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  • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
  • C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
  • C07D213/60—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
  • C07D213/72—Nitrogen atoms
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  • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
  • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
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  • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings

Definitions

• the present invention relates to kinase inhibitors exhibiting novel and unexpected properties useful for the treatment of various diseases including hyperproliferative diseases and cancer. More particularly, the invention is concerned with such compounds, methods of treating diseases, and methods of synthesis of the compounds. Preferably, the compounds are useful for the modulation of activity of c-MET kinase, c-MET kinase polymorphs, c-MET kinase mutants, or c-MET kinase fusion proteins in the treatment of mammalian diseases, and in particular human hyperproliferative diseases and human cancers. In some embodiments, compounds disclosed herein exhibit unexpected selectivity for modulation of c-MET kinase activity.
• c-MET is a receptor tyrosine kinase (RTK) located on chromosome 7p and activated via its natural ligand hepatocyte growth factor.
• RTK receptor tyrosine kinase
• c-MET is found mutated in a variety of solid tumors (Ma, P. C. et al. Cancer Metastasis (2003) 22: 309). Mutations in the tyrosine kinase domain are associated with hereditary papillary renal cell carcinomas (Schmidt, L. et al. Nat. Genet . (1997) 16: 68; Schmidt, L. et al.
• the TPR-MET oncogene is a transforming variant of the c-MET RTK and was initially identified after treatment of a human osteogenic sarcoma cell line transformed by the chemical carcinogen N-methyl-N′-nitro-N-nitrosoguanidine (Park, M. et al. Cell (1986) 45: 895).
• the TPR-MET fusion oncoprotein is the result of a chromosomal translocation, placing the TPR3 locus on chromosome 1 upstream of a portion of the c-MET gene on chromosome 7 encoding only for the cytoplasmic region.
• Studies suggest that TPR-MET is detectable in experimental cancers (e.g., Yu, J. et al. Cancer (2000) 88: 1801).
• TPR-MET activates wild-type c-MET RTK and can activate crucial cellular growth pathways, including the Ras pathway (Aklilu, F. et al. Arm. J. Physiol . (1996) 271: E277) and the phosphatidylinositol 3-kinase (PI3K)/AKT pathway (Ponzetto, C. et al. Mol. Cell. Biol . (1993) 13: 4600).
• TPR-MET is ligand independent, lacks the CBL-like SH2 domain binding site in the juxtamembrane region in c-MET, and is mainly cytoplasmic.
• c-MET immunohistochemical expression seems to be associated with abnormal ⁇ -catenin expression, a hallmark feature of epithelial to mesenchymal transition (EMT) and provides good prognostic and predictive factors in breast cancer patients.
• Protein kinases constitute an important therapeutic protein family. There are approximately 518 human protein kinases. While inhibition of a desired kinase ‘on target’ is desirable for a human therapeutic, it is also desirable in many cases to provide a selective kinase inhibitor which does not substantially inhibit other kinase ‘off targets’ from within this protein family. Monoclonal antibodies are one approach to providing specific inhibitors to a specific kinase without inhibiting ‘off targets.’ Achieving this level of selectivity with small molecule inhibitors, however, is not as easily achievable nor as straightforward. Accordingly, there is a need for kinase inhibitors that are selective for a particular protein kinase. It is theorized that an unexpected increase in potency for c-MET kinase inhibition or an unexpected increase in selective c-MET inhibition relative to other kinases is observed for one or more of the embodiments disclosed herein.
• Compounds described herein find utility in the treatment of mammalian cancers and especially human cancers including, but not limited to, solid tumors, gastric cancers, melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, non small cell lung cancer, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, colonic cancers, myeloproliferative diseases, diseases wherein the etiology or progression is dependent on c-MET kinase activity, or on the activity of oncogenic forms, aberrant fusion protein forms, and mutant forms of c-MET kinase.
• X and F are regiochemically oriented with respect to each other in a mutual para-orientation; X is halogen or C1-C6 alkyl; and R3 is a non-hydrogen moiety regiochemically oriented ortho- to the B ring nitrogen.
• Compounds described herein exhibit unexpected potency for c-MET kinase inhibition and/or an unexpected increase in selective c-MET kinase inhibition relative to other kinases, particularly in comparison to other purported MET kinase inhibitors.
• X is halogen
• Z1 and Z2 are independently and individually CR2 or N;
• Z3 is CH or N
• each R1 is independently and individually halogen, H, C1-C6 alkyl, branched C3-C7 alkyl, C3-C7 cycloalkyl, or —CN;
• each R2 is individually and independently H, halogen, C1-C6 alkyl, or cyano;
• R3 is —C(O)R4, —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl, wherein
• R4 is C1-C7 alkyl, C3-C8 cycloalkyl, —(CH 2 ) p —CN, —(CH 2 ) p —OR6, —(CH 2 ) p —NR6(R7), —(CH 2 ) p —SO 2 —C1-C6-alkyl, —(CH 2 ) p —C6-C10-aryl, —(CH 2 ) p —C5-C6-heteroaryl, or —(CH 2 ) p —C4-C6-heterocyclyl, wherein
• each R6 and R7 is individually and independently H, C1-C6 alkyl, or C3-C8 branched alkyl;
• each cycloalkyl, aryl, heteroaryl and heterocyclyl is independently substituted with —(R25) m ;
• each R25 is individually and independently C1-C6 alkyl, branched C3-C8 alkyl, halogen, —(CH 2 ) m —CN, —(CH 2 ) m —OR6, —(CH 2 ) m —NR6(R7), —(CH 2 ) m —SO 2 —C1-C6-alkyl, —(CH 2 ) m —C(O)NR6(R7), —(CH 2 ) m —C(O)—C4-C6-heterocyclyl, or —(CH 2 ) m —C4-C6-heterocyclyl, wherein each alkyl or alkylene is optionally substituted with one or two C1-C6 alkyl;
• each m is individually and independently 0, 1, 2, or 3;
• p 1, 2, or 3.
• Z1 and Z2 are CR2, and Z3 is CH.
• the compound is a compound of Formula Ic,
• n 0, 1, or 2.
• R3 is —C(O)R4.
• R3 is —C(O)R4 and R4 is C1-C7 alkyl, C3-C8 cycloalkyl, —(CH 2 ) p —CN, —(CH 2 ) p —OR6, —(CH 2 ) p —NR6(R7), —(CH 2 ) p —SO 2 —C1-C6-alkyl, or —(CH 2 ) p —C4-C6-heterocyclyl, and wherein each alkyl or alkylene is optionally substituted with one or two C1-C6 alkyl.
• R3 is —C(O)R4 and R4 is C1-C7 alkyl or C3-C8 cycloalkyl, and wherein each alkyl or alkylene is optionally substituted with one or two C1-C6 alkyl.
