Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
  • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
  • C07D487/04—Ortho-condensed systems
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
  • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P21/00—Drugs for disorders of the muscular or neuromuscular system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
  • C07D239/70—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings condensed with carbocyclic rings or ring systems
  • C07D239/72—Quinazolines; Hydrogenated quinazolines
  • C07D239/78—Quinazolines; Hydrogenated quinazolines with hetero atoms directly attached in position 2
  • C07D239/80—Oxygen atoms
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
  • C07D471/04—Ortho-condensed systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D519/00—Heterocyclic compounds containing more than one system of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring system not provided for in groups C07D453/00 or C07D455/00

Definitions

• the present invention relates to compounds useful as inhibitors of protein kinases.
• the invention also provides pharmaceutically acceptable compositions comprising compounds of the present invention and methods of using said compositions in the treatment of various disorders.
• Protein kinases constitute a large family of structurally related enzymes that are responsible for the control of a variety of signal transduction processes within the cell. Protein kinases are thought to have evolved from a common ancestral gene due to the conservation of their structure and catalytic function. Almost all kinases contain a similar 250-300 amino acid catalytic domain. The kinases may be categorized into families by the substrates they phosphorylate (e.g., protein-tyrosine, protein-serine/threonine, lipids, etc.).
• protein kinases mediate intracellular signaling by effecting a phosphoryl transfer from a nucleoside triphosphate to a protein acceptor that is involved in a signaling pathway. These phosphorylation events act as molecular on/off switches that can modulate or regulate the target protein biological function. These phosphorylation events are ultimately triggered in response to a variety of extracellular and other stimuli.
• Examples of such stimuli include environmental and chemical stress signals (e.g., osmotic shock, heat shock, ultraviolet radiation, bacterial endotoxin, and H 2 0?.), cytokines (e.g., interleukin-1 (IL-1) and tumor necrosis factor a (TNF-a)), and growth factors (e.g., granulocyte macrophage-colony-stimulating factor (GM-CSF), and fibroblast growth factor (FGF)).
• IL-1 interleukin-1
• TNF-a tumor necrosis factor a
• growth factors e.g., granulocyte macrophage-colony-stimulating factor (GM-CSF), and fibroblast growth factor (FGF)
• An extracellular stimulus may affect one or more cellular responses related to cell growth, migration, differentiation, secretion of hormones, activation of transcription factors, muscle contraction, glucose metabolism, control of protein synthesis, and regulation of the cell cycle.
• R 1 is a warhead group.
• Compounds of the present invention are useful for treating a variety of diseases, disorders or conditions, associated with abnormal cellular responses triggered by protein kinase-mediated events. Such diseases, disorders, or conditions include those described herein.
• Compounds provided by this invention are also useful for the study of kinases in biological and pathological phenomena; the study of intracellular signal transduction pathways mediated by such kinases; and the comparative evaluation of new kinase inhibitors.
• Figure 1 Mass Modification of FGFR4 by 1-1.
• Figure 2 Data showing that compound 1-69 has prolonged duration of action (PDA) against pFGFR4 signalling in MDA-MB-453 cells consistent with the resynthesis rate of FGFR4.
• Figure 3 Data showing that compound 1-1 has PDA against pFGFR4 signalling in MDA-MB-453 cells consistent with the resynthesis rate of FGFR4, whereas its noncovalent, reversible analog, 1-234 does not have PDA.
• Figure 4 The amino acid sequence of FGFR4 (SEQ ID NO. 1).
• the present invention provides irreversible inhibitors of FGFR4.
• such compounds include those of the formulae described herein, or a pharmaceutically acceptable salt thereof, wherein each variable is as defined and described herein.
• aliphatic or "aliphatic group”, as used herein, means a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as “carbocycle” "cycloaliphatic” or “cycloalkyl”), that has a single point of attachment to the rest of the molecule.
• aliphatic groups contain 1-6 aliphatic carbon atoms.
• aliphatic groups contain 1-5 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms. In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms, and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms.
• cycloaliphatic (or “carbocycle” or “cycloalkyl”) refers to a monocyclic C3-C6 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule.
• Exemplary aliphatic groups are linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.
• bridged bicyclic refers to any bicyclic ring system, i.e. carbocyclic or heterocyclic, saturated or partially unsaturated, having at least one bridge.
• a "bridge” is an unbranched chain of atoms or an atom or a valence bond connecting two bridgeheads, where a "bridgehead” is any skeletal atom of the ring system which is bonded to three or more skeletal atoms (excluding hydrogen).
• a bridged bicyclic group has 7-12 ring members and 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• bridged bicyclic groups are well known in the art and include those groups set forth below where each group is attached to the rest of the molecule at any substitutable carbon or nitrogen atom. Unless otherwise specified, a bridged bicyclic group is optionally substituted with one or more substituents as set forth for aliphatic groups. Additionally or alternatively, any substitutable nitrogen of a bridged bicyclic group is optionally substituted. Exemplary bridged bicyclics include:
• lower alkyl refers to a Ci_ 4 straight or branched alkyl group.
• exemplary lower alkyl groups are methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and tert-butyl.
• lower haloalkyl refers to a Ci_ 4 straight or branched alkyl group that is substituted with one or more halogen atoms.
• heteroatom means one or more of oxygen, sulfur, nitrogen, or phosphorus (including, any oxidized form of nitrogen, sulfur, or phosphorus; the quaternized form of any basic nitrogen or; a substitutable nitrogen of a heterocyclic ring, for example N (as in 3,4- dihydro-2H-pyrrolyl), ⁇ (as in pyrrolidinyl) or NR + (as in N-substituted pyrrolidinyl)).
• Ci_g (or Ci_ 6 ) saturated or unsaturated, straight or branched, hydrocarbon chain
• bivalent alkylene, alkenylene, and alkynylene chains that are straight or branched as defined herein.
• alkylene refers to a bivalent alkyl group.
• An "alkylene chain” is a polymethylene group, i.e., -(CH 2 ) n -, wherein n is a positive integer, preferably from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3.
• a substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.
• alkenylene refers to a bivalent alkenyl group.
• a substituted alkenylene chain is a polymethylene group containing at least one double bond in which one or more hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.
• cyclopropylenyl refers to a bivalent cyclopropyl group of the following structure:
• halogen means F, CI, Br, or I.
• aryl used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl”, refers to monocyclic and bicyclic ring systems having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains three to seven ring members.
• aryl is used interchangeably with the term “aryl ring”.
• aryl refers to an aromatic ring system.
• Exemplary aryl groups are phenyl, biphenyl, naphthyl, anthracyl and the like, which optionally includes one or more substituents.
• aryl is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like.
• heteroaryl and “heteroar-”, used alone or as part of a larger moiety refer to groups having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms; having 6, 10, or 14 ⁇ electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms.
• heteroatom refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quatemized form of a basic nitrogen.
• Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl.
• heteroaryl and “heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring.
• Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H-quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3-b]-l,4-oxazin- 3(4H)-one.
