Classifications

• • A—HUMAN NECESSITIES
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  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/529—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim forming part of bridged ring systems
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/445—Non condensed piperidines, e.g. piperocaine
  • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
  • A61K31/4545—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a six-membered ring with nitrogen as a ring hetero atom, e.g. pipamperone, anabasine
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/66—Phosphorus compounds
  • A61K31/675—Phosphorus compounds having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
• • 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
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
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  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/90—Enzymes; Proenzymes
  • G01N2333/91—Transferases (2.)
  • G01N2333/912—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

• compositions comprising the compounds and the use of the compounds in therapy. More particularly, provided herein are certain macrocyclic compounds which exhibit ROS1 protein kinase inhibition, and which are useful in the treatment of cancer.
• ROS1 is a receptor tyrosine kinase that is closely related to ALK, and, like ALK, it undergoes genomic rearrangement that creates fusion proteins in various cancers (Davies K D and Doebele R C (2013) Clin Cancer Res 19: 4040-4045). It is well established that these fusion proteins act as oncogenic drivers and that ROS1 inhibition is anti-proliferative in cells that express ROS1 fusions (Davies K D, Le A T, Theodoro M F, Skokan M C, Aisner D L, et al. (2012) Clin Cancer Res 18: 4570-4579). Thus, it appears that ROS1 targeted therapy will likely soon be the standard of care for this patient population. However, based on the experiences with other kinase inhibitors in various cancers, it is fully expected that acquired resistance to ROS1 inhibition will occur, and this will ultimately limit the treatment options for patients.
• macrocyclic compounds are inhibitors of ROS1 kinase, and are useful for treating various cancers.
• Compounds which are inhibitors of ROS1 may be useful in the treatment of multiple types of cancer including cancers exhibiting resistance to ROS1 inhibition.
• the methods provided include administration of a ROS1 inhibitor, wherein the ROS1 inhibitor is a compound of Formula I
• ring A, ring B, W, m, D, R 2 , R 2a , R 3 , R 3a , and Z are as defined herein.
• a compound of Formula I has the general formula:
• the compound of Formula I is selected from the compounds of Table 1, or a pharmaceutically acceptable salt or solvate thereof. In some embodiments, the compound of Formula I is selected from the group consisting of Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• a method for treating a cancer in a patient in need thereof comprising:
• a method for treating a cancer in a patient in need thereof comprising:
• Also provided herein is a method for treating cancer in a patient in need thereof, the method comprising administering to a patient identified or diagnosed as having a ROS1-associated cancer a therapeutically effective amount of a ROS1 inhibitor, wherein the ROS1 inhibitor is a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• a method of treating cancer in a patient in need thereof comprising:
• a method of treating cancer in a patient in need thereof comprising:
• Also provided herein is a method of treating a subject having a cancer, wherein the method comprises:
• a method of treating a subject having a cancer comprising:
• Also provided herein is a method of treating a subject having a cancer, wherein the method comprises:
• a method of treating a subject having a cancer comprising:
• Also provided herein is a method of treating a subject having a cancer, wherein the method comprises:
• a method of treating a subject having a cancer comprising:
• Also provided herein is a method of treating a patient, the method comprising administering a therapeutically effective amount of a compound of Formula I, or a pharmaceutically acceptable salt or solvate thereof, to a patient having a clinical record that indicates that the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• a method of selecting a treatment for a patient comprising selecting a treatment comprising administration of a compound of Formula I, or a pharmaceutically acceptable salt or solvate thereof, for a patient identified or diagnosed as having a ROS1-associated cancer.
• a method of selecting a treatment for a patient having a cancer comprising:
• Also provided herein is a method of selecting a patient for treatment including administration of a therapeutically effective amount of a compound of Formula I, or a pharmaceutically acceptable salt or solvate thereof, the method comprising:
• a method of selecting a patient having cancer for treatment including administration of a therapeutically effective amount of a compound of Formula I, or a pharmaceutically acceptable salt or solvate thereof, the method comprising:
• ring B is ring B-2 having the structure:
• ring A is ring A-1 having the structure
• ring A when represented by structure A-1 include the structures:
• ring A is ring A-2 having the structure
• ring A when represented by ring A-2 are the structures:
• ring A is ring A-3 having the structure
• ring A when represented by ring A-3 are the structures:
• W is O.
• W is NH
• W is CH 2 .
• D is carbon
• R 2 and R 2a are independently H, F, (1-3 C)alkyl or OH (provided that R 2 and R 2a are not both OH)
• R 3 and R 3a are independently H, (1-3 C)alkyl or hydroxy(1-3 C)alkyl.
• R 2 and R 2a are independently H, F, methyl or OH, provided that R 2 and R 2a are not both OH.
• R 2 and R 2a are both H.
• R 2 is H and R 2a is F.
• R 2 and R 2a are both F.
• R 2 is H and R 2a is OH.
• R 2 is H and R 2a is methyl.
• R 2 and R 2a are both methyl.
• R 3 and R 3a are independently H, (1-3C)alkyl or hydroxy(1-3 C)alkyl.
• R 3a is H. In some embodiments, R 3 is H. In some embodiments, both R 3 and R 3a are H.
• R 3a is (1-3C)alkyl. Examples include methyl, ethyl, propyl and isopropyl. In some embodiments, R 3 is (1-3C)alkyl. Examples include methyl, ethyl, propyl and isopropyl.
• R 3a is (1-3C)alkyl and R 3 is H. In some embodiments, R 3a is methyl and R 3 is H.
• both R 3a and R 3 are (1-3C)alkyl. In some embodiments, R 3a and R 3a are both methyl.
• R 3 is hydroxy(1-3C)alkyl. Examples include hydroxymethyl, 2-hydroxyethyl, 2-hydroxypropyl, and 3-hydroxypropyl. In some embodiments, R 3 is hydroxymethyl, 2-hydroxyethyl, 2-hydroxypropyl, or 3-hydroxypropyl and R 3a is H.
• D is carbon or nitrogen
• R 2 and R 3 are absent
• R 2a and R 3a together with the atoms to which they are attached form a 5-6 membered heteroaryl ring having 1-2 ring heteroatoms.
• R 2a and R 3a together with the atoms to which they are attached form a 5-6 membered heteroaryl ring having 1-2 ring nitrogen atoms.
• heteroaryl rings include pyridyl and pyrazolyl rings. Specific examples of heteroaryl rings include the structures:
• Z is *—NR 4a C( ⁇ O)—.
• R 4a is H.
• R 4a is (1-6C)alkyl. Examples include methyl, ethyl, propyl, isopropyl, butyl, and isobutyl.
• R 4a is fluoro(1-6C)alkyl. Examples include fluoromethyl and 2-fluoroethyl.
• R 4a is difluoro(1-6C)alkyl.
• Example include difluoromethyl and 2,2-difluoroethyl.
• R 4a is trifluoro(1-6C)alkyl. Examples include trifluoromethyl and 2,2,2-trifluoroethyl.
• R 4a is hydroxy(1-6C alkyl). Examples include hydroxymethyl, 2-hydroxyethyl, 2-hydroxypropyl and 3-hydroxypropyl.
• R 4a is dihydroxy(2-6C alkyl).
• An example includes 2,3-dihydroxypropyl.
• R 4a is H or (1-6C)alkyl. In some embodiments, R 4a is H or Me.
• Z is *—NR 4b CH 2 —.
• R 4b is H.
• R 4b is selected from (1-6C)alkyl, fluoro(1-6C)alkyl, difluoro(1-6C)alkyl, and trifluoro(1-6C)alkyl.
• R 4b is (1-6C)alkyl. Examples include methyl, ethyl, propyl, isopropyl, butyl and tert-butyl. In some embodiments, R 4b is methyl.
• R 4b is fluoro(1-6C)alkyl. Examples include fluoromethyl and 2-fluoroethyl.
• R 4b is difluoro(1-6C)alkyl.
• Example include difluoromethyl and 2,2-difluoroethyl.
• R 4b is trifluoro(1-6C)alkyl. Examples include trifluoromethyl and 2,2,2-trifluoroethyl.
• R 4b is selected from (1-6C alkyl)C(O)—, (3-6C cycloalkyl)C(O)—, Ar 1 C(O)— and HOCH 2 C(O)—.
• R 4b is (1-6C alkyl)C(O)—. Examples include CH 3 C(O)—, CH 3 CH 2 C(O)—, CH 3 CH 2 CH 2 C(O)—, and (CH 3 ) 2 CHC(O)—. In some embodiments, R 4 is CH 3 C(O)—.
• R 4b is (3-6C cycloalkyl)C(O)—. Examples include cyclopropylC(O)—, cyclobutylC(O)—, cyclopentylC(O)— and cyclohexylC(O)—.
• R 4b is Ar 1 C(O)—.
• An example is phenylC(O)—.
• R 4b is HOCH 2 C(O)—.
• R 4b is selected from (1-6C alkyl)sulfonyl, (3-6C cycloalkyl)sulfonyl, and Ar 2 (SO 2 )—.
• R 4b is (1-6C alkyl)sulfonyl. Examples include methylsulfonyl, ethylsulfonyl and propylsulfonyl.
• R 4b is (3-6C cycloalkyl)sulfonyl. Examples include cyclopropylsulfonyl, cyclobutylsulfonyl, cyclopentylsulfonyl and cyclohexylsulfonyl. In some embodiments, R 4 is methylsulfonyl.
• R 4b is Ar 2 (SO 2 )—.
• An example is phenylsulfonyl.
• R 4b is HO 2 CCH 2 —.
• R 4b is (1-6C alkyl)NH(CO)—. Examples include CH 3 NHC(O)—, CH 3 CH 2 NHC(O)—, CH 3 CH 2 CH 2 NHC(O)—, and (CH 3 ) 2 CHNHC(O)—. In some embodiments, R 4 is CH 3 NHC(O)—.
• R 4b is selected from H, methyl, —C(O)CH 3 , methylsulfonyl, —C(O)CH 2 OH, —CH 2 COOH and —C(O)NHCH 2 CH 3 .
• Z is *—OC( ⁇ O)—.
• ring B is ring B-1:
• R 5 and R 6 are independently H, F, OH, (1-6C)alkyl or hydroxy(1-6C)alkyl. In some embodiments, R 5 is H and R 6 is H, F, OH, (1-6C)alkyl or hydroxy(1-6C)alkyl.
• R 5 and R 6 are independently H, F, OH, (1-3C)alkyl or hydroxy(1-3C)alkyl. In some embodiments, R 5 is hydrogen and R 6 is H, F, OH, (1-3C)alkyl or hydroxy(1-3C)alkyl.
• R 5 and R 6 are independently H, F, OH, methyl, ethyl, HOCH 2 — or HOCH 2 CH 2 —. In some embodiments, R 5 is hydrogen and R 6 is H, F, OH, methyl, ethyl, HOCH 2 — or HOCH 2 CH 2 —.
• R 5 and R 6 are independently H, F, or methyl. In some embodiments, R 5 is H and R 6 is H, F, or methyl.
• R 5 is H and R 6 is F.
• R 5 is H and R 6 is methyl.
• R 5 and R 6 are both H.
• R 5 and R 6 are both F.
• R 5 and R 6 are both methyl.
• ring B is ring B-1 which is optionally substituted with one or two substituents independently selected from OH and F, provided that two OH substituents are not on the same ring carbon atom.
• ring B when represented by ring B-1 include the structures:
• ring B is ring B-2 having the formula:
• m is 0.
• m is 1.
• n is 2.
• Formula IA includes compounds wherein:
• X is N. In some embodiments, X is CH.
• Formula IA includes compounds wherein:
• Formula IA includes compounds wherein:
• Formula IA includes compounds wherein:
• Formula IA includes compounds wherein:
• X is N. In some such embodiments of Formula IA where ring A is ring A-1, W is O. In some embodiments of Formula IA where ring A is ring A-1, W is CH 2 . In some embodiments of Formula IA where ring A is ring A-1, R 2 and R 2a are H. In some embodiments of Formula IA where ring A is ring A-1, R 2 and R 2a are independently F, (1-3 C)alkyl, or OH. In some embodiments of Formula IA where ring A is ring A-1, R 3 is (1-3 C)alkyl. In some embodiments of Formula IA where ring A is ring A-1, R 3 is H. In some embodiments of Formula IA where ring A is ring A-1, Z is *—NR 4a C( ⁇ O)—. In some embodiments of Formula IA where ring A is ring A-1, R 5 and R 6 are H.
• Formula IA includes compounds wherein:
• Y is F.
• R 2 and R 2a are H.
• R 2 and R 2a are independently H or (1-3 C)alkyl.
• R 3 is (1-3 C)alkyl.
• R 5 and R 6 are H.
• Formula IA includes compounds wherein:
• Y is F. In some embodiments of Formula IA where ring A is ring A-3, Y is H. In some embodiments of Formula IA where ring A is ring A-3, R 2 and R 2a are H. In some embodiments of Formula IA where ring A is ring A-3, R 2 and R 2a are independently H or (1-3 C)alkyl. In some embodiments of Formula IA where ring A is ring A-3, R 3 is (1-3 C)alkyl. In some embodiments of Formula IA where ring A is ring A-3, R 3 is H. In some embodiments of Formula IA where ring A is ring A-3, R 5 and R 6 are H.
• certain compounds as provided herein may contain one or more centers of asymmetry and may therefore be prepared and isolated as a mixture of isomers such as a racemic or diastereomeric mixture, or in an enantiomerically or diastereomerically pure form. It is intended that all stereoisomeric forms of the compounds provided herein, including but not limited to, diastereomers, enantiomers and atropisomers, as well as mixtures thereof such as racemic mixtures, form part of the present disclosure.
• compounds of the general Formula I wherein Ring B is ring B-1 have the absolute configuration of Formula 1-a:
• compounds of the general Formula I wherein Ring B is ring B-1 have the absolute configuration of Formula 1-b:
• stereochemistry of any particular chiral atom is not specified, then all stereoisomers are contemplated and included as the compounds of the disclosure. Where stereochemistry is specified by a solid wedge or dashed line representing a particular configuration, then that stereoisomer is so specified and defined.
• (1-3C)alkyl and “(1-6C)alkyl” as used herein refer to saturated linear or branched-chain monovalent hydrocarbon radicals of one to three carbon atoms and one to six carbon atoms, respectively. Examples include, but are not limited to, methyl, ethyl, 1-propyl, isopropyl, 1-butyl, isobutyl, sec-butyl, tert-butyl, 2-methyl-2-propyl, pentyl, and hexyl.
• fluoro(1-6C)alkyl refers to saturated linear or branched-chain monovalent hydrocarbon radicals of one to six carbon atoms as defined herein, wherein one of the hydrogens is replaced by a fluorine atom.
• difluoro(1-6C)alkyl refers to saturated linear or branched-chain monovalent hydrocarbon radicals of one to six carbon atoms as defined herein, wherein two of the hydrogens are replaced by fluorine atoms.
• trifluoro(1-6C)alkyl refers to saturated linear or branched-chain monovalent hydrocarbon radicals of one to six carbon atoms as defined herein, wherein three of the hydrogens are replaced by fluorine atoms.
• hydroxy(1-6Calkyl) refers to saturated linear or branched-chain monovalent hydrocarbon radicals of one to six carbon atoms, wherein one of the hydrogens is replaced by a hydroxy (OH) group.
• dihydroxy(2-6C alkyl) refers to saturated linear or branched-chain monovalent hydrocarbon radicals of two to six carbon atoms as defined herein, wherein two of the hydrogens are replaced by hydroxy (OH) groups, provided the hydroxy groups are not on the same carbon atom.
