOCi- , alkyl, -Si(Ci-6 alkyl)3, -OSi(Ci-6 alkyl -C(=S)N(Ci-6 alkyl)2,
Figure imgf000024_0006
C{ ())S(C i Λ alkyl), - C(=S)SCi-6 alkyl,
Figure imgf000024_0007
alkyl, -P(=0)2(Ci-6 alkyl), alkyl)2, OPi 0)(Ci alkyl)2, -OP(=0)(OC1-6 alkyl)2, Ci-e alkyl, Ci-6 perhaloalkyl, C2-0 alkenyl, C2--6 alkynyi, heteroCi-ealkyl,
Figure imgf000024_0008
heteroC2-6alkynyl, C3-J0 carbocyclyi, C6-io aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal Rgg substituents can be joined to form =0 or =S; wherein X~ is a counted on.
[0081] In certain embodiments, the carbon atom substituents are independently halogen, substituted or unsubstituted Ci-e alkyl, -OR88, -SRaa, -N(R )2, -CN, -SCN, -NO2, -C(=0)Raa, -C02Raa,
Figure imgf000024_0009
OH 0)R:ui. -OC02Raa OC( 0)N(Rbb)>, -NR C(-0)Raa, -NRbDC02Raa, or
Figure imgf000024_0010
In certain embodiments, the carbon atom substituents are independently halogen, substituted or unsubstituted Ci-e alkyl, -ORaa, ~SRaa -N(Rbb)2, -CN, -
Figure imgf000024_0011
[0082] The term "halo" or "halogen" refers to fluorine (fluoro, -F), chlorine (chloro, -CI), bromine (bromo, -Br), or iodine (iodo, -I),
[0083] The term "-hydroxyl" or "-OH" refers to the group -OH. The term "substituted hydroxyl" or "substituted -OH," by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from -OR83, -ON(R )2, -OC(=0)SRaa, -OC(=0)Raa, -OC02Raa, - OC(=0)N(Rbb)2, OCi \RM,)R ; -OC(===NR )ORaa, -OC(=NRb )N(R )2, -OS(==())Raa, - QSQ2Raa, -OSi(Raa)3, -OP(Rcc)2, -OP(Rcc)3, -OP(=0)2Raa, -OP(=0)(Raa)2, -OP(=0)(ORcc)2, -
Figure imgf000025_0001
wherein Raa, R b, and Rcc are as defined herein,
[0084] The term "amino" refers to the group - H2. The term "substituted amino," by extension, refers to a rnonosubstituted amino, a disubstituted amino, or a tri substituted amino. In certain embodiments, the "substituted amino" is a rnonosubstituted amino or a disubstituted amino group.
[0085] The term "rnonosubstituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with one hydrogen and one group other than hydrogen, and includes groups selected from -NH(Rbb), -NHC(=0)Raa, -NHC02Raa, - HC(=0)N(R )2, -NHC (=NRb )N(Rb )2 , -NHS02Raa, -NHP(=0)(ORcc)2, and - NHP(=0)(NR b)2, wherein Raa, Rbb and Rcc are as defined herein, and wherein Rb of the group - NH(Rbb) is not hydrogen.
[0086] The term "disub tituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with two groups other than hydrogen, and includes groups selected from -N(R b)2, -NR C(=0)Raa, -NRbbC02Raa, -NRbbC(=0)N(R b)2, - NRbbC(== Rbb) (Rbb)2, -NRbbS()2Raa, -NRbbP(===0)(0Rcc)2, and -NRbbP( ))(NRbb)2, wherein Raa, R , and Rcc are as defined herein, with the proviso that the nitrogen atom directly attached to the parent molecule is not substituted with hydrogen.
[0087] The term "tri substituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with three groups, and includes groups selected from -N(RDD)3 and -N(R )3÷X~, wherein R and X~ are as defined herein.
[0088] The term "carbonyl" refers a group wherein the carbon directly attached to the parent molecule is sp2 hybridized, and is substituted with an oxygen, nitrogen or sulfur atom, e.g., a group selected from ketones f-C(=Q)Raa), carboxylic acids (-C02H), aldehydes (-CHO), esters ( ί Ό '!<:,·!
Figure imgf000026_0001
- C(-S)N(Rbb)2), and i mi nes (-C(==NRb )Raa, C( N Rhb)ORa;i). -C(-NR )N(R b)2), wherein Ra and RM1 are as defined herein.
[0089] The term "oxo" refers to the group =0, and the term "thiooxo" refers to the group =S.
[0090] Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quaternary nitrogen atoms. Exemplary nitrogen atom substituents include, but are not limited to, hydrogen, -OH, -OR33, -N(Rce)2, -CN, -C(==0)Raa, -
Figure imgf000026_0002
S02N(RCC)2, -S02RCC, -S020RCC, -SORaa, -C(==S)N(RCC)2, ('( 0)SR";, -C(-S)SRCC, -
Figure imgf000026_0003
-P(=Q)(NRCC)2, Ci-io alkyl, Ci-io perhaloalkyl, C2-10 alkenyl, C2-10 alkynyl, heteroCi -ioalkyl, heteroC2-10alkenyl, heteroC2-ioalkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, Ce.-i4 aryl, and 5-14 membered heteroaryl, or two Rc groups attached to an N atom are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl , alkynyl, heteroalkyl, heteroalkenyl, heteroaikynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Raa groups, and wherein Raa, R¾¾, Rcc and Rdd are as defined above.
[0091] In certain embodiments, the substituent present on the nitrogen atom is an nitrogen protecting group (also referred to herein as an "amine protecting group" or an "amino protecting group"). The protecting group may be represented as "-PG". An amine group bearing a nitrogen protecting group, or two nitrogen protecting groups, may be referred to as a "protected amine." Nitrogen protecting groups include, but are not limited to, -OH, -ORaa, -N(RCC)2, -C(=0)Raa, -
Figure imgf000026_0004
S02N(RCC)2, -S02Rcc, S( ) :OR- -SORaa,
Figure imgf000026_0005
Ci~io alkyl (e.g., aralkyl, heteroaralkyl), C2-10 alkenyl, C2-10 alkynyl, heteroCi-io alkyl, heteroC2-io alkenyl, heteroC2-10 alkynyl, C3-10 carbocyclyl, 3-14 membered heterocyclyl, C6-14 aryl, and 5-14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroaikynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1 , 2, 3, 4, or 5 RdQ groups, and wherein Raa, R b, Rcc and Rdd are as defined herein. Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W . Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference. [0092] For example, nitrogen protecting groups such as amide groups (e.g., -C(=0)Raa) include, but are not limited to, formamide, acetamide, chloroacetamide, tri chloroacetamide, trifluoroacetamide, phenyl acetamide, 3-phenylpropanamide, picolinamide, 3- pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, »-phenylbenzamide, o- nitophenylacetamide, o-nitrophenoxy acetamide, acetoacetamide, (Ν'- dithiobenzyloxyacylamino)acetamide, 3-(p— OHphenyl)propanamide, 3-(o- mtrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o- pheny 1 azophenoxy )propanami de, 4-chl orobutanami de, 3 -methyl -3 -ni trobutan ami de, o- nitrocinnamide, Λ-acetylmethionine derivative, o-nitrobenzamide and o- (benzoyloxymethyl)benzamide.
[0093] Nitrogen protecting groups such as carbamate groups (e.g., ~C(=O)ORaa) include, but are not limited to, methyl carbamate, ethyl carbamante, 9-fiuorenylmethyl carbamate (Fmoc), 9- (2-suifo)fluorenylmethyi carbamate, 9-(2,7-dibromo)fluoroenyir ethyl carbamate, 2,7-di-t- buty l-[9-( 10, 10-dio o- 10, 10, 10, 10-tetrahy drothioxanthy ] )]methyl carbamate (DBD-Tmoc), 4- methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyi carbamate (Troc), 2- trimethylsiiylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), l-(i-adamantyl)-l- methyl ethyl carbamate (Adpoc), l,l-dimethyl-2-haloethyl carbamate, 1, 1 -dim ethyl- 2,2- dibromoethyl carbamate (DB-i-BOC), l, l-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), l-methyl-l-(4-biphenyiyl)ethyi carbamate (Bpoc), l-(3,5-di-t-butylphenyl)-l-methylethyl carbamate ( -Bumeoc), 2-(2'- and 4'-pyridyl)ethyl carbamate (Pyoc), 2- N,N- dicyclohexylcarboxamido)ethy] carbamate, /-butyl carbamate (BOC or Boc), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropyiailyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N- -OHpiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), -methoxybenzyl carbamate (Moz), 7-nitobenzyl carbamate, /^-bromobenzyl carbamate, -chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfmylbenzyl carbamate (Msz), 9- anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2- methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2— (1,3— dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4- dimethylthiophenyl carbamate (Bmpc), 2-phosphomoethyl carbamate (Peoc), 2- triphenylphosphonioisopropyl carbamate (Ppoc), l, l-dimethyl-2-cyanoethyl carbamate, nils chioro- -acyloxybenzyl carbamate, >-(di-OHboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6- nitrobenzyl carbamate, phenyl(o-nitrophenyl)methyl carbamate, r-amyl carbamate, S-benzyl thiocarbamate, p -cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2- dimethoxyacylvinyl carbamate, o~(N,N~4i m ethylcarboxami do)benzy 1 carbamate, 1 , 1-dimethyl-
3- (N,N-dimethylcarboxamido)propyl carbamate, 1, 1-dimethylpropynyl carbamate, di(2— pyridyl)methyl carbamate, 2-furanyl methyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p -methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-l- cyclopropylmethyl carbamate, l-methyl-l-(3,5-dimethoxyphenyl)ethyl carbamate, 1-methyl- l-(p~-phenylazophenyl)ethyl carbamate, 1-methyl-l-phenylethyl carbamate, 1 -methyl- l-(4- pyridyl)ethyl carbamate, phenyl carbamate, ?-(phenylazo)benzyl carbamate, 2,4,6-tri-t- butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzyl carbamate.
[0094] Nitrogen protecting groups such as sulfonamide groups (e.g., S( 0) 'RJ") include, but are not limited to, jo-toluenesulfonamide (Ts), benzenesultonarnide, 2,3,6,-tiimethyl-4- methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-
4- methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6- dimethoxy-4-methylbenzenesuifonamide (iMds), 2,2,5, 7,8-pentamethylchroman-6- sulfonamide (Pmc), methanesulfonamide (Ms), β-trimethylsilylethanesulfonamide (SES), 9- anthracenesulfonamide, 4-(4' , 8 '-dimethoxynaphthylmethyl)benzenesulfonamide (DNMB S), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.
[0095] Other nitrogen protecting groups include, but are not limited to, phenothiazinyi-(lO)- acyl derivative, /V'-p-toluenesulfonylaminoacyl derivative, N -phenylaminothioacyl derivative, Λ-benzoylphenyialanyl derivative, Λ-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2- one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, A-2,5- dimethylpyrrole, N-l ,l,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5- substituted l,3-dimethyl-l,3,5-triazacyclohexan-2-one, 5-substituted l,3-dibenzyl-l,3,5- triazacyclohexan-2-one, 1- substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), Λ-3-acetoxypropylamine, A-( 1 -isopropyl-4- nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, A-di(4- methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N-[(4- methoxyphenyl)di phenyl methyl] amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7- dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), A-2-picolylamino N '~ oxide, N-l, 1-dimethylthiomethyleneamine, N-benzylideneamine, N-p-- methoxybenzyli deneamine, N-diphenylmethyleneamine, N-[(2- pyridyl)mesityl]methyleneamine, N~(N ',Ν -dimethylaminomethylene)amine, Ν,Ν'- isopropylidenediamine, N- --p-nitrobenzylideneamine, N-salicylideneamine, N--5- chlorosalicylideneamine, N-(5-chloro-2— OHphenyl)phenylmethyleneamine, N- cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-l-cyclohexenyl)amine, N-borane derivative, A-diphenylborinic acid derivative, N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N- copper chelate, A?:-zinc chelate, N-nitroamine, N-nitrosoamine, amine S oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).
[0096] In certain embodiments, the substituent present on an oxygen atom is an oxygen protecting group (also referred to herein as an "hydroxy! protecting group"). The protecting group may be represented as "-PG". A hydroxyl group bearing an oxygen protecting group may be referred to as a "protected hydroxyl." Oxygen protecting groups include, but are not limited to, -Raa, -N(R B)2, -€(=G)SRaa, -C(=0)Raa, -COJ.R33, -€(=0)N(R )2, -C(=NR )Raa, -
Figure imgf000029_0001
S{ ())Ra;i. -S02Raa, Si( .;i;i) :. -P(RCC)2, -P(RCC)3, - P(=0)2Raa, -P(=0)(Raa)2, -P(=0)(ORcc)2, -P(=0)2N(Rbb)2, and -P(=0)(NR )2, wherein R33, R , and Rcc are as defined herein. Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3ld edition, John Wiley & Sons, 1999, incorporated herein by reference.
[0097] Exemplary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyl oxymethyl (BOM), p - methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-
(tri methyl silyl)ethoxymethyl (SEMO ), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4- methoxytetrahydrothiopyranyl, 4-methoxy tetrahydrothiopyranyl S,S-di oxide, l-[(2-chloro-4- methyl)phenyl]-4-methoxypiperidin-4-yl (CT MP), 1 ,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a~octahydro-7,8,8-trimethyi-4,7-methanobenzofuran"2- yl, 1-ethoxy ethyl, l-(2-chloroethoxy)ethyl, 1-m ethyl- 1-methoxy ethyl, 1 -methyl- 1- benzyloxyethyl, 1-methy 1-1 -benzyl oxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2- trimethylsilylethyl, 2-(phenylselenyl)ethyl, /--butyl, allyl, -chlorophenyl, 7-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), -methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p- nitrobenzyl, -halobenzyl, 2,6-dichlorobenzyl, ?-cyanobenzyl, ^-phenyl benzyl, 2-picolyl, 4- picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl, p,p -dinitrobenzhydryl, 5- dibenzosuberyl, triphenylmethyl, a-naphthyldiphenylmethyl, 7-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4'- bromophenacyloxyphenyl)diphenylmethyl, 4,4',4"-tris(4,5-dichlorophthalimidophenyl)methyl, 4,4',4"-tris(levulinoyloxyphenyl)methyl, 4,4',4"-tris(benzoyloxyphenyl)methyl, 3-(imidazol-l- yl)bis(4',4"-dimethoxyphenyl)methyl, l, l-bis(4-methoxyphenyl)-l '-pyrenylmethyl, 9-anthryi, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl, l.,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), tnethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, /- butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p— xy ly 1 sily 1 , triphenylsilyl, diphenylmethyl sily 1 (DPM S), /-butyl methoxyphenyl si lyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, tri phenyl rnethoxyacetate, phenoxyacetate, -chlorophenoxy acetate, 3- phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p- phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), methyl carbonate, 9-fluorenyl methyl carbonate (Fmoc), ethyl carbonate, 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), isobutyl carbonate, vinyl carbonate, allyl carbonate, /-butyl carbonate (BOC or Boc), p -nitrophenyl carbonate, benzyl carbonate, -methoxybenzyl carbonate, 3,4- dimethoxybenzyl carbonate, o-nitrobenzyl carbonate, p-nitrobenzyl carbonate, S-benzyl thioc arbon ate, 4-ethoxy-l-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4- azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2- foraiylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2- (methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4- (l , l,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(l,l-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o- (methoxyacyl)benzoate, a-naphthoate, nitrate, alkyl Ν,Ν,Ν',Ν -tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).
[0098] In certain embodiments, the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a "thiol protecting group"). The protecting group may be represented as "~PG". A thiol group bearing a sulfur protecting group may be referred to as a "protected thiol." Sulfur protecting groups include, but are not limited to, -Raa, -N(R b)2, -C(=0)SRaa, -C(=0)Raa, -C02Raa,
Figure imgf000031_0001
- SQ2Raa, -Si(Raa)3; -P(Rcc)2, -P(RCC)3,
Figure imgf000031_0002
and -P(=0)(NRbbX wherein Raa, Rbb, and Rcc are as defined herein. Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.
[0099] The term "leaving group" is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. Examples of suitable leaving groups include, but are not limited to, halogen (such as F, CI, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy, arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,O- dimethyihydroxylamino, pixyl, and haloformates. In some cases, the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate, -OTs), methanesulfonate (mesylate, -OMs), p- bromobenzenesulfonyloxy (brosylate, -OBs), -OS(=0)2(CF2)3CF3 (nonaflate, -ONf), or trifluoromethanesulfonate (inflate, -OTf). In some cases, the leaving group is a brosylate, such as />-bromobenzenesulfonyloxy. In some cases, the leaving group is a nosylate, such as 2- nitrobenzenesulfonyloxy. In some embodiments, the leaving group is a sulfonate-containing group. In some embodiments, the leaving group is a tosylate group. The leaving group may also be a phosphineoxide (e.g., formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. In certain embodiments, the leaving group is of the formula SR;ia. - S(0)Raa, S(0).<R;i . <)('(() )R:s', -OS(0)Raa, ()S{()) 'R. -OP(0)(Raa)2, - OP(0)(ORaa)2,
Figure imgf000032_0001
Raa is as defined herein. Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
[00100] As used herein, the term "oxidizing agent" or "oxidant" refers to a substance that has the ability to oxidize another substance (i.e., cause the other substance to lose electrons). Exemplary oxidizing agents include acyl sulfoxide reagents, halides, hypervalent halide reagents, hexavalent chromium reagents, permanganate reagents, and peroxide reagents.
[00101] As used herein, the term "reducing agent" refers to a substance that has the ability to reduce another substance (i.e., cause the other substance to gain electrons). Exemplary reducing agents include elemental hydrogen (e.g., in the presence of a transition metal catalyst such as palladium, platinum, rhodium, iridium or nickel), reducing metals (e.g., lithium, sodium, iron, aluminum, tin, and the like), borane reagents (e.g., diborane), metal hydride reagents (e.g., sodium borohydride, sodium triacetoxyborohydride, lithium aluminum hydride, diisobutyl aluminum hydride, and the like), and phosphorous reagents (e.g., ph ophites, phosphines such as triphenylphosphine, and the like).
[00102] Other suitable oxidizing and reducing agents are known to those skilled in the art of organic synthesis, and are disclosed, for example, in Smith, Michael B.; March, Jerry (2007), Advanced Organic Chemistry: Reactions, Mechanisms, and. Structure (6th ed.), New York: Wiley-Interscience, incorporated herein by reference.
[00103] The following definitions are more general terms used throughout the present application.
[00104] The term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et at describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1 -19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids, such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids, such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods known in the art such as ion exchange. Other pharmaceutically acceptable salts inciude adipate, alginate, ascorbate, aspartate, benzenesuifonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2— GH- ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, pi crate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium, and NP(Ci-4 alkyl)4 " salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quateraary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxyiate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
[00105] The terms "composition" and "formulation" are used interchangeably.
[00106] A "subject" to which administration is contemplated refers to a human {i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal. In certain embodiments, the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, cows, pig, horse, sheep, goat, cat, or dog), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey)). In certain embodiments, the non-human animal is a fish, reptile, or amphibian. The non-human animal may be a male or female at any stage of development. The non-human animal may be a transgenic animal or genetically engineered animal. A "patient" refers to a human subject in need of treatment of a disease. The subject may also be a plant. In certain embodiments, the plant is a land plant. In certain embodiments, the plant is a non-vascular land plant. In certain embodiments, the plant is a vascular land plant. In certain embodiments, the plant is a seed plant. In certain embodiments, the plant is a cultivated plant. In certain embodiments, the plant is a dicot. In certain embodiments, the plant is a monocot. In certain embodiments, the plant is a flowering plant. In some embodiments, the plant is a cereal plant, e.g., maize, corn, wheat, rice, oat, barley, rye, or millet. In some embodiments, the plant is a legume, e.g., a bean plant, e.g., soybean plant. In some embodiments, the plant produces fruit. In some embodiments, the plant is a tree or shrub.
[00107] The term "administer," "administering," or "administration" refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound described herein, or a composition thereof, in or on a subject,
[00108] The terms "treatment," "treat," and "treating" refer to reversing, alleviating, delaying the onset of, or inhibiting the progress of a disease (e.g., a bacterial infection) described herein. In some embodiments, treatment may be administered after one or more signs or symptoms of the disease have developed or have been observed. In other embodiments, treatment may be administered in the absence of signs or symptoms of the disease. For example, treatment may be administered to a susceptible subject prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of exposure to a pathogen). Treatment may also be continued after symptoms have resolved, for example, to delay and/or prevent recurrence.
[00109] The term "prevent," "preventing," or "prevention" refers to a prophylactic treatment of a subject who is not and was not with a disease (e.g., a bacterial infection) but is at risk of developing the disease or who was with a disease, is not with the disease, but is at risk of regression of the disease. In certain embodiments, the subject is at a higher risk of developing the disease or at a higher risk of regression of the disease than an average healthy member of a population of subjects.
[00110] The terms "condition," "disease," and "disorder" are used interchangeably. Development of Semisynthetic Aminoglycosides
[00111] The first semisynthetic aminoglycoside came as early as 1946, when hydrogenation of streptomycin in the presence of a platinum catalyst yielded dihydrostreptomycin, a compound with equipotent antibiotic properties but greatly improved chemical stability (Figure 4). It was shown much later that the ototoxic symptoms of dihydrostreptomycin differ from those of streptomycin. By 1950, the annual production of streptomycin and dihydrostreptomycin reached almost 100 tons. Both antibiotics found widespread clinical applications and continue to be used in veterinary medicine.
[00112] Widespread clinical resistance and identification of aminoglycoside modifying enzymes (AMEs) led to the development of several important semisynthetic derivatives with improved activities against resistant strains. Dibekacin was prepared in 6 steps from kanamycin B and developed by Meiji Seika in Japan (Figure 5). Deoxygenation of the€3 ' and€4' positions overcame modifications by APH(3 ) and ANT(4I) enzymes, but at the same time increased the toxicity level. Dibekacin was active against resistant strains of Staphlococci and Pseudomonas and has been marketed worldwide, except in the United States, since 1975.
[00113] Historically, the most impactful aminoglycoside arguably is amikacin, which was first prepared in three steps from kanamycin A in 1972 by scientists at Bristol-Myers (Figure 6). The inspiration for amikacin came with the isolation of butirosin, which carries the (S)~2- hydroxyaminobutyric acid (HABA) sidechain. Comparison of butirosin with ribostamycin, which does not contain the acyl sidechain, revealed that butirosin exhibited antibacterial activities against some strains, including Pseudomonas, that are resistant to ribostamycin and kanamycin. Introduction of the identical sidechain to kanamycin A provides complete protection of amikacin, likely through steric shielding, against modifications of the 2 "-hydroxy! by AMEs and reduces its susceptibility to AAC(3) and APH(3!). In addition, acylation of the 1 -amino group alleviated nephrotoxic side effects in humans compared to kanamycin and gentamicin. This outcome was attributed to reduced binding to lysosomal phospholipids as a result of removing a basic amino group. While the conversion of kanamycin A to amikacin took place in three steps overall with an acceptable yield for manufacturing, difficulties in differentiating the reactivities of the amine groups contributed to the low yields observed in the coupling reactions.
[00114] The success of amikacin led to the synthesis of arbekacin in 1973 (Figure 7), which is an acyiated derivative of dibekacin, and isepamicin in 1978, which was prepared from gentamicin B (Figure 8). The synthesis of arbekacin proceeds in five steps from dibekacin and employs a zinc-chelation reaction to attenuate the reactivity of the 3 "~ and 1 -amino groups. Conversion of gentamicin to isepamicin requires four steps and suffers from low yields due to poor regioselectivity in the acyiation steps.
[00115] In addition to acyiation, alkylation of sisomicin produced netilmicin in 1976, which was approved for worldwide use in 1985. The original synthesis of netilmicin involves an one- step reductive alkylation of sisomicin (Figure 9, top). The issue of low regioselectivity was overcome through the formation of a chelation complex, which allows selective protection of the 3-, 2 -, and 6 -amino groups. In the improved procedure, conversion of sisomicin to netilmicin proceeds in three steps and 60% yield (Figure 9, bottom).
[00116] Widespread resistance to both amikacin and gentamicin developed within ten years after the introduction of amikacin. Prevalent resistance to fluoroquinolones and carbapenenis has highlighted the urgency for new and improved aminoglycosides for combating infections caused by Gram-negative bacteria, A next-generation aminoglycoside, plazomicin, is currently under clinical development. Plazomicin is a semisynthetic derivative of sisomicin and is prepared in 7 steps in 0.16% yield (Figure 10).
[00117] A common strategy for the generation of new aminoglycoside analogs is glyxodi versification, in which selective hydrolysis of the more labile ring III (and IV) of a naturally occurring aminoglycoside provides a neamine or paromomine derivative, which, after protection of the polar functional groups, is coupled with carbohydrate building blocks to generate a library of new aminoglycoside analogs. The advantage of such an approach is that the 2-deoxystreptamine-glucosamine motif, which is important for ribosome recognition, is conserved while diversity is introduced to the substituent at the C5~ or C6-hydroxyl groups of 2- deoxystreptamine. In 2009, Meiji Seika successfully employed this strategy for the synthesis of 2-hydroxyarbekacin, a novel aminoglycoside antibiotic (Figure 1 1), from 2-hydroxygentamicin. 2-Hydroxygentamicin is produced by a mutant strain of M. purpurea, the producer of gentamicin. Hydrolysis of 2-hydroxygentamicin yielded 3',4'-dideoxyneamine, which was processed in 6 steps to provide a substrate for the introduction of the HABA sidechain. Subsequent glycosylation and deprotection furnished 2-hydroxyarbekacin in a total of 1 1 steps. Introduction of a hydroxy! group at C2 provided a 4-fold to 64-fold improvement against MRS A clinical isolates resistant to arbekacin and led to a reduction in nephrotoxicity. 5-Epi-2-deoxystreptamine Aminoglycosides
[00118] Given the importance of aminoglycosides, a large number of semisynthetic analogs have been prepared since the discovery of streptomycin. Among them, inversion and modification of the C5 stereogenic center in 4, 6-di substituted 2-deoxystreptamine aminoglycosides led to a large number of analogs (see, e.g., Figures 12 and 13).
[00119] The mesylate intermediate in the chemical preparation of 5-episisomicin (Figure 13) served as a branching point for the synthesis of 5-amino- and 5-fluorosisomicin derivatives. Among them, SCH 22703 and SCH 27082, prepared in 3 steps from 5-episisomicin in a similar sequence as that employed for the synthesis of netilmicin (Figure 9), exhibited remarkable activity against resistant strains of P. aeruginosa (Figure 14).
[00120] 5-Deoxy~5-epifluoro derivatives of arbekacin and amikacin were reported to have similar antibiotic activities as their parent compound but much reduced toxicities. These compounds provide indications that the toxicity of aminoglycosides is correlated with the number and the basicity of amino groups on the scaffold. More recently, a new 5-epiarbekacin derivative, TS2037, was prepared in 1 1 steps from arbekacin (Figure 15).
[00121] Studies on the structure-activity relationship of sisomicin have clearly shown that sisomicins with an axial substituent at C5 are more active than their natural stereoisomers.22 It appears that inversion of the C5 stereogenic center has led to compounds with more potent activity against resistant pathogens, but at the same time, elevated levels of toxicity. The 5-fluoro derivatives of 2-deoxystreptamine aminoglycosides are exceptions to this trend, which are less toxic than their C5-equitorial counterparts. At this point, it is unclear whether the observed improvement in antibiotic activity is a result of enhanced ribosomal binding or permeability. A better understanding of the conformational change resulting from the stereochemical inversion could allow scientists to decouple the favorable spectrum of activity of 5-epiaminoglycosides from their toxic side effects. This would in turn have a profound influence on the design of future aminoglycoside therapies.
[00122] Since the initial isolation of streptomycin, six semisynthetic derivatives, prepared in 1-6 steps from a naturally occurring aminoglycoside, have been approved by the FDA for the treatment of bacterial infections. In 2016, plazomicin, a third-generation aminoglycoside which showed both improved antibiotic and safety profiles, completed Phase III clinical trials. A summary of these seven important clinical agents, along with several other promising semisynthetic analogs, is provided in Figure 16. The biosynthetic relationship between aminoglycosides, which are natural products, and these semisynthetic derivatives are depicted through the genealogy tree in Figure 1 7.
Compounds of the Invention
[00123] The present disclosure provides compounds of Formulae (I) and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopicallv labeled derivatives, and prodrugs thereof, collectively referred to as compounds of the invention.
[00124] In one aspect, rovided herein is a compound of Formula (I):
Figure imgf000038_0001
or a pharmaceutically acceptable salt thereof, wherein:
R.2b is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R.3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rsd is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group; or
R.3c and R3a together form a ring,
R4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
R4a and R3c are combined to form a five or six-membered ring, or
R4a and R3d are combined to form a five or six-membered ring; R b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
R4a and The are combined to form a five or six-membered ring; or
R4a and R3d are combined to form a five or six-membered ring;
R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rub is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rjsb is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Riea is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Riga, Risb, and Risd independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or two of Risa, Ri8b, and Risd are combined to form a ring.
[00125] Unless otherwise stated, any formulae described herein are also meant to include salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, and isotopically labeled derivatives thereof. In certain embodiments, the provided compound is a salt of any of the formulae described herein. In certain embodiments, the provided compound is a pharmaceutically acceptable salt of any of the formulae described herein. In certain embodiments, the provided compound is a solvate of any of the formulae described herein . In certain embodiments, the provided compound is a hydrate of any of the formulae described herein. In certain embodiments, the provided compound is a polymorph of any of the formulae described herein. In certain embodiments, the provided compound is a co-crystal of any of the formulae described herein. In certain embodiments, the provided compound is a tautomer of any of the formulae described herein. In certain embodiments, the provided compound is a stereoisomer of any of the formulae described herein. In certain embodiments, the provided compound is of an isotopicallv labeled form of any of the formulae described herein. For example, compounds having the present stmctures except for the replacement of hydrogen by deuterium or tritium, replacement of i 9F with lSF, or the replacement of a f 2C by a 1 C or 14C are within the scope of the disclosure. In certain embodiments, the provided compound is a deuterated form of any of the formulae or compounds described herein.
Group I b
[00126] As generally defined herein, Rib is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary] or heteroaryl .
[00127] In certain embodiments, Ra is fluorine, chlorine, bromine or iodine. In certain embodiments, Rib is hydroxyl. In certain embodiments, Ri i s protected hydroxyl. In certain embodiments, Rib is amino (e.g., -NH2, - H(alkyl) or -N(alkyl)2). In certain embodiments, ib is protected amino. In certain embodiments, i is cyano. In certain embodiments, Rib is unsubstituted aliphatic (e.g. , unsubstituted 0-6 akyl). In certain embodiments, Rib is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, R : i s unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyi). In certain embodiments, Rib is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyi). In certain embodiments, Rib is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-e heteroakyl). In certain embodiments. Rib is substituted heteroaliphatic (e.g. , substituted Ci-6 heteroakyl). In certain embodiments, Rib is unsubstituted cyclic heteroaliphatic (e.g. , unsubstituted C2-6 heterocyclyl). In certain embodiments, ib is substituted cyclic heteroaliphatic (e.g., substituted C2-0 heterocyclyl). In certain embodiments, Rib is unsubstituted Ce-io aryl. In certain embodiments, Rib is substituted Ce-io aryl. In certain embodiments, Rib is unsubstituted C3-10 heteroaryl. In certain embodiments, Rib is substituted C3- 10 heteroaryl.
[00128] In certain particular embodiments, Rib is hydroxyl. In certain particular embodiments, Group Rsc
[00129] As generally defined herein, Bee is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group.
[00130] In certain embodiments, R3c is hydrogen. In certain embodiments, R3c i s a nitrogen protecting group. In certain embodiments, R.¾ is unsubstituted aliphatic {e.g. , unsubstituted Ci-e akyl). In certain embodiments, R3c i s substituted aliphatic e.g. , substituted Ci-e. akyl). In certain embodiments, R3c is unsubstituted cyclic aliphatic {e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R.3c is substituted cyclic aliphatic {e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R3c is unsubstituted heteroaliphatic {e.g. , unsubstituted Ci-6 heteroakyl). In certain embodiments, Bee is substituted heteroaliphatyl {e.g., substituted Ci-6 heteroakyl). In certain embodiments, Rsc is unsubstituted cyclic heteroaliphatic {e.g. , unsubstituted C2-6 heterocyclyl). In certain embodiments, R3c is substituted cyclic heteroaliphatic (e.g. , substituted C2-0 heterocyclyl). In certain embodiments, R3c is unsubstituted Ce-io aryl . In certain embodiments, R3c is substituted Ce-io aryl. In certain embodiments, Bee is unsubstituted C3-10 heteroaryl. In certain embodiments, R3c is substituted€3-10 heteroaryl,
[00131] In certain particular embodiments, sc is hydrogen. In certain particular embodiments,
Figure imgf000041_0001
[00132] In certain embodiments, Rsc is CHO, -C(=0)Raa, ( Ί l >(OR ! :, -C02Raa -
C( 0)SR:u, -C(-S)SRaa), -C(-0)N(Rbb)2, C( 0)\RbilSO ,:R-i , C( S)N< Rbb).- ). -C(= Rbb)Raa,
-C(==:NR b)ORaa), or Π \ Rbi;)N(Ri;i;) }. wherein each instance of Rm independently is as defined herein, and wherein each instance of Rs independently is as defined herein.
[00133] In certain embodiments, modification of R3c is used to overcome ArmA-medidated resistance.
Group Rsd
[00134] As generally defined herein, R3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
[00135] In certain embodiments, B d is a nitrogen protecting group. In certain embodiments, R3d is unsubstituted aliphatic (e.g. , unsubstituted Ci-e. akyl ). In certain embodiments, R3d is substituted aliphatic (e.g., substituted Ci-& akyl). In certain embodiments, Rsd is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R3d is substituted cyclic aliphatic (e.g., subsituted C3-0 cycloakyl). In certain embodiments, R3d is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-e heteroakyl). In certain embodiments, R3d is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl). In certain embodiments, RM is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-6 heterocyclyi). In certain embodiments, R3d is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyi). In certain embodiments, ad is unsubstituted C6-io aryl. In certain embodiments, R3d is substituted Ce-io aryl. In certain embodiments, R3d is unsubstituted C3-10 heteroaryl. In certain embodiments, Rsdis substituted C3- 10 heteroaryl.
[00136] In certain particular embodiments, R3d is methyl. In certain particular embodiments,
Figure imgf000042_0001
[00137] In certain embodiments, modification of R3d is used to overcome ArmA-medidated resistance,
[00138] In certain embodiments, R3d is -CHG, -C(=0)Raa, -CH2C02Raa, -CG2Raa - C( ())SRa;i, -C(-S)SRaa), C( ())N( bb},% -C(==0)NR bS02Raa, -C(==S)N(R b)2), -C(= RBB)RAA, -C(=NRbb)ORaa), or -C(=NRBB)N(RBB)2), wherein each instance of R33 independently is as defined herein, and wherein each instance of R independently is as defined herein.
Groups R:<c and RM
[00139] As generally provided herein, R3c and R3d are optionally combined to form a ring. In certain embodiments, the ring is optionally substituted heterocyclyi (e.g., oxiranyl, butyrolactonyl, aziridinyl, azetidinyl, and the like). In certain embodiments, the ring is a 3, 4, 5, 6 or 7 membered ring.
Group R4a
[00140] As generally defined herein, R¾a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl .
[00141] In certain embodiments, R4A is fluorine, chlorine, bromine or iodine. In certain embodiments, R4A is hydroxyl. In certain embodiments, R4A is protected hydroxyl. In certain embodiments, R4a is cyano. In certain embodiments, R4a is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl). In certain embodiments, R4a is substituted aliphatic (e.g., substituted Ci- 6 akyl). In certain embodiments, R4a is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R4a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R4a is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-e heteroakyl). In certain embodiments, R4a is substituted heteroaliphatyl (e.g. , substituted Ci-6 heteroakyl). In certain embodiments, R4a is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R4a is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl). In certain embodiments, R4a is unsubstituted Ce-io aryl . In certain embodiments, R4a is substituted Ce-io aryl. In certain embodiments, R a is unsubstituted C3-10 heteroaryl. In certain embodiments, R4a is substituted C3-10 heteroaryl.
[00142] In certain particular embodiments, R4a is hydroxyl ,
Group R4b
[00143] As generally defined herein, R4b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaiyl.
[00144] In certain embodiments, R4b is fluorine, chlorine, bromine or iodine. In certain embodiments, R4b is hydroxyl. In certain embodiments, R4b is protected hydroxyl. In certain embodiments, R4b i s cyano. In certain embodiments, R4b is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl). In certain embodiments, R4b is substituted aliphatic (e.g. , substituted Ci- 6 akyl). In certain embodiments, R4b is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R4a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R4b is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, R4b is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl). In certain embodiments, R4b is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R*b is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl). In certain embodiments, R4b is unsubstituted Ce-io aryl. In certain embodiments, R4b is substituted Ce.-io aryl. In certain embodiments, R4b is unsubstituted C3-10 heteroaiyl. In certain embodiments, R4b is substituted C3-10 heteroaiyl.
[00145] In certain particular embodiments, R4b is methyl . Group R7d
[00146] As generally defined herein, R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaiyl, or a nitrogen protecting group.
