WO2008131253A1 - Kinase inhibitors useful for the treatment of myleoproliferative diseases and other proliferative diseases - Google Patents

Kinase inhibitors useful for the treatment of myleoproliferative diseases and other proliferative diseases Download PDF

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WO2008131253A1
WO2008131253A1 PCT/US2008/060867 US2008060867W WO2008131253A1 WO 2008131253 A1 WO2008131253 A1 WO 2008131253A1 US 2008060867 W US2008060867 W US 2008060867W WO 2008131253 A1 WO2008131253 A1 WO 2008131253A1
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group
c6alkyl
kinase
pyrazol
branched
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PCT/US2008/060867
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French (fr)
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Daniel L. Flynn
Peter A. Petillo
Michael D. Kaufman
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Deciphera Pharmaceuticals, Llc
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Priority to AU2008242697A priority Critical patent/AU2008242697A1/en
Priority to CA002684950A priority patent/CA2684950A1/en
Priority to EP08746306A priority patent/EP2146718A4/en
Publication of WO2008131253A1 publication Critical patent/WO2008131253A1/en

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    • C07ORGANIC CHEMISTRY
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    • C07D401/00Heterocyclic 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
    • C07D401/14Heterocyclic 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
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    • C07D403/14Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing three or more hetero rings
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    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic 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
    • A61K31/505Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/506Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
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    • A61P43/00Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P9/00Drugs for disorders of the cardiovascular system
    • A61P9/10Drugs for disorders of the cardiovascular system for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
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    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D413/00Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D413/14Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing three or more hetero rings
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    • C07D417/00Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/14Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing three or more hetero rings

Definitions

  • the present invention relates to novel kinase inhibitors and modulator compounds useful for the treatment of various diseases. More particularly, the invention is concerned with such compounds, kinase/compound adducts, methods of treating diseases, and methods of synthesis of the compounds. Preferrably, the compounds are useful for the modulation of kinase activity of C-AbL c-Kit, VEGFR, PDGFR kinases, Flt-3, c-Met, FGFR, the HER family and disease causing polymorphs thereof.
  • proliferative diseases relevant to this invention include cancer, rheumatoid arthritis, atherosclerosis, and retinopathies.
  • Important examples of kinases which have been shown to cause or contribute to the pathogensis of these diseases include C-AbI kinase and the oncogenic fusion protein bcr-Abl kinase; c-Kit kinase, PDGF receptor kinase; VEGF receptor kinases; and Flt-3 kinase.
  • C-AbI kinase is an important non-receptor tyrosine kinase involved in cell signal transduction. This ubiquitously expressed kinase — upon activation by upstream signaling factors including growth factors, oxidative stress, integrin stimulation, and ionizing radiation — localizes to the cell plasma membrane, the cell nucleus, and other cellular compartments including the actin cytoskeleton (Van Etten, Trends Cell Biol. (1999) 9: 179). There are two normal isoforms of AbI kinase: AbI- IA and AbI- IB.
  • the N-terminal half of c-Abl kinase is important for auto inhibition of the kinase domain catalytic activity (Pluk et al, Cell (2002) 108: 247). Details of the mechanistic aspects of this autoinhibition have recently been disclosed (Nagar et al, Cell (2003) 112: 859).
  • the N-terminal myristolyl amino acid residue of AbI-I B has been shown to intramolecularly occupy a hydrophobic pocket formed from alpha-helices in the C -lobe of the kinase domain.
  • Such intramolecular binding induces a novel binding area for intramolecular docking of the SH2 domain and the SH3 domain onto the kinase domain, thereby distorting and inhibiting the catalytic activity of the kinase.
  • an intricate intramolecular negative regulation of the kinase activity is brought about by these N- terminal regions of c-Abl kinase.
  • An aberrant dysregulated form of c-Abl is formed from a chromosomal translocation event, referred to as the Philadelphia chromosome (P.C. Nowell et al, Science (1960) 132: 1497; J.D. Rowley, Nature (1973) 243: 290).
  • This abnormal chromosomal translocation leads aberrant gene fusion between the AbI kinase gene and the breakpoint cluster region (BCR) gene, thus encoding an aberrant protein called bcr-Abl (G. Q. Daley et al, Science (1990) 247: 824; M. L. Gishizky et al, Proc. Natl. Acad. ScI USA (1993) 90: 3755; S. Li et al, J. Exp. Med. (1999) 189: 1399).
  • the bcr-Abl fusion protein does not include the regulatory myristolylation site (B. Nagar et al.
  • CML chronic myeloid leukemia
  • CML is a malignancy of pluripotent hematopoietic stem cells.
  • the p210 form of bcr-Abl is seen in 95% of patients with CML 3 and in 20% of patients with acute lymphocytic leukemia and is exemplified by sequences such as el4a2 and el3a2.
  • the corresponding p!90 form, exemplified by the sequence ela2 has also been identified.
  • a pi 85 form has also been disclosed and has been linked to being causative of up to 10% of patients with acute lymphocytic leukemia.
  • C-KIT (Kit, CD 117, stem cell factor receptor) is a 145 kDa transmembrane tyrosine kinase protein that acts as a type-Ill receptor (Pereira et al. J Carcin. (2005), 4: 19).
  • the c-KIT proto-oncogene located on chromosome 4ql 1-21, encodes the c-KIT receptor, whose ligand is the stem cell factor (SCF, steel factor, kit ligand, mast cell growth factor, Morstyn G, et al Oncology (1994) SI(2):205. Yarden Y, et al. Embo J (1987) 6(1 1):3341).
  • the receptor has tyrosine-protein kinase activity and binding of the ligands leads to the autophosphorylation of KIT and its association with substrates such as phosphatidylinositol 3-kinase (Pi3K).
  • Tyrosine phosphorylation by protein tyrosine kinases is of particular importance in cellular signalling and can mediate signals for major cellular processes, such as proliferation, differentiation, apoptosis, attachment, and migration.
  • Defects in KIT are a cause of piebaldism. an autosomal dominant genetic developmental abnormality of pigmentation characterized by congenital patches of white skin and hair that lack melanocytes.
  • Gain-of-function mutations of the c-KIT gene and the expression of phosphorylated KIT are found in most gastrointestinal stromal tumors and mastocytosis. Further, almost all gonadal seminomas/dysgerminomas exhibit KIT membranous staining, and several reports have clarified that some (10-25%) have a c- KIT gene mutation (Sakuma, Y. et al Cancer Sci (2004) 95:9, 716). KIT defects have also been associated with testicular tumors including germ cell tumors (GCT) and testicular germ cell tumors (TGCT).
  • GCT germ cell tumors
  • TGCT testicular germ cell tumors
  • c-kit expression has been studied in hematologic and solid tumours, such as acute leukemias (Cortes J. et al Cancer (2003) 97(11):2760) and gastrointestinal stromal tumors (GIST, Fletcher CD. et al Hum Pathol (2002) 33(5):459).
  • the clinical importance of c-kit expression in malignant tumors relies on studies with Gleevec ® (imatinib mesylate, STI571, Novartis Pharma AG Basel, Switzerland) that specifically inhibits tyrosine kinase receptors (Lefevre G. et al J Biol Chem (2004) 279(30):31769).
  • c-MET is a unique 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 a Cancer Metastasis (2003) 22:309). Mutations in the tyrosine kinase domain are associated with hereditary papillary renal cell carcinomas (Schmidt L et a Nat. Genet.
  • 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 iV-methyl-iV'-mtro-JV-nitrosoguanidirie (Park M. et a 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.
  • TPR-MET acts to activated wild-type c-MET RTK and can activate crucial cellular growth pathways, including the Ras pathway (Aklilu F. et a Am J Physiol (1996) 271 :E277) and the phosphatidylinositol 3-kinase (PI3K)/AKT pathway (Ponzetto C. et a MoI Cell Biol (1993) 13:4600).
  • TPR-MET is ligand independent, lacks the CBL binding site in the juxtamembrane region in c-MET, and is mainly cytoplasmic.
  • c-Met irnmunoliistochemical expression seems to be associated with abnormal ⁇ -catenin expression, and provides good prognostic and predictive factors in breast cancer patients.
  • kinases are regulated by a common activation/deactivation mechanism wherein a specific activation loop sequence of the kinase protein binds into a specific pocket on the same protein which is referred to as the switch control pocket.
  • a specific activation loop sequence of the kinase protein binds into a specific pocket on the same protein which is referred to as the switch control pocket.
  • Such binding occurs when specific amino acid residues of the activation loop are modified for example by phosphorylation, oxidation, or nitrosylation.
  • the binding of the activation loop into the switch pocket results in a conformational change of the protein into its active form (Huse, M. and Kuriyan, J. Cell (109) 275)
  • Compounds of the present invention find utility in the treatment of mammalian cancers and especially human cancers including but not limited to malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, 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, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, a disease caused by c-Abl kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, or a disease caused by c-Kit, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof.
  • Cycloalkyl refers to monocyclic saturated carbon rings taken from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptanyl and cyclooctanyl;
  • Aryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon atoms of at least one carbocyclic ring; preferred aryl rings are taken from phenyl, naphthyl, tetrahydronaphthyl, indenyl, and indanyl;
  • Heteroaryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring; heteroaryl rings are taken from, but not limited to, pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazolyl, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, tetrazolyl, pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, be
  • Heterocyclyl refers to monocyclic rings containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms; heterocyclyl rings include, but are not limited to.
  • oxetanyl azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, thiazolinyl, thiazolidinyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, thiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl;
  • Poly-aryl refers to two or more monocyclic or fused aryl bicyclic ring systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon atoms of at least one carbo cyclic ring wherein the rings contained therein are optionally linked together;
  • Poly-heteroaryl refers to two or more monocyclic or fused bicyclic systems characterized by delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring wherein the rings contained therein are optionally linked together, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heteroaryl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above;
  • Poly-heterocyclyl refers to two or more monocyclic or fused bicyclic ring systems containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized ⁇ electrons (aromaticity) shared among the ring carbon or heteroatoms wherein the rings contained therein are optionally linked, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heterocyclyl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above;
  • Alkyl refers to straight or branched chain Cl-C6alkyls;
  • Halogen refers to fluorine, chlorine, bromine, and iodine
  • Alkoxy refers to -O-(alkyl) wherein alkyl is defined as above;
  • Alkoxylalkyl refers to -(alkyl)-O-(alkyl) wherein alkyl is defined as above;
  • Alkoxylcarbonyl refers to -C(O)O-(alkyl) wherein alkyl is defined as above;
  • CarboxylCl-C ⁇ alkyl refers to -(Cl-C ⁇ alkyFj-CChH wherein alkyl is defined as above;
  • Substituted in connection with a moiety refers to the fact that a further substituent may be attached to the moiety to any acceptable location on the moiety.
  • salts 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 examples of which are formic, acetic, propionic, succinic, glycolic, gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic, fumaric.
  • Suitable pharmaceutically-acceptable salts of free acid- containing compounds of Formula I include metallic salts and organic salts.
  • More preferred metallic salts include, but are not limited to appropriate alkali metal (group Ia) salts, alkaline earth metal (group Ha) salts and other physiological acceptable metals.
  • Such salts can be made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc.
  • Preferred organic salts can be made from primary amines, secondary amines, tertiary amines and quaternary ammonium salts, including in part, tromethamine, diethylamine, /etr ⁇ -N-methylammonium, N.N'-diben2ylethyIenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
  • prodrug refers to derivatives of active compounds which revert in vivo into the active form.
  • a carboxylic acid form of an active drug may be esterified to create a prodrug, and the ester is subsequently converted in vivo to revert to the carboxylic acid form. See Ettmayer et. al, J Med. Chem (2004) 47: 2393 and Lorenzi et. al, J Pharm. Exp. Therpeiitics (2005) 883 for reviews.
  • 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.
  • Enatiomers are defined as one of a pair of molecular entities which are mirror images of each other and non-superimpo sable. 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.
  • Tautomerisra is defined as isomerism of the general form
  • Tautomers are defined as isomers that arise from tautomerism, independent of whether the isomers are isolable.
  • pyrimidine ring may be optionally substituted with one or more R20 moieties;
  • each D is individually taken from the group consisting of C, CH, C-R20, N-Z3, N, O and S, such that the resultant ring is taken from the group consisting of pyrazolyl, triazolyl, isoxazolyl, isothiazolyl, oxazolyl, imidazoyl, and thiadiazolyl;
  • E is selected from the group consisting phenyl, pyridyl, and pyrimidinyl;
  • Rl 6 may be optionally substituted with one or two Rl 6 moieties
  • A is a ring system selected from the group consisting of cyclopentyl, cyclohexyl, Gl, G2, and G3;
  • Gl is a heteroaryl taken from the group consisting of pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazol-4-yl, isoxazol-5-yI, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, and tetrazolyl;
  • G2 is a fused bicyclic heteroaryl taken from the group consisting of indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, benzothiazolonyl, benzoxazolyl, benzoxazolonyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl, benzimidazolonyl, benztriazolyl, imidazopyridinyl, pyrazolopyridinyl, imidazolonopyridinyl, thiazolopyridinyl, thiazolonopyridinyl, oxazolopyridinyl, oxazolonopyridinyl.
  • dihydropurinonyl pyrrolopyrimidinyl, purinyl, pyrazolopyrimidinyl, phthalimidyl, phthaliniidinyl, pyrazinylpyridinyl, pyridinopyrimidinyl, pyrimidinopyrimidinyl, cinnolinyl, quinoxalinyl, quinazolinyl, quinolinyl, isoquinolinyl, phthalazinyl.
  • G3 is a heterocyclyl taken from the group consisting of oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, imidazolonyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, tliiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropaiiyl;
  • the A ring may be optionally substituted witli-one or two R2 moieties;
  • X is selected from the group consisting of -O-, -S(CH 2 ),,-, -N(R3)(CH 2 ) n -, -(CH 2 ) P -, and wherein the carbon atoms of -(CH 2 )H-, -(CH 2 )p-, of X may be further substituted by oxo or one or more Cl-C6alkyl moieties;
  • each respective sp2 hybridized carbon atom may be optionally substituted with a Zl substituent;
  • each respective sp3 hybridized carbon atom may be optionally substituted with a Z2 substituent; when A, Gl, G2 or G3 has one or more substitutable nitrogen atoms, each respective nitrogen atom may be optionally substituted with a 24 substituent;
  • each Zl is independently and individually selected from the group consisting of Cl- ⁇ alkyl, branched C3-C7alkyl, C3-C8cycloalkyl, halogen, fluoroCl-C ⁇ alkyl wherein the alkyl moiety can be partially or fully fluorinated, cyano, Cl-C6alkoxy, fluoroCl- C ⁇ alkoxy wherein the alkyl moiety can be partially or fully fluorinated, -(CH 2 ) ⁇ OH, oxo, Cl-C6alkoxyCl-C6alkyl, (R4) 2 N(CH 2 ) ⁇ -, (R3) 2 N(CH 2 ) ⁇ -, (R4) 2 N(CH 2 ) q N(R4)(CH 2 ) n -, (R4) 2 N(CH 2 ) q O(CH 2 ) n -, (R3) 2 NC(O)-, (R4) 2 NC(O)-, (R4)
  • each Z2 is independently and individually selected from the group consisting of aryl, Cl- C ⁇ alkyl, C3-C8cycloalkyl, branched C3-C7alkyl, hydroxyl, hydroxyCl-C ⁇ alkyl-, cyano, (R3) 2 N-, (R4) 2 N-, (R4) 2 NC1-C6alkyl-, (R4) 2 NC2-C6alkylN(R4)(CH 2 ) n -, (R4) 2 NC2- C6alkylO(CH 2 ) n -, (R3) 2 NC(O>, (R4) 2 NC(O)-, (R4) 2 NC(O)-Cl-C6alkyl-, carboxyL - carboxyC 1 -C ⁇ alkyl, C 1 -C ⁇ alkoxycarbonyl-, Cl-C6alkoxycarbonylC 1 -C ⁇ alkyl-, (R3) 2 NSO 2 -, (R4) 2 NSO 2 -,
  • each Z3 is independently and individually selected from the group consisting of H, Cl- C ⁇ alkyl, branched C3-C7alkyl, C3-C8cycloalkyl, fluoroCl-C ⁇ alkyl wherein the alkyl moiety can be partially or fully fluorinated, hydroxyC2-C6 alkyl-, Cl-C6alkoxycarbonyl-, -C(O)RS, R5C(O)(CH 2 )n-, (R4) 2 NC(O)- 5 (R4) 2 NC(O)C1-C6alkyl-, R8C(O)N(R4)(CH 2 ) q - , (RS) 2 NSO 2 -, (R4) 2 NSO 2 -, -(CH 2 ) q N(R3) 2 , and -(CH 2 )
  • each R2 is selected from the group consisting of H, Cl-C6alkyl, branched CS-C ⁇ alkyl, Rl 9 substituted CS-C ⁇ cycloalkyl-, fluoroCl-C ⁇ alkyl- wherein the alkyl is fully or partially fluorinated, halogen, cyano, Cl-C6alkoxy-, and fluoroCl-C ⁇ a ⁇ koxy- wherein the alkyl group is fully or partially fluorinated, hydroxyl substituted Cl-C6alkyl-, hydroxyl substituted branched C3-C8alkyl-, cyano substituted Cl-C6alkyl-, cyano substituted branched C3-C8alkyl-, (R3) 2 NC(O)C1-C6alkyl-, and (R3) 2 NC(O)C3-C8 branched alkyl-;
  • each R3 is independently and individually selected from the group consisting of H, Cl-C6alkyl, branched C3-C7alkyl, and C3 -CScycloalkyl;
  • each R6 is independently and individually selected from the group consisting of Cl- C ⁇ alkyl, branched C3-C7alkyl, and Rl 9 substituted C3-C8cyc ⁇ oalkyl-;
  • each R7 is independently and individually selected from the group consisting of H, Cl- C ⁇ alkyl, hydroxyC2-C6alkyl-, dihydroxyC2-C6alkyl ⁇ , Cl-C6alkoxyC2-C6alkyl-, branched C3-C7alkyl, branched hydroxyC2-C6alkyl-, branched Cl-C6alkoxyC2- C ⁇ alkyl-, branched dihydroxyC2-C6alkyl-, -(CH 2 ) n C(O)OR3, Rl 9 substituted C3- C ⁇ cycloalkyl- and -(CH 2 ) n R17;
  • each R8 is independently and individually selected from the group consisting of Cl- C6alkyl, branched C3-C7alkyl, fluoroCl-C6alkyl- wherein the alkyl moiety is partially or fully fluorinated, Rl 9 substituted C3-C8cycloalkyl-, -OH, Cl-C6alkoxy, -N(R3) 2 , and - N(R4) 2 ;
  • each RlO is independently and individually selected from the group consisting Of -CO 2 H, -CO 2 Cl-C6alkyl, -C(O)N(R4) 2 , OH, Cl-C6alkoxy, and -N(R4) 2 ;
  • each Rl 9 is independently and individually selected from the group consisting of H, OH and Cl-C6alkyl;
  • each R20 is independently and individually selected from the group consisting of Cl- C ⁇ alkyl, branched C3 ⁇ C7alkyl, Rl 9 substituted C3-C8cycloalkyl-, halogen, fluoroCl- C ⁇ alkyl- wherein the alkyl moiety can be partially or fully fluormated, cyano, hydroxyl, Cl-C6alkoxy, fluoroCl-C ⁇ alkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(RS) 2 , -N(R4) 2 , -N(R3)C(O)R3, -C(O)N(R3) 2 and nitro and wherein two R4 moieties independently and individually taken from the group consisting of Cl- C ⁇ alkyl, branched C3-C6alkyl, hydroxyalkyl-, and alkoxyalkyl and attached to the same nitrogen heteroatom may cyclize to form a C3-C7 heterocyclyl
  • tlie symbol (**) indicates the point of attachment to the pyrimidine ring.
  • A is any possible isomer of pyrazole.
  • the invention includes methods of modulating kinase activity of a variety of kinases, e.g.
  • the method comprises the step of contacting the kinase species with compounds of the invention and especially those set forth in sections section 1.
  • the kinase species may be activated or unactivated, and the species may be modulated by phosphorylations, sulfation, fatty acid acylations glycosylations, nitrosylation, cystinylation (i.e. proximal cysteine residues in the kinase react with each other to form a disulfide bond) or oxidation.
  • the kinase activity may be selected from the group consisting of catalysis of phospho transfer reactions, inhibition of phosphorylation, oxidation or nitrosylation of said kinase by another enzyme, enhancement of dephosphorylation, reduction or denitrosylation of said kinase by another enzyme, kinase cellular localization, and recruitment of other proteins into signaling complexes through modulation of kinase conformation.
  • the methods of the invention also include treating individuals suffering from a condition selected from the group consisting of cancer and hyperproliferative diseases.
  • These methods comprise administering to such individuals compounds of the invention, and especially those of section 1, said diseases including, but not limited to, malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor secondary sites, myeloproliferative diseases, 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 including diabetic retinopathy and age-related macular degeneration, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, mastocytosis, mast cell leukemia, a disease caused by c-Abl kin
  • compositions may include an additive selected from the group consisting of adjuvants, excipients, diluents, and stablilizers.
  • ureas of general formula I can be readily prepared by the union of amines of general formula 2 with isocyanates 3 or isocyanate surrogates 4 (trichloroethyl carbamates) or 5 . (isopropenyl carbamates).
  • Preferred conditions for the preparation of compounds of general formula 1 involve heating a solution of 4 or 5 .
  • a tertiary base such as diisopropylethylamine, triethylamine or N- methylpyrrolidine in a solvent such as dimethylformamide, dimethylsulfoxide, tetrahydrofuran or 1,4-dioxane at a temperature between 50 and 100 0 C for a period of time ranging from 1 hour to 2 days.
  • isocyanates 3 can be prepared from amines A-NH 2 6-With phosgene, or a phosgene equivalent such as diphosgene. triphosgene, or N 5 N- dicarbonylimidazole.