• (1-6C alkyl)sulfonyl refers to a (1-6C alkyl)SO 2 — group, wherein the radical is on the sulfur atom and the (1-6C alkyl) portion is as defined above. Examples include methylsulfonyl (CH 3 SO 2 —) and ethylsulfonyl (CH 3 CH 2 SO 2 —).
• (3-6C cycloalkyl)sulfonyl refers to a (3-6C cycloalkyl)SO 2 — group, wherein the radical is on the sulfur atom.
• An example is cyclopropylsulfonyl.
• (1-3C)alkoxy and “(1-6C)alkoxy”, as used herein refer to saturated linear or branched-chain monovalent alkoxy radicals of one to three carbon atoms or one to six carbon atoms, respectively, wherein the radical is on the oxygen atom. Examples include methoxy, ethoxy, propoxy, isopropoxy, and butoxy.
• halogen includes fluoro, chloro, bromo and iodo.
• Non-limiting examples of the compounds of Formula I include those in Table 1.
• the compounds of Formula I include salts thereof.
• the salts are pharmaceutically acceptable salts.
• the compounds of Formula I include other salts of such compounds which are not necessarily pharmaceutically acceptable salts, and which may be useful as intermediates for preparing and/or purifying compounds of Formula I and/or for separating enantiomers of compounds of Formula I.
• pharmaceutically acceptable indicates that the substance or composition is compatible chemically and/or toxicologically, with the other ingredients comprising a formulation, and/or the mammal being treated therewith.
• the compounds provided herein may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds. That is, an atom, in particular when mentioned in relation to a compound according to Formula I, comprises all isotopes and isotopic mixtures of that atom, either naturally occurring or synthetically produced, either with natural abundance or in an isotopically enriched form.
• the compounds provided herein therefore also comprise compounds with one or more isotopes of one or more atom, and mixtures thereof, including radioactive compounds, wherein one or more non-radioactive atoms has been replaced by one of its radioactive enriched isotopes.
• Radiolabeled compounds are useful as therapeutic agents, e.g., cancer therapeutic agents, research reagents, e.g., assay reagents, and diagnostic agents, e.g., in vivo imaging agents. All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are intended to be encompassed within the scope of the present disclosure.
• the compounds of Formula I or a salt thereof as defined herein can be prepared as described in U.S. Pat. No. 8,933,084, which is incorporated by reference in its entirety herein.
• a process for preparing a compound of Formula I or a salt thereof as defined herein can include:
• ring B is ring B-1 having the structure:
• D is carbon
• R 2 and R 2a are independently H, F, (1-3 C)alkyl or OH (provided that R 2 and R 2a are not both OH)
• R 3 is H, (1-3 C)alkyl or hydroxy(1-3 C)alkyl
• ring A, W, m, Z, Y, R 3a , R 5 and R 6 are as defined for Formula I.
• the cyclization may be performed using conventional amide bond formation conditions, for example by treating the carboxylic acid with an activating agent, followed by addition of the amine in the presence of a base.
• Suitable activating agents include EDCI, oxalyl chloride, thionyl chloride, HATU, and HOBt.
• Suitable bases include amine bases, for example triethylamine, diisopropylethylamine, pyridine, or excess ammonia.
• Suitable solvents include DCM, DCE, THF and DMF.
• the leaving atoms L 1 and L 2 may be, for example a halogen atom such as Br, Cl or I.
• L 1 and L 2 can be a leaving group, for example an arylsulfonyloxy group or an alkylsulfonyloxy group, such as a mesylate or a tosylate group.
• Suitable bases include alkali metal carbonates, such as sodium carbonate, potassium carbonate or cesium carbonate.
• Convenient solvents include aprotic solvents such as ethers (for example tetrahydrofuran or p-dioxane), DMF, or acetone.
• the reaction can be conveniently performed at elevated temperatures, for example 50-150° C., for example at 85° C.
• suitable coupling reagents include HATU, HBTU, TBTU, DCC, DIEC, and any other amide coupling reagents well known to persons skilled in the art.
• Suitable bases include tertiary amine bases such as DIEA and triethylamine.
• Convenient solvents include DMF, THF, DCM and DCE.
• suitable reducing agents include Me 4 N(OAc) 3 BH, Na(OAc) 3 BH and NaCNBH 3 .
• Suitable solvents include neutral solvents such as acetonitrile, THF and DCE. The reaction can be conveniently performed at ambient temperature.
• the triphenylphosphine reagent is used in the form of a polystyrene-bound PPh 3 resin (sold as PS-PPh 3 by Biotage Systems).
• the reaction is conveniently performed at ambient temperature.
• Suitable solvents include neutral solvents, for example DCM.
• the leaving atom L 3 may be a halogen, for example Cl or Br.
• Suitable bases include tertiary amine bases such as diisopropylethylamine and triethylamine. The reaction is conveniently performed at ambient temperature.
• suitable bases include tertiary amine bases such as DIEA and triethylamine.
• the reaction is conveniently performed at ambient temperature.
• the fluorination reagent may be, for example, bis(2-methoxyethyl)amino-sulfur trifluoride (Deoxo-FluorTM) or diethylaminosulfur trifluoride (DAST).
• Suitable solvents include dichloromethane, chloroform, dichloroethane, and toluene. The reaction is conveniently performed at ambient temperature.
• base may be, for example, an alkali metal carbonate, such as for example sodium carbonate, potassium carbonate or cesium carbonate.
• Convenient solvents include aprotic solvents such as ethers (for example tetrahydrofuran or p-dioxane) or toluene.
• the reaction can be conveniently performed at a temperature between ambient temperature and reflux, for example at 85° C.
• Amine groups in compounds described in any of the above methods may be protected with any convenient amine protecting group, for example as described in Greene & Wuts, eds., “Protecting Groups in Organic Synthesis”, 2 nd ed. New York; John Wiley & Sons, Inc., 1991.
• amine protecting groups include acyl and alkoxycarbonyl groups, such as t-butoxycarbonyl (BOC), and [2-(trimethylsilyl)ethoxy]methyl (SEM).
• carboxyl groups may be protected with any convenient carboxyl protecting group, for example as described in Greene & Wuts, eds., “Protecting Groups in Organic Synthesis”, 2 nd ed.
• carboxyl protecting groups include (1-6C)alkyl groups, such as methyl, ethyl and t-butyl.
• Alcohol groups may be protected with any convenient alcohol protecting group, for example as described in Greene & Wuts, eds., “Protecting Groups in Organic Synthesis”, 2 nd ed. New York; John Wiley & Sons, Inc., 1991.
• Examples of alcohol protecting groups include benzyl, trityl, silyl ethers, and the like.
• test compounds to act as ROS1 inhibitors may be demonstrated by the assay described in Example A. IC 50 values are shown in Table 17.
• inhibition of L2026M is similar to, or better than, that observed for wild-type ROS1.
• inhibition of L2026M is within about 2-fold (e.g., about 5-fold, about 7-fold, about 10-fold) of inhibition of wild-type ROS1 (i.e. the compounds are similarly potent against wild-type ROS1 and L2026M).
• inhibition of L2026M is about the same as inhibition of wild-type ROS1.
• inhibition of L2026M is about 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, or greater than inhibition of wild-type ROS1.
• selectivity for a wildtype or L2026M ROS1 kinase over another kinase is measured in an enzyme assay (e.g., an enzyme assay as provided herein).
• an enzyme assay e.g., an enzyme assay as provided herein.
• the compounds provided herein exhibit selective cytotoxicity to ROS1-mutant cells.
• inhibition of D2033N is similar to, or better than, that observed for wild-type ROS1. In some embodiments, inhibition of D2033N is within about 2-fold (e.g., about 5-fold, about 7-fold, about 10-fold) of inhibition of wild-type ROS1 (i.e. the compounds are similarly potent against wild-type ROS1 and D2033N). In some embodiments, inhibition of D2033N is about the same as inhibition of wild-type ROS1. In some embodiments, inhibition of D2033N is about 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, or greater than inhibition of wild-type ROS1.
• selectivity for a wildtype or D2033N ROS1 kinase over another kinase is measured in an enzyme assay (e.g., an enzyme assay as provided herein).
• an enzyme assay e.g., an enzyme assay as provided herein.
• the compounds provided herein exhibit selective cytotoxicity to ROS1-mutant cells.
• ROS1-associated diseases and disorders e.g., proliferative disorders such as cancers, including hematological cancers and solid tumors.
• treat or “treatment” refer to therapeutic or palliative measures.
• Beneficial or desired clinical results include, but are not limited to, alleviation, in whole or in part, of symptoms associated with a disease or disorder or condition, diminishment of the extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state (e.g., one or more symptoms of the disease), and remission (whether partial or total), whether detectable or undetectable.
• Treatment can also mean prolonging survival as compared to expected survival if not receiving treatment.
• the terms “subject,” “individual,” or “patient,” are used interchangeably, refers to any animal, including mammals such as mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, primates, and humans.
• the patient is a human.
• the subject has experienced and/or exhibited at least one symptom of the disease or disorder to be treated and/or prevented.
• the subject has been identified or diagnosed as having a cancer with a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same (a ROS1-associated cancer) (e.g., as determined using a regulatory agency-approved, e.g., FDA-approved, assay or kit).
• the assay is a liquid biopsy.
• the subject has a tumor that is positive for a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same (e.g., as determined using a regulatory agency-approved assay or kit).
• the subject can be a subject with a tumor(s) that is positive for a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same (e.g., identified as positive using a regulatory agency-approved, e.g., FDA-approved, assay or kit).
• the assay is a liquid biopsy.
• the subject can be a subject whose tumors have a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or a level of the same (e.g., where the tumor is identified as such using a regulatory agency-approved, e.g., FDA-approved, kit or assay).
• the subject is suspected of having a ROS1-associated cancer.
• the subject has a clinical record indicating that the subject has a tumor that has a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same (and optionally the clinical record indicates that the subject should be treated with any of the compositions provided herein).
• the patient is a pediatric patient.
• the term “pediatric patient” as used herein refers to a patient under the age of 21 years at the time of diagnosis or treatment.
• the term “pediatric” can be further be divided into various subpopulations including: neonates (from birth through the first month of life); infants (1 month up to two years of age); children (two years of age up to 12 years of age); and adolescents (12 years of age through 21 years of age (up to, but not including, the twenty-second birthday)).
• Berhman R E, Kliegman R, Arvin A M Nelson W E. Nelson Textbook of Pediatrics, 15th Ed. Philadelphia: W.B. Saunders Company, 1996; Rudolph A M, et al. Rudolph's Pediatrics, 21st Ed.
• a pediatric patient is from birth through the first 28 days of life, from 29 days of age to less than two years of age, from two years of age to less than 12 years of age, or 12 years of age through 21 years of age (up to, but not including, the twenty-second birthday).
• a pediatric patient is from birth through the first 28 days of life, from 29 days of age to less than 1 year of age, from one month of age to less than four months of age, from three months of age to less than seven months of age, from six months of age to less than 1 year of age, from 1 year of age to less than 2 years of age, from 2 years of age to less than 3 years of age, from 2 years of age to less than seven years of age, from 3 years of age to less than 5 years of age, from 5 years of age to less than 10 years of age, from 6 years of age to less than 13 years of age, from 10 years of age to less than 15 years of age, or from 15 years of age to less than 22 years of age.
• compounds of Formula I are useful for preventing diseases and disorders as defined herein (for example, cancer).
• preventing means the prevention of the onset, recurrence or spread, in whole or in part, of the disease or condition as described herein, or a symptom thereof.
• ROS1-associated disease or disorder refers to diseases or disorders associated with or having a dysregulation of a ROS1 gene, a ROS1 kinase (also called herein ROS1 kinase protein), or the expression or activity or level of any (e.g., one or more) of the same (e.g., any of the types of dysregulation of a ROS1 gene, a ROS1 kinase, a ROS1 kinase domain, or the expression or activity or level of any of the same described herein).
• a non-limiting example of a ROS1-associated disease or disorder includes cancer.
• ROS1-associated cancer refers to cancers associated with or having a dysregulation of a ROS1 gene, a ROS1 kinase (also called herein ROS1 kinase protein), or expression or activity, or level of any of the same.
• ROS1 kinase protein also called herein ROS1 kinase protein
• Non-limiting examples of a ROS1-associated cancer are described herein.
• the phrase “dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same” refers to a genetic mutation (e.g., a ROS1 gene translocation that results in the expression of a fusion protein, a deletion in a ROS1 gene that results in the expression of a ROS1 protein that includes a deletion of at least one amino acid as compared to the wild-type ROS1 protein, a mutation in a ROS1 gene that results in the expression of a ROS1 protein with one or more point mutations, or an alternative spliced version of a ROS1 mRNA that results in a ROS1 protein having a deletion of at least one amino acid in the ROS1 protein as compared to the wild-type ROS1 protein) or a ROS1 gene amplification that results in overexpression of a ROS1 protein or an autocrine activity resulting from the overexpression of a ROS1 gene in a cell that results in a
• a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same can be a mutation in a ROS1 gene that encodes a ROS1 protein that is constitutively active or has increased activity as compared to a protein encoded by a ROS1 gene that does not include the mutation.
• a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same can be the result of a gene or chromosome translocation which results in the expression of a fusion protein that contains a first portion of ROS1 that includes a functional kinase domain, and a second portion of a partner protein that is not ROS1.
• dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity or level of any of the same can be a result of a gene translocation of one ROS1 gene with another non-ROS1 gene.
• Non-limiting examples of fusion proteins are described in Table 2.
• Non-limiting examples of ROS1 kinase protein point mutations are described in Table 3 and Table 3a. Additional examples of ROS1 kinase protein mutations (e.g., point mutations) are ROS1 inhibitor resistance mutations.
• Non-limiting examples of ROS1 inhibitor resistance mutations are described in Table 4.
• wildtype when referring to a ROS1 nucleic acid or protein describes a nucleic acid (e.g., a ROS1 gene or a ROS1 mRNA) or protein (e.g., a ROS1 protein) that is found in a subject that does not have a ROS1-associated disease, e.g., a ROS1-associated cancer (and optionally also does not have an increased risk of developing a ROS1-associated disease and/or is not suspected of having a ROS1-associated disease), or is found in a cell or tissue from a subject that does not have a ROS1-associated disease, e.g., a ROS1-associated cancer (and optionally also does not have an increased risk of developing a ROS1-associated disease and/or is not suspected of having a ROS1-associated disease).
• a ROS1-associated disease e.g., a ROS1-associated cancer
• regulatory agency refers to a country's agency for the approval of the medical use of pharmaceutical agents with the country.
• FDA U.S. Food and Drug Administration
• a method of treating cancer e.g., a ROS1-associated cancer
• the method comprising administering to the patient a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof or a pharmaceutical composition thereof.
• methods for treating a ROS1-associated cancer in a patient in need of such treatment comprising a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the patient; and b) administering a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same includes one or more fusion proteins.
• ROS1 gene fusion proteins are described in Table 2.
• the fusion protein is one of SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same includes one or more ROS1 kinase protein point mutations, insertions, and/or deletions.
• ROS1 kinase protein point mutations are described in Table 3 and Table 3a.
• the ROS1 kinase protein point mutations, insertions, and/or deletions are point mutations selected from the group consisting of A15G, R118N, G1025R, T1735M, R1948H, and R2072N.
• a compound of Formula I is selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the cancer e.g., ROS1-associated cancer
• the cancer is a hematological cancer.