• R3 is —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl.
• Z1 and Z2 are CR2, and Z3 is N.
• the compound of Formula I is a compound of Formula If
• n 0, 1, or 2.
• R3 is —C(O)R4.
• R3 is —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl.
• Z1 is CR2, Z2 is N, and Z3 is CH.
• the compound of Formula I is a compound of Formula Ij,
• R3 is —C(O)R4.
• R3 is —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl.
• Z1 is CR2, and Z2 and Z3 are N.
• the compound of Formula I is a compound of Formula Im
• R3 is —C(O)R4.
• R3 is —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl.
• the present invention is directed to a compound selected from the group consisting of N-(4-(2-acetamidopyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide, N-(4-(2-acetamidopyridin-4-yloxy)-5-chloro-2-fluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide, N-(4-(2-acetamidopyridin-4-yloxy)-2,5-difluorophenyl)-N′-phenylcyclopropane-1,1-dicarboxamide, N-(4-(2-(2-(dimethylamino)acetamido)pyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluoroph
• the present invention is directed to a compound selected from the group consisting of N-(4-(2-(cyclopropanecarboxamido)pyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide, N-(2,5-difluoro-4-(2-propionamidopyridin-4-yloxy)phenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide, N-(2,5-difluoro-4-(2-isobutyramidopyridin-4-yloxy)phenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide, N-(4-(2-acetamidopyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-(4-
• the present invention comprises a method of treating mammalian disease wherein the disease etiology or progression is at least partially mediated by a kinase activity, wherein the kinase is a wildtype form, a mutant oncogenic form, an aberrant fusion protein form or a polymorph, the method comprising administering to a mammal in need thereof an effective amount of a compound of any of claims 1 - 21 .
• the disease etiology or progression is at least partially mediated by the kinase activity of c-MET, mutant oncogenic forms, aberrant fusion proteins, or polymorphs thereof.
• the invention is directed to a pharmaceutical composition, comprising a compound of any of claims 1 - 21 and a pharmaceutically acceptable carrier.
• the pharmaceutical composition further comprises an additive selected from adjuvants, excipients, diluents, or stabilizers.
• the present invention is directed to a method of treating cancer, gastrointestinal stromal tumors, hyperproliferative diseases, metabolic diseases, neurodegenerative diseases, or diseases characterized by angiogenesis, such as solid tumors, melanomas, glioblastomas, ovarian cancer; pancreatic cancer, prostate cancer, lung cancers, breast cancers, renal cancers, hepatic cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, chronic myelogenous leukemia, leukemias, papillary thyroid carcinoma, non-small cell lung cancer, mesothelioma, hypereosinophilic syndrome, colonic cancers, ocular diseases characterized by hyperproliferation leading to blindness including retinopathies, diabetic retinopathy, age-related macular degeneration, hypereosinophilic syndrome, rheumatoid arthritis, asthma, chronic obstructive pulmonary, mastocytosis, or mast cell leukemia, the method comprising of cancer
• the compound is administered orally, parenterally, by inhalation, or subcutaneously.
• the compounds of this disclosure include any and all possible isomers, stereoisomers, enantiomers, diastereomers, tautomers, pharmaceutically acceptable salts, and solvates thereof, as well as crystalline polymorphic forms of the disclosed compounds and any and all possible isomers, stereoisomers, enantiomers, diastereomers, tautomers, pharmaceutically acceptable salts, and solvates thereof.
• the terms “compound” and “compounds” as used in this disclosure refer to the compounds of this disclosure and any and all possible isomers, stereoisomers, enantiomers, diastereomers, tautomers, pharmaceutically acceptable salts, and solvates, and crystalline polymorphs thereof.
• alkyl refers to a straight chain alkyl, wherein alkyl chain length is indicated by a range of numbers.
• alkyl refers to an alkyl chain as defined above containing 1, 2, 3, 4, 5, or 6 carbons (i.e., C1-C6 alkyl).
• alkyl group include, but are not limited to, methyl, ethyl, propyl, butyl, pentyl, and hexyl.
• branched alkyl refers to an alkyl chain wherein a branching point in the chain exists, and the total number of carbons in the chain is indicated by a range of numbers.
• branched alkyl refers to an alkyl chain as defined above containing from 3, 4, 5, 6, 7, or 8 carbons (i.e., branched C3-C8 alkyl). Examples of a branched alkyl group include, but are not limited to, iso-propyl, iso-butyl, secondary-butyl, and tertiary-butyl.
• alkoxy refers to —O— (alkyl), wherein “alkyl” is as defined above.
• branched alkoxy refers to —O— (branched alkyl), wherein “branched alkyl” is as defined above.
• alkylene refers to an alkyl moiety interposed between two other atoms.
• alkylene refers to an alkyl moiety as defined above containing 1, 2, or 3 carbons.
• Examples of an alkylene group include, but are not limited to —CH 2 —, —CH 2 CH 2 —, and —CH 2 CH 2 CH 2 —.
• alkylene groups are branched.
• alkynyl refers to a carbon chain containing one carbon-carbon triple bond.
• alkynyl refers to a carbon chain as described above containing 2 or 3 carbons (i.e., C2-C3 alkynyl).
• alkynyl group include, but are not limited to, ethyne and propyne.
• aryl refers to a cyclic hydrocarbon, where the ring is characterized by delocalized ⁇ electrons (aromaticity) shared among the ring members, and wherein the number of ring atoms is indicated by a range of numbers.
• aryl refers to a cyclic hydrocarbon as described above containing 6, 7, 8, 9, or ring atoms (i.e., C6-C10 aryl). Examples of an aryl group include, but are not limited to, benzene, naphthalene, tetralin, indene, and indane.
• cycloalkyl refers to a monocyclic saturated carbon ring, wherein the number of ring atoms is indicated by a range of numbers.
• “cycloalkyl” refers to a carbon ring as defined above containing 3, 4, 5, 6, 7, or 8 ring atoms (i.e., C3-C8 cycloalkyl).
• Examples of a cycloalkyl group include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
• halogen refers to fluorine, chlorine, bromine, and iodine.
• heterocycle or “heterocyclyl” as used herein refers to a cyclic hydrocarbon, wherein at least one of the ring atoms is an O, N, or S, wherein the number of ring atoms is indicated by a range of numbers.
• Heterocyclyl moieties as defined herein have C or N bonding hands.
• a ring N atom from the heterocyclyl is the bonding atom to —C(O) to form an amide, carbamate, or urea.
• heterocyclyl refers to a cyclic hydrocarbon as described above containing 4, 5, or 6 ring atoms (i.e., C4-C6 heterocyclyl).