• heteroaryl group is optionally mono- or bicyclic.
• heteroaryl is used interchangeably with the terms “heteroaryl ring”, “heteroaryl group”, or “heteroaromatic”, any of which terms include rings that are optionally substituted.
• heteroarylkyl refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.
• heterocycle As used herein, the terms “heterocycle”, “heterocyclyl”, “heterocyclic radical”, and “heterocyclic ring” are used interchangeably and refer to a stable 5- to 7-membered monocyclic or 7-10-membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above.
• nitrogen includes a substituted nitrogen.
• the nitrogen is N (as in 3,4-dihydro- 2H-pyrrolyl), ⁇ (as in pyrrolidinyl), or ⁇ NR (as in N-substituted pyrrolidinyl).
• a heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted.
• saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothiophenyl pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and quinuclidinyl.
• heterocycle used interchangeably herein, and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl, where the radical or point of attachment is on the heterocyclyl ring.
• a heterocyclyl group is optionally mono- or bicyclic.
• heterocyclylalkyl refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.
• partially unsaturated refers to a ring moiety that includes at least one double or triple bond.
• partially unsaturated is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties, as herein defined.
• an "optionally substituted” group has a suitable substituent at each substitutable position of the group, and when more than one position in any given structure is substituted with more than one substituent selected from a specified group, the substituent is either the same or different at every position.
• Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds.
• stable refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.
• Suitable monovalent substituents on R° are independently halogen, -(CH 2 ) 0 2 R*, -(haloR*), -(CH 2 ) 0 2 OH, -(CH 2 ) 0 2 OR*, -(CH 2 ) 0 2 CH(OR*) 2 ; -O(haloR'), -CN, -N 3 , -(CH 2 ) 0 2 C(0)R*, -(CH 2 ) 0 2 C(0)OH, -(CH 2 ) 0 2 C(0)OR*, -(CH 2 ) 0 2 SR*, -(CH 2 )o 2 SH, -(CH 2 )o 2 NH 2 , -(CH 2 ) 0 2 NHR*, -(CH 2 ) 0 2 NR* 2 , -N0 2 , -SiR*
• Suitable divalent substituents that are bound to vicinal substitutable carbons of an "optionally substituted” group include: -0(CR 2 ) 2 3O-, wherein each independent occurrence of R is selected from hydrogen, Ci_6 aliphatic which is optionally substituted as defined below, or an unsubstituted 5-6- membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• Suitable substituents on the aliphatic group of R * include halogen, -R*, -(haloR*), -OH, -OR*, -O(haloR'), -CN, -C(0)OH, -C(0)OR*, -NH 2 , -NHR*, -NR* 2 , or -N0 2 , wherein each R* is unsubstituted or where preceded by "halo" is substituted only with one or more halogens, and is independently Ci_ 4 aliphatic, -CH 2 Ph, -O(CH 2 ) 0 iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• Suitable substituents on a substitutable nitrogen of an "optionally substituted" group include -R ⁇ , -NR ⁇ 2 , -C(0)R ⁇ , -C(0)OR ⁇ , -C(0)C(0)R ⁇ , -C(0)CH 2 C(0)R ⁇ , -S(0) 2 R ⁇ , -S(0) 2 NR ⁇ 2 , -C(S)NR ⁇ 2 , -C(NH)NR ⁇ 2 , or -N(R ⁇ )S(0) 2 R ⁇ ; wherein each R ⁇ is independently hydrogen, Ci_6 aliphatic which is optionally substituted as defined below, unsubstituted -OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R ⁇ , taken together with their intervening atom(
• Suitable substituents on the aliphatic group of R ⁇ are independently halogen, -R*, -(haloR*), -OH, -OR*, -O(haloR'), -CN, -C(0)OH, -C(0)OR*, -NH 2 , -NHR*, -NR* 2 , or -N0 2 , wherein each R* is unsubstituted or where preceded by "halo" is substituted only with one or more halogens, and is independently Ci_ 4 aliphatic, -CH 2 Ph, -O(CH 2 ) 0 iPh, or a 5-6- membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• the term "pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
• Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference.
• Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases.
• Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
• inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid
• organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
• salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate,
• Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and salts.
• Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
• Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.
• structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention.
• structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
• compounds having the present structures including the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 13 C- or 14 C-enriched carbon are within the scope of this invention.
• Such compounds are useful, for example, as analytical tools, as probes in biological assays, or as therapeutic agents in accordance with the present invention.
• the R 1 group comprises one or more deuterium atoms.
• the term "irreversible” or “irreversible inhibitor” refers to an inhibitor (i.e. a compound) that is able to be covalently bonded to a target protein kinase in a substantially non-reversible manner. That is, whereas a reversible inhibitor is able to bind to (but is generally unable to form a covalent bond) the target protein kinase, and therefore can become dissociated from the target protein kinase, an irreversible inhibitor will remain substantially bound to the target protein kinase once covalent bond formation has occurred. Irreversible inhibitors usually display time dependency, whereby the degree of inhibition increases with the time with which the inhibitor is in contact with the enzyme. In certain embodiments, an irreversible inhibitor will remain substantially bound to a kinase once covalent bond formation has occurred and will remain bound for a time period that is longer than the life of the protein.
• an irreversible inhibitor will remain substantially bound to a kinase once covalent bond formation
• Methods for identifying if a compound is acting as an irreversible inhibitor are known to one of ordinary skill in the art. Such methods include, but are not limited to, enzyme kinetic analysis of the inhibition profile of the compound with the protein kinase target, the use of mass spectrometry of the protein drug target modified in the presence of the inhibitor compound, discontinuous exposure, also known as "washout," experiments, and the use of labeling, such as radiolabeled inhibitor, to show covalent modification of the enzyme, as well as other methods known to one of skill in the art.
• warheads reactive functional groups
• the term "warhead” or "warhead group” refers to a functional group present on a compound of the present invention wherein that functional group is capable of covalently binding to an amino acid residue (such as cysteine, lysine, histidine, or other residues capable of being covalently modified) present in the binding pocket of the target protein, thereby irreversibly inhibiting the protein.
• an amino acid residue such as cysteine, lysine, histidine, or other residues capable of being covalently modified
• the -L-Y group provides such warhead groups for covalently, and irreversibly, inhibiting the protein.
• a "pro-warhead group” is used in place of a warhead groups. Such pro-warhead groups convert to a warhead group in vivo or in vitro.
• an inhibitor is defined as a compound that binds to and /or inhibits the target protein kinase with measurable affinity.
• an inhibitor has an IC 50 and/or binding constant of less about 50 ⁇ , less than about 1 ⁇ , less than about 500 nM, less than about 100 nM, or less than about 10 nM.
• measurable affinity and “measurably inhibit,” as used herein, means a measurable change in FGFR4 activity between a sample comprising a compound of the present invention, or composition thereof, and FGFR4, and an equivalent sample comprising FGFR4, in the absence of said compound, or composition thereof.