[00147] In certain embodiments, R?d is hydrogen. In certain embodiments, R?d is a nitrogen protecting group. In certain embodiments, R:?d is unsubstituted aliphatic (e.g., unsubstituted d-6 akyl). In certain embodiments, R?d i s substituted aliphatic (e.g. , substituted Ci-e akyl). In certain embodiments, R?d is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R.?d is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R?d is unsubstituted heteroaliphatic (e.g. , unsubstituted d-6 heteroakyl). In certain embodiments, R?d is substituted heteroaliphatyl (e.g. , substituted d-6 heteroakyl). In certain embodiments, R?d is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R?d is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, R?d is unsubstituted C6-10 aryl . In certain embodiments, R-'d is substituted Ce-io aryl. In certain embodiments, R?d is unsubstituted C3-10 heteroaiyl. In certain embodiments, R?d is substituted C3-10 heteroaiyl .
[00148] In certain embodiments, R?d is -CHO, -C(=0)Raa, -COiR33, -€(=0)SRaa, - C(-S)SRaa), CI 0)N( Rbb) % -C(-0)NRbbS02Raa,
Figure imgf000044_0001
-C(-NRb )Raa, -
Figure imgf000044_0002
wherein each instance of Raa independently is as defined herein, and wherein each instance of R independently i s as defined herein .
[00149] In certain embodiments, R?d has the structure:
O
wherein R7f is alkyl or heteroalkyl. In certain embodiments, R?f is halogenated. In an embodiment, R?f is d-6 alkyl or d-6 heteroalkyl. In a particular embodiment, R?f is substituted. In another particular embodiment, R?f is unsubstituted.
[00150] In certain embodiments, R?d has the structure:
Figure imgf000044_0003
00151 In certain embodiments, R?d has the structure:
Figure imgf000045_0001
[00152] n certain embodiments, R?d has the structure:
Figure imgf000045_0002
wherein R7g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acyclic, linear or branched aliphatic (e.g. , alkyl or cycloalkyl), cyclic or acyclic, linear or branched heteroaliphatic (e.g. , heteroalkvl or heterocyclvl), arvl or heteroaryl, or R7g and R/h are combined to form a ring. In a particular embodiment, R7 and R7 are independently substituted. In another particular embodiment, R?g and R?h are unsubstituted. In another particular
embodiment, R7g and R?h are combined to form an optionally substituted 5- or 6-membered ring (e.g. , pyrrolidinyi, piperidinyl, morpholinyl, and the like).
[00153] In certain particular embodiments, R?dis hydrogen. In certain particular embodiments, R?d has the structure:
Figure imgf000045_0003
In certain embodiments, R?d has the structure:
Figure imgf000045_0004
[00154] In certain embodiments, modification of R?d is used to overcome A T(2")-medi dated resistance and/or AAC(3)-mediated resistance.
GrOUp R.9a
[00155] As generally defined herein, ja is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, arvl, or heteroaryl. [00156] In certain embodiments, l a is hydrogen. In certain embodiments, R9?. is a nitrogen protecting group. In certain embodiments, R.9a is unsubstituted aliphatic (e.g. , unsubstituted d-6 akyl). In certain embodiments, Ι½ι is substituted aliphatic (e.g. , substituted Ci-e akyl). In certain embodiments, R9a is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R.9a is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, R9a is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, I¾a is substituted heteroaliphatyl (e.g., substituted Ci-6 heteroakyl). In certain embodiments, R a is unsubstituted cyclic heteroaliphatic (e.g. , unsubstituted C2-6 heterocyclyl). In certain embodiments, Rga is substituted cyclic heteroaliphatic (e.g. , substituted C2-0 heterocyclyl). In certain embodiments, Rsa is unsubstituted C0-10 aryl . In certain embodiments, R.9a is substituted Ce-io aryl. In certain embodiments, R¾ is unsubstituted C3-10 heteroaryl. In certain embodiments, l¾a is substituted C3-10 heteroaryl. In certain embodiments, ga is an aldehyde (e.g., -CHO), a carboxylic acid (e.g., CO2H), a carboxyalkyl (e.g., -C02(alkyl), or an amide (e.g., --CONH2, -CONH(alkyl) or -CON(alkyl)2).
[00157] In certain particular embodiments, R9a is hydroxymethyl. In certain particular embodiments, R<:, is cycloproyl. In certain particular embodiments, R.9a is -CHO, In certain particular embodiments, R9a is -CO2CH3. In certain particular embodiments, R9a is hydrogen.
[00158] In certain embodiments, modification of R9a is used to overcome AAC(3)-mediated resistance.
Group R.9d
[00159] As generally defined herein, R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
[00160] In certain embodiments, 9d is hydrogen. In certain embodiments, R9d is a nitrogen protecting group. In certain embodiments, R9d is unsubstituted aliphatic (e.g. , unsubstituted C i-e akyl). In certain embodiments, R9d is substituted aliphatic (e.g. , substituted Ci-e akyl). In certain embodiments, R¾i is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, R<M is substituted cyclic aliphatic (e.g. , subsituted C3-0 cycloakyl). In certain embodiments, R.9d is unsubstituted heteroaliphatic (e.g. , unsubstituted d-6 heteroakyl). In certain embodiments, 9d is substituted heteroaliphatyl (e.g. , substituted C1-0 heteroakyl). In certain embodiments, Rad is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyelyi). In certain embodiments, R.9d is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyelyi). In certain embodiments, 9d is unsubstituted Ce-io aryl. In certain embodiments, R d is substituted C6-i0 aryl. In certain embodiments, d is unsubstituted C io heteroaryl. In certain embodiments, R9d is substituted C3-10 heteroaryl.
[00161] In certain particular embodiments, R9d is hydrogen.
[00162] In certain embodiments, 9d is CI ID, -C( ))Rm, -CChR83, -C( ))SRaa, -■
Figure imgf000047_0001
Figure imgf000047_0002
wherein each instance of Raa independently is as defined herein, and wherein each instance of Rbb independently is as defined herein.
Group Rub
[00163] As generally defined herein, R is halogen, hvdroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
[00164] In certain embodiments, Rub is fluorine, chlorine, bromine or iodine. In certain embodiments, Rub is hydroxyl. In certain embodiments, Rub i s protected hydroxyl . In certain embodiments, Rub is cyano. In certain embodiments, Rub is unsubstituted aliphatic (e.g. , unsubstituted Ci-& akyl). In certain embodiments, Rub is substituted aliphatic (e.g. , substituted Ci-6 akyl). In certain embodiments, Rub is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, Rub i s substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, Rub is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl). In certain embodiments, Rub is substituted heteroaliphatic (e.g. , substituted Ci-6 heteroakyl). In certain embodiments, Rub is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyelyi). In certain embodiments, Ra is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyelyi). In certain embodiments, Rub is unsubstituted Ce-io aryl. In certain embodiments, Rub is substituted Ce-io aryl. In certain embodiments, R» is unsubstituted C3-10 heteroaryl. In certain embodiments, Rub is substituted C3-10 heteroaryl.
[00165] In certain particular embodiments, Rub is hydroxyl. Group Ri4d
[00166] As generally defined herein, Ri4d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary], heteroaryl, or a nitrogen protecting group.
[00167] In certain embodiments, Ri4d is hydrogen. In certain embodiments, Rwd is a nitrogen protecting group. In certain embodiments, R14d is unsubstituted aliphatic (e.g., unsubstituted Ci-e akyl). In certain embodiments, R14d is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, Ri4d is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyl). In certain embodiments, Rj4d is substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyl). In certain embodiments, Ri d is unsubstituted heteroaliphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, Ri4d is substituted heteroaliphatyl (e.g., substituted Ci-e heteroakyl). In certain embodiments, R i .■..< is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, R14d is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Ri4d is unsubstituted C0-10 aryl. In certain embodiments, R14d is substituted Ce-io aryl. In certain embodiments, Ri4d is unsubstituted C3-10 heteroaryl. In certain embodiments, Ri4d is substituted C3-10 heteroaryl.
[00168] In certain particular embodiments, Rnd is hydrogen.
[00169] In certain embodiments, Ri4d is -CHG, -C(=Q)Raa, -CG2Raa -C(=0)SRaa, - C(-S)SRaa),
Figure imgf000048_0001
S)N(R b)2), -C(-NRb )Raa, - C(=NR )ORaa), or -C(=NRbb)N(Rbb)2), wherein each instance of Raa independently is as defined herein, and wherein each instance of R b independently is as defined herein.
Group Risb
[00170] As generally defined, Risb is hydrogen, halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, ary! or heteroaryl.
[00171] In certain embodiments, Ri.¾ is hydrogen. In certain embodiments, Risb is fluorine, chlorine, bromine or iodine. In certain embodiments, Ru is hydroxy!. In certain embodiments, Risb is protected hydroxyl. In certain embodiments, Ri.¾ is cyano. In certain embodiments, Risb is unsubstituted aliphatic (e.g., unsubstituted Ci-6 akyl). In certain embodiments, Risb is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, Ri?b is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyi ). In certain embodiments, Risb i s substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyi). In certain embodiments, Risb is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, Risb is substituted heteroaiiphatic (e.g., substituted Ci-e heteroakyl). In certain embodiments, Risb is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, Risb is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Risb is unsubstituted Ce.-io aryl. In certain embodiments, Risb is substituted Ce-io aryl. In certain embodiments, RL¾ is unsubstituted C3-10 heteroaryi. In certain embodiments, Risb is substituted C3-10 heteroaryi .
[00172] In certain particular embodiments, RL¾ is hydrogen.
GrOUp Rl6a
[00173] As generally defined, R16a is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryi.
[00174] As generally defined, Riea is hydrogen. In certain embodiments, Ri6a is fluorine, chlorine, bromine or iodine. In certain embodiments, Ri6a is hydroxyl. In certain embodiments, Ri6a is protected hydroxyl. In certain embodiments, R½a is cyano. In certain embodiments, Riea is unsubstituted aliphatic (e.g., unsubstituted Ci-e akyl). In certain embodiments, Ri6a is substituted aliphatic (e.g., substituted Ci-6 akyl). In certain embodiments, Ri6a is unsubstituted cyclic aliphatic (e.g., unsubsituted C3-6 cycloakyi). In certain embodiments, Ri6a is substituted cyclic aliphatic (e.g., subsituted C3-0 cycloakyi). In certain embodiments, Riea is unsubstituted heteroaiiphatic (e.g., unsubstituted Ci-6 heteroakyl). In certain embodiments, Riea is substituted heteroaiiphatic (e.g., substituted Ci-6 heteroakyl). In certain embodiments, Riea is unsubstituted cyclic heteroaiiphatic (e.g., unsubstituted C2-0 heterocyclyl). In certain embodiments, Riea is substituted cyclic heteroaiiphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Ri6a is unsubstituted Ce-io aryl. In certain embodiments, Riea is substituted Ce-io aryl. In certain embodiments, Ri6a is unsubstituted C3-10 heteroaryi. In certain embodiments, Riea is substituted C3-10 heteroaryi.
[00175] In certain particular embodiments, Riea is hydrogen. GrOlip RlHa
[00176] As generally defined, Riga is halogen, hydroxvl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl .
[00177] In certain embodiments, Riga is fluorine, chlorine, bromine or iodine. In certain embodiments, Ri8a is hydroxyl. In certain embodiments, Riga is protected hydroxy!. In certain embodiments, Riga is cyano. In certain embodiments, Ri8a i s unsubstituted aliphatic (e.g., unsubstituted C i-e akyl). In certain embodiments, Ri8a i s substituted aliphatic (e.g. , substituted Ci-6 akyl). In certain embodiments, Risa is unsubstituted cyclic aiiphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, Risa is substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloaky!). In certain embodiments, Riga is unsubstituted heteroaliphatic (e.g. , unsubstituted Cw heteroakyl). In certain embodiments, Risa is substituted heteroaliphatic (e.g. , substituted Ci-e heteroakyl). In certain embodiments, Rixa is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, Riga is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl). In certain embodiments, Risa is unsubstituted Cr io aryl. In certain embodiments, Risa is substituted Ce-io aryl. In certain embodiments, Riga is unsubstituted C3-10 heteroaryl. In certain embodiments, Risa is substituted C3-10 heteroaryl.
[00178] In certain particular embodiments, Risa is hydrogen. In certain particular embodiments, Risa is hydroxy methyl. In certain particular embodiments, Risa is -CH(OH)CH3 hydroxyeth-l-yl (e.g., the (S) stereoisomer of -CH(OH)CH3 or the (R) stereoisomer of - CH(OH)CH3). In certain particular embodiments, Risa is -CH2NHCH(CH2)2.
[00179] In certain embodiments, modification of Risa is used to overcome NpmA-medidated resistance and/or AAC(6')-mediated resistance.
Group Risb
[00180] As generally defined, Risb is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
[00181] In certain embodiments, Risb is fluorine, chlorine, bromine or iodine. In certain embodiments, Risb is hydroxyl. In certain embodiments, Risb is protected hydroxy!. In certain embodiments, Risb is cyano. In certain embodiments, Risb i s unsubstituted aliphatic (e.g. , unsubstituted Ci-& akyl). In certain embodiments, Risa is substituted aliphatic (e.g. , substituted Ci-6 akyl). In certain embodiments, Risb is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-6 cycloakyl). In certain embodiments, R i s substituted cyclic aliphatic (e.g. , subsituted C3-6 cycloakyl). In certain embodiments, Risb is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl). In certain embodiments, Risb is substituted heteroaliphatic (e.g. , substituted Ci-e heteroakyl). In certain embodiments, Risb is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl). In certain embodiments, Risb is substituted cyclic heteroaliphatic (e.g., substituted C2-6 heterocyclyl). In certain embodiments, Risb is unsubstituted Ce-io aryl. In certain embodiments, Risb is substituted Ce-io aryl . In certain embodiments, Rm is unsubstituted C3-10 heteroaryl. In certain embodiments, Ri8b is substituted C3-10 heteroaryl.
[00182] In certain particular embodiments, Risb is hydrogen. In certain particular embodiments, Risb is hydroxy methyl. In certain particular embodiments, Risb is -CH(OH)CH3 hydroxyeth-l-yl (e.g., the (S) stereoisomer of -CH(OH)CH3 or the (R) stereoisomer of - CH(OH)CH3). In certain particular embodiments, isb is -CH2 HC (CH2)2.
Group Risd
[00183] As generally defined herein, Risd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
[00184] In certain embodiments, Risd is hydrogen. In certain embodiments, Risd is a nitrogen protecting group. In certain embodiments, Risd is unsubstituted aliphatic (e.g. , unsubstituted Ci-6 akyl). In certain embodiments, Risd is substituted aliphatic (e.g. , substituted Ci-& akyl). In certain embodiments, Risd is unsubstituted cyclic aliphatic (e.g. , unsubsituted C3-0 cycloakyl). In certain embodiments, Risd is substituted cyclic aliphatic (e.g., subsituted C3-6 cycloakyl). In certain embodiments, Ri8d is unsubstituted heteroaliphatic (e.g. , unsubstituted Ci-6 heteroakyl). In certain embodiments, Risd is substituted heteroaliphatyl (e.g., substituted Ci-6 heteroakyl). In certain embodiments, Risd is unsubstituted cyclic heteroaliphatic (e.g., unsubstituted C2-6 heterocyclyl).
In certain embodiments, Risd is substituted cyclic heteroaliphatic (e.g. , substituted C2-6 heterocyclyl). In certain embodiments, Risd is unsubstituted Ce-io aryl. In certain embodiments, Ri8d is substituted Ce-io aryl. In certain embodiments, Ri»d is unsubstituted C3-10 heteroaryl. In certain embodiments, Risd is substituted C3-10 heteroaryl.
[00185] In certain particular embodiments, Risd is hydrogen.
[00186] In certain embodiments, Risd is -CHG, -C(=Q)Raa, -CG2Raa -C(=0)SRaa, - C(-S)SRaa),
Figure imgf000052_0001
-
Figure imgf000052_0002
wherein each instance of R:sa independently is as defined herein, and wherein each instance of R b independently is as defined herein.
Groups Ri8a, Risb arulRmd
[00187] As generally provided herein, any two of R18a, Risb and Risd are optionally combined to form a ring. In cerain embodiments, Rj.8a and Ri8b are combined to form a ring. In cerain embodiments, R18a and Risd are combined to form a ring. In cerain embodiments, Risb and Risd are combined to form a ring. In certain embodiments, the ring is optionally substituted carbocyclyl (e.g., C3-10 cycloalkyl, or C3-10 cycloalkenyl, or C3-10 cycloalkynyl). In certain embodiments, the ring is optionally substituted C2-10 heterocvclyl (e.g., oxiranyl, butyrolactonyl, aziridinyl, azetidinyl, and the like). In certain embodiments, the ring is a 3, 4, 5, 6, 7, 8, 9 or 10 membered ring.
Embodiments of Formula (I)
[00188] In certain embodiments of Formula (I), or a pharmaceutically acceptable salt thereof, wherein I b, I c, Rsd, 4a, Rtb, R?d, R a, 9d, Riib, Ri4d, Ri.¾, Ri&a, Risa, Risb, and R18d are as defined herein.
[00189] In certan embodiments of Formula (I),
R2b is halogen, -OH, -G(aikyi), -OC(0)alkyl, -NH2, -NHC(0)alkyl, or heteroaryl;
ic is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl;
R d is alkyl, cycloalkyl, heteroalkyl or heterocyclyl; or
RJC and R3d together form a ring;
R4a is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
Ri is alkyl, cycloalkyl, heteroalkyl, or heterocyclyl,
R?d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl;
R9a is hydrogen, alkyl, carboxyalkyl, cycloalkyl, heteroalkyl, or heterocyclyl; R.9d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl;
Rub is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
Ri4d is hydrogen, alkyl, cycloalkyl, heteroalkyl, or heterocyclyl;
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, - HC(0)alkyl, alkyl heteroalkyl,
Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl; and
Risa, Risb, and Ri8d independently are hydrogen, alkyl, cycloalkyl, heteroalkyl heterocyclyl, or two of Risa, Ri8t>, and Risd are combined to form a ring,
[00190] In certain embodiments, the compound of Formula (I) is of Formula (II):
Figure imgf000053_0001
or a pharmaceutically acceptable salt thereof, wherein Rib, R:¾, 4a, Rib, R?d, 9a, R9d, Rub, Ri4d, Risb, Riea, Risa, Risb, and isa are as defined herein.
[00191 ] In an embodiment, the compound of Formula (II) is of Formula (II- 1):
Figure imgf000053_0002
or a pharmaceutically acceptable salt thereof wherein jc, sd, R*, Rvd, RM, Ri isb, and Ri8d are as defined herein.
[00192] In an embodiment, the compound of Formula (II) is of Formula (II~2):
Figure imgf000053_0003
or a pharmaceutically acceptable salt thereof, wherein R3ci, R4b, R?d, R d, Ri4d, Ri8a, Ri8 and Ri8d are as defined herein.
[00193] In an embodiment, the compound of Fonnuia (II) is of Formula (11-3):
Figure imgf000054_0001
or a pharmaceutically acceptable salt thereof, wherein Rsd, R4b, R?d, Rsd, Ri4d, Risa, and Ri8d are as defined herein.
[00194] In an embodiment, the compound of Formula (II) is of Formula (Π-4):
Figure imgf000054_0002
or a pharmaceutically acceptable salt thereof, wherein R3d, R-4 , R?d, Rsd, Ri4d, Risb, and Ri8d are as defined herein.
Ϊ5] In an embodim nt, the compound of Formula (II) is of Formula (II-5):
Figure imgf000054_0003
or a pharmaceutically acceptable salt thereof.
] In certain embodiments, the compound of Formula (II) is of Formula (Π-6):
Figure imgf000054_0004
or a pharmaceutically acceptable salt thereof wherein R<d, d, Rsa, Risb, Ri6a, Ri8a, Ris and Ri8d are as defined herein.
[00197 ] In certain embodiments, the compound of Formula (I) is selected from the following compounds:
Figure imgf000055_0001
and pharmaceutically acceptable salts thereof.
00198] In another aspect, provided herein is a compound of Formula (I-a):
Figure imgf000055_0002
or a salt thereof, wherein:
X is a leaving group;
Ri5b is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl,
Riea is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Ri8a and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
Risa and Risb are combined to form a ring.
00199] In certain embodiments of Formula (I-a):
Ri5b is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
Ri6a is hydrogen, halogen, ~OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl; and
Risa and Rssb are hydrogen, alkyl, cycloalkyl, heteroalkyl or heterocyclyi; or
Ri8a and Risb are combined to form a ring. In certain embodiments of Formula (I-a), X is - SPh, -S(0)Ph or -S(0)2Ph. In certain embodiments Fommla (I-a) is of Formulae (I-al)-(I-a4):
Figure imgf000056_0001
or a salt thereof, wherein:
R?e is -N3 or -N(R?c)(R7d), wherein:
R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl; and
Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring.
[00203] In certain embodiments of Formula I-b), R?e is a radical of the formula:
Figure imgf000056_0002
wherein R?f is Ci-e alkyl or C1-0 heteroalkyl.
[00204] In certain embodiments of Formula (I-b),
R?c is hydrogen or a nitrogen protecting group;
R?d is hydrogen or a nitrogen protecting group;
R9a is hydrogen, alkyl, carboxyalkyl, cycloalkyl, heteroalkyl or heterocyclyl; and
Riib is halogen, protected hydroxy!, -O(alkyl), -OC(0)alkyl, ~ HC(0)alkyl, or heteroaryl; and
Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring.
[00205] In certain embodiments of Formula (I-b),
R9a is hydrogen;
Riib is protected hydroxyl; and Ri2a is an oxygen protecting group.
In certain embodiments of Formula (I-b),
R9a is hydrogen;
Riib and R12a are combined to form a five or six-membered ring.
[00206] In certain embodiments Formula (I-b) is of Formulae (I~bl)-(l-b8):
Figure imgf000057_0001
(I-b4)
Figure imgf000058_0001
Figure imgf000058_0002
Figure imgf000058_0003
or a salt thereof, wherein:
R?e is -N3 or -N(R?c)(R7d), wherein:
R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rvd is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rsa is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl ;
Riib is halogen, hydroxvl, protected hvdroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl; and
Ri2a is an oxygen protecting group; or
Riib and R12a are combined to form a five or six-membered ring;
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl; Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl; and
Risa and Risb are hydrogen, alkyl, cycloalkyl, heteroalkyl or heterocyclyl; or
Risa and Rss are combined to form a ring.
[00208] In certain embodiments of Formula (I-c), R?e is a radical of the formula:
Figure imgf000059_0001
wherein R?f is Ci-ό alkyl or Ci-e heteroalkyl.
[00209] In certain embodiments Formula (I-c):
R \ is -N3 or ·Ν( ! ·,)(! ·.:}:
R?c is hydrogen or a nitrogen protecting group;
R?d is hydrogen or a nitrogen protecting group,
R9a is hydrogen, alkyl, carboxvalkyl, cycloalkyl, heteroalkyl or heterocyclyl;
Rub is halogen, protected hydroxyl, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, heteroaryl;
Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring;
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl; and
Risa and Rssb independently are hydrogen, alkyl, cycloalkyl, or cyclic or acyclic heteroalkyl.
[00210] In certain embodiments Formula (I-c):
R9a is hydrogen;
Rub is hydroxyl or protected hydroxyl; and
Ri2a is an oxygen protecting group; or
Rub and Ri2a are combined to form a five or six-membered ring;
Risb and R16a are hydrogen; and
Risa and Ri8b independently are hydrogen, alkyl, or heteroalkyl. [00211] In certain embodiments Formula (I-c):
R-9a is hydrogen,
Riib is protected hydroxy], and R12a is an oxygen protecting group.
[00212] In certain embodiments of Formula (I-c),
R9a is hydrogen;
Riib and R12a are combined to form a five or six-membered ring.
00213] In certain embodiments, Formula (I-c) is of Formulae (I-cl)-(I-c6):
Figure imgf000060_0001
or a salt thereof, wherein:
X is a leaving group, R2 is halogen, hydroxy!, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Rsc is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
'3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group, or
Rsc and R3d together form a ring;
R»a is halogen, hydroxy!, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R4b is halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R4a and R3c are combined to form a five or six-membered ring; or
ia and R3d are combined to form a five or six-membered ring.
[00215] In certain embodiments of Formula (I-d),
X is a leaving group,
Ra is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -TMH2, protected amino, -NHC(0)a!ky!, or heteroaryl;
R3c is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
Rsd is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group,
R a is halogen, -Oil protected hydroxyl, -O(alkyl), -OC(0)alkyl, alkyl, cycioalkyl heteroaikyi, or heterocyciyl; and
i is alkyl, cycioalkyl, heteroaikyi or heterocyciyl; or
R4a and R3c are combined to form a five or six-membered ring; or
R4a and R3d are combined to form a five or six-membered ring,
[00216] In certain embodiments of Formula (I-d),
X is -SPh, -S(0)Ph or -S(0)2Ph,
Ri is protected hydroxyl;
R3c i alkyl
R d is alkyl or benzyl;
R4a is protected hydroxyl; and b is alkyl .
In certain embodiments of Formula (I-d),
a and R.3c are combined to form a five or six-membered ring; or Ua and R.3d are combined to form a five or six-membered ring.
In certain embodiments, Formula (I-d) is of Formulae (I-dl)-(I-d6)
Figure imgf000062_0001
Figure imgf000062_0002
Figure imgf000062_0003
In another aspect, provided herein is a compound of Formula (I-
Figure imgf000062_0004
or a salt thereof wherein; R.2b is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Rsc is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
'3d is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group, or
Rsc and R3d together form a ring;
R a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R4b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R?e is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group,
R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Rub is halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Ri5b is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Ri6a is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Ri8a and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
[00220] In certain embodiments of Formula (I-e),
Ra> is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -TMH2, protected amino, -NHC(0)alkyl, or heteroaryl;
R3c is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
R'3d is alkyl, cycioalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
R4a is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, alkyl, cycioalkyl heteroaikyi, or heterocyciyl; and P b is alkyl, cycioalkyl, heteroalkyl or heterocyclyl; or
R4a and R3c are combined to form a five or six-membered ring; or
R4a and R3d are combined to form a five or six-membered ring;
R-/e is -N3 or ~N(R7c)(R7d);
R?c is hydrogen or a nitrogen protecting group;
R'?d is hydrogen or a nitrogen protecting group;
R9a is hydrogen, alkyl, cycioalkyl, heteroalkyl or heterocyclyl,
Rub is halogen, protected hydroxyl, -OH, -O(alkyl), -QC(0)alkyl, -NHC(0)alkyl, heteroaryl;
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, heteroaikvi; and
Ri8a and Risb independently are hydrogen, alkyl, cycioalkyl, or cyclic or acyclic heteroalkyl.
[00221] In certain embodiments of Formula (I-e),
Ra> is protected hydroxyl;
3d is alkyl;
R4a is protected hydroxyl;
Rtb is alkyl or benzyl, or
R a and Rsc are combined to form a five-membered ring; or
4a and 3d are combined to form a five-membered ring;
e is -N3 or -N(R7c)(R7d);
R?c is hydrogen or a nitrogen protecting group;
R is hydrogen or a nitrogen protecting group;
R9a is hydrogen;
Rub is hydroxyl or protected hydroxyl; and
Risb and Riea are hydrogen; and
Risa and Risb independently are hydrogen, alkyl, or heteroalkyl.
[00222] In certain embodiments, Formula (I-e) is of Formulae (I-el)-(I-e6):
Figure imgf000065_0001
Figure imgf000065_0002
Figure imgf000065_0003
Method of Preparation
[00223] Provided herein is a modular, fully synthetic approach to the synthesis of aminoglycosides, providing access to new aminoglycosides with antibacterial activity.
[00224] In one aspect, provided herein is a method of making a compound of Formula (I):
Figure imgf000065_0004
or a pharmaceutically acceptable salt thereof, the method comprising reducing a compound of Formula (I-e):
Figure imgf000066_0001
or a salt thereof, to form the compound of Formula (I), wherein Formulae (I) and (I-e) are as defined above,
[00225] In an embodiment, the method further comprises contacting the compound of Formula (I-e), or a salt thereof wherein R18a and Risb are hydrogen, with a base and an electrophile to produce a compound of Formula (I-e), or a salt thereof, wherein one or both of Ri8a and Risb are not hydrogen. In certain particular embodiments, R18a and Ri8b are independently alky] .
[00226] In certain embodiments, the base is selected from a carbonate (e.g., sodium carbonate, potassium carbonate, and the like), a tertiary amine (e.g., trimethylamme, diisopropylethylamine, l ,8-diazabicyclo[5.4.0]undec-7-ene, and the like), a hydride (e.g., sodium hydride, potassium hydride, and the like), and an amide (lithium diisopropyl amide, sodium hexamethyidisilazide, potassium hexamethyidisilazide, and the like).
[00227] In certain embodiments, the electrophile has the structure of R18a-X or Rssb-X, wherein Risa and Risb are not hydrogen, and wherein X is a leaving group as defined herein. In certain particular embodiments, the electrophile is an aldehyde (e.g., formaldehyde), an activated carboxylic acid derivative (e.g., an acid chloride, carboxylic acid anhydride, or the like), an activated carbonate acid derivative (e.g., an alkoxy carbonyl chloride), a halogen or haiogenating agent (e.g., bromine, N-bromosuccinimide, or the like), or a Schiff base (e.g., a formal dimine).
[00228] In certain embodiments, said reducing a compound of Formula (I-e), or a salt thereof, comprises:
(a) reducing the nitro group to a primary amine with a first reducing agent;
(b) optionally alkylating or acylating the primary amine of (a);
(c) reducing one or more azido groups to corresponding primary amines with a second reducing agent; and
(d) optionally alkylating or acylating the corresponding primary amines of (c). [00229] In certain embodiments, the first reducing agent and the second reducing agent are the same, and the nitro group and azide groups are reduced simultaneously. In certain embodiments, the first reducing agent and the second reducing agent are different.
[00230] In certain embodiments of the method of preparing Formula (I), the method further comprises coupling a comp nd of Formula (I-c):
Figure imgf000067_0001
or a salt thereof, with a compound of Formula (I-d):
Figure imgf000067_0002
or a salt thereof, under suitable conditions to form the compound of Formula (I-e), wherein Formulae (I-c) and (I-d) are as defined above.
[00231] In certain embodiments, the suitable conditions comprise an oxidizing agent.
[00232] In certain embodiments, said coupling a compound of Formula (I-c), or a salt thereof, with a compound of Formula (I-d), or a salt thereof, comprises:
(a) contacting the compound of Formula (I-c), or a salt thereof, with a compound of Formula (I-d) , or a salt thereof, under suitable conditions to produce a compound of Formula (I-e), wherein R7e is N(R?c)(R7d) and wherein R7c and R?d are nitrogen protecting groups;
(b) removing the nitrogen protecting groups of Formula (I-e) under suitable
condi tions to produce a compound of Formula (I-e), wherein Rye is NII2; and
iating the product of (b) with a compound having the formula:
Figure imgf000067_0003
wherein X is a leaving group and R?f is C1-6 alky] or Ci-e heteroalkyl, to produce a compound of Formula (I-e) wherein R7e has the structure: H
O
$] In certain embodiments R?e has a structure selected from:
Figure imgf000068_0001
, wherein
PG is a protecting group; and
R?g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acy clic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl, or vg and R?h are combined to form a ring.
[00234] In certain embodiments, the suitable conditions of (a) comprise an oxidizing agent.
[00235] In certain embodiments, the suitable conditions of (b) comprise an oxidizing agent, hydrogenolysis, acid hydrolysis, or base hydrolysi s.
[00236] In certain embodiments of the method of preparing Formula (I), the method further comprises coupling a compound of Formula (I-a):
Figure imgf000068_0002
or a salt thereof, with a compound of Formula (I-
Figure imgf000068_0003
or a salt thereof, under suitable conditions to produce a compound of Formula (I-c), wherein Formulae (I-a) and (I-b) are as defined above.
[00237] In certain embodiments, the suitable conditions comprise an oxidizing agent.
[00238] In certain embodiments, said coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof, comprises: (a) coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof, under suitable conditions to produce a compound of Formula (I-c), wherein R12a is an oxygen protecting group; and
(b) removing the oxygen protecting group under suitable conditions to produce a compound of Formula (I-c), wherein Ri2a is hydrogen.
[00239] In certain embodiments, the suitable conditions of (a) comprise an oxidizing agent.
[00240] In certain embodiments, the suitable conditions of (b) comprise hydrogenolysis, acid hydrolysis or base hydrolysis.
[00241] In another aspect, provided herein is a method of making a compound of Formula (I):
Figure imgf000069_0001
or a pharmaceutically acceptable salt thereof wherein R2 , Rsc, Rsd, R.4a, R.4b, Rvd, R9a, 9d, Rub, Ri4d, Ri 5b, Ri&a, Risa, Ri»b, and i8d are as defined above, comprising:
(i) coupling a compound of Formula (I-a) with a compound of Formula (I-b) under suitable conditions to produce a compound of Formula (I-c), wherein the compounds of Formulae (I-a), (I-b) and (I-c) are as defined above;
(ii) coupling the compound of Formula (I-c) with a compound of Formula (I-d) under suitable conditions to produce the compound of Formula (I-e), wherein the compounds of Formulae (I-d) and (I-e) are as defined above;
(iii) converting the compound of Formula (I-e) to the compound of Formula (I).
[00242] In certain embodiments of the method of making Formula (I), step (i) comprises:
(i-a) coupling a compound of Formula (I-a) with a compound of Formula (I-b) under suitable conditions to produce a compound of Formula (I~c), wherein Ri 2a is an oxygen protecting group; and
(i-b) removing the oxygen protecting group under suitable conditions to produce a compound of Formula (I-c), wherein R12a is hydrogen. [00243] In certain embodiments of Formulae (I-b) and (I-c), R?e is N(R.7c)(R7d), wherein R?c and R?d are nitrogen protecting groups, and step (ii) comprises:
(ii-a) coupling the compound of Formula (I-c) with a compound of Formula (I-d) under suitable conditions to produce a compound of Formula (I-e), wherein R?e is N(R7c)(R7d) and wherein R?c and R7d are nitrogen protecting groups;
(ii-b) removing the nitrogen protecting groups of Formula (I-e) under suitable conditions to produce a compound of Formula (1-e) wherein R7e is NH2; and
ii-c) acylating the product of step (ii-b) with a compound having the formula:
Figure imgf000070_0001
, wherein
X is a leaving group and R?f is Ci-6 alkyl or Ci-e heteroalkyl,
to produce a compound of Formula (I-e) wherein R?e has the structure:
Figure imgf000070_0002
In certain particular embodiments, R?e has the structure:
PC o H
O
[00245] In certain particular embodiments, R?e has the structure:
PG H R7h o
wherein R7g and R?h are as defined herein.
[00246] In certain particular embodiments, R?d is hydrogen. In certain particular embodiments, R?d has the structure:
Figure imgf000070_0003
[00247] In certain embodiments, the method of making Formula (I) further comprises contacting the compound of Formula (I-e), or a salt thereof wherein Riga and i8 are hydrogen, with a base and an electrophile to produce a compound of Formula (I-e), or a salt thereof, wherein one or both of Risa and Risb are not hydrogen. In certain embodiments, Riga and Ri8b are independently alkyl.
[00248] In certain embodiments, the base is selected from carbonate (e.g., sodium carbonate, potassium carbonate, and the li ke), tertiary amine (e.g., trimethylamine, diisopropyl ethyl amine, l,8-diazabicyclo[5.4.0]undec-7-ene, and the like), hydride (e.g., sodium hydride, potassium hydride, and the like), and amide (lithium diisopropyl amide, sodium hexamethyldisilazide, potassium hexamethyldisilazide, and the like).
[00249] In certain embodiments, the electrophile has the structure of Risa-X or Ri8b-X, wherein Riga and Risb are not hydrogen, and wherein X is a leaving group as defined herein. In certain particular embodiments, the electrophile is an aldehyde (e.g., formaldehyde), an activated carboxylic acid derivative (e.g., an acid chloride, carboxylic acid anhydride, or the like), an activated carbonate acid derivative (e.g., an alkoxy carbonyl chloride), a halogen or haiogenating agent (e.g., bromine, N-bromosuccinimide, or the li ke), or a Schiff base (e.g., a formal dimine).
[00250] In certain embodiments, step (iii) comprises reducing both the azido and nitro groups of the compound of Formula (I-e) with the same reducing agent. In certain embodiments, step (iii) comprises orthogonal reduction of the azido and nitro groups with different reducing agents.
[00251] In certain embodiments, step (iii) comprises:
(iii-a) reducing the nitro group to a primary amine with a first reducing agent;
(iii-b) optionally, alkylating or acylating the primary amine of (iii-a);
(iii-c) reducing one or more azido groups to corresponding primary amines with a second reducing agent; and
(iii-d) optionally, alkylating or acylating the primary amines of (iii-c).
[00252] Exemplar}' reaction conditions are described herein, for example, in the Examples, Figures and Definitions.
[00253] In certain embodiments, the suitable conditions of steps (i) and (i-a) independently comprise an oxidizing agent. Exemplary conditions are disclosed herein, for example, in Figure 8 and Figure 21.
[00254] In certain embodiments, the suitable conditions of steps (ii) and (ii-a) independently comprise an oxidizing agent. [00255] In certain embodiments, the suitable conditions of step (ii-b) comprises acid hydrolysis (e.g., aqueous hydrochloric acid) or hydrogenolysis (e.g., catalytic hydrogenation), or oxidation (e.g., eerie ammonium nitrate). Other exemplary conditions are disclosed in the Examples and Figures herein.
[00256] In another aspect, provided herein is a method of making a compound of Formula (1- c), comprising coupling a compound of Formula (I-a) with a compound of Formula (I-b) under suitable conditions, wherein the compounds of Formulae (I-a), (I-b) and (I-e) have structures as described herein. In certain embodiments, the suitable conditions comprise an oxidizing agent. Exemplary conditions are disclosed herein, for example, in Figure 18 and Figure 21.