• heterocycle group include, but are not limited to, aziridine, oxirane, thiirane, azetidine, oxetane, thietane, pyrrolidine, tetrahydrofuran, pyran, thiopyran, thiomorpholine, thiomorpholine S-oxide, thiomorpholine'S-dioxide, oxazoline, tetrahydrothiophene, piperidine, tetrahydropyran, thiane, imidazolidine, oxazolidine, thiazolidine, dioxolane, dithiolane, piperazine, oxazine, dithiane, and dioxane.
• heteroaryl refers to a cyclic hydrocarbon, where at least one of the ring atoms is an O, N, or S, the ring is characterized by delocalized it electrons (aromaticity) shared among the ring members, and wherein the number of ring atoms is indicated by a range of numbers. Heteroaryl moieties as defined herein have C or N bonding hands. For example, in some embodiments, a ring N atom from the heteroaryl is the bonding atom to —C(O) to form an amide, carbamate, or urea.
• heteroaryl refers to a cyclic hydrocarbon as described above containing 5 or 6 ring atoms (i.e., C5-C6 heteroaryl).
• heteroaryl group include, but are not limited to, pyrrole, furan, thiene, oxazole, thiazole, isoxazole, isothiazole, imidazole, pyrazole, oxadiazole, thiadiazole, triazole, tetrazole, pyridine, pyrimidine, pyrazine, pyridazine, and triazine.
• substituted in connection with a moiety as used herein refers to a further substituent which is attached to the moiety at any acceptable location on the moiety. Unless otherwise indicated, moieties can bond through a carbon, nitrogen, oxygen, sulfur, or any other acceptable atom.
• salts as used herein embraces pharmaceutically acceptable salts commonly used to form alkali metal salts of free acids and to form addition salts of free bases.
• the nature of the salt is not critical, provided that it is pharmaceutically acceptable.
• Suitable pharmaceutically acceptable acid addition salts may be prepared from an inorganic acid or from an organic acid.
• Exemplary pharmaceutical salts are disclosed in Stahl, P. H., Wermuth, C. C., Eds. Handbook of Pharmaceutical Salts: Properties, Selection and Use ; Verlag Helvetica Chimica Acta/Wiley-VCH: Zurich, 2002, the contents of which are hereby incorporated by reference in their entirety.
• inorganic acids are hydrochloric, hydrobromic, hydroiodic, nitric, carbonic, sulfuric and phosphoric acid.
• Appropriate organic acids include, without limitation, aliphatic, cycloaliphatic, aromatic, arylaliphatic, and heterocyclyl containing carboxylic acids and sulfonic acids, for example formic, acetic, propionic, succinic, glycolic, gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic, fumaric, pyruvic, aspartic, glutamic, benzoic, anthranilic, mesylic, stearic, salicylic, p-hydroxybenzoic, phenylacetic, mandelic, embonic (pamoic), methanesulfonic, ethanesulfonic, benzenesulionic, pantothenic, toluenesulfonic, 2-hydroxyethane
• Suitable pharmaceutically acceptable salts of free acid-containing compounds disclosed herein include, without limitation, metallic salts and organic salts.
• Exemplary metallic salts include, but are not limited to, appropriate alkali metal (group Ia) salts, alkaline earth metal (group IIa) salts, and other physiological acceptable metals.
• Such salts can be made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc.
• Exemplary organic salts can be made from primary amines, secondary amines, tertiary amines and quaternary ammonium salts, for example, tromethamine, diethylamine, tetra-N-methylammonium, N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
• salts as used herein embraces pharmaceutically acceptable salts commonly used to form alkali metal salts of free acids and to form addition salts of free bases.
• the nature of the salt is not critical, provided that it is pharmaceutically acceptable.
• Suitable pharmaceutically acceptable acid addition salts may be prepared from an inorganic acid or from an organic acid. Examples of such inorganic acids are hydrochloric, hydrobromic, hydroiodic, nitric, carbonic, sulfuric and phosphoric acid.
• Appropriate organic acids may be selected from aliphatic, cycloaliphatic, aromatic, arylaliphatic, and heterocyclyl containing carboxylic acids and sulfonic acids, for example formic, acetic, propionic, succinic, glycolic, gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic, fumaric, pyruvic, aspartic, glutamic, benzoic, anthranilic, mesylic, stearic, salicylic, p-hydroxybenzoic, phenylacetic, mandelic, embonic (pamoic), methanesulfonic, ethanesulfonic, benzenesulfonic, pantothenic, toluenesulfonic, 2-hydroxyethanesulfonic, sulfanilic, cyclohexylaminosulfonic, algenic, 3-hydroxybutyric, galactaric and galactu
• Suitable pharmaceutically acceptable salts of free acid-containing compounds disclosed herein include metallic salts and organic salts.
• Exemplary metallic salts include, but are not limited to, appropriate alkali metal (group Ia) salts, alkaline earth metal (group IIa) salts, and other physiological acceptable metals.
• Such salts can be made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc.
• Exemplary organic salts can be made from primary amines, secondary amines, tertiary amines and quaternary ammonium salts, for example, tromethamine, diethylamine, tetra-N-methylammonium, N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
• administer refers to either directly administering a compound or pharmaceutically acceptable salt of the compound or a composition to a subject.
• carrier encompasses carriers, excipients, and diluents, meaning a material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material involved in carrying or transporting a pharmaceutical agent from one organ, or portion of the body, to another organ or portion of the body.
• disorder is used in this disclosure to mean, and is used interchangeably with, the terms disease, condition, or illness, unless otherwise indicated.
• an effective amount and “therapeutically effective amount” are used interchangeably in this disclosure and refer to an amount of a compound that, when administered to a subject, is capable of reducing a symptom of a disorder in a subject.
• the actual amount which comprises the “effective amount” or “therapeutically effective amount” will vary depending on a number of conditions including, but not limited to, the particular disorder being treated, the severity of the disorder, the size and health of the patient, and the route of administration. A skilled medical practitioner can readily determine the appropriate amount using methods known in the medical arts.
• the isolate and “purified” as used herein refer to a component separated from other components of a reaction mixture or a natural source.
• the isolate contains at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 98% of the compound or pharmaceutically acceptable salt of the compound by weight of the isolate.
• phrases “pharmaceutically acceptable” as used herein refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio:
• the term “subject” includes, without limitation, a human or an animal.
• exemplary animals include, but are not limited to, mammals such as mouse, rat, guinea pig, dog, cat, horse, cow, pig, monkey, chimpanzee, baboon, or rhesus monkey.
• treating refers to improving at least one symptom of the subject's disorder. Treating can be curing, improving, or at least partially ameliorating the disorder.
• hydrate refers to a compound disclosed herein which is associated with water in the molecular form, i.e., in which the H—OH bond is not split, and may be represented, for example, by the formula R ⁇ H 2 O, where R is a compound disclosed herein.