  • Trichloroethyl carbamates 4 and isopropenyl carbamates 5 are readily prepared from amines A-NH 2 (6) by reaction with trichloroethyl chloroformate or isopropenyl chloroformate by standard conditions familiar to those skilled in the art.
  • Preferred conditions for the preparation of 4 and 5 include include treatment of compound __ with the appropriate chloroformate in the presence of pyridine in an aprotic solvent such as dichloromethane or in the presence of aqueous hydroxide or carbonate in a biphasic aqueous/ethyl acetate solvent system.
  • compounds of formula 1 can also be prepared from carboxylic acids 7 by the intermediacy of in ⁇ situ generated acyl azides (Curtius rearrangement) as indicated in Scheme 3.
  • Preferred conditions for Scheme 3 include the mixing of acid 7 with amine 2 and diphenylphosphoryl azide in a solvent such as 1,4-dioxane or dimethylformamide in the presence of base, such as triethylamine, and raising the temperature of the reaction to about 80-120 0 C to affect the Curtius rearrangement.
  • Isocyanates 8 can be prepared from general amines 2 by standard synthetic methods. Suitable methods for example, include reaction of 2 with phosgene, or a phosgene equivalent such as diphosgene, triphosgene, or N,N- dicarbonylimidazole. In addition to the methods above for converting amines 2 into isocyanates _5, the isocyanates 8 can also be prepared in situ by the Curtius rearrangement and variants thereof.
  • isocycanates J_ need not be isolated, but may be simply generated in situ. Accordingly, acid 9 can be converted to compounds of formula I either with or without isolation of _5. Preferred conditions for the direct conversion of acid 9 to compounds of formula I involve the
  • compounds of formula 1 can also be prepared from amines 2 by first preparing stable isocyanate equivalents, such as carbamates (Scheme 5).
  • carbamates include trichloroethyl carbamates QO) and isopropenyl carbamates (11) which are readily prepared from amine 2 by reaction with trichloroethyl chloroformate or isopropenyl cliloroformate respectively using standard conditions familiar to those skilled in the art. Further reaction of carbamates J_0 or JJ_ with amine A- NHT 6 provides compounds of formula X.
  • carbamates can also be prepared from acid 9 by Curtius rearrangement and trapping with an alcoholic co-solvent. For example, treatment of acid 9 (Scheme 5) with diphenylphosphoryl azide and trichloroethanol at elevated temperature provides trichloroethyl carbamate H).
  • Z4-substituted pyrazol-5-yI amines 14 are available by the condensation of hydrazines ⁇ 2 and beta-keto nitriles L3 in the presence of a strong acid. Preferred conditions for this transformation are by heating in ethanolic HCl. Many such hydrazines 12 are commercially available. Others can be prepared by conditions familiar to those skilled in the art, for example by the diazotization of amines followed by reduction or, alternately from the reduction of hydrazones prepared from carbonyl precursors.
  • Scheme 6 Another preferred method for constructing Z4-substituted pyrazoles is illustrated by the general preparation of pyrazole acids 19 and 20. (Scheme 7), aspects of of general acid A-CO 2 H 7 (Scheme 3). As indicated in Scheme 7, pyrazole 5-carboxylic esters ⁇ 1_ and 18 can be prepared by the alkylation of pyrazole ester 16 with Z4-X 15, wherein X represents a leaving group on a Z4 moiety such as a halide, triflate. or other sulfonate.
  • Preferred conditions for the alkylation of pyrazole J_6 include the use of strong bases such as sodium hydride, potassium tert-butoxide and the like in polar aprotic solo vents such as dimethylsulfoxide, dimethylformamide or tetrahydrofuran.
  • Z4-substituted pyrazoles ⁇ 1_ and J_8 are isomers of one another and can both be prepared in the same reactions vessel and separated by purification methods familiar to those skilled in the art.
  • esters 17 and j_8 in turn can be converted to acids 19 and 20 using conditions familiar to those skilled in the art, for example saponification in the case of ethyl esters, hydrogenation in the case of benzyl esters or acidic hydrolysis in the case of tert-butyl esters.
  • Scheme 8 illustrates the preparation of pyrazole amine 25 ⁇ a further example of general amine A-NHT 6.
  • Acid-catalyzed condensation of R2-substituted hydrazine 21 with 1,1,3,3-tetramethoxypropane 22 provides R2-substituted pyrazole 23-
  • R2-substituted pyrazole 23 can also be prepared by direct alkylation of pyrazole.
  • Pyrazole 23 can be regioselectively nitrated to provide nitro-pyrazole 24 by standard conditions familiar to those skilled in the art.
  • hydrogenation of nitro-pyrazole 24 employing a hydrogenation catalyst, such as palladium or nickel provides pyrazole amine 25, an example of general amine A-NH? 6.
  • keto-ester 26 can be reacted with N,N- dimetliylforrnamide dimethyl acetal to provide 27.
  • Reaction of 27 with either 21 or 28 (wherein P is an acid-labile protecting group) in the presence of acid provides 29 or 3_0.
  • both 29 and 30 can be obtained from the same reaction and can be separated by standard chromatographic conditions.
  • esters 29 and 30 can be converted to acids 3_1 and 32 respectively as previously described in Scheme 7.
  • NH-pyrazole 34 can be prepared by reaction of acrylate 33 with hydrazine (Scheme 10). Alkylation of 34 with R2-X 35 as described above for Scheme 7 provides mixtures of pyrazole esters 3_6 and 32 which are separable by standard chromatographic techniques. Further conversion of esters 36 and 3_7 to acids 38 and 3_£ can be accomplished as described above in Scheme 7.
  • General amines 6 containing an isoxazole ring can be prepared as described in Scheme 11.
  • reaction of keto-nitrile 9 with hydroxylamine can provide the 5-ammoisoxazole 40.
  • Preferred conditions for the formation of 5- aminoisoxazole 40 include the treatment of 9 with hydroxylamine in the presence of aqueous sodium hydroxide, optionally in the presence of an alcoholic co-solvent at a temperature between 0 and 100 °C.
  • Amines 2 useful for the invention can be synthesized according to methods commonly known to those skilled in the art.
  • Amines of general formula 2 contain three rings and can be prepared by the stepwise union of three monocyclic subunits as illustrated in the following non-limiting Schemes.
  • Scheme 12 illustrates one mode of assembly in which an E-containing subunit 41 is combined with the central pyridine ring 42 to provide the bicyclic intermediate 43.
  • the "M" moiety of 41 represents a hydrogen atom of a heteroatom on the X linker that participates in a nucleophilic aromatic substitution reaction with monocycle 42.
  • M may also represent a suitable counterion (for example potassium, sodium, lithium, or cesium) within an alkoxide, sulfide or amide moiety.
  • the "M" group can represent a metallic species (for example, copper, boron, tin, zirconium, aluminum, magnesium, lithium, silicon, etc.) on a carbon atom of the X moiety that can undergo a transition-metal-mediated coupling with monocycle 42.
  • the "Y” group of monocyclic species 4J_ is an amine or an amine surrogate, such as an amine masked by a protecting group ("P" in formula 44), a nitro group, or a carboxy acid or ester that can be used to prepare an amine via known rearrangement.
  • suitable protecting groups “P” include but are not limited to tert- butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz), and acetarnide.
  • the "LG" of monocycle 42 represents a moiety that can either be directly displaced in a nucleophilic substitution reaction (with or without additional activation) or can participate in a transition-mediated union with fragment 4L
  • the W group of monocycle 42 or bicycle 43 represents a moiety that allows the attachment of the pyrazole.
  • the "W” group represents a halogen atom that will participate in a transition-metal-mediated coupling with a pre-formed heterocyclic reagent (for example a boronic acid or ester, or heteroaryl stannane) to give rise to amine 2.
  • the "W" group of 42 and 43 represents a functional group that can be converted to a f ⁇ ve-membered hetero cycle by an annulation reaction.
  • Non-limiting examples of such processes would include the conversion of a cyano, formyl, carboxy, acetyl, or alkynyl moiety into a f ⁇ ve-membered heterocycle moiety.
  • annulations may in fact be reaction sequences and that the reaction arrows in Scheme 12 may represent either a single reaction or a reaction sequence.
  • the "W" group of 43 may represent a leaving group (halogen or triflate) that can be displaced by a nucleophilic nitrogen atom of a pyrazole, triazole or imidazole ring.
  • Scheme 13 illustrates another general method of preparing amines 2 by first attaching the 5-membered heterocycle to the pyrimidine ring (42).
  • the "LG" of rnonocycle 42 represents a moiety that can either be directly displaced in a nucleophilic substitution reaction (with or without additional activation) or can participate in a transition-mediated union with fragment 4J_.
  • the "W” group of monocycle 42 represents a moiety that allows the attachment of a 5-membered heterocycle.
  • the "W” group represents a halogen atom that will participate in a transition-metal-mediated coupling with a pre-formed heterocyclic reagent (for example, a boronic acid or ester, or heteroaryl stannaiie) to give rise to amine 2.
  • a pre-formed heterocyclic reagent for example, a boronic acid or ester, or heteroaryl stannaiie
  • the "W” group of 42 represents a functional group that can be converted to a five-membered heterocycle by an annulation reaction.
  • the "W” group of 42 may represent a leaving group (halogen or triflate) that can be displaced by a nucleophilic nitrogen atom of a pyrazole, triazole or imidazole ring.
  • Scheme 16 illustrates the preparation amine 56 as a non-limiting example of general Scheme 12.
  • 2.4-dichloropyrimidine (53) can be reacted with phenol 54 in the presence of a base to provide 5_5, an example of general intermediate 43 (Scheme 12).
  • Further reaction of chloropyrimidine 55 with pyrazole boronate 4£ in the presence of palladium catalyst provides amine 56, an example of general amine 2.
  • Scheme 17 illustrates the preparation of amine 62, an additional example of general amine 2.
  • 4,6- dichloropyrimidine (57) an example of general pyrimidine 42 (Scheme 13) wherein "W” is chloro
  • 1,2,4-triazole 58 is reacted with 1,2,4-triazole 58 to provide 59, an example of general intermediate 46 (Scheme 13) wherein "LG” is chloro.
  • Further reaction of 59 with phenol 60 provides the Boc-protected amine 6J_, corresponding to general intermediate 44 (Scheme 13 wherein "P” is tert-butoxycarbonyl [Boc]).
  • Treatment of 6J_ with an acid, for example trifluoracetic acid provides amine 61, an example of general amine 2.
  • additional non-limiting examples of general amine 2 can also be prepared from chloropyrimidine 47 by the three step sequence of Scheme 15 (Step 1 : palladium-catalyzed cross-coupling reaction; Step 2: Sulfide oxidation to sulfone; Step 3: Displacement of sulfone with phenol 7JL wherein Rl 6 is an optional substituent as described above and x is 0-2).
  • Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 1.
  • chloropyrimidine 47 can be combined with tributylstannane 63_ (see; Cheng et al., Biorg. Med. Chem Lett., 2006. 2076), stannane 64 (Aldrich Chemical), boronate 65. (BoroPharm), tributylstannane 66 (see: Sakamoto, et al. Tetrahedron, 1991, 5111), boronate 67 (Frontier Scientific), boronate 68 (see: Blackaby, et al., US 7030128), trimethyl stannane 69 (see: Wentland, et al. J Med. Chem., 1993, 1580) or stannane 70 (see: Nicolaou, et. aL Chem, Med, Chem., 2006, 41) to provide general amines 72-79 respectively.
  • additional non-limiting examples of general amine 2 can also be prepared from dicliloropyrimidine 53 by the two-step sequence of Scheme 16 (Step 1 : Displacement of chloride with phenol 71, wherein Rl 6 is an optional substituent as described above and x is 0-2; Step 2: palladium-catalyzed cross-coupling reaction). Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 2.
  • chloropyrimidine 53 can first be combined with phenol TL and the resultant phenoxy chloropyrimidine (not shown) can be reacted with a palladium catalyst and tributylstannane 63 (see: Cheng et al, Biorg. Med. Chem Lett, 2006, 2076), stannane 64 (Aldrich Chemical), boronate 65_ (BoroPharm), tributylstannane 66 (see: Sakamoto, et al.
  • Scheme 19 As indicated in Scheme 20, additional non-limiting examples of general amine 2 can also be prepared from dichloropyrimidine 57 using the two-step sequence of Scheme 16 and Scheme 19 (Step 1 : Displacement of chloride with phenol 71, wherein R16 is an optional substituent as described above and x is 0-2; Step 2: palladium-catalyzed cross- coupling reaction) Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 2.
  • Step 1 Displacement of chloride with phenol 71, wherein R16 is an optional substituent as described above and x is 0-2;
  • Step 2 palladium-catalyzed cross- coupling reaction
  • Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 2.
  • chloropyrimidine 57 can first be combined with phenol 71.
  • phenoxy chloropyrimidine (not shown) can be reacted with a palladium catalyst and tributylstannane 63 (see: Cheng et al., Biorg. Med. Chem Lett, 2006, 2076), stannane 64 (Aldrich Chemical), boronate 65 (BoroPharm), tributylstannane 66 (see: Sakamoto, et al. Tetrahedron, 1991, 5111), boronate 67 (Frontier Scientific), boronate 68 (see: Blackaby, et al., US 7030128), trimethylstannane 69 (see: Wentland, et al. J. Med.
  • Example Al 4-Fluoro-2-methyl-phenol (25 g, 0.2 mol) was added to a solution of sodium hydroxide (9.7 g, 0.24 mol) in water (160 mL) and the resultant solution was cooled to 0 0 C. Methyl chloroformate (24.2 g, 0.26 mol) was added dropwise at 0 0 C. At the completion of the reaction, the pH was adjusted to pH 8 with saturated aqueous Na 2 CO 3 and then mixture was extracted with ethyl acetate (3 x 300 mL).
  • Example A2 Methyl chloroformate (77.3 g, 0.82 mol) was added dropwise to a -10 0 C solution of 2-chloro-4-fluorophenol (10Og, 0.68 mol) and sodium hydroxide (32.8 g, 0.82 mol) in water (550 mL). After complete addition, the precipitated solid was collected by filtration and washed with water to give 2-chloro-4-fluorophenyl methyl carbonate (110 g, 79 % yield).
  • Example Bl t-Butylhydrazine and 1,1,3,3-tetrametlioxypropane were combined according to literature procedures to yield l-t-butyl-lH-pyrazoI-4-amine. See Ger. Offen., DE3332270, 21 March 1985.
  • Example 1 To a biphasic solution of Example Al (0.071 g, 0.23 mmol) in EtOAc (5 ml) and NaHCO 3 (10 ml) was added prop-l-en-2-yl carbonochloridate (0.043 g, 0.35 mmol) and the mixture was stirred for 2h at RT. The layers were separated and the aqueous layer was extracted with EtOAc (1x5 mL).
  • Example 2 To a biphasic solution of Example Al (0.075 g, 0.26 mmol) in EtOAc (5 ml) and NaHC ⁇ 3 (10 ml) was added prop-l-en-2-yl carbonochloridate (0.048 g, 0.35 mmol) and the mixture was stirred for 2h at RT. The layers were separated and the aqueous layer was extracted with EtOAc (1x5 mL).
  • Example 3 Using General Method A, 3 -tert-butyl-1 -methyl- lH-pyrazole-5-carboxylic acid (0.074 g, 0.4 mmol), Example Al (0.081 g, 0.27 mmol), triethylamine (0.082 g, 0.8 mmol) and DPPA (0.15 g, 0.54 mmol) were combined and purified via chromatography (EtOAc/hexanes) to afford l-(3-tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-4- methyl-5-(4-(l -methyl- lH-pyrazoI-4 ⁇ yl)pyrimidin-2-yloxy)phenyl)urea as white solid (0.07 g, 54% yield).
  • Example 4 Using General Method A, S-tert-butyl-l-methyl-lH-pyrazole-S-carboxylic acid (0.072 g, 0.39 mmol), Example A2 (0.075 g, 0.26 mmol), triethylamine (0.08 g, 0.79 mmol) and DPPA (0.14 g, 0.52 mmol) were combined and purified via chromatography (EtOAc/hexanes) to afford l-(3-tert-butyI-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-5-(4- (1 -methyl -lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea as white solid (0.062 g, 51% yield).
  • AbI kinase Activity of AbI kinase (SEQ ID NO:1) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A 34O n n O was continuously monitored spectrophometrically. The reaction mixture (100 ⁇ l) contained AbI kinase (1 nM.
  • the absorption at 340 nm was monitored continuously for 2 hours at 30 0 C on Polarstar Optima plate reader (BMG).
  • the reaction rate was calculated using the 1.0 to 2.0 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.
  • T315I AbI kinase Activity of T315I AbI 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, e ⁇ al. Science (2000) 289, 1938- 1942). In this assay, the oxidation of NADH (thus the decrease at A3 4 o n m) was continuously monitored spectrophometrically. The reaction mixture (100 ⁇ l) contained AbI kinase (4.4 nM.
  • M315I AbI from deCode Genetics peptide substrate (EAIYAAPFAKKJC, 0.2 rnM), 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 T315I AbI (SEQ ID NO:2) and other reaction reagents at 30 0 C for 1 h before ATP (500 ⁇ M) was added to start the reaction.
  • T315I AbI SEQ ID NO:2
  • other reaction reagents at 30 0 C for 1 h before ATP (500 ⁇ M) was added to start the reaction.
  • the absorption at 340 nm was monitored continuously for 2 hours at 30 0 C on Polarstar Optima plate reader (BMG).
  • the reaction rate was calculated using the 1.0 to 2.0 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.
  • c-Kit kinase Activity of c-Kit kinase (SEQ ID NO:9) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340nm) was continuously monitored spectrophometrically.
  • the reaction mixture (100 ⁇ l) contained c-Kit (cKIT residues T544-V976, from ProQinase, 5.4 nM), polyE4Y (1 mg/ml), MgC12 (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 3 pH 7.5.
  • Test compounds were incubated with C-Met (SEQ ID NO:9) and other reaction reagents at 22 0 C for ⁇ 2 min before ATP (200 ⁇ M) was added to start the reaction.
  • the absorption at 340 run was monitored continuously for 0.5 hours at 30 0 C on Polarstar Optima plate reader (BMG).
  • BMG Polarstar Optima plate reader
  • the reaction rate was calculated using the 0 to 0.5 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound).
  • IC50 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.
  • C-Met kinase (SEQ ID NO: 10) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340nm) was continuously monitored spectrophometrically.
  • the reaction mixture (100 ⁇ l) contained C-Met (c-Met residues: 956-1390, from Invitrogen, catalogue #PV3143, 6 nM), polyE4Y (1 mg/rnl), MgC12 (10 niM), 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: 10) and other reaction reagents at 22 0 C for 0.5 h before ATP (100 ⁇ M) was added to start the reaction.
  • the absorption at 340 nrn was monitored continuously for 2 hours at 30 0 C on Polarstar Optima plate reader (BMG).
  • BMG Polarstar Optima plate reader
  • the reaction rate was calculated using the 1.0 to 2.0 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound).
  • IC50 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.
  • biochemical IC 50 values of other compounds disclosed herein are at least 10 ⁇ M against AbI enzyme.
  • BaF3 cells parental or transfected with the following: wild type p210 BCR-AbI and T3151 p210 BCR-AbI was obtained from Professor Richard Van Etten (New England Medical Center, Boston, MA). Briefly, cells were grown in RPMI 1640 supplemented with 10% characterized fetal bovine serum (HyClone, Logan, UT) at 37 degrees Celsius, 5% CO 2 , 95% humidity. Cells were allowed to expand until reaching 80% saturation at which point they were subciiltured or harvested for assay use.
  • test compound was dispensed into a 96 well black clear bottom plate (Corning, Corning, NY). For each cell line, three thousand cells were added per well in complete growth medium. Plates were incubated for 72 hours at 37 degrees Celsius, 5% CO 2 , 95% humidity. At the end of the incubation period Cell Titer Blue (Promega. Madison, WI) was added to each well and an additional 4.5 hour incubation at 37 degrees Celsius, 5% CO 2 , 95% humidity was performed. Plates were then read on a BMG Fluostar Optima (BMG, Durham, NC) using an excitation of 544 nM and an emission of 612 nM. Data was analyzed using Prism software (Graphpad. San Diego, CA) to calculate IC50 ! s.

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Abstract

Compounds of the present invention find utility in the treatment of mammalian cancers and especially human cancers including but not limited to malignant, melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, 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, rheumatoid arthritis, asthma, chronic obstructive pulmonary disease, mastocyctosis, mast cell leukemia, a disease caused by c-Abl kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, or a disease caused by c-Kit kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof.

Description

Kinase Inhibitors Useful for the Treatment of Myleoproliferative Diseases and other Proliferative Diseases
Cross-Reference to Related Applications
This application claims the benefit of Provisional Application 60/913.216 filed April 20th,
2007. This provisional application is incorporated by reference herein in its entirety.
Sequence Listing
This application contains a Sequence Listing in both paper and computer readable format in accordance with 37 C.F.R. 1.821 (c) and (e), the contents of which are hereby incoiporated by reference in their entirety.
Field of the Invention
The present invention relates to novel kinase inhibitors and modulator compounds useful for the treatment of various diseases. More particularly, the invention is concerned with such compounds, kinase/compound adducts, methods of treating diseases, and methods of synthesis of the compounds. Preferrably, the compounds are useful for the modulation of kinase activity of C-AbL c-Kit, VEGFR, PDGFR kinases, Flt-3, c-Met, FGFR, the HER family and disease causing polymorphs thereof.
Background of the invention
Several members of the protein kinase family have been clearly implicated in the pathogenesis of various proliferative and myleoproliferative diseases and thus represent important targets for treatment of these diseases. Some of the proliferative diseases relevant to this invention include cancer, rheumatoid arthritis, atherosclerosis, and retinopathies. Important examples of kinases which have been shown to cause or contribute to the pathogensis of these diseases include C-AbI kinase and the oncogenic fusion protein bcr-Abl kinase; c-Kit kinase, PDGF receptor kinase; VEGF receptor kinases; and Flt-3 kinase.