[00257] In another aspect, provided herein is a method of making a compound of Formula (I- e), comprising coupling the compound of Formula (I-c) with a compound of Formula (I-d) wherein the compounds of Formulae (I~d) and (Ι-ε) have structures as described herein. In certain embodiments, the suitable conditions comprise an oxidizing agent. Exemplar}' conditions are disclosed herein, for example, in Figure 18 and Figure 21 ,
Pharmaceutical Compositions and Administration
[00258] The present disclosure provides pharmaceutical compositions comprising an aminoglycoside compound as described herein (e.g., a compound of Formulae (I), (II), (II-l), (ΙΪ-2), (Π-3), (Π-4), (Π-5), (Π-6), FSA-38240, FSA-38252, FSA-382SS, FSA-392S4
(compound 1), or a pharmaceutically acceptable salt thereof) and a pharmaceutically acceptable excipient.
[00259] Pharmaceutically acceptable excipients include any and all solvents, diluents, or other liquid vehicles, dispersions, suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. General considerations in formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).
[00260] Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the aminoglycoside of the present invention into association with a carrier and/or one or more other accessor}' ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
[00261] Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, ami/or as a plurality of single unit doses. As used herein, a "unit dose" is discrete amount of the pharmaceutical composition comprising a predetermined amount of the aminoglycoside of the present invention. The amount of the aminoglycoside is generally equal to the dosage of the aminoglycoside which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
[00262] Relative amounts of the aminoglycoside, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1% and 100% (w/w) aminoglycoside.
[00263] Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
[00264] Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the aminoglycosides, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, soiubilizing agents, and emulsifiers, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates of the invention are mixed with soiubilizing agents, and mixtures thereof.
[00265] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium.
[00266] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the aminoglycoside is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or di calcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitoi, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.
[00267] Dosage forms for topical and/or transdermal administration of an aminoglycoside of this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, the aminoglycoside is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any needed preservatives and/or buffers as can be required.
[00268] Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.
[00269] Aminoglycosides provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily amount of the aminoglycoside will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific aminoglycoside employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject, the time of administration, route of administration, and rate of excretion of the specific aminoglycoside employed; the duration of the treatment; drugs used in combination or coincidental with the specific aminoglycoside employed; and like factors well known in the medical arts.
[00270] The aminoglycosides and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation, and/or as an oral spray, nasal spray, and/or aerosol. In general, the most appropriate route of administration will depend upon a variety of factors including the nature of the agent, the therapeutic regimen, and/or the condition of the subject. Oral administration is the preferred mode of administration. However, in certain embodiments, the subject may not be in a condition to tolerate oral administration, and thus intravenous, intramuscular, and/or rectal administration are also preferred altermative modes of administration.
[00271] An effective amount may be included in a single dose (e.g., single oral dose) or multiple doses (e.g., multiple oral doses). In certain embodiments, when multiple doses are administered to a subject or applied to a tissue or cell, any two doses of the multiple doses include different or substantially the same amounts of a compound described herein. In certain embodiments, when multiple doses are administered to a subject or applied to a tissue or cell, the frequency of administering the multiple doses to the subject or applying the multiple doses to the tissue or cell is three doses a day, two doses a day, one dose a day, one dose every other day, one dose every third day, one dose every week, one dose every two weeks, one dose every three weeks, or one dose every four weeks. In certain embodiments, a dose (e.g., a single dose, or any dose of multiple doses) described herein includes independently between 0.1 g and 1 ug, between 0.001 nig and 0.01 mg, between 0.01 mg and 0.1 mg, between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg, between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and 300 mg, between 300 mg and 1 ,000 mg, or between 1 g and 10 g, inclusive, of a compound described herein.
[00272] It will be also appreciated that an aminoglycoside or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. The aminoglycoside or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of the inventive aminoglycoside with the additional therapeutical ly active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
[00273] Exemplary additional therapeutically active agents include, but are not limited to, antibiotics, anti-viral agents, anesthetics, anti-coagulants, inhibitors of an enzyme, steroidal agents, steroidal or non-steroidal anti-inflammatory agents, antihistamine, immunosuppressant agents, antigens, vaccines, antibodies, decongestant, sedatives, opioids, pain-relieving agents, analgesics, anti-pyretics, hormones, and prostaglandins. Therapeutical ly active agents include small organic molecules such as drug compounds (e.g., compounds approved by the US Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucieoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells.
[00274] In certain embodiments, the additional therapeutically active agent is an antibiotic. Exemplar}' antibiotics include, but are not limited to, penicillins (e.g., penicillin, amoxicillin), cephalosporins (e.g., cephalexin), macrolides (e.g., erythromycin, clarithormycin, azithromycin, troieandomycin), fluoroquinolones (e.g., ciprofloxacin, levofloxacin, ofloxacin), sulfonamides (e.g., co-trimoxazole, trimethoprim), tetracyclines (e.g., tetracycline, chlortetracyciine, oxytetracycline, demeclocycline, methacycline, sancycline, doxycline, aureomycin, terramycin, minocycline, 6-deoxytetracycline, iymecycline, meclocycline, methacycline, roiitetracycline, and glycyicycline antibiotics (e.g., tigecycline)), aminoglycosides (e.g., gentamicin, tobramycin, paromomycin), aminocyclitol (e.g., spectinomycin), chloramphenicol, sparsomycin, and quinupristin/daifoprisin (Syndercid™).
[00275] Also encompassed by the invention are kits (e.g., pharmaceutical packs). The kits provided may comprise an inventive pharmaceutical composition or aminoglycoside and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or aminoglycoside. In some embodiments, the inventive pharmaceutical composition or aminoglycoside provided in the container and the second container are combined to form one unit dosage form.
[00276] Also encompassed by the invention are kits (e.g., pharmaceutical packs). The kits provided may comprise an inventive pharmaceutical composition or aminoglycoside and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or aminoglycoside. In some embodiments, the inventive
pharmaceutical composition or aminoglycoside provided in the container and the second container are combined to form one unit dosage form.
Mechanism of Action
[00277] The bacterial ribosome is composed of ribosomal RNA (rRNA) and proteins, which are organized into two subu its, the 30S and the 50S (Figure 34). There are three sites on the ribosome that allow tRNA binding: the A site, P site, and E site. Prior to the formation of a peptide bond, an aminoacyl-tRNA, which carries the correct amino acid for the codon displayed by the mRNA, is selected by the A site. The P site is bound to the peptidyi-tRNA, which carries the nascent peptide. The E site houses uncharged tRNA, which is subject to ejection from the ribosome. [00278] The process of protein synthesis can be divided into four phases: initiation, elongation, termination, and recycling (Figure 34), The 2-deoxystreptamine class of aminoglycosides (for example, compounds of Formula (I)), exert their antibacterial action by binding to the bacterial ribosome, which affects protein synthesis in multiple stages.
[00279] For example, interactions of aminoglycosides with an internal loop of helix 44 (li44) in the 30S subunit of the ribosome compromises the fidelity of tR A selection in the elongation phase, and binding of aminoglycosides to helix 69 (h69) in the SOS subunit of the ribosome interferes with the translocation process in the elongation phase and ribosome recycling.
Bacterial Resistance to Aminoglycosides
[00280] The use of aminoglycosides has steadily declined over the past decades due to a rise in bacterial resistance. The emergence of multidrug-resistant bacteria is a major public health concern. The most problematic of all, the ESKAPE pathogens (Enterococcus faecium, Staphlococcus aureus, Klebsiella pneumonia, Acinetohacter baumannii, Pseudomonas aeruginosa, and Enterobacteria), have been responsible for a large number of nosocomical infections and cany resistance to aminoglycosides (Figure 35) and many (or all) other classes of antibiotics.
[00281] There are several biochemical mechanisms by which bacteria evade the antibiotic action of aminoglycosides, including modification of the aminoglycoside substrate, mutations and enzymatic modifications of the ribosome target, and efflux pumps and change in membrane permeability.
[00282] Aminoglycoside Modifying Enzymes (AMEs): The most prevalent mechanism of resistance to aminoglycosides is through the action of aminoglycoside modifying enzymes (AMEs), which carry out cofactor-dependent modifications of the polar functional groups on these antibiotics. AMEs can occur alone or in combination in both Gram-positive and Gram- negative pathogens, and exhibit a high level of substrate promiscuity. Most are encoded on mobile elements such as plasmids, transposons, and integrons, which facilitate rapid dissemination of resistance.
[00283] There are three types of AMEs: aminoglycoside JV-acetyltransf erase (AAC), aminoglycoside ^-phosphotransferase (APH), and aminoglycoside ^-nucleotidyltransferase or O-adenyltransferase (ANT). The nomenclature convention dictates that the site of modification is denoted as a number in parenthesis. This is followed by a Roman numeral designating the resistance profile, and a subsequent letter indicating a specific gene. As an example: AAC(6')-Ia and AAC(6')-Ib both acetylate the 6 -amino group of aminoglycosides and have identical resistance profiles. But they are two unique proteins encoded by two different genes.
[00284] Depending on the substitution pattern and the location of carbohydrate attachment, individual aminoglycosides have different susceptibilities to AMEs (Figure 36). Kinetic studies show that these enzymes are highly effective at low concentrations of aminoglycoside substrates. By inactivating the drug molecules as they enter the ceil, the AMEs reduce the intracellular accumulation of active antibiotics, which precludes the rapid uptake during energy-dependent phase II (EDPII) that leads to cell death.
[00285] Mutations and Enzymatic Modifications to the Ribosome: Direct mutations of the 16S rRNA to confer aminoglycoside resistance are rare, owing to the importance and universally conserved function of the ribosome. It has been shown however, that a single point mutation, A1408G, in a single-stranded loop leads to disruption of stabilizing interactions between the aminoglycosides and h44. This results in resistance to ail 2-deoxystreptamine aminoglycosides. It is likely of lesser clinical importance however, due to the presence of multiple copies of rRN A genes, except in mycobacteria, which carry a single copy of rRNA genes.
[00286] Another method of resistance through changes to the bacterial ribosome involves the action of rRNA methyltransferases (RMTs). RMTs were initially present only in aminoglycoside-producing actinomycetes, which through the actions of RMTs avoid the antibiotic effects of their secondary metabolites. In 2003, plasmid-encoded RMTs, known as ArmA (aminoglycoside resistance methylase) and RmtA-D, were isolated in clinical strains of P. aeruginosa and K. pneumoniae . Since then, ArmA has been found in other clinical strains, including A. baumannii. This class of RMTs is related to ones found in the gentamicin producing-producing strain Micromonospora purpurea, and methylates the N7 position of G1405, which is located in close proximity to the 3 "-amino group on ring III of 4,6-disubstituted aminoglycosides. Methylation results in the introduction of a positive charge on the nucleotide and, together with increased steric bulk, disfavors aminoglycoside binding and confers high-level resistance to all 4,6-disubstituted 2-deoxystreptamine aminoglycosides. On the other hand, methylation of G1405 does not lead to resistance to neomycin and paromomycin, which lack a carbohydrate attachment on the C6-hydroxyi functional group (Figure 37). [00287] A second class of RMT, NmpA, was found in a clinical isolate of E. coli in Japan in 2007, which methylates Nl of AMOS, Strains carrying the nmpA gene exhibited resistance to all aminoglycosides, including the 4, 5 -di substituted aminoglycoside neomycin and the atypical aminoglycoside apramycin.
[00288] Efflux Pumps and Change in Membrane Permeability: Resistance to aminoglycosides in P, aeruginosa is associated with changes to the outer membrane lipopolysaccharides. Structural changes to the outer membrane composition is partly regulated by the two-component regulatory system, PhoP-PhoQ, which reduces permeability of the outer membrane to aminoglycosides under Mg2÷ starvation or in the presence of polyamines. Additionally, both mutations to the electron-transport chain and nitric oxide-mediated repression of respiratory activity result in inhibition of the energy-dependent phase of aminoglycoside uptake. This attenuates the threshold buildup of aminoglycosides that is necessary for cell death and confers antibiotic resistance.
[00289] Synergistic with inherently low permeability of the outer membrane, efflux of aminoglycosides is a significant contribution to clinically observed bacterial resistance to aminoglycosides, particularly in Gram-negative pathogens such as P. aeruginosa and A. baumannii. Aminoglycoside efflux pumps are energy dependent and belong to the resistance nodulation division (RND) family, one of five classes of transmembrane efflux systems. Restricted to Gram-negative bacteria, the RND family of efflux pumps functions by forming a three-component protein complex, which consists of the RND membrane pump, a periplasmic membrane fusion protein (MFP), and an outer-membrane factor (OMF). This tripartite assembly spans all layers of the cell membrane and allows efflux of antibiotics directly into the external medium.
[00290] The aminoglycoside efflux systems are named AcrAD-TolC in E. coli, AdeAB-AdeC in A. baumannii, and MexXY-OprM in P. aeruginosa. They are distinct from RND pumps used for the active export of other classes of antibiotics, which have hydrophobic binding pockets that make aminoglycosides poor substrates. Overexpression of efflux pumps, often induced by exposure to aminoglycosides, are well correlated with multidrug resistance in clinical isolates.
[00291] The resistance mechanisms outlined above can occur alone or in combination. Because of difference in usage pattern, the frequency of resistance mechanisms also differs depending on geographical location. Each pathogenic strain of bacteria expresses different levels of resistance, with pan-resistance observed in some species that cany clusters of resistance genes. The occurrence of aminoglycoside resistance mechanism in ESKAPE pathogens is shown in the following table:
Pathogen Prevalent resistance mechanisms
Enterococci APH(3")-IIIa, AAC(6')/APH(2")
S. aureus AAC(6')-le/APH(2"), ANT(4')-Ia, APH(3')-liia
K. pneumoniae AAC(6')-Ib, ANT(3")-ia, ANT(2")-Ia
Acinetobacter spp. permeability/efflux, AAC(3)-I, APH(3')-VI, AAC(6')-I, ANT(2")-I, AAC(3)-IL
ArmA
P. aeruginosa permeability/efflux, A AC(6')-! !. ANT(2")-I, APH(3 1I (chromosomal),
AAC(6')-I, AAC(3)-I, ArmA
Enterobacteriaceae AAC(3)-IL AAC(6')-I, ANT(2")-I, Ann A, AAC(3)-I
Methods of Treatment and Uses
[00292] The present disclosure contemplates the use of the aminoglycosides as described herein as antibacterial agents.
[00293] Thus, as generally described herein, provided is a method of treating a bacterial infection comprising administering an effective amount of an aminoglycoside of the present invention (e.g., a compound of Formulae (1), (II), (H-l), (0-2), (II-3), (0-4), (H-5), (II-6), FSA-38240, FSA-38252, FSA-38255, FSA-39254 (compound 1), or a pharmaceutically acceptable salt thereof) to a subject in need thereof. Such a method can be conducted in vivo (i.e., by administration to a subject) or in vitro (e.g. , upon contact with the pathogen, biological sample, tissue, or cell culture). Treating and treatment, as used herein, encompasses therapeutic treatment and prophylactic treatment.
[00294] In certain embodiments, the effective amount is a therapeutically effective amount. For example, in certain embodiments, administering an effective amount of an aminoglycoside kills or stops the growth of the bacteria. In certain embodiments, administering an effective amount of an aminoglycoside slows the progress of a bacterial infection in the subject. In certain embodiments, administering an effective amount of an aminoglycoside improves the condition of the subject suffering from a bacterial infection. In certain embodiments, the subject has a suspected or confirmed bacterial infection. [00295] In certain embodiments, the effective amount is a prophylatically effective amount. For example, in certain embodiments, the method prevents or reduces the likelihood of a bacterial infection, e.g., in certain embodiments, the method comprises administering an aminoglycoside of the present invention to a subject in need thereof in an amount sufficient to prevent or reduce the likelihood of a bacterial infection. In certain embodiments, the subject is at risk of a bacterial infection (e.g. , has been exposed to another subject who has a suspected or confirmed bacterial infection or has been exposed or thought to be exposed to a bacterium).
[00296] In another aspect, provided is a method of inhibiting bacterial growth comprising contacting an effective amount of the aminoglycoside of the present invention with a bacterium. In certain embodiments, the method is in vitro. In certain embodiments, the method is in vivo.
[00297] As used herein, "bacterial infection" refers to an infection with a bacterium, such as a gram-negative or a gram-positive bacterium. In certain embodiments, the bacterial infection is caused by a bacterium resistant to other treatments. In certain embodiments, the bacterial infection is caused by a bacterium that is multi-drag tolerant or resistant, e.g., the bacterial infection is caused by a bacterium that neither grows nor dies in the presence of or as a result of other treatments.
[00298] In certain embodiments, the aminoglycoside of the present invention has a mean inhibitory concentration (MIC), with respect to a particular bacteria, of less than 50 μ^πιΐ,, less than 25 μg/mL, less than 20 μ^πύ^, less than 10 ,ug/mL, less than 5 ug/mL, or less than 1 ^ig/mL.
[00299] In certain embodiments, the bacteria is susceptible (e.g., responds to) or resistant to known commercial aminoglycosides, such as plazomicin, kanamycin A, amikacin, tobramycin, dibekacin, gentamicin, sisomicin, netilmicin, neomycins B, C, and E, streptomycin, and the like. In certain embodiments, the bactera is resistant to a known aminoglycoside.
[00300] In certain embodiments, the bacterial infection is resistant to other antibiotics therapy. For example, in certain embodiments, the bacteria is vancomycin resistant (VR). In certain embodiments, the bacteria is methicillin-resistant (MR), e.g., in certain embodiments, the bacterial infection is a methicillin-resistant S. aureus infection (a MRS A infection). In certain embodiments, the bacteria is quinolone resistant (QR). In certain embodiments, the pathogen is fluoroquinolone resistant (FR), [00301] In certain embodiments, the bacteria is selected from Enterococcus faecium, Staphlococcus aureus, Klebsiella pneumonia, Acinetohacter haumannu, Pseudomonas aeruginosa, and Enter obacteria.
[00302] In certain embodiments, the bacteria has an efflux {e.g., mef, msr) genotype. In certain embodiments, the bacteria has a methylase {e.g., erm) genotype. In a particular embodiment, the bacteria has an ArmA genotype. In a particular embodiment, the bacterial infection is associated with bacteria expressing ribosomal methylase ArmA, In certain embodiments, the bacteria has a constitutive genotype. In certain embodiments, the bacteria has an inducible genotype.
[00303] Exemplary bacterial infections include, but are not limited to, infections with a Gram positive bacteria {e.g., of the phylum Actinobacteria, phylum Firmicutes, or phylum Tenericutes); Gram negative bacteria {e.g., of the phylum Aquifieae, phylum Deinococcus- Thermus, phylum Fibrobacteres/Chlorobi/Bacteroidetes (FCB), phyium Fusobacteria, phyium Gemraatimonadest, phylum Ntrospirae, phylum Planctomycetes/Verrucomicrobia/Chlamydiae (PVC), phylum Proteobacteria, phylum Spirochaetes, or phylum Synergistetes); or other bacteria {e.g., of the phyium Acidobacteria, phylum Chlroflexi, phylum Chrystiogenetes, phylum Cyanobacteria, phylum Deferrubacteres, phylum Dictyoglomi, phylum Thermodesuifobacteria, or phylum Thermotogae).
[00304] In certain embodiments, the bacterial infection is an infection with a Gram positive bacteria. In certain embodiments, the Gram positive bacteria is a bacteria of the phylum Firmicutes,
[00305] In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Enterococcus, i.e., the bacterial infection is an Enterococcus infection. Exemplary Enter ococci bacteria include, but are not limited to, E. avium, E. durans, E. fa.eca.lis, E. faecium, E. gallinarum, E. solitarius, /·„'. casseliflavus, and /.'. raffmosus.
[00306] In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Staphylococcus, i.e., the bacterial infection is a Staphylococcus infection. Exemplary Staphylococci bacteria include, but are not limited to, . arlettae, S. aureus, S. auricularis, S. capitis, S. caprae, S. carnous, S. chromogenes, S. cohii, S. condimenti, S. croceolyticus, S. delphini, S. devriesei, S. epidermis, S. equorum, S. felis, S. fluroettii, S. gallinarum., S. haemolyticus, S. hominis, S. hyicus, S. intermedins, S. kloosii, S. leei, S. lenus, S. lugdunesis, S. lutrae, S. lyticcms, S. massiliensis, S. microti, S. muscae, S. nepalensis, S. pasteuri, S. pentlenkoferi, S. piscifermentans, S. psuedointermedius, S. psudolugdensis, S. pulvereri, S. rosiri, S. saccharolyticus, S. saprophytics, S. schleiferi, S. sciuri, S. simiae, S. simulans, S. stepanovicii, S. s ccinus, S, vitulinus, S. w rneri, and S, xylosus. In certain embodiments, the Siaphylococcus infection is an S. aureus infection. In certain embodiments, the S. aureus has an efflux (e.g., mef, msr) genotype. In certain embodiments, the S. aureus has a methylase (e.g., erm) genotype.
[00307] In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Bacillus, i.e., the bacterial infection is a Bacillus infection. Exemplary Bacillus bacteria include, but are not limited to, B. alcalophilus, B. alvei, B. aminovorans, B. amyloliquefaciens, B. aneurinolyticus, B. anihracis, B. aquaemaris, B. atrophaeus, B. horoniphilus, B. brevis, B. caldolyticus, B. cenirosporus, B. cereus, B. circulans, B. coagulans, B. firmus, B. flavothermus, B. fusiformis, B. glohigii, B. infernus, B. larvae, B. laterosporus, B. lentiis, B. licheniformis, B. megaterium, B. mesentericus, B. mucilaginosus, B. mycoides, B. natto, B. pantothenticus, B. polymyxa, B. pseudoanihracis, B. pumilus, B. schlegelii, B. sphaericus, B. sporothermodurans, B. stearothermophilus, B. suhtilis, B. thermoglucosidasius, B. thuringiensis, B. vulgatis, and B. weihenstephanensis . In certain embodiments, the Bacillus infection is a B. subtilis infection. In certain embodiments, the B. subtilis has an efflux (e.g., mef, msr) genotype. In certain embodiments, the B. subtilis has a methylase (e.g., erm) genotype.
[00308] In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Streptococcus, i.e., the bacterial infection is a Strepococctis infection. Exemplar}' Streptococcus bacteria include, but are not limited to, S. agalactiae, S. anginosus, S. bovis, S. can is, S. constellatus, S. dysgalactiae , S. equinus, S. iniae, S. intermedins, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. per or is, S. pneumoniae, S. pyogenes, S. ratii, S. salivarius, S. thennophilus, S. sanguinis, S. sobrinus, S. suis, S. uberis, S. vestibularis, S. viridans, and S. zooepidemicus. In certain embodiments, the Strepococcus infection is an S. pyogenes infection. In certain embodiments, the Strepococcus infection is an .V. pneumoniae infection. In certain embodiments, the S. pneumoniae has an efflux (e.g., mef, msr) genotype. In certain embodiments, the S. pneumoniae has a methylase (e.g. , erm) genotype.
[00309] In certain embodiments, the bacterial infection is an infection with a Gram negative bacteria. o ozn [00310] In certain embodiments, the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Escherichia, i.e., the bacterial infection is an Escherichia infection. Exemplary Escherichia bacteria include, but are not limited to, E. alhertii, E. blattae, E. coli, E. fergusonii, E. hermannii, and E. vulneris. In certain embodiments, the Escherichia infection is an E. coli infection.
[00311] In certain embodiments, the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Haemophilus, i.e., the bacterial infection is an Haemophilus infection. Exemplary Haemophilus bacteria include, but are not limited to, H. aegyptius, H. aphrophilus, H. avium, //. ducreyi, //. felis, //. haemoiyticus, H. influenzae, H. parainfluenzae, H. paracuniculus, H. parahaemolyticus, H. pittmaniae, Haemophilus segnis, and / . so nus. In certain embodiments, the Haemophilus infection is an //, influenzae infection.
[00312] In certain embodiments, the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Acinetobacter . i.e., the bacterial infection is an Acinetobacter infection. Exemplary Acinetobacter bacteria include, but are not limited to, A. haurnanii, A. haemoiyticus, and A. Iwoffii. In certain embodiments, the Acinetobacter infection is an A. haurnanii infection.
[00313] In certain embodiments, the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Klebsiella, i.e., the bacterial infection is a Klebsiella infection. Exemplar}- Klebsiella bacteria include, but are not limited to, K granulomatis, K, oxytoca, K. michiganensis, K. pneumoniae, K. quasi pneumoniae, and K. variicola. In certain embodiments, the Klebsiella infection is a K. pneumoniae infection.
[00314] In certain embodiments, the Gram negative bacteria is a bacteria of the phylum Proteobacteria and the genus Pseudomonas. i.e., the bacterial infection is a Pseudomonas infection. Exemplary Pseudomonas bacteria include, but are not limited to, P. aeruginosa, P. oryzihabitans, P. plecoglissicida, P. syringae, P. putida, and P. fluoroscen . In certain embodiments, the Pseudomonas infection is a P. aeruginosa infection.
[00315] In certain embodiments, the bacteria is an atypical bacteria, i.e., are neither Gram positive nor Gram negative.
[00316] The antibiotic activity of synthetic gentamicin Cia (FSA-38219) and the three C6'~ modified analogs was evaluated, along with gentamicin C complex, against a panel of Gram- positive and Gram-negative strains. Both diastereomers of C6'-hydroxymethyl gentamicin (FSA- 38240 and FSA-38255) exhibited comparable activity as synthetic gentamicin Ci?. (FSA-38219) with minor improvement against a clinical strain of E. coli resistant to fluoroquinolones. The C6!-tetrasuhstituted structural analog FSA-382S2 showed inferior activity compared to gentamicin but was nevertheless active against wild-type Gram-positive and Gram-negative bacteria. See Figure 38,
EXAMPLES
General Experimental Procedures
[00317] All reactions were performed in round-bottom flasks fitted with rubber septa under a positive pressure of argon or nitrogen, unless otherwise noted. Air- and moisture-sensitive liquids were transferred via syringe or stainless-steel cannula. Organic solutions were concentrated by rotary evaporation (house vacuum, ca. 25-40 torr) at ambient temperature, unless otherwise noted. Analytical thin-layer chromatography (TLC) was performed using glass plates pre-coated with silica gel (0,25 mm, 60 A pore-size, 230-400 mesh, Merck KGA) impregnated with a fluorescent indicator (254 nm). TLC plates were visualized by exposure to ultraviolet light, then were stained with an aqueous sulfuric acid solution of eerie ammonium molybdate (CAM), or an aqueous sodium carbonate solution of potassium permanganate ( Mn04), then briefly heated on a hot plate. Flash-column chromatography was performed as described by Still et ai., employing silica gel (60 A, 32-63 uM, standard grade, Dynamic Adsorbents, Inc.).
[00318] The Minimum Inhibitor}' Concentrations (MICs) for both test articles and control articles were performed in accordance with guidelines of the Clinical Laboratory Standards Institute (CLSI) for broth microdilution susceptibility testing (reference: Clinical and Laboratory Standards Institute. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically— Tenth Edition: Approved Standard M07-A10. CLSI, Wayne, PA, USA, 2015). S. aureus strains ATCC 29213 and E. coli strain ATCC 25922 were purchased from American Type Culture Collection (ATCC). All other strains were supplied by Macrolide Pharmaceuticals. Materials
[00319] Dry solvents were purchased from the Aldrich Chemical Company in Sure/SealTM glass bottles and used without purification. All reagents were purchased and used without purification with the following exceptions: benzaldehyde, 3-methyl-2-butenal, trimethylsilyi chloride, trifluoromethanesulfonic anhydride, and trimethylsilyi trifluoromethanesulfonate were distilled under an atmosphere of argon. Benzyl bromide and methyl iodide were filtered neat through a column of oven-dried basic alumina immediately prior to use.
Instrumentation
[00320] Proton magnetic resonance (!H NMR) spectra were recorded on Varian INOVA 500 (500 MHz) or 600 (600 MHz) NMR spectrometers at 23 °C. Proton chemical shifts are expressed in parts per million (ppm, δ scale) and are referenced to residual protium in the NMR solvent (CHC13, δ 7.26; D2HCOD: δ 3 ,31), Data are represented as follows; chemical shift, integration, multiplicity (s = singlet, d = doublet, t = triplet q = quartet, m = muitiplet and/or multiple resonances, br = broad, app = apparent), and coupling constant (J) in Hertz. Carbon nuclear magnetic resonance spectra (1JC NMR) were recorded on a Varian INOVA 500 (125 MHz) NMR spectrometer at 23 °C. Carbon chemical shifts are expressed in parts per million (ppm, δ scale) and are referenced to the carbon resonances of the NMR solvent (CDCb, δ 77.0; CD3OD, δ 49.0). Infrared (IR) spectra were obtained using a Shimadzu 8400S FT-IR spectrometer and were referenced to a polystyrene standard. Data are represented as follows: frequency of absorption (cm"1), intensity of absorption (s = strong, m = medium, w = weak, br = broad).
Synthesis O vervie w
[00321] Preparation of Compound 1 : l-N-4-amino-2-hydroxybutanoyl-gentamicin Cla (1- HABA-gentamicin Cia): The synthetic route to a representative target, l-N-4-amino-2- hydroxybutanoyl-gentamiciti Cia ( 1 -H AB A-gentamicin Cia, 1), is shown in Figure 18. The aminoglycoside scaffold is assembled through two convergent coupling reactions of three components (2-4), which proceeds from the glvcosyl donor 3 (a purpurosamine derivative) and the glvcosyl acceptor 4 (an orthogonally protected 2-deoxystreptamine). The first glycosylation reaction forges the C4-C1' bond and affords the glycoside 140 in 43% yield. Alternative conditions are shown in Figure 19. The p-methoxybenzyl groups on the CI amine are then cleaved (CAN), and the resulting primary amine is coupled with the activated 4-amino-2- hydroxybutanoic acid (HABA) sidechain 5 to provide the glycoside 141 in 62% yield over two steps. Unveiling the diol functional group in 141 (TFA, 83%) gives the glycosyl acceptor 139, which undergoes the second convergent coupling with the glycosyl donor 2 (a garosamine derivative) to furnish the fully protected aminoglycoside 138 in 37% yield. A one-step hydrogenolytic deprotection in the presence of palladium hydroxide affords a fully synthetic aminoglycoside (1) in a total of six steps.
[00322] The feasibility and diversifiable nature of the disclosed synthetic strategy is demonstrated in the syntheses of gentamicin itself and three new aminoglycoside antibiotics (Figure 21). In this case, 3 is used as the purpurosamine component, and 50, prepared similarly as 2 {vide infra), serves as the garosamine component. The simplified 2-deoxystreptamine derivative 118 is employed as the glycosyl acceptor. The coupling of 118 with the purpurosamine component 3 is best achieved by the combination of l -(phenylsulfinyl)piperidine (43), and Tf20. The a anomer of the product diazide 147 is isolated as the major product (α:β = 3: 1) in 61% yield. Both the methoxymethyl ether and the acetate ester are cleaved in the presence of methanolic hydrochloric acid to give the diol 148 in 80% yield. Formation of the C6-C1" glycosidic bond occurs through the coupling of 148 with the activated garosamine 50 to provide the glycoside 149 as a mixture of anomers (α:β = 4: 1), which is separated by reverse- phase HPLC to give the pure anomer of 149 in 58% yield. The diversifiable nitro group in 149 now serves as a branching point for introduction of diversity at the C6' position. Specifically, treatment of a solution of 149 with potassium carbonate and aqueous formaldehyde leads to partial conversion of the starting material to afford the nitroaldol adduct 150 as a mixture of C6! diastereomers in 59% yield (dr = 1 : 1). Unreacted 149 is isolated in 10% yield, as well as the diol 151 (18%). The diastereomers of the Henry adduct 150 can be separated by reverse-phase HPLC, and both can be deprotected in two steps (Pd(OH)2, Hz, then NaOH) to give aminoglycoside antibiotic candidates FSA-38240 and FSA-38255. Similarly, the gentamicin derivative FSA- 38252 is obtained in two steps from the diol 151, while deprotection of 149 provides gentamicin Cia (FSA-38219). Overall, the synthesis of gentamicin Cla (FSA-38219) proceeds in five steps and 16% yield from 3 and 118, The structures of the three synthetic derivatives prepared herein deviate from the gentamicin Cia scaffold by the hydroxymethyl groups at the C6' position, which would be difficult to access via semisynthetic modifications of gentamicin itself.
[00323] Garosamme Compounds 2 and 50: Garosamine is an amino sugar that is biosynthetically derived from xylose (Figure 3). It is a component of the gentamicin and sisomicin classes of aminoglycosides (Figure 22), and its unique C- and N-methylation patterns improve the antibiotic activities of gentamicin and sisomicin, relative to kanamycin, against bacteria carrying aminoglycoside modifying enzymes (AMEs). Compared to ring I of the aminoglycosides, few medicinal chemical modifications have been made to the garosamine subunit (ring III). The recently identified ribosome methyltransferase, ArmA, selectively inactivates 4,6-disubsituted aminoglycosides by methylation of the N7 amine of G1405, which introduces steric and electronic repulsions with the garosamine sugar. The efficient synthesis of garosamine described herein allows systematic investigations of the carbohydrate scaffold. Intermediates in the synthesis are amenable to late-stage diversification, particularly at the C3"~ amino group, providing access to compounds capable of overcoming resistance to bacteria expressing ArmA, among other resistance phenotypes.
[00324] The syntheses of compounds 2 and 50 are achieved through the union of two building blocks. First, a highly diastereoselective nitroaldol coupling reaction of the building blocks 6 and 7 has enabled the synthesis of the glycosyl donors 2 and 50. As shown in Figure 23, the coupling of 6 and 7 affords the nitroaldol adduct 42 in 77% yield and >10: 1 diastereoselectivity. Alternative conditions are shown in Figure 24. The nitro group in 42 is then reduced to an amine (Pd(OH)2, 1 1 <), which gives 47 after benzyl ether formation. The protecting groups in 47 (Boc, acetonide, and the JV,O-acetal) are cleaved by heating in a solution of hydrochloric acid. Subsequent transformation to the phenyl thiogiycoside 48 proceeds in 77% yield over two steps. The thiogiycoside 48 serves as a branching point for the syntheses of glycosyl donors 2 and 50. A one-pot reductive ami nation with benzaldehyde, then formaldehyde, affords the amino alcohol 51 (77%), which is converted to the glycosyl donor 2 in 99% yield (LiHMDS, CbzCl). The alternative glycosyl donor 50 is prepared by first treatment of 48 with phosgene (79%), followed by methylation of the carbamate in 86% yield (Mel, NaH). The route to 2 and 50 proceeds in a total of seven steps, which is shorter and higher yielding than all previous syntheses of garosamine derivatives. In addition, all prior syntheses of activated garosamine derivatives use carbohydrates as starting materials, which inherently limit the positions available for modification and do not offer any distinct advantage over semi synthesis. In contrast, the present approach allows flexible access to the entire scaffold of 2. In particular, late-stage modifications of the C3 "-amino group provides access to analogs with activity against bacteria expressing the ribosomal methylase ArmA, which confers pan-resi stance to all aminoglycosides, including the next-generation aminoglycoside, plazomicin, by introducing steric and/or electrostatic repulsion near the C3 " amine binding site.
[00325] The large-scale preparations of the building blocks 6 and 7 are depicted in Figure 25 , The synthesis of 6 begins with an enantioselective Henry reaction of nitromethane (11) and ethyl pyruvate, catalyzed by the cinchona alkaloid 28, to give the adduct 29 in 93% yield and 96% ee. The ester in 29 is then reduced to afford diol 23 (72%), which is transformed to the acetonide 6 in 95% yield. The aldehyde 7 can be obtained by the condensation of (l S,2R)~(+)-norephedrine with 3-methyl-2-butenal followed by treatment of the resulting imine (without purification) with di-tert-butyl di carbonate (92%). The olefin is then cleaved through ozonolysis to provide the norephedrine oxazoiine 7 in 76%> yield. Notably, while norephedrine has been used in diastereoselective conjugate addition and carbonyl addition reactions, the coupling of 6 and 7 represents the first example of a diastereoselective intermolecular nitroaldol reaction using norephedrine as the auxiliary.
[00326] Purpurosamine Compound 3: Purpurosamines A-C are the ring-I amino sugars in gentamicin C complex, a clinically important antibiotic (Figure 26). They are present in gentamicins Ci, i, and Cia, respectively, and differ in the methylation patterns at the C6' position and C6'-amino group (aminoglycoside numbering). As a part of a conserved 2- deoxystreptamine-glucosamine motif in aminoglycoside natural products, purpurosamine plays a key role in the recognition and binding of gentamicin to the bacterial ribosome. Biosynthetically, it is derived from glucose, and distinguishes itself from other glucosamine components (ring I) in aminoglycosides by a lack of hydroxyl ations at the C3' and C4' positions. The widespread dissemination of APH(3') and ANT(4'), enzymes which inactivate aminoglycosides by phosphorylation and adenylation of the C3'~ and C4'-hydroxyl groups, has rendered aminoglycoside antibiotics such as kanamycin clinically obsolete. Gentamicin is the most commonly prescribed aminoglycoside due to its inherent immunity to the actions of these two prevalent resistance mechanisms. [00327] Because the ring I of aminoglycosides engages in key hydrogen-bonding interactions with the bacterial ribosome, efforts have been undertaken to probe the structure-activity relationship of glucosamine and its derivatives. Due to their inherent limitations, semisynthetic modifications of ring I have primarily been restricted to heteroatom deletion and interconversion. The efficient synthesis of purpurosarnine described herein allows systematic investigation of the carbohydrate scaffold at positions previously inaccessible through semi synthesis.