• the present invention provides a compound of formula I,
• X 1 is -NR 4 , N, -CR 4 R 4' , or -CR 4 ;
• X 2 is -NR 5 , N, -CR 5 R 5' , or -CR 5 ;
• X 3 is N or CR 6 ;
• X 4 is N or CR 7 ;
• X 5 is N, C, or CH; wherein at least one of X 1 , X 2 , X 3 , X 4 , or X 5 is N;
• G is H, O, OR, or N(R)(R);
• Ring A is an optionally substituted group selected from phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 5-6 membered monocyclic heteroaryl ring having 1 - 4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic saturated, partially unsaturated or aryl ring;
• each R is independently hydrogen or an optionally substituted group selected from Ci_ 6 aliphatic, phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 4-7 membered heterocylic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or
• R 1 is a warhead group; wherein R 1 is attached to an atom adjacent to the atom where T is attached;
• each R 2 is independently -R, halogen, -haloalkyl, -OR, -SR, -CN, -N0 2 , -S0 2 R, -SOR, -C(0)R, -C0 2 R, -C(0)N(R) 2 , -NRC(0)R, -NRC(0)N(R) 2 , -NRS0 2 R, or -N(R) 2 ;
• R 3 is hydrogen, C 2 _ 6 alkenyl, -W-Cy, or Ci_ 6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-3 groups independently selected from halogen, -CN, oxo, -OR', or -C(0)0(Ci_ 6 alkyl);
• W is absent or is a bivalent Ci_ 3 alkylene chain optionally substituted with one or more R' ' and wherein one methylene unit of W is optionally replaced with -O- , -S-, or -NR'-;
• each R is independently hydrogen or Ci_ 6 alkyl
• each R is independently halogen or Ci_ 6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-3 groups independently selected from halogen, -CN, oxo, or -OR'; Cy is phenyl, C3_ 7 cycloalkyl, or a 3-7 membered monocyclic or 5-10 membered bicyclic saturated, partially unsaturated, or heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x ; each R x is independently H, -CN, oxo, -NH 2 , Ci_ 6 alkyl, halogen, -OR , -N(R') 2 , -NHC(0)(Ci_ 6 alkyl), -C(0)N(R') 2 , -C(0)0(Ci_ 6 alkyl), -NHS0 2 (Ci_ 6 alkyl), or -S0 2 N(R') 2
• R 3 is absent if not allowed by valence
• each of R 4 and R 4 is independently hydrogen or an optionally substituted group selected from Ci_6 aliphatic, phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring which is optionally bridged, a 4-7 membered heterocylic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic saturated, partially unsaturated or aryl ring, which is optionally bridged;
• each of R 5 and R 5 is independently -R, halogen, -OR, -SR, -CN, -N0 2 , -S0 2 R, -SOR, -C(0)R,
• Y is O or NR a ;
• R a is hydrogen or an optionally substituted Ci_ 6 aliphatic group
• T is a covalent bond or a bivalent straight or branched, saturated or unsaturated Ci_ 6 hydrocarbon chain wherein one or more methylene units are optionally replaced by -0-, -S-, -N(R)-, - C(O)-, -OC(O)-, -C(0)0-, -C(0)N(R)-, -N(R)C(0)-, -N(R)C(0)N(R)-, -S(O)-, -S0 2 -, - S0 2 N(R)-, -N(R)S0 2 -, or -N(R)S0 2 N(R)-;
• each of R 6 and R 7 is independently -R, halogen, -OR, -SR, -CN, -N0 2 , -S0 2 R, -SOR, -C(0)R,
• X 1 is -NR 4 . In certain embodiments, X 1 is N. In certain embodiments, X 1 is -CR 4 R 4 . In certain embodiments, X 1 is -CR 4 .
• X 2 is -NR 5 . In certain embodiments, X 2 is N. In certain embodiments, X 2 is -CR 5 R 5 . In certain embodiments, X 2 is -CR 5 .
• X 3 is N. In certain embodiments, X 3 is CR 6 .
• X 4 is N. In certain embodiments, X 4 is CR 7 .
• X 5 is N. In certain embodiments, X 5 is C. In certain embodiments, X 5 is CH.
• G is H. In certain embodiments, G is O. In certain embodiments, G is OR. In certain embodiments, G is N(R)(R).
• G is OMe. In certain embodiments, G is NH 2 .
• Y is O. In certain embodiments, Y is NR a .
• Ring A is an optionally substituted group selected from phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic saturated, partially unsaturated or aryl ring.
• Ring A is an optionally substituted phenyl group. In some embodiments, Ring A is an optionally substituted a 3-8 membered saturated or partially unsaturated carbocyclic ring. In some embodiments, Ring A is an optionally substituted 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, Ring A is an optionally substituted 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, Ring A is an optionally substituted 7-10 membered bicyclic saturated, partially unsaturated or aryl ring.
• Ring A is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, cyclooctyl, [3.3.0]bicyclooctanyl, [4.3.0]bicyclononanyl, [4.4.0]bicyclodecanyl, [2.2.2]bicyclooctanyl, fluorenyl, phenyl, naphthyl, indanyl, tetrahydronaphthyl, acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolinyl, carb
• Ring A is phenyl, cyclohexyl, cyclohexenyl, cyclopentyl, cyclobutyl, cyclopropyl, pyridine, pyrmidine, pyrazine, pyridazine, pyrrole, pyrazole, piperidine, piperidin-one, pyrrolidine, tetrahydropyran, tetrahydrofuran, tetrahydrothiophene dioxide, or cyclobutene dione.
• Ring A is an optionally substituted group selected from phenyl, cyclohexyl, a 7-8 membered saturated or partially unsaturated carbocyclic ring, or a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• Ring A is an optionally substituted group selected from phenyl or cyclohexyl.
• Ring A is substituted as defined herein. In some embodiments, Ring A is substituted with one, two, or three R 2 groups each of which is independently selected. Exemplary substituents on Ring A include Br, I, CI, F, Me, -CF 3 , -OMe, -OR, -N(R) 2 , pyrazolyl, thiazolyl, piperidinyl, piperazinyl, or morpholinyl.
• Ring A comprises one or more chiral centers which are of a particular configuration.
• Ring A is a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic saturated or partially unsaturated ring, wherein substituents -T-Y- and R 1 of Ring A are in a "cis" configuration.
• X J , G, Y, T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• a compound of the present invention is of formula I-cis(l):
• X J , G, Y, T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the present invention provides a compound of formula I-cis(l), wherein Ring A is a 3-8 membered saturated or partially unsaturated carbocyclic ring.
• the present invention provides a compound of formula I-cis(l), wherein Ring A is a a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• the present invention provides a compound of formula I-cis(l), wherein Ring A is a 7-10 membered bicyclic saturated or partially unsaturated ring.
• the present invention provides a compound of formula I- cis(l), wherein Ring A is optionally substituted and is selected from cyclohexyl, cyclohexenyl, cyclopentyl, cyclobutyl, cyclopropyl, piperidine, piperidin-one, pyrrolidine, tetrahydropyran, tetrahydrofuran, tetrahydrothiophene dioxide, or cyclobutene dione.