C-AbI kinase is an important non-receptor tyrosine kinase involved in cell signal transduction. This ubiquitously expressed kinase — upon activation by upstream signaling factors including growth factors, oxidative stress, integrin stimulation, and ionizing radiation — localizes to the cell plasma membrane, the cell nucleus, and other cellular compartments including the actin cytoskeleton (Van Etten, Trends Cell Biol. (1999) 9: 179). There are two normal isoforms of AbI kinase: AbI- IA and AbI- IB. The N-terminal half of c-Abl kinase is important for auto inhibition of the kinase domain catalytic activity (Pluk et al, Cell (2002) 108: 247). Details of the mechanistic aspects of this autoinhibition have recently been disclosed (Nagar et al, Cell (2003) 112: 859). The N-terminal myristolyl amino acid residue of AbI-I B has been shown to intramolecularly occupy a hydrophobic pocket formed from alpha-helices in the C -lobe of the kinase domain. Such intramolecular binding induces a novel binding area for intramolecular docking of the SH2 domain and the SH3 domain onto the kinase domain, thereby distorting and inhibiting the catalytic activity of the kinase. Thus, an intricate intramolecular negative regulation of the kinase activity is brought about by these N- terminal regions of c-Abl kinase. An aberrant dysregulated form of c-Abl is formed from a chromosomal translocation event, referred to as the Philadelphia chromosome (P.C. Nowell et al, Science (1960) 132: 1497; J.D. Rowley, Nature (1973) 243: 290). This abnormal chromosomal translocation leads aberrant gene fusion between the AbI kinase gene and the breakpoint cluster region (BCR) gene, thus encoding an aberrant protein called bcr-Abl (G. Q. Daley et al, Science (1990) 247: 824; M. L. Gishizky et al, Proc. Natl. Acad. ScI USA (1993) 90: 3755; S. Li et al, J. Exp. Med. (1999) 189: 1399). The bcr-Abl fusion protein does not include the regulatory myristolylation site (B. Nagar et al. Cell (2003) 112: 859) and as a result functions as an oncoprotein which causes chronic myeloid leukemia (CML). CML is a malignancy of pluripotent hematopoietic stem cells. The p210 form of bcr-Abl is seen in 95% of patients with CML3 and in 20% of patients with acute lymphocytic leukemia and is exemplified by sequences such as el4a2 and el3a2. The corresponding p!90 form, exemplified by the sequence ela2 has also been identified. A pi 85 form has also been disclosed and has been linked to being causative of up to 10% of patients with acute lymphocytic leukemia. It will be appreciated by one skilled in the art that "p210 form", "pi 90 form" and "pi 85 form" each describe a closely related group of fusion proteins, and that Sequence ID's used herein are merely representative of each form and are not meant to restrict the scope solely to those sequences.
C-KIT (Kit, CD 117, stem cell factor receptor) is a 145 kDa transmembrane tyrosine kinase protein that acts as a type-Ill receptor (Pereira et al. J Carcin. (2005), 4: 19). The c-KIT proto-oncogene, located on chromosome 4ql 1-21, encodes the c-KIT receptor, whose ligand is the stem cell factor (SCF, steel factor, kit ligand, mast cell growth factor, Morstyn G, et al Oncology (1994) SI(2):205. Yarden Y, et al. Embo J (1987) 6(1 1):3341). The receptor has tyrosine-protein kinase activity and binding of the ligands leads to the autophosphorylation of KIT and its association with substrates such as phosphatidylinositol 3-kinase (Pi3K). Tyrosine phosphorylation by protein tyrosine kinases is of particular importance in cellular signalling and can mediate signals for major cellular processes, such as proliferation, differentiation, apoptosis, attachment, and migration. Defects in KIT are a cause of piebaldism. an autosomal dominant genetic developmental abnormality of pigmentation characterized by congenital patches of white skin and hair that lack melanocytes. Gain-of-function mutations of the c-KIT gene and the expression of phosphorylated KIT are found in most gastrointestinal stromal tumors and mastocytosis. Further, almost all gonadal seminomas/dysgerminomas exhibit KIT membranous staining, and several reports have clarified that some (10-25%) have a c- KIT gene mutation (Sakuma, Y. et al Cancer Sci (2004) 95:9, 716). KIT defects have also been associated with testicular tumors including germ cell tumors (GCT) and testicular germ cell tumors (TGCT).
The role of c-kit expression has been studied in hematologic and solid tumours, such as acute leukemias (Cortes J. et al Cancer (2003) 97(11):2760) and gastrointestinal stromal tumors (GIST, Fletcher CD. et al Hum Pathol (2002) 33(5):459). The clinical importance of c-kit expression in malignant tumors relies on studies with Gleevec® (imatinib mesylate, STI571, Novartis Pharma AG Basel, Switzerland) that specifically inhibits tyrosine kinase receptors (Lefevre G. et al J Biol Chem (2004) 279(30):31769). Moreover, a clinically relevant breakthrough has been the finding of anti-tumor effects of this compound in GIST, a group of tumors regarded as being generally resistant to conventional chemotherapy (de Silva CM, Reid R: Pathol Oncol Res (2003) 9(1): 13-19). GIST most often become Gleevec resistant and molecularly targeted small therapies that target c-KIT mutations remain elusive.
c-MET is a unique receptor tyrosine kinase (RTK) located on chromosome 7p and activated via its natural ligand hepatocyte growth factor. c-MET is found mutated in a variety of solid tumors (Ma P. C. et a Cancer Metastasis (2003) 22:309). Mutations in the tyrosine kinase domain are associated with hereditary papillary renal cell carcinomas (Schmidt L et a Nat. Genet. (1997)16:68; Schmidt L, et a Oncogene (1999) 18:2343), whereas mutations in the sema and juxtamembrane domains are often found in small cell lung cancers (SCLC; Ma P.C. et a Cancer Res (2003) 63:6272). Many activating mutations are also found in breast cancers (Nakopoulou et a Histopath (2000) 36(4): 313). The panoply of tumor types for which c-Met mediated growth has been implicated suggests this is a target ideally suited for modulation by specific c-MET small molecule inhibitors.
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 iV-methyl-iV'-mtro-JV-nitrosoguanidirie (Park M. et a 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 ah Cancer (2000) 88:1801). Dimerization of the Mx 65.000 TPR-MET oncoprotein through a leucine zipper motif encoded by TPR leads to constitutive activation of the c-MET kinase (Zhen Z. et ah Oncogene (1994) 9:1691). TPR-MET acts to activated wild-type c-MET RTK and can activate crucial cellular growth pathways, including the Ras pathway (Aklilu F. et a Am J Physiol (1996) 271 :E277) and the phosphatidylinositol 3-kinase (PI3K)/AKT pathway (Ponzetto C. et a MoI Cell Biol (1993) 13:4600). Conversely, in contrast to c-MET RTK, TPR-MET is ligand independent, lacks the CBL binding site in the juxtamembrane region in c-MET, and is mainly cytoplasmic. c-Met irnmunoliistochemical expression seems to be associated with abnormal β-catenin expression, and provides good prognostic and predictive factors in breast cancer patients.
The majority of small molecule kinase inhibitors that have been reported have been shown to bind in one of three ways. Most of the reported inhibitors interact with the ATP binding domain of the active site and exert their effects by competing with ATP for occupancy. Other inhibitors have been shown to bind to a separate hydrophobic region of the protein known as the "DFG-in-conformation" pocket wherein such a binding mode by the inhibitor causes the kinase to adopt the "DFG-out" conformation, and still others have been shown to bind to both the ATP domain and the "DFG-in-conformation" pocket again causing the kinase to adopt the "DGF- out" conformation. Examples specific to inhibitors of Raf kinases can be found in Lowinger et al, Current Pharmaceutical Design (2002) 8: 2269; Dumas, J. et al, Current Opinion in Drug Discovery & Development (2004) 7: 600; Dumas, J. et al, WO 2003068223 Al (2003); Dumas, J., et al, WO 9932455 Al (1999), and Wan, P.T.C., et al, Cell (2004) 116: 855.
Physiologically, kinases are regulated by a common activation/deactivation mechanism wherein a specific activation loop sequence of the kinase protein binds into a specific pocket on the same protein which is referred to as the switch control pocket. Such binding occurs when specific amino acid residues of the activation loop are modified for example by phosphorylation, oxidation, or nitrosylation. The binding of the activation loop into the switch pocket results in a conformational change of the protein into its active form (Huse, M. and Kuriyan, J. Cell (109) 275)
Summary of the Invention
Compounds of the present invention find utility in the treatment of mammalian cancers and especially human cancers including but not limited to malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor sites, myeloproliferative diseases, 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, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, a disease caused by c-Abl kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, or a disease caused by c-Kit, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof.
Section 1 - Description of the Preferred Embodiments
The following descriptions refer to various compounds, stereo-, regioisoraers and tautomers of such compounds and individual moieties of the compounds thereof.
Cycloalkyl refers to monocyclic saturated carbon rings taken from cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptanyl and cyclooctanyl;
Aryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized π electrons (aromaticity) shared among the ring carbon atoms of at least one carbocyclic ring; preferred aryl rings are taken from phenyl, naphthyl, tetrahydronaphthyl, indenyl, and indanyl;
Heteroaryl refers to monocyclic or fused bicyclic ring systems characterized by delocalized π electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring; heteroaryl rings are taken from, but not limited to, pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazolyl, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, tetrazolyl, pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, benzothiazolonyl, benzoxazolyl, benzoxazolonyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl, benzimidazolonyl, benztriazolyl, imidazopyridinyl, pyrazolopyridinyl, imidazolonopyridinyl, thiazolopyridinyl, tliiazolonopyridinyl, oxazolopyridinyl, oxazolonopyridinyl, isoxazolopyridinyl, isothiazolopyridinyl. triazolopyridinyl, imidazopyrimidinyl, pyrazolopyrimidinyl, imidazolonopyrimidinyl, thiazolopyridiminyl, thiazolonopyrimidinyl, oxazolopyridirninyl, oxazolonopyrimidinyl, isoxazolopyrimidmyl, isotliiazolopyrimidinyl, triazolopyrimidinyl, dihydropurinonyl, pyrrolopyrimidinyl, purinyl, pyrazolopyrimidinyl, phthalimidyl, phtlialimidinyl, pyrazinylpyridinyl, pyridinopyrimidinyl, pyrimidinopyrimidinyl, cinnolinyl, quinoxalinyl, quinazolinyl, quinolinyl, isoquinolinyl, phthalazinyl, benzodioxyl, benzisotliiazoline- 1 , 1 ,3 -trionyl, dihydroquinolinyl, tetrahydroquinolinyl, dihydroisoquinolyl, tetrahydroisoquinolinyL benzoazepinyl, benzodiazepinyl, benzoxapinyl, and benzoxazepinyl;
Heterocyclyl refers to monocyclic rings containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized π electrons (aromaticity) shared among the ring carbon or heteroatoms; heterocyclyl rings include, but are not limited to. oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, thiazolinyl, thiazolidinyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, thiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl;
Poly-aryl refers to two or more monocyclic or fused aryl bicyclic ring systems characterized by delocalized π electrons (aromaticity) shared among the ring carbon atoms of at least one carbo cyclic ring wherein the rings contained therein are optionally linked together;
Poly-heteroaryl refers to two or more monocyclic or fused bicyclic systems characterized by delocalized π electrons (aromaticity) shared among the ring carbon or heteroatoms including nitrogen, oxygen, or sulfur of at least one carbocyclic or heterocyclic ring wherein the rings contained therein are optionally linked together, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heteroaryl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above;
Poly-heterocyclyl refers to two or more monocyclic or fused bicyclic ring systems containing carbon and heteroatoms taken from oxygen, nitrogen, or sulfur and wherein there is not delocalized π electrons (aromaticity) shared among the ring carbon or heteroatoms wherein the rings contained therein are optionally linked, wherein at least one of the monocyclic or fused bicyclic rings of the poly-heteroaryl system is taken from heterocyclyl as defined broadly above and the other rings are taken from either aryl, heteroaryl, or heterocyclyl as defined broadly above; Alkyl refers to straight or branched chain Cl-C6alkyls;
Halogen refers to fluorine, chlorine, bromine, and iodine;
Alkoxy refers to -O-(alkyl) wherein alkyl is defined as above;
Alkoxylalkyl refers to -(alkyl)-O-(alkyl) wherein alkyl is defined as above;
Alkoxylcarbonyl refers to -C(O)O-(alkyl) wherein alkyl is defined as above;
CarboxylCl-Cόalkyl refers to -(Cl-CόalkyFj-CChH wherein alkyl is defined as above;
Substituted in connection with a moiety refers to the fact that a further substituent may be attached to the moiety to any acceptable location on the moiety.
The term salts 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, examples of which are 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, ethane sulfonic, benzenesulfonic, pantothenic, toluenesulfonic, 2- hydroxyethanesulfonic, sulfanilic, cyclohexylaminosulfonic, algenic, 3 -hydroxy butyric, galactaric and galacturonic acid. Suitable pharmaceutically-acceptable salts of free acid- containing compounds of Formula I include metallic salts and organic salts. More preferred metallic salts include, but are not limited to appropriate alkali metal (group Ia) salts, alkaline earth metal (group Ha) salts and other physiological acceptable metals. Such salts can be made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc. Preferred organic salts can be made from primary amines, secondary amines, tertiary amines and quaternary ammonium salts, including in part, tromethamine, diethylamine, /etrø-N-methylammonium, N.N'-diben2ylethyIenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
The term prodrug refers to derivatives of active compounds which revert in vivo into the active form. For example, a carboxylic acid form of an active drug may be esterified to create a prodrug, and the ester is subsequently converted in vivo to revert to the carboxylic acid form. See Ettmayer et. al, J Med. Chem (2004) 47: 2393 and Lorenzi et. al, J Pharm. Exp. Therpeiitics (2005) 883 for reviews.
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 P. Mϋller, Pure Appl. Chem., 66, 1077-1184 (1994) and Basic Terminology of Stereochemistry (IUPAC Recommendations 1996) as summarized by G.P. Moss Pure and Applied Chemistry, 68, 2193-2222 (1996). Specific definitions are as follows:
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.
Regioisomers or structural isomers are defined as isomers involving the same atoms in different arrangements.
Enatiomers are defined as one of a pair of molecular entities which are mirror images of each other and non-superimpo sable. 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.
Tautomerisra is defined as isomerism of the general form
G-X-Y=Z -^-X=Y-Z-G
where the isomers (called tautomers) are readily interconvertible; the atoms connecting the groups X, Y3Z are typically any of C, H, O, or S, and G is a group which becomes an electrofuge or nucleofuge during isomerization. The commonest 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.
L First aspect of the invention - Compounds, Methods, Preparations and
Adducts
Figure imgf000013_0001
and wherein the pyrimidine ring may be optionally substituted with one or more R20 moieties;
each D is individually taken from the group consisting of C, CH, C-R20, N-Z3, N, O and S, such that the resultant ring is taken from the group consisting of pyrazolyl, triazolyl, isoxazolyl, isothiazolyl, oxazolyl, imidazoyl, and thiadiazolyl;
wherein E is selected from the group consisting phenyl, pyridyl, and pyrimidinyl;
E may be optionally substituted with one or two Rl 6 moieties;
wherein A is a ring system selected from the group consisting of cyclopentyl, cyclohexyl, Gl, G2, and G3;
Gl is a heteroaryl taken from the group consisting of pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazol-4-yl, isoxazol-5-yI, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl, and tetrazolyl;
G2 is a fused bicyclic heteroaryl taken from the group consisting of indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, benzothiazolonyl, benzoxazolyl, benzoxazolonyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl, benzimidazolonyl, benztriazolyl, imidazopyridinyl, pyrazolopyridinyl, imidazolonopyridinyl, thiazolopyridinyl, thiazolonopyridinyl, oxazolopyridinyl, oxazolonopyridinyl. isoxazolopyridinyl, isothiazolopyridinyl. triazolopyridinyl, imidazopyrimidinyl, pyrazolopyrimidinyl, imidazolonopyrimidinyl. thiazolopyridiminyl, thiazolonopyrimidinyl, oxazolopyridiminyl, oxazolonopyrimidinyl, isoxazolopyrimidinyl, isothiazolopyrimidinyl, triazolopyrimidinyl. dihydropurinonyl, pyrrolopyrimidinyl, purinyl, pyrazolopyrimidinyl, phthalimidyl, phthaliniidinyl, pyrazinylpyridinyl, pyridinopyrimidinyl, pyrimidinopyrimidinyl, cinnolinyl, quinoxalinyl, quinazolinyl, quinolinyl, isoquinolinyl, phthalazinyl. benzodioxyl, benzisothiazoline-l,l,3-trionyl, diliydroquinolinyl, tetrahydroquinolinyl, dihydroisoquinolyl, tetrahydroisoquinolinyl, benzoazepinyl, benzodiazepinyl, benzoxapinyl, and benzoxazepinyl;
G3 is a heterocyclyl taken from the group consisting of oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, imidazolonyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, tliiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropaiiyl;
the A ring may be optionally substituted witli-one or two R2 moieties;
X is selected from the group consisting of -O-, -S(CH2),,-, -N(R3)(CH2)n-, -(CH2)P-, and wherein the carbon atoms of -(CH2)H-, -(CH2)p-, of X may be further substituted by oxo or one or more Cl-C6alkyl moieties;
when A, Gl, G2 or G3 has one or more substitutable sp2-hybridϊzed carbon atoms, each respective sp2 hybridized carbon atom may be optionally substituted with a Zl substituent;
when A, Gl, G2 or G3 has one or more substitutable sp3 -hybridized carbon atoms, each respective sp3 hybridized carbon atom may be optionally substituted with a Z2 substituent; when A, Gl, G2 or G3 has one or more substitutable nitrogen atoms, each respective nitrogen atom may be optionally substituted with a 24 substituent;
each Zl is independently and individually selected from the group consisting of Cl- όalkyl, branched C3-C7alkyl, C3-C8cycloalkyl, halogen, fluoroCl-Cόalkyl wherein the alkyl moiety can be partially or fully fluorinated, cyano, Cl-C6alkoxy, fluoroCl- Cθalkoxy wherein the alkyl moiety can be partially or fully fluorinated, -(CH2)πOH, oxo, Cl-C6alkoxyCl-C6alkyl, (R4)2N(CH2)π-, (R3)2N(CH2)π-, (R4)2N(CH2)qN(R4)(CH2)n-, (R4)2N(CH2)qO(CH2)n-, (R3)2NC(O)-, (R4)2NC(O)-, (R4)2NC(O)C1-C6alkyl-, - (R4)NC(O)R8, Cl-Cόalkoxycarbonyl-, -carboxyCl-Cόalkyl, Cl-C6alkoxycarbonylCl- C6alkyl-: (R3)2NSO2-5 -SOR3, (R4)2NSO2-5 -N(R4)SO2R8, -O(CH2)qOCl-C6alkyl, - SO2R3, -SOR4, -C(O)R8, -C(O)R6, ~C(=NOH)R6, -C(=NOR3)R6, - (CH2)πN(R4)C(O)R8, -N(R3)(CH2)qO-alkyl, -N(R3)(CH2)qN(R4)2, nϊtro, CH(OH)CH(OH)R4, -C(-NH)N(R4)2j -C(=NOR3)N(R4)2, -NHC(=NH)R8, Rl 7 substituted G3, Rl 7 substituted pyrazolyl and Rl 7 substituted imidazolyl;
in the event that Zl contains an alkyl or alkylene moiety, such moieties may be further substituted with one or more Cl-C6alkyls;
each Z2 is independently and individually selected from the group consisting of aryl, Cl- Cδalkyl, C3-C8cycloalkyl, branched C3-C7alkyl, hydroxyl, hydroxyCl-Cόalkyl-, cyano, (R3)2N-, (R4)2N-, (R4)2NC1-C6alkyl-, (R4)2NC2-C6alkylN(R4)(CH2)n-, (R4)2NC2- C6alkylO(CH2)n-, (R3)2NC(O>, (R4)2NC(O)-, (R4)2NC(O)-Cl-C6alkyl-, carboxyL - carboxyC 1 -Cόalkyl, C 1 -Cόalkoxycarbonyl-, Cl-C6alkoxycarbonylC 1 -Cβalkyl-, (R3)2NSO2-, (R4)2NSO2-, -SO2RS, -(CH2)nN(R4)C(O)R8, -C(O)R8, =0, =N0H, and =N(0R6);
in the event that Z2 contains an alkyl or alkylene moiety, such moieties may be further substituted with one or more Cl-C6alkyls; each Z3 is independently and individually selected from the group consisting of H, Cl- Cδalkyl, branched C3-C7alkyl, C3-C8cycloalkyl, fluoroCl-Cδalkyl wherein the alkyl moiety can be partially or fully fluorinated, hydroxyC2-C6 alkyl-, Cl-C6alkoxycarbonyl-, -C(O)RS, R5C(O)(CH2)n-, (R4)2NC(O)-5 (R4)2NC(O)C1-C6alkyl-, R8C(O)N(R4)(CH2)q- , (RS)2NSO2-, (R4)2NSO2-, -(CH2) qN(R3)2, and -(CH2)qN(R4)2;
each ZA is independently and individually selected from the group consisting of Cl- Cόalkyl, branched C3-7alkyl, hydroxyC2-C6alkyl-, Cl-C6alkoxyC2-C6alkyl-, (R4)2N- C2-C6alkyl-, (R4)2N-C2-C6alkylN(R4)-C2-C6alkyl-, (R4)2N-C2-C6alkyl-O-C2- Cόalkyl- (R4)2NC(O)Cl-C6alkyK carboxyCl-Cβalkyl, Cl-C6alkoxycarbonylCl- Cδalkyl-, -C2-C6alkyIN(R4) C(O)RS, R8-C(=NR3)-5 -SO2R8, and -CORS;
in the event that Z4 contains an alkyl or alkylene moiety, such moieties may be further substituted with one or more Cl-C6alkyls;
each R2 is selected from the group consisting of H, Cl-C6alkyl, branched CS-Cδalkyl, Rl 9 substituted CS-Cδcycloalkyl-, fluoroCl-Cβalkyl- wherein the alkyl is fully or partially fluorinated, halogen, cyano, Cl-C6alkoxy-, and fluoroCl-Cόaϊkoxy- wherein the alkyl group is fully or partially fluorinated, hydroxyl substituted Cl-C6alkyl-, hydroxyl substituted branched C3-C8alkyl-, cyano substituted Cl-C6alkyl-, cyano substituted branched C3-C8alkyl-, (R3)2NC(O)C1-C6alkyl-, and (R3)2NC(O)C3-C8 branched alkyl-;
wherein each R3 is independently and individually selected from the group consisting of H, Cl-C6alkyl, branched C3-C7alkyl, and C3 -CScycloalkyl;
each R4 is independently and individually selected from the group consisting of H, Cl- Cδalkyl, hydiOxyCl-Cόalkyl", dihydroxyCl-C6alkyl-, Cl-C6alkoxyCl-C6alkyk branched C3-C7alkyl, branched hydroxyC 1 -Cόalkyl-, branched Cl-C6alkoxyCl- Cόalkyl-, branched diliydroxyCl -Cόalkyl-, -(CH2)PN(R7)2, -(CH2)PC(O)N(R7)2, - (CH2)nC(O)OR3, and Rl 9 substituted C3-C8cycloalkyl-; each R5 is independently and individually selected from the group consisting of
Figure imgf000017_0001
and wherein the symbol (##) is the point of attachment to Z3;
each R6 is independently and individually selected from the group consisting of Cl- Cόalkyl, branched C3-C7alkyl, and Rl 9 substituted C3-C8cycϊoalkyl-;
each R7 is independently and individually selected from the group consisting of H, Cl- Cβalkyl, hydroxyC2-C6alkyl-, dihydroxyC2-C6alkyl~, Cl-C6alkoxyC2-C6alkyl-, branched C3-C7alkyl, branched hydroxyC2-C6alkyl-, branched Cl-C6alkoxyC2- Cόalkyl-, branched dihydroxyC2-C6alkyl-, -(CH2)nC(O)OR3, Rl 9 substituted C3- Cδcycloalkyl- and -(CH2)nR17;
each R8 is independently and individually selected from the group consisting of Cl- C6alkyl, branched C3-C7alkyl, fluoroCl-C6alkyl- wherein the alkyl moiety is partially or fully fluorinated, Rl 9 substituted C3-C8cycloalkyl-, -OH, Cl-C6alkoxy, -N(R3)2, and - N(R4)2;
each RlO is independently and individually selected from the group consisting Of -CO2H, -CO2Cl-C6alkyl, -C(O)N(R4)2, OH, Cl-C6alkoxy, and -N(R4) 2;
each Rl 6 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, branched C3-C7alkyl, R19 substituted C3-C8cycloalkyl-, halogen, fluoroCl- Cβalkyl- wherein the alkyl moiety can be partially or fully fluorinated, cyano, hydroxyl, Cl-C6alkoxy, fluoroCl-Cόalkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(R3)2, -N(IU)2, R3 substituted C2-C3alkynyl- and nitro; each Rl 7 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, branched C3-C7alkyl, Rl 9 substituted CS-Cδcycloalkyl-, halogen, fluoroCl- Cόalkyl- wherein the alkyl moiety can be partially or fully fluormated, cyano, hydroxyl, Cl-C6alkoxy, fluoroCl-Cόalkoxy- wherein the alky] moiety can be partially or fully fluorinated, -N(RS)2, -N(R4)2, and nitro;
each Rl 9 is independently and individually selected from the group consisting of H, OH and Cl-C6alkyl;
each R20 is independently and individually selected from the group consisting of Cl- Cδalkyl, branched C3~C7alkyl, Rl 9 substituted C3-C8cycloalkyl-, halogen, fluoroCl- Cβalkyl- wherein the alkyl moiety can be partially or fully fluormated, cyano, hydroxyl, Cl-C6alkoxy, fluoroCl-Cόalkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(RS)2, -N(R4)2, -N(R3)C(O)R3, -C(O)N(R3)2 and nitro and wherein two R4 moieties independently and individually taken from the group consisting of Cl- Cόalkyl, branched C3-C6alkyl, hydroxyalkyl-, and alkoxyalkyl and attached to the same nitrogen heteroatom may cyclize to form a C3-C7 heterocyclyl ring;
k is O or l; n is 0-6; p is 1-4; q is 2-6; r is 0 or 1; t is 1-3; v is 1 or 2; x is 0-2;
and stereo-, regioisomers and tautomers of such compounds.