[00328] Referring to Figure 27, to prepare the component 3, the building block azido aldehyde 24 is obtained in three steps from D-glutamic acid. First, glutamic acid is converted to its dimethyl ester (TMSC1 in methanol), which is transformed to the azide 87 in 86% yield by the treatment of trifluoromethanesulfonyl azide. Regioselective reduction of the less hindered methyl ester (DIBAL-FI) affords 10, which undergoes a convergent, diastereoselective coupling with nitromethane (11) in 83% yield. Diastereoselectivity of the nitroaldol addition to set the C5' stereocenter (>15: 1 dr) is achieved through the use of the chirai diamine ligand 86. Partial reduction of the methyl ester in 81 (D1BAL-H), followed by spontaneous intramolecular cyclization leads to the formation of the nitropurpurosamine derivative 80 in 88% yield. The anomeric position of 80 was then activated by transformation to the corresponding phenyl thioglycoside 3, which is isolated in 94% yield. The disclosed synthetic approach allows opportunities for modifications of the entire scaffold of component 3, i.e., through alkylations of the intermediate 87 at the C3' and C4' positions. In addition, masking of the C6' amine as a nitro group permits late-stage introduction of diversity at the C6' position, as shown in Figure 21. Because enzymatic modification of the C6' amino group is a common and widespread mechanism of bacterial resistance to aminoglycosides, the disclosed fully synthetic route could give rise to new C6'-modified analogs with activity against multi drug-resistant bacteria.
[00329] 2-Deoxystreptamine Compound 4 and Differentially Protected 2-Deoxystreptamines: 2-Deoxystreptamine is a conserved structural motif in the 4,5- and 4,6-disubstituted aminoglycoside antibiotics (Figure 28). Together with the ring I hexose, 2-deoxystreptamine engages in key stabilizing interactions with the RNA bases in the bacterial ribosome. Because of its relevance in ribosome recognition, minor perturbations to the 2-deoxystreptamine structure have been shown to greatly influence both the antibiotic property and the safety profile of the resulting analogs. [00330] Several resistance mechanisms target polar functional groups on 2- deoxystreptamine for enzymatic modification. In particular, a family of aminoglycoside acetyltransferases, the AAC(3) enzymes, are widely found in Gram-negative bacteria, and inactivate all aminoglycosides currently in clinical use by acylating the C3 -amino group. The most recently approved next-generation aminoglycoside, plazomicin, has only limited activity (MIC = 8 ^ig/niL) against P. aeruginosa carrying the aac(3) gene. Because the C3 amine plays an important role in the binding of aminoglycosides to the ribosome, attempts to overcome the action of the AAC(3) enzyme by derivatization of the C3 amine through semisynthesis have resulted in complete loss of antibiotic activity.
[00331] Compound 4, an orthogonally protected 2-deoxystreptamine, is a conserved structural motif in all clinically relevant aminoglycoside antibiotics. Currently, the primary source of 2-deoxystreptamine for synthetic and biological studies is the degradation of naturally occurring aminoglycosides to give /Me.so-2-deoxystreptamine, which is enantiomerically enriched through enzymatic resolution. The fully synthetic approach is depicted in Figure 29 and begins with the protected dimethyl tartrate 8. Desymmetrization of 8 is achieved by its convergent coupling with the lithiated ethyl vinyl ether (9) to give the vinyl ketone 121 in 73% yield. The hvdroxyester 122 is obtained by Luche reduction of 122, which installs the C4 stereocenter in 60% yield and >20: 1 diastereoselectivity. Mitsunobu inversion of the C4 hydroxyl group proceeds in 78% yield with benzoic acid as the nucleophiie to afford the allylic benzoate 126. Partial reduction of the methyl ester in 126 and cleavage of the benzoate ester occurs in one pot (DIBAL-H) and the resulting crude hydroxyaldehyde is treated with bis(p-methoxybenzyl)amine and ytterbium trifluoromethanesulfonate to provide the all trans-6,6-bicycie 119 (35%) as a single diastereomer. The diethyl ketal 127 and the mixed benzyl ethyl ketal 128 are also isolated in 10% and 9% yield, respectively, which can be hvdrolyzed with hydrochloric acid in acetone to afford the amino ketone 119 in 68% yield. Together, the reduction-Mannich cyclization sequence from 126 provides the ketone 119 in two steps and 48% yield. Finally, the C3 amine can be installed in a three-step sequence in 58% overall yield: Formation of the methyl oxime of 119, which is reduced in a mixture of lithium aluminum hydride and sodium methoxide (5: 1 dr), followed by transformation of the amine 36 to the corresponding azide 4. The synthesis of component 4 described here is the shortest and most efficient synthesis of an orthogonally protected 2-deoxystreptamine. A notable feature of the disclosed synthesis is the differentiation of the CI and the C3 amino groups, which allows regioselective introduction of the HABA sidechain at any stage of the disclosed synthetic route, a significant advantage over all prior syntheses of aminoglycoside antibiotics. In addition, the ketone 119 is a strategic intermediate that offers opportunity for denvatization of the C3 position, which has been inaccessible through semi synthesis. This is particularly important owing to the widespread resistance caused by enzymatic modification of the C3 amine (The most recently approved next-generation aminoglycoside, plazomicin, has only limited activity (MIC = 8 g/niL) against P. aeruginosa carrying this resistance mechanism).
[00332] Preparation of the 4-Amino-2-Hydroxyaminobutyric Acid (HABA) Sidechain and Synthesis of the 2-Deoxystreptamine Glycosyl Acceptor 137: The synthesis of an activated HAB A sidechain followed preparations of similar compounds in the literature (Figure 30). First, the terminal amine in (S)-2-hydroxy-4-aminobutyric acid (132) was converted to an azide functional group. The resulting hydroxyacid (not shown) was benzylated to give 133 in 49% over 2 steps. The benzyl ester in 133 was then hydrolyzed to give the acid 134, which was coupled with N-hydroxysuccinimide to afford the HABA sidechain coupling partner 5 in 94% yield.
[00333] To explore the giycosylation reaction with the purpurosamine glycosyl donor 3, an alternative 2-deoxystreptamine glycosyl acceptor was prepared, which incorporated the HABA chain (Figure 31). Treatment of the azido alcohol 4 with eerie ammonium nitrate (CAN) at 23 °C led to the formation of the p-methoxybenzyl imine 135, which underwent in situ transimination with hydroxylamine to give 136. Coupling of 136 with the activated HABA sidechain 5 then afforded the 2-deoxystreptamine glycosyl acceptor 137 in 56% yield over two steps.
Synthesis of Gentamicin Cia and Late-Stage Modifications of the C 6' Position
[00334] Prior to the completion of the fully synthetic route to 1 -HAB A-gentamiein Cia (1), conditions for the glycosidic couplings of activated garosamine and purpurosamine components were explored using the 2-deoxystreptamine glycosyl acceptor 118, prepared in six steps through semisynthesis (Figure 39). The coupling of 118 with the purpurosamine component 3 was best achieved by the treatment of a solution of 3 and l-(phenylsulfinyl)piperidine with triiluoromethanesulfonic anhydride at -78 °C followed by the addition of the glycosyl acceptor 118 (Figure 32). The a anomer of the product diazide 147 was isolated as the major product (α:β = 3 : 1) in 61% yield after purification by column chromatography. Both the methoxymethyl ether and the acetate ester could be cleaved in the presence of methanolic hydrochloric acid to give the diol 148 in 80% yield. Formation of the C6-C 1" giycosidic bond occurred through the coupling of 148 with the activated garosamine 50 to provide the glycoside 149 as a mixture of anomers (α:β = 4: 1 ), which was separated by reverse-phase HPLC to give the pure a anomer of 149 in 58% yield. It should be noted that the glycosyl donor 50 was preferred in the preparation of 149, as an analogous coupling reaction between the garosamine glycosyl donor 2 and the diol 148 provided the corresponding glycosylation product 152 in only 43% yield, and 1 : 1 diastereoselectivity (α:β = 1 : 1). Subsequently, a two-step deprotection sequence, which involved first hydrogenation of 149 followed by hydrolysis of the intermediate carbamate, completed the component-based approach to gentamicin Cia (FSA-38219). Overall, the synthesis of gentamicin Cia proceeded in five steps and 16% yield from the glycosyl donor 3 and the semisynthetic glycosyl acceptor 118.
[00335] The diversifiable nitro group at the C6' position of 149 offered opportunities for the introduction of structural diversity at a late stage. To demonstrate the feasibility of the approach, three C6'-modified gentamicin derivatives were prepared from the glycoside 149 (Figure 33).
[00336] Treatment of a solution of 149 in tetrahydrofuran with potassium carbonate and aqueous formaldehyde (5.00 equiv) at 23 °C led to partial conversion of the starting material to afford the nitroaldol adduct 150 as a mixture of C6' diastereomers in 59% yield (dr = 1 : 1) after purification by column chromatography. Unreacted 149 was isolated in 10% yield, as well as a small amount (18%) of the diol 151. The diastereomers of the Henry adduct 150 could be separated by reverse- phase HPLC, and both could be deprotected in two steps to give aminoglycoside antibiotic candidates FSA-38240 and FSA-38255. Similarly, the gentamicin derivative FSA-38252 was obtained in two steps from the diol 151. The structures of the three synthetic derivatives prepared herein deviate from the gentamicin Cia scaffold by the hydroxymethyl groups at the C6' position, which would be difficult to access via semisynthetic modifications of gentamicin itself.
Figure imgf000095_0001
[00337] Example 1, Ethyl 2-hydroxy-2-methyl-3-nitropropanoate (29)
Synthesis of (±)-29: triethyianiine (2.50 mL, 17.9 mmol, 0.20 equiv) was added to a solution of nitrom ethane (48.3 mL, 896 mmol, 10.0 equiv) and ethyl pyruvate ( 10 mL, 90.0 mmol, 1 equiv) in dichloromethane (90.0 mL) at 23 °C. The resulting yellow solution was stirred for 2 h and then concentrated to give a yellow oil. The crude reaction mixture was purified by flash-column chromatography ( 100% dichloromethane initially, grading to 3% ethyl ether-dichloromethane), affording (±)-ethyl 2-hydroxy-2-methyl-3-nitropropanoate (29, 103.4 g, 93%) as a clear and colorless oil.
Synthesis of (R)-29: Cinchona alkaloid catalyst 28 (13.0 g, 31.4 mmol, 0.050 equiv) was dissolved in dichloromethane (500 mL) and the resulting solution was cooled to an internal temperature of -20 °C using a -25 °C cooling bath. Nitromethane (11, 338 mL, 6.27 mol, 10.0 equiv) was then added. The addition was quantitated with dichloromethane (100 mL). After the internal temperature of the reaction has stabilized at -20 °C, ethyl pyruvate (70.0 mL, 627 mmol, I equiv) was added dropwise via a dropping funnel over 30 min while maintaining the internal temperature below -18 °C. The addition was quantitated with dichloromethane (27.0 mL). The resulting solution was stirred at -20 °C. After 2 h, white precipitate appeared. The resulting heterogeneous mixture was stirred at -20 °C for an additional 12 h, at which point the reaction had become homogeneous and analysis by thin-layer chromatography indicated full consumption of the ethyl pyruvate starting material. The crude reaction mixture was concentrated and then re- dissolved in ethyl acetate (1 L). The organic layer was washed with 1 M aqueous hydrochloric acid (2 x 500 mL). The aqueous layers were combined and was saturated with sodium chloride. The combined aqueous layers were back-extracted with ethyl acetate (3 x 500 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to afford (i )-ethyl 2-hydroxy-2-methyl-3- nitropropanoate (29, 103.4 g, 93%) as a yellow oil, which was used in the next step without further purification. The enantiomeric ratio of the product was determined to be 98:2 by HPLC analysis (Chiralcei AS-H, 95:5 hexane:isopropanol, 1 mL/min, λ = 210 nm, tii (minor) = 20.6 min, ti (major) =:: 24.9 min).
Figure imgf000096_0001
[00338] Example 2. (R)-2-methyl-3-nitropropane-l,2-diol (23)
A solution of the nitroester 29 (1.1.3 g, 64.0 mmol, 1 equiv) in tetrahydrofuran (213 mL) was added dropwise over 90 min via dropping funnel to a solution of lithium borohydnde (2.00 M, 6.40 mL, 12.8 mmol, 0.20 equiv) and borane-tetrahydrofuran (1.00 M, 77.0 mL, 77.0 mmol, 1.20 equiv) in tetrahydrofuran (110 mL) at 23 °C. The temperature of the solution was maintained at 23 °C with the use of a 23 °C cooling bath. The addition was quantitated with tetrahydrofuran (13.0 mL). The resulting solution was stirred at 23 °C for 12 h, at which point methanol (1.55 mL, 38.4 mmol, 0.60 equiv) was added. The resulting solution was stirred at 23 °C for an addition 8 h. Residual borane was then quenched by the addition of a solution of /?- toluenesuifonic acid monohydrate (2.43 g, 12.8 mmol, 0.20 equiv) in methanol (50.0 mL). The resulting solution was concentrated to give a clear oil. Methanol ( 100 ml.) was added to the crude reaction mixture and the resulting solution was concentrated again. This process was repeated a total of three times to allow the full conversion of borane to trimethyl borate. The crude reaction mixture was then purified by flash-column chromatography (2% methanol- dichloromethane initially, grading to 6% methanol-dichloromethane), affording (R)-2-methyl-3- nitropropane-l ,2-diol (23, 7.63 g, 76%) as a clear and colorless oil, which solidified to give a white waxy solid upon refrigeration at -20 °C. The enantiomeric ratio of the product was determined to be 98:2 by HPLC analysis (Chiralcei AD-H, 90: 10 hexane:isopropanol, 1 mL/min, λ = 210 nm, tR (minor) = 17.7 min, tR (major) = 20.9 min).
TLC (5% methanol-dichloromethane): Rf 0.24 (UV, KMn04).
!! f NMR (500 MHz, CDCta), δ: 4.61 (d, J = 1 1.7 Hz, 1 1 1, O2NCH2), 4.47 (d, J = 1 1.6 Hz, 1 1 1, O2NCH2), 3.58 (s, M l CH2OH, OH), 2.94 (s, 1H, OH), 1.30 (s, 3H, CH2CCH3).
13C NMR (125 MHz, CDCb), δ: 81.5, 72.2, 67.6, 21.8. FTIR (neat), cm-1 : 3399 (br), 2984 (w), 2943 (w), 2361 (m), 2342 (m), 1545 (s), 1379 (m), 1225 (w), 1128 (w), 1049 (s), 920 (m), 806 (m), 741 (m), 627 (m).
Figure imgf000097_0001
0 aC, 95%
95% ee
[00339] Example 3. (R)-nitroacetonide 6
(R)-2-methyl-3-nitropropane-l,2-diol (23, 2,80 g, 20.7 mmol, 1 equiv) was dissolved in acetone (207 mL). The resulting clear and colorless solution was cooled to 0 °C. ?-Toluenesulfonic acid monohydrate (197 mg, 1.04 mmol, 0.050 equiv) was then added in one portion. 2,2- Dimethoxypropane (25.5 mL, 207 mmol, 10.0 equiv) was then added dropwise. The resulting solution was stirred at 0 °C for 3 h, whereupon tnethylamine (0.159 mL, 1.14 mmol, 0.055 equiv) was added dropwise. The resulting solution was concentrated. The crude product was purified by flash-column chromatography (1% ethyl ether-hexanes initially, grading to 10% ethyl ether-hexanes), affording (R)-2,2,4-trimethyl-4-(nitromethyl)-l ,3-dioxolane (6, 3,45 g, 95%) as a clear and colorless oil (volatile), which solidified to give a white waxy solid upon refrigeration at -20 °C. The enantiomeric ratio of the product was determined to be 97.5:2.5 by HPLC analysis (Chiralcel AD-H, 95:5 hexane:isopropanol, 1 mL/min, λ = 210 nm, tR (minor) = 6.2 min, tR (major) = 7.0 min).
TLC (25% ethyl ether-hexanes): Rr 0,26 (UV, Mn04).
¾ vlR (500 MHz, CDCI3), δ: 4.47 (d, J = 11.2 Hz, 1H, CH2NO2), 4.43 (d, J = 11.2 Hz, 1H,
CH2NO2), 4,25 (d, J = 9,4 Hz, l it CH2O), 3.83 (d, J = 9.3 Hz, 1H, CH2O), 1 .46 (s, 3H,
O2NCH2CCH3), 1.42 (s, 3H, ΟΓίΠΙΙ }, 1.40 (s, 3H, OCiC'f ! ;},:}.
-(. NMR (125 MHz, CDCb), δ: 110,6, 81 ,3, 78.5, 72.2, 27.0, 26.1, 22.4,
FTiR (neat), cm"1 : 2988 (m), 2938 (w), 2880 (w), 1551 (s), 1480 (w), 1456 (w), 1428 (w), 1380
(s), 1284 (w), 1243 (s), 1216 (s), 1155 (m), 1118 (s), 1060 (s), 1016 (w), 977 (m), 902 (m), 851
(m), 816 (m), 652 (m), 520 (m).
HRMS (APCI): Caicd for
Figure imgf000097_0002
176.0917. Found: 176,0918.
Figure imgf000098_0001
[00340] Example 4, Norephedrine oxazoline 41
(lS,2R)-Norephedrine (3.00 g, 19.8 mmol, 1 equiv) was suspended in dichlorom ethane (40.0 rnL) at 23 °C. 3 -Methyl -2-butenal (1.91 mL, 19.8 mmol, 1.00 equiv) was then added dropwise to give a clear and colorless solution. After stirring at 23 °C for 10 min, the solution turned cloudy. The resulting cloudy solution was stirred for an additional 20 min, at which point sodium sulfate (10 g) was added. The dried solution was fi ltered and the filtrate was concentrated to give a clear and colorless oil. The crude oil was dissolved in dichloromethane (40.0 mL) at 23 °C. Oi-tert- butyl-di carbonate (5.07 mL, 21 .8 mmol, 1 . 10 equiv) was then added dropwise. The resulting solution was stirred at 23 °C for 2.5 h, at which point analysis of an aliquot of the solution by ¾ NMR shows complete conversion to the product. The reaction solution was then concentrated to give a pale yellow oil. The crude product was purified by flash-column chromatography (4% ethyl ether-hexanes + 1% triethylamine initially, grading to 10% ethyl ether-hexanes + 1% triethylamine), affording norephedrine oxazoline 41 as a clear and colorless oil (5.79 g, 92%). TLC (10% ethyl ether-hexanes + 1% triethylamine): Rf = 0.29 (UV, KMn04).
fTi NMR (25 : 1 ratio of C3-epimers, asteri sk (*) denotes minor epimer, 500 MHz, CDCI 3), δ:
7.36-7.30 (m, 4H, ArH), 7.30-7.26 (m, 1H, ArH), 5.75 (br-s, 1H, BocNCHO), 5.44-5.37* (m, H i ), 5.33-5.27* (m, l i s ), 5, 1 8 (dq, J - 8,5, 1 ,5 Hz, I I I , CI ί (Π ΐ ), 5,06 (d, J = 5, 5 Hz, l it OCHPh), 4.22 (br-s, 1H, B0CNCHCH3), 1.84 (s, 3H, CH=(CH3)2), 1.81 (d, J = 1.5 Hz, 3H, (Ί I (Π ί Κ 1.46 (s, 9H, Γ(Π ! ), 0.82 (d, J = 6.7 Hz, 3H, BocNCHCH3).
13C MR (125 MHz, CDCb), δ: 152.7, 138.5, 136.4, 128.1, 127.5, 126.1, 124.1, 84.6, 80.8, 79.7, 55.7, 28.4, 25.9, 18.1 , 15.9.
FTIR (neat), cm"1: 2978 (m), 2361 (m), 2350 (m), 1694 (s), 1478 (w), 1454 (m), 1398 (s), 1375 (s), 1366 (s), 1306 (w), 1280 (w), 1 175 (m), 1017 (s), 909 (s), 706 (s), 646 (m).
HRMS (ESI): Calcd for (Ο ι 318.2064. Found: 318,2068.
Figure imgf000099_0001
[00341] Example 5. Norephedrine oxazoline aldehyde 7
Sudan III (5 rag) was added to a solution of norephedrine oxazoline 41 (5.69 g, 17.9 mmol, 1 equiv) in a mixture of acetone (170 mL) and water (9.00 mi). The resulting pink solution was cooled to -78 °C. After stirring for 10 min at -78 °C, a stream of ozone was passed through the solution via a glass pipette. After about 30 min, the pink color disappeared and the solution turned pale blue. The ozone stream was stopped, and nitrogen was bubbled through the solution until the blue color dissipated. The resulting colorless solution was then warmed to 23 °C and concentrated to a final volume of ~20 mL. The bright yellow solution was poured into a mixture of ethyl ether (300 mL) and half saturated aqueous sodium chloride solution (300 mL). The layers were separated and the aqueous layer was extracted with ethyl ether (3 x 200 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil. The crude product was purified by flash-column chromatography (5% ethyl ether-hexanes initially, grading to 40% ethyl ether-hexanes) to give norephedrine oxazoline aldehyde 7 as a clear and colorless oil (3.98 g, 76%, 90% purity). The aldehyde 7 was used in the subsequent coupling reaction without further purification.
Figure imgf000099_0002
2
12] Example 6. Nitroalcohol 42
Nitroacetonide 6 (1.20 g, 6.83 mmol, 1 equiv) and norephedrine oxazoline aldehyde 7 (3.98 g, 13.7 mmol 2.00 equiv) were dissolved in tetrahydrofuran (68.3 mL). The resulting solution was cooled to -20 °C. A solution of potassium ter -butoxide in tetrahydrofuran (1.0 M, 0.410 mL, 0.410 mmol, 0.06 equiv) was added dropwise by syringe. The resulting solution was stirred at - 20 °C for 30 min. Saturated aqueous ammonium chloride solution (50 mL) and ethyl ether (100 mL) were then added and the resulting mixture was wanned to 23 °C. The layers were separated and the aqueous layer was extracted with ethyl ether (3 x 100 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl ether-hexanes initially, then grading to 30% ethyl ether-hexanes) to provide pure nitroalcohol 42 as a white foam (2.47 g, 77%).
TLC (30% ethyl ether-hexanes): Rr 0,34 (UV, Mn04).
¾ NMR (500 MHz, CDCta), δ: 7.38-7.32 (m, 2H, ArH), 7.32-7.28 (m, 1H, ArH), 7.24 (m, 2H, ArH), 5.64 (br-s, 1 1 1, OH), 5.43 (d, J = 6,5 Hz, 1H, BocNCHO), 5.14 (d, J = 5.7 Hz, 1 1 1.
OCHPh), 5.05 (br-s, 1H, CHNO2), 4.35 (d, J = 9.6 Hz, 1H, CH2O), 4.27 (m, 2H, HOCH, BocNCHCHs), 3.99 (d, J = 9,6 Hz, H i, ( 1■()).. 1.62 (s, 31 L O2NCHCCH3), 1 ,50 (s, 91 1.
C(CH3», 1.46 (s, 3H, OC(CH3 .), 1.40 (s, 31 1, OC(CH3)?.), 0,80 (d, J = 6,7 Hz, 3H,
BocNCHCH.).
! T N.MR ( 125 MHz, CDCh), δ: 155.5, 135.2, 128.3, 128.0, 125.9, 109.8, 89.2, 89.0, 82.2, 81.4, 80.8, 73.4, 73.1, 56.3, 28.3, 26.9, 26.6, 22.9, 16.4.
FTIR (neat), cm-1: 3283 (br), 2984 (s), 2935 (w), 2877 (w), 1698 (m), 1663 (s), 1552 (s), 1479 (w), 1455 (m), 1411 (s), 1381 (s), 1370 (s), 1336 (w), 1276 (w), 1254 (m), 1200 (m), 1 165 (s), 1 1 10 (s), 1060 (s), 986 (m), 852 (m), 755 (s), 706 (s).
Hi MS (ESI): Calcd for (C. l h iN OxNa) " : 489.2207. Found: 489.2185.
Figure imgf000100_0001
42
[00343] Example 7. Enantiomeric excess determination of nitroalcohol 22
To determine the enantiomeric excess of nitroalcohol 42, aqueous hydrogen chloride (2.00 M, 7,50 mL, 15.0 mmol, 7.0 equiv) was added to a solution of 42 (1.00 g, 2, 14 mmol, 1 equiv) in a mixture of dioxane (20.0 mL) and water (12.5 mL) at 23 °C. The flask was then immersed in an oil bath preheated to 55 °C, After 15 h, the heating bath was removed and the solution was allowed to cool to 23 °C. The cooled solution was concentrated under reduced pressure. The residue was purified by flash-column chromatography on silica gel (2% methanol- dichloromethane initially, then grading to 7% methanoi-diehloromethane) to provide nitrogarosamine 22 as a white foam (1 : 1 ratio of α:β anomers, 340 mg, 82%), The enantiomeric ratio of the product was determined to be >99: 1 by HPLC analysis (Chiralpak 1C, 85 : 15 hexane:isopropanol, 1 mL/min, λ = 210 nm, tR (a anomer, major) = 1 1.2 min, tR (a anomer, minor) = 13.3 min, tR (β anomer, minor) = 17.4 min), tR (β, anomer, major) = 20.0 min).
β-22: !H MR (500 Mi l/. CD3OD), δ: 4.49 (d, J = 10.5 Hz, 1H, ¾»), 4.48 (d, J = 7.8 Hz, 1 H, Hi-), 4.16 (dd, J = 10.5, 7,8 Hz, 111 H2"), 3.65 (d, J = 12.4 Hz, H I , Hs"), 3.54 (d, J = 12.4 Hz, i l l
Figure imgf000101_0001
α-22: Ή N\ IR (500 MHz, CD3OD), δ: 5.19 (d, J = 3.9 Hz, 1H, Hi-), 4,69 (d, J = 10.7 Hz, I I I, ft-), 4.45 (dd, J = 10,5, 3 ,5 Hz, 111 1 l.r), 3.93 (d, J = 12.1 Hz, 111 Hs-), 3.32 (d, J = 12. 1 Hz, i l l
Figure imgf000101_0002
Figure imgf000101_0003
42 41
[00344] Example 8. Amino alcohol 46
Palladium hydroxide on carbon (20 wt%, 269 mg, 0.383 mmol) was added in one portion to a solution of nitroalcohol 42 (1 ,79 g, 3.83 mmol, 1 equiv) and acetic acid (2, 19 mL, 38.3 mmol , 10.0 equiv) in methanol (70.9 ml) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 aim) for 10 min. The heterogeneous mixture was stirred at 23 °C for 24 h. Excess hydrogen was then removed by flushing with argon (1 aim) for 10 min. The resulting htereogeneous mixture was filtered through a plug of Celite© and the filter cake was washed with methanol (20 mL). The filtrate was concentrated to afford amino alcohol 46 (1.66 g, 99%) as a white foam, which was used directly in the next step without further purification.
TLC (5% methanoi-diehloromethane): .r 0.51 (UV, KM1 O4).
¾ NMR (500 MHz, CDCb), δ: 7.37-7.3 1 (m, 2H, ArH), 7.31-7.23 (m, 3H, ArH), 5.33-5.25 (m, 1 Π , BocNCHO), 5.10 (d, J = 5 ,7 Hz, 1H, OCHPh), 4.25 (br-s, i l l BocNCHCH3), 4,22 (d, J 0,0 Hz, 1H, CH2O), 3.98 (br-s, 1H, HOCH), 3.72 (d, J = 8.9 Hz, 1H, CH2O), 3.29 (d, J = 1.2 Hz, I H, H2NCH), 1.50 (s, 9H, Π( Ί ί ). 1 .46 (s, 3H, ΟΠΠ Ι ψ ), 1.43 (s, 3H, Οί ϊΠ ! = 1.39 (s, 3H, H2NCHCCH3), 0.77 (d, J = 6.7 Hz, 3H, BocNCHCH3).
°C NMR (125 MHz, CDCI3), δ: 155.4, 135.7, 128.3, 127.8, 125.9, 108.6, 89.7, 83.7, 81.7, 80.9, 74.4, 71.6, 56.1 (H2NC, BocNCHCHs), 28.4, 27.3, 26.9, 22.8, 16.3.
FTIR (neat), cm"1: 3340 (br), 2980 (s), 2933 (m), 2873 (m), 1697 (s), 1664 (s), 1479 (w), 1455 (m), 1409 (s), 1378 (s), 1368 (s), 1277 (w), 1255 (m), 1206 (s), 1 167 (s), 1 103 (s), 1051 (s), 1031 (w), 1033 (m), 985 (m), 852 (m), 756 (s), 706 (s).
HRMS (ESI): Calcd for (C -Ί f -X -{),, ) : 437.2646. Found: 437.2667
Figure imgf000102_0001
[00345] Example 9. Amino benzyl ether 47
Sodium hydride (60% dispersion in mineral oi l, 0.300 g, 7.49 mmol, 2.00 equiv) was added in one portion to a solution of amino alcohol 46 (1.63 g, 3.74 mmol, 1 equiv) in dimethylformamide (37.4 mL) at 0 °C. The resulting suspension was stirred for 10 min. Benzyl bromide (0.980 mL, 8.24 mmol, 2.20 equiv) was then added dropwise. The reaction mixture was stirred at 0 °C for 2 h. Saturated aqueous ammonium chloride solution (20 mL) was added, and the resulting suspension was warmed to 23 °C. Ethyl acetate (200 mL) and half-saturated aqueous ammonium chloride (200 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 200 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (1% ethyl acetate-hexanes initially, then grading to 40% ethyl acetate-hexanes) to provide pure amino benzyl ether 47 as a white foam (1.64 g, 83%).
TLC (40% ethyl acetate-hexanes): \ 0.29 (UV, K M11O 1 ).
ί NMR (500 MHz, CDCI3), 6: 7.41-7.30 (m, 6H, ArH), 7.30-7.25 (m, 4H, ArH), 5.49 (s, IH, BocNCHO), 5,06 (d, J - 5.9 Hz, IH, OCHPh), 4.97 (br-s, H, OCH2Ph), 4.68 (br-s, i l l.
OCHzPh), 4.40 (br-s, I H, CHOBn), 4.32-4.20 (br-s, I H, BocNCHCHs), 4.25 (d, J = 8.7 Hz, IH, CH2O), 3.73 (hr-s. I ! L CH2O), 3.10 (s, i l l. CHNH2), 1 .53 (s, 9H, C(CH3)3), 1.39 (s, 3H, (>C((' l h ).·. ). 1.34 (s, 3H, OC(CI-l3)2), 1.28 (s, 3H, H2NCHCCH3), 0.87 (d, J = 6.7 Hz, 3H, BocNCHCHs).
13C MR (125 MHz, CDC ), δ: 153.8, 138.3, 135.6, 128.3, 128.2, 127.8, 127.4, 127.3, 126.0, 109. 1 , 89.6, 82.8, 81 ,4, 80,8, 75 ,9, 74,2, 72.0, 56.4, 55.5, 28.4, 27.1, 27.0, 20.5, 16.9.
FTIR (neat), cm4: 2979 (m), 2933 (m), 2871 (m), 1698 (s), 1605 (w), 1455 (m), 1368 (s), 1278 (w), 1255 (m), 1203 (w), 1 170 (m), 1 102 (s), 1056 (s), 1029 (s), 997 (m), 885 (m), 858 (m), 751 (s), 704 (s).
FIRMS (ESI): Calcd for (θ3θΗ43Ν2θβ)+: 527,31 16, Found: 527.3098.
Figure imgf000103_0001
47 S1
[00346] Example 10. Phenyl thioglycoside 48
To a solution of amino benzyl ether 47 (650 rng, 1.23 mmol, I equiv) in dioxane (10.8 mL) and water (2.50 mL) at 23 °C was added aqueous hydrogen chloride (2.00 M, 4.32 mL, 8.64 mmol, 7.00 equiv). The flask was then immersed in an oil bath preheated to 55 °C. After 15 h, the heating bath was removed and the solution was allowed to cool to 23 °C. The cooled solution was concentrated under reduced pressure. The crude reaction mixture was dried to afford a 1 : 1 mixture of glycoside S I and (lS,2R)-norephedrine as a white solid. The crude mixture was suspended in acetonitrile (24.7 mL). Thiophenol (0.445 mL, 4.32 mmol, 3.50 equiv) was then added. The resulting suspension was cooled to 0 °C. Trifluoromethanesulfonic acid (0,274 mL, 3.09 mmol, 2.50 equiv) was added dropwise, after which the suspension became a pale yellow homogeneous solution. Trimethylsilyl trifluoromethanesulfonate (1.12 mL, 6. 18 mmol, 5,00 equiv) was then added dropwise. The resulting yellow solution was stirred at 0 °C for 40 min. Saturated aqueous sodium bicarbonate solution (20 mL) and ethyl acetate (40 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 100 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (1 % methanoi-dichioromethane initially, then grading to 7% methanol -dichloromethane) to provide phenyl thioglycoside 48 as pale yellow oil (329 mg, 77% over two steps),
TLC (6% methanol-dichloromethane + 1% saturated aqueous ammonium hydroxide solution): Rf = 0.37 (UV, KMn04).
lH NMR (1 :2 ratio of α:β anomers, asterisk (*) denotes the minor a anomer, 500 MHz, CDCb), δ: 7.63-7.52 (m, 2H, ArH), 7.53-7.43* (m, 2H, ArH), 7.44-7.25 (m, 8H, ArH), 5.77* (d, J = 5.2 Hz, ! I ί CHSPh), 5.05 (d, J = 11.0 Hz, 1H, OCH2Ph), 4.76* (d, J = 11.2 Hz, 1 H, OCPfcPh), 4.69 (d, J = 9.3 Hz, 1H, CHSPh), 4.61 (d, J = 11.0 Hz, I I I. OCH2Ph), 4.47* (d, J = 1 1.2 Hz, 1H, ΟΠ I -Ph.), 4.12* (d, J = 12.5 Hz, H I, CH2O), 3.82* (dd, J - 10, 1 , 5,2 Hz, I I I, CHOBn) 3.81 (d, J = 12.3 Hz, 1H, CH2O), 3.55* (d, J = 12.5 Hz, I I I. CH2O), 3.38 (d, J = 12.2 Hz, I I I. CH2O), 3.35 (t, J = 9,2 Hz, I I I, CHOBn), 3.01 * (d, J = 10.1 Hz, i l l. CHNH2), 2,68 (d, J - 9.0 Hz, IH, CHNH2), 1 , 14* (s, 3H, CH3), 1.14 (s, 3H, CH3).
13C NMR (125 MHz, CDCb), δ: 137.8, 137.3*, 134.6*, 134.0, 131.3, 131.1 *, 128.9, 128.8*, 128.4, 128,4*, 128.1, 128.1 *, 127.9*, 127,9, 127.3, 126.8*, 89.1 , 86.8*, 79.7, 76,8*, 75, 1, 74.8, 71.6*, 70.5, 70.3*, 66.6*, 60.7, 55.4*, 22.6*, 21.8.
FTIR (neat), cm:1: 3363 (w), 3061 (w), 3031 (w), 2968 (w), 2862 (w), 1583 (m), 1496 (w), 1479 (m), 1454 (m), 1439 (m), 1374 (w), 1307 (w), 1266 (w), 1208 (w), 1064 (s), 1026 (m), 992 (wj, 952 (m), 911 (w), 883 (w), 822 (m), 736 (s), 691 (s), 643 (m), 629 (m).
HRMS (ESI): Calcd for (( :■»! h =NO = S) : 346.1471. Found: 346.1473.
Figure imgf000104_0001
p-49 a-4§
54% 25%
[00347] Example 11. Phenyl thioglycoside 49
A solution of phosgene in toluene (15 wt¾, 0.816 mL, 1.14 mmol, 1.20 equiv) was added dropwise to a solution of thioglycoside 48 (329 mg, 0.953 mmol, 1 equiv) and
diisopropylethylamine (0,499 mL, 2.86 mmol, 3.00 equiv) at -78 °C. The resulting solution was stirred for 30 min at -78 °C. Saturated aqueous sodium bicarbonate solution (20 mL) was added and the resulting heterogeneous mixture was warmed to 23 °C. Ethyl acetate (40 mL) was added. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 50 niL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash- column chromatography on silica gel (30% ethyl acetate-hexanes initially, then grading to 80% ethyl acetate-hexanes) to provide phenyl thioglycoside β-49 (189 mg, 54%) and a-49 (89.0 mg, 25%>) as white solids.
β-49: TLC (70% ethyl acetate-hexanes): Rf = 0.63 (UV, KMn04).
! ] [ NMR (500 MHz, CDCh), δ: 7.53-7.48 (ni, 2H, ArH), 7.43-7.28 (m, 8H, Ari l ), 5.1 5 (d, J 6.2 Hz, 1H, CHSPh), 4.97 (br-s, IH, H), 4.90 (d, J = 1 1.6 Hz, 1H, OCHzPh), 4.58 (d, J = 1 1.6 Hz, i l l OC! l -Ph 4.15 (d, J = 12.4 Hz, IH, CH20), 3.60 (d, J = 12.4 Hz, IH, CH2O), 3.60 (t, J 6.4 Hz, IH, CHOBn), 3.49 (dd, J = 6.6, 0.9 Hz, IH, CHNH), 1 .50 (s, 3H, CH3).
1 C NMR (125 MHz, CDCh), δ: 158.5, 137.2, 134,0, 131 ,7, 129.0, 128.6, 128.3, 128.0, 127,6,
86.3, 79.4, 78.5, 73.8, 66.8, 60.0, 23.9.
FTIR (neat), cm4: 1754 (s), 1275 (m), 1261 (m), 1069 (m), 1026 (w), 985 (w), 764 (s), 750 (s), 698 (m).