• R is a compound disclosed herein.
• a given compound may form more than one hydrate including, for example, monohydrates (R ⁇ H 2 O), dihydrates (R ⁇ 2H 2 O), trihydrates (R ⁇ 3H 2 O), and the like.
• solvate refers to a compound disclosed herein which is associated with solvent in the molecular form, i.e., in which the solvent is coordinatively hound, and may be represented, for example, by the formula R ⁇ (solvent), where R is a compound disclosed herein.
• a given compound may form more than one solvate including, for example, monosolvates (R ⁇ (solvent)) or polysolvates (R ⁇ n(solvent)), wherein n is an integer greater than 1) including, for example, disolvates (R ⁇ 2(solvent)), trisolvates (R ⁇ 3(solvent)), and the like, or hemisolvates, such as, for example, R ⁇ n/2(solvent), R ⁇ n/3(solvent), R ⁇ n/4(solvent) and the like, wherein n is an integer.
• Solvents herein include mixed solvents, for example, methanol/water, and as such, the solvates may incorporate one or more solvents within the solvate.
• acid hydrate refers to a complex that may be formed through association of a compound having one or more base moieties with at least one compound having one or more acid moieties or through association of a compound having one or more acid moieties with at least one compound having one or more base moieties, said complex being further associated with water molecules so as to form a hydrate, wherein said hydrate is as previously defined and R represents the complex herein described above.
• Structural, chemical and stereochemical definitions are broadly taken from IUPAC recommendations, and more specifically from Glossary of Terms used in Physical Organic Chemistry (IUPAC Recommendations 1994) as summarized by Müller, P. Pure Appl. Chem. 1994, 66, pp. 1077-1184 and Basic Terminology of Stereochemistry (IUPAC Recommendations 1996) as summarized by Moss, G. P. Pure Appl. Chem. 1996, 68, pp. 2193-2222.
• Atropisomers are defined as a subclass of conformers which can be isolated as separate chemical species and which arise from restricted rotation about a single bond.
• Enantiomers are defined as one of a pair of molecular entities which are mirror images of each other and non-superimposable.
• Diastereomers or diastereoisomers are defined as stereoisomers other than enantiomers. Diastereomers or diastereoisomers are stereoisomers not related as mirror images. Diastereoisomers are characterized by differences in physical properties, and by some differences in chemical behavior towards achiral as well as chiral reagents.
• tautomer refers to compounds produced by the phenomenon wherein a proton of one atom of a molecule shifts to another atom. See March, Advanced Organic Chemistry: Reactions, Mechanisms and Structures, 4th Ed., John Wiley & Sons, pp. 69-74 (1992). Tautomerism is defined as isomerism of the general form
• Tautomers are readily interconvertible; the atoms connecting the groups X, Y and Z are typically any of C, H, O, or S, and G is a group which becomes an electrofuge or nucleofuge during isomerization.
• electrofuge H +
• prototropy The most common case, when the electrofuge is H + , is also known as “prototropy.”
• Tautomers are defined as isomers that arise from tautomerism, independent of whether the isomers are isolable.
• ChemDraw version 8.0 or 10 was used to name structures.
• ADP is adenosine diphosphate
• ATP is adenosine triphosphate
• dba is dibenzylideneacetone
• DIEA is N,N-diisopropylethylamine
• DMA is N,N-dimethylacetamide
• DMF is N,N-dimethylformamide
• DMSO is dimethylsulfoxide
• DTT is dithiothreitol
• EGTA is ethylene glycol tetraacetic acid
• ESI electrospray ionization
• GST is glutathione S-transferase
• “h” is hour or hours
• HATU is 2-(7-Aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
• HEPES is 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
• HPLC is
• IC 50 half maximal inhibitory concentration
• MS mass spectrometry
• min minutes
• NADH nicotinamide adenine dinucleotide
• NMR nuclear magnetic resonance
• PBS phosphate buffered saline
• RT room temperature
• THF tetrahydrofuran
• Tris tris(hydroxymethyl)aminomethane
• xantphos is 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene.
• X, B, Z1, Z2, Z3, R1, R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I;
• each heterocyclyl and heteroaryl individually and independently has a C or N bonding hand.
• a ring N atom from the heterocyclyl is the bonding atom to —C(O) to form an amide, carbamate, or urea.
• a ring N atom from the heteroaryl is the bonding atom to —C(O) to form an amide, carbamate, or urea.
• compounds of the Formula I are compounds of the Formula Ib:
• X, R1, R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I;
• n 0, 1, or 2;
• compounds of the Formula I are compounds of the Formula Ic:
• R2, R3, R4, R6, R7, R25, m, n, and p are as defined above for Formula Ib.
• compounds of the Formula I are compounds of the Formula Ie:
• X, R1, R2, R3, R4, R6, R7, R25, m, n, and p are as defined above for Formula Ib.
• compounds of the Formula I are compounds of the Formula If:
• R2, R3, R4, R6, R7, R25, m, n, and p are as defined above for Formula Ib.
• compounds of the Formula I are compounds of the Formula Ih:
• X, R1, R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I.
• compounds of the Formula I are compounds of the Formula Ij:
• R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I.
• compounds of the Formula I are compounds of the Formula Il:
• X, R1, R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I.
• compounds of the Formula I are compounds of the Formula Im:
• R2, R3, R4, R6, R7, R25, m, n and p are as defined above for Formula I.
• X is halogen. In other embodiments, X is F or Cl. In further embodiments, X is F.
• each R1 is individually and independently halogen. In other embodiments, each R1 is individually and independently F or Cl. In further embodiments, each R1 is F.
• m is 1 and R1 is halogen. In other embodiments, m is 1 and R1 is F or Cl. In further embodiments, m is 1 and R1 is F.
• X and each R1 is individually and independently halogen. In other embodiments, X and each R1 is individually and independently F or Cl. In further embodiments, X and each R1 is F.
• m is 1 and X and each R1 is individually and independently halogen. In other embodiments, m is 1 and X and each R1 is individually and independently F or Cl. In further embodiments m is 1 and X and each R1 is F.
• R3 is —C(O)R4 and R4 is C1-C7 alkyl, C3-C8 cycloalkyl, —(CH 2 ) p —CN, —(CH 2 ) p —OR6, —(CH 2 ) p —NR6(R7), or —(CH 2 ) p —C4-C6-heterocyclyl, wherein each alkyl or alkylene is optionally substituted with one or two C1-C6 alkyl.
• one alkyl or alkylene is substituted by one C1-C6 alkyl.
• one alkyl or alkylene is substituted by one C1-alkyl.
• R3 is —C(O)—C6-C10-aryl, —C(O)—C4-C6-heterocyclyl, or —C(O)—C5-C6-heteroaryl.