1.1 Compounds of Formula Ia which exemplify preferred D moieties
Figure imgf000018_0001
In a preferred embodiment of compounds of formula Ia, said compounds have preferred
Λ Dθ"-""/ moieties of the formula: R20- jfΛ NZ3
Figure imgf000019_0001
Figure imgf000019_0002
wherein tlie symbol (**) indicates the point of attachment to the pyrimidine ring.
1.1.1 Compounds of Formula Ia which exemplify preferred A moieties
In a preferred embodiment of compounds of formula Ia, said compounds have structures of formula Ib
Figure imgf000019_0003
wherein A is any possible isomer of pyrazole.
1.1.2 Compounds of Formula Ia which exemplify preferred A, D, and RI 6 moieties In a more preferred embodiment of compounds of formula Ib, said compounds have structures of formula Ic
Figure imgf000020_0001
1.1.3 Compo unds of Formula Ia which exemplify preferred A1 D, and Rl 6 mo ieties In a more preferred embodiment of compounds of formula Ib, said compounds have structures of formula Id
Figure imgf000020_0002
1.1.4 Compounds of Formula Ia which exemplify preferred A, D, and RI 6 moieties
In a more preferred embodiment of compounds of formula Ib, said compounds have structures of formula Ie
Figure imgf000020_0003
1.1.5 Compounds of Formula Ia which exemplify preferred A, D, and Rl 6 moieties In a more preferred embodiment of compounds of formula Ia, said compounds have structures of formula If
Figure imgf000020_0004
1.1.6 Compounds of Formula Ia which exemplify preferred A and D moieties In a more preferred embodiment of compounds of formula Ia, said compounds have structures of formula Ig
Figure imgf000021_0001
1.1.7 Compounds of Formula Ia which exemplify preferred A, D, and Rl 6 moieties
In a more preferred embodiment of compounds of formula Ig, said compounds have structures of formula Ih
Figure imgf000021_0002
1.L8 Most preferred compounds of formula Ia
1 -( 1 -tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-4-methyl-5-(4-( 1 -methyl- 1 H-pyrazol-4- yI)pyrirnidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl- 1 H-pyrazol-4-yl)-3-(2-fluoro-5-(4-( 1 - methyl- 1 H-pyrazol-4-yl)pyrimidin-2 -y loxy )phenyl)urea, 1 -(3 -tert-butyl - 1 -methyl- IH- pyrazol-5-yl)-3-(2-fluoro-4-methyI-5-(4-( 1 -methyl- 1 H-pyrazol-4-yl)pyrimidin-2~ yloxy)phenyl)urea, and 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)-3 -(2-fiuoro-5 -(4-( 1 - methyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea.
1.2 Methods
1.2a Methods of Protein Modulation
The invention includes methods of modulating kinase activity of a variety of kinases, e.g.
C-AbI kinase, bcr-Abl kinase, Flt-3. VEGFR-2 kinase mutants, c-Met, c-Kit, PDGFR and the HER family of kinases. The kinases may be wildtype kinases, oncogenic forms thereof, aberrant fusion proteins thereof or polymorphs of any of the foregoing. The method comprises the step of contacting the kinase species with compounds of the invention and especially those set forth in sections section 1. The kinase species may be activated or unactivated, and the species may be modulated by phosphorylations, sulfation, fatty acid acylations glycosylations, nitrosylation, cystinylation (i.e. proximal cysteine residues in the kinase react with each other to form a disulfide bond) or oxidation. The kinase activity may be selected from the group consisting of catalysis of phospho transfer reactions, inhibition of phosphorylation, oxidation or nitrosylation of said kinase by another enzyme, enhancement of dephosphorylation, reduction or denitrosylation of said kinase by another enzyme, kinase cellular localization, and recruitment of other proteins into signaling complexes through modulation of kinase conformation.
1.2b Treatm ent Methods
The methods of the invention also include treating individuals suffering from a condition selected from the group consisting of cancer and hyperproliferative diseases. These methods comprise administering to such individuals compounds of the invention, and especially those of section 1, said diseases including, but not limited to, malignant melanomas, glioblastomas, ovarian cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, kidney cancers, cervical carcinomas, metastasis of primary tumor secondary sites, myeloproliferative diseases, 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 including diabetic retinopathy and age-related macular degeneration, rheumatoid arthritis, asthma, chronic obstructive pulmonary disorder, mastocytosis, mast cell leukemia, a disease caused by c-Abl kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, or a disease caused by a c-Kit kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof.. The administration method is not critical, and may be from the group consisting of oral, parenteral, inhalation, and subcutaneous.
1.3 Pharmaceutical Preparations The compounds of the invention, especially those of section 1 may form a part of a pharmaceutical composition by combining one or more such compounds with a pharamaceutically acceptable carrier. Additionally, the compositions may include an additive selected from the group consisting of adjuvants, excipients, diluents, and stablilizers.
Section 2. Synthesis of compounds of the present invention
The compounds of the invention are available by the general synthetic methods illustrated in the Schemes below and the accompanying examples.
As indicated in Scheme 1, ureas of general formula I can be readily prepared by the union of amines of general formula 2 with isocyanates 3 or isocyanate surrogates 4 (trichloroethyl carbamates) or 5. (isopropenyl carbamates). Preferred conditions for the preparation of compounds of general formula 1 involve heating a solution of 4 or 5. with 2 in the presence of a tertiary base such as diisopropylethylamine, triethylamine or N- methylpyrrolidine in a solvent such as dimethylformamide, dimethylsulfoxide, tetrahydrofuran or 1,4-dioxane at a temperature between 50 and 100 0C for a period of time ranging from 1 hour to 2 days.
A-N=C=O 3 or
Figure imgf000023_0001
Scheme 1
As shown in Scheme 2, isocyanates 3 can be prepared from amines A-NH2 6-With phosgene, or a phosgene equivalent such as diphosgene. triphosgene, or N5N- dicarbonylimidazole. Trichloroethyl carbamates 4 and isopropenyl carbamates 5. are readily prepared from amines A-NH2 (6) by reaction with trichloroethyl chloroformate or isopropenyl chloroformate by standard conditions familiar to those skilled in the art. Preferred conditions for the preparation of 4 and 5 include include treatment of compound __ with the appropriate chloroformate in the presence of pyridine in an aprotic solvent such as dichloromethane or in the presence of aqueous hydroxide or carbonate in a biphasic aqueous/ethyl acetate solvent system.
Figure imgf000024_0001
Scheme 2
Additionally, compounds of formula 1 can also be prepared from carboxylic acids 7 by the intermediacy of in~situ generated acyl azides (Curtius rearrangement) as indicated in Scheme 3. Preferred conditions for Scheme 3 include the mixing of acid 7 with amine 2 and diphenylphosphoryl azide in a solvent such as 1,4-dioxane or dimethylformamide in the presence of base, such as triethylamine, and raising the temperature of the reaction to about 80-120 0C to affect the Curtius rearrangement.
Figure imgf000024_0002
Scheme 3
By analogy to Schemes 1 and 3 above, it will be recognized by those skilled in the art that the compounds' of formula 1 can also be prepared by the union of amines A-NHT 6 with isocyanates __ (Scheme 4). Isocyanates 8 can be prepared from general amines 2 by standard synthetic methods. Suitable methods for example, include reaction of 2 with phosgene, or a phosgene equivalent such as diphosgene, triphosgene, or N,N- dicarbonylimidazole. In addition to the methods above for converting amines 2 into isocyanates _5, the isocyanates 8 can also be prepared in situ by the Curtius rearrangement and variants thereof. Those skilled in the art will further recognize that isocycanates J_ need not be isolated, but may be simply generated in situ. Accordingly, acid 9 can be converted to compounds of formula I either with or without isolation of _5. Preferred conditions for the direct conversion of acid 9 to compounds of formula I involve the
ZO mixing of acid 9. amine A-NH? 6, diphenylphosphoryl azide and a suitable base, for example triethylamine, in an aprotic solvent, for example dioxane. Heating said mixture to a temperature of between 80 and 120 0C provides the compounds of formula 1.
Figure imgf000025_0001
Scheme 4
Additionally, compounds of formula 1 can also be prepared from amines 2 by first preparing stable isocyanate equivalents, such as carbamates (Scheme 5). Especially preferred carbamates include trichloroethyl carbamates QO) and isopropenyl carbamates (11) which are readily prepared from amine 2 by reaction with trichloroethyl chloroformate or isopropenyl cliloroformate respectively using standard conditions familiar to those skilled in the art. Further reaction of carbamates J_0 or JJ_ with amine A- NHT 6 provides compounds of formula X. Those skilled in the art will further recognize that certain carbamates can also be prepared from acid 9 by Curtius rearrangement and trapping with an alcoholic co-solvent. For example, treatment of acid 9 (Scheme 5) with diphenylphosphoryl azide and trichloroethanol at elevated temperature provides trichloroethyl carbamate H).
Scheme 5
Many methods exist for the preparation of amines A-NH2 6 and acids A-CO2H 7, depending on the nature of the A-moiety. Indeed, many such amines (6) and acids (7) useful for the preparation of compounds of formula 1 are available from commercial vendors. Some non-limiting preferred synthetic methods for the preparation of amines 6 and acids 7 are outlined in the following schemes and accompanying examples.
As illustrated in Scheme 6. Z4-substituted pyrazol-5-yI amines 14 (a preferred aspect of A-NH2 6, Scheme 2) are available by the condensation of hydrazines \2 and beta-keto nitriles L3 in the presence of a strong acid. Preferred conditions for this transformation are by heating in ethanolic HCl. Many such hydrazines 12 are commercially available. Others can be prepared by conditions familiar to those skilled in the art, for example by the diazotization of amines followed by reduction or, alternately from the reduction of hydrazones prepared from carbonyl precursors.
Figure imgf000026_0002
12 13 14
Scheme 6 Another preferred method for constructing Z4-substituted pyrazoles is illustrated by the general preparation of pyrazole acids 19 and 20. (Scheme 7), aspects of of general acid A-CO2H 7 (Scheme 3). As indicated in Scheme 7, pyrazole 5-carboxylic esters \1_ and 18 can be prepared by the alkylation of pyrazole ester 16 with Z4-X 15, wherein X represents a leaving group on a Z4 moiety such as a halide, triflate. or other sulfonate. Preferred conditions for the alkylation of pyrazole J_6 include the use of strong bases such as sodium hydride, potassium tert-butoxide and the like in polar aprotic solo vents such as dimethylsulfoxide, dimethylformamide or tetrahydrofuran. Z4-substituted pyrazoles \1_ and J_8 are isomers of one another and can both be prepared in the same reactions vessel and separated by purification methods familiar to those skilled in the art. The esters 17 and j_8 in turn can be converted to acids 19 and 20 using conditions familiar to those skilled in the art, for example saponification in the case of ethyl esters, hydrogenation in the case of benzyl esters or acidic hydrolysis in the case of tert-butyl esters.
Figure imgf000027_0001
18 20
Scheme 7
Scheme 8 illustrates the preparation of pyrazole amine 25^ a further example of general amine A-NHT 6. Acid-catalyzed condensation of R2-substituted hydrazine 21 with 1,1,3,3-tetramethoxypropane 22 provides R2-substituted pyrazole 23- Those skilled in the art will further recognize that R2-substituted pyrazole 23 can also be prepared by direct alkylation of pyrazole. Pyrazole 23 can be regioselectively nitrated to provide nitro-pyrazole 24 by standard conditions familiar to those skilled in the art. Finally, hydrogenation of nitro-pyrazole 24 employing a hydrogenation catalyst, such as palladium or nickel provides pyrazole amine 25, an example of general amine A-NH? 6.
-
Figure imgf000028_0001
21 22 23
Figure imgf000028_0002
24 23
Scheme 8
Additional pyrazoles useful for the synthesis of compounds of formula 1 can be prepared as described in Scheme 9. Thus, keto-ester 26 can be reacted with N,N- dimetliylforrnamide dimethyl acetal to provide 27. Reaction of 27 with either 21 or 28 (wherein P is an acid-labile protecting group) in the presence of acid provides 29 or 3_0. In practice, both 29 and 30 can be obtained from the same reaction and can be separated by standard chromatographic conditions. In turn, esters 29 and 30 can be converted to acids 3_1 and 32 respectively as previously described in Scheme 7.
Figure imgf000028_0003
Scheme 9 In a manner similar to Scheme 9, NH-pyrazole 34 can be prepared by reaction of acrylate 33 with hydrazine (Scheme 10). Alkylation of 34 with R2-X 35 as described above for Scheme 7 provides mixtures of pyrazole esters 3_6 and 32 which are separable by standard chromatographic techniques. Further conversion of esters 36 and 3_7 to acids 38 and 3_£ can be accomplished as described above in Scheme 7.
Figure imgf000029_0001
Scheme 10
General amines 6 containing an isoxazole ring can be prepared as described in Scheme 11. Thus, by analogy to Scheme 6, reaction of keto-nitrile 9 with hydroxylamine can provide the 5-ammoisoxazole 40. Preferred conditions for the formation of 5- aminoisoxazole 40 include the treatment of 9 with hydroxylamine in the presence of aqueous sodium hydroxide, optionally in the presence of an alcoholic co-solvent at a temperature between 0 and 100 °C.
Figure imgf000029_0002
9 40
Scheme 11
Amines 2 useful for the invention can be synthesized according to methods commonly known to those skilled in the art. Amines of general formula 2 contain three rings and can be prepared by the stepwise union of three monocyclic subunits as illustrated in the following non-limiting Schemes. Scheme 12 illustrates one mode of assembly in which an E-containing subunit 41 is combined with the central pyridine ring 42 to provide the bicyclic intermediate 43. In one aspect this general Scheme, the "M" moiety of 41 represents a hydrogen atom of a heteroatom on the X linker that participates in a nucleophilic aromatic substitution reaction with monocycle 42. Such reactions may be facilitated by the presence of bases (for example, potassium tert-butoxide), thus M may also represent a suitable counterion (for example potassium, sodium, lithium, or cesium) within an alkoxide, sulfide or amide moiety. Alternately, the "M" group can represent a metallic species (for example, copper, boron, tin, zirconium, aluminum, magnesium, lithium, silicon, etc.) on a carbon atom of the X moiety that can undergo a transition-metal-mediated coupling with monocycle 42.
The "Y" group of monocyclic species 4J_ is an amine or an amine surrogate, such as an amine masked by a protecting group ("P" in formula 44), a nitro group, or a carboxy acid or ester that can be used to prepare an amine via known rearrangement. Examples of suitable protecting groups "P" include but are not limited to tert- butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz), and acetarnide. In the instances wherein the "Y"-group of intermediate 4_L is not an amine, the products of Scheme 12 will be amine surrogates such as 44 or 45 that can be converted to amine 2 by a deprotection, reduction or rearrangement (for example, Curtius rearrangement) familiar to those skilled in the art.
In these instances, the "LG" of monocycle 42 represents a moiety that can either be directly displaced in a nucleophilic substitution reaction (with or without additional activation) or can participate in a transition-mediated union with fragment 4L The W group of monocycle 42 or bicycle 43 represents a moiety that allows the attachment of the pyrazole. In one aspect, the "W" group represents a halogen atom that will participate in a transition-metal-mediated coupling with a pre-formed heterocyclic reagent (for example a boronic acid or ester, or heteroaryl stannane) to give rise to amine 2. hi another aspect, the "W" group of 42 and 43 represents a functional group that can be converted to a fϊve-membered hetero cycle by an annulation reaction. Non-limiting examples of such processes would include the conversion of a cyano, formyl, carboxy, acetyl, or alkynyl moiety into a fϊve-membered heterocycle moiety. It will be understood by those skilled in the art that such annulations may in fact be reaction sequences and that the reaction arrows in Scheme 12 may represent either a single reaction or a reaction sequence. Additionally, the "W" group of 43 may represent a leaving group (halogen or triflate) that can be displaced by a nucleophilic nitrogen atom of a pyrazole, triazole or imidazole ring.
Figure imgf000031_0001
Scheme 12
Scheme 13 illustrates another general method of preparing amines 2 by first attaching the 5-membered heterocycle to the pyrimidine ring (42). As before, the "LG" of rnonocycle 42 represents a moiety that can either be directly displaced in a nucleophilic substitution reaction (with or without additional activation) or can participate in a transition-mediated union with fragment 4J_. The "W" group of monocycle 42 represents a moiety that allows the attachment of a 5-membered heterocycle. In one aspect, the "W" group represents a halogen atom that will participate in a transition-metal-mediated coupling with a pre-formed heterocyclic reagent (for example, a boronic acid or ester, or heteroaryl stannaiie) to give rise to amine 2. In another aspect, the "W" group of 42 represents a functional group that can be converted to a five-membered heterocycle by an annulation reaction. Additionally, the "W" group of 42 may represent a leaving group (halogen or triflate) that can be displaced by a nucleophilic nitrogen atom of a pyrazole, triazole or imidazole ring. After conversion of 42 to 46, the "LG" moiety can be replaced with an "X" linkage to the E-sub-unit to provide the tricylic amine 2, as described above in Scheme 12. Those skilled in the art will recognize that amines 2 may be accessed directly from the union of 46 and 4\_ or may arise indirectly via the intermediacy of 44 or 45, as described previously.
Figure imgf000032_0001
Scheme 13
A specific example of Scheme 13 is illustrated by the preparation of amine 55 in Scheme 14. Thus, commercially available pyrimidine 47, an example of general intermediate 42, undergoes a palladium-catalyzed coupling with the commercially available pyrazole boronate 4£ to provide the bicycle 49, an example of general intermediate 46. Oxidation of the sulfide moiety of 49 (The "LG" group of general intermediate 46) with m-chloroperbenzoic acid further activates this moiety toward nucleopliilic displacement and gives rise to intermediate 50. Treatment of sulfone 50 with phenol 5J, in the presence of a base provides tricylic amine 52, an example of general amine 2. Preferred bases for the later transformation include potassium carbonate and potassium tert-butoxide in polar aprotic solvents such as dimethylformamide or dimethylacetamide.