HRMS (ESI): Calcd for (0 <.,H.v \'O i S ) " : 372.1264. Found: 372.1284.
a-49: TLC (70% ethyl acetate-hexanes): 0.38 (UV, KMnO-s).
! ! f NMR (500 MHz, CDCh), 6: 7.55-7.46 (m, 2Ή, ArH), 7.39 (d, J = 4.4 Hz, 4H, ArH), 7.37- 7,22 (rn, 4H, ArH), 5.65 (d, J = 4.8 Hz, IH, CHSPh), 5 ,56 (br~s, I H, NH), 4.79 (d, J = 1 1 .3 Hz, IH, OCH2Ph), 4.58 (d, J = 1 1.3 Hz, I H, OCH2Ph), 4.13 (d, J = 13.0 Hz, IH, CH2O), 3.93 (t, J = 4.9 Hz, IH, CHOBn), 3.78 (d, J = 13.0 Hz, I H, CH2O), 3.66 (d, J = 4.8 Hz, I H, CHNH), 1.42 (s, 3H, CH3).
l3C NMR (125 MHz, CDCh), δ: 158.6, 136.8, 134.5, 131. 1, 129.0, 128.6, 128.4, 128.1, 127.2,
85.4, 80.9, 76.2, 74.1, 65.5, 57.3, 23.0.
FTIR (neat), cm"! : 3079 (w), 2978 (w), 2937 (w), 2864 (w), 1759 (s), 1602 (m), 1522 (s), 1454 (w), 1346 (s), 1258 (w), 1217 (w), 1 152 (w), 1 109 (m), 1060 (m), 1048 (m), 997 (m), 914 (rn), 858 (m), 840 (m), 763 (m), 731 (s).
HRMS (ESI): Calcd for (CioIfeNCUS)*: 372.1264. Found: 372. 1284.
Figure imgf000106_0001
■4 1!9
[00348] Example 12, β-Phenyl thioglycoside 50
Sodium hydride (60% dispersion in mineral oil, 22,2 mg, 0.555 mmol, 3.00 equiv) was added in one portion to a solution of β-phenyi thioglycoside 49 (68.7 mg, 0.185 mmol, 1 equiv) in dimethylformamide (3.70 mL) at 0 °C. The resulting suspension was stirred for 10 min.
Iodomethane (23.1 μ 0.370 mmol, 2.00 equiv) was then added dropwise. The reaction mixture was stirred at 0 °C for 0,5 h. Saturated aqueous ammonium chloride solution (2 mL) was added, and the resulting suspension was warmed to 23 °C. Ethyl acetate (30 mL) and ha if- saturated aqueous ammonium chloride (20 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (2 x 20 mL). The organic layers were combined. The combined solution was washed with half-saturated aqueous ammonium chloride (3 x 30 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 40% ethyl ether-hexanes) to provide pure thioglycoside β-50 as a white solid (61.3 mg, 86%).
LLC (40% ethyl acetate-hexanes): Rr 0.31 (UV, MnO i).
lH NMR (500 MHz, CDCI3), δ: 7.50-7.43 (m, 2H, ArH), 7.41-7.26 (m, 8H, ArH), 5.34 (d, J = 3 ,2, 1H, { 1 1 SPh), 4.84 (d, J = 1 1 .5 Hz, 1 H, OCifcPh), 4.55 (d, J = 11.6 Hz, 1H, OCH2Ph), 4, 17 (d, J = 12.2 Hz, 1 1 1, CH2O), 3.83 (dd, J = 4.0, 3.2 Hz, 1 1 1, CHOBn), 3.63 (d, J = 12.2 Hz, 1H, CH2O), 3,45 (dd, J = 3,9, 0,8 Hz, 1H, CHNCH3), 2.86 (s, 3H, NCH3), 1 ,53 (s, 31 1. CH3).
l3C NMR (125 MHz, CDCb), δ: 157.4, 136.8, 134.1 , 131.4, 129.0, 128.5, 128.2, 127.7, 127.6, 85,4, 75.8, 75.4, 72.8, 66.3, 64.0, 30.2, 23.9.
FTIR (neat), cm"1: 3061 (w), 2974 (w), 2876 (w), 1755 (s), 1584(w), 1427 (m), 1375 (m), 1 09
(s), 1088 (w), 1026 (s), 1001 (m), 739 (w), 692 (s), 677 (s).
HRMS (ESI): Calcd for (C2iH24N04S)+: 386.1421. Found: 386, 1422.
Figure imgf000107_0001
Example 13. a-Phenyl thioglycoside 50
Sodium hydride (60% dispersion in mineral oi l, 1.45 mg, 0,061 mmol, 3.00 equiv) was added in one portion to a solution of ot-phenyl thioglycoside 49 (7.50 mg, 0.020 mmol, 1 equiv) in dimethylformamide (455 μΐ,) at 0 °C. The resulting suspension was stirred for 10 min.
Iodomethane (2.53 μΕ, 0.040 mmol, 2.00 equiv) was then added dropwise. The reaction mixture was stirred at 0 °C for 0.5 h. Saturated aqueous ammonium chloride solution (2 mL) was added, and the resulting suspension was warmed to 23 °C, Ethyl acetate (10 mL) and half- saturated aqueous ammonium chloride (10 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (2 x 10 mL). The organic layers were combined. The combined solution was washed with half-saturated aqueous ammonium chloride (3 x 10 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 45% ethyl ether-hexanes) to provide pure thioglycoside a-50 as a white solid (6.90 mg, 89%).
TLC (45% ethyl acetate-hexanes): Rr 0.27 (UV, KMn04).
¾ NMR (500 MHz, CDCI3), δ: 7.54-7.47 (m, 2H, ArH), 7.43-7.33 (m, 41 1, ArH), 7.35-7.27 (m, 2I-I, ArH), 7.28-7.22 (m, 2H, ArH), 5.51 (d, J = 4,9 Hz, 1H, CHSPh), 4.84 (d, J = 1 1.3 Hz, i l l OCH2PI1), 4.61 (d, J ==: 1 1 .4 Hz, 11 1 OCH2PI1), 4. 1 (d, J = 12.9 Hz, i l l CH2O), 4.03 (t, J - 4.5 Hz, 1H, CHOBn), 3.73 (d, J = 12.8 Hz, 1H, CH2O), 3.40 (d, J = 4.1 Hz, 1H, CHNCH3), 2.80 (s, 3H, NCH3), 1.39 (s, 3H, CH3).
13C MR (125 MHz, CDCb), δ: 157.5, 136.6, 134.7, 130.9, 129.0, 128.7, 128.5, 128.4, 127.2, 85.4, 77.6, 74.4, 74.1 , 66.0, 62,3, 30, 1, 23 ,3.
FTIR (neat), cm4: 2925 (m), 2853 (wj, 1754 (s), 1584 (w), 1481 (w), 1454 (w), 1430 (m), 1405 ( m l 1378 (m), 1339 (w), 1296 (m), 1265 (rn), 1219 (m), 1 151 (m), 1 1 13 (s), 1087 (w), 1068 (s), 739 (s), 696 (s).
HRMS (ESI): Calcd for (O M I I. NO I S) " : 386.1421. Found: 386.1422.
Figure imgf000108_0001
ii-51 a-51
67% 20%
[00349] Example 14. Benzyl methylamine 51
Benzaldehyde (36.4 μΐ,, 35.9 mmol, 2.30 equiv) was added dropwise to a solution of
aminoalcohol 48 (53.9 mg, 0.156 mmol, 1 equiv) and acetic acid (89 μ]_, 1.56 mmol, 10.0 equiv) in dichloromethane (3 ,47 raL) and methanol (433 fiL) at 23 °C. Sodium cyanoborohydride (32.4 mg, 0.515 mmol, 3.30 equiv) was then added in one portion. The resulting solution was stirred for 1 h at 23 °C, at which point thin-layer chromatographic analysis indicated complete consumption of the starting aminoalcohol 48. A solution of formaldehyde in water (37 wt%, 58.1 μΐ , 0.780 mmol, 5,00 equiv) was then added, followed by another portion of sodium
cyanoborohydride (32.4 mg, 0.515 mmol, 3 ,30 equiv). The resulting solution was stirred for 40 min at 23 °C. Saturated aqueous sodium bicarbonate solution (10 mL), water (10 mL) and ethyl acetate (20 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (10% ethyl ether-hexanes initially, then grading to 50% ethyl ether-hexanes) to provide benzyl methylamine β-51 (40.2 mg, 57%) and a-51 (13.7 mg, 20%).
β-Sl: TLC (50° o ethyl ether-hexanes): Rf = 0.42 (UV, KMn04).
¾ NMR (500 MHz, CDCb), δ: 7.59-7.53 (m, 21 1. ArH), 7.51-7.46 (m, 2H, ArH), 7.42-7,36 (m, 2H, ArH), 7.35-7.26 (m, 81 1, ArH), 7.24-7.18 (m, ! l i. ArH), 5, 18 (d, J 10,3 Hz, I I I, OCPfcPh), 4,81 (d, J = 10.2 Hz, 1H, OCH2Ph), 4.73 (d, J = 9.2 Hz, 1H, CHSPh), 4.07 (d, J = 13.5 Hz, IH, NCFbPh), 3 ,97 (t, J = 9.6 Hz, ! I ! CHOBn), 3.83 (d, J = 13.5 Hz, I I I, NCH2Ph), 3.66 (d, J = 12.0 Hz, IH, CH2O), 3.35 (d, J = 11.9 Hz, IH, CH2O), 2.64 (d, J = 9.9 Hz, IH, CHNCHsBn), 2.55 (s, 3H, NC I ! :), 2. 1 1 (s, H, OH), 1.25 (s, 3H, CH3).
l3C NMR (125 MHz, CDCb), δ: 140.7, 138.3, 134.1 , 131.7, 129.0, 128.7, 128.4, 128.2, 128. 1 , 127.8, 127.5, 126.7, 90.9, 76.9, 76.6, 74,6, 73,6, 71 ,2, 62,3, 39,2, 22.4,
!· ] ]]< (neat), cm"1: 3488 (br), 3061 (w), 3028 (w), 2966 (w), 2927 (w), 2855 (w), 2795 (w), 2199 (w), 2027 (w), 1954 (w), 1879 (w), 181 1 (w), 1602 (w), 1584 (m), 1495 (w), 1479 (m), 1453 (m), 1440 (m), 1370 (w), 1355 (w), 1307 (w), 1276 (w), 11 1 1 (m), 1070 (s), 1027 (s), 1001 (m),
956 (ml 910 (m l 871 (m), 801 (m), 739 (s), 698 (s).
HRMS (ESI): Calcd for (C H ί ; ·Χί ) : 450.2097. Found: 450.2093.
a-51 : TLC (50% ethyl ether-hexanes): Rf = 0.23 (UV, KMn04).
!] [ NMR (500 MHz, CDCb), δ: 7.52-7.44 (m, 41 1, ArH), 7.41-7.28 (m, 8H, ArH), 7.28-7,21 (m, 3H, ArH), 5.95 (d, J = 5.3 Hz, 1H, CHSPh), 4.81 (d, J = 10.9 Hz, 1H, GCH2PI1), 4.56 (d, J = 10.9 Hz, ! I ί OCH2PI1), 4.43 (dd, J = 10.8, 5.3 Hz, i l l, CHOBn), 4.16 (d, J = 12.2 Hz, 1 1 1 CH2O), 4.03 (d, J = 13.5 Hz, 1H, NCH2PI1), 3.80 (d, J = 13.5 Hz, 1H, NCH2PI1), 3.42 (d, J = 12.2 Hz, 1H, CH2O), 2,78 (d, J - 10,9 Hz, 111 CHNCH3Bn), 2,49 (s, 3H, NCH3), 1.96 (s, H I, OH), 1.27 (s, 3H, CHs).
l3C NMR (125 M! I/., CDCb), δ: 140,6, 137.7, 134.6, 131.4, 128,9, 128,7, 128.4, 128.2, 128.1, 127.8, 127.0, 126.7, 88.3, 74.9, 74.9, 70.8, 69,2, 65,7, 62,3, 39,4, 22.9.
FTIR (neat), cm"1: 3464 (br), 3061 (w), 3028 (w), 2924 (s), 2853 (s), 2798 (w), 2178 (w), 1967 (w), 1585 (w), 1495 (m), 1480 (m), 1454 (s), 1439 (s), 1365 (m), 1315 (m), 1280 (m), 1 103 (w), 1064 (s), 1027 (s), 951 (s), 762 (w), 736 (s), 698 (s),
HRMS (ESI): Calcd for ( C H h S ) : 450,2097, Found: 450.2093.
Figure imgf000109_0001
[00350] Example 15. Thioglycoside β-2
A solution of lithium hexamethyldisilazane in toluene (1.0 M, 153 μΐ.,, 15.3 rnmol, 2.10 equiv) was added drop wise to a solution of aminoalcohol β-51 (32.7 mg, 0.073 mmol, 1 equiv) at 0 °C. The resulting solution was warmed to 23 °C and stirred for 30 min. Benzyl chloroformate (20.8 μΐ.., 14.5 mmol, 2.00 equiv) was then added dropwise. The resulting solution was stirred for 40 min at 23 °C. Saturated aqueous ammonium chloride solution (10 mL) and ethyl acetate (20 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl ether-hexanes initially, then grading to 20% ethyl ether-hexanes) to provide thioglycoside β-2 (42.1 mg, 99%). TLC (20% ethyl ether - hexanes): Rr 0.33 (UV).
'■\ \ NMR (600 MHz, CDCb), δ: 7,56-7,50 (m, 211 ArH), 7.49-7.44 (m, 21 L Aril), 7.41-7.30 (m, 7H, ArH), 7.30-7.24 (m, 5H, ArH), 7.23-7.20 (m, 41 1, ArH), 5.17 id, j 10.5 Hz, 1H, QCHiPh), 5.13 (d, J = 9.0 Hz, 2H, OCH2PI1), 4.80 (d, J = 12.9 Hz, 1H, CH2O), 4.71 (d, J = 10.2 Hz, 1H, OCH2Ph), 4.70 (d, J ==: 9.0 Hz, 1H, CHSPh), 4, 14 (t, J = 9.5 Hz, 1 1 1. CHOBn), 4.06 (br-s, 1H, NCH2PI1), 3.77 (br-s, 1H, NCH2PI1), 3.23 (d, J = 12.9 Hz, i l l. CH2O), 2.64 (d, J = 9.9 Hz, i l l CHNCH3B1 ), 2.50 ( s. 3H, NCH3), 1.56 (s, 3H, { ! ! .).
13C MR (125 MHz, CDCb), δ: 153.1, 140.5, 138.3, 135.4, 134.2, 131.2, 128.9, 128.8, 128.5, 128.3, 128,3, 128, 1, 128.0, 128.90, 127.7, 127,2, 126.7, 90.6, 86.1, 75.6, 73.5, 72.4, 70.9, 68.8, 18.4. 13C signals corresponding to NCHVPh and NCH3 were not visible due to broadening.
FTIR (neat), cm'1: 3063 (w), 3032 (w), 2938 (w), 2853 (w), 1742 (s), 1496 (w), 1454 (m), 1280 (w), 1287 (s), 1252 (s), 1 196 (m), 1078 (s), 1027 (m), 960 (w), 867 (w), 848 (w), 788 (w), 741 (s), 697 (s).
HRMS (ESI): Calcd for (CssHseNOsS)*: 584.2465. Found: 584,2464.
Figure imgf000110_0001
[00351] Example 16. Thioglycoside a-2
A solution of lithium hexamethyldisilazane in toluene (1.0 M, 64.0 μί, 0.064 mmol, 2.10 equiv) was added dropwise to a solution of aminoalcohol a-51 (13.7 mg, 0.030 mmol, 1 equiv) at 0 °C. The resulting solution was warmed to 23 °C and stirred for 15 min. Benzyl chloroformate (8.70 μΐ.., 0,061 mmol, 2.00 equiv) was then added dropwise. The resulting solution was stirred for 20 min at 23 °C. Saturated aqueous ammonium chloride solution (10 mL) and ethyl acetate (20 niL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl ether-hexanes initially, then grading to 20% ethyl ether-hexanes) to provide thioglycoside β-2 (15.0 mg, 84%). a-2: TLC (20% ethyl ether-hexanes): R,- 0,40 (UV). lH NMR (600 MHz, CDCI3), δ: 7.53-7.43 (m, 4H, ArH), 7.43-7.16 (m, 16H, ArH), 5.94 (d, J = 4,9 Hz, I I I, CHSPh), 5.13 (d, J = 12.2 Hz, i l l OCHiPh), 5.06 (d, J = 12.3 Hz, H i, OCH2P 1), 4.82 (d, J = 10.7 Hz, 1H), OCH2Ph, 4.59-4.46 (m, 3H, OCH2PI , CHOBn, CH2O), 4.01 (d, J = 13.0 Hz, 1H, CH2O), 4.01 (br-s, IH, NCH2PI1), 3.80 (br-s, 1H, NCH2PI1), 2.80 (d, J = 10.7, IH, CHNCHsBn), 2,49 (s, 3H, NCH3), 1.57 (s. M l CH3).
1 :C W !R ( 125 X !i !z, CDCI3), δ: 153.2, 140.7, 137.8, 135.5, 134.3, 131.7, 129.1, 128.9, 128.5, 128.4, 128.3, 128.1 , 128.0, 128,0, 127.8, 127.1, 126.7, 88.4, 87.0, 74.7, 70.9, 68.8, 66,5, 63,3, 18.4, 13C signals corresponding to NCH2Ph and NCH3 were not visible due to broadening.
FTIR (neat), cm'1: 3031 (w), 2937 (w), 2878 (w), 2859 (w), 2220 (w), 2155 (w), 2147 (w), 2042 (w), 2032 (w), 1978 (w), 1958 (w), 1742 (s), 1454 (m), 1381 (m), 1300 (m), 1252 (s), 1198 (w), 1075 (s), 1027 (m), 947 (m), 738 (s), 698 (s).
HRMS (ESI): Calcd for (CssHseNOsS)*: 584.2465. Found: 584.2464.
Figure imgf000111_0001
D-gluiamic acid
0 °C, 86%
[00352] Example 17. (R)-dimethyl 2-azidopentanedioate (87)
To a suspension of D-glutamic acid (5.00 g, 34.0 mmol, 1 equiv) in methanol (89.0 mL) at 0 °C was added freshly distilled trimethylsiiyl chloride (19.1 mL, 150 mmol, 4.40 equiv) dropwise over 5 min. After the addition was complete, the mixture was allowed to warm to 23 °C to afford a clear solution. After stirring for 17 h at 23 °C, the reaction mixture was concentrated and dried under high vacuum for 2 h. The resulting sticky oil was dissolve in water (44.0 mL) and cooled to 0 °C. Sodium bicarbonate (11.4 g, 221 mmol, 4.00 equiv) and copper(II) sulfate pentahydrate (424 nig, 1.70 mmol, 0.05 equiv) were added in sequence. The resulting suspension was diluted with methanol (295 mL) and a freshly prepared solution of trifluoromethanesulfonyl azide (1.0 M in toluene, 74.8 mL, 74.8 mmol, 2.20 equiv) was added dropwise over 10 min to give a green emulsion. The ice bath was then removed. After stirring for 2,5 h at 23 °C, a saturated aqueous solution of ammonium chloride (30 mL) was added. The resulting suspension was concentrated under reduced pressure. The residual blue mixture was diluted with water (20 mL) and extracted with ethyl acetate (3 χ 50 mL), The combined organic layers were washed sequentially with 1 M aqueous hydrochloric acid (60 mL), a half saturated aqueous solution of sodium chloride (60 mL) and dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a yellow oil, which was purified by flash-column chromatography on silica gel (15% acetone in hexanes) to afford (i?)-dimethyl 2-azidopentanedioate (87, 5.90 g, 86%) as a light yellow oil.
lH NMR (500 MHz, CDCI3), δ: 4.01 (dd, J = 8.7, 5.1 Hz, 1H, Hr), 3.80 (s, 3H, OCH3), 3.69 (s, 3H, OCH3), 2.46 (td, J - 7, 1 , 6.5, 2.2 Hz, 2H, l ! r), 2 1 8 (did, J = 14.2, 7.6, 5.1 Hz, ! I ! ¾■), 2.01 (dddd, J = 14.1 , 8.7, 7.5, 6.5 Hz, 1 H, i ).
1 C NMR (125 MHz, CDCh), δ: 172.6 (Cr), 170.4 ((». 61.0 ((». 52,7 (OCH3), 51 ,8 (OCH3), 29.8 (C r), 26.5 (C3-).
FTIR (neat), cm"1: 2956, 21 10, 1739, 1438, 1259, 1207, 1 174, 1062, 1020, 987,
HRMS (ESI): Calcd for (0-l l i i \' <O i\'a) " : 224.0642, Found: 224.0667.
Figure imgf000112_0001
Example 18. (R)-methyl 2-azido-5-oxopentanoate (10)
To a stirring solution of the diester 87 (120 mg, 0.596 mmol, 1 equiv) in ethyl ether (6.00 mL) at -78 °C was added diisobutylaluminum hydride (1 .0 M in toluene, 716 |jL, 716 mmol, 1.20 equiv) dropwise over 3 min. After stirring for 1 h at -78 °C, water (0.200 mL) was added and the resulting suspension was allowed to warm to 23 °C under vigorous stirring to afford an opaque gel . The mixture was dried over magnesium sulfate and the resulting white suspension was filtered over Celite®. The filtrate was concentrate and the cmde oil was purified by flash-column chromatography on silica gel (20% ethyl ether-hexanes initially, then grading to 50% ethyl ether-hexanes) to afford (R)-methyl 2-azido-5-oxopentanoate (10) as a colorless volatile liquid (69.5 mg, 68%).
lH NMR (600 MHz, CDCh), δ: 9.75 (d, J = 1.0 Hz, 1H, ¾■), 3.99 (dd, J = 8.4, 5.2 Hz, 1H, Hr), 3.78 (s, 3H, OCH3), 2.61 (tt, J = 7.3, 1. 1 Hz, 2H, I ί r), 2.17 (dtd, J = 14.5, 7.3, 5.2 Hz, i l l. Hr), 2,06-1 ,92 ins. 1 H, I I ;·). l3C NMR (125 MHz, CDCh), δ: 200.1 (C5'), 170.3 (Cr), 60.9 (C?.'), 52.7 (OCH3), 39.5 (Cr), 23.7 CO. ).
!· ] ]]< (neat), cm"1: 2959, 2849, 2731, 2360, 2341, 21 10, 1743, 1724, 1439, 1260, 1207, 1179, 999, 667.
HRMS (ESI): Calcd for (Cd-feNsNaOsf: 194,0536, Found: 194,0543,
Figure imgf000113_0001
[00353] Example 19. Nitroalcohol 81
To a blue suspension of copper(II) chloride di hydrate ( 102 mg, 0.599 mmol, 0.050 equiv) in tetrahydrofuran (60.0 ml.) was added the chiral diamine ligand 86 (142 mg, 0,599 mmol, 0.050 equiv). The resulting green solution was stirred for 1 h at 23 °C and then cooled to 0 °C, A solution of the aldehyde 10 (2.05 g, 12.0 mmol, 1 equiv) in tetrahydrofuran (6.00 mL) was added. Diisopropylethylamine (2,09 mL, 12.0 mmol, 1.00 equiv) and nitromethane (11, 6,46 mL, 120 mmol, 10.0 equiv) were then added sequentially. The reaction was stirred for 18 h at 0 C'C. A saturated aqueous solution of ammonium chloride (40 mL) and 0.01 M aqueous hydrochloric acid (50 mL) were added. The layers were separated. The pH of the aqueous layer was adjusted to 3 by the dropwise addition of 2 M aqueous hydrochloric acid whereupon the color of the aqueous layer changed from green to yellow. The aqueous layer was extracted with
dichloromethane (4 χ 50 mL) and the combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude reaction mixture was purified by flash-column chromatography on silica gel (15% ethyl acetate-hexanes initially, then grading to 45% ethyl acetate-hexanes) to afford the nitroalcohol 81 as a yellow oil (2,31 g, 83%).
¾ NMR. (600 MHz, CDCh), δ: 4,47-4,32 (m, 3H, 1 b: He'), 4.00 (dd, J = 8.4, 4.9 Hz, i l l. llr), 3.82 (s, 3H, OCH3), 2.12 (ddt, J = 14.9, 10.2, 5.3 Hz, 1H, Hi'), 1.84 (dddd, J = 13.9, 9.7, 8.5, 5.6 Hz, H i, t-Iv), 1.70 - 1.57 (m, 2H, M i ).
I l l l3C NMR (125 MHz, CDCh), δ: 170.5 (Cr), 80.3 (CV), 68.0 (C.v), 61.7 (C?), 52.8 (OCH3), 29.5 (Ca 27.4 ((>)
M IR (neat), cm"1: 3514, 2959, 2108, 1742, 1555, 1439, 1381, 1253, 12 1, 1107, 1084, 1005, 887.
HRMS (ESI): Calcd for (C7Hi2N4NaOs)+: 255,0700. Found: 255,0729,
Figure imgf000114_0001
[00354] Example 20. Nitroglycoside 80
To a solution of the nitroalcohol 81 (1.68 g, 7.24 mmol, 1 equiv) in dichloromethane (72,4 mL) at - 78 °C was added dropwise diisobutylaluminum hydride (1.0 M in toluene, 17.4 mL, 17.4 mmol, 2.40 equiv) over 5 min. The resulting yellow solution was stirred for 3 h at -78 °C. Propionaldehyde (882 uL, 12.30 mmol, 1.70 equiv) was then added dropwise. After stirring for an additional 10 min at -78 °C, 1 M aqueous hydrochloric acid (20 mL) was added and the resulting mixture was allowed to warm to 23 °C. Water (40 mL) was added. The layers were separated and the aqueous layer was extracted with dichloromethane (3 χ 30 mL), The combined organic layers were washed with a saturated solution of sodium chloride (50 mL) and dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude reaction mixture was purified by flash-column chromatography on silica gel (10% ethyl acetate- hexanes initially, then grading to 30% ethyl acetate-hexanes) to afford the nitroglycoside 80 as a white solid (2:1 ratio of α:β anomers, 1.29 g, 88%).
lH NMR (2:1 ratio of α:β anomers, asterisk (*) denotes the minor β anomer, 600 MHz, CDCh), δ: 5.27 (d, J = 3.2 Hz, Hi, Π; }..4.75 (dddd, J = 12.1, 8.4, 3.9, 2.5 Hz, 11 L ¾■), 4.66 (d, J = 7.8 Hz, 1H, Hi-), 4.52 (dd, J = 12.9, 8.8 Hz, 111. He'*), 4.44-4.36 (m, 3H, Η6', H6', He'*), 4.30-4.25 (m, HI, ¾·*), 3,29-3,20 (m, 2H, 11··, ¾'*), 2.24-2.13 (m, 311.11 v, ¾·*, ¾'*), 1.98 (dq, J = 12.4, 4.0 Hz, 111. I i v).1.88 (dq, J = 13,4, 3,2 Hz, lit !ir), 1,79 - 1,74 (m, lit M ).1,59-1,45 (m, 2H, H4', H4'*).
13C NMR. (2:1 ratio of α:β anomers, asterisk (*) denotes the minor β anomer, 125 MHz, CDCh), δ: 97.9* (Cr), 91.8 (Cr), 78.7* (('.-, ).78.3 {(V).72.1* (Cs'), 65.1 ((' ·}.60.9* (C-), 57.5 (C2'), 27.3* (C.3'), 27.0 (Cr)..26.7* (Cvi 21.4(C3'). FTiR (neat), cm"1: 3454, 2941 , 2360, 2332, 2106, 1557, 1373, 1259, 1070, 1041 , 1014, 734. HRMS (ESI): Calcd for ( (V,l l i X iXaO .) ' : 225.0594. Found: 225.061 1.
Figure imgf000115_0001
94%. α:β = 2.5:1
80 3
[00355] Example 21. Phenyl thioglycoside 3
To a solution of the nitroglycoside 80 (1.25 g, 6.18 mmol, 1 equiv) in dichloromethane (124 mL) at 0 °C was added thiophenol (2.04 mL, 19,8 mmol, 3.20 equiv) and freshly distilled
trimethylsilyi trifluoromethanesulfonate (6,03 μΕ, 33.4 mmol, 5.40 equiv) sequentially. After stirring for 1.5 h at 0 °C, a saturated aqueous solution of sodium bicarbonate (10 mL) was added. The resulting mixture was poured into a saturated solution of sodium chloride (50 mL) and sodium bicarbonate (50 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (100 mL) and dichloromethane ( 100 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude reaction mixture was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 30% ethyl acetate-hexanes) to afford the
purpurosamiiie phenyl thioglycosyl donor 3 as a colorless oil (2,5 : 1 ratio of α:β anomers, 1 .72 g, 94%). The anomers could be partially separated by flash-column chromatography on silica gel (10% ethyl ether-hexanes initially, then grading to 50% ethyl ether-hexanes) to obtain small amounts of pure samples, which were used for characterization purposes.
a-3: ¾ NMR (500 MHz, CDCh), δ: 7.49-7.44 (m, 2H, ArH), 7.34-7.26 (m, 3H, ArH), 5,48 (dd, J = 4,9, 1 ,5 Hz, I I I, Hr), 5 , 1 -5.00 (m, 1H, Hs1), 4,52- 4.37 (m, 21 L I I,,·), 3.83 (dt, J = 12.0, 4.6 Hz, 1 H, ί i ··), 2, 10-2.01 (m. 1 1 1. ILr), 1 .99- 1 .86 (m, 2H, ILr, l l r). 1.66-1.52 (m, 1H, l l r) 13C NMR (125 MHz, CDCh), δ: 133.0, 132.7, 129.1, 127.9, 89.3, 78.5, 65.9, 58.5, 27.1, 24.3. HRMS (ESI): Calcd for (CuHu aChS)*: 317.0679. Found: 317.0656.
β-3: Ή NMR (500 MHz, CDCh), δ: 7.52-7.41 (m, 2H, ArH), 7.38-7.28 (m, 3H, ArH), 4.48 (d, J = 3 ,5 Hz, I I I, Hr), 4.45-4.33 (m, 2H, He), 4,30 (tq, J = 8.0, 3.6 Hz, 1 1 1 , ¾■), 3.68 (dt, J = 10. 1, 3.5 Hz, 1H, Hr), 2.20-2.06 (m, 1H, ¾■), 1.86 (dtd, J = 14.8, 10.2, 5. 1 Hz, 1 1 1. 1 1 ;·), 1.67 (ddt, J = 14.4, 9.4, 4.6 Hz, 1 1 L I i ,·), 1 .58-1.45 (m, i l l. 1 1 ,·).
1 C NMR (125 MHz, CDCh), δ: 133.2, 132,7, 129.3, 129.3, 80.3, 68.3, 65.3, 65.1, 30.5, 27.8. HRMS (ESI): Calcd for (C " : h :N iXaO ^S) : 317.0679. Found: 317.0656.
(+
Figure imgf000116_0001
[00356] Example 22. Diester 8
To a solution of (+)-dimethyl tartrate (8.00 g, 44.9 mmol, 1 equiv) in methanol (44.9 mL) was added sequentially 2,3-butanedione (4,73 mL, 53.9 mmol, 1.20 equiv), trimethylorthoformate (14.7 mL, 135 mmol, 3 ,00 equiv), and (±)-camphorsulfonic acid (1.04 g, 4.49 mmol, 0.10 equiv). The resulting light yel low solution was heated to 75 °C. After stirring for 21 hours at 75 °C, the dark brown reaction mixture was cooled to 23 °C. Sodium bicarbonate (7 g) was added. The resulting heterogeneous mixture was stirred for 1 h at 23 °C and then filtered. The filtrate was concentrated to give a brown oil. The residue was purified by flash-column chromatography on silica gel (10% ethyl ether-hexanes initially, then grading to 50% ethyl ether-hexanes) to provide the diester 8 (90% purity) as a yellow solid, which was dried on high vacuum for 3 h. The yellow solid was then triturated with 5% ethyl ether-hexanes to give pure 8 as a white solid (8.41 g, 64%).
Figure imgf000116_0002
[00357] Example 23, Vinyl ketone 121
Ethyl vinyl ether (9, 2.57 mL, 26.7 mmol, 2.60 equiv) was dissolved in tetrahydropyran (6. 1 mL) and the resulting solution was cooled to -78 °C. A titrated solution of t-butyl lithium in pentane (1.56 M, 13.2 mL, 20.5 mmol, 2.00 equiv) was added dropwise. The resulting light yellow slurry was stirred at -78 °C for 10 min and then warmed to 0 °C, at which point the reaction mixture became clear and colorless. After stirring at 0 °C for 30 min, the reaction mixture was cooled again to -78 °C, at which point tetrahydrofuran (21.0 mL) was added. A solution of the diester 8 (3.00 g, 10.3 mmol, 1 equiv) in tetrahydrofuran (5.00 mL) was then added dropwise. The addition was quantitated with tetrahydrofuran (5.00 mL). The resulting solution was stirred at -78 °C for 1 h. Aqueous dipotassium hydrogen phosphate buffer solution (pH 7.0, 0.2 M, 100 mL) and ethyl ether (100 mL) were added and the resulting mixture was allowed to warm to 23 °C. The pH of the aqueous layer was adjusted to 7 by the addition of 1 M aqueous hydrochloric acid. The layers were separated and the aqueous layer was extracted with ethyl ether (2 x 300 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 20% ethyl acetate-hexanes) to provide pure vinyl ketone 121 as a clear and colorless oil (2.49 g, 73%).
TLC (30% ethyl acetate-hexanes): Rf = 0.47 (UV, CAM).
f NMR (500 MHz, CDCh), δ: 5.3 1 (d, J = 2.6 Hz, i l l. Π b ); 5.12 (d, J = 10.0 Hz, 1 1 L OCHC(=0)), 4.67 (d, J = 10.0 Hz, 1H, ΟίΊ ίΠ ())()( ' ! h), 4.52 (d, J = 2.6 Hz, 1 H, =CH2), 3.88- 3.81 (m, 2H, OCH2CH3), 3.69 (s, 3H, CO2CH3), 3.38 (s, 3H, OCH3), 3.34 (s, 3H, OCH3), 1.37 (s, 3H, { ! ! .), 1 .37 (t, J = 7.0 Hz, 3H, OCH2CH3), 1 ,32 (s, 3H, CH3).
13C NMR (125 MHz, CDCh), δ: 191.8, 168.8, 156.4, 99.3, 99.2, 92.8, 68.3, 66.7, 63.9, 52.2, 48.6, 48.4, 17.5, 17.4, 14.3.
FTIR (neat), cm"1: 2993 (w), 2953 (m), 1739 (s), 1608 (m), 1441 (m), 1378 (m), 121 1 (m), 142 (s), 1 1 13 (s), 1034 (s), 889 (m),
HRM:S (ESI): Calcd for ((VI l - iOxNa ) " : 355.1363. Found: 355.1371.
Figure imgf000117_0001
[00358] Example 24. Allylic alcohol 122
Vinyl ketone 1.21 (494 mg, 1 .49 mmol, 1 equiv) was dissolved in methanol (21.2 mL) and the resulting solution was cooled to -40 °C. Cerium trichloride heptahydrate (609 mg, 1.64 mmol, 1.10 equiv) was added in one portion. Sodium borohydride (67.5 mg, 1.78 mmol, 1.20 equiv) was then added as a solid, in two portions. The resulting solution was stirred at -40 °C for 30 min and then warmed to 23 °C. After stirring at 23 °C for 5 min, triethylamine (622 μΐ,, 4.46 mmol, 3.00 equiv) was then added, followed by ethyl acetate (10 mL) and water (10 mL). The resulting mixture was concentrated under reduced pressure to give a light yellow slurry. The slurry was diluted with ethyl acetate (50 mL) and poured into half saturated aqueous sodium bicarbonate solution (50 mL) and half saturated aqueous sodium chloride solution (50 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 50 mL). The organic layers were combined. The combined orgamc layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 30% ethyl ether-hexanes) to provide pure allylic alcohol 122 as a clear and colorless oil (296 mg, 60%). TLC (30% ethyl acetate-hexanes): Rr 0.30 (CAM).
¾ MR (500 MHz, ( V.D,-.), δ: 4.67 (d, J = 9.9 Hz, 1H, OCi iCi 0)00 L). 4.61 (dd, J = 9.9, 5.8 Hz, 1H, OCHCOH), 4.39 (d, J = 2.1 Hz, 1H, C'j [.> }.. 4.33 (t, J = 6.3 Hz, i l l CHOI I ). 3.95 (d, J
2. 1 Hz, 1H, =CH2), 3.40 (q, J = 7.0 Hz, 2H, QCH2CH3), 3.36 (s, 3H, CO2CH3), 3.13 (s, 3H, OCH3), 3.07 (s, 3H, OCH3), 2.48 (d, J = 7.0 Hz, 1H, OH), 1.3 1 (s, 3H, CH3), 1.25 (s, 3H, O h ). 1 ,03 (t, J = 7.0 Hz, 3H, OCH2CH3),
13C NMR (125 MHz, ('.-,!>.). δ: 169.4, 160.3, 99.2, 98.9, 83.5, 73.3, 70.7, 69.8, 63.0, 51.6, 47.9, 47.7, 17.8, 17.5, 14.3.
FTIR (neat), cm4: 3497 (br-w), 2990 (w), 2950 (m), 1751 (s), 1637 (w), 1438 (m), 1376 (m),
1295 (m), 1201 (m), 1 142 (s), 1 120 (s), 1035 (s), 877 (w).
HRMS (ESI): Calcd for (CisHzeOsNa)*: 357.1520. Found: 357.1502.