• the cancer e.g., ROS1-associated cancer
• the cancer e.g., ROS1-associated cancer
• lung cancer e.g., small cell lung carcinoma or non-small cell lung carcinoma
• papillary thyroid cancer medullary thyroid cancer, differentiated thyroid cancer, recurrent thyroid cancer, refractory differentiated thyroid cancer, lung adenocarcinoma, bronchioles lung cell carcinoma, multiple endocrine neoplasia type 2A or 2B (MEN2A or MEN2B, respectively), pheochromocytoma, parathyroid hyperplasia, breast cancer, colorectal cancer (e.g., metastatic colorectal cancer), papillary renal cell carcinoma, ganglioneuromatosis of the gastroenteric mucosa, inflammatory myofibroblastic tumor, or cervical cancer.
• lung cancer e.g., small cell lung carcinoma or non-small cell lung carcinoma
• papillary thyroid cancer medullary thyroid cancer
• differentiated thyroid cancer differentiated thyroid cancer
• recurrent thyroid cancer refractory differentiated thyroid cancer
• the cancer e.g., ROS1-associated cancer
• ALL acute lymphoblastic leukemia
• AML acute myeloid leukemia
• adrenocortical carcinoma anal cancer
• appendix cancer astrocytoma, atypical teratoid/rhabdoid tumor
• basal cell carcinoma bile duct cancer
• bladder cancer bone cancer
• brain stem glioma brain tumor, breast cancer, bronchial tumor, Burkitt lymphoma
• carcinoid tumor unknown primary carcinoma, cardiac tumors, cervical cancer, childhood cancers, chordoma, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), chronic myeloproliferative neoplasms, colon cancer, colorectal cancer, craniopharyngioma, cutaneous T-cell lymphoma, bile duct cancer, duct
• a hematological cancer is selected from the group consisting of leukemias, lymphomas (non-Hodgkin's lymphoma), Hodgkin's disease (also called Hodgkin's lymphoma), and myeloma, for instance, acute lymphocytic leukemia (ALL), acute myeloid leukemia (AML), acute promyelocytic leukemia (APL), chronic lymphocytic leukemia (CLL), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), chronic neutrophilic leukemia (CNL), acute undifferentiated leukemia (AUL), anaplastic large-cell lymphoma (ALCL), prolymphocytic leukemia (PML), juvenile myelomonocyctic leukemia (JMML), adult T-cell ALL, AML with triline
• ALL acute lymphocytic leukemia
• AML acute myeloid leukemia
• hematological cancers include myeloproliferative disorders (MPD) such as polycythemia vera (PV), essential thrombocytopenia (ET) and idiopathic primary myelofibrosis (IMF/IPF/PMF).
• MPD myeloproliferative disorders
• PV polycythemia vera
• ET essential thrombocytopenia
• IMF/IPF/PMF idiopathic primary myelofibrosis
• the hematological cancer e.g., the hematological cancer that is a RET-associated cancer
• AML or CMML.
• the cancer is a solid tumor.
• solid tumors e.g., solid tumors that are ROS1-associated cancers
• the cancer is selected from the group consisting of lung cancer (including, e.g., non-small-cell lung cancer), colorectal cancer, gastric cancer, adenocarcinoma (including, e.g., small bowel adenocarcinoma), cholangiocarcinoma, glioblastoma, ovarian cancer, angiocarcinoma, congenital gliobastoma multiforme, papillary thyroid carcinoma, inflammatory myofibroblastic tumour, a spitzoid neoplasm, anaplastic large cell lymphoma, diffuse large B cell lymphoma, and B-cell acute lymphoblastic leukemia.
• lung cancer including, e.g., non-small-cell lung cancer
• colorectal cancer gastric cancer
• adenocarcinoma including, e.g., small bowel adenocarcinoma
• cholangiocarcinoma including, e.g., small bowel a
• the patient is a human.
• a method for treating a patient diagnosed with or identified as having a ROS1-associated cancer comprising administering to the patient a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, or a pharmaceutical composition thereof as defined herein.
• Dysregulation of a ROS1 kinase, a ROS1 gene, or the expression or activity or level of any (e.g., one or more) of the same can contribute to tumorigenesis.
• a dysregulation of a ROS1 kinase, a ROS1 gene, or expression or activity or level of any of the same can be a translocation, overexpression, activation, amplification, or mutation of a ROS1 kinase, a ROS1 gene, or a ROS1 kinase domain.
• a translocation can include a translocation involving the ROS1 kinase domain
• a mutation can include a mutation involving the ROS1 ligand-binding site
• an amplification can be of a ROS1 gene.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes overexpression of wild-type ROS1 kinase (e.g., leading to autocrine activation).
• the dysregulation of a ROS1 gene, a ROS1 kinase protein, or expression or activity or level of any of the same includes overexpression, activation, amplification, or mutation in a chromosomal segment comprising the ROS1 gene or a portion thereof, including, for example, the kinase domain portion, or a portion capable of exhibiting kinase activity.
• the dysregulation of a ROS1 gene, a ROS1 kinase protein, or expression or activity or level of any of the same includes one or more chromosome translocations or inversions resulting in a ROS1 gene fusion.
• the dysregulation of a ROS1 gene, a ROS1 kinase protein, or expression or activity or level of any of the same is a result of genetic translocations in which the expressed protein is a fusion protein containing residues from a non-ROS1 partner protein, and includes a minimum of a functional ROS1 kinase domain.
• ROS1 fusion proteins are shown in Table 2.
• Non-small-cell lung cancer 1 SLC34A2 including Non-small-cell lung cancer 1 , Colorectal SLC34A2-ROS(S) 28 , cancer 14 , Gastric cancer 15 , Lung SLC34A2-ROS(L) 28 , and adenocarcinoma 24 SLC34A2-ROS(VS) 28 , SLC34A2-ROS (with a breakpoint at chr6: 117653720, chr4: 25678781) 24 TPM3 Non-small-cell lung cancer 1 SDC4 Non-small-cell lung cancer 1 , Adenocarcinoma 10 EZR Non-small-cell lung cancer 1 LRIG3 Non-small-cell lung cancer 1 KDELR2 Non-small-cell lung cancer 1 CCDC6 Non-small-cell lung cancer 1 FIG (GOPC, PIST) Non-small-cell lung cancer 2 , including FIG-ROS1(L) 29 , Cholangiocarcinoma 5 ,
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes one or more deletions, insertions, or point mutation(s) in a ROS1 kinase. In some embodiments, the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, includes a deletion of one or more residues from the ROS1 kinase, resulting in constitutive activity of the ROS1 kinase domain.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes at least one point mutation in a ROS1 gene that results in the production of a ROS1 kinase that has one or more amino acid substitutions, insertions, or deletions as compared to the wild-type ROS1 kinase (see, for example, the point mutations listed in Table 3).
• ROS1 Point Mutations ROS1 Mutation ROS1-Associated Cancer
• Amino acid position 15 Diffuse large B cell lymphoma 1 (e.g., A15G) Amino acid position 118 B-cell acute lymphoblastic (e.g., R118N) leukemia 2 Amino acid position 122 Gastrointestinal stromal tumors (e.g., A122T) (GISTs) 3 Amino acid position 245 Uterine Corpus Endometrioid (e.g., R245I) Carcinoma 4 Amino acid position 1025 B-cell acute lymphoblastic (e.g., G1025R) leukemia 2 Amino acid position 1186 Non-Small-Cell Lung Cancer 5 (e.g., S1186F) Amino acid position 1539 Skin Cutaneous Melanoma 7 (e.g., P1539S) Amino acid position 1735 B-cell acute lymphoblastic (e.g., T17) Am
• Amino acid position 1186 (e.g., S1186F 11 ) Amino acid position 1935 (e.g., E1935G6 10 ) Amino acid position 1945 (e.g., L1945Q 7 ) Amino acid position 1946 (e.g., T1946S 7 ) Amino acid position 1947 (e.g., L1947R 6, 10 , L1947M 7 ) Amino acid position 1948 (e.g., R1948S 7 ) Amino acid position 1951 (e.g., L1951R 5 , L1951V 7 ) Amino acid position 1958 (e.g., E1958V 7 ) Amino acid position 1959 (e.g., V1959E 7 ) Amino acid position 1961 (e.g., E1961K 7 ) Amino acid position 1962 (e.g., G1962E 7 ) Amino acid position 1971 (e.g., G1971E 6, 10 ) Amino acid position 1945 (e
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes a splice variation in a ROS1 mRNA which results in an expressed protein that is an alternatively spliced variant of ROS1 having at least one residue deleted (as compared to the wild-type ROS1 kinase) resulting in a constitutive activity of a ROS1 kinase domain.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes a splice variation in a ROS1 mRNA which results in an expressed protein that is an alternatively spliced variant of ROS1 having at least one residue added (as compared to the wild-type ROS1 kinase) resulting in a constitutive activity of a ROS1 kinase domain.
• a “ROS1 kinase inhibitor” as defined herein includes any compound exhibiting ROS1 inhibition activity.
• a ROS1 kinase inhibitor is selective for a wild type and/or mutant ROS1 kinase.
• ROS1 kinase inhibitors can exhibit inhibition activity (IC 50 ) against a ROS1 kinase of less than about 1000 nM, less than about 500 nM, less than about 200 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, or less than about 1 nM as measured in an assay as described herein.
• a ROS1 kinase inhibitors can exhibit inhibition activity (IC 50 ) against a ROS1 kinase of less than about 25 nM, less than about 10 nM, less than about 5 nM, or less than about 1 nM as measured in an assay as provided herein.
• the ROS1 kinase inhibitor is a compound of Formula I.
• a “first ROS1 kinase inhibitor” or “first ROS1 inhibitor” is a ROS1 kinase inhibitor as defined herein, but which does not include a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as defined herein.
• a “second ROS1 kinase inhibitor” or a “second ROS1 inhibitor” is a ROS1 kinase inhibitor as defined herein. In some embodiments, a second ROS1 inhibitor does not include a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as defined herein.
• ROS1 inhibitors When more than one ROS1 inhibitor is present in a method provided herein (e.g., both a first and a second ROS1 inhibitor are present in a method provided herein), the two ROS1 inhibitors are different (e.g., the first and second ROS1 kinase inhibitor are different). As provided herein, different ROS1 inhibitors are structurally distinct from one another.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes at least one point mutation in a ROS1 gene that results in the production of a ROS1 kinase that has one or more amino acid substitutions or insertions or deletions as compared to the wild-type ROS1 kinase.
• the resulting ROS1 kinase is more resistant to inhibition of its phosphotransferase activity by one or more first ROS1 kinase inhibitor(s), as compared to a wildtype ROS1 kinase or a ROS1 kinase not including the same mutation.
• Such mutations optionally, do not decrease the sensitivity of the cancer cell or tumor having the ROS1 kinase to treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof (e.g., as compared to a cancer cell or a tumor that does not include the particular ROS1 inhibitor resistance mutation).
• a ROS1 inhibitor resistance mutation can result in a ROS1 kinase that has one or more of an increased V max , a decreased K m for ATP, and an increased K D for a first ROS1 kinase inhibitor, when in the presence of a first ROS1 kinase inhibitor, as compared to a wildtype ROS1 kinase or a ROS1 kinase not having the same mutation in the presence of the same first ROS1 kinase inhibitor.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes at least one point mutation in a ROS1 gene that results in the production of a ROS1 kinase that has one or more amino acid substitutions as compared to the wild-type ROS1 kinase, and which has increased resistance to a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, as compared to a wildtype ROS1 kinase or a ROS1 kinase not including the same mutation.
• a ROS1 inhibitor resistance mutation can result in a ROS1 kinase that has one or more of an increased V max , a decreased K m , and a decreased K D in the presence of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, as compared to a wildtype ROS1 kinase or a ROS1 kinase not having the same mutation in the presence of the same compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• ROS1 inhibitor resistance mutations can, e.g., include point mutations, insertions, or deletions in and near the ATP binding site in the tertiary structure of ROS1 kinase, including but not limited to the gatekeeper residue, P-loop residues, residues in or near the DFG motif, and ATP cleft solvent front amino acid residues. Additional examples of these types of mutations include changes in residues that may affect enzyme activity and/or drug binding including but are not limited to residues in the activation loop, residues near or interacting with the activation loop, residues contributing to active or inactive enzyme conformations, changes including mutations, deletions, and insertions in the loop proceeding the C-helix and in the C-helix.
• ROS1 inhibitor resistance mutations include but are not limited to those listed in Table 4 based on the human wildtype ROS1 protein sequence (e.g., SEQ ID NO: 1). Changes to these residues may include single or multiple amino acid changes, insertions within or flanking the sequences, and deletions within or flanking the sequences.
• compounds of Formula I and pharmaceutically acceptable salts and solvates are useful in treating patients that develop cancers with ROS1 inhibitor resistance mutations (e.g., that result in an increased resistance to a first ROS1 inhibitor, e.g., a substitution at amino acid position 2032 (e.g., G2032R), amino acid position 2026 (e.g., L2026M), amino acid position 2033 (e.g., D2033N), and/or one or more ROS1 inhibitor resistance mutations listed in Table 4) by either dosing in combination or as a follow-up therapy to existing drug treatments (e.g., ALK kinase inhibitors, TRK kinase inhibitors, other ROS1 kinase inhibitors, e.g., first and/or second ROS1 kinase inhibitors).
• a first ROS1 inhibitor e.g., a substitution at amino acid position 2032 (e.g., G2032R), amino acid position 2026 (e.g., L
• Exemplary ALK kinase inhibitors are described herein.
• Exemplary TRK kinase inhibitors are described herein.
• Exemplary first and second ROS1 kinase inhibitors are described herein.
• a first or second ROS1 kinase inhibitor can be selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib.
• compounds of Formula I or pharmaceutically acceptable salts and solvates thereof are useful for treating a cancer that has been identified as having one or more ROS1 inhibitor resistance mutations (that result in an increased resistance to a first or second ROS1 inhibitor, e.g., a substitution at amino acid position 2032 (e.g., G2032R), amino acid position 2026 (e.g., L2026M), amino acid position 2033 (e.g., D2033N)).
• ROS1 inhibitor resistance mutations are listed in Table 4.
• Amino acid position 1186 (e.g., S1186F 11 ) Amino acid position 1935 (e.g., E1935G6 10 ) Amino acid position 1945 (e.g., L1945Q 7 ) Amino acid position 1946 (e.g., T1946S 7 ) Amino acid position 1947 (e.g., L1947R 6, 10 , L1947M 7 ) Amino acid position 1948 (e.g., R1948S 7 ) Amino acid position 1951 (e.g., L1951R 5 , L1951V 7 ) Amino acid position 1958 (e.g., E1958V 7 ) Amino acid position 1959 (e.g., V1959E 7 ) Amino acid position 1961 (e.g., E1961K 7 ) Amino acid position 1962 (e.g., G1962E 7 ) Amino acid position 1971 (e.g., G1971E 6, 10 ) Amino acid position 1945 (e
• ROS1 proto-oncogene is expressed in a variety of tumor types, and belongs to the sevenless subfamily of tyrosine kinase insulin receptor genes.
• the protein encoded by this gene is a type I integral membrane protein with tyrosine kinase activity.
• ROS1 shares structural similarity with the anaplastic lymphoma kinase (ALK) protein.
• ALK anaplastic lymphoma kinase
• ROS1 fusions have been detected in multiple other tumor histologies, including ovarian carcinoma, sarcoma, cholangiocarcinomas and others.
• ALK is a receptor tyrosine kinase that belongs to the insulin growth factor receptor superfamily. ALK is believed to play a role in the development of the nervous system.
• a variety of ALK gene fusions have been described, such as EML4, KIF5B, KLC1, and TRK-fused gene (TFG). Such fusion products result in kinase activation and oncogenesis.