Figure imgf000032_0002
Scheme 15
Similarly, Scheme 16 illustrates the preparation amine 56 as a non-limiting example of general Scheme 12. Thus, 2.4-dichloropyrimidine (53) can be reacted with phenol 54 in the presence of a base to provide 5_5, an example of general intermediate 43 (Scheme 12). Further reaction of chloropyrimidine 55 with pyrazole boronate 4£ in the presence of palladium catalyst provides amine 56, an example of general amine 2.
Figure imgf000033_0001
Scheme 16
As an additional example of general Scheme 13, Scheme 17 illustrates the preparation of amine 62, an additional example of general amine 2. In this instance, 4,6- dichloropyrimidine (57), an example of general pyrimidine 42 (Scheme 13) wherein "W" is chloro, is reacted with 1,2,4-triazole 58 to provide 59, an example of general intermediate 46 (Scheme 13) wherein "LG" is chloro. Further reaction of 59 with phenol 60 provides the Boc-protected amine 6J_, corresponding to general intermediate 44 (Scheme 13 wherein "P" is tert-butoxycarbonyl [Boc]). Treatment of 6J_ with an acid, for example trifluoracetic acid, provides amine 61,, an example of general amine 2.
Figure imgf000033_0002
Scheme 17
As indicated in Scheme 18, additional non-limiting examples of general amine 2 can also be prepared from chloropyrimidine 47 by the three step sequence of Scheme 15 (Step 1 : palladium-catalyzed cross-coupling reaction; Step 2: Sulfide oxidation to sulfone; Step 3: Displacement of sulfone with phenol 7JL wherein Rl 6 is an optional substituent as described above and x is 0-2). Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 1. Thus, in a 3-step sequence as indicated in Scheme 18, chloropyrimidine 47, can be combined with tributylstannane 63_ (see; Cheng et al., Biorg. Med. Chem Lett., 2006. 2076), stannane 64 (Aldrich Chemical), boronate 65. (BoroPharm), tributylstannane 66 (see: Sakamoto, et al. Tetrahedron, 1991, 5111), boronate 67 (Frontier Scientific), boronate 68 (see: Blackaby, et al., US 7030128), trimethyl stannane 69 (see: Wentland, et al. J Med. Chem., 1993, 1580) or stannane 70 (see: Nicolaou, et. aL Chem, Med, Chem., 2006, 41) to provide general amines 72-79 respectively.
Figure imgf000034_0001
Scheme 18
As indicated in Scheme 19, additional non-limiting examples of general amine 2 can also be prepared from dicliloropyrimidine 53 by the two-step sequence of Scheme 16 (Step 1 : Displacement of chloride with phenol 71, wherein Rl 6 is an optional substituent as described above and x is 0-2; Step 2: palladium-catalyzed cross-coupling reaction). Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 2. Thus, in the 2- step sequence of Scheme 19, chloropyrimidine 53., can first be combined with phenol TL and the resultant phenoxy chloropyrimidine (not shown) can be reacted with a palladium catalyst and tributylstannane 63 (see: Cheng et al, Biorg. Med. Chem Lett, 2006, 2076), stannane 64 (Aldrich Chemical), boronate 65_ (BoroPharm), tributylstannane 66 (see: Sakamoto, et al. Tetrahedron, 1991, 5111), boronate 67 (Frontier Scientific), boronate 6£ (see: Blackaby, et al., US 7030128), trimethylstannane 69 (see: Wentland, et al. J. Med. Chem., 1993, 1580) or stannane 70 (see: Nicolaou, et. al., Chem. Med. Chem., 2006, 41) to provide general amines 80-87 respectively.
Figure imgf000036_0001
Scheme 19 As indicated in Scheme 20, additional non-limiting examples of general amine 2 can also be prepared from dichloropyrimidine 57 using the two-step sequence of Scheme 16 and Scheme 19 (Step 1 : Displacement of chloride with phenol 71, wherein R16 is an optional substituent as described above and x is 0-2; Step 2: palladium-catalyzed cross- coupling reaction) Suzuki cross-coupling reactions using readily available boronates or Stille cross-coupling reactions using readily available stannanes are interchangeable for Step 2. Thus, in the 2- step sequence of Scheme 20, chloropyrimidine 57, can first be combined with phenol 71. and the resultant phenoxy chloropyrimidine (not shown) can be reacted with a palladium catalyst and tributylstannane 63 (see: Cheng et al., Biorg. Med. Chem Lett, 2006, 2076), stannane 64 (Aldrich Chemical), boronate 65 (BoroPharm), tributylstannane 66 (see: Sakamoto, et al. Tetrahedron, 1991, 5111), boronate 67 (Frontier Scientific), boronate 68 (see: Blackaby, et al., US 7030128), trimethylstannane 69 (see: Wentland, et al. J. Med. Chem,, 1993, 1580) or stannane 70 (see: Nicolaou, et. al., Chem. Med. Chem., 2006, 41) to provide general amines 88-95 respectively. Those skilled in the art will recognize that due to the symmetry of dichloropyrimidine 57. the general amine products of Scheme 20 can also be prepared by reversing the order of the 2-step sequence (Step 1 : Palladium-catalyzed cross-coupling reaction of 57 with 63-70; Step 2: Displacement of chloride with phenol 71).
Figure imgf000038_0001
Scheme 20 Additional synthetic methods for the preparation of compounds of formula 1 are found in the following examples.
Section 3. Examples
General method A: To a stirring solution of the carboxylic acid (0.24 mmol) and TEA (1.2 mmol) in 1,4-dioxane (4.5 niL) at RT was added DPPA (0.29 mmol). After stirring for 0.5 h at RT, the appropriate amine (0.71 mmol) was added and the reaction was stirred with heating at 100 0C for 2h. The reaction was cooled to RT, diluted with brine (15 mL) and extracted with EtOAc (3x30 mL). The combined organic layers were dried (MgSO4) and concentrated. The residue was purified by chromatography to afford the target compound.
Example Al : 4-Fluoro-2-methyl-phenol (25 g, 0.2 mol) was added to a solution of sodium hydroxide (9.7 g, 0.24 mol) in water (160 mL) and the resultant solution was cooled to 0 0C. Methyl chloroformate (24.2 g, 0.26 mol) was added dropwise at 0 0C. At the completion of the reaction, the pH was adjusted to pH 8 with saturated aqueous Na2CO3 and then mixture was extracted with ethyl acetate (3 x 300 mL). The combined organic extracts were washed with water and brine, dried (MgSO4) and were concentrated under reduced pressure to provide carbonic acid 4-fluoro-2-methyl~phenyl ester methyl ester (30 g, 82% yield). 1H NMR (300 MHz, DMSO-rfβ): δ 7.22-7.13 (m, 2 H), 7.05 (m, 1 H), 3.81 (s, 3 H), 2.12 (s, 3 H).
To a solution of carbonic acid 4-fluoro-2-methyl-phenyl ester methyl ester (15 g, 81.5 mmol) in cone, sulfuric acid (100 mL) at 0 0C was added powdered KNO3 (8.3 g, 82.2 mmol) in several portions. The reaction mixture was stirred for 1 hour at 0 °C and was then poured into ice water and extracted with ethyl acetate (3 x 100 mL). The extracts were washed with water and brine, dried (MgSO4), concentrated in vacuo and purified by silica gel chromatography to provide carbonic acid 4-fluoro-2-methyl-5-mtro- phenyl ester methyl ester (2.0 g, 11% yield). 1H NMR (300 MHz, DMSO-rf*): δ 8.14 (d, J= 6.9, 1 H), 7.60 (d, J= 12.0 Hz, 1 H), 3.86 (s, 3 H), 2.25 (s, 3 H). To a solution of aqueous sodium hydroxide (1.2 N, 20 mL, 24 mmol) was added 4- fluoro~2-methyl-5-nitro-phenyl ester methyl ester (2.0 g, 8.7 mmol), then the resultant mixture was refluxed for 2 hours. The reaction was cooled to RT and partitioned between EtOAc and water. The organic layer was washed with water and brine, dried (MgSO4), and concentrated in vacuo to provide 4-fluoro-2-methyl-5-nitro-phenol (1.4 g, 93 % yield). 1H NMR (300 MHz, OMSO-d6) δ 10.33 (s, 1 H), 7.45 (d, J= 6.6, 1 H), 7.32 (d, J= 12.3 Hz, 1 H), 2.19 (s, 3 H).
A mixture of 4-fluoro-2-methyl-5-nitro-phenol (1.4 g, 8.2 mmol) and 10% PdVC (0.3 g, 20%/w) in MeOH (80 mL) was stirred under H2 (30 psi) for 2h. The Pd/C was removed by filtration and the filtrate was concentrated to give 5-amino-4-fluoro-2- methyl-phenol (0.68 g, 62% yield). 1H NMR (300 MHz, DMSO→fc) δ 8.75 (s, 1 H), 6.62 (d, J= 12.0 Hz, 1 H), 6.21 (d, J= 8.1 Hz, 1 H), 4.69 (s, 2 H), 1.93 (s, 3 H).
The mixture of 2-methanesulfonyl-4-(l -methyl- lH-pyrazol-4-yl)-pyrimidine and 2- methanesulfinyl-4-(l-metliyI-lH-pyrazol-4-yl)-pyrimidine from Example AlO (1 g, 4.2 mmol), 5-amino-4-fluoro-2-rnethylphenol (1.2 g, 8.5 mmol) and K2CO3 (1.2 g, 8.6 mmol) were combined in DMF (10 mL) using a procedure analogous to Example AlO to provide 2 -fluoro-4-methyl-5 -(4-(I -methyl- 1 H-pyr azol-4-y l)pyrimidin-2 -yloxy)benzenamine (420 mg). 1H NMR (400 MHz, DMSO-<4): δ 8.42 (d, J= 5.2 Hz, 1 H), 8.39 (s, 1 H), 8.07 (s, 1 H), 7.40 (d, J= 5.2 Hz, 1 H), 6.90 (d, J= 9.6 Hz, 1 H), 6.47 (d, J- 8.4 Hz, 1 H), 5.02 (br s, 2 H), 3.88 (s, 3 H), 1.88 (s, 3 H); MS (ESI) m/z: 300.2 (M+H*).
Example A2: Methyl chloroformate (77.3 g, 0.82 mol) was added dropwise to a -10 0C solution of 2-chloro-4-fluorophenol (10Og, 0.68 mol) and sodium hydroxide (32.8 g, 0.82 mol) in water (550 mL). After complete addition, the precipitated solid was collected by filtration and washed with water to give 2-chloro-4-fluorophenyl methyl carbonate (110 g, 79 % yield). 1H NMR (300 MHz, DMSO-^6): δ 7.62 (dd, J = 8.1, 2.7 Hz, 1 H), 7.50 (dd, J = 9.0, 5.4 Hz, 1 H), 7.30 (td, J = 8.1, 3.0 Hz, 1 H), 3.86 (s, 3 H); MS (ESI) m/z: 205.2 (M+H÷).
To a suspension of 2-chloro-4-fluorophenyl methyl carbonate (110 g, 0.54 mol) in cone. H2SO4 (50 mL) was slowly added a mixture comprised of cone. H2SO4 (40 mL) and fuming HNO3 (40.8 mL, 0.89 mol). The resultant mixture was stirred for 30 min at 0 0C. The reaction mixture was poured into ice water and the precipitated solid was collected by filiation and washed with water to give 2-cliloro-4-fiuoro-5-nitrophenyl methyl carbonate (12O g, 90% yield). 1H NMR (400 MHz, DMSO-J6): δ 8.45 (d, J= 7.2 Hz, 1 H), 8.12 (d, J= 10.8 Hz, 1 H), 3.89 (s, 3 H); MS (ESI) m/z: 250.1 (M^-H+).
2-Chloro-4-fluoro-5-nitrophenyl methyl carbonate (12Og 0.48mol) was combined with a solution of sodium hydroxide (22.7 g, 0.57 mol) in water (300 mL) and the resultant mixture was refluxed for 4h. The insoluble solids were removed by filtration and the filtrate was acidified with dilute HCl. The precipitated solid was collected by filtration and washed with water to give 2-chloro-4-fluoro-5-m'trophenol (90 g, 98% yield). 1H NMR (400 MHz, DMSO-^6): δ 11.18 (s ,1 H), 8.10 (d, J = 10.4 Hz, 1 H), 7.62 (d, J=7.2 Hz5 1 H); MS (ESI) m/z: 192.1 (M+If).
2-Chloro-4-fluoro-5-nitrophenol (85 g, 0.45 mol) and 10% Pd/C (25g, 0.023 mol) were combined in EtOH and hydrogenated (50 psi) for 12h. The reaction mixture was filtered. The filtrate was concentrated in vacuo and purified by silica gel chromatography to provide 3-amino-4-fluorophenol (40 g 70%, yield). 1H NMR (400 MHz, DMS(W6): δ 8.87 (s, 1 H), 6.70 (dd, J- 11.2, 8.8 Hz, 1 H), 6.14 (dd, J= 7.8, 2.4 Hz, 1 H), 5.84 (m, 1 H), 4.92 (s, 2 H); MS (ESI) m/z: 128.2 (M+H+).
4-Chloro-2-methylsulfanyl-pyrimidine (1.4 g, 8.8 mmol), 1 -methyl-4-(4, 4,5,5 - tetramethyl-[L3,2]dioχaborolan-2-yl)-lH-pyrazole (2.0 g, 1.1 eq), Na2CO3 (2.8 g, 3 eq) and Pd(PPli3)4 (500 mg, 0.43 rnmol) were combined in a solvent comprised of toluene/EtOH/H2θ (4/4/1, 20 mL). The reaction mixture was purged with argon and heated to 100 0C overnight. The reaction was filtered to remove insolubles and the filtrate was concentrated in vacuo. The residue was purified by silica gel chromatography to provide 4-(l -methyl- lH-pyrazol-4-yl)-2-(methyltliio)pyrimidine contaminated with triphenylphoshine oxide (2.0 g, >100% yield). 1H NMR (300 MHz, DMSCWtf): δ 8.49 (d, J= 5.1 Hz, 1 H), 8.46 (s, 1 H), 8.12 (s, 1 H), 7.38 (d, J = 5.1 Hz, 1 H), 3.89 (s, 3 H), 2.52 (s, 3 H).
A solution of 4-(l-memyl-lH-pyrazol-4-yl)-2-metliylsulfanyl-pyrimidine (2.O g crude, 8.8 mmol) in dichloromethane (20 mL) was treated with m-CPBA (3.0 g, 17.4 mmol) portionwise at RT. The reaction was stirred 2h and was quenched with saturated aqueous NaS2SO3 (3 mL). The mixture was partitioned with saturated aq Na2CO3 and the organics were washed with brine, dried (Na2SO4), and concentrated to provide a mixture (2.0 g) of 2-methanesulfonyl-4-(l-methyl-lH-pyrazol-4-yl)-ρyrimidine and 2- methanesulfmyI-4-(l -methyl- lH-pyrazol-4-yl)-pyrimidine with a molar ratio of 1 :0.3. 1H NMR (400 MHz5 DMSO-^): δ 8.83 (d, J= 5.2 Hz, 1 H), 8.82 (d, J - 5.2 Hz, 0.24 H), 8.57 (s, 1 H), 8.57 (s, 0.24 H), 8.21 (s, 1 H), 8.21 (s, 0.23 H), 7.80 (d, J= 5.6 Hz, 1 H), 7.80 (d, J= 5.6 Hz, 0.25 H), 3.48 (s, 3 H), 2.88 (s. 0.7 H).
The above mixture of 2-methanesulfonyl-4-(l -methyl- lH-pyrazol-4-yl)- pyrimidine and 2-methanesulfinyI-4~(l -methyl- lH-pyrazol-4-yl)-pyrimidine (1 g, 4.2 mmol), 4-amino -3 -fluoro -phenol (1.1 g, 8.6 mmol) and K2CO3 (1.2 g, 8.6 mmol) in DMF (10 niL) was heated at 100 0C for 12h. The reaction was partitioned between H2O and EtOAc (3 x 50 niL). The combined organics were dried (Na2SO4), concentrated in vacuo and chromatographed to 2-fluoro-5 -(4-(I -methyl- 1 H-pyrazol-4-y l)pyrimidin-2- yloxy)benzenamine (402 mg). 1H NMR (400 MHz, OMSO-d6): δ 8.44 (d, J= 5.2 Hz, 1 H), 8.39 (s, 1 H)5 8.07 (s, 1 H), 7.41 (d, J= 5.2 Hz5 1 H)5 6.98 (t, J= 9.6 Hz, 1 H)5 6.53 (dd, J = 5.6, 2.0 Hz, 1 H), 6.28 (d, J= 8.4 Hz, 1 H)5 5.25 (br s, 2 H), 3.88 (s, 3 H). MS (ESI) m/z: 286.2 (M+H+).
Example Bl: t-Butylhydrazine and 1,1,3,3-tetrametlioxypropane were combined according to literature procedures to yield l-t-butyl-lH-pyrazoI-4-amine. See Ger. Offen., DE3332270, 21 March 1985.
Example 1: To a biphasic solution of Example Al (0.071 g, 0.23 mmol) in EtOAc (5 ml) and NaHCO3 (10 ml) was added prop-l-en-2-yl carbonochloridate (0.043 g, 0.35 mmol) and the mixture was stirred for 2h at RT. The layers were separated and the aqueous layer was extracted with EtOAc (1x5 mL). The combined organics were washed with brine, dried (Na2SO4) and concentrated in vacuo to afford prop-l-en-2-yl 2-fiuoro~4-methyl-5- (4-(l-metliyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenylcarbamate as an off-white solid. MS (ESI) m/z: 384.2 (M+tT).
A solution of prop-l-en-2-yl 2-fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazol-4- yl)pyrimidm-2-yloxy)phenylcarbamate, Example Bl (0.033 g, 0.237 mmol) and DBU (catalytic) was dissolved in THF (2 ml) and stirred at 55 0C for 6h. Solvents were removed and the crude residue was purified by column chromatography (methanol /CH2Cl2) to afford l-(l-tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-4-metliyl-5-(4-tl-methyl- lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea as a white solid, (0.089 mg, 81% yield). 1H NMR (400 MHz, DMSO-^6): δ 8.66 (s, IH), 8.50 (d, J- 1.6 Hz5 IH), 8.44 (d, J = 5.2 Hz, IH), 8.42 (s, IH), 8.09 (s, IH), 7.91 (d, J= 7.2 Hz, IH), 7.77 (s, IH), 7.44 (d, J = 5.2 Hz, IH), 7.36 (s, IH), 7.18 (d, J- 12.0 Hz, IH), 3.87 (s, 3H), 2.01 (s, 3H), 1.46 (s, 9H); MS (ESI) m/z: 465.3 (M+H÷).
Example 2: To a biphasic solution of Example Al (0.075 g, 0.26 mmol) in EtOAc (5 ml) and NaHCθ3 (10 ml) was added prop-l-en-2-yl carbonochloridate (0.048 g, 0.35 mmol) and the mixture was stirred for 2h at RT. The layers were separated and the aqueous layer was extracted with EtOAc (1x5 mL). The combined organics were washed with brine, dried (Na2SO4) and concentrated in vacuo to afford prop~l-en-2-yl 2-fluoro-5-(4-(l- meώyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenylcarbamate as an off-white solid. MS (ESI) m/z: 370.2 (M+H*).
A solution of prop-l-en-2-yl 2-fluoro-5-(4-(l -methyl- lH-pyrazol-4-yl)pyrirnidm- 2-yloxy)phenylcarbamate, Example Bl (0.037 g, 0.26 mmol), DBU (catalytic) in THF (2 ml) was stirred at 55 0C for 6h. Solvents were removed and the crude residue was purified by column chromatography (methanol/ CH2Cl2) to afford l-(l-tert-butyl-lH- pyrazoI-4-yl)-3-(2-fluoro-5-(4-(l-methyl-lH"pyrazol-4-yl)pyrimidin-2~yloxy)phenyl)urea as a white solid. (0.089 mg, 75% yield). 1H NMR (400 MHz, DMSO-Cf6): δ 8.73 (s, IH), 8.61 (d, J= 2.4 Hz, IH), 8.46 (d, J= 5.2 Hz, IH), 8.42 (s, IH), 8.10 (s, IH), 8.04 (dd, J= 12 Hz, 2.8 Hz, IH), 7.79 (s, IH), 7.45 (d, J = 5.2 Hz, IH), 7.38 (s, IH), 7.26 (dd, J = 10.8 Hz, 8.8 Hz, IH), 6.81-6.78 (m, IH), 3.87 (s, 3H), 1.46 (s, 9H); MS (ESI) m/z: 451.2 (M+H+).
Example 3: Using General Method A, 3 -tert-butyl-1 -methyl- lH-pyrazole-5-carboxylic acid (0.074 g, 0.4 mmol), Example Al (0.081 g, 0.27 mmol), triethylamine (0.082 g, 0.8 mmol) and DPPA (0.15 g, 0.54 mmol) were combined and purified via chromatography (EtOAc/hexanes) to afford l-(3-tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-4- methyl-5-(4-(l -methyl- lH-pyrazoI-4~yl)pyrimidin-2-yloxy)phenyl)urea as white solid (0.07 g, 54% yield). 1H NMR (400 MHz, OMSO-d6): δ 8.88 (s, IH), 8.82 (d, J= 2.4 Hz, IH), 8.44 (d, J= 4.8 Hz, IH), 8.42 (s, IH), 8.08 (s, IH)5 7.89 (d. J= 7.6 Hz5 IH), 7.44 (d, J- 5.2 Hz, IH), 7.22 (d, J = 11.6 Hz, IH)5 6.02 (s, IH), 3.87 (s, 3H), 3.57 (s, 3H), 2.02 (s, 3H), 1.15 (s, 9H); MS (ESI) m/z: 479.3 (M+H4).