Figure imgf000118_0001
[00359] Example 25, Benzoyl ester 126
Allylic alcohol 122 (1.24 g, 3.71 mmol, 1 equiv) and triphenylphosphine (3.40 g, 13.0 mmol, 3.50 equiv) were dissolved in tetrahydrofuran (28.0 mL). The temperature of the resulting solution was maintained at 23 °C using a room-temperature water bath. Diisopropyl
azodicarboxylate (2.52 mL, 13.0 mmol, 3.50 equiv) was then added dropwise. The solution turned yellow and then white precipitate appeared. A solution of benzoic acid (498 mg, 4.08 mmol, 1.10 equiv) in tetrahydrofuran (8.00 mL) was then added dropwise via syringe. The addition was quantitated with tetrahydrofuran (1.00 mL). The resulting heterogeneous mixture was stirred at 23 °C for 2 h. The reaction mixture was filtered, and the solids were washed with 50% ethyl ether-hexanes (200 mL). The filtrate was poured into saturated aqueous sodium bicarbonate solution (200 mL). The layers were separated and the aqueous layer was extracted with ethyl ether (2 x 200 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (5% acetone-hexanes initially, then grading to 25% acetone-hexanes) to provide pure benzoyl ester 126 as a clear and colorless oil (980 mg, 60%) and a mixture of benzoyl ester 126 and diisopropyl 1- benzoylhydrazine- 1 ,2-dicarboxyfate (510 mg, not shown). The mixture was again purified by flash-column chromatography on silica gel (0% ethyl ether-dichloromethane initially, then grading to 5% ethyl ether-dichloromethane) to provide pure benzoyl ester 126 (283 mg, 18%). TLC (30% acetone-hexanes): Rf = 0.36 (CAM).
fH NMR (500 MHz, CDC13), δ: 8, 14 (dd, J = 8,3, 1.4 Hz, 2H, ArH), 7.64-7,55 (m, ! I ! An I ), 7.53-7.42 (m, 2H, ArH), 5.49 (d, J = 3.0 Hz, 1H, CHOBz), 4.50 (d, J = 9.9 Hz, 1H,
OC! iCi Ο Κ Χ Ί ΐ 4.41 (dd, J = 9.9, 3.0 Hz, 1H, OCHCOBz), 4, 15 (d, J = 2,8 Hz, I S !. C\ h ). 4.08 (d, J = 2.8 Hz, 1H, Π H. 3.78 (dq, J = 9.4, 7.0, 6.6 Hz, 1H, OCH2CH3), 3.69-3.74 (m, 1H, OCH2CH3), 3.70 (s, 3H, CO2CH3), 3.26 (s, 3H, OCH3), 3.23 (s, 3H, OCH3), 1.35 (s, 3H, CH3), 1.31 (s, 3H, CH3), 1.29 (t, J = 7.0 Hz, 3H, OCH2CH3).
13C MR (125 MHz, CDCh), δ: 168.7, 165.2, 156,3, 133 , 1, 129.9, 129.9, 128.4, 99. 1 , 99.0, 82.3, 71 .8, 69.1 , 67.7, 63.1 , 52.2, 48,2, 47,7, 17,5, 17,3, 14.3.
FTIR (neat), cm4: 2984 (m), 2951 (m), 1753 (s), 1730 (s), 1667 (m), 1452 (m), 1377 (m), 1269 (s), 1250 (s), 1 132 (s), 1 1 19 (s), 1070 (m), 1038 (m), 964 (m), 714 (s),
HRMS (ESI): Calcd for (C22H3o09Na)+: 461. 1782. Found: 461.1766.
Figure imgf000120_0001
35% 128 (R = 8n) 9%
† HCi, H2Q
acetone
SO "C, 88%
[00360] Example 26. Amino ketone 119
Step 1 , reduction. A solution of diisobutylaluminum hydride (1.0 M solution in dichlorom ethane, 547 .uL, 0.547 mmol, 6.00 equiv) was added dropwise to a solution of the benzoyl ester 126 (40.0 mg, 0.091 mmol, 1 equiv) in dichloromethane (1.82 mL) at -85 °C. The resulting solution was stirred for 15 min, at which point propanal (39.2 iL, 0.547 mmol, 6.00 equiv) was then added. The reaction mixture was stirred at -85 °C for another 5 min, at which point ethyl acetate (4 mL) was added. The cooling bath was then removed and saturated aqueous sodium potassium tartrate (4 mL) and sodium bicarbonate (4 mL) were added at once. The mixture was warmed to 0 °C. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a colorless oil. Step 2, cyclization. The crude material from step 1 above was di ssolved in acetonitrile (1.07 mL) and magnesium sulfate (96.0 mg, 0.798 mmol, 8.32 equiv) was added. The resulting suspension was cooled to 0 °C. Bis(4-methoxybenzyI)amine (27.2 mg, 0.106 mmol, 1.10 equiv) and ytterbium trif!uoromethanesulfonate ( 1 .9 mg, 0.019 mmol, 0.20 equiv) were then added sequentially. The resulting mixture was stirred at 0 °C for 1.5 h, after which the reaction was filtered through a fritted funnel . The filtrate was poured into saturated aqueous sodium
bicarbonate (10 mL) and ethyl acetate (10 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL), The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil. The residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes + 1% tri ethyl amine initially, then grading to 50% ethyl acetate-hexanes + 1% tri ethyl amine) to provide aminoketone 119 (9: 1 mixture of 119 and bis(4- methoxybenzyl)amine, 17.3 mg, 35%), benzyl ethyl ketal 128 (impure, 5.60 mg, 9%), and diethyl ketal 127 (5.60 mg, 10%).
Step 3, ketal hydrolysis. To a solution of diethyl ketai 127 (48.7 mg, 0.083 mmol, 1 equiv) and benzyl ethyl ketal 128 (43.1 mg, 0.066 mmol, 1 equiv) in acetone (7.42 mL) was added a solution of hydrochloric acid (2.0 M in water, 744 jiL, 1 ,49 mmol, 10.0 equiv). The resulting solution was heated to 50 °C. After stirring for 1.5 h at 50 °C, the reaction mixture was cooled to 23 °C and concentrated to give a pale yellow oil. The residue was poured into aqueous sodium bicarbonate (20 mL) and ethyl acetate (20 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil. The residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes + 1% triethylamine initially, then grading to 50% ethyl acetate-hexanes + 1% triethylamine) to provide aminoketone 119 (9: 1 mixture of 119 and bis(4- methoxybenzyl)amine, 52.2 mg, 68%).
TLC (50% ethyl acetate-hexanes): Rr 0.27 (UV, CAM).
¾ NMR (500 MHz, CDCb), δ: 7.28 (d, J = 8.6 Hz, 4H, ArH), 6.84 (d, J = 8.6 Hz, 4H, ArH), 4.31 (dd, J = 10.4, 9.4 Hz, 1 1 1. H6), 4, 15 (dd, J - 11 ,0, 1.2 Hz, 1H, H4), 3.88 (d, J = 13.7 Hz, 2H, NCHzAr), 3.79 (s, 6H, (',-·! 1 :(){'! I 3.66 (d, J = 13.7 Hz, 2H, NCH2Ar), 3.43 (s, 3H, OCH3), 3,42 (dd, J = 10.9, 9,5 Hz, I I I, Hs), 3.23 (s, 3H, OCH3), 3,09 (ddd, J - 12,9, 10,5, 4,3 Hz, I I I, Hi), 2,65 (dd, J = 14,2, 4,3 Hz, 1 1 1. H2), 2.49 (t, J = 13.9 Hz, 1 1 1. H2), 1.42 (s, 3H, CHs), 1.37 (s, 31 1 , Cl h )
13C NMR (125 MHz, CDCI3), δ: 205.6, 158,6, 131.3, 129,4, 113.7, 99.4, 99.4, 75.4, 72.7, 68.9, 55.2, 55.2, 53.2, 49.0, 47.9, 40.0, 17.8.
FTIR (neat), cm-1: 3476 (w), 2994 (w), 2949 (m), 2834 (m), 1721 (m), 1611 (m), 1510 (s), 1463 (m), 1376 (m), 1301 (m), 1243 (s), 1131 (s), 1112 (s), 1032 (s), 850 (m), 823 (m), 736 (m), 524(m).
Hi MS (ESI): Calcd for ( C -sl hnNOx} ' ; 516,2592, Found: 516.2597.
Figure imgf000122_0001
3. TfN3, GuS04 4 3-ep/-4
NaHCO 60% 12%
[00361] Example 27. Azido alcohol 4
Step 1, oxime formation. Methanol (3.64 mL) was added to a suspension of the aminoketone 119 (131 mg, 0.254 mmol, 1 equiv), sodium bicarbonate (34.2 mg, 0,407 mmol, 1.60 equiv) and O- methylhydroxylamine hydrochloride (31.0 mg, 0.382 mmol, 1.50 equiv). The resulting suspension was heated to 65 °C for 3 h and then cooled to 23 °C. The reaction mixture is poured into a saturated aqueous solution of sodium bicarbonate (20 mL), sodium chloride (20 mL) and ethyl acetate (20 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give the crude methyl oxime (not depicted) as a clear and colorless oil.
Step 2, reduction, A flame-dried flask was charged with sodium methoxide (138 mg, 2,55 mmol, 10.0 equiv) and lithium aluminum hydride (145 mg, 3.83 mmol, 15.0 equiv) and cooled with a 23 °C water bath. Tetrahydrofuran (3.00 ml) was then added, which led to gas evolution. After gas evolution has subsided, the resulting suspension was cooled to -78 °C. To the resulting suspension was then added a solution of the crude methyl oxime from step 1 above in tetrahydrofuran (1.00 mL) dropwise via cannula. The addition was quantitated with
tetrahydrofuran (1.50 mL). The resulting reaction mixture was stirred at -78 °C for 1 h. The cooling bath was then removed and the suspension was stirred at 23 °C. After 1 h, the reaction mixture was heated to 65 °C. After 1.5 h, the mixture was cooled to 0 °C with an ice bath. Then water (140 (u,L) was added dropwise, followed by a solution of sodium hydroxide (2.0 M in water, 280 μL), and then water (420 μL). The suspension was then warmed to 23 °C and stirred for 30 rain. The resulting white precipitate was filtered through celite, washing with ethyl acetate (30 mL). The filtrate was poured into a saturated aqueous solution of sodium bicarbonate (20 mL), sodium chloride (20 mL) and ethyl acetate (20 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give the crude amine 36 as a pale yellow oil.
Step 3, azide formation. Sodium bicarbonate (107 mg, 1.28 mmol, 5.00 equiv) was added to a solution of the crude amine 36 from step 2 above in methanol (4.05 mL) and water (604 μΐ,) at 23 °C. A solution of trifluoromethanesulfonyl azide (1.0 M in toluene, 1.02 mL, 1 .02 mmol, 4,00 equiv) was then added. Copper(II) sulfate pentahydrate (6.38 mg, 0.026 mmol, 0.100 equiv) was then added in one portion as a solid. The resulting suspension was stirred at 23 °C for one hour and then filtered through a cotton plug. The filtrate was poured into a saturated aqueous solution of sodium bicarbonate (20 mL), sodium chloride (20 mL) and ethyl acetate (20 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil. ¾ NMR.
analysis revealed that the diastereomeric ratio was 5: 1. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 35% ethyl acetate-hexanes) to provide the aminoalcohol 4 (82,6 mg, 60%) and its diastereomer 3-epi~4 (16.5 mg, 12%) as white foams.
Azido alcohol 4 (major): TLC (35% ethyl acetate-hexanes): Rr 0,42 (UV, CAM).
!! f NMR (500 MHz, CDCta), 6: 7.29 (d, J = 8.4 Hz, 4H, ArH), 6.84 (d, J = 8.6 Hz, 4H, ArH), 3 ,84 (t, J = 10.0 Hz, i l l He), 3 ,81 (d, J - 12.5 Hz, 2H, NCH2Ar), 3.79 (s, 6H, CeTLOCTL), 3,64 (d, J = 13.6 Hz, 2H, NCHiAr), 3.49 (t, J = 9.6 Hz, 1H, H4), 3.38 (s, 3H, OCH3), 3.36 (t, J = 9.7 Hz, 1H, Hs), 3.26 (dt, J = 7,3, 3 ,5 Hz, 1 1 1, H3), 3.23 (s, 3H, OCH3), 2.89 (ddd. .! 12,4, 10.3, 3 ,8 Hz, 1H, Hi), 2.54 (s, l it OH), 2.00 (dt, J = 13.2, 4.4 Hz, i l l, H2), 1 .44 (q, J = 12.6 Hz, ! I ! H2), 1.39 (s, 3H. CH3), 1.33 (s, 3H, CH3).
13C NMR (125 MHz, CDCh), δ: 158,5, 132.0, 129.5, 1 13.6, 99.4, 99.3, 73,8, 72,2, 69,0, 61 ,3, 55.2, 54.5, 53.3, 48.9, 47.8, 30.5, 17.8, 17.8.
FTIR (neat), cm'1: 3489 (br), 2994 (w), 2949 (w), 2834 (w), 2101 (s), 1611 (m), 1585 (w), 1511 (s), 1456 (m), 1374 (m), 1301 (m), 1245 (s), 1169 (m), 1134 (s), 1035 (s), 980 (w), 883 (w), 854 (m l 824 (m),
HRMS (ESI): Calcd for (C28H39N4O7) ": 543.2813. Found: 543.2808.
Diastereomer 3~epi~4 (minor): TLC (35%> ethyl acetate-hexanes): Rf = 0.21 (LTV, CAM). ! ! f NMR (500 MHz, CDCI3), δ: 7.30-7.24 (m, 4H, ArH), 6.85-6.77 (m, 4H, ArH), 4.00 (q, J = 3 ,3 Hz, I I I, l ), 3.85-3.79 (m, 3H, He, NCHzAr), 3.79 (s, 6H, Cd OCHs), 3.75-3 ,69 (rn, i l l Hs), 3 ,70-3.62 (m, 3H, H4, NCI f -Ar), 3.38 (s, 3H, OCH3), 3.25 (s, 3H, OCH3), 3.17 (ddd, J = 12.3, 10.3, 3.7 Hz, 1H, Hi), 1.93 (dt, J = 14.3, 3.6 Hz, 1H, Hz), 1.52 (ddd, J = 14.9, 12.4, 3.0 Hz, 1 H, H2), 1 ,38 (s, 3H, CH3), 1 ,33 (s, 3H, CH3).
1 :C W !R ( 1 25 MHz, CDCI3), δ: 158.5, 132.2, 129.4, 1 13.6, 99.5, 99.4, 71.8, 70.5, 69.6, 60.1, 55 ,2, 53.6, 53.6, 48.9, 47.9, 29.6, 17.9, 17.9.
I- TI R (neat), cm"1 : 2493 (br), 2994 (w), 2925 (s), 2132 (w), 2097 (s), 1725 (w), 161 1 (m), 1585 (w), 1510 (s), 1464 (m), 1376 (rn), 1300 (m), 1246 (s), 1 168 (m), 1 37 (s), 1 1 14 (s), 1033 (s), 994 (w), 909 (m), 732 (s).
HRMS (ESI): Caicd lot ( C - ! f ^X iO- } - 543.2813. Found: 543.2808.
Figure imgf000124_0001
{S)-^amino-2-hydraxybiiianoie acid
(132)
[00362] Example 28. (,S)-benzyl 4-azido-2-(benzyloxy)butanoate (133)
Step 1, azide formation. To a mixture of (S)-4-amino-2-hydroxybutanoic acid (132, 2,00 g, 16,8 mmol, 1 equiv) in water (21 .7 mL) was added sodium bicarbonate (5.64 g, 67.2 mmol, 4.00 equiv) and copper(II) sulfate pentahydrate (210 mg, 0.839 mmol, 0.05 equiv). A solution of trifluoromethanesulfonyl azide (1.0 M in toluene, 36.9 mL, 36.9 mmol, 2.20 equiv) was then added dropwise. The resulting solution was diluted with methanol (145 mL) to afford a green homogenous emul sion. After stirring for 2.5 h at 23 °C, 1 M aqueous hydrochloric acid (30 mL) was added. The methanol in the reaction mixture was then concentrated under reduced pressure. The residue was diluted with ethyl acetate. The layers were separated and the pH of the aqueous layer was adjusted to 1 by the addition of 1 M aqueous hydrochloric acid (40 mL), The aqueous layer was extracted with ethyl acetate (2 χ 50 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give the crude azide, which was used in the subsequent step without further purification.
Step 2, benzylation. The crude azide from Step 1 above was dissolved in dimethylformamide (84.0 mL) and cooled to 0 °C. Sodium hydride (2.69 g, 67.2 mmol, 4.00 equiv) was added in one portion and the resulting suspension was stirred for 15 min at 0 °C. Benzyl bromide (11.5 g, 8.0 mL 67.2 mrnol, 4.00 equiv) was then added dropwise and the reaction mixture was allowed to warm to 23 °C. After stirring for 3 h at 23 °C, a second portion of benzyl bromide (11.5 g, 8.0 mL 67.2 mmol, 4.00 equiv) was added. The resulting mixture was heated to 50 °C. After stirring for 19 h at 50 °C, the reaction mixture was cooled to 23 °C. Ethyl ether (100 mL) and a saturated aqueous solution of ammonium chloride (50 mL) were added sequentially. The layers were separated. The organic layer was washed with a saturated solution of ammonium chloride (2 χ 100 mL) and dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude material was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 15% ethyi acetate-hexanes) to provide (S)-benzyl 4-azido-2~(benzyloxy)butanoate (133, 2.71 g, 49%).
fH NMR (500 MHz, CDCb), δ: 7,42 - 7.28 (m, 10H, ArH), 5.24 (d, J = 12,2 Hz, 1H, OCPfcPh), 5.19 (d, J = 12.2 Hz, 1H, OCH2Ph), 4.74 (d, J = 11.3 Hz, 1H, OCH2PI1), 4.43 (d, J = 11.4 Hz, 1H, OCH2PI1), 4.11 (dd, J = 8.2, 4.6 Hz, 1 1 1. CHOBn), 3,47-3,37 (m, 2H, CH2 3), 2,08- 1 ,95 (m, 2H,
Figure imgf000125_0001
13C NMR (125 MHz, CDCb), δ: 171 ,9, 137.1, 135.4, 128.6, 128.5, 128,4, 128.4, 128.2, 128.1, 74.8, 72.6, 66.8, 47.4, 32.2.
FTIR (neat), cm'1: 3065, 3034, 2949, 2878, 2363, 2101, 1749, 1499, 1456, 1 184, 1123, 1028, 740, 698.
HRMS (ESI): Calcd for (CieHwNsNaOs)*: 348.1319. Found: 348.1303.
Figure imgf000125_0002
[00363] Example 29. (5)-4-azido-2-(benzyloxy)butanoic acid (134)
To a solution of (S)-benzyi 4-azido-2-(benzyloxy)butanoate (133, 4.87 g, 15.0 mmol, 1 equiv) in water (17.8 mL) and 1,4-dioxane (35.6 mL) at 23 °C was added a solution of sodium hydroxide (2.0 M in water, 53.5 mL, 107 mmol, 7.10 equiv). The resulting opaque solution was heated to 55 °C, which turned clear. After stirring for I h at 55 °C, the solution was cooled to 23 °C and the dioxane in the reaction mixture was evaporated under reduced pressure. Water (100 mL) was then added. The aqueous layer was washed with ethyl acetate (3 χ 60 mL) and then cooled to 0 °C. The pH of the aqueous layer was adjusted to 0 by the dropwise addition of 2 M aqueous hydrochloric acid (65 mL). The resulting cloudy mixture was extracted with dic-hloromethane (4 x 150 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give (S)-4-azido-2-(benzyloxy)butanoic acid (134, 14.7 mmol, 98%) as a thick yellow oil .
lH NMR (600 MHz, CDCI3), δ: 7.41 - 7.30 (m, 5H, ArH), 4.79 (dd, J = 1 1.4, 2.3 Hz, 1H, OCi-bPh), 4,50 (dd, J = 11.3, 3.6 Hz, 1H, OCH2Ph), 4, 14 (dd, J = 8,4, 4,3 Hz, l it CHOBn), 3.53-3.42 (m, 2H, CH2 3), 2.13-2.00 (m, 2H, CH2CH2N3).
1 C MR (125 MHz, CDCh), δ: 177.6, 136.7, 128,6, 128,3, 128.2, 74.3, 72.9, 47.2, 32.0.
FTIR (neat), cm"1: 3034, 2938, 2878, 2099, 1717, 1496, 1454, 1260, 1209, 1 15, 1028, 739, 698. HRMS (ESI): Calcd for (C11H12N3O3)": 234,0884. Found: 234,0991 ,
Figure imgf000126_0001
[00364] Example 30. (S)-2,5-dioxopyrrolidin-l-yl 4-azido-2-(benzyloxy)butanoate (5)
To a mixture of (S)-4-azido-2-(benzyloxy)butanoic acid (134, 520 mg, 2.21 mmol, 1 equiv) in ethyl acetate (22.0 mL) at 0 °C was added N-hydroxysuccinimide (280 mg, 2,43 mmol, 1 , 10 equiv). The resulting suspension was stirred for 20 min at 0 °C, at which point
dicyclohexylcarbodiimide (502 mg, 2.43 mmol, 1 .10 equiv) was added in one portion. The resulting suspension was warmed to 23 °C. After stirring for 2 h at 23 °C, the reaction mixture was filtered through a fritted funnel and the filtrate was concentrated. The crude residue was purified by flash-column chromatography on silica gel (15% ethyl acetate-hexanes initially, then grading to 35% ethyl acetate-hexanes) to provide (S)-2,5-dioxopyrrolidin-l-yl 4-azido-2- (benzyloxy)butanoate (5, 694 mg, 2,09 mmol, 94%) as a colorless oil.
lH NMR (500 MHz, CDCh), δ: 7,40-7,31 (m, 5H, ArH), 4.84 (d, J = 1 1.3 Hz, 1 1 1 , OCH2Ph), 4,52 (d, J - 11.2 Hz, 1 1 1. OCH2Ph), 4,41 (t, J = 6.5 Hz, 1H, CHOBn), 3.56-3.50 (m, 2H, CH2N3), 2.88 (s, 4H, C(=0)CH2CH2), 2.17 (q, J = 6.5 Hz, 2H, CH2CH2N3).
13C NMR (125 MHz, CDCh), δ: 168.6, 167.8, 136,3, 128,6, 128.4, 128.4, 1 10.0, 73.2, 72,9, 46,9,
32.5, 25.6. FTIR (neat), cm"1: 2361, 2342, 2104, 1817, 1786, 1741, 1456, 1429, 1358, 1206, 1070, 745, 700. HRMS (ESI): Calcd for
Figure imgf000127_0001
355.1013. Found: 355.1010.
Figure imgf000127_0002
[00365] Example 31. 2-Deoxystreptamine glycosyl acceptor 137
Step 1, oxidative cleavage of the p-methoxybenzyl groups. Ceric ammonium nitrate (393 mg, 0.717 mrnol, 8.00 equiv) was added in one portion to a solution of the azido alcohol 4 (48.6 mg, 0.090 mmoi, 1 equiv) in acetonitrile (1 .40 mL) and water (0.350 mL) at 23 °C. The resulting orange solution was stirred for 1.5 h at 23 °C. A second portion of ceric ammonium nitrate (246 mg, 0.448 mmol, 5,00 equiv) was added. The resulting orange solution was stirred for another 30 min at 23 °C at which point analysis by mass spectrometry (ESI-MS) indicated the formation of an 1 : 1 mixture of the primary amine 136 and its p-methoxybenzylidene imine 135 (not shown). A buffered aqueous solution (2 mL) of hydroxylamine (1 M, pH 6, prepared by dissolving 1.39 g of hydroxy 1 amine hydrochloride in water (10 mL), and then adjusting the pH of the resulting solution to 6 by the addition of a saturated aqueous solution of sodium bicarbonate (10 mL)) was then added. Immediately, the reaction mixture turned colorless and the resulting white suspension was stirred at 23 °C for 1 h. The pH of the solution was adjusted to 0 by the addition of 2 M aqueous solution of hydrochloric acid (3 mL). Water (10 mL) and dichloromethane (5 mL) were then added. The layers were separated and the aqueous layer was washed with dichloromethane (2 x 5 mL). The pH of the aqueous layer was then adjusted to 12 by the addition of 2 M aqueous sodium hydroxide to give an opaque solution. The solution was diluted with a saturated solution of sodium chloride (10 mL) and extracted with ethyl acetate (3 x 8 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give the crude amine 136 (27. 1 mg, 100%) as a yellow foam.
Step 2, sidechain coupling. Diisopropylethylamine (47.0 0.269 mmol, 3.00 equiv) was added to a solution of (S)-2,5-dioxopyrrolidin-l-yl 4-azido-2-(benzyloxy)butanoate (5, 35.7 mg, 0.108 mmol, 1 .20 equiv) and the crude amine 136 (27. 1 mg, 0.090 mmoi, 1 equiv) from step 1 above in tetrahydrofuran (1.80 mL) at 23 °C. The resulting solution was stirred at 23 °C for 2.5 h. An aqueous solution of sodium bicarbonate (8 mL) was added. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 5 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude material was purified by flash-column chromatography on silica gel (1.0% ethyl acetate-hexanes initially, then grading to 40% ethyl acetate-hexanes) to provide 137 (26.2 mg, 56%) as a white foam.
lH NMR (500 MHz, CDCh), δ: 7.39-7.27 (m, 5H, ArH), 6.52 (d, J = 7, 1 Hz, 1H, NH), 4.61 (d, J = 1 1.3 Hz, IH, OCH2PI1), 4.50 (d, J = 1 1.3 Hz, 1H, OCHzPh), 3.99 (dd, J = 6.8, 4.5 Hz, IH, CHOBn), 3.87-3.79 (m, 1 1 L Hi), 3.57 (td, J = 9.3, 1.7 Hz, IH, H¾), 3.51-3 ,31 (m, 5H, H3, H5, He, CH2N3), 3.25 (s, 3H, OCH3), 3.08 (s, 3H, OCH3), 2.70 (d, J = 2.3 Hz, IH, OH), 2.36 (dt, J = 13. 1, 4.5 Hz, 1 1 1 H2), 2,08 (dtd, J = 14.3, 7.6, 4.6 Hz, I H, CH2CH2N3), 1 .98 ( did.. J = 14.2, 7.1, 5.6 Hz, 1 1 1, CH2CH2N3), 1.30 (s, 3H, CH3), 1.30-1.26 (m, IH, H2), 1.25 (s, 3H, CH3).
1 :C NMR ( 1 25 MHz, CDC13), δ: 171.6, 136.7, 128.7, 128.5, 127.9, 99.5, 99.4, 77.6, 73.7, 73.2, 71 ,5, 69.5, 60.6, 48.0, 47.8, 47.2, 47.0, 33.0, 31 .6, 17.5, 17.5.
FTIR (neat), cm"1: 3400, 2948, 2103, 1663, 1527, 1455, 1377, 1262, 1 133, 1 1 17, 103 1, 858, 743, 699, 660.
Hi MS (ESI): Calcd for (C. l i «N-NaO-) " : 542.2334. Found: 542.2371.
Figure imgf000128_0001
[00366] Example 32. Glycoside 140
A mixture of the azido alcohol 4 (50,0 mg, 0.092 mmol, 1 equiv) and the thioglycoside 3 (40,7 mg, 0.138 mmol, 1.50 equiv) was dried by azeotropic distillation from benzene (3 x 5 mL) to produce a colorless oil, which was held under high vacuum for 12 h. A stir bar was added, followed by dichloromethane (0.380 mL) and ethyl ether (0,380 mL). The resulting solution was cooled to -20 °C. A solution of trifluoromethanesulfonic acid (1.126 M in dichloromethane, 94.0 ah, 0, 106 mmol, 1.15 equiv) was added dropwise, N-iodosuccinimide (31 , 1 mg, 0.138 mmol, 1 .50 equiv) was then added in one portion. Immediately, the solution turned bright red. The resulting solution was stirred for 1 h at -20 °C. Saturated aqueous sodium bicarbonate solution (2 mL) and sodium thiosulfate solution (2 mL) were added. The resulting suspension was wanned to 23 °C and vigorously stirred until the red color has faded. The mixture was then diluted with ethyl acetate (10 mL) and water (10 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. ¾ NMR analysis revealed that the diastereomenc ratio (α:β) was 1 : 1. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 30% ethyl acetate-hexanes) to provide giycosylation products a-140 (29.0 mg, 43%) and β~140 (31.8 mg, 47%),
a-140: TLC (30% ethyl acetate-hexanes): Rf = 0.38 (UV, CAM).
f NMR (600 MHz, CDCh), δ: 7.29 (d, J = 8.6 Hz, 41 1. ArH), 6.84 (d, J = 8.7 Hz, 4H, ArH), 5.66 (d, J = 3.4 Hz, 1H, Hr), 4.84 (dddd, J = 12.0, 7.2, 4.6, 2.5 Hz, I I I, Hv), 4.47-4.34 (m, 21 L He1), 3.88-3.83 (m, IH, He), 3.81 (d, J = 13.8 Hz, 2H, NCH2Ar), 3.80 (s, 6H, CeH4OCH3), 3.71- 3 ,56 (m, 4H, NCH2Ar, l ! i. ¾), 3.36 (s, 3H, OCH3), 3,36-3.32 (m, IH, H3), 3.32 (s, 3H, OCH3), 3.05 (ddd, J = 12.7, 4.5, 3.4 Hz, IH, ! ! ··). 2.87 (ddd, J = 12.5, 10.4, 3.8 Hz, IH, Hi), 2.22 (qd, J = 12.8, 3.9 Hz, I H, Rr), 2,05 (dt, J = 13.1, 4.3 Hz, IH, H2), 1 .94 (dq, J = 12.0, 3.9 Hz, I H, ¾■), 1.91-1.86 (m, IH, Hr), 1.59-1.48 (m, 2H, Hv, H2), 1.37 (s, 3H, CH3), 1.27 (s, 3H, CH3).
13C NMR (125 MHz, CDCb), δ: 158,5, 132.0, 129.5, 1 13.6, 99.2, 99. 1, 96.6, 78.7, 74,5, 73,9, 69.2, 64.7, 61.4, 57.0, 55.2, 54.2, 53.3, 48.9, 47.4, 30.6, 27.2, 21.2, 17.9.
FTIR (neat), cm"1: 2994 (w), 2836 (w), 2101 (s), 161 1 (w), 1557 (m), 1510 (m), 1456 (w), 1374 (w), 1301 (w), 1248 (m), 1 139 (m), 1 1 11 (m), 1027 (m), 732 (w).
HRMS (ESI): Calcd for
Figure imgf000129_0001
727.3410. Found: 727.3409.
Figure imgf000130_0001
44
[00367] Example 33. Diol 144
Glycoside 140 (36.4 rng, 0.050 mmol, I equiv) was dissolved in an aqueous solution of trifluoroacetic acid (95% w/w, 1.85 niL, 24.0 mmol, 480 equiv) and the resulting solution was heated to 55 °C. After stirring for 2 h at 55 °C, the reaction mixture was cooled to 23 °C and diluted with toluene. The resulting solution was concentrated, re-suspended in ethyl acetate (10 mL) and poured into a saturated aqueous solution of sodium bicarbonate (10 mL), and sodium chloride (10 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil . The residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes initially, then grading to 45% ethyl acetate-hexanes) to provide diol 144 (18.8 mg, 61%).
TLC (50% ethyl acetate-hexanes): Rf = 0.36 (UV, CAM).
lH NMR (600 MHz, CDCI3), δ: 7.20-7.10 (m, 4H, ArH), 6.93-6.79 (m, 4H, ArH), 5.52 (d, J = 3 ,4 Hz, 1H, H i ). 4.88-4.73 (m, 1H, I ί<·). 4,51-4.32 (m, 2H, He'), 3 ,80 (s, 6H, ( Υ.ϋ ιϋΠ ί 3.78 (d, J = 13.3 Hz, 2H, NCHzAr), 3.52-3.36 (m, 3H, H4, Hs, ¾), 3.36-3.23 (m, 4H, NCHzAr, Hr, H3), 3.1 1 (br-s, I I I , OH), 2, 53 (ddd, J - 12,9, 9,8, 3 ,4 Hz, I I I , Hi), 2.22 (dt, J - 12,7, 4,0 Hz, l ! i I f 2.12 (qd, J = 12.8, 4.0 Hz, 1H, i I ;·). 1 .95 (dq, J = 12.1, 4.0 Hz, 1 H, I ! = ). 1 .90 (dq, J = 13.4, 3 ,3 Hz, I I I, H i ). 1.60-1.53 (m, I I I, H41), 1.50 (q, J = 12,6 Hz, 1H, H2).
13C MR (125 MHz, CDCh), δ: 159.0, 130.4, 129.9, 1 14.1, 97.4, 80.2, 78.9, 77.7, 71.0, 65.4, 60.8, 57.7, 56.9, 55.2, 52.8, 27,3, 25,2, 21 ,7.
FTIR (neat), cm"1: 3420 (br), 2929 (w), 2837 (w), 2099 (s), 161 1 (m), 1555 (s), 1510 (s), 1457 (w), 1370 (m), 1301 (m), 1249 (s), 1 173 (m), 1 141 (m), 1 104 (m), 1021 (s), 849 (w), 823 (m), 732 (m), 620 (w).
HRMS (ESI): Calcd for
Figure imgf000130_0002
613.2729. Found: 613.2746.
Figure imgf000131_0001
3 1 1
Figure imgf000131_0002
[00368] Example 34, Glycoside 141
From the azido alcohol 137: A mixture of the azido alcohol 137 (8.1.0 mg, 0.016 mmol, 1 equiv) and the thioglycoside 3 (5.74 mg, 0.019 mmol, 1.25 equiv) was dried by azeotropic distillation from benzene (3 x 5 nil.) to produce a colorless oil, which was held under high vacuum for 12 h. A stir bar was added, fol lowed by dichloromethane (0.100 mL) and ethyl ether (0.100 niL). The resulting solution was cooled to -20 °C. A solution of trifluoromethanesulfonic acid (1.126 M in dichloromethane, 1 5.9 \iL, 0.018 mmol, 1.1 5 equiv) was added dropwise. N-iodosuccinimide (4.91 mg, 0.022 mmol, 1.40 equiv) was then added in one portion. Immediately, the solution turned bright red. The resulting solution was stirred for 1.5 h at -20 °C. Saturated aqueous sodium bicarbonate solution (2 mL) and sodium thiosulfate solution (2 mL) were added. The resulting suspension was warmed to 23 °C and vigorously stirred until the red color has faded. The mixture was then diluted with ethyl acetate (10 mL) and water ( 10 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. XH NMR analysis revealed that the diastereomeric ratio (α:β) was 1 :2. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 60% ethyl acetate-hexanes) to provide glycosylation product a-141 (1.60 mg, 15%) and β-141 (2.13 mg, 19%).
From the glycoside 140: Step 1, oxidative cleavage of the p-methoxybenzyl groups. Ceric ammonium nitrate (355 mg, 8.00 equiv) was added in one portion to a solution of glycoside 140 (58.9 mg, 0.081 mmol, 1 equiv) in acetonitrile (1.30 mL) and water (324 ylS) at 23 °C. The resulting orange solution was stirred for 30 min at 23 °C, at which point analysis by mass spectrometry (ESI-MS) indicated the form ation of an 1 : 1 mixture of the primary amine 143 and its p-methoxybenzylidene imine 142 (See Figure 20). A buffered aqueous solution (2 mL) of hydroxylamine (1 M, pH 6, prepared by dissolving 1.39 g of hydroxylamine hydrochloride in water (10 raL), and then adjusting the pH of the resulting solution to 6 by the addition of a saturated aqueous solution of sodium bicarbonate (10 mL)) was then added. Immediately, the reaction mixture turned colorless and the resulting white suspension was stirred at 23 °C for 1 h. The pH of the solution was adjusted to 1 by the addition of 2 M aqueous hydrochloric acid (3 mL). Water (10 mL) and ethyl ether (10 mL) were then added. The layers were separated and the organic layer was extracted with 1 M hydrochloric acid (3 x 10 mL). The aqueous layers were then combined. The combined solution was cooled to 0 °C with stirring. The pH of the cold solution was adjusted to 9 by the portion wise addition of solid sodium bicarbonate. The solution was removed from the cooling bath and allowed to warm to 23 °C. The solution was diluted with ethyl acetate (20 mL) and poured into saturated sodium chloride solution (10 mL), pH 10 phosphate buffer solution (3 mL), and water (5 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 20 mL). The organic layers were combined. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to give a pale yellow oil.
Step 2, sidechain coupling. Diisopropylethylamine (21.2 μΐ,, 0.121 mmol, 1 .50 equiv) was added to a solution of (S)-2,5-dioxopyrrolidin-l-yl 4-azido-2-(benzyloxy)butanoate (5, 32.3 mg, 0.097 mmol, 1.20 equiv) and the crude amine (143) from step 1 above in tetrahydrofuran (1.62 mL) at 23 °C. The resulting solution was stirred at 23 °C for 12 h and then concentrated to give a pale yellow oil. The residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes initially, then grading to 40% ethyl acetate-hexanes) to provide glycoside 141 (35.5 mg, 62%).