• NSCLC Non-small-cell lung cancer
• ALK anaplastic lymphoma kinase gene
• crizotinib which is an inhibitor of ALK and ROS1.
• the additional therapeutic agent(s) includes any one of the above listed therapies or therapeutic agents which are standards of care in cancers wherein the cancer has a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same.
• the additional therapeutic agent(s) includes any one of the above listed therapies or therapeutic agents which are standards of care in cancers wherein the cancer has a dysregulation of an ALK gene, an ALK protein, or expression or activity, or level of any of the same (e.g., an ALK-associated cancer).
• the additional therapeutic agent(s) includes any one of the above listed therapies or therapeutic agents which are standards of care in cancers wherein the cancer has a dysregulation of a TRK gene, a TRK protein, or expression or activity, or level of any of the same (e.g., a TRK-associated cancer).
• ALK-associated cancer refers to cancers associated with or having a dysregulation of an ALK gene, an ALK protein, or expression or activity, or level of any of the same. Exemplary ALK-associated cancers are provided herein.
• the phrase “dysregulation of an ALK gene, an ALK kinase, or the expression or activity or level of any of the same” refers to a genetic mutation (e.g., an ALK gene translocation that results in the expression of a fusion protein, a deletion in an ALK gene that results in the expression of an ALK protein that includes a deletion of at least one amino acid as compared to the wild-type ALK protein, a mutation in an ALK gene that results in the expression of an ALK protein with one or more point mutations, or an alternative spliced version of an ALK mRNA that results in an ALK protein having a deletion of at least one amino acid in the ALK protein as compared to the wild-type ALK protein) or an ALK gene amplification that results in overexpression of an ALK protein or an autocrine activity resulting from the overexpression of an ALK gene in a cell that results in a pathogenic increase in the activity of a kinase domain of an ALK protein (e.g.,
• a dysregulation of an ALK gene, an ALK protein, or expression or activity, or level of any of the same can be a mutation in an ALK gene that encodes an ALK protein that is constitutively active or has increased activity as compared to a protein encoded by an ALK gene that does not include the mutation.
• a dysregulation of an ALK gene, an ALK protein, or expression or activity, or level of any of the same can be the result of a gene or chromosome translocation which results in the expression of a fusion protein that contains a first portion of ALK that includes a functional kinase domain, and a second portion of a partner protein that is not ALK.
• dysregulation of an ALK gene, an ALK protein, or expression or activity or level of any of the same can be a result of a gene translocation of one ALK gene with another non-ALK gene.
• Non-limiting examples of fusion proteins are described in Table 5. Additional examples of ALK kinase protein mutations (e.g., point mutations) are ALK inhibitor resistance mutations.
• wildtype when referring to an ALK nucleic acid or protein describes a nucleic acid (e.g., an ALK gene or an ALK mRNA) or protein (e.g., an ALK protein) that is found in a subject that does not have an ALK-associated disease, e.g., an ALK-associated cancer (and optionally also does not have an increased risk of developing an ALK-associated disease and/or is not suspected of having an ALK-associated disease), or is found in a cell or tissue from a subject that does not have an ALK-associated disease, e.g., an ALK-associated cancer (and optionally also does not have an increased risk of developing an ALK-associated disease and/or is not suspected of having an ALK-associated disease).
• the dysregulation of an ALK gene, an ALK kinase protein, or expression or activity or level of any of the same includes one or more chromosome translocations or inversions resulting in an ALK gene fusion.
• the dysregulation of an ALK gene, an ALK kinase protein, or expression or activity or level of any of the same is a result of genetic translocations in which the expressed protein is a fusion protein containing residues from a non-ALK partner protein, and includes a minimum of a functional ALK kinase domain.
• Non-limiting examples of ALK fusion proteins are shown in Table 5.
• Anaplastic large cell lymphoma 1 Diffuse large B-cell lymphoma 1 , Neuroblastoma 8 , Lung adenocarcinoma 9
• ALO17/RNF213 Anaplastic large cell lymphoma 1 TFG (e.g., TFGs, Anaplastic large cell lymphoma 1 , TFG L , TFG XL ) 38
• Non-small cell lung cancer 1 Anaplastic thyroid carcinoma 1 MSN (e.g., MSNa Anaplastic large cell lymphoma 1 and MSNb) 38 TPM3 Anaplastic large cell lymphoma 1 , Inflammatory myofibroblastic tumour 1 , Renal medulla carcinoma/renal cell carcinoma 1 , Spitzoid neoplasm 5 TPM4 (e.g., type 1 Anaplastic large cell lymphoma 1 , and type 2) 38 Inflammatory myofibroblastic tumour 1 , Oesoph
• the dysregulation of an ALK gene, an ALK kinase, or expression or activity or level of any of the same includes at least one point mutation in an ALK gene that results in the production of an ALK kinase that has one or more amino acid substitutions, insertions, or deletions as compared to the wild-type ALK kinase.
• an ALK-associated cancer has been identified as having one or more ALK inhibitor resistance mutations (that result in an increased resistance to an ALK inhibitor.
• Tropomyosin-related kinase is a receptor tyrosine kinase family of neurotrophin receptors that are found in multiple tissues types. Three members of the TRK proto-oncogene family have been described: TrkA, TrkB, and TrkC, encoded by the NTRK1, NTRK2, and NTRK3 genes, respectively.
• TrkA, TrkB, and TrkC encoded by the NTRK1, NTRK2, and NTRK3 genes, respectively.
• the TRK receptor family is involved in neuronal development, including the growth and function of neuronal synapses, memory development, and maintenance, and the protection of neurons after ischemia or other types of injury (Nakagawara, Cancer Lett. 169:107-114, 2001).
• TRK was originally identified from a colorectal cancer cell line as an oncogene fusion containing 5′ sequences from tropomyosin-3 (TPM3) gene and the kinase domain encoded by the 3′ region of the neurotrophic tyrosine kinase, receptor, type 1 gene (NTRK1) (Pulciani et al., Nature 300:539-542, 1982; Martin-Zanca et al., Nature 319:743-748, 1986).
• TPM3 tropomyosin-3
• NTRK1 neurotrophic tyrosine kinase, receptor, type 1 gene
• TRK gene fusions follow the well-established paradigm of other oncogenic fusions, such as those involving ALK and ROS1, which have been shown to drive the growth of tumors and can be successfully inhibited in the clinic by targeted drugs (Shaw et al., New Engl. J. Med. 371:1963-1971, 2014; Shaw et al., New Engl. J. Med. 370:1189-1197, 2014).
• Oncogenic TRK fusions induce cancer cell proliferation and engage critical cancer-related downstream signaling pathways such as mitogen activated protein kinase (MAPK) and AKT (Vaishnavi et al., Cancer Discov. 5:25-34, 2015).
• MAPK mitogen activated protein kinase
• AKT AKT
• NTRK1 and its related TRK family members NTRK2 and NTRK3 have been described (Vaishnavi et al., Cancer Disc. 5:25-34, 2015; Vaishnavi et al., Nature Med. 19:1469-1472, 2013). Although there are numerous different 5′ gene fusion partners identified, all share an in-frame, intact TRK kinase domain.
• Trk inhibitors have been developed to treat cancer (see, e.g., U.S. Patent Application Publication No. 62/080,374, International Application Publication Nos.
• TRK-associated cancer refers to cancers associated with or having a dysregulation of a TRK gene, a TRK protein, or expression or activity, or level of any of the same. Exemplary TRK-associated cancers are provided herein.
• the phrase “dysregulation of a TRK gene, a TRK kinase, or the expression or activity or level of any of the same” refers to a genetic mutation (e.g., a TRK gene translocation that results in the expression of a fusion protein, a deletion in a TRK gene that results in the expression of a TRK protein that includes a deletion of at least one amino acid as compared to the wild-type TRK protein, a mutation in a TRK gene that results in the expression of a TRK protein with one or more point mutations, or an alternative spliced version of a TRK mRNA that results in a TRK protein having a deletion of at least one amino acid in the TRK protein as compared to the wild-type TRK protein) or a TRK gene amplification that results in overexpression of a TRK protein or an autocrine activity resulting from the overexpression of a TRK gene in a cell that results in a pathogenic increase in the activity of a kinase domain
• a dysregulation of a TRK gene, a TRK protein, or expression or activity, or level of any of the same can be a mutation in a TRK gene that encodes a TRK protein that is constitutively active or has increased activity as compared to a protein encoded by a TRK gene that does not include the mutation.
• a dysregulation of a TRK gene, a TRK protein, or expression or activity, or level of any of the same can be the result of a gene or chromosome translocation which results in the expression of a fusion protein that contains a first portion of TRK that includes a functional kinase domain, and a second portion of a partner protein that is not TRK.
• dysregulation of a TRK gene, a TRK protein, or expression or activity or level of any of the same can be a result of a gene translocation of one TRK gene with another non-TRK gene.
• Non-limiting examples of fusion proteins are described in Tables 6-8. Additional examples of TRK kinase protein mutations (e.g., point mutations) are TRK inhibitor resistance mutations.
• wildtype when referring to a TRK nucleic acid or protein describes a nucleic acid (e.g., a TRK gene or a TRK mRNA) or protein (e.g., a TRK protein) that is found in a subject that does not have a TRK-associated disease, e.g., a TRK-associated cancer (and optionally also does not have an increased risk of developing a TRK-associated disease and/or is not suspected of having a TRK-associated disease), or is found in a cell or tissue from a subject that does not have a TRK-associated disease, e.g., a TRK-associated cancer (and optionally also does not have an increased risk of developing a TRK-associated disease and/or is not suspected of having a TRK-associated disease).
• the dysregulation of a TRK gene, a TRK kinase protein, or expression or activity or level of any of the same includes one or more chromosome translocations or inversions resulting in a TRK gene fusion.
• the dysregulation of a TRK gene, a TRK kinase protein, or expression or activity or level of any of the same is a result of genetic translocations in which the expressed protein is a fusion protein containing residues from a non-TRK partner protein, and includes a minimum of a functional TRK kinase domain. See, for example, Tables 6-8.
• TrkA Fusion Proteins and Cancers Non-limiting Exemplary Trk-and Synonyms of Associated Fusion Protein Non-TrkA Fusion Partner Cancer(s) TP53-TrkA 1,11 Tumor Protein P53 Spitzoid Melanoma, Spitz tumors LMNA-TrkA 1, 12 Lamin A/C Spitzoid Melanoma, Spitz tumors, Undifferentiated Sarcoma, Adult Soft Tissue Sarcoma (e.g., Soft Tissue Sarcoma Metastatic to Lung), Soft Tissue Fibrosarcoma, Spindle Cell Sarcoma G , Congenital Infantile Fibrosarcoma H , Pediatric haemangiopericytoma-like sarcoma I , Colorectal Cancer K CD74-TrkA 2 MHC class II invariant chain Non-Small Cell Lung Cancer (NSCLC) Lung adenocarcimona TFG-TrkA (TRK-T3) 3 TRK-Fused Gene Pa
• the dysregulation of a TRK gene, a TRK kinase, or expression or activity or level of any of the same includes at least one point mutation in a TRK gene that results in the production of a TRK kinase that has one or more amino acid substitutions, insertions, or deletions as compared to the wild-type TRK kinase.
• a TRK-associated cancer has been identified as having one or more TRK inhibitor resistance mutations (that result in an increased resistance to a TRK inhibitor.
• methods for treating a patient diagnosed with (or identified as having) a cancer that include administering to the patient a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• methods for treating a patient identified or diagnosed as having a ROS1-associated cancer that include administering to the patient a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof or a pharmaceutical composition thereof.
• the patient that has been identified or diagnosed as having a ROS1-associated cancer through the use of a regulatory agency-approved, e.g., FDA-approved test or assay for identifying dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, in a patient or a biopsy sample from the patient or by performing any of the non-limiting examples of assays described herein.
• the test or assay is provided as a kit.
• the assay is a liquid biopsy.
• the cancer is a ROS1-associated cancer.
• the ROS1-associated cancer can be a cancer that includes one or more ROS1 inhibitor resistance mutations.
• Some embodiments of these methods further include administering to the subject one or more additional anticancer agents (e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor).
• one or more additional anticancer agents e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor
• one or more additional anticancer agents are administered after a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• one or more additional anticancer agents are administered with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the subject was previously treated with a first ROS1 inhibitor or previously treated with another anticancer treatment, e.g., treatment with another anticancer agent, resection of the tumor or radiation therapy.
• the subject was previously treated with an ALK inhibitor, a TRK inhibitor, or both.
• the patient is determined to have a ROS1-associated cancer through the use of a regulatory agency-approved, e.g., FDA-approved test or assay for identifying dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, in a patient or a biopsy sample from the patient or by performing any of the non-limiting examples of assays described herein.
• the test or assay is provided as a kit.
• the assay is a liquid biopsy.
• the cancer is a ROS1-associated cancer.
• the ROS1-associated cancer can be a cancer that includes one or more ROS1 inhibitor resistance mutations.
• Also provided are methods of treating a patient that include performing an assay on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, and administering (e.g., specifically or selectively administering) a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof or a pharmaceutical composition thereof to the patient determined to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• Some embodiments of these methods further include administering to the subject one or more additional anticancer agents (e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor).
• one or more additional anticancer agents e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor
• one or more additional anticancer agents e.g., a second ROS1 inhibitor (e.g., a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof), an ALK inhibitor, and/or a TRK inhibitor) are administered after a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• one or more additional anticancer agents e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor
• the subject was previously treated with a first ROS1 inhibitor or previously treated with another anticancer treatment, e.g., treatment with another anticancer agent, resection of a tumor or radiation therapy.
• the subject was previously treated with an ALK inhibitor, a TRK inhibitor, or both.
• the patient is a patient suspected of having a ROS1-associated cancer, a patient presenting with one or more symptoms of a ROS1-associated cancer, or a patient having an elevated risk of developing a ROS1-associated cancer.
• the assay utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved assay, e.g., FDA-approved kit.
• the assay is a liquid biopsy. Additional, non-limiting assays that may be used in these methods are described herein. Additional assays are also known in the art.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• an assay e.g., an in vitro assay
• a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof for the manufacture of a medicament for treating a ROS1-associated cancer in a patient identified or diagnosed as having a ROS1-associated cancer through a step of performing an assay on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same where the presence of dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, identifies that the patient has a ROS1-associated cancer.
• Some embodiments of any of the methods or uses described herein further include recording in the patient's clinical record (e.g., a computer readable medium) that the patient is determined to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, through the performance of the assay, should be administered a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof or a pharmaceutical composition thereof.
• the assay utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved assay, e.g., FDA-approved kit. In some embodiments, the assay is a liquid biopsy. In some embodiments, the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof for use in the treatment of a cancer in a patient in need thereof or a patient identified or diagnosed as having a ROS1-associated cancer. Also provided is the use of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof for the manufacture of a medicament for treating a cancer in a patient identified or diagnosed as having a ROS1-associated cancer.
• the cancer is a ROS1-associated cancer, for example, a ROS1-associated cancer having one or more ROS1 inhibitor resistance mutations.
• a patient is identified or diagnosed as having a ROS1-associated cancer through the use of a regulatory agency-approved, e.g., FDA-approved, kit for identifying dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, in a patient or a biopsy sample from the sample.
• a ROS1-associated cancer includes those described herein and known in the art.
• the patient has been identified or diagnosed as having a cancer with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the patient has a tumor that is positive for a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the patient can be a patient with a tumor(s) that is positive for a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the patient can be a patient whose tumors have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the patient is suspected of having a ROS1-associated cancer (e.g., a cancer having one or more ROS1 inhibitor resistance mutations).