• Compounds described herein rind utility in the treatment of mammalian cancers and especially human cancers including, but not limited to, solid tumors, gastric cancers, melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, non small cell lung cancer, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, colonic cancers, myeloproliferative diseases, diseases wherein the etiology or progression is dependent on c-MET kinase activity, or on the activity of oncogenic forms-, aberrant fusion protein forms, and mutant forms of c-MET kinase.
• the compound is administered by a method selected from the group consisting of oral, parenteral, inhalation, and subcutaneous.
• the disclosed methods also include treating individuals suffering from a condition selected from the group consisting of cancer, hyperproliferative diseases, metabolic diseases, neurodegenerative diseases or diseases characterized by angiogenesis.
• These methods comprise administering to such individuals compounds disclosed herein, and especially those of section 1, said diseases including, but not limited to, solid tumors, malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, hepatic cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, chronic myelogenous leukemia, leukemias, papillary thyroid carcinoma, non-small cell lung cancer, mesothelioma, hypereosinophilic syndrome, gastrointestinal stromal tumors, colonic cancers, ocular diseases characterized by hyperproliferation leading to blindness including various retinopathies, diabetic retinopathy and age-related macular degeneration and hypereosinophilic syndrome, r
• compositions may form a part of a pharmaceutical composition by combining one or more such compounds with a pharmaceutically acceptable carrier.
• the compositions may include an additive selected from the group consisting of adjuvants, excipients, diluents, and stabilizers.
• carboxylic acid 2 is also, in some embodiments, first coupled with aniline 5 to yield intermediate 6, which is then in turn coupled with 3 to yield desired compound 1.
• Scheme 2 illustrates the preparation of compound 10, an example of general formula 1 (wherein R1 is F, Z1, Z2, and Z3 are CH and R3 is —C(O)CH 3 ) by the general sequence of 2 ⁇ 4 ⁇ 1 (Scheme 1).
• R1 is F
• Z1, Z2, and Z3 are CH
• R3 is —C(O)CH 3
• Scheme 2 illustrates the preparation of compound 10, an example of general formula 1 (wherein R1 is F, Z1, Z2, and Z3 are CH and R3 is —C(O)CH 3 ) by the general sequence of 2 ⁇ 4 ⁇ 1 (Scheme 1).
• R1 is F
• Z1, Z2, and Z3 are CH
• R3 is —C(O)CH 3
• Coupling agents for the later transformation include TBTU (O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate), PyBOP (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate), EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride) and BOP-Cl (bis(2-oxo-3-oxazolidinyl)phosphonic chloride).
• Amines of the general formula 3 that are useful for the invention are prepared by standard methods familiar to those skilled in the art. Several non-limiting examples are shown in the following schemes. A mixture of phenol 14 and benzamide 15, wherein LG is a leaving group such as a halide or sulfonate, are coupled in the presence of a base such as potassium tert-butoxide and a polar aprotic solvent at elevated temperatures (e.g., 100° C.) to yield 16 (Scheme 4). Protection of the aniline NH 2 of 16 with the appropriate protecting group (PG) familiar to one skilled in the art, such as a tert-butoxycarbonyl (BOC) group, followed by subjection to Hofmann rearrangement conditions results in the formation of 17.
• PG protecting group
• BOC tert-butoxycarbonyl
• the reagent R3-LG (18) is a carboxylic acid (wherein LG is OH) that is coupled with the amino moiety of 17 using standard peptide Coupling agents, as described above.
• reagent R3-LG (18) is an activated carboxylic acid derivative, such as an acid halide (wherein LG is halo) that undergoes reaction with amine 17 to provide 3.
• Conditions for the Hofmann rearrangement include bromine in aqueous KOH or addition of oxidants such as lead tetraacetate or hypervalent iodine reagents such as bis(trifluoroacetyl)iodobenzene in pyridine. Subsequent acylation of 22 with acetyl chloride (an example of R3-LG wherein LG is chloro) in a solution of pyridine yields 23. Removal of the BOC protecting group in a solution of HCl provides amine 7, an example of amine 3 wherein Z1, Z2, and Z3 are CH and R3 is —C(O)CH 3 .
• Amines of the general formula 3 are also accessed via 26 wherein Y is a typical leaving group in transition metal mediated coupling reactions (for example, chloride, bromide, or triflate) (Scheme 7).
• Y is a typical leaving group in transition metal mediated coupling reactions (for example, chloride, bromide, or triflate) (Scheme 7).
• an aprotic solvent for example 1,4-dioxane
• Pd(OAc) 2 or Pd 2 (dba) 3 and xantphos in the presence of cesium carbonate at elevated temperatures between 45° C. and 110° C. yields intermediate 3 (see Buchwald, et. al. Org. Lett . (2000), 2(8): 1101).
• intermediate 28 is assembled from 26 and 6 using methods described in Scheme 3 and subsequently reacted with 27 using catalytic palladium and xantphos (vide supra) to yield compounds of formula 1.
• Amine 26 is synthesized in a variety of ways, including those shown below in the following non-limiting examples. As depicted, in Scheme 8, amino-phenol 14 and 29 (wherein LG is a leaving group in a nucleophilic substitution reaction, such as a halide or sulfonate) is coupled upon addition of a base such as potassium tert-butoxide in a solution of DMA at elevated temperatures of 80° C. to 100° C.
• a base such as potassium tert-butoxide
• General amine 26 is also accessed via the 1-fluoro-4-nitrobenzene intermediate 30 (Scheme 9).
• the coupling of 30 with 31 proceeds at temperatures ranging from 0° C. to 80° C. in the presence of a base, for example sodium hydride.
• the resultant nitro intermediate 32 is then reduced using a variety of methods familiar to one skilled in the art to afford amine 26.
• Scheme 7 A non-limiting example of Scheme 7 is illustrated in Scheme 11, beginning with intermediate 36, prepared in Scheme 10.
• 36 readily reacts with acid chloride 13 (see. Scheme 3) in the presence of triethylamine to yield chloro-pyridine 37.
• Chloro-pyridine 37 is then converted to 38, a specific example of 1 wherein R1 is F, X is F, Z1, Z2, and Z3 are CH and R3 is —C(O)CH 3 , upon treatment with acetamide (an example of R3-NH 2 27 where R3 is acetyl) and cesium carbonate in the presence of a catalytic amount of palladium acetate and xantphos.
• the reaction mixture was concentrated under reduced pressure to remove the majority of DMF in the mixture, and was then partitioned between ethyl acetate (300 mL) and 10% aqueous lithium chloride (150 mL). A precipitate formed which was removed via suction filtration and then the layers were separated. The organic layer was washed with additional 10% aqueous lithium chloride (2 ⁇ 150 mL), saturated aqueous sodium bicarbonate (150 mL) and brine (150 mL).