TLC (35% ethyl acetate-hexanes): Rf = 0.23 (UV, CAM).
i XM . (600 MHz, CDC13), δ: 7,45-7,33 (m, 3H), 7.33-7.27 (m, 2H), 6,52 (d, J - 6.9 Hz, I I I, NH), 5.65 (d, J = 3.3 Hz, 1H, S i r), 4.88 (dtd, J = 12.3, 6.2, 2.5 Hz, 1H, ¾■), 4.62 (d, J = 11.3 Hz, lit OCH2Ph), 4.50 (d, J = 1 1.3 Hz, i l l. OCHiPh), 4,43 (d, J - 6,4 Hz, 2H, He1), 4,00 (dd, J 6.8. 4.5 Hz, 1H, CHOBn), 3.84 (tdd, J = 1 1.3, 6.9, 4.3 Hz, 1H, Hi), 3.76 (t, J = 9.5 Hz, 1H, Hs), 3,71 (t, J = 9.5 Hz, 1H, l i s ). 3,51 (ddd, J = 12.3, 9,3, 4,6 Hz, 1 1 1, ¾), 3.45-3.39 (m, 2H, He, CH2N3), 3.39-3.35 (m, I I I. CH2N3), 3.34 (s, 3H, OCH3), 3.10-3.06 (m, 1H, ¾), 3.06 (s, 3H, OCH3), 2.48 (dt, J = 13.1, 4.5 Hz, 1H, II2), 2.24 (qd, J = 12.9, 4.0 Hz, i l l Ha1), 2.09 (ddt, J = 14.9, 7.6, 3.8 Hz, 1H, CH2CH2N3), 2.02-1.94 (m, 2H, CH2CH2N3, H3'), 1 -92 (dt, J = 13.3, 3.3 Hz, H i, M r). 1.59-1.50 (m, 1H, M r). 1.31 (q, J = 12.5 Hz, i l l H2), 1.25 (s, 3H, CH3), 1.23 (s, 3H, CH3).
1 :C MR ( 125 MHz, CDCI3), δ: 171.7, 136.6, 128.8, 128.6, 128.0, 99.4, 99.3, 96.8, 78.8, 77.6, 74,5, 73.3, 73.3, 69.7, 64.9, 60.4, 57.0, 47.8, 47.6, 47.2, 46.8, 33,2, 31 ,7, 27, 1 , 21 ,2, 17,6, 17,5, I lR (neat), cm"1 : 3325 (br), 2952 (m), 2925 (m), 2102 (s), 1733 (w), 1660 (m), 1557 (s), 1529 (rn), 1456 (w), 1376 (rn), 1258 (m), 1140 (s), 1108 (s), 1028 (s), 865 (w), 743 (m), 700 (w). HRMS (ESI): Calcd for (C29H4iNnOioNa)+: 726.2930. Found: 726.2954.
Figure imgf000133_0001
Example 35, Diol 139
Glycoside 141 (35.5 mg, 0.050 mmoi, 1 equiv) was dissolved in an aqueous solution of trifluoroacetic acid (95% w/w, 1.96 mL, 24.2 mmol, 480 equiv). The resulting solution was stirred at 23 °C for 10 min and then diluted with toluene. The diluted solution was concentrated to give a white solid. The residue was purified by flash-column chromatography on silica gel (15% ethyl acetate-hexanes initially, then grading to 65% ethyl acetate-hexanes) to provide diol 139 (24.8 mg, 83%) as a white solid.
TLC (35% ethyl acetate-hexanes): Rr 0.23 (UV, CAM).
¾ NMR (600 MHz, CDCI3), δ: 7.46-7.35 (m, 3H, ArH), 7.35-7,29 (m, 21 1, ArH), 6.60 (d, J = 7.8 Hz, 1 1 L NH), 5.42 (d, J = 3.4 Hz, H i, Hr), 4.79 (ddt, J = 11.9, 7.1, 3 ,3 Hz, 1 1 1, I f -}.. 4.65 (d, J = 1 1 .6 Hz, 1 H, OCH2Ph), 4.52 (d, J = 1 1.6 Hz, 1H, OCH2Ph), 4,49-4,34 (m, 2H, He'), 4,03 (dd, J = 6.4, 4.8 Hz, 1H, CHOBn), 3.93-3.77 (m, 1H, Hi), 3.57 (t, J = 8.9 Hz, 1H, Hs), 3.50-3.32 (m, 5H, 1 1 ·■·, H3, H4, CH2N3), 3.26 (t, J = 9.6 Hz, 2H, He), 2.21-2.15 (m, 2H, H2, 1 1 =·), 2.15-1 ,96 (m, 3H, H3 >, CH2CH2N3), 1.92 (dd, J = 13.3, 3.2 Hz, H i, i n ). 1.57 (qd, J = 13.1, 4.1 Hz, i l l ! ! , ·-), 1.35 (q, J = 12.4 Hz, 1H, H2). l3C NMR (125 MHz, CDCb), δ: 173.0, 136.6, 128.9, 128.7, 128.2, 97.7, 80.7, 78.9, 77.2, 77.1, 75,5, 73.5, 65.6, 59.6, 58.0, 48.8, 47.1, 32.7, 31.7, 27.2, 21.8.
!· ] ]]< (neat), cm"1: 3418 (br), 3308 (br), 2922 (w), 2094 (s), 1636 (m), 1551 (m), 1532 (w), 1455 (w), 1375 (w), 1249 (m), 1 114 (w), 1071 (w), 1032 (m), 741 (w), 698 (w), 608 (w).
HRMS (ESI): Calcd for (CisHsiNuOsNa)*: 612.2249. Found: 612,2247.
Figure imgf000134_0001
[00369] Example 36. Glycoside 138
A mixture of diol 139 (5.00 mg, 8.48 μηιοΐ, 1 equiv) and the thioglycoside 2 (7.43 mg, 0.013 rnmol, 1.50 equiv) was dried by azeotropic distillation from benzene (3 x 3 mL) to produce a pale yellow solid, which was held under high vacuum for 12 h. A stir bar, 2,6-di-tert-butyl -4- methylpyridine (8.71 mg, 0,042 mmol, 5.00 equiv) and 4-A molecular sieves (6.0 mg, activated by heating at 200 °C under 0.1 Torr for 16 h, then cooling to 23 °C under dry argon) were added, followed by dichloromethane (0.400 mL). The resulting suspension was cooled to 0 °C. A solution of dimethyl(methylthio)sulfonium triflate (0.613 M in dichloromethane, 27.7 ,uL, 0.017 mmol, 2.00 equiv) was added dropwise. The resulting solution was stiired for 3 h at 0 °C.
Saturated aqueous sodium bicarbonate solution (1 mL) and sodium thiosulfate solution (1 mL) were added. The resulting suspension was diluted with ethyl acetate (5 mL) and was filtered through a cotton plug. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. ¾ NMR analysis revealed that the diastereomeric ratio (α:β) was 4: 1 , The residue was purified by flash- column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 30% ethyl acetate-hexanes) to provide glycosylation product a-138 (3.40 mg, 38%).
TLC (30% ethyl acetate-hexanes): Rf = 0.31 (UV, CAM).
¾ NMR (500 MHz, CDCh), δ: 7,44-7,20 (m, 20H, ArH), 6.69 (d, J = 6.7 Hz, 1H, NH), 5.69 (d, J = 3.3 Hz, 1H, Hr), 5.12 (d, J = 12.3 Hz, 1H, OCH2Ph), 5.06 (d, J = 12.3 Hz, 1 1 1. OCH2Ph), 4.90 (d, J = 3.5 Hz, 1H, Hr), 4.91-4.81 (m, 1H, S k), 4.66 (d, J = 1 1.5 Hz, 1H, OCH2Ph), 4.54 (d, J = 1 1.6 Hz, 1H, OCH2PI1), 4.54 (d, J = 2.3 Hz, 2H, OH), 4.51-4.42 (m, 5H, OCH2PI1, Η5», He'), 4.14 (dd, J = 1 1.0, 3.5 Hz, 1H, Hr), 3.87 (dd, J = 8.1, 5.1 Hz, I I I. CHOBn), 3.87-3.80 (m, 1H, Hi), 3.67-3.59 (ni, 2H, Η5», Hs), 3.53-3.46 (m, 1H, H3), 3.43 (dd, J = 10.0, 8.7 Hz, 1H, H4), 3.30-3.22 (ni, 2H, CH2N3), 3.12 (dt, J = 12.7, 4.0 Hz, 1H, i k), 2.93 (t, J = 9.7 Hz, 1 H, He), 2.83 (d, J = 10.7 Hz, 1H, I ί :· ). 2.44 (dt, J = 12.9, 4.2 Hz, 1H, H2), 2.40 (s, 3H, NCH3), 2.25-2.14 (m, } \ \, H:v), 1.99-1.85 (m, 5H, CH2CH2N3, Hr, I ), 1 ,57 (s, 3H, CH3), 1.1 8 (q, J = 12.4 Hz, 111 H2). !H signals corresponding to NCH2Ph were not visible due to broadening.
1 C NMR (125 MHz, CDCh), δ: 172.5, 153.2, 140,6, 137,7, 136.6, 135.4, 128.9, 128.8, 128,7, 128.6, 128,6, 128.4, 128.3, 128.2, 128.2, 128.1 , 128.0, 126.8, 97.8, 97.1, 87.0, 83.9, 79.0, 78.1, 77,6, 76.9, 76.2, 73.5, 73.1, 68.9, 65.8, 65.2, 63.5, 59.5, 57.2, 47.7, 47.5, 32,8, 32,6, 27,3, 21 ,8, 18,5, i3C signals corresponding to NCH2PI1 and NCH3 were not. visible due to broadening, HRMS (ESI): Ca!cd ibr (C-l ί, Χ -Ο ι : 1063.4632. Found: 1063.4640.
Figure imgf000135_0001
[00370] Example 37. Glycoside 147
The azido alcohol 118 (35,2 mg, 0.1 17 mmol, I equiv) was dried by azeotropic distillation from benzene (3 x 5 mL) to produce a yellow oil, which was held under high vacuum for 12 h. In a separate flask, the thioglycoside 3 (51.8 mg, 0.176 mmol, 1.50 equiv) and 1- (phenylsulfmyl)piperidine (38. 1 mg, 0.182 mmol, 1.55 equiv) were dried by azeotropic distillation from benzene (3 x 5 mL) to produce a clear and colorless oil, which was held under high vacuum for 12 h. The vessel containing thioglycoside 3 was flushed with argon, A stir bar, 4-A molecular sieves (72 mg, activated by heating at 200 °C under 0.1 Torr for 16 h, then cooling to 23 °C under dry argon), and 2,6-di-tert-butyl-4-methylpyridine (72,3 mg, 0.352 mmol , 3.00 equiv) were added, followed by dichloromethane (0.500 mL). The resulting solution was cooled to -78 °C. Trifluoromethanesulfonic anhydride (30.7 L, 0.182 mmol, 1 .55 equiv) was then added dropwise to produce a bright orange solution. After the solution was stirred at -78 °C for 20 min, a solution of alcohol 1 18 in dichloromethane (0.200 mL) was added dropwise via cannula. The addition was quantitated with dichloromethane (2 x 0.200 mL). The resulting solution was allowed to warm to -25 °C over 2.5 h, at which point the orange color faded. The resulting solution was stirred at -25 °C for 12 h. Triethyl phosphite (43.1 μΐ,, 0.246 mmol, 2.10 equiv) was added and the resulting solution was warmed to 23 °C. The suspension was filtered through a cotton plug. Saturated aqueous sodium bicarbonate solution (10 mL) and ethyl acetate (10 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. ¾ NMR analysis revealed that the diastereomeric ratio was 3 : 1 in favor of the a glycoside. The residue was purified by flash-column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 35% ethyl acetate-hexanes) to provide glycosylation product a-147, mixed with several uncharacterized impurities related to l-(phenylsulfinyl)piperidine. The mixture was again purified by flash-column chromatography on silica gel (5% acetone-hexanes initially, then grading to 15% acetone-hexanes) to provide the pure glycosylation product a-147 (34.6 mg, 61%).
TLC (35% ethyl acetate-hexanes): Rr 0.39 (CAM),
lH NMR (600 MHz, CDCI3), δ: 5.44 (d, J = 3.4 Hz, 1H, Hr), 4.93 (t J = 9.7 Hz, 1H, He), 4.87 (dddd, J = 12,0, 7.2, 4.4, 2,6 Hz, 1 H, ¾■), 4.80 (d, J = 6.8 Hz, ! I ! CH2OCH3), 4.71 (d, J = 6.8 Hz, I I I, CH2QCH3), 4.47-4.35 (m, 2H, ¾<), 3.63 (dd, J = 9.9, 9.1 Hz, 1H, Hi), 3.56 (t, J = 9.2 Hz, 1H, Hs), 3.51-3.42 (m, 2H, Hi, I L L 3.31 (s, 3H, OCH3), 3.12 (dt J = 12.6, 4.0 Hz, 1 1 L I S <■}, 2.33 (dt, J = 13.3, 4.5 Hz, 1H, H2), 2.21-2.1 1 (m, 1H, 1 1 ;·). 2.14 (s, 3H, COCH3), 1.98 (dq, J = 12,2, 3 ,9 Hz, 1 1 1, Hr), 1.93 (dq, J = 13.5, 3.3 Hz, H i, 1 1 . ), 1.64-1.52 (m, 2H, H2, I I ··).
13C NMR (125 MHz, CDCb), δ: 170.0, 99.6, 97.3, 84.1, 78.8, 77.4, 74.6, 65.3, 59.3, 58.3, 57.1, 56.6, 31.9, 27.2, 21.5, 21.1.
FTIR (neat), cm"1: 2953 (w), 2101 (s), 1746 (m), 1 557 (s), 1373 (m), 1256 (m), 1225 (s), 1 130
(w), 1 101 (w), 1030 (s), 101 1 (s), 974 (w), 916 (m), 731 (m).
HRMS (ESI): Calcd for (Ci6H24Nio06Na)+: 507. 1671. Found: 507.1686.
Figure imgf000137_0001
147
[00371] Example 38. Diol 148
Acetyl chloride (401 L, 5.65 mmol, 50.0 equiv) was added dropwise to a solution of the glycosylation product 147 (54.7 mg, 0.1 13 mmol, 1 equiv) in anhydrous methanol (1.88 mL) at 0 °C. The resulting solution was warmed to 23 °C. After stirring for 24 h, the solution was concentrated to give a light yellow oil. The residue was purified by flash-column
chromatography on silica gel ( 0% ethyl acetate-hexanes initially, then grading to 45% ethyl acetate-hexanes) to provide diol 148 (35.9 mg, 80%).
TLC (45% ethyl acetate-hexanes): Rr 0.26 (CAM).
lH NMR (600 MHz, CDCb), δ: 5.31 (d, J = 3.3 Hz, 1 1 1. Hr), 4.76 (dddd, J = 12.0, 7.2, 4.1, 2.5 Hz, IH, Hs'), 4.54-4.33 (m, 2H, He1), 3.62 (br-s, 1H, OH), 3.57-3.51 (m, IH, Hs), 3.49-3.33 (m, 5H, Hi, H , i l l, He, ¾), 2,86 (br-s, i l l, OH), 2,32 (dt, J = 14,0, 3,7 Hz, l it H2), 2.21-2.08 (m, 1H, ! ! - 2.03 (dt, J = 12.6, 4.0 Hz, IH, ¾■), 1.93 (dt, J = 13.5, 3.3 Hz, IH, H*), 1.65-1.56 (m, i l l, l-Lvl 1.56-1.47 (m, IH, i H.
13C MR (125 MHz, CDCb), δ: 97,8, 81.1, 78.8, 76.3, 75.5, 65.7, 59.8, 59.2, 58.1, 32.0, 27.1, 21.8.
FTIR (neat), cm4: 3420 (br), 2923 (w), 2098 (s), 1555 (s), 1372 (m), 1257 (s), 1 142 (w) , 1 105 (m), 1025 (s), 990 (m), 734 (m).
HRM:S (ESI): Calcd for (C HisNioOeNa)*: 421 .1303, Found: 421.1305.
Figure imgf000137_0002
[00372] Example 39, Glycoside 149
The diol 148 (43.2 mg, 0.108 mmol, 1 equiv) was dried by azeotropic distillation from benzene (3 x 5 mL) to produce a yellow oil, which was held under high vacuum for 12 h. In a separate flask, the thioglycoside 50 (62.7 mg, 0.163 mmol, 1.50 equiv) and l-(phenylsulfinyl)piperidine (35.2 mg, 0.168 mmol, 1.55 equiv) were dried by azeotropic distillation from benzene (3 x 5 mL) to produce a clear and colorless oil, which was held under high vacuum for 12 h. The vessel containing thioglycoside 50 was flushed with argon. A stir bar, 4-A molecular sieves (160 mg, activated by heating at 200 °C under 0.1 Torr for 16 h, then cooling to 23 °C under dry argon), and 2,6-di-tert-butyl-4-methylpyridine (66.8 mg, 0.325 mmol, 3.00 equiv) were added, followed by dichloromethane (1.00 mL). The resulting solution was cooled to -78 °C.
Trifluoromethanesulfonic anhydride (28.4 ,uL, 0.168 mmol, 1.55 equiv) was then added dropwise to produce a bright orange solution. After the solution was stirred at -78 °C for 20 min, a solution of diol 148 in dichloromethane (0.500 mL) was added dropwise via cannula. The addition was quantitated with dichloromethane (2 x 0.300 mL). The resulting solution was allowed to warm to -25 °C over 2.5 h, at which point the orange color faded. The resulting solution was stirred at -25 °C for 12 h. Tri ethyl phosphite (39.8 μΐ., 0.228 mmol, 2.10 equiv) was added and the resulting solution was warmed to 23 °C. The suspension was filtered through a cotton plug. Saturated aqueous sodium bicarbonate solution (10 mL) and ethyl acetate (10 mL) were added sequentially. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. fH NMR analysis revealed that the diastereomeric ratio was 3.8: 1 in favor of the a glycoside. The residue was purified by flash-column chromatography on silica gel (5% acetone-hexanes initially, then grading to 35% acetone-hexanes) to provide a mixture (α:β = 3.8: 1) of a and β anomers. This mixture was purified by preparative HPLC on a Waters SunFire Prep C 18 column [5 μτη, 250 x 19 mm, UV detection at 210 nm, solvent A: water, solvent B: acetonitrile, injection volume: 3.5 mL (1.8 mL water, 1.7 mL acetonitrile), gradient elution with 50— >90% B over 35 min, flow rate: 1 5 mL/min]. Fractions eluting at 21.5-23 min were collected and concentrated, affording glycoside β-149 (1 1.0 mg, 15%) as a clear oil. Fractions eluting at 23-25 min were collected and concentrated, affording glycoside a-149 (42.2 mg, 58%) as a clear oil.
a-149: TLC (40% ethyl acetate-hexanes): Rr = 0,2 (CAM).
fH NMR (600 MHz, CDCb), δ: 7,41-7,35 (m, 2H, ArH), 7,35-7,30 (m, 3H, ArH), 5.73 (d, J = 3.4 Hz, 1H, Hr), 4.94 (d, J = 3.0 Hz, 1H, Hi-), 4.89 (d, J = 1 1.7 Hz, 1H, OCFfcPh), 4.81 (ddt, J = 1 1 .8, 7.3, 3.5 Hz, 1 1 1. ¾■), 4.61 (d, J = 1 1 ,7 Hz, ! I ! OCH2PI1), 4.45 (dd, J = 12.6, 8.1 Hz, 1H, He1), 4.39 (dd, J = 12.6, 4.2 Hz, 1H, He-), 4.16 (d, J = 1.2 Hz, 1H, OH), 4.14 (d, J = 12.2 Hz, i l l. ¾■■), 3.97 (dd, J = 4.1 , 3.1 Hz, IH, ¾»), 3.78 (d, J = 12.3 Hz, 1H, ¾»), 3.67 (td, J = 9.0, 1.3 Hz,
IH, Hs), 3.56 (l. J = 9,4 Hz, I I I, I f i K 3.53-3.42 (m, 3H, Hi, l , Hr), 3.36 (t, J = 9,3 Hz, 1H, He), 3. 16 (dt, J = 12.7, 4.1 Hz, IH, I !,- ), 2.81 (s, 3H, NCHs), 2.30 (dt, J = 13.3, 4.5 Hz, I I I. H2), 2.19 (qd, J = 12.8, 4.0 Hz, IH, Hv), 2.00-1.93 (m, IH, H:v), 1.90 (dd, J = 13.4, 3.3 Hz, IH, ¾■), 1.60- 1 .53 (m, IH, l-lv\ 1.51 (q, .) 12.8 Hz, IH, H2), 1.40 (s, 31 1 ).
l3C NMR (125 MHz, CDCI3), δ: 157.0, 137.3, 128.6, 128.3, 127.9, 97.4, 96.9, 85.9, 78.8, 78.4, 76,8, 75.4, 74.7, 72.8, 67.2, 65.2, 63.0, 59.6, 59.3, 57.1 , 32,2, 30.1 , 27.2, 23,5, 21 ,6.
I- TIR (neat), cm"1 : 3433 (br), 2936 (br), 2102 (s), 1755 (s), 1557 (s), 1454 (w), 1430 (w), 1376 (rn), 1261 (m), 1141 (m), 1102 ( ni 1037 (s).
HilMS (ESI): Calcd for (CH i ^N i iOi.A ) : 696.2461. Found: 696.2446.
β-149: TLC (40% ethyl acetate-hexanes): Rr 0.2 (CAM).
fH NM (600 MHz, CDCI 3), δ: 7,40-7,34 (m, 2H, ArH), 7.35-7.29 (rn, 3H, ArH), 5.24 (d, J = 5.4 Hz, IH, Hi-), 5.12 (d, J = 3.4 Hz, IH, Hr), 4.93 (d, J = 1 1.2 Hz, IH, OCH2PI1), 4.73 (ddt, J =
I I .8, 7.1, 3.6 Hz, I H, ¾■), 4.60 (d, J = 1 1 .2 Hz, I H, OCH2PI1), 4.46 (dd, J = 12.1, 7.4 Hz, IH, He1), 4.40 (dd, J = 12.1, 4.3 Hz, IH, He'), 4.05 (d, J = 12.2 Hz, IH, ¾»), 3.74 (dd, J = 2.5, 0.7 Hz, IH, OH), 3,67 (dd, J = 7,5, 5,5 Hz, IH, H2"), 3,64 (d, J = 12,2 Hz, IH, H5"), 3.62-3.58 (m, 21 L Hs, He), 3.58-3.51 (m, IH, Hr), 3.39-3.26 (m, 4H, Hi, H3, H3 », H4), 2.94 (s, 3H, NCH3), 2.35 (dt, J == 13.4, 4.5 Hz, IH, ! ! · ). 2, 10 (qd, J == 12.8, 4,2 Hz, IH, i h ).. 2.04 (dq, J == 8.7, 5.1, 4,6 Hz, IH, ¾■), 1.94 (dd, J = 13.4, 3.3 Hz, IH, Η4·), 1.59 (qd, J = 12.9, 4.3 Hz, IH, Hr), 1.55-1.47 (m, IH,
Figure imgf000139_0001
f 3C NMR (125 MHz, CDCb), δ: 157.1 , 137.5, 128.6, 128.2, 127.8, 101.3, 98,5, 83.1, 79.2, 79.0,
78.8, 77.0, 73.3, 65,9, 65,9, 64,2, 58,8, 58.7, 58.7, 32.2, 30.7, 27.0, 24.4, 22.0.
FTIR (neat), cm"1: 3428 (br), 2919 (br), 2101 (s), 1739 (s), 1556 (s), 1454 (w), 1433 (w), 1373
(m), 1302 (w), 1258 (s), 1142 (w), 1099 (m), 1028 (s), 989 (m), 909 (s), 729 (s),
HRMS (ESI): Calcd for (C■-! f ^X ; :()i::.Na) . 696,2461 , Found: 696.2446.
Figure imgf000140_0001
152
[00373] Example 40, Glycoside 152
A mixture of the diol 148 (4,90 mg, 0.012 mmol, 1 equiv) and the thioglycoside 2 (10.8 mg, 0,018 mmol, 1.50 equiv) was dried by azeotropic distillation from benzene (3 x 3 mL) to produce a pale yellow oil, which was held under high vacuum for 12 h. A stir bar and 4 molecular sieves (8.0 mg, activated by heating at 200 °C under 0.1 Torr for 16 h, then cooling to 23 °C under dry argon) were added, followed by dichloromethane (0.200 mL) and ethyl ether (0.100 mL). The resulting solution was cooled to -5 °C. A solution of trifluoromethanesulfonic acid (1.126 M in dichloromethane, 13.0 μΐ., 0.014 mmol, 1. 15 equiv) was added dropwise. N- iodosuccinimide (4.15 mg, 0.018 mmol, 1.50 equiv) was then added in one portion. Immediately, the solution turned bright red. The resulting solution was warmed to 0 °C and stirred for 12 h. Saturated aqueous sodium bicarbonate solution (1 mL) and sodium thiosulfate solution (1 mL) were added. The resulting suspension was diluted with ethyl acetate (5 mL) and was filtered through a cotton plug. The layers were separated and the aqueous layer was extracted with ethyl acetate (3 x 10 mL). The organic layers were combined. The combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. !H NMR analysis revealed that the diastereomeiic ratio (α:β) was 1 : 1 , The residue was purified by flash- column chromatography on silica gel (5% ethyl acetate-hexanes initially, then grading to 30% ethyl acetate-hexanes) to provide glycosylation product a-152 (4.60 mg, 43%).
LLC (30% ethyl acetate-hexanes): Rr 0.40 (UV, CAM),
lH NMR (600 MHz, CDCI3), δ: 7.52-7.45 (m, 2H, ArH), 7.45-7.30 (m, 6H, ArH), 7.31-7.24 (m, 5H, ArH), 7,23-7.17 (m, 2H, ArH), 5.70 (d, J = 3.4 Hz, ! I ! Hr), 5,28 (d, J = 3.6 Hz, ! I ! Hr), 5.13 (d, J = 12.3 Hz, 1H, GCH2PI1), 5.08 (d, J = 12.1 Hz, IH, OCH2PI1), 4.83 (qd, J = 8.7, 7.1, 3.4 Hz, 1 1 1. ¾■), 4.75 (d, J = 10.8 Hz, ! I ! OCH2PI1), 4.63 (d, J = 10.8 Hz, IH, OCH2Ph), 4,58 (d, J = 1 .9 Hz, IH, OH), 4.55 (d, J = 12.7 Hz, IH, Hs»), 4.48-4.38 (m, 2H, He1), 4.24 (dd, J = 11.0, 3 ,6 Hz, H, H2"), 3.74 (d, J = 12,8 Hz, IH, 1 ! ■·), 3.67 (id, J = 8.9, 1.9 Hz, IH, H5), 3.51 (dd, J 10.0, 8.8 Hz, IH, H i ). 3.49-3.43 (m, 2H, Hi, H3), 3.26 (t, J = 9.3 Hz, 1 1 1. He), 3.15 (dt, J = 12.6, 4.1 Hz, 1 1 L H2'), 2.92 (d, J = 1 1 .0 Hz, IH, ! ! 2.45 (s, 3H, NCH3), 2.30 (dt, J = 13.2, 4.5 Hz, 1H, I ! 2.24-2.12 (m, I I I. I I ·), 1.95 (dt, J = 12.3, 4.0 Hz, H i, i ), 1.93-1.87 (m, 1H, 1 ! r), 1,59-1 ,56 (m, lit 1 1 · ). 1 ,55 (s, 3H, CH3), 1 ,49 (q, J = 12,7 Hz, 1 1 1, H2), ¾ signals
corresponding to NCH2Ph were not visible due to broadening.
13C MR (125 MHz, CDCb), δ: 153.3, 141.0, 137.9, 135.4, 128.9, 128.6, 128.5, 128.4, 128.3, 128.0, 128,0, 127,8, 126.6, 98.5, 97.2, 86.8, 86.8, 78.9, 78.4, 76.4, 75.2, 71 ,9, 68,9, 65,2, 65, 1 , 63.5, 59.6, 59.4, 57.2, 32.5, 27.3, 21.8, 18.5. 13C signals corresponding to NCHuPh and NO L were not visible due to broadening.
FTIR (neat), cm"1 : 3430 (br), 2928 (w), 2104 (s), 1742 (m), 1557 (m), 1496 (w), 1455 (w), 1378 (w), 1302 (w), 1256 (s), 1145 (w), 1068 (m), 1028 (s), 737 (m), 698 (m).
HRMS (ESI): Calcd for (C4iH5oNnOii)+: 872.3686. Found: 872.3661.
Figure imgf000141_0001
14S 150 (59%) 151 (18%)
[00374] Example 41. Nitroalcohols 150 and 151
A solution of the glycoside 149 (15.5 mg, 0.023 mmol, 1 equiv) and aqueous formaldehyde (37 wt%, 8.60 μΙ_, 0.1 15 mmol, 5.00 equiv) in tetrahydrofuran (1.15 mL) was cooled to 0 °C. An aqueous solution of potassium carbonate (0.10 M, 23.0 μί, 0.100 equiv) was added dropwise. The resulting clear and colorless solution was warmed to 23 °C and stirred for 9 h, at which point saturated aqueous ammonium chloride solution (3 mL) was added. The resulting suspension was diluted with ethyl acetate (10 mL). The layers were separated and the aqueous layer was extracted with ethyl acetate (2 x 10 mL), The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (40% ethyl acetate-hexanes initially, then grading to 70% ethyl acetate-hexanes) to provide recovered glycoside 149 (1.5 mg, 10%), a diastereomeric mixture of the nitroalcohols 150 (dr = : 1) and the nitrodiol 151 (impure).
The mixture of nitroalcohol diastereomers was purified by preparative HPLC on a Waters SunFire Prep CI 8 column [5 um, 250 x 19 mm, UV detection at 210 nm, solvent A: water, solvent B: acetonitrile, injection volume: 3.5 mL (1 .8 mL water, 1.7 mL acetonitrile), gradient elution with 50— » 100% B over 35 min, flow rate: 15 mL/min]. Fractions eluting at 17.5-18.5 min were collected and concentrated, affording nitroalcohol 150, diastereomer A (4.6 mg, 28%) as a clear oil. Fractions eluting at 18.5-20 min were collected and concentrated, affording nitroalcohol 150, diastereomer B (5.0 mg, 31%) as a clear oil.
The nitrodiol 151 was purified by preparative HPLC on a Waters SunFire Prep C18 column [5 μτη, 250 x 19 mm, UV detection at 210 nm, solvent A: water, solvent B: acetonitrile, injection volume: 3.5 mL (2.1 mL water, 1.4 mL acetonitrile), gradient elution with 40- 80% B over 35 min, flow rate: 15 mL/min]. Fractions eluting at 17-20 min were collected and concentrated, affording pure nitrodiol 151 (3,0 mg, 18%) as a clear oil.
Nitroalcohol 150, diastereomer A: TLC (60% ethyl acetate-hexanes): Rf = 0.21 (CAM).
¾NMR (600 MHz, CDC13), δ: 7,41-7,36 (m, 211 ArH), 7.37-7.31 (m, 3H, Aril), 5.76 (d, J = 3.4 Hz, 1H, Hr), 4.94 (d, J = 3.0 Hz, 1H, Hi-), 4.89 (d, J = 11.7 Hz, IH, OCH2PI1), 4.66 (ddd, J = 11.8, 7.1, 2.3 Hz, ill ¾'), 4.61 (d, J = 11.7 Hz, ill OCHiPh), 4.58 (td, J - 7,1, 3.3 Hz, IH, He1), 4.15 (s, III. OH), 4.16-4.09 (m, IH, CH2OH), 4.14 (d, J = 12.2 Hz, IH, H5"), 4.05 (ddd, J = 12.8, 5,3, 3,3 Hz, IH, CH2OH), 3.97 (dd, J = 4.0, 3.1 Hz, IH, Hr), 3.79 (d, J = 12.3 Hz, IH, 1 Ir).3.67 (t, J = 8.3 Hz, IH, Us), 3.52-3.43 (m, 4H, Hi, Hs, H4, Η3»), 3.37 (t, J = 9.4 Hz, IH, He), 3.16 (dt, J = 12.8, 4.0 Hz, IH, ! ! ··).2.81 (s, 3H, NCH3), 2.36-2.24 (m, 2H, H2, CH2OH), 2.16 (qd, J = 13.4, 12,9, 4.3 Hz, IH, H3'), 2,00-1.90 (m, 2H, I i Mr), 1.61 (td, J = 13,6, 13.1, 4,4 Hz, III, ) \y), 1.54-1.45 (m, IH, H2), 1.41 (s, 3H, CH3).
13C NMR (100 MHz, CDCI3), δ: 157.1, 137.2, 128.6, 128.3, 127.9, 97.4, 97,0, 91,0, 85,9, 78,4, 76.8, 75.4, 74.8, 72.8, 67.3, 66.2, 63.0, 60.5, 59.6, 59.4, 57.1, 32.3, 30.1, 26.4, 23.6, 21.7.
FTIR(neat), cm'1: 3429 (br), 2936 (br), 2101 (s), 1744 (s), 1557 (s), 1454 (w), 1434 (w), 1376 (w), 1261 (s), 1141 (m), 1091 (w), 1038 (s), 911 (s), 869 (w), 731 (s).
HRMS (ESI): Calcd for (C28l¾7NiiOiiNa)+: 726.2566, Found: 726.2568.
Nitroalcohol 150, diastereomer B: TLC (60% ethyl acetate-hexanes): Rf = 0.21 (CAM).
¾ NMR (500 MHz, CDCI3), δ: 7.42-7.30 (m, 5H, ArH), 5.69 (d, J = 3.4 Hz, IH, Hr), 4.93 (d, J = 3.1 Hz, IH, Hr), 4.89 (d, J = 11.7 Hz, IH, OCH2PI1), 4,65 (ddd, J = 9.8, 7.0, 3,6 Hz, IH, i I > 4.62 (d, J = 11.8 Hz, IH, OCH2PI1), 4.53 (td, J = 7.0, 3.4 Hz, IH, He-), 4.28 (dd, J = 12.6, 7.0 Hz, IH, CH2OH), 4.16 id. J = 12.2 Hz, ILL 1 ! ··), 4.08 (dd, J = 12.6, 3.3 Hz, IH, CH2OH), 3.99 (dd, J = 3.9, 3.1 Hz, IH, H2"), 3.79 (d, J = 12.3 Hz, III. H5"), 3.69 (t, J = 8.8 Hz, IH, H5), 3.54-3.47 (m, 311, Hi, I!, Hi), 3.46 (d, J = 4.0 Hz, IH, 3.37 (t, J = 9.3 Hz, IH, He), 3.15 (dt, J = 12,7, 4.1 Hz, IH, ¾'), 2.81 (s, 3H, NCH3), 2.33 (dt, J = 13.8, 4.1 Hz, IH, !!··).2,19-2,05 (m, IH, Hv), 2.01-1.86 (m, 2H, y, 11 ; ), 1.61 (qd, J = 13.0, 3.8 Hz, 1H, ¾'), 1.56-1.44 (m, 1H, H2), 1.41 (s,
3H, (Ί!:).
13C MR(125 MHz, CDCb), δ: 157.1, 137.2, 128.6, 128.3, 127.9, 97.4, 97.4, 91.1, 85.9, 78.9, 76.9, 75.3, 74.9, 72.6, 67.3, 66.3, 63.0, 60.8, 59.5, 59.4, 57.2, 32.3, 30.1, 27.3, 23.6, 21.7.
FTIR(neat), cm"1: 3443 (br), 2930 (w), 2361 (m), 2332 (m), 2104 (s), 1753 (s), 1557 (m), 1454 (w), 1379 (ni), 1261 (s), 1038 (s), 700 (w).
HRMS (ESI): Calcd for ( K) h-XwOnNa) .726.2566, Found: 726.2568.
Nitrodiol 151: TLC (60% ethyl acetate-hexanes): Rf = 0,11 (CAM).
f NMR (600 MHz, CDCh), δ: 7.42-7.31 (m, 5H, ArH), 5.79 (d, J = 3,4 Hz, Hi, Hr), 4.92 (d, J = 3.1 Hz, 111, Hr).4.89 (d, J = 11.7 Hz, 1H, OCH2PI), 4.65 (dd, J = 12.1, 2.3 Hz, 1H, Si-), 4.62 (d, J = 11.7 Hz, 111 OC!l-Ph)..4.38 (dd, J = 12.5, 6.7 Hz, IH, CH2OH), 4,28 (dd, J = 12,7, 7,7 Hz, ! I ί CH2OH), 4.22 (d, J = 1.4 Hz, !ii. OH), 4.20 (dd, J = 12,9, 6,0 Hz, III, CH2OH), 4.15 (d, J = 12.2 Hz, IH, !! ·■), 4.11 (dd, J = 12.5, 6.7 Hz, IH, CH2OH), 4.00 (t, J = 3.5 Hz, IH, Hr), 3.79 (d, J = 12,2 Hz, IH, H5"), 3,68 (td, J = 8.8, 1.4 Hz, IH, Hs), 3.54-3,44 (m, 41 ί Hi, !!., Hi, H3 »), 3,37 (t, J = 9.3 Hz, IH, He), 3.12 (dt, J = 12.7, 4.0 Hz, IH, Hr), 2.81 (s, 3H, NCH3), 2.71 (t, J = 7, 1 Hz, H, CH2OH), 2.66 (t, J = 7,0 Hz, H, Ci !■()!!}, 2.31 (dt, J = 13.5, 4.3 Hz, IH, I!,:), 2.16- 2.05 (m, IH, ¾■), 1.95 (dt, J = 11.7.3.7 Hz, 111, IH).1.92-1.84 (m, 111, Hr).1.67 (qd, J = 13.0, 3.9 Hz, IH, I i ,·), 1.50 (q, J = 12.6 Hz, IH, !!·).1.41 (s, 3H, CH3).