• provided herein are methods for treating a ROS1-associated cancer in a patient in need of such treatment, the method comprising a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the patient; and b) administering a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same includes one or more fusion proteins.
• Non-limiting examples of ROS1 gene fusion proteins are described in Table 2.
• the fusion protein is SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same includes one or more ROS1 kinase protein point mutations, insertions, and/or deletions. Non-limiting examples of ROS1 kinase protein point mutations are described in Table 3 and Table 3a.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• ROS1 inhibitor resistance mutations are described in Table 4.
• the ROS1 inhibitor resistance mutation is selected from the group consisting of L2026M, G2032R, and D2033N.
• the cancer with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is determined using a regulatory agency-approved, e.g., FDA-approved, assay or kit.
• the assay is a liquid biopsy.
• the tumor that is positive for a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is a tumor positive for one or more ROS1 inhibitor resistance mutations.
• the tumor with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is determined using a regulatory agency-approved, e.g., FDA-approved, assay or kit.
• the assay is a liquid biopsy.
• the patient has a clinical record indicating that the patient has a tumor that has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same (e.g., a tumor having one or more ROS1 inhibitor resistance mutations).
• the clinical record indicates that the patient should be treated with one or more of the compounds of Formula I or a pharmaceutically acceptable salts or solvates thereof or compositions provided herein.
• the cancer with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is a cancer having one or more ROS1 inhibitor resistance mutations.
• the cancer with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is determined using a regulatory agency-approved, e.g., FDA-approved, assay or kit.
• the assay is a liquid biopsy.
• the tumor that is positive for a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is a tumor positive for one or more ROS1 inhibitor resistance mutations.
• the tumor with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same is determined using a regulatory agency-approved, e.g., FDA-approved, assay or kit.
• the assay is a liquid biopsy.
• Also provided are methods of treating a patient that include administering a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof to a patient having a clinical record that indicates that the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same. Also provided is the use of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof for the manufacture of a medicament for treating a ROS1-associated cancer in a patient having a clinical record that indicates that the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• Some embodiments of these methods and uses can further include: a step of performing an on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, and recording the information in a patient's clinical file (e.g., a computer readable medium) that the patient has been identified to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the assay is an in vitro assay.
• an assay that utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved, e.g., FDA-approved, kit.
• the assay is a liquid biopsy.
• the dysregulation of a ROS1 gene, ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• the method includes performing an assay on a sample obtained from the subject to determine whether the subject has a dysregulation of a ROS1 gene, a ROS1 protein, or expression or level of any of the same.
• the method also includes administering to a subject determined to have a dysregulation of a ROS1 gene, a ROS1 protein, or expression or activity, or level of any of the same a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the dysregulation in a ROS1 gene, a ROS1 kinase protein, or expression or activity of the same is a gene or chromosome translocation that results in the expression of a ROS1 fusion protein (e.g., any of the ROS1 fusion proteins described herein).
• the ROS1 fusion can be selected from a SLC34A2 fusion, a CD74 fusion, a EZR fusion, a TPM3 fusion, or a SDC4 fusion.
• the dysregulation in a ROS1 gene, a ROS1 kinase protein, or expression or activity or level of any of the same is one or more point mutation in the ROS1 gene (e.g., any of the one or more of the ROS1 point mutations described herein).
• the one or more point mutations in a ROS1 gene can result, e.g., in the translation of a ROS1 protein having one or more of the following amino acid substitutions: A15G, R118N, G1025R, T1735M, R1948H, and R2072N.
• the dysregulation in a ROS1 gene, a ROS1 kinase protein, or expression or activity or level of any of the same is one or more ROS1 inhibitor resistance mutations (e.g., any combination of the one or more ROS1 inhibitor resistance mutations described herein).
• the one or more point mutations in a ROS1 gene can result, e.g., in the translation of a ROS1 protein having one or more of the following amino acid substitutions: L2026M, G2032R, and D2033N.
• Some embodiments of these methods further include administering to the subject another anticancer agent (e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor).
• another anticancer agent e.g., a second ROS1 inhibitor, a second compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, an ALK inhibitor, and/or a TRK inhibitor.
• the selected treatment can include administration of a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• Some embodiments can further include a step of performing an assay on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, and identifying and diagnosing a patient determined to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, as having a ROS1-associated cancer.
• the cancer is a ROS1-associated cancer having one or more ROS1 inhibitor resistance mutations.
• the patient has been identified or diagnosed as having a ROS1-associated cancer through the use of a regulatory agency-approved, e.g., FDA-approved, kit for identifying dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, in a patient or a biopsy sample from the patient.
• the assay is a liquid biopsy.
• the ROS1-associated cancers is a cancer described herein or known in the art.
• the assay is an in vitro assay.
• an assay that utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved, e.g., FDA-approved, kit.
• the assay is a liquid biopsy.
• Also provided herein are methods of selecting a treatment for a patient wherein the methods include a step of performing an assay on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same (e.g., one or more ROS1 inhibitor resistance mutations), and identifying or diagnosing a patient determined to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, as having a ROS1-associated cancer. Some embodiments further include administering the selected treatment to the patient identified or diagnosed as having a ROS1-associated cancer.
• the selected treatment can include administration of a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof to the patient identified or diagnosed as having a ROS1-associated cancer.
• the assay is an in vitro assay.
• an assay that utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved, e.g., FDA-approved, kit.
• the assay is a liquid biopsy.
• Also provided are methods of selecting a patient for treatment wherein the methods include selecting, identifying, or diagnosing a patient having a ROS1-associated cancer, and selecting the patient for treatment including administration of a therapeutically-effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• identifying or diagnosing a patient as having a ROS1-associated cancer can include a step of performing an assay on a sample obtained from the patient to determine whether the patient has a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, and identifying or diagnosing a patient determined to have a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same, as having a ROS1-associated cancer.
• the method of selecting a treatment can be used as a part of a clinical study that includes administration of various treatments of a ROS1-associated cancer.
• a ROS1-associated cancer is a cancer having one or more ROS1 inhibitor resistance mutations.
• the assay is an in vitro assay. For example, an assay that utilizes next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH).
• FISH fluorescence in situ hybridization
• the assay is a regulatory agency-approved, e.g., FDA-approved, kit.
• the assay is a liquid biopsy.
• the dysregulation of the ROS1 gene, the ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• an assay used to determine whether the patient has a dysregulation of a ROS1 gene, or a ROS1 kinase, or expression or activity or level of any of the same, using a sample from a patient can include, for example, next generation sequencing, pyrosequencing, immunohistochemistry, an enzyme-linked immunosorbent assay, and/or fluorescence in situ hybridization (FISH) (e.g., break apart FISH or dual-fusion FISH), fluorescence microscopy, Southern blotting, Western blotting, FACS analysis, Northern blotting, and PCR-based amplification (e.g., RT-PCR and quantitative real-time RT-PCR).
• FISH fluorescence in situ hybridization
• the assays are typically performed, e.g., with at least one labelled nucleic acid probe or at least one labelled antibody or antigen-binding fragment thereof.
• Assays can utilize other detection methods known in the art for detecting dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or levels of any of the same (see, e.g., the references cited herein).
• the dysregulation of the ROS1 gene, the ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• the sample is a biological sample or a biopsy sample (e.g., a paraffin-embedded biopsy sample) from the patient.
• the patient is a patient suspected of having a ROS1-associated cancer, a patient having one or more symptoms of a ROS1-associated cancer, and/or a patient that has an increased risk of developing a ROS1-associated cancer).
• dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same can be identified using a liquid biopsy (variously referred to as a fluid biopsy or fluid phase biopsy).
• a liquid biopsy (variously referred to as a fluid biopsy or fluid phase biopsy). See, e.g., Karachialiou et al., “Real-time liquid biopsies become a reality in cancer treatment”, Ann. Transl. Med., 3(3):36, 2016.
• Liquid biopsy methods can be used to detect total tumor burden and/or the dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same.
• Liquid biopsies can be performed on biological samples obtained relatively easily from a subject (e.g., via a simple blood draw) and are generally less invasive than traditional methods used to detect tumor burden and/or dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same.
• liquid biopsies can be used to detect the presence of dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same at an earlier stage than traditional methods.
• the biological sample to be used in a liquid biopsy can include, blood, plasma, urine, cerebrospinal fluid, saliva, sputum, broncho-alveolar lavage, bile, lymphatic fluid, cyst fluid, stool, ascites, and combinations thereof.
• a liquid biopsy can be used to detect circulating tumor cells (CTCs).
• CTCs circulating tumor cells
• a liquid biopsy can be used to detect cell-free DNA.
• cell-free DNA detected using a liquid biopsy is circulating tumor DNA (ctDNA) that is derived from tumor cells.
• Analysis of ctDNA can be used to identify dysregulation of a RET gene, a RET kinase, or the expression or activity or level of any of the same.
• NGS next-generation sequencing
• RET RET kinase
• ctDNA derived from a single gene can be detected using a liquid biopsy.
• ctDNA derived from a plurality of genes e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more, or any number of genes in between these numbers
• a liquid biopsy e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more, or any number of genes in between these numbers
• ctDNA derived from a plurality of genes can be detected using any of a variety of commercially-available testing panels (e.g., commercially-available testing panels designed to detect dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same ).
• Liquid biopsies can be used to detect dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same including, without limitation, point mutations or single nucleotide variants (SNVs), copy number variants (CNVs), genetic fusions (e.g., translocations or rearrangements), insertions, deletions, or any combination thereof.
• a liquid biopsy can be used to detect a germline mutation. In some embodiments, a liquid biopsy can be used to detect a somatic mutation. In some embodiments, a liquid biopsy can be used to detect a primary genetic mutation (e.g., a primary mutation or a primary fusion that is associated with initial development of a disease, e.g., cancer). In some embodiments, a liquid biopsy can be used to detect a genetic mutation that develops after development of the primary genetic mutation (e.g., a resistance mutation that arises in response to a treatment administered to a subject).
• a primary genetic mutation e.g., a primary mutation or a primary fusion that is associated with initial development of a disease, e.g., cancer.
• a liquid biopsy can be used to detect a genetic mutation that develops after development of the primary genetic mutation (e.g., a resistance mutation that arises in response to a treatment administered to a subject).
• a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same identified using a liquid biopsy is also present in a cancer cell that is present in the subject (e.g., in a tumor).
• any of the types of dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same described herein can be detected using a liquid biopsy.
• a genetic mutation identified via a liquid biopsy can be used to identify the subject as a candidate for a particular treatment.
• detection of dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in the subject can indicate that the subject will be responsive to a treatment that includes administration of a compound of Formula I or a pharmaceutically acceptable salt thereof.
• Liquid biopsies can be performed at multiple times during a course of diagnosis, a course of monitoring, and/or a course of treatment to determine one or more clinically relevant parameters including, without limitation, progression of the disease, efficacy of a treatment, or development of resistance mutations after administering a treatment to the subject.
• a first liquid biopsy can be performed at a first time point and a second liquid biopsy can be performed at a second time point during a course of diagnosis, a course of monitoring, and/or a course of treatment.
• the first time point can be a time point prior to diagnosing a subject with a disease (e.g., when the subject is healthy), and the second time point can be a time point after subject has developed the disease (e.g., the second time point can be used to diagnose the subject with the disease).
• the first time point can be a time point prior to diagnosing a subject with a disease (e.g., when the subject is healthy), after which the subject is monitored, and the second time point can be a time point after monitoring the subject.
• the first time point can be a time point after diagnosing a subject with a disease, after which a treatment is administered to the subject, and the second time point can be a time point after the treatment is administered; in such cases, the second time point can be used to assess the efficacy of the treatment (e.g., if the genetic mutation(s) detected at the first time point are reduced in abundance or are undetectable) or to determine the presence of a resistance mutation that has arisen as a result of the treatment.
• a treatment to be administered to a subject can include a compound of Formula I or a pharmaceutically acceptable salt thereof.
• compositions provided herein may be, for example, surgery, radiotherapy, and chemotherapeutic agents, such as kinase inhibitors, signal transduction inhibitors and/or monoclonal antibodies.
• chemotherapeutic agents such as kinase inhibitors, signal transduction inhibitors and/or monoclonal antibodies.
• Compounds of Formula I therefore may also be useful as adjuvants to cancer treatment, that is, they can be used in combination with one or more additional therapies or therapeutic agents, for example a chemotherapeutic agent that works by the same or by a different mechanism of action.
• the compound of Formula I (or a pharmaceutically acceptable salt or solvate thereof) is administered in combination with a therapeutically effective amount of at least one additional therapeutic agent selected from one or more additional therapies or therapeutic (e.g., chemotherapeutic) agents.
• Non-limiting examples of additional therapeutic agents include: other ROS1-targeted therapeutic agents (i.e. a first or second ROS1 kinase inhibitor), ALK-targeted therapeutic agents (e.g., ALK kinase inhibitors), receptor tyrosine kinase-targeted therapeutic agents (e.g., TRK kinase inhibitors), kinase targeted therapeutics, signal transduction pathway inhibitors, checkpoint inhibitors, modulators of the apoptosis pathway (e.g. obataclax); cytotoxic chemotherapeutics, angiogenesis-targeted therapies, immune-targeted agents, including immunotherapy, and radiotherapy.
• ROS1-targeted therapeutic agents i.e. a first or second ROS1 kinase inhibitor
• ALK-targeted therapeutic agents e.g., ALK kinase inhibitors
• receptor tyrosine kinase-targeted therapeutic agents e.g
• the other ROS1-targeted therapeutic is a multikinase inhibitor exhibiting ROS1 inhibition activity. In some embodiments, the other ROS1-targeted therapeutic inhibitor is selective for a ROS1 kinase.
• Exemplary ROS1 kinase inhibitors can exhibit inhibition activity (IC 50 ) against a ROS1 kinase of less than about 1000 nM, less than about 500 nM, less than about 200 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, or less than about 1 nM as measured in an assay as described herein.
• a ROS1 kinase inhibitor can exhibit inhibition activity (IC 50 ) against a ROS1 kinase of less than about 25 nM, less than about 10 nM, less than about 5 nM, or less than about 1 nM as measured in an assay as provided herein.
• ROS1-targeted therapeutic agents include (E)-5-chloro-2-(2-(1-(4-fluorophenyl)ethylidene)hydrazinyl)-N-(2-(isopropylsulfonyl)phenyl)pyrimidin-4-amine ( Eur. J. Org. Chem.
• alectinib alectinib; brigatinib; cabozantinib; ceritinib; crizotinib; entrectinib; foretinib; herbimycin A; lorlatinib; lorlatinib des-methyl analogs; merestinib; ASP3026 (NCT01284192; Astellas Pharma); AZD3634 (AstraZeneca); and ASP3026 (Astrellas Pharma).
• an ALK-targeted therapeutic is a multikinase inhibitor exhibiting ALK inhibition activity.
• the ALK-targeted therapeutic inhibitor is selective for an ALK kinase.
• Exemplary ALK kinase inhibitors can exhibit inhibition activity (IC 50 ) against an ALK kinase of less than about 1000 nM, less than about 500 nM, less than about 200 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, or less than about 1 nM as measured in an assay as described herein.
• an ALK kinase inhibitor can exhibit inhibition activity (IC 50 ) against an ALK kinase of less than about 25 nM, less than about 10 nM, less than about 5 nM, or less than about 1 nM as measured in an assay.
• Non-limiting examples of ALK-targeted therapeutic agents include “Amgen 36”; “Amgen 49”; “Cephalon 30”; “Chugai 13d”; 4-arylaminopyrimidine derivatives (see, e.g., Eur. J. Med. Chem.