• Cyclopropane-1,1-dicarboxylic acid monomethylester (2 g, 13.88 mmol) was dissolved in DMF (28 mL) and 4-fluoroaniline (1.999 mL, 20.82 mmol) was added, followed by diisopropylethylamine (12.12 mL, 69.4 mmol) and O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate (8.91 g, 27.8 mmol).
• Methyl 1-((4-fluorophenyl)carbamoyl)cyclopropanecarboxylate (3.28 g, 14.00 mmol) was dissolved in THF (23.34 mL), water (11.67 mL) was added, followed by lithium hydroxide monohydrate (1.763 g, 42.0 mmol), and the mixture stirred at room temperature for 30 minutes. After this time the THF was removed under reduced pressure and the pH of the water layer was adjusted to ⁇ 5 with 2 M HCl while the solution was cooled in an ice bath. The precipitate that formed was dissolved in ethyl acetate (125 mL) and the layers were separated.
• Cyclopropane-1,1-dicarboxylic acid monomethyl ester (0.4 g, 2.78 mmol) was, dissolved in DMF (5.55 mL) and aniline (0.380 mL, 4.16 mmol) was added, followed by diisopropylethylamine (2.424 mL, 13.88 mmol) and O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate (1.782 g, 5.55 mmol).
• the reaction mixture was stirred at room temperature for 18 hours and was then diluted with ethyl acetate (70 mL) and washed with 10% aqueous lithium chloride (3 ⁇ 40 mL), saturated aqueous ammonium chloride (40 mL), saturated aqueous sodium bicarbonate (40 mL) and brine (40 mL).
• the organic layer was dried over magnesium sulfate and evaporated to yield a dark brown oil. It was purified by silica gel chromatography (0 to 20% ethyl acetate/hexane) to yield methyl 1-(phenylcarbamoyl)cyclopropanecarboxylate (0.607 g, 100% yield) as a light peach solid.
• Example A1 (2.136 g, 8.32 mmol) was dissolved in dry THF (63 mL) and triethylamine (1.508 mL, 10.82 mmol) was added. To this solution was added Example B1 (2.414 g, 9.99 mmol) in dry THF (20 mL). The mixture stirred at room temperature for 30 minutes. The triethylamine hydrochloride was removed from the reaction mixture by suction filtration.
• N-(4-(2-chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (3.819 g, 8.27 mmol), acetamide (2.442 g, 41.3 mmol), cesium carbonate (4.04 g, 12.40 mmol), and xantphos (0.469 g, 0.810 mmol) were stirred in dry dioxane (59.1 mL) while argon was bubbled through the mixture for 15 minutes.
• Example A2 A solution of Example A2 (0.147 g, 0.538 mmol) in dry THF (5.38 mL) with triethylamine (0.098 mL, 0.700 mmol) was added to Example B1 (0.169 g, 0.699 mmol). The mixture was stirred under argon for 20 minutes at room temperature. The reaction mixture was then filtered through a frit in order to remove the solid triethylamine hydrochloride that had precipitated.
• N-(5-chloro-4-(2-chloropyridin-4-yloxy)-2-fluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (0.200 g, 0.418 mmol)
• acetamide (0.124 g, 2.091 mmol
• cesium carbonate (0.136 g, 0.418 mmol)
• xantphos 0.017 g, 0.029 mmol
• the mixture was again degassed for five minutes, and then the reaction flask was fitted with a reflux condenser. The system was flushed with argon and then heated at 100° C. under a balloon of argon for 3 hours.
• the reaction mixture was cooled to room temperature and diluted with water (30 mL) and a 4:1 mixture of ethyl acetate and THF (150 mL). The layers were separated, and the aqueous layer was washed with additional ethyl acetate/THF solution. The organic layers were combined and concentrated to yield a sticky orange oil.
• Example A 1 (0.12 g, 0.468 mmol) was dissolved in dry THF (4.68 mL) and triethylamine (0.085 mL, 0.608 mmol) was added. This solution was added to Example 132 (0.125 g, 0.561 mmol) and the mixture stirred under argon at room temperature for 2 hours.
• reaction mixture was filtered to remove triethylamine hydrochloride salt and the filtrate was evaporated to yield a light peach oil which was purified by silica gel chromatography (10 to 50% ethyl acetate/hexane) to yield N-(4-(2-chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-phenylcyclopropane-1,1-dicarboxamide (0.164 g, 79% yield) as a clear solid.
• N-(4-(2-chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-phenylcyclopropane-1,1-dicarboxamide (0.162 g, 0.365 mmol), acetamide (0.108 g, 1.825 mmol), cesium carbonate (0.178 g, 0.548 mmol), and xantphos (0.021 g, 0.036 mmol) were combined in dry dioxane (2.61 mL) and argon was bubbled through the mixture for 5 minutes. Palladium acetate (6.15 mg, 0.027 mmol) was added, and argon was bubbled through the mixture for an additional 5 minutes.
• the reaction flask was fitted with a reflux condenser and a balloon of argon and the mixture was heated at 100° C. for 20 hours.
• the reaction mixture was cooled to room temperature and partitioned between a 4:1 mixture of ethyl acetate and THF (50 mL) and water (50 mL).
• the aqueous layer was removed and the organic layer was washed with additional water (50 mL) and brine (50 mL).
• the organic layer was dried over magnesium sulfate and evaporated under reduced pressure to yield a light peach-colored film.
• Dichloromethane (10 mL) was added and after a few minutes solid began to precipitate. Sonication was used to precipitate out more solid.
• Example A3 300 mg, 1.07 mmol
• HATU 440 mg, 3.2 mmol
• DIEA 280 mg, 2.1 mmol
• the reaction mixture was stirred at 60° C. under nitrogen overnight. After cooling to room temperature water (30 mL) was added and the solution was extracted with ethyl acetate (3 ⁇ 50 mL). The combined organics were washed with brine (3 ⁇ 50 mL), dried over sodium sulfate, and concentrated.
• N-(4-(2-Chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (0.25 g, 0.541 mmol) (as prepared in Example 1), cyclopropanecarboxamide (0.092 g, 1.083 mmol), xantphos (0.014 g, 0.024 mmol), and cesium carbonate (0.265 g, 0.812 mmol) were dissolved in dry dioxane (5.41 mL) and argon was bubbled through the mixture for 5 minutes.
• N-(4-(2-Chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide 200 mg, 0.43 mmol (as prepared in Example 1), propionamide (95 mg, 1.30 mmol), xantphos (25 mg, 0.043 mmol), and cesium carbonate (280 mg, 0.86 mmol) were dissolved in dry dioxane (3 mL) and argon was bubbled through the mixture for 10 minutes. Pd 2 (dba) 3 (20 mg, 0.022 mmol) was then added, and the solution was degassed for an additional 10 minutes.