• the present invention provides a compound of formula I-cis(l), wherein Ring A is optionally substituted tetrahydrofuran.
• Exemplary compounds of formula I-cis(l) include, for instance, compounds 1-82, I- 92, 1-114, 1-241, 1-186, and the like.
• the present invention provides a compound of formula I- cis(2), wherein Ring A is any of the structures described above and herein which are capable of having chiral centers at the sites depicted in formula I-cis(l).
• a compound of the present invention is of formula I-cis(2):
• Ring A, R 1 , X5 J , G, Y, T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the present invention provides a compound of formula I-cis(2), wherein Ring A is a 3-8 membered saturated or partially unsaturated carbocyclic ring.
• the present invention provides a compound of formula I-cis(2), wherein Ring A is a a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• the present invention provides a compound of formula I-cis(2), wherein Ring A is a 7-10 membered bicyclic saturated or partially unsaturated ring.
• the present invention provides a compound of formula I- cis(2), wherein Ring A is optionally substituted and is selected from cyclohexyl, cyclohexenyl, cyclopentyl, cyclobutyl, cyclopropyl, piperidine, piperidin-one, pyrrolidine, tetrahydropyran, tetrahydrofuran, tetrahydrothiophene dioxide, or cyclobutene dione.
• the present invention provides a compound of formula I-cis(2), wherein Ring A is optionally substituted tetrahydrofuran.
• Exemplary compounds of formula I-cis(2) include, for instance, compounds 1-66, I- 93, 1-119, 1-240, 1-185, and the like.
• the present invention provides a compound of formula I- cis(2), wherein Ring A is any of the structures described above and herein which are capable of having chiral centers at the sites depicted in formula I-cis(2).
• each R 2 is independently -R.
• each R 2 is hydrogen. [0081] In another embodiment, each R 2 is independently halogen, -haloalkyl, -OR, -SR, - CN, -NO 2 , -SO 2 R, -SOR, -C(0)R, -CO 2 R, -C(0)N(R) 2 , -NRC(0)R, -NRC(0)N(R) 2 , -NRS0 2 R, or -N(R) 2 .
• each R 2 is independently methyl, ethyl, propyl, i-propyl, F, CI, Br, I, CF 3 , piperidinyl, piperazinyl, morpholinyl, tetrahydropyridinyl, pyrazolyl, thiazolyl, or tetrazolyl.
• each R 2 is independently -CH 3 , -CI, -F, -CF 3 , or -OMe; or is selected from
• Ring A is selected from
• R 3 is hydrogen
• R 3 is C 2 _ 6 alkenyl, -W-Cy, or Ci_ 6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-3 groups independently selected from halogen, -CN, oxo, - OR', or -C(0)0(Ci_6 alkyl).
• W is absent (i.e., W is a covalent bond).
• W is a bivalent Ci_3 alkylene chain optionally substituted with one or more R" and wherein one methylene unit of W is optionally replaced with -O- , -S-, or -NR'-.
• Cy is phenyl wherein Cy is optionally substituted with 1-3 R x .
• Cy is C3-7 cycloalkyl wherein Cy is optionally substituted with 1-3 R x .
• Cy is a 3-7 membered monocyclic or 5-10 membered bicyclic saturated or partially unsaturated heterocyclic having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• Cy is a 3-7 membered monocyclic or 5-10 membered bicyclic heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• each R x is independently H, -CN, oxo, -NH 2 , Ci_ 6 alkyl, halogen, -OR , -N(R') 2 , -C(0)R', -NHC(0)(Ci_ 6 alkyl), -C(0)N(R') 2 , -C(0)0(Ci_ 6 alkyl), - NHS0 2 (Ci_6 alkyl), or -S0 2 N(R') 2 .
• R x is -C(0)R'. In some embodiments, R x is -C(0)Me.
• R 3 is Ci_6 alkyl.
• R 3 is cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, oxetanyl, phenyl, piperidinyl, pyridinyl, pyrazolyl, thiazolyl, or pyridin-one-yl.
• R 3 is
• R 3 is
• R 3 is absent.
• each of R 4 and R 4 is independently hydrogen.
• each of R 4 and R 4 is independently an optionally substituted phenyl. In certain embodiments, each of R 4 and R 4 is independently an optionally substituted Ci_6 aliphatic. In certain embodiments, each of R 4 and R 4 is independently a 3-8 membered saturated or partially unsaturated carbocyclic ring. In other embodiments, each of R 4 and R 4 is independently an optionally substituted 4-7 membered heterocylic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• each of R 4 and R 4 is independently an optionally substituted phenyl or a 3-8 membered saturated or partially unsaturated carbocyclic ring. In certain embodiments, each of R 4 and R 4 is independently an optionally substituted phenyl.
• each of R 4 and R 4 is independently an optionally substituted cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, oxetanyl, phenyl, piperidinyl, pyridinyl, pyrazolyl, thiazolyl, or pyridin-one-yl.
• each of R 4 and R 4 is independently is ethyl, phenyl, cyclohexyl,
• each of R 5 and R 5 is independently -R.
• each of R 5 and R 5 is independently H. In certain embodiments, both of R 5 and R 5 are H. In certain embodiments, one of R 5 and R 5 is H. In certain embodiments, each of R 5 and R 5 is independently H, or -Me.
• each of R 5 and R 5 is independently halogen, -OR, -SR, - CN, -N0 2 , -S0 2 R, -SOR, -C(0)R, -C0 2 R, -C(0)N(R) 2 , -NRC(0)R, -NRC(0)N(R) 2 , -NRS0 2 R, or -N(R) 2 .
• R a is hydrogen. In some embodiments, R a is optionally substituted Ci_ 6 aliphatic group.
• T is a covalent bond. In another embodiment, T is a bivalent straight or branched, saturated or unsaturated Ci_ 6 hydrocarbon chain wherein one or more methylene units are optionally replaced by -0-, -S-, -N(R)-, -C(O)-, -OC(O)-, -C(0)0-, -C(0)N(R)-, -N(R)C(0)-, -N(R)C(0)N(R)-, -S(O)-, -S0 2 -, -S0 2 N(R)-, -N(R)S0 2 -, or -N(R)S0 2 N(R)-.
• T is a bivalent straight or branched, saturated or unsaturated Ci_6 hydrocarbon chain wherein one or more methylene units are optionally replaced by -0-, -S-, -N(R)-, -C(O)-, -OC(O)-, -C(0)0-, -C(0)N(R)-, -N(R)C(0)-, -N(R)C(0)N(R)-, -N(R)S0 2 -, or -N(R)S0 2 N(R)-.
• T is a covalent bond or a bivalent straight or branched, saturated or unsaturated Ci_ 6 hydrocarbon chain.
• q is 0. In other embodiments, q is 1. In other embodiments, q is 2-6.