Example 4: Using General Method A, S-tert-butyl-l-methyl-lH-pyrazole-S-carboxylic acid (0.072 g, 0.39 mmol), Example A2 (0.075 g, 0.26 mmol), triethylamine (0.08 g, 0.79 mmol) and DPPA (0.14 g, 0.52 mmol) were combined and purified via chromatography (EtOAc/hexanes) to afford l-(3-tert-butyI-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-5-(4- (1 -methyl -lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea as white solid (0.062 g, 51% yield). 1H NMR (400 MHz, DMSCW6): δ 8.95 (s, IH), 8.93 (d, J = 2.0 Hz, IH), 8.46 (d, J= 5.2 Hz, IH)5 8.42 (s, IH)5 8.08 (s, IH), 8.02 (dd, J- 6.8 Hz, 2.8 Hz, IH), 7.45 (d, J = 5.2 Hz, IH), 7.30 (dd, J- 11.2 Hz, 9.2 Hz, IH), 6.87-6.83 (m, IH)5 6.04 (s, IH), 3.87 (s, 3H), 3.58 (s, 31I)5 1.16 (s, 9H); MS (ESI) m/z: 465.3 (M+H÷).
Using the synthetic procedures and methods described herein and methods known to those skilled in the art, the following compounds are made:
1 -(3-tert-butyl- 1 -methyl- 1 H-ρyrazol-5-yl)-3-(2-fluoro-4-methyl-5-(4-(l -methyl-lH- pyrazol-4-yl)pyrimidin-2 -yloxy)pheny l)urea, 1 -(3 -tert-butyl - 1 -methyl - 1 H-pyrazol-5-yl)- 3-(2-fluoro-5-(4-(l -methyl-1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert- butyl-5-methyl-lH-ρyrazol-3-yl)-3-(2-fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazoI-4- yi)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl-5-metliyl-l H-pyrazoI-3-yI)-3-(2- fluoro-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)pheny])urea, l-(l-tert-butyl- 5 -methyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-4-methyl-5 -(4-(I -methyl- 1 H-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea5 l-(l-tert-butyl-5-methyl-lH-pyrazol-4-yl)-3-(2- fluoro-5 -(4-( 1 -methyl - 1 H-pyrazol-4-yl)pyrimidin-2~yloxy)pheny l)urea, 1 -(3 -tert- butylisoxazoI-5-yl)-3-(2-fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, 1- (3 -tert-butyl isoxazol-5-yI)-3-(2-fluoro-5 -(4-(I -methyl- lH-pyrazol- 4-yl)pyrimidin-2-yloxy)phenyl)urea, l-(3-tert-butyl-4-methylisoxazol-5-yl)-3-(2-fluoro- 4-methyl-5-(4-(l -methyI-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3-tert- butyl-4-methylisoxazoI-5-yl)-3-(2-fluoro-5-(4-(l -methyl- 1 H-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, 1 -cyclohexyl-3 -(2-fluoro-4-methyl-5 -(4-( 1 -metliyl- 1 H-pyrazol-4- yl)pyrirnidin-2-yloxy)phenyl)urea, 1 -cyclohexyl-3-(2-fluoro-5-(4-( 1 -methyl- 1 H- pyrazol-4-yl)pyrirnidin-2-yIoxy)phenyl)urea, 1 -(5-tert-butyl-L3,4-thiadiazol-2-yl)-3-(2- fluoro-4-methyl-5-(4-(l -methyl- lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(5- tert-buty 1- 1 ,3 ,4-thiadiazol-2 -yl) -3-(2 -fiuoro-5 -(4-(I -methyl- 1 H-pyrazol-4-yl)pyrimidin- 2-yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-imidazol-4-yl)-3 -(2-fluoro-4-methyl-5 -(4-( 1 - methyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-imidazol-4- y l)-3 -(2-fluoro- 5 - (4-( 1 -methyl- 1 H-pyrazo l-4-yl)pyrimidin-2-y loxy)phenyl)urea, 1 -( 1 - tert-butylpyrrolidin-3 -yl) -3 ~(2-fluoro-4-methyl-5 -(4-(I -methyl- 1 H-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert-butylpyrrolidm-3-yl)-3-(2-fluoro-5-(4-(l - methyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3-tert-butyl- 1 -metliyl- 1 H- pyrazol-5 -yl)-3 -(4-chloro-2-fluoro-5 ~(4-( 1 -methyl- 1 H-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, l-(3-tert-butyI-l-methyl-lH-pyrazol-5-yl)-3-(2,4-difluoro-5-(4-(l- methyl- 1 H-pyrazol-4~yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(5-(4-( 1 H-pyrazol-4- yl)pyrimidin-2-y 1 oxy)-2-fluoro-4-methy lpheny l)-3 -(I -tert-buty 1-5 -methyl- 1 H-pyrazol-4- yl)urea, 1 -(5-(4-(I H-pyrazol-4-yl)pyrimidin-2-yloxy)-2-fluorophenyl)~3-(l -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(3-tert-butylisoxazol-5-yl)-3-(2-fluoro-4-methyl-5-(4-(l - methyl- lH-pyrazoi-4-yl)pyrimidin-2-yloxy)phenyl)urea, l-(5-(4-(lH-pyrazol-4- yl)pyrimidin-2-yloxy)-2,4-difIuorophenyl)-3-(3-tert-butylisoxazol-5-yl)urea, l-(3-tert- butyI-4-methylisoxazol-5-yl)-3-(2-fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, l-(5-(4-(lH-pyrazol-4-yI)pyrimidin-2-yloxy)-4- cliloro-2-fluorophenyl)-3-(3-tert-butylisoxazol-5-yl)urea, 1 -(I -tert-buty 1-1 H-pyrazol-4- yl)-3-(2,4-difluoro-5-(4-(l-methyl-lH-pyrazol~4-yl)pyrimidin-2-yloxy)phenyl)urea, 1- (5-(4-(lH-pyrazoI-4-yl)pyrimidin-2-yloxy)-4-chloro-2-fIuorophenyl)-3-(l-tert-butyl-lH- pyrazol-4-yI)urea, 1 -(3-tert-butyl- 1-methyl-l H-pyrazol-5-yI)-3-(2,4-difluoro-5-(4-
(oxazol-5-yl)pyrimidin-2-yloxy)phenyl)urea, l-(l-tert-butyl-lH-pyrazol-4-yl)-3-(2- fluoro-5-(4-(oxazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H- pyrazol-5 -yl)-3 -(2-fluoro-4-methyl-5 -(4-(oxazol-5 -yl)pyrimidin-2 -yloxy )pheny l)urea, 1 - ( 1 -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-5 -(4-(oxazol-2-yl)pyrimidin-2- yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-5 ~(4-(oxazol-5 - yl)pyrimi din-2 -y loxy)pheny l)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol- 5-yl)-3 -(2 - fluoro-4-methy 1-5 -(4-(I -methyl- 1 H-pyrazol-4-yl)pyrimidin-2 -yloxy)phenyl)urea, 1 - (3-tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, l-(l-tert-butyl-5-methyl-lH-pyrazol-3-yl)-3-(2- fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1- (l-tert-butyl-5-methyI-lH-pyrazol-3-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol~4~ yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl~5~methyl-l H-pyrazol-4-yl)-3-(2- fluoro-4-metliyl- 5 - (4-( 1 -methyl - 1 H-pyrazol-4-yI)pyrimidin-2-yloxy)pheny l)urea, 1 - (1 -tert-butyl-5-methyl-l H-pyrazol-4-yl)-3-(2-fluoro-5-(4-(l -metliyl- 1 H-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, l-(3-tert-butylisoxazol-5-yl)-3-(2-fluoro-4-methyl~ 5-(4-(l-methyl-lH~pyrazol-4-yl)pyrimidin-2~yloxy)phenyl)urea, 1 -(3-tert- butylisoxazol-5-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, 1 -(3-tert-butyl-4-methylisoxazol-5-yl)-3-(2-fluoro-4-methyl-5 -(4- ( 1 -metliyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3-tert-butyl-4- methyIisoxazol-5-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, 1 -eye lohexyl-3 - (2-fluoro -4-me tliyl-5 -(4-(I -methyl- 1 H-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, 1 -cyclohexyl-3 -(2-fluoro-5 ~(4-( 1 -methyl- 1 H- pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(5-tert-butyl- 1 ,3,4-thiadiazol-2-yl)-3- (2-fluoro-4-metliyl-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, l-(5-tert-butyl-l,3,4-thiadiazol-2-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl-l H-imidazol-4-yl)-3-(2-fluoro-4- methyl- 5 - (4-( 1 -methyl- 1 H-pyrazo l-4~yl)pyrimi din-2 -yloxy)phenyl)urea, 1 -( 1 -tert- butyl-lH-imidazol-4-yl)-3-(2-fluoro-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2- yl oxy)phenyl)urea, 1 -( 1 -tert-butylpyrrolidin-3 -yl)-3 -(2-fluoro-4-methyl-5-(4-( 1 - methyl- 1 H-pyrazol-4-yl)pyrimIdin-2-yIoxy)phenyl)urea, 1 -( 1 -tert-butylpyrrolidm-3 - yl)-3 -(2-fluoro-5 -(4-( 1 -methyl- 1 H-pyrazol-4-yl)pyriniidin-2~yloxy)phenyl)urea, 1 -(3 - tert-butyl-l-metliyl-lH-pyrazol-5-yl)-3-(4-chloro-2-fluoro-5-(4-(l-metliyl-lH-pyrazol- 4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5-yl)-3 -
(2,4-difluoro-5-(4-( 1 -methyl- 1 H-pyrazol-4-yl)pyτimidm-2-yloxy)phenyl)urea, 1 -(5- (4-( 1 H-pyrazol-4-yl)pyrimidin-2 -y loxy)-2 -fluoro-4-methy lphenyl)-3 -(I -tert-buty 1-5 - methyl- lH-pyrazol-4-yl)urea, l-(5-(4-(lH-pyrazol-4-yl)pyrimidin-2-yloxy)-2- fluorophenyl)-3 -(I -tert-butyl- lH-pyrazol-4-yl)urea, l-(3-tert-butylisoxazol-5-yl)-3- (2-fluoro-4-methyl-5-(4-(l-methyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, l-(5-(4-(lH-pyrazoI-4-yl)pyrimϊdin-2-yloxy)-2,4-difluorophenyl)-3-(3-tert- butylisoxazoI-5-yl)urea, l-(3-tert-butyl-4-methylisoxazol-5-yl)-3-(2-fluoro-4-methyl- 5-(4-( 1 -metliyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(5-(4-( 1 H-pyrazol- 4-yI)pyrimidin-2-yloxy)-4-chloro-2-fluorophenyl)-3-(3-tert-butylisoxazol-5-yl)urea, 1- (l"tert-butyl-lH-pyrazol-4-yl)-3-(2,4-difluoro-5-(4-(l-methyl-lH-pyrazol-4- yl)pyrimidin-2-yloxy)pheny l)urea, l-(5-(4-(l H-pyrazol-4-yl)pyrimidin-2-yloxy)-4- chloro-2-fluorophenyl)-3-(l-tert-butyl-lH-pyrazol-4-yl)urea, 1 -(3 -tert-butyl- l- methyI-lH-pyrazol-5-yl)-3-(2,4-difluoro-5-(4-(oxazol-5-yl)pyrimidin-2~ yloxy)phenyl)urea. l-(l-tert-butyl-lH-pyrazol-4-yI)-3-(2-fluoro-5-(4-(oxazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazoI-5-yl)~3-(2- fluoro-4-methyl-5-(4-(oxazol-5-yl)pyrirnidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl- IH- pyrazol-4-yl)-3-(2-fluoro-5~(4-(oxazol~2-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -( 1 -tert- butyI-lH-pyrazol-4-yl)-3-(2-fluoro-5-(4-(oxazol-5-yl)pyrimidin-2-yloxy)plienyl)urea, l-(3-tert-butyl-l-metliyl-lH-pyrazol-5-yl)-3-(2-fluoro-5-(4-(3-methyIisoxazol-5- yl)pyrimidin-2 -yloxy )phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)-3 -(2 - fluoro-5-(4-(isoxazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, l-(3-tert-butylisoxazol-5-yl)- 3-(2-fluoro-5-(4-(l -methyl- lH-imidazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(5-(4- (IH-1.2,4-triazol- 1 -yl)pyrimidin-2-yloxy)-2-fluorophenyl)-3-(3-tert-butyl- 1 -metliyl- 1 H- pyrazol-5-yI)urea, l-(3-tert-butylisoxazol-5-yl)-3-(2-fluoro-4-(4-(isothiazol-4- yl)pyrimidin-2-yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2- fluoro-5-(4-(3-metliylisothiazol-5-yl)pyrimidin-2-yloxy)phenyl)urea, 1-(5-(4-(4H- l,2.4-triazol-3 "yl)pyrimidin-2-yloxy)-2-fluorophenyl)-3 -(I -tert-butyl - 1 H-pyrazol-4- yl)urea, l-(5-(4-(lH-l,2,3-triazol-l-yl)pyrimidin-2-yloxy)-2-fluorophenyl)-3-(l-tert- butyl-lH-pyrazol-4-yl)urea, l-(5-(4-(l,3,4-thiadiazol-2-yl)pyrimidin-2-yloxy)-2- fluorophenyl)-3 -(I -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(3-tert-butyl- 1 -methyl- IH- pyrazol-5-yl)-3-(2-fluoro-5-(2-(l-methyl-lH-pyrazol-4-yl)pyrimidin-4- yloxy)phenyl)urea, l-(5-(2-(lH-pyrazol-4-yl)pyrimidin-4-yloxy)-2-fluorophenyl)-3- (3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)urea, l-(5-(2-(l H-pyrazol-3 -y l)pyriniidin-4- yloxy)-2-fluorophenyl)-3-(3-tert-butyl-l-methyl-lH-pyrazol-5-yl)urea, l-(3-tert-butyl- 1 -metliyl- 1 H-pyrazol-5-yl)-3 -(2-fluoro-5-(2-(oxazol-4-yl)pyrimidIn-4- yloxy)phenyl)urea, 1 -(3-tert-butyl-l -methyl~lH-pyrazol-5-yI)-3-(2-fiuoro-5-(2-
(oxazol-2-yl)pyrimidIn-4-yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-lH-pyrazol-5- y I )-3 -(2-fluoro-5 -(2 -(oxazo 1-5 -yI)pyrimidin-4-yloxy)pheny l)urea, 1 -( 1 -tert-butyl- 1 H- pyrazol-4-yl)-3-(2-fluoro-5-(2-(3-methylisoxazol-5-yl)pyrimidin-4-yloxy)phenyl)urea, l-(l-tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-5-(2-(isoxazol-4-yI)pyrimidin-4- yloxy)phenyl)urea, l-(l-tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-5-(2-(isothiazol-4- yl)pyrimidin-4-yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-5 -(2- (3 -methylisothiazol-5 -yl)pyrimidin-4-y loxy)pheny l)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol - 4-yl)-3-(2-fluoro-5-(2-(l -methyl-1 H-imidazol-4-yl)pyrimidm-4-yloxy)phenyl)urea, 1 - (5 -(2-(I H- 1 ,2,4-triazol- 1 -yI)pyrimidin-4-yloxy)-2-fluorophenyl)-3-( 1 -tert-butyl- 1 H- pyrazol-4-yl)urea, 1 -(5-(2-(4H- 1 ,2,4-triazol-3-yl)pyrimidin-4-yIoxy)-2-fiuorophenyl)- 3-( 1 -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(5-(2-( 1 H- 1 ,2,3 -triazol- 1 -yl)pyrimidin-4- yloxy)-2-fluorophenyl)-3 -( 1 -tert-butyl- 1 H-pyrazoI-4-yl)urea, 1 -(5-(2-( 1 ,3 ,4- thiadiazoI-2-yI)pyrimidiii-4-yioxy)-2-fluorophenyl)-3-( 1 -tert-butyl- 1 H-pyrazol-4- yl)urea, 1 -(3 -tert-butylisoxazol-5-yl)-3 -(2-fluoro-4-(2-( 1 -methyl- 1 H- 1 ,2,3-triazol-4- yl )pyrimidin-4-y loxy)phenyl)urea, 1 - (3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)-3 -(2 - fluoro-4-(2-( 1 -methyl- 1 H-pyrazol-4-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(4-(2-( 1 H- pyrazol-4-yl)pyrimidin-4-y I oxy)-2-fluorophenyl)-3 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol- 5-yl)urea, 1 -(4-(2-(I H-pyrazol-3-yl)pyrimidin-4-yloxy)-2-fluorophenyl)-3-(3-tert- butyI-l-methyl-lH-pyrazol-5-yl)urea, 1 -(3-tert-butyl-l -methyl-1 H-pyrazol-5-yl)-3-(2- fluoro-4-(2-(oxazol-4-yl)pyrimidin-4-yloxy)phenyI)urea, 1 -(3 -tert-butyl- 1 -methyl- lH-pyrazol-5-yl)-3-(2-fluoro-4-(2-(oxazol-2-yl)pyrimidin-4-yloxy)phenyl)urea, l-(3- tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-4-(2-(oxazol-5-yI)pyrimidin-4- yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-l H-pyrazol -5-yl)-3-(2-fluoro-4-(2-(3- methylisoxazoI-5-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(3-tert-butyl- 1 -methyl- 1 H- pyrazol-5-yl)-3-(2-fluoro-4-(2-(isoxazol-4-yI)pyrimidin-4-yloxy)phenyl)urea, l-(3- tert-butyl- 1 -methyl- 1 H-pyrazo 1-5 -y I )-3 -(2 -fluoro-4-(2-(isothi azol-4-yl)pyrimidin-4- yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-4-(2-(3 - methylisothiazol-5-yl)pyrimidIn-4-yloxy)phenyl)urea, 1 -(3 -tert-butylisoxazol-5-yl)-3 - (2-£hioro-4-(2-( 1 -methyl- 1 H-imidazol-4-yl)pyrimidin-4-yIoxy)phenyl)urea, 1 -(4-(2- ( 1 H- 1 ,2 ,4-triazol- 1 -yl)pyrimidin-4-y loxy)-2 -fluorophenyl) -3-(3 -tert-butyl- 1 -methyl- 1 H- pyrazol-5 -y l)urea, 1 -(4-(2 - (4H- 1 ,2 ,4-triazol-3 -yl)pyrimidin-4-y loxy )-2- fiuorophenyl)-3 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(4-(2-( 1 H- 1.2,3-triazoI- 1 - yl)pyrimidin-4-yloxy) -2-fluorophenyl)-3 -(I -tert-butyl - 1 H-pyrazol-4-y l)urea, 1 -(4-(2- (l,354-thiadiazol-2-yl)pyrimidm-4-yloxy)-2-fluorophenyl)-3-(l-tert-butyl-lH-pyrazol-4- yl)urea, 1 -(5 -(6-( 1 H-pyrazol-4-yl)pyrimidin-4-yloxy)-2 -fluorophenyl)-3-( 1 -tert- butyl- lH-pyrazol-4-yl)urea, 1 -(3 -tert-butyl- 1 -methyl- lH-pyrazol-5-yl)-3-(2-fluoro-5- (6-( 1 -methyl- 1 H-pyrazol-4-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(5-(6-( 1 H-pyrazol- 3 -yl)pyrimidin-4-yloxy)-2-fluorophenyl)-3 -(3-tert-butyl- 1 -methyl- 1 H-pyrazol-5-yl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5-yl)-3-(2-fluoro-5-(6-( 1 -metliyl-1 H-pyrazol-4- yl)pyrimidin-4-yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-lH-pyrazoI-5-yl)-3-(2- fluoro-5-(6-(oxazol-4-yI)pyrimidin-4-yloxy)phenyl)urea; 1 -(3-tert-butyl- 1 -methyl- IH- pyrazol-5-yl)-3-(2-fiuoro-5-(6-(oxazoI-2-yI)pyrimidin-4-yloxy)phenyl)urea, l-(3- tert-butyl-l-methyl-lH-pyrazol-5-yl)-3-(2-fluoro-5-(6-(oxazol-5-yl)pyrimidin-4- yloxy)phenyl)urea, l-(l-tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-5-(6-(3- methylisoxazol-5-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(I -tert-butyl- lH-pyrazol-
4-yl)-3-(2-fluoro-5-(6-(isoxazol-4-yl)pyrimidin-4-yloxy)ρhenyl)urea, 1 -( 1 - tert-butyl- 1 H-pyrazol-4-yl)-3 -(2 -fluoro-5 -(6-(isothiazol -4-y l)pyrimidin-4- y 1 oxy)phenyl)urea, 1 -(3 -tert-butylisoxazol- 5-yl)-3-(2-fluoro-5-(6-(3 -methy Ii sothiazol- 5 -yl)pyrimidin-4-yloxy)pheny l)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -y I)-
3-(2-fluoro-5-(6-(l -methyl- lH-imidazol-4-yl)pyrimidin-4-yloxy)phenyl)urea. 1 -(5- (6-( 1 H- 1 ,2,4-triazol- 1 -yl)pyrimidin-4-yloxy)-2-fiuorophenyl)-3 -( 1 -tert-butyl- 1 H- pyrazol-4-yl)urea, 1 -(5-(6-(4H-1 ,2}4-triazol-3-yl)pyrimidin-4-yloxy)-2- fluorophenyl)-3-( 1 -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(5-(6-( IH-1 ,2,3-triazol- 1 - yl)pyrimidin-4-yloxy)~2-fluorophenyl)-3-(3-tert-butyl-l-methyl-lH-pyrazol-5-yl)urea, 1 -(5 -(6-( 1 ,3 ,4-thiadiazol-2-yl)pyrimidin-4-yIoxy)-2-fluorophenyI)-3 -(3 -tert- butylisoxazol-5-yI)urea, l-(3-tert-butyl-l-methyl-lH-pyrazol-5-yI)-3-(2-fluoro-5-(6- ( 1 -methyl- 1 H- 1 ,2,3 -triazol-4-yl)pyrimi din-4-yloxy)phenyl)urea, 1 -(4-(6-(I H-pyrazol- 4-yl)pyrimidin-4-yloxy)-2-fiuorophenyl) -3-(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)urea,
1.( i -tert-butyl- 1 H-ρyrazol-4-yl)-3 -(2-fluoro-4-(6-( 1 -methyl- 1 H-pyrazol-4- yl)pyrimidin-4-yloxy)phenyl)urea, l-(4-(6-(lH-pyrazol-3-yl)pyrimidin-4-yloxy)-2- fiuorophenyl)-3-(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5-yl)urea, 1 -( 1 -tert-butyl- 1 H- pyrazol-4-yl)-3-(2-fluoro-4-(6-( 1 -methyl- 1 H-pyrazoI-4-yl)pyrimidin-4- yloxy )phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)-3 -(2 -fϊ uoro-4- (6- (oxazol-4-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazol-
5-yl)-3-(2-fluoro-4-(6-(oxazol-2-yl)pyrimidin-4-yloxy)phenyl)urea, l-(3- tert-butyl- 1 -memyl-1 H-pyrazol-5~yl)-3-(2-fluoro-4-(6-(oxazol-5-yl)pyrimidin-4- yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-lH-pyrazoI-5-yl)-3-(2-fluoro-4-(6-(3- methylisoxazol-5-yl)pyrimidin-4-yloxy)phenyl)urea, l-(3-tert-butyl-l-methyl-lH- pyra2ol-5-yl)-3-(2-fluoro-4-(6-(isoxazol-4-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -(I - tert-butyl-lH-pyrazol-4-yl)-3-(2-fluoro-4-(6-(isothiazol-4-yl)pyrimidIn-4- yloxy)phenyl)urea, 1 -(I -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2 -fluoro-4-(6-(3- methyIisothiazol-5-yl)pyrirnidin-4-yloxy)phenyl)urea, 1 -(I -tert-butyl- lH-pyrazoI-4-y I)- 3 -(2-fluoro-4-(6-( 1 -methyl- 1 H~imidazol-4-yl)pyrimidin-4-yloxy)phenyl)urea, 1 -( 1 -tert- butyl-lH-ρyrazoi-4-yl)-3-(2-fluoro-4-(6-(l-methyI-lH-l,2,3-tria2θl-4-yl)pyrimidin-4- yloxy)phenyl)urea, 1 -(4-(6-(1H-1 ,2,4-triazol-l -yl)pyrimidin-4-yloxy)-2- fluorophenyl)-3 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)urea, 1 -(4-(6-(4H- 1 ,2,4-triazol-3 - yl )pyrimidin-4-yloxy)-2-fluoropheny l)-3 -( 1 -tert-butyl- 1 H-pyr azol-4-yl)urea, 1 -(4-(6- ( 1 H-1 ,2,3 -triazol-1 -yl)pyrimidin-4-yloxy)-2-fluorophenyl)-3-(l -tert-butyl- lH-pyrazol-4- yl)urea, 1 -(4-(6-( 1 ,3 ,4-thiadiazol-2-yl)pyrimidin-4-yloxy)-2-fluorophenyl)-3 -( 1 - tert-butyl- lH-pyrazol-4-yl)urea, l-(5-(4-(lH-pyrazol-4-yI)pyrimidin-2-yloxy)-2- fluoropheny l)-3 -(3 -tert-butylisoxazol-5-yI )urea, 1 -(5 -(4- ( 1 H-pyrazol-4-y l)pyrimidiπ- 2-yloxy)-2-fluorophenyI)-3-( 1 -tert-butyl- 1 H-pyrazol-3-yl)urea, 1 -(5-(4-( 1 H-pyrazol- 4-yl)pyrimidin-2-yloxy)-2-fluorophenyI)-3-(5-tert-butyltliiophen-3-yl)urea. l-(5-(4- ( 1 H-pyrazol-4-yl)pyrimidm-2 -yloxy)-2 -fluorophenyI)-3 -( 1 -tert-butyl -lH-imidazol-4- yl)urea. l-(5-(4-(lH-pyrazol-4-yl)pyrimidin-2-yloxy)-2-fluorophenyl)-3-(3-tert-butyl- 1 -methyl- 1 H-pyrazol-5 -yl)urea, 1 -(I -tert-butyl- 1 H-pyrazol-4-yl)-3-(2-fluoro-5-(4-(l - methyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol-3- y l)-3 - (2-fluoro-5 -(4-(I -methyl - 1 H-pyrazol-4-yl)pyrimidin-2 -yloxy)phenyl)urea, 1 -(5 - tert-buty 1 thi ophen-3 -yl)- 3 -(2-fluoro-5 -(4-(I -methyl - 1 H-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, 1 -(5-(4-(I H-pyrazoI-4-yl)pyrimidin-2-yloxy)-2-fluoro-4- methylphenyI)-3 -(3 -tert-butyl- 1 -methyl- 1 H-pyrazoI-5-yI)urea, 1 -(5-(4-( 1 H-pyrazol-4- yl)pyrimidin-2-yloxy)-2-fluoro-4-methylphenyI)-3-(3-tert-butyIisoxazol-5-yI)urea, H- pyrazoI-4-yI)urea, l-(5-(4-(lH-pyrazol-4-yl)pyrimidin-2-yloxy)-2-fluoro-4- methylpheπyl)-3-( 1 -tert-butyl- 1 H-pyrazol-3-yl)urea, 1 -(5-(4-(I H-pyrazol-4- yl)pyrimidin-2-yloxy)-2-fluoro-4-methylphenyl)-3-(5-tert-butyMiiophen-3-yl)urea, 1- (5-(4-( 1 H-pyrazoI-4~yl)pyrimidin-2-yloxy)-2-fluoro-4-metliylphenyl)-3 -( 1 -tert-butyl- 1 H-imidazol-4-yl)urea, 1 -( 1 -tert-butyl- 1 H-pyrazol-4-yl)-3 -(2-fluoro-4-methy 1-5 -(4-( 1 - methyl-lH-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea, 1 -(I -tert-butyl- lH-pyrazol-3- yl)-3-(2-fluoro-4-methyl-5-(4-(l-methyI-lH-pyrazol-4-yl)pyrimidin-2- yloxy)phenyl)urea, and 1 -(5-tert-butylthiophen-3-yI)-3-(2-fiuoro-4-methyI-5-(4-(l - methyl- 1 H-pyrazol-4-yl)pyrimidin-2-yloxy)phenyl)urea.