1 C NMR (125 MHz, CDCh), δ: 157.1, 137.2, 128.6, 128.3, 127.9, 97.5, 97.1, 94.5, 86.1, 78.4, 76,8, 75.4, 74.9, 72.5, 68.8, 67.4, 63.0, 62.9, 62.2, 59.6, 59.5, 57,2, 32,4, 30,1, 24,7, 23,6, 21,8, FTIR (neat), cm"1: 3429 (br), 2939 (br), 2102 (s), 1747 (s), 1544 (s), 1454 (w), 1434 (w), 1408 (w), 1377 (w), 1261 (s), 1038 (s), 913 (m), 736 (s).
HRMS (ESI): Calcd for (CigHjgNiiOnNa)*: 756.2672. Found: 756.2688.
Figure imgf000143_0001
S2 · TFA
[00375] Example 42. Carbamate S2
Palladium hydroxide on carbon (20% wt, 26.3 mg, 0.037 mmol, 2.00 equiv) was added in one portion to a solution of the glycoside 149 (12.6 mg, 3.8:1 mixture of α,β-anomers at Cr, 0.019 mmol, 1 equiv) and acetic acid (623 μΕ, 10.9 mmol, 582 equiv) in ethyl acetate (623 μΕ), methanol (623 μί,), and water (623 (uL) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm) for 5 min. The resulting heterogeneous mixture was stirred at 23 °C for 7 h, and then was filtered through a plug of Ceiite®. The filter cake was washed with water (10 mL). The filtrate was concentrated to afford a clear and colorless oil. The residue was loaded onto a column of CM-Sephadex C-25 (NtFv form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.05 --> 0.1 M). The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XBridge BEH C 18 column [5 μπι, 250 x 10 mm, UV detection at 210 nm, solvent A: 10 mM ammonium hydroxide in water, solvent B : 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0— >20% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 19-19.6 min were collected and concentrated, affording the carbamate S2 (2.9 mg, 41%). For the purpose of characterization, the carbamate S2 was dissolved in water (1.5 mL). Trifluoroacetic acid (30 μΐ,) was added. The resulting solution was concentrated to afford carbamate S2 * 4TFA as a clear and colorless foam.
TLC (chloroform:methanol:ammonium hydroxide :=: 9:4: 1): Rf = 0.28 (ninhydrin).
M i NMR (500 MHz, D2O), 0: 5.78 (d, J = 3.6 Hz, IH, Hr), 5.02 i d, J = 3.8 Hz, IH, Hi»), 4.38 (t, J = 4.2 Hz, 1H, H2"), 4.23-4.13 (m, i l l ! i ). 4.16 (d, J = 13.1 Hz, 1 1 1. H5"), 3.97 (t, J = 9.3 Hz, I H), 3.90-3.80 (m, 4Fi), 3.64-3.51 (m, 3H), 3.26 (dd, J = 13.5, 3.4 Hz, IH, He), 3.12 (dd, J = 13.6, 6.9 Hz, IH, He1), 2.92 (s, 3H, NCH3), 2.55 (dt, J = 12.5, 4.2 Hz, IH, H2), 2. 1 1-1.97 (m, 2H, I i :■), 1 .98-1.88 (m, 2H, Fir, H2), 1.72-1.58 (m, I I I , M r). 1.43 (s, 31 L CH3).
Figure imgf000144_0001
>2 geniarnincin C1a ' SHCi
{FSA-3S219)
[00376] Example 43, Gentamicin C (FSA-38219)
An aqueous solution of sodium hydroxide (2.0 M, 407 μΐ^, 0.814 mmol, 133 equiv) was added to a solution of the carbamate S2 (2,90 mg, 6.10 μτηοΐ , 1 equiv) in ethanol (407 μΐ,). The resulting solution was heated to 80 °C. After stirring for 3 h at 80 °C, the resulting light yellow solution was cooled to 23 °C. An aqueous solution of hydrochloric acid (2 M, 450 μΐ,) was added and the mixture was concentrated to give a white solid. The solid was loaded onto a column of CM- Sephadex C-25 (NH4 + form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0,05— 0.1 M), The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XB ridge BEH C 18 column [5 μηι, 250 x 10 mm, UV detection at 210 nm, solvent A: 10 mM ammonium hydroxide in water, solvent B: 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0—»25% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 15.5- 16.5 min were collected and concentrated, affording gentamicin Cia as a colorless film. Gentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 μΐ.) was added. The resulting solution was concentrated to give gentamicin Cia * 5HC1 (FSA-38219, 3.80 mg, 99%) as a clear and colorless foam.
TLC (chloroform:methanol:ammonium hydroxide = 9:4: 1): Rf = 0.15 (ninhydrin).
f NMR (500 MHz, D2O), 6: 5,82 (d, J - 3 ,6 Hz, 1 1 1, ! i r). 5, 12 (d, J - 3 ,7 Hz, 1 1 1, Hi-), 4,26 (dd, J = 10.9, 3.8 Hz, 1H, S i -}, 4.23-4. 1 7 (m, 1 H, Hv), 4.04 (d, J = 12.8 Hz, 1 1 1. 1 1- ), 4.02 (t, J = 9,7 Hz, I I I ), 3.86 (t, J = 9.0 Hz, H i ), 3 ,81 (t, J = 9.5 Hz, IH), 3 ,68-3 ,49 (m, 5H, Hi, H3, ! ] · , H5", 1-Ϊ3"), 3.29 (dd, J = 13.5, 3.5 Hz, IH, ! !.v). 3.14 (dd, J = 13.6, 6.9 Hz, ! I ! ί i,v), 2,95 (s, NCH3), 2.58 (dt, J = 12.5, 4.3 Hz, IH, H2), 2.12-2.02 (m, 2H, Hr), 2.02-1.90 (m, 2H, H2, H4'), 1.73-1.58 (m, I H, Η4·), 1.38 (s, 3H, CH3). The spectroscopic data obtained for gentamicin Cia * 5HC1 (FSA-38219) were in agreement with those of gentamicin gentamicin Cia · 5HC1, purified from a commercial sample of gentamicin sulfate (see below).
Purification of gentamicin Cia · 5HC1 from a commercial sample of gentamicin sulfate: A sample of gentamicin sulfate (25 mg) was loaded onto a column of CM-Sephadex C-25 (NH4 ÷ form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.05— » 0.1 M). The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XBridge BEH CI 8 column [5 μιη, 250 x 10 mm, UV detection at 210 nm, solvent A: 10 mM ammonium hydroxide in water, solvent B : 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0→25% B over 15 min, flow rate: 5 mL/min] . A total of five peaks were observed. Fractions eluting at 15,3-15,7 min were collected and concentrated, affording gentamicin Cia as a colorless film , Gentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 μΕ) was added. The resulting solution was concentrated to give gentamicin Cia * 5HC1 as a clear and colorless foam.
Figure imgf000146_0001
150 Hydroxyrnei yigeritarnidri C1a" 5HGi
G6' diastereomer A C8' diastereomer A {FSA-38255)
[00377] Example 44. Hydroxymethylgentamicin Cia, diastereomer A (FSA-38255)
Step 1 , hydrogenation. Palladium hydroxide on carbon (20% wt, 18,0 nig, 0.026 mmol, 3.00 equiv) was added in one portion to a solution of the nitroalcohol 150 (C6' diastereomer A, 6.00 mg, 8.53 μπιοΐ, 1 equiv) in acetic acid (620 μΕ) and water (155 μΐ.) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm) for 5 min. The resulting heterogeneous mixture was stirred at 23 °C for 3.5 h, and then was filtered through a plug of Celite®. The filter cake was washed with water (10 mL). The filtrate was concentrated to afford a clear and colorless oil.
Step 2, hydrolysis. An aqueous solution of sodium hydroxide (2 M, 568 μΙ_, 1.14 mmol, 133 equiv) was added to a solution of the residue from step 1 above in ethanoi (568 μΤ). The resulting solution was heated to 80 °C. After stirring for 3 h at 80 °C, the resulting light yellow solution was cooled to 23 °C. An aqueous solution of hydrochloric acid (2 M, 600 μΕ) was added and the mixture was concentrated to give a white solid. The solid was loaded onto a column of CM-Sephadex C-25 (Ν1Τ form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.05 --> 0.1 M). The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XB ridge BEH C18 column [5 μηι, 250 x 10 mm, UV detection at 210 iiffl, solvent A: 0 niM ammonium hydroxide in water, solvent B: 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0— 15% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 19.5-20 min were collected and concentrated, affording hydroxymethylgentamicin Cia (diastereomer A) as a colorless film.
Hydroxymethylgentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 μϋ) was added. The resulting solution was concentrated to give diastereomer A of hydroxymethylgentamicin Cia ® 5HC1 (FSA-38255, 1.8 rng, 32%) as a clear and colorless foam.
¾ NMR (500 MHz, D20), δ: 5.83 (d, 1 = 3.6 Hz, 1H, Hr), 5.13 (d, J = 3.7 Hz, 1H, Hr), 4.26 (dd, J = 10.9, 3 ,7 Hz, 1H, H2"), 4,25-4, 18 (m, l it ¾■), 4,04 (d, J = 12,9 Hz, 111 H5"), 4,02 (dd, J = 10.3, 8.9 Hz, 1H), 3.92-3.78 (m, 4H), 3.68-3.57 (m, 3H), 3.54 (d, J = 12.9 Hz, 1H, Η5»), 3.53 (d, J = 10.9 Hz, 1 1 1. H r ), 3.45 (q, J = 5.5 Hz, i l l), 2,95 (s, M l. NCH3), 2.58 (dt, J - 12,6, 4,2 Hz, 1H, ! ! ··). 2.11-2.03 (m, 3H, i I■■: i I r). 2.01 (q, J = 12.6 Hz, 1H, H2), 1.72 (p, J = 10.6 Hz, 1 1 1. Hr), 1.38 (s, 311 CM).
Figure imgf000147_0001
150 Hydroxyrciethyigerrtamicin Cl3 e 5HC!
C6' diasteraomar B C6' diastereomer B (FSA-38248)
[00378] Example 45. Hydroxymethylgentamicin Cja, diastereomer B (FSA-38240)
Step 1, hydrogenation. Palladium hydroxide on carbon (20% wt, 13.0 mg, 0,018 mmol, 2.00 equiv) was added in one portion to a solution of the nitroaicohol 150 (C61 diastereomer B, 6.50 mg, 9,24 μηιοΐ, 1 equiv) in acetic acid (680 μΐ) and water (170 ,L) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm) for 5 min. The resulting heterogeneous mixture was stirred at 23 °C for 3 h, and then was filtered through a plug of Celite®. The filter cake was washed with water (10 mL). The filtrate was concentrated to afford a clear and colorless oil.
Step 2, hydrolysis. An aqueous solution of sodium hydroxide (2 M, 616 μΐ, 1.232 mmol, 133 equiv) was added to a solution of the residue from step 1 above in ethanoi (616 μΐ). The resulting solution was heated to 80 °C. After stirring for 3 h at 80 °C, the resulting light yellow solution was cooled to 23 °C. An aqueous solution of hydrochloric acid (2 M, 700 μΐ) was added and the mixture was concentrated to give a white solid. The solid was loaded onto a column of CM-Sephadex C-25 (ΝΗ form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.05— » 0.1 M). The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XB ridge BEH CI 8 column [5 μιη, 250 x 10 mm, UV detection at 210 nm, solvent A: 10 mM ammonium hydroxide in water, solvent B: 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0— 15% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 18.5-19.5 min were collected and
concentrated, affording hydroxymethylgentamicin Cia (diastereomer B) as a colorless film.
Hydroxymethylgentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 μΙΛ was added. The resulting solution was concentrated to give diastereomer B of hydroxymethylgentamicin Cia * 5HC1 (FSA-38240, 1. 10 mg, 18%) as a clear and colorless foam.
TLC (chloroform:methanol:ammonium hydroxide = 9:4: 1): Rf = 0.08 (ninhydrin).
¾ MR (500 MHz, D20), δ: 5.75 (d, J = 2.7 Hz, i l l. Hr), 5.09 (s, 1H, Hi-), 4.22 (d, J = 10.7 Hz, 2H, Hr, H.v), 4.01 (d, J = 12.8 Hz, 1H, ! !«··), 3.96 (t, J = 9.7 Hz, 1H), 3.89-3.73 (m, 4H), 3.64-3.46 (m, 6H), 2,91 (s, 3H, NCH3), 2.54 (d, J = 12.9 Hz, i l l. ! !.:), 2.15-1.87 (m, 41 1. Ή3; HA; H2), 1.65 (q, J = 12.9 Hz, 1H, H r). 1.34 (s, 3H, CH3).
Figure imgf000148_0001
Bisifsydraxymethyljgeniamicin C|„» 5HC!
(FSA-382S2)
[00379] Example 46, Bis(hydroxymethyl)gentamicin Cia (FSA-38252)
Step 1 , hydrogenation. Palladium hydroxide on carbon (20% wt, 6.51 mg, 9.27 μτηοΐ, 4.00 equiv) was added in one portion to a solution of the dioi 151 (1.70 mg, 2.32 μηιοΐ, 1 equiv) in acetic acid (500 L) and water (125 μΐ.) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm) for 5 min. The resulting heterogeneous mixture was stirred at 23 °C for 3 h, and then was filtered through a plug of Celite®. The filter cake was washed with water (10 mL). The filtrate was concentrated to afford a clear and colorless oil.
Step 2, hydrolysis. An aqueous solution of sodium hydroxide (2 M, 1 54 μΙ_, 0.308 mmol, 133 equiv) was added to a solution of the residue from step 1 above in ethanoi (154 μΤ). The resulting solution was heated to 80 °C. After stirring for 3 h at 80 °C, the resulting light yellow solution was cooled to 23 °C. An aqueous solution of hydrochloric acid (2 M, 300 μΕ) was added and the mixture was concentrated to give a white solid. The solid was loaded onto a column of CM-Sephadex C-25 (NH4 + form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.05— 0. 1 M). The ninhvdrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XB ridge BEH C 18 column [5 μηι, 250 x 10 mm, UV detection at 210 iiffl, solvent A: 0 niM ammonium hydroxide in water, solvent B: 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0— 15% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 15.5-16.5 min were collected and
concentrated, affording bis(hydroxymethyl)gentamicin C ia as a colorless film.
Bis(hydroxymethyl)gentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 fiL) was added. The resulting solution was concentrated to give bis(hydroxymethyl)gentamicin Cia * 5HC1 (FSA-38252, 0.90 mg, 56%) as a clear and colorless foam.
TLC (chloroform:methanol:ammonium hydroxide = 9:4: 1 ): Rf = 0.08 (ninhydrin).
f NMR (500 MHz, D2O), 6: 5.81 (s, 1H, Hr), 5.1 1 (s, H I , Hr), 4.30-4.20 (m, 2H), 4,02 (d, J 12.8 Hz, H i ), 3.98-3.86 (m, 1H), 3.88-3.72 (m, 61 1 ), 3.62-3.45 (m, 5H), 2.93 (s, 3H, NCH3), 2,57-2,45 (m, H I , H2), 2.16-1.86 (m, 41 1 , Hy, Hr, H2), 1.70 (dd, J = 24.4, 10.3 Hz, 1 1 L I i r), 1.36
Figure imgf000149_0001
$80] Example 47. 1-HABA-gentamicin Cla (1)
Palladium hydroxide on carbon (20% wt, 17.8 mg, 0.025 mmol, 5.00 equiv) was added in one portion to a solution of the glycoside 138 (5.40 mg, 5.08 μηιοΐ, 1 equiv) in acetic acid (810 ,L) and water (200 μΕ) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm) for 5 min. The resulting heterogeneous mixture was stirred at 23 °C for 20 h, and then was filtered through a plug of Celite®. The filter cake was washed with an aqueous solution of acetic acid in water (10% v./v, 10 mL), The filtrate was concentrated to afford a colorless oil . The residue was loaded onto a column of CM- Sephadex C-25 (NH4 + form). After washing the column with water (50 mL), the product was eluted with a solution of ammonium hydroxide (0.1 -- 0.2 M). The ninhydrin-positive fractions were collected and concentrated to give a white film. The residue was purified by preparative HPLC on a Waters XB ridge BEH C 18 column [5 μηι, 250 x 10 mm, UV detection at 210 nm, solvent A: 10 mM ammonium hydroxide in water, solvent B: 10 mM ammonium hydroxide in acetonitrile, injection volume: 2.0 mL (water), gradient elution with 0—»15% B over 15 min, flow rate: 5 mL/min]. Fractions eluting at 20.5-21 min were collected and concentrated, affording l-N-(4"'-amino-2'"-hydroxylbutanoyl)gentamicin Cla free base. 1-HABA-gentamicin Cia free base was dissolved in water and an aqueous solution of hydrochloric acid (2 M, 30 ΐ . ) was added. The resulting solution was concentrated to give 1-HABA-gentamicin Cia (1, FSA- 39254) ® 5HC1 (1 .00 mg, 36%) as a clear and colorless foam ,
TLC (chloroform:methanol:ammonium hydroxide = 5 :8 :2): Rf = 0.05 (ninhydrin).
f NMR (500 MHz, D2O), 6: 5,76 (d, J - 3 ,6 Hz, 1H, Hr), 5, 14 (d, J - 3 ,9 Hz, 1H, Hr), 4.25 (dd, J = 9.4, 3.7 Hz, 1H, CHOH), 4.19-4.12 (m, 1H, ! 1-), 4.12-4.09 (m, 1H, Hi), 4.09 (d, J = 12.8 Hz, H i, Hs"), 4,02 (dd, J = 1 1.0, 3 ,8 Hz, H i, i f -). 3 ,91 (t, J = 9.7 Hz, i l l H¾), 3.83 (t J = 9,6 Hz, 1H, He), 3.76 (t, J - 9,3 Hz, I I I , H5), 3.57-3.52 (m, 1H, H2'), 3.52-3.44 (m, 1H, H3), 3.40 (d, J = 12.9 Hz, 1H, Hs-), 3.31 (d, J = 10.9 Hz, 1H, H3 »), 3.24 (dd, J = 13.5, 3.5 Hz, 1H, He'), 3.15 (t, J = 7.4 Hz, 2H, CH2NH2), 3.10 (dd, J = 13.5, 7.2 Hz, IH, He'), 2.88 (s, 3H, NCH3), 2.21 (dt, J = 12.7, 4.1 Hz, IH, H2), 2.18-2.1 1 (m, IH, CH2CH2NH2), 2.05-1.89 (m, 4H, I i · 1 h | f r.
CH2CH2NH2), 1.82 (q, J = 12,5 Hz, IH, H2), 1.66-1.54 (m, I I I , H i ).. 1.31 (s, 31 L CH3).
13C NMR (125 MHz, D2O), δ: 175.3, 97.9, 95.0, 79.2, 77.4, 74.5, 69.7, 69.4, 66.9, 65.8, 65.7, 64. 1, 48.7, 48.6, 48.4, 42.4, 36,8, 34,9, 30,6, 30,3, 25.2, 20.8, 20.3 ,
Equivalents and Scope
[00381] In the claims articles such as "a," "an," and "the" may mean one or more than one unless indicated to the contraiy or otherwise evident from the context. Claims or descriptions that include "or" between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or othenvise evident from the context. The invention includes embodiments in which exactly one member of the group is present in. employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or ail of the group members are present in, employed in, or otherwise relevant to a given product or process.
[00382] Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms "comprising" and "containing" are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.
[00383] This application refers to various issued patents, published patent applications, journal articles, and other publications, ail of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the invention can be excluded from any claim, for any reason, whether or not related to the existence of prior art.
[00384] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims.

Claims

CL. S
What is claimed is:
1. A compound havin the structure of Formula (I):
Figure imgf000153_0001
c Ί )
or a pharmaceutically acceptable salt thereof, wherein:
R-2b is halogen, hydroxy!, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl
3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group;
R.3d i s cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group; or
R3c and R3d together form a ring;
R4a is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or R4a and R3c are combined to form a five or six-membered ring; or
R4a and R3d are combined to form a five or six-membered ring;
R'Sb is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; or R4a and R3c are combined to form a five or six-membered ring, or
R4a and R¼ are combined to form a five or six-membered ring;
R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group; l a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
R9d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rub i s halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Ri d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Ri5b is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Riea is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Risa, Risb, and Risd independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or two of Risa, Ri»b, and Ri8d are combined to form a ring.
The compound of claim 1 , wherein:
Rib is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NH2, protected amino, -NHC(0)alkyl, or
heteroaryl;
I¾3c is hydrogen, alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
R.3d is alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
R.3c and R:<d together form a ring;
Rta is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
Rib is alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
R?d is hydrogen, alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
R-9a is hydrogen, alkyl, carboxy alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
R9d is hydrogen, alkyl, cycloaikyi, heteroalkyl or heterocyclyl;
Rub is halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, or heteroaryl;
Ri4d is hydrogen, alkyl, cycloaikyi, heteroalkyl or heterocyclyl; Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, - HC(0)alkyl, alkyl, or heteroalkyl;
Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyi, alkyl, or heteroalkyl;
Ri8a, Risb, and Risd independently are hydrogen, alkyl, cvcloalkyl, heteroalkyl, or heterocyclyl; or two of Riga, Risb, and Risd combine to form a ring.
3. The compound of any one of claims 1-2, wherein Rsd, Ri4d, and Ri8d are hydrogen.
4. The compound of an one of claims 1-3, having the structure of Formula (II):
Figure imgf000155_0001
or a pharmaceutically acceptable salt thereof.
5, The compound of claim 4, having a structure selected from:
Figure imgf000155_0002
Figure imgf000156_0001
and pharmaceutically acceptable salts thereof. e compound of any one of claims 1-5, wherein R?d has the structure:
Figure imgf000156_0002
wherein R?f is (Ci-6)alkyl, or (Ci-6)heteroaikyl
7. The compound of claim 6, wherein R? has the structure:
Figure imgf000156_0003
wherein R7g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; or
R?g and R?h are combined to form a ring.
The compound of any one of claims 1 -5, selected from the group consisting of:
Figure imgf000156_0004
Figure imgf000157_0001
and pharmaceutically acceptable salts thereof. 9. A compound of Formula (1-a):
Figure imgf000157_0002
or a salt thereof, wherein:
X is a leaving group,
Risb is hydrogen, halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
Ri6a is hydrogen, halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Riga and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or
branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl, or
Riga and Risb are combined to form a ring.
10. The compound of claim 9, wherein:
X is a leaving group;
Risb is hydrogen, halogen, -OH, -O(alkyl), -QC(0)alkyl, -NHC(0)alkyl, alkyl, heteroalkyl;
Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(O)alky), alkyl, heteroalkyl; and
Riga and Risb are hydrogen, alkyl, cvcloalkyi, heteroalkyl or heterocyclvi; or
Riga and Risb are combined to form a ring.
1 1. The compound of claim 9 or 10, wherein X is -SPh, -S(0)Ph or - S(0)2Ph.
12. The compound of claim 9, wherein Formula (I-a) is selected from Formulae (I-al)- a4):
Figure imgf000158_0001
(I-al) a)
Figure imgf000158_0002
(I-a3) ( I
13. A compound of Formul 1-b):
Figure imgf000158_0003
or a salt thereof, wherein:
R?e is -N3 or -N(R7c)(R?d), wherein: R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryi, or a nitrogen protecting group;
R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryi, or a nitrogen protecting group;
Rsa is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryi;
Rub is halogen, hydroxy!, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryi; and Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring.
14. The compound of claim 13, wherein:
R?e is a radical of the formula:
Figure imgf000159_0001
wherein R7f is Ci-6 alkyl or Ci-e heteroalkyl.
15. The compound of claim 13 or 14, wherein:
R?c is hydrogen or a nitrogen protecting group;
R?d is hydrogen or a nitrogen protecting group;
R9a is hydrogen, alkyl, carboxyalkyi, cye!oalkyl, heteroalkyl or heterocyclyl; and
Rub is halogen, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -NHC(O)alky), or heteroaryi, and
Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring.
16. The compound of claim 15, wherein:
R.9a is hydrogen;
Rub is protected hydroxyl; and
Ri2a is an oxygen protecting group.
17. The compound of claim 15, wherein:
R.9a is hydrogen; and
Rub and R12a are combined to form a five or six-membered ring.
18. The compound of any one of claims 13-17, wherein Formula (I-b) is selected from Formulae (I-bl -(I-b8):
Figure imgf000160_0001
-b7)
19. A compound of Formula 1-c):
Figure imgf000161_0001
or a salt thereof, wherein:
R?e is -N3 or ~N(R?c)( 7d), wherein:
R?c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl, heteroaryl, or a nitrogen protecting group;
R?d is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl, heteroaryl, or a nitrogen protecting group;
R9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl;
Rub is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroahphatic, aryl, heteroaryl; and Ri2a is an oxygen protecting group; or
Rub and R12a are combined to form a five or six-membered ring;
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl; and
Ri8a and Risb are hydrogen, alkyl, cycloaikyi, heteroalkyl or heterocvclyl; or
Ri8a and Risb are combined to form a ring.
20. The compound of claim 19, wherein:
R?c is a radical of the formula:
H
R-
O
wherein R7f is Ci-e. alkyl or Ci-6 heteroalkyl.
21. The compound of claim 19 or 20, wherein:
Rv is -N3 or -N ( R \- )( -,i ):
R?c is hydrogen or a nitrogen protecting group;
R.7d is hydrogen or a nitrogen protecting group;
R9a is hydrogen, alkyl, carboxyalkyl, cycloalkyl, heteroalkyl or heterocyclyl;
Riib is halogen, protected hydroxy!, -OH, -O(alkyl), ~OC(0)alkyl, -NHC(0)alkyl, heteroaryl;
Ri2a is an oxygen protecting group; or
Riib and R12a are combined to form a five or six-membered ring;
Ri5b is hydrogen, halogen, -OH, -O(alkyl), ~OC(0)a!kyl, -NHC(0)a!kyl, alkyl, heteroalkyl;
Ri6a is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, - HC(0)alkyl, alkyl, heteroalkyl; and
Riga and Ri8b independently are hydrogen, alkyl, cycloalkyl, or cyclic or acyclic heteroalkyl
22. The compound of claim 21, wherein:
R9a is hydrogen;
Rub is hydroxyl or protected hydroxy!; and
Ri2a is an oxygen protecting group; or
Riib and Ri2a are combined to form a five or six-membered ring;
Ri5b and Riea are hydrogen; and
Ri8a and Risb independently are hydrogen, a!ky!, or heteroalkyl.
23. The compound of claim 22, wherein:
R a is hydrogen;
Rub is protected hydroxy!; and
Ri2a is an oxygen protecting group.
24. The compound of claim 22, wherein:
R a is hydrogen; and Riib and R12a are combined to form a five or six-membered ring.
5. The compound of claim 19, wherein Formula (I-c) is selected from Formulae (I-cl)-(I-
Figure imgf000163_0001
(I-cl) (I-c2)
Figure imgf000163_0002
I-c3)
Figure imgf000163_0003
(I-e5)
6. A compound of Formula (l~d):
Figure imgf000163_0004
(I-d)
or a salt thereof, wherein:
X is a leaving group; I b is halogen, hydroxyl, protected hydroxyl, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R:¾c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group;
Rsd is cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl, heteroaryl, or a nitrogen protecting group; or
I¾3c and Rsd together form a ring;
R.4a is halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R4b is halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl;
R4a and R c are combined to form a five or six-membered ring; or
R.4a and R3d are combined to form a five or six-membered ring.
27. The compound of claim 26, wherein:
X is a leaving group,
R?.b is halogen, -OH, protected hydroxyl, -O(aikyi), -OC(0)alkyl, - H2, protected amino, -NHC(0)alkyl, or heteroary!;
R3c is alkyl, cycloalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group;
Rsd is alkyl, cycloalkyl, heteroaikyi, heterocyciyl, or a nitrogen protecting group,
R4a is halogen, -OH, protected hydroxy!, -O(alkyl), -OC(0)alkyl, alkyl, cycloalkyl heteroaikyi, or heterocyciyl; and
Ri is al kyl , cycloalkyl, heteroaikyi or heterocyciyl; or
R4a and R3c are combined to form a five or six-membered ring; or
4a and R3d are combined to form a five or six-membered ring.
28. The compound of claim 27, wherein:
X is -SPh, -S(0)Ph or -S(0)2Ph,
Ra is protected hydroxyl;
R3c is alkyl R3d is alkyl or benzyl;
R4a is protected hydroxy!, and
4 is alkyl.
The compound of claim 27, wherein :
R4a and R3c are combined to form a five or six-membered ring; or
R.4a and R3d are combined to form a five or six-membered ring.
The compound of claim 26, wherein Formula (I~d) is selected from Fommlae (I-dl)-(I-
Figure imgf000165_0001
( I ■dl) (I-d2)
Figure imgf000165_0002
I- d3) I ■d4'
Figure imgf000165_0003
(I-d5) (I-d6)
Figure imgf000166_0001
or a salt thereof, wherein:
R.2b is halogen, hydroxyl, protected hydroxy!, amino, protected amino, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroary!;
R3c is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group;
R.3d i s cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group; or
3c and R3d together form a ring;
4a is halogen, hydroxy!, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl;
R4b is halogen, hydroxyl, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl;
R?e is hydrogen, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl, or a nitrogen protecting group;
R.9a is hydrogen, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl;
Rub is halogen, hydroxy!, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl, heteroaryl;
Ri5b is hydrogen, halogen, hydroxyl, protected hydroxy!, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaiiphatic, aryl or heteroaryl; Ri6a is hydrogen, halogen, hydroxy!, protected hydroxyl, cyano, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl; and
Ri8a and Risb independently are hydrogen, halogen, cyano, cyclic or acyclic, linear or
branched aliphatic, cyclic or acyclic, linear or branched heteroaliphatic, aryl or heteroaryl.
32. The compound of claim 31, wherein:
i is halogen, -OH, protected hydroxyl, -O(alkyl), -OC(0)alkyl, -NH2, protected amino, -NHC(0)alkyi, or heteroaryl;
Rsc is alkyl, cycioaikyi, heteroalkyl, heterocyclyl, or a nitrogen protecting group;
Rsd is alkyl, cycioaikyi, heteroalkyl, heterocyclyl, or a nitrogen protecting group,
R4a is halogen, -OH, protected hydroxy!, -O(alkyl), -OC(0)aikyi, alkyl, cycioaikyi heteroalkyl, or heterocyclyl; and
R4 is alkyl, cycioaikyi, heteroalkyl or heterocyclyl; or
R.4a and Rjc are combined to form a five or six-mernbered ring; or
R4a and R3d are combined to form a five or six-membered ring;
R - is - V or -N(R7c)(R-7d);
R?c is hydrogen or a nitrogen protecting group;
R?d is hydrogen or a nitrogen protecting group;
R9a is hydrogen, alkyl, carboxyalkyl, cycioaikyi, heteroalkyl or heterocyclyl;
Ru is halogen, protected hydroxyl, -OH, -O(aikyl), -OC(0)alkyl, - HC(0)alkyl, or heteroaryl,
Risb is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl;
Riea is hydrogen, halogen, -OH, -O(alkyl), -OC(0)alkyl, -NHC(0)alkyl, alkyl, or heteroalkyl; and
Riga and Risb independently are hydrogen, alkyl, cycioaikyi, or cyclic or acyclic heteroalkyl.
33. The compound of cl aim 3 1 , wherein :
Ra> is protected hydroxyl;
Rsd is alkyl;
R4a is protected hydroxyl;
R4 is alkyl or benzyl; or
R4a and R3c are combined to form a five-membered ring; or
R4a and R3d are combined to form a five-membered ring;
ve is -N3 or -N(R7c)(R7d);
R?c is hydrogen or a nitrogen protecting group;
R?d is hydrogen or a nitrogen protecting group,
R9a is hydrogen;
Rub is hydroxyl or protected hydroxy!; and
Ri5b and Ri6a are hydrogen; and
Riga and Risb independently are hydrogen, alkyl, or heteroalkvl.
34. The compound of any one of claims 31 -33, wherein Formula (I-e) is selected from F rmulae (I-el)-(I-e6):
Figure imgf000168_0001
(I-el) (I- ■e2
Figure imgf000168_0002
(I~e3) 4)
Figure imgf000169_0001
(I~e5)
55. A method of preparing a compound of Formula (I):
Figure imgf000169_0002
or a pharmaceutically acceptable salt thereof, wherein Formula (I) is defined according to any one of claims 1-7, the method comprising reducing a compound of Formula (I-e):
Figure imgf000169_0003
or a salt thereof, to form the compound of Formula (I), wherein Formula (I-e) is defined according to any one of claims 31-34.
36. The method of claim 35, further comprising contacting the compound of Formula (I-e), or a salt thereof, wherein Risa and Risb are hydrogen, with a base and an electrophile to produce a compound of Formula (I-e), or a salt thereof, wherein one or both of Riga and Risb are not hydrogen.
37. The method of claim 36, wherein Riga and Risb are independently alkyl.
38. The method of claim 36, wherein the base is selected from a carbonate, a tertiary amine, a hydride, and a metal amide.
39. The method of claim 36, wherein the electrophile is formaldehyde, Risa-X or Ri sb-X, wherein Risa and Ri8b are not hydrogen, and wherein X is a leaving group.
40. The method of claim 35, wherein said reducing a compound of Formula (I-e), or a salt thereof, comprises:
(a) reducing the nitro group to a primary amine with a first reducing agent;
(b) optionally alkylating or acylating the primary amine of (a);
(c) reducing one or more azido groups to corresponding primary amines with a
second reducing agent; and
(d) optionally alkylating or acylating the corresponding primary amines of (c).
41. The method of claim 40, wherein the first reducing agent and the second reducing agent are the same, and the nitro group and azide groups are reduced simultaneously.
42. The method of claim 40, wherein the first reducing agent and the second reducing agent are different.
43. The method of claim 35, further comprising coupling a compound of Formula (I-c):
Figure imgf000170_0001
or a salt thereof, with a compound of Formula (I-d):
Figure imgf000171_0001
or a salt thereof, under suitable conditions to form the compound of Formula (l-e), wherein Formula (I-c) is defined according to any one of claims 19-25, and wherein Formula (I- d) is defined according to any one of claims 26-30,
44. The method of claim 43, wherein the suitable conditions comprise an oxidizing agent.
45. The method of claim 43, wherein said coupling a compound of Formula (I-c), or a salt thereof, with a compound of Formula (I-d), or a salt thereof, comprises;
(a) contacting the compound of Formula (I-c), or a salt thereof, with a compound of Formula (I-d) , or a salt thereof, under suitable conditions to produce a compound of Formula (I-e), wherein R?e is N(R7C)(R?d) and wherein R7c and R?d are nitrogen protecting groups,
(b) removing the nitrogen protecting groups of Formula (l-e) under suitable
conditions to produce a compound of Formula (l-e), wherein R7e is NEb; and lating the product of (b) with a compound having the formula;
Figure imgf000171_0002
wherein X is a leaving group and R?f is Ci-e. alkyl or Ci-e heteroalkyl, to produce a compound of Formula (I~e) wherein R7e has the structure:
Figure imgf000171_0003
46. The method of claim 45, wherein the suitable conditions of (a) comprise an oxidizing agent.
47. The method of claim 45, wherein the suitable conditions of (b) comprise oxidation, hydrogenolysis, acid hydrolysis or base hydrolysis.
48. The method of claim 45 wherein R7e has structure selected from:
Figure imgf000172_0001
wherein PG is a protecting group; and
R'?g and R?h are independently hydrogen, a nitrogen protecting group, cyclic or acyclic, linear or branched aliphatic, cyclic or acyclic, linear or branched heteroaliphati c, aryl or heteroaryl, or R7g and R? are combined to form a ring.
The method of claim 38, further comprising coupling a compound of Formula (I-a)
Figure imgf000172_0002
or a salt thereof, with a compound of Formula (I-
Figure imgf000172_0003
or a salt thereof, under suitable conditions to produce a compound of Formula (I-c), wherein Formula (I-a) is defined according to any one of claims 9- 2, and wherein Formula ( d) is defined according to any one of claims 13-18.
50. The method of claim 49, wherein the suitable conditions comprise an oxidizing agent.
51. The method of claim 49, wherein said coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof, comprises:
(a) coupling a compound of Formula (I-a), or a salt thereof, with a compound of Formula (I-b), or a salt thereof, under suitable conditions to produce a compound of Formula (I-c), wherein Ri2a is an oxygen protecting group; and (b) removing the oxygen protecting group under suitable conditions to produce a compound of Formula (I-c), wherein R12a is hydrogen.
52. The method of claim 51, wherein the suitable conditions of (a) comprise an oxidizing agent.
53. The method of claim 51 , wherein the suitable conditions of (b) comprise hydrogenolysis, acid hydrolysis or base hydrolysis.
54. A pharmaceutical composition comprising a compound of any one of claims 1-8 and a pharmaceutically acceptable excipient.
55. The pharmaceutical composition of claim 54, further comprising an additional therapeutic agent.
56. A kit comprising a compound of any one of claims 1 -8, and a container.
57. A method of treating an infection in a subject in need thereof, comprising administering to the subject a compound of any one of claims 1-8, or a pharmaceutical composition of claim 54,
58. The method of claim 57, wherein the bacterial infection is associated with bacteria expressing ribosomal methylase ArmA.
59. The method of claim 57, wherein the bacterial infection i s associated with a Gram negative bacteria.
60. The method of claim 57, wherein the bacterial infection is associated with a Gram positive bacteria.
61 . The method of claim 58, wherein the bacterial infection is associated with one or more bacteria selected from Enlerococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetohacter baumannii, Psendomonas aeruginosa, and Enterohacteria.
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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE PUBCHEM SUBSTANCE [online] 12 June 2009 (2009-06-12), XP055597024, retrieved from NCBI Database accession no. 77087000 *
DATABASE PUBCHEM substance [online] 6 January 2015 (2015-01-06), XP055597008, retrieved from NCBI Database accession no. 223658860 *

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