• the present invention provides a compound of formula I-a,
• R 1 , R 2 , R 3 , R 4 , R 5 , R 5 , R a , T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the compound is of formula I-b:
• Ring A, R 1 , R 2 , R 3 , R 4 , T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-c:
• R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-d:
• R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-e:
• Ring A, R 1 , R 2 , R 3 , R 5 , R 5 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-f:
• Ring A, R 1 , R 2 , R 3 , R 5 , R 5 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-g:
• Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-h:
• Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the present invention provides a compound of formula I-h, wherein Ring A is an optionally substituted group selected from phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic saturated, partially unsaturated or aryl ring.
• Ring A is an optionally substituted group selected from phenyl, a 3-8 membered saturated or partially unsaturated carbocyclic ring, a 5-6 membered monocyclic heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or a 7-10 membered bicyclic
• a compound is of formula I-h and Ring A is an optionally substituted monocyclic ring. In some embodiments, a compound is of formula I-h and Ring A is an optionally substituted monocyclic carbocycle. In some embodiments, a compound is of formula I-h and Ring A is an optionally substituted monocyclic heterocycle. [00118] In some embodiments, a compound is of formula I-h and Ring A is optionally substituted aryl. In certain embodiments, a compound is of formula I-h and Ring A is optionally substituted phenyl.
• a compound is of formula I-h and Ring A is optionally substituted heteroaryl. In certain embodiments, a compound is of formula I-h and Ring A is optionally substituted pyridinyl.
• a compound is of formula I-h and Ring A is an optionally substituted 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• a compound is of formula I-h and Ring A is an optionally substituted 5 membered saturated heterocyclic ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
• a compound is of formula I-h and Ring A is phenyl, cyclohexyl, cyclohexenyl, cyclopentyl, cyclobutyl, cyclopropyl, pyridine, pyrmidine, pyrazine, pyridazine, pyrrole, pyrazole, piperidine, piperidin-one, pyrrolidine, tetrahydropyran, tetrahydrofuran, tetrahydrothiophene dioxide, or cyclobutene dione.
• a compound is of formula I-h and Ring A is an optionally substituted group selected from tetrahydropyran, tetrahydrofuran, or tetrahydrothiophene dioxide.
• a compound is of formula I-h and Ring A is optionally substituted tetrahydropyran.
• a compound is of formula I-h and Ring A is unsubstituted tetrahydropyran.
• a compound is of formula I-h and Ring A is optionally substituted tetrahydrofuran.
• a compound is of formula I-h and Ring A is unsubstituted tetrahydrofuran.
• a compound is of formula I-h and Ring A is optionally substituted tetrahydrothiophene dioxide. In certain embodiments, a compound is of formula I-h and Ring A is unsubstituted tetrahydrothiophene dioxide.
• a compound is of formula I-h and Ring A is substituted as defined herein.
• a compound is of formula I-h and Ring A is substituted with one, two, or three R 2 groups each of which is independently selected.
• exemplary substituents on Ring A include Br, I, CI, F, Me, -CF 3 , -OMe, -OR, -N(R) 2 , pyrazolyl, thiazolyl, piperidinyl, piperazinyl, or morpholinyl.
• a compound is of formula I-h and Ring A is substituted with one, two, or three R 2 groups each of which is independently selected.
• a compound is of formula I-h and Ring A is a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Ring A is substituted with one, two, or three R 2 groups each of which is independently selected.
• a compound is of formula I-h and Ring A is tetrahydropyran substituted with one, two, or three R 2 groups each of which is independently selected.
• a compound is of formula I-h and Ring A is tetrahydrofuran substituted with one, two, or three R 2 groups each of which is independently selected.
• a compound is of formula I-h and Ring A is tetrahydrothiophene dioxide substituted with one, two, or three R 2 groups each of which is independently selected.
• a compound is of formula I-h and each R 2 is independently methyl, ethyl, propyl, i-propyl, F, CI, Br, I, CF 3 , piperidinyl, piperazinyl, morpholinyl, tetrahydropyridinyl, pyrazolyl, thiazolyl, or tetrazolyl.
• a compound is of formula I-h and R 2 is optionally substituted pyrazolyl. In some embodiments, a compound is of formula I-h and R 2 is n-substituted pyrazolyl. In some embodiments, a compound is of formula I-h and R 2 is n-alkyl pyrazolyl. In some embodiments, a compound is of formula I-h and R 2 is n-methyl pyrazolyl.
• a compound is of formula I-h and R 2 is optionally substituted pyridinyl. In some embodiments, a compound is of formula I-h and R 2 is unsubstituted pyridinyl.
• a compound is of formula I-h and R 2 is n-substituted tetrazolyl. In some embodiments, a compound is of formula I-h and R 2 is n-alkyl tetrazolyl. In some embodiments, a compound is of formula I-h and R 2 is n-methyl tetrazolyl. [00134] In some embodiments, a compound is of formula I-h and R 2 is optionally substituted piperazinyl. In some embodiments, a compound is of formula I-h and R 2 is n-substituted piperazinyl.
• a compound is of formula I-h and R 2 is n-alkyl piperazinyl. In some embodiments, a compound is of formula I-h and R 2 is n-methyl piperazinyl. In some embodiments, a compound is of formula I-h and R 2 is n-ethyl piperazinyl.
• a compound is of formula I-h and each R 2 is independently halogen, -haloalkyl, -OR, -SR, -CN, -N0 2 , -S0 2 R, -SOR, -C(0)R, -C0 2 R, -C(0)N(R) 2 , - NRC(0)R, -NRC(0)N(R) 2 , -NRS0 2 R, or -N(R) 2 .
• a compound is of formula I-h and R 2 is -OR. In certain embodiments, a compound is of formula I-h and R 2 is -OH.
• a compound is of formula I-h and R 2 is -C(0)R. In certain embodiments, a compound is of formula I-h and R 2 is -C(0)Me.
• a compound is of formula I-h and each R 2 is independently - R.
• a compound is of formula I-h and R 2 is optionally substituted cycloalkyl. In some embodiments, a compound is of formula I-h and R 2 is optionally substituted cyclopropyl. In some embodiments, a compound is of formula I-h and R 2 is unsubstituted cyclopropyl.
• a compound is of formula I-h and R 3 is C 2 _ 6 alkenyl, -W-Cy, or Ci_6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-3 groups independently selected from halogen, -CN, oxo, -OR', or -C(0)0(Ci_ 6 alkyl).
• a compound is of formula I-h and R 3 is Ci 6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-3 -OH groups.
• a compound is of formula I-h and R 3 is Ci_6 alkyl, wherein the Ci_ 6 alkyl is optionally substituted with 1-2-OH groups.
• a compound is of formula I-h and R 3 is C 3 _ 6 alkyl optionally substituted with 1-3 -OH groups.
• a compound is of formula I-h and R 3 is C 3 _ 6 alkyl optionally substituted with 1-2 -OH groups.
• a compound is of formula I-h and R 3 is Ci 6 alkyl. In some embodiments, a compound is of formula I-h and R 3 is methyl, ethyl, or propyl. In certain embodiments, a compound is of formula I-h and R 3 is methyl. In certain embodiments, a compound is of formula I-h and R 3 is ethyl. In certain embodiments, a compound is of formula I-h and R 3 is propyl, e.g., isopropyl.