• the flask was fitted with a balloon of N 2 and slowly heated to 100° C. and stirred overnight.
• the reaction mixture was cooled to room temperature and diluted with a 4:1 mixture of ethyl acetate and THF (60 mL) and water (40 mL).
• the organic layer was separated and washed with brine and the aqueous layer was back extracted with the ethyl acetate/THF solution, which was then extracted with brine.
• N-(4-(2-Chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (3 g, 6.5 mmol) (as prepared in Example 1), tert-butyl carbamate (2.3 g, 19.5 mmol), Xantphos (0.37 g, 0.65 mmol), and cesium carbonate (4.2 g, 13 mmol) were dissolved in dry dioxane (50 mL) and argon was bubbled through the mixture for 10 minutes.
• the mixture was cooled to room temperature and diluted with ethyl acetate (30 mL) and filtered to remove solids.
• the filtrate was washed with aq NaHCO 3 (30 mL) and brine (30 mL).
• the organic phase was dried over Na 2 SO 4 and evaporated at reduced pressure to give a foam.
• the foam was purified by reverse phase silica gel chromatography (35-80% acetonitrile/water/0.1% TFA). Fractions containing product were combined and evaporated at reduced pressure.
• the resultant aqueous mixture was then treated with saturated aq NaHCO 3 (4 mL) and allowed to stand.
• the solid was collected by filtration, washed with water (2 ⁇ 5 mL) and dried on high vacuum line at 80° C.
• N-(4-((2-aminopyridin-4-yl)oxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide (150 mg, 0.34 mmol) (as prepared in Example 9) and 2-cyanoacetic acid (44 mg, 0.51 mmol) in DMF (2 mL) was added HATU (258 mg, 0.68 mmol) and DIEA (130 mg, 1 mmol) and the mixture was stirred at 60° C. under nitrogen overnight.
• N-(4-(2-chloropyridin-4-yloxy)-2,5-difluorophenyl)-N′-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide 160 mg, 0.34 mmol (as prepared in Example 1), 2,2-dimethyl-propionamide (100 mg, 1 mmol), xantphos (40 mg, 0.068 mmol), and cesium carbonate (222 mg, 0.68 mmol) were dissolved in dry dioxane (2 mL) and argon was bubbled through the mixture for 10 minutes. Pd(OAc) 2 (8 mg, 0.034 mmol) was then added, and the solution was degassed for an additional 10 minutes.
• e-MET kinase Activity of e-MET kinase (Seq. ID No. 2) was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler et al. Science 2000, 289, pp. 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophotometrically.
• the reaction mixture (100 ⁇ l) contained c-MET (c-MET residues: 956-1390, from Invitrogen, catalogue #PV3143, 6 nM), polyE4Y (1 mg/mL), MgCl 2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM Tris buffer containing 0.25 mM DTT, 0.2% octyl-glucoside and 1% DMSO, pH 7.5. Test compounds were incubated with c-MET (Seq. ID No. 2) and other reaction reagents at 22° C.
• ATP 100 ⁇ M
• BMG Polarstar Optima plate reader
• Activity of c-KIT kinase was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler et al. Science 2000, 289, pp. 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophotometrically.
• the reaction mixture (100 ⁇ l) contained c-KIT (cKIT residues T544-V976, from ProQinase, 5.4 nM), polyE4Y (1 mg/mL), MgCl 2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM Tris buffer containing 0.2% octyl-glucoside and 1% DMSO, pH 7.5. Test compounds were incubated with c-KIT (Seq. ID No. 1) and other reaction reagents at 22° C.
• ATP 200 ⁇ M
• BMG Polarstar Optima plate reader
• KDR kinase The activity of KDR kinase was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g., Schindler et al. Science 2000, 289, pp. 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophotometrically. The reaction mixture (100 ⁇ l) contained KDR (Seq ID No.
• reaction rate was calculated using the 1 h to 2 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e., with no test compound).
• IC 50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routines as implemented in the GraphPad Prism software package.
• KDR kinase assay K2 is the same as for assay K1 except that (1) a nominal concentration of 2.1 nM of enzyme was employed (2) the reaction was pre-incubated at 30° C. for 2 h prior to initiation with ATP and (3) 1.0 mM ATP (final concentration) was used to initiate the reaction.
• KDR kinase assay K3 is the same as for assay K1 except that (1) a nominal concentration of 1.1 nM of enzyme was employed, (2) the buffer components per 100 ⁇ l reaction mixture were as follows: 75 mM Tris buffer containing 0.066% octyl-glucoside, 17 mM MgCl 2 , and 1% DMSO at pH 7.5, (3) the final concentration of DTT was 0.66 mM, (4) the reaction was pre-incubated at 30° C. for 1 h prior to initiation with ATP, and (5) 1.0 mM ATP (final concentration) was used to initiate the reaction.
• KDR protein sequence used for screening (Seq. ID No. 3) DPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKML KEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEF VPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLA RDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEF CRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQD FMS kinase Assay
• FMS kinase activity was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (e.g. Schindler et al. Science 2000, 289, pp. 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophotometrically.
• the reaction mixture (100 ⁇ l) contained FMS (purchased from Invitrogen or Millipore, 6 nM), polyE4Y (1 mg/mL), MgCl 2 (10 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM) and NADH (0.28 mM) and ATP (500 mM) in a 90 mM Tris buffer containing 0.2% octyl-glucoside and 1% DMSO, pH 7.5.
• the inhibition reaction was started by mixing serial diluted test compound with the above reaction mixture. The absorption at 340 nm was monitored continuously for 4 hours at 30° C.
• IC 50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routine's as implemented in the GraphPad Prism software package.
• EBC-1 cells (catalog #JCRB0820) were obtained from the Japan Health Science Research Resources Bank, Osaka, Japan. Briefly, cells were grown in DMEM supplemented with 10% characterized fetal bovine serum (Invitrogen, Carlsbad, Calif.) at 37° C., 5% CO 2 , 95% humidity. Cells were allowed to expand until reaching 70-95% confluency at which point they were subcultured or harvested for assay use.
• test compound A serial dilution of test compound was dispensed into a 96-well black clear bottom plate (Corning, Corning, N.Y.). For each cell line, five thousand cells were added per well in 200 ⁇ L complete growth medium. Plates were incubated for 67 hours at 37° C., 5% CO 2 , 95% humidity. At the end of the incubation period 40 ⁇ L of a 440 ⁇ M solution of resazurin (Sigma, St. Louis, Mo.) in PBS was added to each well and incubated for an additional 5 hours at 37° C., 5% CO 2 , 95% humidity.