• a receptor tyrosine kinase targeted therapeutic is a multikinase inhibitor (e.g., TRK-targeted therapeutic inhibitor) exhibiting TRK inhibition activity.
• the TRK-targeted therapeutic inhibitor is selective for a TRK kinase.
• Exemplary TRK kinase inhibitors can exhibit inhibition activity (IC 50 ) against a TRK kinase of less than about 1000 nM, less than about 500 nM, less than about 200 nM, less than about 100 nM, less than about 50 nM, less than about 25 nM, less than about 10 nM, or less than about 1 nM as measured in an assay as described herein.
• a TRK kinase inhibitor can exhibit inhibition activity (IC 50 ) against a TRK kinase of less than about 25 nM, less than about 10 nM, less than about 5 nM, or less than about 1 nM as measured in an assay.
• IC 50 inhibition activity against a TRK kinase of less than about 25 nM, less than about 10 nM, less than about 5 nM, or less than about 1 nM as measured in an assay.
• a TRK inhibitor assay can be any of those provided in U.S. Pat. No. 8,933,084 (e.g., Example A or B).
• Non-limiting examples of receptor tyrosine kinase (e.g., Trk) targeted therapeutic agents include afatinib, cabozantinib, cetuximab, crizotinib, dabrafenib, entrectinib, erlotinib, gefitinib, imatinib, lapatinib, lestaurtinib, nilotinib, pazopanib, panitumumab, pertuzumab, sunitinib, trastuzumab, 1-((3 S,4R)-4-(3-fluorophenyl)-1-(2-methoxyethyl)pyrrolidin-3-yl)-3-(4-methyl-3-(2-methylpyrimidin-5-yl)-1-phenyl-1H-pyrazol-5-yl)urea, AG 879, AR-772, AR-786, AR-256, AR-618, AZ-23,
• Additional Trk targeted therapeutic agents include those described in U.S. Pat. Nos. 8,450,322; 8,513,263; 8,933,084; 8,791,123; 8,946,226; 8,450,322; 8,299,057; and 8,912,194; U.S. Publication No. 2016/0137654; 2015/0166564; 2015/0051222; 2015/0283132; and 2015/0306086; International Publication No.
• Trk inhibitors can be found in U.S. Pat. No. 8,637,516, International Publication No. WO 2012/034091, U.S. Pat. No. 9,102,671, International Publication No. WO 2012/116217, U.S. Publication No. 2010/0297115, International Publication No. WO 2009/053442, U.S. Pat. No. 8,642,035, International Publication No. WO 2009092049, U.S. Pat. No. 8,691,221, International Publication No. WO2006131952, all of which are incorporated by reference in their entireties herein.
• Exemplary Trk inhibitors include GNF-4256, described in Cancer Chemother. Pharmacol.
• Trk inhibitors include those disclosed in U.S. Publication No. 2010/0152219, U.S. Pat. No. 8,114,989, and International Publication No. WO 2006/123113, all of which are incorporated by reference in their entireties herein.
• Exemplary Trk inhibitors include AZ623, described in Cancer 117(6):1321-1391, 2011; AZD6918, described in Cancer Biol. Ther. 16(3):477-483, 2015; AZ64, described in Cancer Chemother. Pharmacol.
• a Trk inhibitor can include those described in U.S. Pat. Nos. 7,615,383; 7,384,632; 6,153,189; 6,027,927; 6,025,166; 5,910,574; 5,877,016; and 5,844,092, each of which is incorporated by reference in its entirety.
• Trk inhibitors include CEP-751, described in Int. J. Cancer 72:672-679, 1997; CT327, described in Acta Derm. Venereol. 95:542-548, 2015; compounds described in International Publication No. WO 2012/034095; compounds described in U.S. Pat. No. 8,673,347 and International Publication No. WO 2007/022999; compounds described in U.S. Pat. No. 8,338,417; compounds described in International Publication No. WO 2016/027754; compounds described in U.S. Pat. No. 9,242,977; compounds described in U.S. Publication No.
• sunitinib N-(2-diethylaminoethyl)-5-[(Z)-(5-fluoro-2-oxo-1H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide
• sunitinib N-(2-diethylaminoethyl)-5-[(Z)-(5-fluoro-2-oxo-1H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide
• 4-aminopyrazolylpyrimidines e.g., AZ-23 (((S)-5-chloro-N2-(1-(5-fluoropyridin-2-yl)ethyl)-N4-(5-isopropoxy-1H-pyrazol-3-yl)pyrimidine-2,4-diamine)), as described in J. Med. Chem. 51(15):4672-4684, 2008; PHA-739358 (danusertib), as described in Mol. Cancer Ther.
• Trk inhibitor to act as a TrkA, TrkB, and/or Trk C inhibitor may be tested using the assays described in Examples A and B in U.S. Pat. No. 8,513,263, which is incorporated herein by reference.
• signal transduction pathway inhibitors include Ras-Raf-MEK-ERK pathway inhibitors (e.g., binimetinib, selumetinib, encorafinib, sorafenib, trametinib, and vemurafenib), PI3K-Akt-mTOR-S6K pathway inhibitors (e.g.
• everolimus, rapamycin, perifosine, temsirolimus), and other kinase inhibitors such as baricitinib, brigatinib, capmatinib, danusertib, ibrutinib, milciclib, quercetin, regorafenib, ruxolitinib, semaxanib, AP32788, BLU285, BLU554, INCB39110, INCB40093, INCB50465, INCB52793, INCB54828, MGCD265, NMS-088, NMS-1286937, PF 477736 ((R)-amino-N-[5,6-dihydro-2-(1-methyl-1H-pyrazol-4-yl)-6-oxo-1Hpyrrolo[4,3,2-ef][2,3]benzodiazepin-8-yl]-cyclohexaneacetamide), PLX3397, PLX7486, PLX8394
• Non-limiting examples of checkpoint inhibitors include ipilimumab, tremelimumab, nivolumab, pidilizumab, MPDL3208A, MEDI4736, MSB0010718C, BMS-936559, BMS-956559, BMS-935559 (MDX-1105), AMP-224, and pembrolizumab.
• cytotoxic chemotherapeutics are selected from arsenic trioxide, bleomycin, cabazitaxel, capecitabine, carboplatin, cisplatin, cyclophosphamide, cytarabine, dacarbazine, daunorubicin, docetaxel, doxorubicin, etoposide, fluorouracil, gemcitabine, irinotecan, lomustine, methotrexate, mitomycin C, oxaliplatin, paclitaxel, pemetrexed, temozolomide, and vincristine.
• Non-limiting examples of angiogenesis-targeted therapies include aflibercept and bevacizumab.
• an immunotherapy refers to an agent that modulates the immune system.
• an immunotherapy can increase the expression and/or activity of a regulator of the immune system.
• an immunotherapy can decrease the expression and/or activity of a regulator of the immune system.
• an immunotherapy can recruit and/or enhance the activity of an immune cell.
• the immunotherapy is a cellular immunotherapy (e.g., adoptive T-cell therapy, dendritic cell therapy, natural killer cell therapy).
• the cellular immunotherapy is sipuleucel-T (APC8015; ProvengeTM; Plosker (2011) Drugs 71(1): 101-108).
• the cellular immunotherapy includes cells that express a chimeric antigen receptor (CAR).
• the cellular immunotherapy is a CAR-T cell therapy.
• the CAR-T cell therapy is tisagenlecleucel (KymriahTM).
• the immunotherapy is an antibody therapy (e.g., a monoclonal antibody, a conjugated antibody).
• the antibody therapy is bevacizumab (MvastiTM, Avastin®), trastuzumab (Herceptin®), avelumab (Bavencio®), rituximab (MabTheraTM, Rituxan®), edrecolomab (Panorex), daratumuab (Darzalex®), olaratumab (LartruvoTM), ofatumumab (Arzerra®), alemtuzumab (Campath®), cetuximab (Erbitux®), oregovomab, pembrolizumab (Keytruda®), dinutiximab (Unituxin®), obinutuzumab (Gazyva®), tremelimumab (CP-675,206), ramucirumab (C
• the immunotherapy is an antibody-drug conjugate.
• the antibody-drug conjugate is gemtuzumab ozogamicin (MylotargTM), inotuzumab ozogamicin (Besponsa®), brentuximab vedotin (Adcetris®), ado-trastuzumab emtansine (TDM-1; Kadcyla®), mirvetuximab soravtansine (IMGN853) or anetumab ravtansine
• the immunotherapy includes blinatumomab (AMG103; Blincyto®) or midostaurin (Rydapt).
• the immunotherapy includes a toxin. In some embodiments, the immunotherapy is denileukin diftitox (Ontak®).
• the immunotherapy is a cytokine therapy.
• the cytokine therapy is an interleukin 2 (IL-2) therapy, an interferon alpha (IFN ⁇ ) therapy, a granulocyte colony stimulating factor (G-CSF) therapy, an interleukin 12 (IL-12) therapy, an interleukin 15 (IL-15) therapy, an interleukin 7 (IL-7) therapy or an erythropoietin-alpha (EPO) therapy.
• the IL-2 therapy is aldesleukin (Proleukin®).
• the IFN ⁇ therapy is IntronA® (Roferon-A®).
• the G-CSF therapy is filgrastim (Neupogen®).
• the immunotherapy is an immune checkpoint inhibitor. In some embodiments, the immunotherapy includes one or more immune checkpoint inhibitors. In some embodiments, the immune checkpoint inhibitor is a CTLA-4 inhibitor, a PD-1 inhibitor or a PD-L1 inhibitor. In some embodiments, the CTLA-4 inhibitor is ipilimumab (Yervoy®) or tremelimumab (CP-675,206). In some embodiments, the PD-1 inhibitor is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In some embodiments, the PD-L1 inhibitor is atezolizumab (Tecentriq®), avelumab (Bavencio®) or durvalumab (ImfinziTM).
• the immunotherapy is mRNA-based immunotherapy.
• the mRNA-based immunotherapy is CV9104 (see, e.g., Rausch et al. (2014) Human Vaccin Immunother 10(11): 3146-52; and Kubler et al. (2015) J. Immunother Cancer 3:26).
• the immunotherapy is bacillus Calmette-Guerin (BCG) therapy.
• the immunotherapy is an oncolytic virus therapy.
• the oncolytic virus therapy is talimogene alherparepvec (T-VEC; Imlygic®).
• the immunotherapy is a cancer vaccine.
• the cancer vaccine is a human papillomavirus (HPV) vaccine.
• the HPV vaccine is Gardasil®, Gardasil9® or Cervarix®.
• the cancer vaccine is a hepatitis B virus (HBV) vaccine.
• the HBV vaccine is Engerix-B®, Recombivax HB® or GI-13020 (Tarmogen®).
• the cancer vaccine is Twinrix® or Pediarix®.
• the cancer vaccine is BiovaxID®, Oncophage®, GVAX, ADXS11-001, ALVAC-CEA, PROSTVAC®, Rindopepimut®, CimaVax-EGF, lapuleucel-T (APC8024; NeuvengeTM), GRNVAC1, GRNVAC2, GRN-1201, hepcortespenlisimut-L (Hepko-V5), DCVAX®, SCIB1, BMT CTN 1401, PrCa VBIR, PANVAC, ProstAtak®, DPX-Survivac, or viagenpumatucel-L (HS-110).
• the immunotherapy is a peptide vaccine.
• the peptide vaccine is nelipepimut-S(E75) (NeuVaxTM), IMA901, or SurVaxM (SVN53-67).
• the cancer vaccine is an immunogenic personal neoantigen vaccine (see, e.g., Ott et al. (2017) Nature 547: 217-221; Sahin et al. (2017) Nature 547: 222-226).
• the cancer vaccine is RGSH4K, or NEO-PV-01.
• the cancer vaccine is a DNA-based vaccine.
• the DNA-based vaccine is a mammaglobin-A DNA vaccine (see, e.g., Kim et al. (2016) Oncolmmunology 5(2): e1069940).
• immune-targeted agents are selected from aldesleukin, interferon alfa-2b, ipilimumab, lambrolizumab, nivolumab, prednisone, and sipuleucel-T.
• Non-limiting examples of radiotherapy include radioiodide therapy, external-beam radiation, and radium 223 therapy.
• Additional kinase inhibitors include those described in, for example, U.S. Pat. Nos. 7,514,446; 7,863,289; 8,026,247; 8,501,756; 8,552,002; 8,815,901; 8,912,204; 9,260,437; 9,273,051; U.S. Publication No. US 2015/0018336; International Publication No.
• kinase inhibitors include those described in, for example, WO 2016/081450; WO 2016/022569; WO 2016/011141; WO 2016/011144; WO 2016/011147; WO 2015/191667; WO 2012/101029; WO 2012/113774; WO 2015/191666; WO 2015/161277; WO 2015/161274; WO 2015/108992; WO 2015/061572; WO 2015/058129; WO 2015/057873; WO 2015/017528; WO/2015/017533; WO 2014/160521; and WO 2014/011900, each of which is hereby incorporated by reference in its entirety.
• a kinase inhibitor as provided herein may have activity against more than one kinase (i.e. may be a multikinase inhibitor).
• a mechanism of action e.g., ROS1, ALK, or TRK kinase inhibition
• each of the compounds recited are structurally distinct from one another (e.g., the ROS1 inhibitor and the TRK inhibitor are not the same compound).
• a method of treating cancer comprising administering to a patient in need thereof a pharmaceutical combination for treating cancer which comprises (a) a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, (b) an additional therapeutic agent, and (c) optionally at least one pharmaceutically acceptable carrier for simultaneous, separate or sequential use for the treatment of cancer, wherein the amounts of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof and the additional therapeutic agent are together effective in treating the cancer.
• additional therapeutic agents may be administered with one or more doses of the compound of Formula I, or a pharmaceutically acceptable salt or solvate thereof, or pharmaceutical composition thereof, as part of the same or separate dosage forms, via the same or different routes of administration, and/or on the same or different administration schedules according to standard pharmaceutical practice known to one skilled in the art.
• a pharmaceutical combination for treating a cancer in a patient in need thereof which comprises (a) a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, (b) at least one additional therapeutic agent (e.g., any of the exemplary additional therapeutic agents described herein or known in the art), and (c) optionally at least one pharmaceutically acceptable carrier for simultaneous, separate or sequential use for the treatment of cancer, wherein the amounts of the compound of Formula I or pharmaceutically acceptable salt or solvate thereof and of the additional therapeutic agent are together effective in treating the cancer; (ii) a pharmaceutical composition comprising such a combination; (iii) the use of such a combination for the preparation of a medicament for the treatment of cancer; and (iv) a commercial package or product comprising such a combination as a combined preparation for simultaneous, separate or sequential use; and to a method of treatment of cancer in a patient in need thereof.
• the patient is a human.
• the cancer is a ROS1-associated cancer
• pharmaceutical combination refers to a pharmaceutical therapy resulting from the mixing or combining of more than one active ingredient and includes both fixed and non-fixed combinations of the active ingredients.
• fixed combination means that a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof and at least one additional therapeutic agent (e.g., a chemotherapeutic agent), are both administered to a patient simultaneously in the form of a single composition or dosage.
• non-fixed combination means that a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof and at least one additional therapeutic agent (e.g., chemotherapeutic agent) are formulated as separate compositions or dosages such that they may be administered to a patient in need thereof simultaneously, concurrently or sequentially with variable intervening time limits (e.g., 1 hour, 1 day, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months), wherein such administration provides effective levels of the two or more compounds in the body of the patient.