• a compound is of formula I-h and R 3 is -W-Cy. In certain embodiments, a compound is of formula I-h, R 3 is -W-Cy, and W is absent (i.e., W is a covalent bond).
• a compound is of formula I-h, R 3 is -W-Cy, and W is a bivalent Ci_3 alkylene chain optionally substituted with one or more R" and wherein one methylene unit of W is optionally replaced with -0-, -S-, or -NR'-.
• a compound is of formula I-h, R 3 is -W-Cy, and Cy is C3-7 cycloalkyl wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, and Cy is a 3-7 membered monocyclic saturated ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, W is a bivalent Ci_ 3 alkylene chain optionally substituted with one or more R", and Cy is a 3-7 membered monocyclic saturated ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, W is a bivalent Ci alkylene chain optionally substituted with one or more R", and Cy is a 3-7 membered monocyclic saturated ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, W is a bivalent Ci_ 3 alkylene chain optionally substituted with one or more R", and Cy is a 3-5 membered monocyclic saturated ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, W is a bivalent Ci alkylene chain optionally substituted with one or more R", and Cy is a 5 membered monocyclic saturated ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• a compound is of formula I-h, R 3 is -W-Cy, W is a bivalent Ci alkylene chain optionally substituted with one or more R", and Cy is a 5 membered monocyclic saturated ring having 1 heteroatom independently selected from nitrogen, oxygen, or sulfur, wherein Cy is optionally substituted with 1-3 R x .
• R 3 is as described above and R x is C(0)R'.
• R 3 is as described above and R x is -C(0)Me.
• a compound is of formula I-h and R 3 is
• a compound is of formula I-h and R 3 is:
• a compound is of formula I-h and R 4 is optionally substituted phenyl.
• a compound is of formula I-h and R 4 is phenyl optionally substituted with 1-5 halogens.
• a compound is of formula I-h and R 4 is phenyl optionally substituted with 1-5 alkoxy groups.
• a compound is of formula I-h and R 4 is phenyl optionally substituted with 1-5 groups independently selected from halogen and alkoxy groups.
• a compound is of formula I-h and R 4 is phenyl optionally substituted with 1-5 groups independently selected from chloro, fluoro, methoxy, and ethoxy.
• a compound is of formula I-h and R 4 is optionally substituted phenyl, wherein the optional substitution is any of those described above and herein.
• a compound is of formula I-h and R 4 is ethyl, phenyl, cyclohexyl,
• a compound is of formula I-h and R 4 is
• a compound of formula I-h is of formula I-h(cis)(l) or I- h(cis)(2):
• Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• a compound of formula I-h is of formula I-h(cis)(l):
• Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• a compound of formula I-h is of formula I-H(cis)(2): I-h(cis)(2) or a pharmaceutically acceptable salt thereof, wherein each of Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-j :
• Ring A, R 1 , R 2 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-k:
• Ring A, R 1 , R 2 , R 3 , R 4 , R a , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound of formula I-n:
• Ring A, R 1 , R 2 , R 3 , R 4 , and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the compound is of formula I-q:
• Ring A, R 1 , R 2 , R 3 , R 4 , T, and q is as defined above and described in embodiments, classes and subclasses above and herein, singly or in combination.
• the invention provides a compound selected from Table 1 or Table 2:
• the invention provides a compound selected from Table 2: TABLE 2
• the invention provides a compound selected from:
• the present invention provides a compound selected from Table 3
• the present invention provides a compound selected from those depicted above, or a pharmaceutically acceptable salt thereof.
• R 1 group of any of the formulae herein is -L-Y, wherein:
• Y is hydrogen, Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN, or a 3-10 membered monocyclic or bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein said ring is substituted with 1-4 R e groups; and
• each R e is independently selected from -Q-Z, oxo, N0 2 , halogen, CN, a suitable leaving group, or a Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN, wherein:
• Q is a covalent bond or a bivalent Ci_ 6 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by -N(R)-, -S-, -0-, -C(O)-, -OC(O)-, -C(0)0-, -SO-, or -S0 2 -, -N(R)C(0)-, -C(0)N(R)-, -N(R)S0 2 -, or -S0 2 N(R)-; and
• Z is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN.
• L is a covalent bond
• L is a bivalent Ci_8 saturated or unsaturated, straight or branched, hydrocarbon chain. In certain embodiments, L is -CH 2 -. [00166] In certain embodiments, L is a covalent bond, -CH 2 -, -NH-, -CH 2 NH-, -NHCH 2 -, - NHC(O)-, -NHC(0)CH 2 OC(0)-, -CH 2 NHC(0)-, -NHS0 2 -, -NHS0 2 CH 2 -, -NHC(0)CH 2 OC(0)-, or -S0 2 NH-.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two additional methylene units of L are optionally and independently replaced by -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, -C(0)0-, cyclopropylene, -0-, -N(R)-, or -C(O)-.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-, -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, or -C(0)0-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-.
• L is a bivalent C 2 _g straight or branched, hydrocarbon chain wherein L has at least one double bond.
• a double bond may exist within the hydrocarbon chain backbone or is "exo" to the backbone chain and thus forming an alkylidene group.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, or -C(0)0-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-.
• NRC(0)C( CH 2 )CH 2 -, -CH 2 NRC(0)-, -CH 2 CH 2 NRC(0)-, or -CH 2 NRC(0)cyclopropylene-; wherein R is H or optionally substituted Ci_ 6 aliphatic; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one triple bond.
• L has at least one triple bond and at least one methylene unit of L is replaced by -N(R)-, -N(R)C(0)-, -C(O)-, -C(0)0-, or -OC(O)-, or -0-.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein one methylene unit of L is replaced by cyclopropylene and one or two additional methylene units of L are independently replaced by -C(O)-, -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, or -S0 2 N(R)-.
• Exemplary L groups include -NHC(0)-cyclopropylene-S0 2 - and -NHC(O)- cyclopropylene-.
• Y is hydrogen, Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN, or a 3-10 membered monocyclic or bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein said ring is substituted with at 1-4 R e groups, each R e is independently selected from -Q-Z, oxo, N0 2 , halogen, CN, a suitable leaving group, or Ci_ 6 aliphatic, wherein Q is a covalent bond or a bivalent Ci_ 6 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by -N(R)-, -S-, -0-, -C(O)-, -OC(O)-, -C(0)0-, -SO-, or -S0 2
• Y is hydrogen
• Y is Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN.
• Y is C 2 _ 6 alkenyl optionally substituted with oxo, halogen, N0 2 , or CN.
• Y is C 2 _ 6 alkynyl optionally substituted with oxo, halogen, N0 2 , or CN.
• Y is C 2 _ 6 alkenyl.
• Y is C 2 _ 4 alkynyl.
• Y is Ci_ 6 alkyl substituted with oxo, halogen, N0 2 , or CN.