Section 4. Biological Data AbI kinase (SEQ ID NO:1) assay
Activity of AbI kinase (SEQ ID NO:1) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A34OnnO was continuously monitored spectrophometrically. The reaction mixture (100 μl) contained AbI kinase (1 nM. AbI from deCode Genetics), peptide substrate (EAIYAAPFAKKK, 0.2 niM), MgCl2 (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 3.5 % DMSO, pH 7.5. Test compounds were incubated with AbI (SEQ ID NO:1) and other reaction reagents at 30 0C for 2 h before ATP (500 μM) was added to start the reaction. The absorption at 340 nm was monitored continuously for 2 hours at 30 0C on Polarstar Optima plate reader (BMG). The reaction rate was calculated using the 1.0 to 2.0 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound). IC50 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.
AbI kinase (SEOIDNO:!)
GTSMDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKΎSLTVAVKTLKEDTMEVE
EFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAWLL YMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKF PIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERP EGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQE
AbI kinase (SEQ ID NO:2) assay
Activity of T315I AbI 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, eϊ al. Science (2000) 289, 1938- 1942). In this assay, the oxidation of NADH (thus the decrease at A34onm) was continuously monitored spectrophometrically. The reaction mixture (100 μl) contained AbI kinase (4.4 nM. M315I AbI from deCode Genetics), peptide substrate (EAIYAAPFAKKJC, 0.2 rnM), MgCl2 (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 T315I AbI (SEQ ID NO:2) and other reaction reagents at 30 0C for 1 h before ATP (500 μM) was added to start the reaction. The absorption at 340 nm was monitored continuously for 2 hours at 30 0C on Polarstar Optima plate reader (BMG). The reaction rate was calculated using the 1.0 to 2.0 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound). IC50 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.
AbI T315I kinase fSEQ ID NO:2)
GTSMDPSSPISrYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTIy[EVE
E FLKEAAVMKE I KHPNLVQLLGVCTRE P P F YI 11 EFMT YGNLLDYLRE CNRQEVNAWLL
YMATQISSAMEYLEIOα^FIHRDIiAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKF
PIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERP
EGCPEKVYELMRACWQWHPSDRPSFAEIHQAFETMFQE
BCR-AbI p210-el4a2 (SEO ID NO:3)
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLEQEVNQERFRMIYLQ TLLAKEKKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAEEPEARPDGE GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV EFHHERGLVICVNDKEVSDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSΞESSC GVDGDYEDAΞLNPRFLKDNLIDANGGSRPPWPPLEYQPYQSIYVGGIMEGEGKGPLLRSQ STΞEQEKRLTWPRRSYSPRΞFEDCGGGYTPDCSSNENLTSSEEDFSSGQSSRVSPSPTTY RMFRDKSRSPSQNSQQSFDSSSPPTPQCHKRHRHCPVWSEATIVGVRKTGQIWPNDDEG AFHGDADGSFGTPPGYGCAADRAEEQRRHQDGLPYIDDSPSSSPHLSSKGRGSRDALVSG ALKSTKASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTS QQIETIFFIWPELYEIHKESYDGLFPRVQQWSHQQRVGDLFQKLASQLGVYRAFVDNYGV AMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDL LKHTPASHPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEHRQLLKDSFMVELVE GARKLRHVFLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDELEAVPNIPLVP DEELDALKIKISQIKSDIQREKRANKGSKATΞRLKKKLSEQESLLLLMSPSMAFRVHSRN GKSYTFLISSDYERAEWRENIREQQKKCFRSFSLTSVELQMLTNSCVKLQTVHSIPLTIN KEDDESPGLYGFLNVIVHSATGFKQSSKALQRPVASDFEPQGLSEAARWNSKENLLAGPS ENDPNLFVALYDFVAΞGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV NSLEKHSWYHGPVSRNAAEYPLSSGINGSFLVRESESSPSQRSISLRYΞGRVYHYRINTA
SDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMER TDITMKHKLGGGQYGEVΫEGVWKKYΞLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLV QLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAWLLYMATQISSAMEYLEKKNF
IHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIK SDVWAFGVLLWEIATYGMSPYPGIDRSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWN PSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVTTLLQAPELPTKTRTSRRAA EHRDTTDVPEMPHSKGQGSSDPLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNL FSALIIGTKKKTAPTPPKRSSSFREMDGQPERRGAGΞΞEGRDISNGALAFTPLDTADPAKS PKPSNGAGVPNGALRESGGSGFRΞPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSV SCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKΞEKPALPRKRAGENRSDQVTRGT VTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAWKG SALGTPAAAEPVTPTSKAGSGAPRGTSKGPAEESRVRRHKHSSESPGRDKGKLSKLKPAP PPPPAASAGKAGGKPΞQRPGQEAAGΞAVLGAKTKATSLVDAVNSDAAKPSQPAEGLKKPV
LPATPKPHPAKPSGTPΣSPAPVPLSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQP PERASGAITKGWLDSTEALCLAISGNΞΞQMASHSAVLEAGKNLYTFCVΞYVDSIQQMRN KFAFREAINKLENNLRELQICPASAGSGPAATQDFSKLLSSVKEISDIVQR
BCR-AbI p210-el3a2 fSEQ ID NO:4)
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLΞQEVNQERFRMIYLQ
TLLAKEKKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAEEPEARPDGE
GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV
EFHHERGLVKVNDKEVSDRISSLGSQAMQMERKKΞQHGAGSSVGDASRPPYRGRSSESSC
GVDGDYΞDAELNPRFLKDNLIDANGGSRPPWPPLΞYQPYQSIYVGGIMEGEGKGPLLRSQ
STSEQEKRLTWPRRSYSPRSFEDCGGGYTPDCSSNENLTSSEEDFSSGQSSRVSPSPTTY RMFRDKSRSPSQNSQQSFDSSSPPTPQCHKRHRHCPVWΞEATIVGVRKTGQIWPNDDEG AFHGDADGSFGTPPGYGCAADRAEEQRRHQDGLPYIDDSPSSSPHLSSKGRGSRDALVSG ALKSTKASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTS QQIETIFFKVPELYEIHKESYDGLFPRVQQWSHQQRVGDLFQKLASQLGVYRAFVDNYGV
AMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDL LKHTPASHPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEHRQLLKDSFMVELVE GARKLRHVFLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDELEAVPNIPLVP DEEIiDALKIKISQIKSDIQREKRANKGSKATERLKKKLSEQESLLLLMSPSMAFRVHSRN GKSYTFLISSDYERAEWRENIREQQKKCFRSFSLTSVELQMLTNSCVKLQTVHSIPLTIN
KEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITK GEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAΞYPLSSG INGSFLVRESESSPSQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAΞLVHHHST VADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKY SLTVAVKTLKEDTMEVEΞFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLL DYLRECNRQEVNAWLLYMATQISSAMEYLΞKKNFIHRDLAARNCLVGEMHLVKVADFGL SRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKΞDVWAFGVLLWEIATYGMSPYPGID RSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWNPSDRPSFAΞIHQAFETMFQESSISD EVEKELGKQGVRGAVTTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDH EPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREM DGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSP HLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSVSCVPHGAKDTEWRSVTLPRDLQSTG RQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMES SPGSΞPPNLTPKPLRRQVTVAPASGLPHKEEAWKGSALGTPAAAEPVTPTSKAGSGAPRG TSKGPAEESRVRRHKHSSESPGRDKGKLSKLKPAPPPPPAASAGKAGGKPSQRPGQEAAG EAVLGAKTKATSLVDAVNSDAAKPSQPAEGLKKPVLPATPKPHPAKPSGTPISPAPVPLS TLPΞASSALAGDQPSSTAFIPLIΞTRVSLRKTRQPPERASGAITKGWLDSTEALCLAIS GNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPASA GSGPAATQDFSKLLSSVKEISDIVQR
BCR-AbI pl90-ela2 fSEO ID NQ:5)
MVDPVGFAEAWKAQFPDSEPPRMΞLRSVGDIEQELERCKASIRRLEQEVNQERFRMIYLQ TLLAKE-KKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAEEPEARPDGE GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV EFHHERGLVKVNDKEVSDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSSΞSSC GVDGDYEDAELNPRFLKDNLIDANGGSRPPWPPLEYQPYQSIYVGGIMEGEGKGPLLRSQ STSEQEKRLTWPRRSYSPRSFEDCGGGYTPDCSSNENLTSSEEDFΞSGQSSRVSPSPTTY RMFRDKSRSPSQNSQQSFDSSSPPTPQCHK-RHRHCPVWSEATIVGVRKTGQIWPNDDEG
AFHGDAΞALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTL SITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVΞRNAAEYP LSSGINGΞFLVREΞESSPSQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVH HHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGV WKKYΞLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTY GNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLSKKNFIHRDLAARNCLVGENHLVKVA DFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPY PGIDRSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES SISDEVEKELGKQGVRGAVTTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESD PLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSS FREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSG FRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSVΞCVPHGAKDTEWRSVTLPRDL QSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKD IMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAWKGSALGTPAAAEPVTPTSKAGSG APRGTSKGPAEESRVRRHKHSSESPGRDKGKLSKLKPAPPPPPAASAGKAGGKPSQRPGQ EAAGEAVLGAKTKATSLVDAVNSDAAKPSQPAEGLKKPVLPATPKPHPAKPSGTPISPAP VPLSTLPSAΞSALAGDQPΞSTAFIPLIΞTRVSLRKTRQPPERASGAITKGWLDSTEALC LAISGNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLΞNNLRELQIC PASAGSGPAATQDFSKLLSSVKEISDIVQR
BCR-AbI p210-el4a2 T315I (SEQ ID NO:6)
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLEQEVNQSRFRMIYLQ TLLAKEKKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAEΞPΞARPDGE GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV EFHHERGLVKVNDKEVSDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSSESSC GVDGDYEDAELNPRFLKDNLIDANGGSRPPWPPLEYQPYQSIYVGGIMEGEGKGPLLRΞQ STSEQEKRLTWPRRSYSPRSFΞDCGGGYTPDCSSNΞNLTSSEEDFSSGQSSRVSPSPTTY RMFRDKSRSPSQNΞQQSFDSSSPPTPQCHKRHRHCPWVSEATIVGVRKTGQIWPNDDEG AFHGDADGSFGTPPGYGCAADRAEEQRRHQDGLPYIDDSPSSSPHLSSKGRGSRDALVSG ALKSTKASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTS QQIETIFFKVPELYEIHKESYDGLFPRVQQWSHQQRVGDLFQKLASQLGVYRAFVDNYGV AMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDL LKHTPASHPDHPLLQDALRISQNFLSSINΞEITPRRQSMTVKKGEHRQLLKDSFMVELVE GARKLRHVFLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDELEAVPNIPLVP
DEELDALKIKISQIKSDIQREK-RANKGSKATERLKKKLSEQESLLLLMSPSMAFRVHSRN GKSYTFLISSDYERAEWRENIREQQKKCFRSFSLTΞVELQMLTNSCVKLQTVHSIPLTIN KEDDESPGLYGFLNVIVHSATGFKQSSKALQRPVASDFEPQGLSEAARWNSKENLLAGPS EITOPNLFVALYDFVASGDNTLSITKGEK-LRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV
NSLEKHSWYHGPVSRNAAEYPLSSGINGSFLVRESESSPSQRSISLRYEGRVYHYRINTA SDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWΞMER TDITMKΉKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKΞIKHPNLV QLLGVCTREPPFYIIIEFMTYGNLLDYLRECNRQEVNAWLLYMATQISSAMEYLEKKNF
IHRDLJAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIK SDVWAFGVLLWEIATYGMSPYPGIDRSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWN PSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVTTLLQAPELPTKTRTSRRAA EHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKERGPPSGGLNEDΞRLLPKDKKTNL FSALIIOCKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKS PKPSNGAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGΞΞΞKRFLRSCSV SCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAGENRΞDQVTRGT VTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAWKG SALGTPAAAEPVTPTSKAGSGAPRGTSKGPAEESRVRRHKHSSESPGRDKGKLSKLKPAP PPPPAASAGKAGGKPSQRPGQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPAEGLKKPV LPATPKPHPAKPSGTPISPAPVPLSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQP PERASGAITKGWLDSTEALCLAISGNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRN KFAFREAINKLENNLRELQICPASAGSGPAATQDFSKLLSSVKEISDIVQR
BCR-AbI p210-el3a2 T315I TSEO IDNO:7^
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLEQEVNQERFRMIYLQ TLLAKEKKSYDRQRWGFRRAAQAPDGAΞEPRASASRPQPAPADGADPPPAEEPEARPDGE GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV EFHHERGLVKVNDKEVSDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSSESSC GVDGDYEDAELNPRFLKDNLIDANGGSRPPWPPLEYQPYQSIYVGGIMEGEGKGPLLRSQ STSEQEKRLTWPRRSYSPRSFEDCGGGYTPDCSSNEMLTSSEEDFSSGQSSRVSPSPTTY RMFRDKSRSPSQNSQQSFDSSSPPTPQCHKRHRHCPVWSEATIVGVRKTGQIWPNDDEG AFHGDADGSFGTPPGYGCAADRAΞEQRRHQDGLPYIDDSPSSSPHLSSKGRGSRDALVSG ALKSTKASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTS QQIETIFFKVPELYEIHKESYDGLFPRVQQWSHQQRVGDLFQKLASQLGVYRAFVDNYGV AMEMAEKCCQANAQFAEISENLRARΞNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDL LKHTPASHPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEHRQLLKDSFMVELVE GARKLRHVFLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDELΞAVPNIPLVP
DEELDALKIKISQIKSDIQREK-RANKGSKATERLKKKLSEQESLLLLMSPSMAFRVHSRN GKSYTFLϊSSDYERAEWRENIREQQKKCFRSFSLTSVELQMLTNSCVKLQTVHSIPLTIN KEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITK GEKLRVLGYNHNGEWCEAQTKNGQGWVPΞNYITPVNSLEKHSWYHGPVSRNAAEYPLSSG INGSFLVRESESSPSQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHST VADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYΞGVWKKY SLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYITIEFMTYGNLL
DYLRECNRQEWAWLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGL SRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGID RSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWNPSDRPSFAΞIHQAFETMFQESSISD EVEKELGKQGVRGAVTTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDH EPAVSPLLPRKERGPPEGGIANEDERLLPKI)KKTNLFSALIKKKKKTAPTPPKRSSSFREM DGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSP HLWKKSSTLTSSRLATGΞΞΞGGGSSSKRFLRSCSVSCVPHGAKDTEWRSVTLPRDLQSTG RQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMES SPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAWKGSALGTPAAAEPVTPTSKAGSGAPRG TSKGPAEEΞRVRRHKHSSESPGRDKGKLSKLKPAPPPPPAASAGKAGGKPSQRPGQEAAG EAVLGAKTKATΞLVDAVNSDAAKPSQPAEGLKKPVLPATPKPHPAKPSGTPISPAPVPLS TLPSASSALAGDQPSΞTAFIPLISTRVSLRKTRQPPERASGAITKGWLDSTEALCLAIS GNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNLRELQICPASA GSGPAATQDFSKLLSSVKEISDIVQR
BCR-AbI pl90-ela2 fSEO IDNO:8)
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLEQEVNQERFRMIYLQ TLLAKEKKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAΞEPEARPDGE GSPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNV EFHHΞRGLVKVNDKEVΞDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSSESSC GVDGDYEDAELNPRFLKDNLIDANGGSRPPWPPLEYQPYQSIYVGGIMEGEGKGPLLRSQ STSEQEKRLTWPRRSYSPRSFEDCGGGYTPDCSSNENLTSSEEDFSΞGQSSRVSPSPTTY RMFRDKSRSPSQNSQQSFDSSSPPTPQCHKRHRHCPVWSEATIVGVRKTGQIWPNDDEG AFHGDAEALQRPVASDFSPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTL SITKGEKLRVLGYNHNGΞWCEAQTKMGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYP LSSGINGSFLVRESESSPSQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVH HHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGV WKKYSLTVAVKTLKEDTMEVΞEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIIIEFMTY GNLLDYLRECNRQEVNAWLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVA
DFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPY PGIDRSQVYELLEKDYRMKRPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES SISDEVEKELGKQGVRGAVTTLLQAPELPTKTRTΞRRAAEHRDTTDVPEMPHSKGQGESD PLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSS FREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSG FRSPHLWKKSSTLTSSRLATGEΞΞGGGSSSKRFLRSCSVSCVPHGAKDTEWRSVTLPRDL QSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKD IMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAWKGSALGTPAAAEPVTPTSKAGSG APRGTSKGPAEESRVRRHKHSSESPGRDKGKLSKLKPAPPPPPAASAGKAGGKPSQRPGQ EAAGEAVLGAKTKATSLVDAVNSDAAKPSQPAEGLKKPVLPATPKPHPAKPSGTPISPAP VPLSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERASGAITKGWLDSTEALC LAISGNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLΞNNLRELQIC PASAGSGPAATQDFΞKLLSSVKEISDIVQR
C-Kit kinase (SEQ ID NO:9) assay
Activity of c-Kit kinase (SEQ ID NO:9) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340nm) was continuously monitored spectrophometrically. The reaction mixture (100 μl) contained c-Kit (cKIT residues T544-V976, from ProQinase, 5.4 nM), polyE4Y (1 mg/ml), MgC12 (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 % DMSO3 pH 7.5. Test compounds were incubated with C-Met (SEQ ID NO:9) and other reaction reagents at 22 0C for < 2 min before ATP (200 μM) was added to start the reaction. The absorption at 340 run was monitored continuously for 0.5 hours at 30 0C on Polarstar Optima plate reader (BMG). The reaction rate was calculated using the 0 to 0.5 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound). IC50 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.