• variable intervening time limits e.g., 1 hour, 1 day, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months
• a method of treating a cancer comprising administering to a patient in need thereof a pharmaceutical combination for treating cancer which comprises (a) a compound of Formula I or pharmaceutically acceptable salt or solvate thereof, (b) an additional therapeutic agent, and (c) optionally at least one pharmaceutically acceptable carrier for simultaneous, separate or sequential use for the treatment of cancer, wherein the amounts of the compound of Formula I or pharmaceutically acceptable salt or solvate thereof and the additional therapeutic agent are together effective in treating the cancer.
• the compound of Formula I or pharmaceutically acceptable salt or solvate thereof, and the additional therapeutic agent are administered simultaneously as separate dosages.
• the compound of Formula I or pharmaceutically acceptable salt or solvate thereof, and the additional therapeutic agent are administered as separate dosages sequentially in any order, in jointly therapeutically effective amounts, e.g. in daily or intermittently dosages.
• the compound of Formula I or pharmaceutically acceptable salt or solvate thereof, and the additional therapeutic agent are administered simultaneously as a combined dosage.
• the cancer is a ROS1-associated cancer.
• a ROS1-associated cancer having one or more ROSlinhibitor resistance mutations.
• the disease or disorder mediated by ROS1 is a dysregulation of ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same includes one or more ROS1 inhibitor resistance mutations.
• a disease or disorder mediated by ROS1 can include any disease, disorder or condition that is directly or indirectly linked to expression or activity of ROS1, including overexpression and/or abnormal activity levels.
• the disease is cancer (e.g., a ROS1-associated cancer).
• the cancer is any of the cancers or ROS1-associated cancers described herein.
• tumorigenesis may vary between different cancer types, the cellular and molecular mechanisms required for metastasis appear to be similar for all solid tumor types.
• the cancer cells lose growth inhibitory responses, undergo alterations in adhesiveness and produce enzymes that can degrade extracellular matrix components. This leads to detachment of tumor cells from the original tumor, infiltration into the circulation through newly formed vasculature, migration and extravasation of the tumor cells at favorable distant sites where they may form colonies.
• a number of genes have been identified as being promoters or suppressors of metastasis.
• the method comprising administering to the patient a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof or a pharmaceutical composition thereof.
• Such methods can be used in the treatment of one or more of the cancers described herein. See, e.g., US Publication No. 2013/0029925; International Publication No. WO 2014/083567; and U.S. Pat. No. 8,568,998.
• the cancer is a ROS1-associated cancer.
• the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof is used in combination with an additional therapy or another therapeutic agent, including a chemotherapeutic agent, such as a kinase inhibitor, for example, a first or second ROS1 kinase inhibitor.
• a chemotherapeutic agent such as a kinase inhibitor, for example, a first or second ROS1 kinase inhibitor.
• tumor is an art known term and means the formation of an additional tumor (e.g., a solid tumor) at a site distant from a primary tumor in a subject or patient, where the additional tumor includes the same or similar cancer cells as the primary tumor.
• additional tumor e.g., a solid tumor
• Also provided are methods of decreasing the risk of developing a metastasis or an additional metastasis in a patient having a ROS1-associated cancer that include: selecting, identifying, or diagnosing a patient as having a ROS1-associated cancer, and administering a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof to the patient selected, identified, or diagnosed as having a ROS1-associated cancer. Also provided are methods of decreasing the risk of developing a metastasis or an additional metastasis in a patient having a ROS1-associated cancer that includes administering a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvent thereof to a patient having a ROS1-associated cancer.
• the decrease in the risk of developing a metastasis or an additional metastasis in a patient having a ROS1-associated cancer can be compared to the risk of developing a metastasis or an additional metastasis in the patient prior to treatment, or as compared to a patient or a population of patients having a similar or the same ROS1-associated cancer that has received no treatment or a different treatment.
• the ROS1-associated cancer is a ROS1-associated cancer having one or more ROSlinhibitor resistance mutations.
• risk of developing a metastasis means the risk that a subject or patient having a primary tumor will develop an additional tumor (e.g., a solid tumor) at a site distant from a primary tumor in a subject or patient over a set period of time, where the additional tumor includes the same or similar cancer cells as the primary tumor.
• additional tumor e.g., a solid tumor
• risk of developing additional metastases means the risk that a subject or patient having a primary tumor and one or more additional tumors at sites distant from the primary tumor (where the one or more additional tumors include the same or similar cancer cells as the primary tumor) will develop one or more further tumors distant from the primary tumor, where the further tumors include the same or similar cancer cells as the primary tumor. Methods for reducing the risk of developing additional metastasis are described herein.
• the presence of one or more ROS1 inhibitor resistance mutations in a tumor causes the tumor to be more resistant to treatment with a first ROS1 inhibitor.
• Methods useful when a ROS1 inhibitor resistance mutation causes the tumor to be more resistant to treatment with a first ROS1 inhibitor are described below.
• methods of treating a subject having a cancer that include: identifying a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations; and administering to the identified subject a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof is administered in combination with the first ROS1 inhibitor.
• the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof is administered in combination with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• methods for treating a ROS1-associated cancer in a subject in need of such treatment comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a compound of Formula I, or a pharmaceutically acceptable salt of solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the first ROS1 inhibitor of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a compound of Formula I selected from Example No.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more fusion proteins of Table 2 and/or one or more ROS1 kinase protein point mutations, insertions, and/or deletions (e.g., one or more point mutations of Table 3 or Table 3a) in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations of Table 4; and (d) administering a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the first ROS1 inhibitor of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more of the fusion proteins SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1 in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more of the ROS1 inhibitor resistance mutations L2026M, G2032R, or D2033N; and (d) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof selected from the group consisting of a compound of Formula I selected from Example No.
• a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor, wherein the first ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a compound of Formula I, or a pharmaceutically acceptable salt of solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the first ROS1 inhibitor of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor, wherein the first ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the first ROS1 inhibitor of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more fusion proteins of Table 2 and/or one or more ROS1 kinase protein point mutations, insertions, and/or deletions (e.g., one or more point mutations of Table 3 or Table 3a) in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor, wherein the first ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations of Table 4; and (d) administering a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the first ROS1 inhibitor of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more of the fusion proteins SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROSlin a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a first ROS1 inhibitor, wherein the first ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more of the ROS1 inhibitor resistance mutations L2026M, G2032R, or D2033N; and (d) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof selected from the group consisting of a compound of Formula I selected from Example No.
• methods for treating a ROS1-associated cancer in a subject in need of such treatment comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I, or a pharmaceutically acceptable salt of solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a second ROS1 inhibitor, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a second ROS1 inhibitor, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more fusion proteins of Table 2 and/or one or more ROS1 kinase protein point mutations, insertions, and/or deletions (e.g., one or more of the point mutations of Table 3 or Table 3a) in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations of Table 4; and (d) administering a second ROS1 inhibitor, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more of the fusion proteins SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1 in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more of the ROS1 inhibitor resistance mutations L2026M, G2032R, or D2033N; and (d) administering a second ROS1 inhibitor, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I, or a pharmaceutically acceptable salt of solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a second ROS1 inhibitor, wherein the second ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the second ROS1 inhibitor is selected from the group consisting of alectinib
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering a second ROS1 inhibitor, wherein the second ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the second ROS1 inhibitor is selected from the group consisting of alectinib
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more fusion proteins of Table 2 and/or one or more ROS1 kinase protein point mutations, insertions, and/or deletions (e.g., one or more of the point mutations of Table 3 or Table 3a) in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations of Table 4; and (d) administering a second ROS1 inhibitor, wherein the second ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the second ROS1 inhibitor is selected from the group consisting of alect
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more of the fusion proteins SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1 in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more of the ROS1 inhibitor resistance mutations L2026M, G2032R, or D2033N; and (d) administering a second ROS1 inhibitor, wherein the second ROS1 inhibitor is selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib, as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (e) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject as a monotherapy or in conjunction with another anticancer agent (e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof) or anticancer therapy (e.g., surgery or radiation) if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations.
• another anticancer agent e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof
• anticancer therapy e.g., surgery or radiation
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting a dysregulation of a ROS1 gene, a ROS1 kinase, or the expression or activity or level of any of the same in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected from Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (d) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject as a monotherapy or in conjunction with another anticancer agent (e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof) or anticancer therapy (e.g., surgery or radiation) if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations.
• another anticancer agent e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof
• anticancer therapy e.g., surgery or radiation
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more ROS1 fusion proteins of Table 2 and/or one or more ROS1 kinase protein point mutations, insertions, and/or deletions (e.g., one or more of the point mutations of Table 3 or Table 3a) in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof selected from the group consisting of a compound of Formula I selected from Example No.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations of Table 4; and (d) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject as a monotherapy or in conjunction with another anticancer agent (e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof) or anticancer therapy (e.g., surgery or radiation) if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations.
• another anticancer agent e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof
• anticancer therapy e.g., surgery or radiation
• a second ROS1 inhibitor selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib is administered in step (d).
• provided herein are methods for treating a ROS1-associated cancer in a subject in need of such treatment, the method comprising (a) detecting one or more of the fusion proteins SLC34A2-ROS1, CD74-ROS1, EZR-ROS1, TPM3-ROS1, or SDC4-ROS1 in a sample from the subject; and (b) administering to the subject a therapeutically effective amount of a compound of Formula I selected Example No. 2, 3, 7, 9, 14, 19, 20, 22, 33-A, 33-B, 35, 36, and 45, or a pharmaceutically acceptable salt or solvate thereof.
• the methods further comprise (after (b)) (c) determining whether a cancer cell in a sample obtained from the subject has one or more of the ROS1 inhibitor resistance mutations L2026M, G2032R, or D2033N; and (d) administering additional doses of the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof of step (b) to the subject as a monotherapy or in conjunction with another anticancer agent (e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof) or anticancer therapy (e.g., surgery or radiation) if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations.
• another anticancer agent e.g., a second ROS1 inhibitor, a second compound of Formula I, an ALK inhibitor, a TRK inhibitor, or a pharmaceutically acceptable salt thereof
• anticancer therapy e.g., surgery or radiation
• a second ROS1 inhibitor selected from the group consisting of alectinib, brigatinib, cabozantinib, ceritinib, crizotinib, entrectinib, foretinib, lorlatinib, and mesestinib is administered in step (d).
• Also provided are methods of selecting a treatment for a subject having a cancer that include: identifying a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations; and selecting a treatment that includes administration of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with a first ROS1 inhibitor.
• the compound of Formula I or a pharmaceutically acceptable salt or solvate thereof is administered in combination with the first ROS1 inhibitor.
• Also provided are methods of selecting a treatment for a subject having a cancer that include: selecting a treatment that includes administration of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof for a subject identified as having a cancer cell that has one or more ROS1 inhibitor resistance mutations. Also provided are methods of selecting a subject having a cancer for a treatment that does not include a first ROS1 inhibitor as a monotherapy that include: identifying a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations; and selecting the identified subject for a treatment that includes a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• Also provided are methods of selecting a subject having a cancer for a treatment that does not include a first ROS1 inhibitor as a monotherapy that include: selecting a subject identified as having a cancer cell that has one or more ROS1 inhibitor resistance mutations for a treatment that includes administration of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• Also provided are methods of determining the likelihood that a subject having a cancer e.g., a ROS1-associated cancer
• determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations has a decreased likelihood of having a positive response (i.e. an increased likelihood of having a negative response) to treatment with a first ROS1 inhibitor as a monotherapy.
• Also provided are methods of determining the likelihood that a subject having a cancer e.g., a ROS1-associated cancer
• determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that a subject not having a cancer cell that has one or more ROS1 inhibitor resistance mutations has an increased likelihood of having a positive response to treatment with a first ROS1 inhibitor as a monotherapy as compared to a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations.
• Also provided are methods of predicting the efficacy of treatment with a first ROS1 inhibitor as a monotherapy in a subject having cancer that include: determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that treatment with a first ROS1 inhibitor as a monotherapy is less likely to be effective in a subject having a cancer cell in a sample obtained from the subject that has one or more ROS1 inhibitor resistance mutations.
• Also provided are methods of predicting the efficacy of treatment with a first ROS1 inhibitor as a monotherapy in a subject having cancer that include: determining that treatment with a first ROS1 inhibitor as a monotherapy is less likely to be effective in a subject having a cancer cell in a sample obtained from the subject that has one or more ROS1 inhibitor resistance mutations.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• Also provided are methods of treating a subject having a cancer that include: (a) administering a first ROS1 inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) administering additional doses of the first ROS1 inhibitor of step (a) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent (e.g., a second ROS1 inhibitor, an ALK inhibitor, a TRK inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor (e.g., a second ROS1 inhibitor).
• another anticancer agent can be the first ROS1 inhibitor administered in step (a).
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2032, e.g., L2026M, G2032R, or D2033N.
• Also provided are methods of treating a subject having a cancer that include: (a) administering a first ALK inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has one or more ROS1 inhibitor resistance mutations; or (d) administering additional doses of the first ALK inhibitor of step (a) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent (e.g., a second ALK inhibitor, a first ROS1 inhibitor, a TRK inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ALK inhibitor (e.g., a second ALK inhibitor).
• another anticancer agent can be the first ALK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• Also provided are methods of treating a subject having a cancer that include: (a) administering a first TRK inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has one or more ROS1 inhibitor resistance mutations; or (d) administering additional doses of the first TRK inhibitor of step (a) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent (e.g., a second TRK inhibitor, a first ROS1 inhibitor, an ALK inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another TRK inhibitor (e.g., a second TRK inhibitor).
• another anticancer agent can be the first TRK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• the dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same confers increased resistance to a cancer cell or tumor to treatment with the first TRK inhibitor.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• Also provided are methods of treating a subject having a cancer that include: (a) administering a first ROS1 inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) administering a second ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) administering additional doses of the first ROS1 inhibitor step (a) to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• Also provided are methods of treating a subject having a cancer e.g., a ROS1-associated cancer
• a cancer e.g., a ROS1-associated cancer
• methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ROS1 inhibitor, has one or more ROS1 inhibitor resistance mutations; and (b) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first ROS1 inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a cancer e.g., a ROS1-associated cancer
• the subject can also be administered another anticancer agent (e.g., a second ROS1 inhibitor, an ALK inhibitor, a TRK inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent e.g., a second ROS1 inhibitor, an ALK inhibitor, a TRK inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor (e.g., a second ROS1 inhibitor).
• another anticancer agent can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of treating a subject having a cancer e.g., a ROS1-associated cancer
• a cancer e.g., a ROS1-associated cancer
• methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ALK inhibitor has one or more ROS1 inhibitor resistance mutations; and (b) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell having one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first ALK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a cancer e.g., a ROS1-associated cancer
• the subject can also be administered another anticancer agent (e.g., a second ALK inhibitor, a TRK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is can be another ALK inhibitor (e.g., a second ALK inhibitor).
• another anticancer agent can be the first ALK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• Also provided are methods of treating a subject having a cancer e.g., a ROS1-associated cancer
• a cancer e.g., a ROS1-associated cancer
• methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first TRK inhibitor is associated with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same; and (b) administering a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first TRK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a cancer e.g., a ROS1
• the subject can also be administered another anticancer agent (e.g., a second TRK inhibitor, an ALK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is can be another TRK inhibitor (e.g., a second TRK inhibitor).
• another anticancer agent can be the first TRK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• Also provided are methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ROS1 inhibitor has one or more ROS1 inhibitor resistance mutations; and (b) administering a second ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first ROS1 inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ALK inhibitor has one or more ROS1 inhibitor resistance mutations; and (b) administering a ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first ALK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be a ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent can be the first ALK inhibitor administered in step (a).