• Y groups include -CH 2 F, -CH 2 C1, -CH 2 CN, and -CH 2 N0 2 .
• Y is a saturated 3-6 membered monocyclic ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Y is substituted with 1 -4 R e groups, wherein each R e is as defined above and described herein.
• Y is a saturated 3-4 membered heterocyclic ring having 1 heteroatom selected from oxygen or nitrogen wherein said ring is substituted with 1-2 R e groups, wherein each R e is as defined above and described herein.
• exemplary such rings are epoxide and oxetane rings, wherein each ring is substituted with 1-2 R e groups, wherein each R e is as defined above and described herein.
• Y is a saturated 5-6 membered heterocyclic ring having 1-2 heteroatom selected from oxygen or nitrogen wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Such rings include piperidine and pyrrolidine, wherein each ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is -2 , or
• Y is a saturated 3-6 membered carbocyclic ring, wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl, wherein each ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein..
• Y is 1 — * , wherein R e is as defined above and described herein. In certain embodiments, Y is cyclopropyl optionally substituted with halogen, CN or N0 2 .
• Y is a partially unsaturated 3-6 membered monocyclic ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is a partially unsaturated 3-6 membered carbocyclic ring, wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is cyclopropenyl, cyclobutenyl, cyclopentenyl, or cyclohexenyl wherein each ring is substituted with 1-4 R e groups, wherein each R e is as defined
• Y is , wherein each R e is as defined above and described herein.
• Y is a partially unsaturated 4-6 membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is selected from:
• each R and R e is as defined above and described herein.
• Y is a 6-membered aromatic ring having 0-2 nitrogens wherein said ring is substituted with 1-4 R e groups, wherein each R e group is as defined above and described herein.
• Y is phenyl, pyridyl, or pyrimidinyl, wherein each ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein.
• Y is selected from:
• Y is a 5 membered partially unsaturated or aryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein said ring is substituted with 1- 4 R e groups, wherein each R e group is as defined above and described herein.
• rings are isoxazolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, pyrrolyl, furanyl, thienyl, triazole, thiadiazole, and oxadiazole, wherein each ring is substituted with 1-3 R e groups, wherein each R e group is as defined above and described herein.
• Y is selected from:
• Y is an 8-10 membered bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein R e is as defined above and described herein.
• Y is a 9-10 membered bicyclic, partially unsaturated, or aryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein R e is as defined above and described herein.
• Exemplary such bicyclic rings include 2,3-dihydrobenzo[d]isothiazole, wherein said ring is substituted with 1-4 R e groups, wherein R e is as defined above and described herein.
• each R e group is independently selected from -Q-Z, oxo, N0 2 , halogen, CN, a suitable leaving group, or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN, wherein Q is a covalent bond or a bivalent Ci_ 6 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by -N(R)-, -S-, -0-, -C(O)-, -OC(O)-, -C(0)0-, -SO-, or -S0 2 -, - N(R)C(0)-, -C(0)N(R)-, -N(R)S0 2 -, or -S0 2 N(R)-; and Z is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2
• R e is Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN. In other embodiments, R e is oxo, N0 2 , halogen, or CN.
• R e is -Q-Z, wherein Q is a covalent bond and Z is hydrogen (i.e., R e is hydrogen).
• R e is -Q-Z, wherein Q is a bivalent Ci_ 6 saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by -NR-, -NRC(O)-, -C(0)NR-, -S-, -0-, -C(O)-, -SO-, or -S0 2 -.
• Q is a bivalent C 2 _ 6 straight or branched, hydrocarbon chain having at least one double bond, wherein one or two methylene units of Q are optionally and independently replaced by -NR-, -NRC(O)-, -C(0)NR-, -S-, -0-, -C(O)-, -SO-, or -S0 2 -.
• the Z moiety of the R e group is hydrogen.
• R e is a suitable leaving group, ie a group that is subject to nucleophilic displacement.
• a “suitable leaving” is a chemical group that is readily displaced by a desired incoming chemical moiety such as the thiol moiety of a cysteine of interest.
• Suitable leaving groups are well known in the art, e.g., see, “Advanced Organic Chemistry,” Jerry March, 5 th Ed., pp. 351-357, John Wiley and Sons, N.Y.
• Such leaving groups include, but are not limited to, halogen, alkoxy, sulphonyloxy, optionally substituted alkylsulphonyloxy, optionally substituted alkenylsulfonyloxy, optionally substituted arylsulfonyloxy, acyl, and diazonium moieties.
• Suitable leaving groups include chloro, iodo, bromo, fluoro, acetoxy, methanesulfonyloxy (mesyloxy), tosyloxy, triflyloxy, nitro-phenylsulfonyloxy (nosyloxy), and bromo-phenylsulfonyloxy (brosyloxy).
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two additional methylene units of L are optionally and independently replaced by -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, -C(0)0-, cyclopropylene, -0-, -N(R)-, or -C(O)- ; and Y is hydrogen or Ci_6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a bivalent C 2 _g straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-, -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, or -C(0)0-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -C(O)-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or (e) L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by -OC(O)-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond and at least one methylene unit of L is replaced by -C(O)-, -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, or -C(0)0-, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, -0-, -N(R)-, or -C(O)-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein L has at least one triple bond and one or two additional methylene units of L are optionally and independently replaced by -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, or -C(0)0-, and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• (k) L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein one methylene unit of L is replaced by cyclopropylene and one or two additional methylene units of L are independently replaced by -NRC(O)-, -C(0)NR-, -N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -SO 2 -, -OC(O)-, or -C(0)0-; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN; or
• L is a covalent bond and Y is selected from:
• R e is as defined above and described herein; or
• R e is as defined above and described herein; or , wherein each R, Q, Z, and R e is as defined above and described herein; or
• each R and R e is as defined above and described herein;
• each R e is as defined above and described herein;
• each R and R e is as defined above and described herein;
• R e is as defined above and described herein; or
• R e is as defined above and described herein; or , wherein each R, Q, Z, and R e is as defined above and described herein; or
• each R and R e is as defined above and described herein;
• each R e is as defined above and described herein;
• each R and R e is as defined above and described herein;
• R e is as defined above and described herein; or
• R e is as defined above and described herein; or , wherein each R, Q, Z, and R e is as defined above and described herein; or
• each R and R e is as defined above and described herein;
• each R e is as defined above and described herein;
• each R and R e is as defined above and described herein;
• L is a bivalent Ci_8 saturated or unsaturated, straight or branched, hydrocarbon chain; and Y is selected from:
• R e is as defined above and described herein; or
• R e is as defined above and described herein; or , wherein each R, Q, Z, and R e is as defined above and described herein; or
• each R and R e is as defined above and described herein;
• each R e is as defined above and described herein;
• each R and R e is as defined above and described herein;
• (p) L is a covalent bond, -CH 2 -, -NH-, -C(O)-, -CH 2 NH-, -NHCH 2 -, -NHC(O)-, -NHC(0)CH 2 OC(0)-, -CH 2 NHC(0)-, -NHS0 2 -, -NHS0 2 CH 2 -, -NHC(0)CH 2 OC(0)-, or -S0 2 NH-; and Y is selected from:
• R e is as defined above and described herein; or
• R e is as defined above and described herein; or , wherein each R, Q, Z, and R e is as defined above and described herein; or
• each R e is as defined above and described herein; or (xi) a partially unsaturated 4-6 membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein each R e is as defined above and described herein; or 1 -2
• each R and R e is as defined above and described herein;
• each R e is as defined above and described herein;
• each R and R is as defined above and described herein; or (xvii) an 8-10 membered bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R e groups, wherein R e is as defined above and described herein.