• MKN-45 cells (catalog #JCRB0254) were obtained from the Japan Health Science Research Resources Bank, Osaka, Japan. Briefly, cells were grown in RPMI 1640 media supplemented with 10% characterized fetal bovine serum (Invitrogen, Carlsbad, Calif.) at 37° C., 5% CO2, 95% humidity. Cells were allowed to expand until reaching 70-95% confluency at which point they were subcultured or harvested for assay use.
• test compound A serial dilution of test compound was dispensed into a 96-well black clear bottom plate (Corning, Corning, N.Y.). Five thousand cells were added per well in 200 ⁇ L complete growth medium. Plates were incubated for 67 hours at 37° C., 5% CO 2 , 95% humidity. At the end of the incubation period 40 ⁇ L of a 440 ⁇ M solution of resazurin (Sigma, St. Louis, Mo.) in PBS was added to each well and plates were incubated for an additional 5 h at 37° C., 5% CO 2 , 95% humidity.
• RON kinase Activity of RON kinase was determined by a radioactive filtration binding assay where incorporation of 33 P from 33 P- ⁇ -ATP to the substrate was measured. In this assay, detection of 33 P was indicative of RON phosphorylation activity which was directly proportional to the amount of phosphorylated peptide substrate (KKSRGDYMTMQIG).
• the reaction mixture contained: 400 nM RON, 20 mM HEPES, pH 7.5, 10 mM MgCl 2 , 2 mM MnCl 2 , 1 mM EGTA, 0.02% Brij 35, 0.02 mg/ml . . . BSA, 0.1 mM Na 3 VO 4 , and 2 mM DTT.
• the reaction mixture was incubated with compound at room temperature for 30 minutes. To initiate the reaction, an equal volume of 20 ⁇ M ATP and 0.4 mg/mL peptide substrate were added and then incubated at room temperature for 2 hours.
• the final assay conditions were: 200 nM RON, 10 ⁇ M ATP, 0.2 mg/mL substrate 20 mM HEPES, pH 7.5, 10 mM MgCl 2 , 1 mM EGTA, 0.02% Brij 35, 0.02 mg/mL BSA, 0.1 mM Na 3 VO 4 , 2 mM DTT, and 1% DMSO.
• IC 50 values were calculated from a series of % Activity values determined at a range of inhibitor concentrations using software routines as implemented in the GraphPad Prism software package.
• the reaction mixture contained: 400 nM FLT1, 20 mM HEPES, pH 7.5, 10 mM MgCl 2 , 2 mM MnCl 2 , 1 mM EGTA, 0.02% Brij 35, 0.02 mg mL BSA, 0.1 mM Na 3 VO 4 , and 2 mM DTT.
• the reaction mixture was incubated with compound at room temperature for 30 minutes. To initiate the reaction, an equal volume of 20 ⁇ M ATP and 0.2 mg/mL peptide substrate were added and then incubated at room temperature for 2 hours.
• the final assay conditions were: 200 nM FLT1, 10 ⁇ M ATP, 0.1 mg/mL substrate 20 mM HEPES, pH 7.5, 10 mM MgCl 2 , 1 mM EGTA, 0.02% Brij 35, 0.02 mg/mL BSA, 0.1 mM Na 3 VO 4 , 2 mM DTT, and 1% DMSO.
• IC 50 values were calculated from a series of % Activity values determined at a range of inhibitor concentrations using software routines as implemented in the Graph Pad Prism software package.
• RET kinase Activity of RET kinase was determined by following the production of ADP from the kinase reaction through coupling with the pyruvate kinase/lactate dehydrogenase system (see e.g., Schindler et al. Science (2000) 289: 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340 nm) was continuously monitored spectrophotometrically.
• the reaction mixture (100 ⁇ l) contained RET (amino acid residues 658-1114, from Invitrogen, 2 nM), polyE4Y (1.5 mg/ml), MgCl 2 (18 mM), pyruvate kinase (4 units), lactate dehydrogenase (0.7 units), phosphoenol pyruvate (1 mM), and NADH (0.28 mM) in 90 mM iris buffer containing 0.2% octyl-glucoside, 1 mM DTT and 1% DMSO, pH 7.5. Test compounds were incubated with RET kinase and other reaction reagents at 22° C.
• ATP 500 ⁇ M
• the absorption at 340 nm was monitored continuously for 3 hours at 30° C. on BioTek Synergy 2 Reader.
• the reaction rate was calculated using the 1 to 2 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e., with no test compound).
• IC 50 values were calculated from a series of percent inhibition values determined at a range of inhibitor concentrations using software routines as implemented in the Graph Pad Prism software package.
• Compounds, of Formula I exhibit inhibitory activity in one or more of the aforementioned assays when evaluated at concentrations ⁇ 10 ⁇ M.
• Compound F and Compound G are almost identical, with the exception that Compound F is mono-fluorinated in the central phenyl ring whereas Compound G is di-fluorinated wherein the two fluorines are oriented para- with respect to each other in the central phenyl ring.
• Compound D potently inhibits c-MET kinase with an IC 50 value of 4 nM.
• Compound D is 6.5-fold more potent versus c-MET kinase than its mono-fluoro analog Compound E (4 nM versus 26 nM; see Table 1). This 6.5-fold greater potency versus MET kinase is unexpected in view of the c-MET inhibition data for Compound G compared to its corresponding mono-fluoro analog Compound F.
• Compound G and Compound F exhibit essentially equivalent potency versus c-MET kinase (53 nM versus 47 nM, respectively; 1.1-fold ratio of potency). See the '188 application, pp. 96-97.
• Compound H is also reported to be a potent MET kinase inhibitor, with IC 50 of 4 nM. Id.
• Compound H like Compound D, is di-fluorinated, with the two fluorines being oriented para with respect to each other in the central phenyl ring. Compound H, however, does not exhibit the selectivity against c-MET inhibition that has been observed for Compound D.
• Compound D exhibits a much higher kinase selectivity versus RON, RET, VEGFR-1, and VEGFR-2 kinases, compared to Compound E.
• RON is a very close kinase of the MET subfamily of kinases, and inhibitors of MET kinase are often not selective versus RON.
• Compound D is >1,250 fold selective of MET kinase versus RON kinase
• Compound E is only 3.85 fold of MET kinase versus RON kinase. See Table 1.
• Compound D is >825 fold selective of MET kinase versus RET kinase
• Compound E is only 1.65 fold selective of MET kinase versus RET kinase.
• Compound D is 19.75-fold selective of MET kinase versus VEGFR-1 kinase
• Compound E is significantly less selective: 6.15-fold selective of MET kinase versus VEGFR-1 kinase.
• Compound D is 13-fold selective of MET kinase versus VEGFR-2 kinase
• Compound E is significantly less selective: 4.69-fold selective of MET kinase versus VEGFR-2 kinase.

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