• Also provided are methods of treating a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first TRK inhibitor is associated with a dysregulation of a ROS1 gene, a ROS1 kinase, or expression or activity or level of any of the same; and (b) administering a ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent to the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) administering additional doses of the first TRK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the subject can also be administered another anticancer agent.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be a ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent can be the first TRK inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) administering a first ROS1 inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) selecting additional doses of the first ROS1 inhibitor of step (a) for the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent for the subject.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor (e.g., a second ROS1 inhibitor).
• another ROS1 inhibitor can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) administering a first ALK inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) selecting additional doses of the first ALK inhibitor of step (a) for the subject if the subject has a cancer cell that does not have has one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent for the subject.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor.
• another anticancer agent is the first ALK inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) administering one or more doses of a first TRK inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) selecting additional doses of the first TRK inhibitor of step (a) for the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent for the subject.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent can be another ROS1 inhibitor.
• another anticancer agent is the first TRK inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) administering a first ROS1 inhibitor to the subject for a period of time (e.g., 1 month, 2 months, 3 months, 6 months, 9 months, 1 year); (b) after (a), determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and (c) selecting a second ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (d) selecting additional doses of the first ROS1 inhibitor of step (a) for the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent for the subject.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is another ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another ROS1 can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ROS1 inhibitor has one or more ROS1 inhibitor resistance mutations; (b) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) selecting additional doses of the first ROS1 inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof) for the subject.
• another anticancer agent e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is another ROS1 inhibitor (e.g., a second ROS1 inhibitor).
• another ROS1 inhibitor can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of selecting a treatment for a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ALK inhibitor has one or more ROS1 inhibitor resistance mutations; and (b) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) selecting additional doses of the first ALK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a cancer e.g., a ROS1-associated cancer
• the method can further include selecting doses of another anticancer agent (e.g., a second ALK inhibitor, a TRK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent e.g., a second ALK inhibitor, a TRK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is can be another ALK inhibitor (e.g., a second ALK inhibitor).
• another anticancer agent can be the first ALK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• Also provided are methods of selecting a treatment for a subject having a cancer that include: (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first TRK inhibitor has one or more ROS1 inhibitor resistance mutations; and (b) selecting a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) selecting additional doses of the first TRK inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• a cancer e.g., a ROS1-associated cancer
• the method can further include selecting doses of another anticancer agent (e.g., a second TRK inhibitor, an ALK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another anticancer agent e.g., a second TRK inhibitor, an ALK inhibitor, a first ROS1 inhibitor, or a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof.
• the ROS1 inhibitor resistance mutation includes one or more ROS1 inhibitor resistance mutations listed in Table 4.
• a ROS1 inhibitor resistance mutation can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is can be another TRK inhibitor (e.g., a second TRK inhibitor).
• another anticancer agent can be the first TRK inhibitor administered in step (a).
• another anticancer agent can be another ROS1 inhibitor.
• Also provided are methods of selecting a treatment for a subject having a cancer that include (a) determining whether a cancer cell in a sample obtained from a subject having a cancer and previously administered a first ROS1 inhibitor has one or more ROS1 inhibitor resistance mutations; (b) selecting a second ROS1 inhibitor as a monotherapy or in conjunction with another anticancer agent for the subject if the subject has a cancer cell that has one or more ROS1 inhibitor resistance mutations; or (c) selecting additional doses of the first ROS1 inhibitor previously administered to the subject if the subject has a cancer cell that does not have one or more ROS1 inhibitor resistance mutations.
• the method can further include selecting doses of another anticancer agent (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof) for the subject.
• another anticancer agent e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• another anticancer agent is any anticancer agent known in the art.
• another anticancer agent is another ROS1 inhibitor (e.g., a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof).
• another ROS1 can be the first ROS1 inhibitor administered in step (a).
• Also provided are methods of determining a subject's risk for developing a cancer that has some resistance to a first ROS1 inhibitor that include: determining whether a cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and identifying a subject having a cell that has one or more ROS1 inhibitor resistance mutations as having an increased likelihood of developing a cancer that has some resistance to the first ROS1 inhibitor. Also provided are methods of determining a subject's risk for developing a cancer that has some resistance to a first ROS1 inhibitor that include: identifying a subject having a cell that has one or more ROS1 inhibitor resistance mutations as having an increased likelihood of developing a cancer that has some resistance to the first ROS1 inhibitor.
• Also provided are methods of determining the presence of a cancer that has some resistance to a first ROS1 inhibitor that include: determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that the subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations has a cancer that has some resistance to the first ROS1 inhibitor. Also provided are methods of determining the presence of a cancer that has some resistance to a first ROS1 inhibitor in a subject that include: determining that a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations has a cancer that has some resistance to the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations confer increased resistance to a cancer cell or tumor to treatment with the first ROS1 inhibitor.
• the one or more ROS1 inhibitor resistance mutations include one or more ROS1 inhibitor resistance mutations listed in Table 4.
• the one or more ROS1 inhibitor resistance mutations can include a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N.
• a ROS1 inhibitor resistance mutation that confers increased resistance to a cancer cell or tumor to treatment with a first ROS1 inhibitor can be any of the ROS1 inhibitor resistance mutations listed in Table 4 (e.g., a substitution at one or more of amino acid positions 2026, 2032, or 2033, e.g., L2026M, G2032R, or D2033N).
• Also provided are methods of determining the likelihood that a subject having a cancer will have a positive response to treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy that include: determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that the subject having the cancer cell that has one or more ROS1 inhibitor resistance mutations has an increased likelihood of having a positive response to treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy.
• Also provided are methods of determining the likelihood that a subject having cancer will have a positive response to treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy that include: determining that a subject having a cancer cell that has one or more ROS1 inhibitor resistance mutations has an increased likelihood of having a positive response to treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy.
• Also provided are methods of predicting the efficacy of treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy in a subject having cancer that include: determining whether a cancer cell in a sample obtained from the subject has one or more ROS1 inhibitor resistance mutations; and determining that treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy is likely to be effective in a subject having a cancer cell in a sample obtained from the subject that has one or more ROS1 inhibitor resistance mutations.
• Also provided are methods of predicting the efficacy of treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy in a subject having cancer that include: determining that treatment with a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof as a monotherapy is likely to be effective in a subject having a cancer cell in a sample obtained from the subject that has one or more ROS1 inhibitor resistance mutations.
• Methods of determining the level of resistance of a cancer cell or a tumor to a ROS1 inhibitor can be determined using methods known in the art.
• the level of resistance of a cancer cell to a ROS1 inhibitor can be assessed by determining the IC 50 of a ROS1 inhibitor (e.g., any of the ROS1 inhibitors described herein or known in the art) on the viability of a cancer cell.
• the level of resistance of a cancer cell to a ROS1 inhibitor can be assessed by determining the growth rate of the cancer cell in the presence of a ROS1 inhibitor (e.g., any of the ROS1 inhibitors described herein).
• the level of resistance of a tumor to a ROS1 inhibitor can be assessed by determining the mass or size of one or more tumors in a subject over time during treatment with a ROS1 inhibitor (e.g., any of the ROS1 inhibitors described herein).
• the level of resistance of a cancer cell or a tumor to a ROS1 inhibitor can be indirectly assessed by determining the activity of a ROS1 kinase including one or more of the ROS1 inhibitor resistance mutations (i.e., the same ROS1 kinase expressed in a cancer cell or a tumor in a subject).
• the level of resistance of a cancer cell or tumor having one or more ROS1 inhibitor resistance mutations to a ROS1 inhibitor is relative to the level of resistance in a cancer cell or tumor that does not have one or more ROS1 inhibitor resistance mutations (e.g., a cancer cell or tumor that does not have the same ROS1 inhibitor resistance mutations, a cancer cell or a tumor that does not have any ROS1 inhibitor resistance mutations, or a cancer cell or a tumor that expresses a wildtype ROS1 protein).
• the determined level of resistance of a cancer cell or a tumor having one or more ROS1 inhibitor resistance mutations can be greater than about 1%, greater than about 2%, greater than about 3%,greater than about 4%, greater than about 5%, greater than about 6%, greater than about 7%, greater than about 8%, greater than about 9%, greater than about 10%, greater than about 11%, greater than about 12%, greater than about 13%, greater than about 14%, greater than about 15%, greater than about 20%, greater than about 25%, greater than about 30%, greater than about 35%, greater than about 40%, greater than about 45%, greater than about 50%, greater than about 60%, greater than about 70%, greater than about 80%, greater than about 90%, greater than about 100%, greater than about 110%, greater than about 120%, greater than about 130%, greater than about 140%, greater than about 150%, greater than about 160%, greater than about 170%, greater than about 180%, greater than about 190%, greater than about 200%, greater than about 210%, greater than about 220%, greater
• Also provided is a method for inhibiting ROS1 kinase activity in a cell comprising contacting the cell with a compound of Formula I.
• the contacting is in vitro.
• the contacting is in vivo.
• the contacting is in vivo, wherein the method comprises administering an effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof to a subject having a cell having ROS1 kinase activity.
• the cell is a cancer cell.
• the cancer cell is any cancer as described herein.
• the cancer cell is a ROS1-associated cancer cell.
• a method for inhibiting ROS1 kinase activity in a mammalian cell comprising contacting the cell with a compound of Formula I.
• the contacting is in vitro.
• the contacting is in vivo.
• the contacting is in vivo, wherein the method comprises administering an effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof to a mammal having a cell having ROSlkinase activity.
• the mammalian cell is a mammalian cancer cell.
• the mammalian cancer cell is any cancer as described herein.
• the mammalian cancer cell is a ROS1-associated cancer cell.
• contacting refers to the bringing together of indicated moieties in an in vitro system or an in vivo system.
• “contacting” a ROS1 kinase with a compound provided herein includes the administration of a compound provided herein to an individual or patient, such as a human, having a ROS1 kinase, as well as, for example, introducing a compound provided herein into a sample containing a cellular or purified preparation containing the ROS1 kinase.
• Also provided herein is a method of inhibiting cell proliferation, in vitro or in vivo, the method comprising contacting a cell with an effective amount of a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, or a pharmaceutical composition thereof as defined herein
• the phrase “effective amount” means an amount of compound that, when administered to a patient in need of such treatment, is sufficient to (i) treat a ROS1 kinase-associated disease or disorder, (ii) attenuate, ameliorate, or eliminate one or more symptoms of the particular disease, condition, or disorder, or (iii) delay the onset of one or more symptoms of the particular disease, condition, or disorder described herein.
• the amount of a compound of Formula I that will correspond to such an amount will vary depending upon factors such as the particular compound, disease condition and its severity, the identity (e.g., weight) of the patient in need of treatment, but can nevertheless be routinely determined by one skilled in the art.
• the compounds of Formula I can be administered in the form of pharmaceutical compositions.
• These compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including transdermal, epidermal, ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal or intranasal), oral or parenteral.
• Oral administration can include a dosage form formulated for once-daily or twice-daily (BID) administration.
• Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal intramuscular or injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
• Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump.
• Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable
• compositions which contain, as the active ingredient, a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof, in combination with one or more pharmaceutically acceptable carriers (excipients).
• the composition is suitable for topical administration.
• the active ingredient is typically mixed with an excipient, diluted by an excipient or enclosed within such a carrier in the form of, for example, a capsule, sachet, paper, or other container.
• the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient.
• compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders.
• the composition is formulated for oral administration.
• the composition is formulated as a tablet or capsule.
• compositions comprising a compound of Formula I or a pharmaceutically acceptable salt or solvate thereof can be formulated in a unit dosage form, each dosage containing from about 5 to about 1,000 mg (1 g), more usually about 100 mg to about 500 mg, of the active ingredient.
• unit dosage form refers to physically discrete units suitable as unitary dosages for human subjects and other patients, each unit containing a predetermined quantity of active material (i.e., a compound for Formula I as provided herein) calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
• the compositions provided herein contain from about 5 mg to about 50 mg of the active ingredient.
• the active ingredient contains from about 5 mg to about 50 mg.
• One having ordinary skill in the art will appreciate that this embodies compounds or compositions containing about 5 mg to about 10 mg, about 10 mg to about 15 mg, about 15 mg to about 20 mg, about 20 mg to about 25 mg, about 25 mg to about 30 mg, about 30 mg to about 35 mg, about 35 mg to about 40 mg, about 40 mg to about 45 mg, or about 45 mg to about 50 mg of the active ingredient.
• compositions provided herein contain from about 50 mg to about 500 mg of the active ingredient.
• the active ingredient contains from about 50 mg to about 500 mg of the active ingredient.
• One having ordinary skill in the art will appreciate that this embodies compounds or compositions containing about 50 mg to about 100 mg, about 100 mg to about 150 mg, about 150 mg to about 200 mg, about 200 mg to about 250 mg, about 250 mg to about 300 mg, about 350 mg to about 400 mg, or about 450 mg to about 500 mg of the active ingredient.
• the compositions provided herein contain from about 500 mg to about 1,000 mg of the active ingredient.
• the active ingredient contains from about 500 mg to about 1,000 mg of the active ingredient.
• this embodies compounds or compositions containing about 500 mg to about 550 mg, about 550 mg to about 600 mg, about 600 mg to about 650 mg, about 650 mg to about 700 mg, about 700 mg to about 750 mg, about 750 mg to about 800 mg, about 800 mg to about 850 mg, about 850 mg to about 900 mg, about 900 mg to about 950 mg, or about 950 mg to about 1,000 mg of the active ingredient.
• the active compound may be effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It will be understood, however, that the amount of the compound actually administered will usually be determined by a physician, according to the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, and the like.
• kits useful for example, in the treatment of RET-associated diseases or disorders, such as cancer or irritable bowel syndrome (IBS), which include one or more containers containing a pharmaceutical composition comprising a therapeutically effective amount of a compound provided herein.
• kits can further include, if desired, one or more of various conventional pharmaceutical kit components, such as, for example, containers with one or more pharmaceutically acceptable carriers, additional containers, etc., as will be readily apparent to those skilled in the art.
• Instructions, either as inserts or as labels, indicating quantities of the components to be administered, guidelines for administration, and/or guidelines for mixing the components, can also be included in the kit.
• the potency of a compound inhibiting wild type and exemplary mutant ROS1 kinases was determined using CisBio's HTRF Kinease-TK assay technology.
• the assays contained 5 nM wild type ROS1 (SignalChem—Cat. No. R14-11G), 5 nM G2032R ROS1 (SignalChem—Cat. No. R14-12BG), 5 nM L2026M ROS1 (Array Biopharma, p 1965), or 5 nM D2033N ROS1 (Array Biopharma, p 1994).
• Each kinase is incubated with 250 nM TK-substrate biotin (CisBio, Cat. No.
• 62TKOPEC and 1 mM ATP along with test compound in a buffer consisting of 25 mM MOPS [pH 7.4], 5 mM MgCl 2 , 0.005% Triton X-100, and 2% DMSO in a volume of 8 ⁇ L.
• Compounds were prepared in a four-fold serial dilution in DMSO and added to the assay to give the appropriate final concentration. After a 120-minute incubation at 22° C., the reaction was quenched by adding 8 ⁇ L of quench solution containing 31.3 nM Sa-XL665 and 1 ⁇ TK-Ab-Cryptate in HTRF detection buffer (CisBio, Cat. No. 62TKOPEC).
• Table 9 provides averaged IC 50 values for compounds tested in this assay.

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