c-Kit with N-terminal GST fusion fSEO ID NO:9)
LGYWKIKGLVQPTRLLLEYXEEKΥEEHL YERDEGDIKWRNKKFELGLEFPNLPYYIDGDVKL TQSMAI IRYIIWKHMMLGGCPKERAEI SMLEGAVDIRYGVSRI AYSKDFETLKVDFLSKLP EMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALD VVLYMDPMCLDAFPKLVCFKKRI EAI PQ IDKYLKSSK-FLWPLQGWQATFGGGDHPPKSDLVPRHNQTSLYKKAGΞAAAVLEEWLYFQGT YKΎLQKPMYEVQWKVVEEINGISΠNIΎW
ATAYGLIKSDAAMTVAVIMLKPSAHLTΞREALMSELKVLSYLGNHMNIVNLLGACTIGGPT LVITEYCCYGDLLNFLRRK-RDSFICSKQEDHAEAALYKNLLHSKΞSSCSDSTNE YMDMKPG
VSYWPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNC IHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPΞSΪFNCVYTFΞ SDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDAD PLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPWDHSVRINSVGSTASSSQPL LVHDDV
C-Met kinase (SEQ ID NO: 10) assay
Activity of C-Met kinase (SEQ ID NO: 10) 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, 1938-1942). In this assay, the oxidation of NADH (thus the decrease at A340nm) was continuously monitored spectrophometrically. The reaction mixture (100 μl) contained C-Met (c-Met residues: 956-1390, from Invitrogen, catalogue #PV3143, 6 nM), polyE4Y (1 mg/rnl), MgC12 (10 niM), 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: 10) and other reaction reagents at 22 0C for 0.5 h before ATP (100 μM) was added to start the reaction. The absorption at 340 nrn was monitored continuously for 2 hours at 30 0C on Polarstar Optima plate reader (BMG). The reaction rate was calculated using the 1.0 to 2.0 h time frame. Percent inhibition was obtained by comparison of reaction rate with that of a control (i.e. with no test compound). IC50 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.
cMet Kinase fSEQ ID NO: 10)
MSYYHHHHHHDYDIPTTENLYFQGAMLVPRGSPWIPFTMKKRKQIKDLGSELVRYDARVHT PHLDRLVSARSVS PTTEMVSNESVDYRAT FPEDQF PNS SQNGS CRQVQYPLTDMS P I LTSG DSDISSPLLQNTVHIDLSALNPELVQAVQHWIGPSSLIVHFNEVI GRGHFGCVYHGTLLD NDGKKIHCAVKS LNRITDIGEVSQFLTEGI IMKDFSHPNVLSLLGI CLRSEGSPL WLPYM KHGDLRNFIRl^TmPTVKDLIGFGLQVAKGMKY]-ASK-KFVHRD
DFGLARDMYDKE YYSVHNKTGAKL PVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAP PYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRI SAI FST F I GEHYVHVNATYVNVKCVAPYP SLLSS EDNADDEVDTRPAS FWETS
The biochemical IC50 values of other compounds disclosed herein are at least 10 μM against AbI enzyme.
Cell Culture
BaF3 cells (parental or transfected with the following: wild type p210 BCR-AbI and T3151 p210 BCR-AbI was obtained from Professor Richard Van Etten (New England Medical Center, Boston, MA). Briefly, cells were grown in RPMI 1640 supplemented with 10% characterized fetal bovine serum (HyClone, Logan, UT) at 37 degrees Celsius, 5% CO2, 95% humidity. Cells were allowed to expand until reaching 80% saturation at which point they were subciiltured or harvested for assay use.
Cell Proliferation Assay
A serial dilution of test compound was dispensed into a 96 well black clear bottom plate (Corning, Corning, NY). For each cell line, three thousand cells were added per well in complete growth medium. Plates were incubated for 72 hours at 37 degrees Celsius, 5% CO2, 95% humidity. At the end of the incubation period Cell Titer Blue (Promega. Madison, WI) was added to each well and an additional 4.5 hour incubation at 37 degrees Celsius, 5% CO2, 95% humidity was performed. Plates were then read on a BMG Fluostar Optima (BMG, Durham, NC) using an excitation of 544 nM and an emission of 612 nM. Data was analyzed using Prism software (Graphpad. San Diego, CA) to calculate IC50!s.

Claims

Claims
L Compounds of the formula Ia
Figure imgf000059_0001
and wherein the pyrimidine ring may be optionally substituted with one or more R20 moieties;
each D is individually taken from the group consisting of C. CH, C-R20, N-Z3, N, O and S, such that the resultant ring is taken from the group consisting of pyrazolyl, triazolyl, isoxazolyl, isothiazolyl, oxazolyl, imidazoyl, and thiadiazolyl;
wherein E is selected from the group consisting phenyl, pyridyl, and pyrimidinyl;
E may be optionally substituted with one or two Rl 6 moieties;
wherein A is a ring system selected from the group consisting of cyclopentyl, cyclohexyl, Gl, G2, and G3;
Gl is a heteroaryl taken from the group consisting of pyrrolyl, furyl, thienyl, oxazolyl, thiazolyl, isoxazol-4-yl, isoxazol-5-yl, isothiazolyl, imidazolyl, pyrazolyl, oxadiazolyl, thiadiazolyl, triazolyl. and tetrazolyl;
G2 is a fused bicyclic heteroaryl taken from the group consisting of indolyl, indolinyl, isoindolyl, isoindolinyl, indazolyl, benzofuranyl, benzothienyl, benzothiazolyl, benzotliiazolonyl, benzoxazolyl, benzoxazolonyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl, benzimidazolonyl, benztriazolyl, imidazopyridinyl, pyrazolopyridinyl, imidazolonopyridinyl, thiazolopyridinyl, tliiazolonopyridinyl, oxazolopyridinyl, oxazolonopyridinyl, isoxazolopyridinyl, isothiazolopyridinyl, triazolopyridinyl, imidazopyrimidinyl, pyrazolopyriinidinyl, imidazolonopyrimidinyl, thiazolopyridiminyl, thiazolonopyrimidinyl, oxazolopyridiminyl, oxazolonopyrimidinyl, isoxazolopyrimidinyl, isothiazolopyrimidinyl, triazolopyrimidinyl, dihydropurinonyl, pyrrolopyriπiidinyl, purinyl, pyrazolopyriinidinyl, phthalimidyl, phthalimidinyl, pyrazinylpyridinyl, pyridinopyrimidinyl. pyrimidinopyrimidinyl, cinnolinyl, quinoxalinyl, quinazolinyl, quinolinyl, isoquinolinyl, plithalazinyl, benzodioxyl, benzisotliiazoline"l,l,3-trionyl, dihydroquinolinyl, tetrahydroquinolinyl, dihydroisoquinolyl, tetrahydroisoquinolinyl, benzoazepinyl, benzodiazepinyl, benzoxapinyl, and benzoxazepinyl;
G3 is a heterocyclyl taken from the group consisting of oxetanyl, azetadinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, imidazolonyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, rnorpholinyl, thiomorpholinyl, tliiomoφholinyl S-oxide, tbiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl;
the A ring may be optionally substituted with-one or two R2 moieties;
X is selected from the group consisting of -O-, -S(CHj)n-, -N(R3)(CH2)n-, -(CH2)P-, and wherein the carbon atoms of -(CHa)n-, -(CH2)P-, of X may be further substituted by oxo or one or more Cl-C6alkyl moieties;
when A. Gl, G2 or G3 has one or more substitutable sp2-hybridized carbon atoms, each respective sp2 hybridized carbon atom may be optionally substituted with a Zl substituent;
when A. Gl. G2 or G3 has one or more substitutable sp3 -hybridized carbon atoms, each respective sp3 hybridized carbon atom may be optionally substituted with a Z2 substituent; when A, Gl, G2 or G3 has one or more substitutable nitrogen atoms, each respective nitrogen atom may be optionally substituted with a Z4 substituent;
each Zl is independently and individually selected from the group consisting of Cl- όalkyl, branched C3-C7alkyl, C3-C8cycloalkyl, halogen, fluoroCl-Cόalkyl wherein the alkyl moiety can be partially or fully fluorinated, cyano, Cl-C6alkoxy, fluoroCl- Cόalkoxy wherein the alkyl moiety can be partially or fully fluorinated, -(CHa)nOH, oxo, Cl-C6alkoxyCl-C6alkyl, (R4)2N(CH2)n-, (RS)2N(CH2),,-, (R4)2N(CH2)qN(R4)(CH2)n-, (R4)2N(CH2)qO(CH2)n-, (R3)2NC(O)-, (R4)2NC(O)-, (R4)2NC(O)Cl-C6alkyl-; - (R4)NC(O)R8, Cl-Cβalkoxycarbonyl-, -carboxyCl-Cόalkyl, Cl-C6alkoxycarbonylCl- Cόalkyl-, (RS)2NSO2-, -S0R3, (R4)2NSO2-, ~N(R4)SO2R8, -O(CH2)qOCl-C6alkyl, - SO2R3, -S0R4, -C(0)R8, -C(O)R6, -C(=NOH)R6, -C(=NOR3)R6, (CH2)nN(R4)C(O)R8, -N(R3)(CH2)qO -alkyl, -N(R3)(CH2)qN(R4)2, nitro, CH(0H)CH(0H)R4, -C(=NH)N(R4)2, -C(=NOR3)N(R4)2, and -NHC(=NH)R8, R17 substituted G3, Rl 7 substituted pyrazolyl and Rl 7 substituted imldazolyl;
in the event that Zl contains an alkyl or alkylene moiety, such moieties may be further substituted with one or more Cl-C6alkyls;
each Z2 is independently and individually selected from the group consisting of aryl, Cl- Cβalkyl, C3-C8cycloalkyl, branched C3-C7alkyl, hydroxy!, hydroxyCl-Cόalkyl-, cyano, (R3)2N-, (R4)2N-, (R4)2NC1-C6alkyl-, (R4)2NC2-C6alkylN(R4)(CH2)n-, (R4)2NC2- C6alkylO(CH2)n-, (R3)2NC(O)-, (R4)2NC(O)-S (R4)2NC(O)-Cl-C6alkyl-, carboxyl, - carboxyC 1 -Cβalkyl, Cl -Cόalkoxycarbonyl-, C 1 -CόalkoxycarbonylC 1 -Cόalkyl-, (RS)2NSO2-, (R4)2NSO2-, -SO2R8, -(CH2)nN(R4)C(O)R8, -C(O)RS, =0. -NOH, and =N(ORό);
in the event that Z2 contains an alkyl or alkylene moiety, such moieties may be further substituted with one or more Cl-C6alkyls; each Z3 is independently and individually selected from the group consisting of H, Cl- Cβalkyl, branched C3-C7alkyl, C3-C8cycloalkyl, fluoroCl-Cβalkyl wherein the alkyl moiety can be partially or fully fluorinated, hydroxyC2-C6alkyl-, Cl-C6alkoxycarbonyl-, -C(O)RS, R5C(O)(CH2)n-, (R4)2NC(O)-, (R4)2NC(O)C1-C6alkyl-, R8C(O)N(R4)(CH2)q- , (RJ)2NSO2-, (R4)2NSO2-, -(CH2)qN(R3)2, and -(CH2)qN(R4)2;
each ZA is independently and individually selected from the group consisting of Cl- Cδalkyl, branched C3-7alkyl, hydroxyC2-C6alkyl-, Cl-C6alkoxyC2-C6alkyl-, (R4)2N- C2-C6alkyk (R4)2N-C2-C6alkylN(R4)-C2-C6alkyl-, (R4)2N-C2-C6alkyl-O-C2- Cθalkyl- (R4)2NC(O)C1-C6alkyl-, carboxyCl -Cδalkyl, Cl-C6alkoxycarbonylCl- Cδalkyl-, ~C2-C6alkylN(R4)C(O)R8, R8-C(=NR3)-, -SO2R8, and -COR8;
in the event that Z4 contains an alkyl or alkyiene moiety, such moieties may be further substituted with one or more Cl-C6alkyls;
each R2 is selected from the group consisting of H5 Cl-C6alkyl, branched C3-C8alkyl, Rl 9 substituted C3-C8cycloalkyl-, fiuoroCl -Cδalkyl- wherein the alkyl is fully or partially fluorinated, halogen, cyano, Cl-C6alkoxy~, and fluoroCl-Cδalkoxy- wherein the alkyl group is fully or partially fluorinated, hydroxyl substituted Cl-C6alkyl-, hydroxyl substituted branched C3-C8alkyl~, cyano substituted Cl-C6alkyl-, cyano substituted branched C3-C8alkyl-, (R3)2NC(O)C1-C6alkyl-, and (R3)2NC(O)C3-C8 branched alkyl-;
wherein each R3 is independently and individually selected from the group consisting of H, Cl -Cδalkyl, branched C3-C7alkyl, and C3-C8cycloalkyl;
each R4 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, hydroxyCl-Cόalkyl-, dihydroxyCl -Cδalkyl-, Cl-C6alkoxyCl-C6alkyl-, branched C3-C7alkyl, branched hydroxyCl -Cδalkyl-, branched Cl-C6alkoxyCl- Cόalkyl-, branched dihydroxyCl-Cβalkyl-, ~(CH2)PN(R7)2. -(CH2)PC(O)N(R7)2, - (CH2)nC(O)OR3, and Rl 9 substituted C3-C8cycloalkyl-; each R5 is independently and individually selected from the group consisting of
Figure imgf000063_0001
and wherein tlie symbol (##) is tlie point of attachment to Z3;
each R6 is independently and individually selected from the group consisting of Cl- Cόalkyl, branched C3-C7alkyl, and Rl 9 substituted CS-CScycloalkyl-;
each R7 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, hydroxyC2-C6alkyl-, dihydroxyC2-C6alkyl-, Cl-C6alkoxyC2-C6alkyl-, branched C3-C7alkyl, branched hydroxyC2-C6alkyl-, branched Cl-C6alkoxyC2- Cόalkyl-, branched dihydroxyC2-C6alkyl-, -(CH2)nC(O)OR3, Rl 9 substituted C3- Cδcycloalkyl- and -(CH2)nR17;
each R8 is independently and individually selected from tlie group consisting of Cl- Cθalkyl, branched C3-C7alkyl, fluoroCl-C6alkyl- wherein the alkyl moiety is partially or fully fluorinated, Rl 9 substituted C3-C8cycloalkyk -OH, Cl-C6alkoxy, -N(R3)2, and - N(R4)2;
each RlO is independently and individually selected from the group consisting of -CO2H, ~CO2C1-C6alkyl, -C(O)N(R4)2. OH, Cl-C6alkoxy, and -N(R4) 2:
each Rl 6 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, branched C3-C7alkyl, R19 substituted C3-C8cycloalkyl-, halogen, fluoroCl- Cόalkyl- wherein the alkyl moiety can be partially or fully fluorinated, cyano, hydroxy 1, Cl-C6alkoxy, fluoroCl-Cόalkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(R3)2, -N(R4)2, R3 substituted C2-C3alkynyl- and nitro; each Rl 7 is independently and individually selected from the group consisting of H, Cl- Cόalkyl, branched C3-C7alkyl, Rl 9 substituted C3-C8cycloalkyk halogen, fluoroCl- Cόalkyl- wherein the alkyl moiety can be partially or fully fluorinated, cyano, hydroxy 1, Cl-C6alkoxy, fluoroCl-Cβalkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(RS)2, -N(R4)2, and nitro;
each Rl 9 is independently and individually selected from the group consisting of H, OH and Cl-C6alkyl;
each R20 is independently and individually selected from the group consisting of Cl- Cβalkyl, branched C3-C7alkyl, Rl 9 substituted C3-C8cycloalkyl-, halogen, fluoroCl- Cόalkyl- wherein the alkyl moiety can be partially or fully fluorinated. cyano, hydroxyl, Cl-Cόalkoxy, fluoroCl-Cδalkoxy- wherein the alkyl moiety can be partially or fully fluorinated, -N(R3)2, -N(R4)2, -N(R3)C(O)R3, -C(O)N(R3)2 and nitro and wherein two R4 moieties independently and individually taken from the group consisting of Cl- Cόalkyl, branched C3-C6alkyl, hydroxyalkyl-, and alkoxyalkyl and attached to the same nitrogen heteroatom may cyclize to form a C3-C7 heterocyclyl ring;
k is 0 or 1; n is 0-6; p is 1-4; q is 2-6; r is 0 or 1; t is 1-3; v is 1 or 2; x is 0-2;
and stereo-, regioisomers and tautomers of such compounds.
2. Compounds of claim 1 wherein
Figure imgf000064_0001
is selected from the group consisting of
Figure imgf000065_0001
Figure imgf000065_0002
Figure imgf000065_0003
wherein the symbol (**) indicates the point of attachment to the pyrimidine ring.
3. Compounds of claim 2 having formula Ib
Figure imgf000065_0004
wherein A is any possible isomer of pyrazole.
4. Compounds of claim 3 having formula Ic
Figure imgf000065_0005
5. Compounds of claim 3 having formula Id
Figure imgf000066_0001
6. Compounds of claim 3 having formula Ie
Figure imgf000066_0002
7. Compounds of claim 2 having formula If
Figure imgf000066_0003
8. Compounds of claim 2 having formula Ig
Figure imgf000066_0004
9. Compounds of claim 8 having formula Ih
Figure imgf000066_0005
10. A method of treating mammalian disease wherein the disease etiology or progression is at least partially mediated by the kinase activity of c-Abl kinase, bcr-Abl kinase, Flt-3 kinase, VEGFR-2 kinase mutants, c-Met, PDGΕR-alpha kinase, PDGFR- beta kinase, HER-I, HER-2, HER-3, HER-4, FGFR, c-Kit, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs of any of the foregoing, comprising the step of administering to the mammal a compound of claim 1.
11. A method of claim 10 wherein said kinase is selected from the group consisting of bcr-Abl fusion protein kinases p210, bcr-Abl fusion protein kinases pi 90, bcr-Abl fusion protein kinases bearing the T315I gatekeeper mutant in the AbI kinase domain of p2I0, bcr-Abl fusion protein kinases bearing the T315I gatekeeper mutant in the AbI kinase domain of pi 90, and other bcr-Abl polymorphs of any of the foregoingkinases.
12. The method of claim 11, wherein said bcr-Abl fusion protein kinases p210 having SEQ ID NO:3 & SEQ ID NO:4, wherein said bcr-Abl fusion protein kinase pi 90 has SEQ ID NO:5, wherein said bcr-Abl fusion protein kinases p210 bearing the T315I mutation in the AbI kinase domain has SEQ ID NO:6 & SEQ ID NO:7, and wherein said bcr-Abl fusion protein kinase pi 90 bearing the T315I mutation in the AbI kinase domain has SEQ ID NO:8.
13. A method of claim 10 wherein said kinase is selected from the group consisting of cKit protein kinase, PDGFR-alpha kinase, and any fusion protein, mutation and polymorphs of any of the foregoing.
14. A method of claim 10 wherein said kinase is selected from the group consisting of c-Met protein kinase, and any fusion protein, mutation and polymorphs of any of the foregoing.
15. A pharmaceutical composition comprising a compound of claim 1 , together with a pharmaceutically acceptable carrier, optionally containing an additive selected from the group including adjuvants, excipients, diluents, and stabilizers.
16. A method of treating an individual suffering from a condition selected from the group consisting of cancer, 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, gastrointestinal stromal tumors, colonic cancers, ocular diseases characterized by hyperproliferation leading to blindness including retinopathies, diabetic retinopathy, age-related macular degeneration and hypereosinophilic syndrome, rheumatoid arthritis, asthma, chronic obstructive pulmonary, mastocytosis, mast cell leukemia, or disease a disease caused by c-Kit kinase, oncogenic forms thereof, aberrant fusion proteins thereof and polymorphs thereof, comprising the step of administering to such individual a compound of claim 1.
17. The method of claim 16, said compound being administered by a method selected from the group consisting of oral, parenteral, inhalation, and subcutaneous.
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