• L is a bivalent C 2 _8 straight or branched, hydrocarbon chain wherein two or three methylene units of L are optionally and independently replaced by -NRC(O)-, -C(0)NR-, - N(R)S0 2 -, -S0 2 N(R)-, -S-, -S(O)-, -S0 2 -, -OC(O)-, -C(0)0-, cyclopropylene, -0-, -N(R)-, or -C(O)- ; and Y is hydrogen or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N0 2 , or CN.
• (r) L-Y is "pro-warhead" that is converted in vitro or in vivo to an irreversible warhead.
• L-Y is , wherein LG is a leaving group.
• L-Y is .
• the "pro-warhead” is converted to an irreversible warhead according to the following:
• the Y group of any of the formulae herein is selected from those set forth in Table 1, Table 2, Table 3, Table 7, or Table 8, wherein each wavy line indicates the point of attachment to the rest of the molecule.
• R 1 is -L-Y, wherein:
• L is a covalent bond or a bivalent Ci_g saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one, two, or three methylene units of L are optionally and independently replaced by -N(R)-, -N(R)C(0)-, -N(R)S0 2 -, -0-, -C(O)-, or -S0 2 -; and
• Y is hydrogen, or Ci_ 6 aliphatic optionally substituted with oxo, halogen, N(R) 2 , N0 2 , or CN.
• the Y group of R 1 group, -L-Y is selected from those set forth in Table 4, below, wherein each wavy line indicates the point of attachment to the rest of the molecule.
• each R e is independently a suitable leaving group, N0 2 , CN, or oxo.
• R 1 is selected from those set forth in Table 5, below, wherein each wavy line indicates the point of attachment to the rest of the molecule.
• each R e is independently a suitable leaving group, N0 2 , CN, or oxo.
• R 1 is selected from
• R 1 is selected from
• R 1 is selected from:
• R 1 is selected from those depicted in Table 1, Table 2, Table 3, Table 7, or Table 8.
• R 1 is a warhead group.
• R 1 groups i.e. warhead groups
• Protein kinases having a cysteine residue in the binding domain are known to one of ordinary skill in the art and include FGFR4, or a mutant thereof.
• Figure 4 provides SEQ ID NO. 1, which is the amino acid sequence of FGFR4.
• compounds of the present invention have a warhead group characterized in that inventive compounds target the cysteine 552 residue (which is highlighted by a box in Figure 4 and in bold with underlining below):
• R 1 is characterized in that the -L-Y moiety is capable of covalently binding to the cysteine 552 residue thereby irreversibly inhibiting the enzyme.
• the cysteine residue is Cys552 of FGFR4, or a mutant thereof, where the provided residue numbering is in accordance with Uniprot P22455).
• R 1 is characterized in that the -L-Y moiety is capable of covalently binding to a cysteine residue of FGFR4, thereby irreversibly inhibiting the enzyme.
• the cysteine residue is Cys 552.
• R 1 groups include, but are not limited to, those described herein and depicted above.
• the present invention provides any compound depicted in any table above, or a pharmaceutically acceptable salt thereof.
• compounds of the present invention are irreversible inhibitors of FGFR4, or a mutant thereof.
• the present invention provides a conjugate of the formula A:
• Cys552 is Cys552 of FGFR4;
• the modifier is a bivalent group resulting from covalent bonding of a warhead group with the Cys552 of FGFR4 kinase;
• the warhead group is a functional group capable of covalently binding to Cys552;
• the inhibitor moiety is a moiety that binds in the binding site of the FGFR4 kinase.
• the inhibitor moiety of conjugate A is of formula l-i:
• the inhibitor moiety of conjugate A is of formula 1-a-i:
• the inhibitor moiety of conjugate A is of formula l-b-i:
• the inhibitor moiety of conjugate A is of formula 1-c-i:
• the inhibitor moiety of conjugate A is of formula l-d-i:
• the inhibitor moiety of conjugate A is of formula I-e-i:
• the inhibitor moiety of conjugate A is of formula I-f-i:
• the inhibitor moiety of conjugate A is of formula l-g-i:
• the inhibitor moiety of conjugate A is of formula 1-h-i:
• the inhibitor moiety of conjugate A is of formula I-j-i:
• the inhibitor moiety of conjugate A is of formula I-k-i:
• the inhibitor moiety of conjugate A is of formula I-n-i:
• the inhibitor moiety of conjugate A is of formula I-q-i:
• the present invention provides a conjugate of any of the formulae below:
• each of Cys552, Modifier, Ring A, R 2 , R ⁇ R 4 , R 5 , R 5 , R a , X 1 , X 2 , X ⁇ X 4 , X 5 , T, Y, G and q, with respect to the above formulae is as defined and described in embodiments herein for formulae I, I-a, I-b, I-c, I-d, I-e, I-f, I-g, I-h, I-j, I-k, I-n, and I-q.
• the modifier moiety of any of conjugate described above is selected from those set forth in Table 6, below.
• Exemplary modifiers further include any bivalent group resulting from covalent bonding of a warhead moiety found in Table 1, Table 2, Table 3, Table 5, Table 7, or Table 8 with cysteine 552 of FGFR4. It will be understood that the exemplary modifiers below are shown as conjugated to the sulfhydryl of Cys552.
• the invention provides a composition comprising a compound of this invention or a pharmaceutically acceptable derivative thereof and a pharmaceutically acceptable carrier, adjuvant, or vehicle.
• the amount of compound in compositions of this invention is such that is effective to measurably inhibit a protein kinase, particularly FGFR4, or a mutant thereof, in a biological sample or in a patient.
• the amount of compound in compositions of this invention is such that is effective to measurably inhibit FGFR4, or a mutant thereof, in a biological sample or in a patient.
• a composition of this invention is formulated for administration to a patient in need of such composition.
• a composition of this invention is formulated for oral administration to a patient.
• patient means an animal, preferably a mammal, and most preferably a human.
• compositions of this invention refers to a nontoxic carrier, adjuvant, or vehicle that does not destroy the pharmacological activity of the compound with which it is formulated.
• Pharmaceutically acceptable carriers, adjuvants or vehicles that are used in the compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene- polyoxypropylene-
• a "pharmaceutically acceptable derivative” means any non-toxic salt, ester, salt of an ester or other derivative of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
• compositions of the present invention are administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir.
• parenteral as used herein includes subcutaneous, intravenous, intramuscular, intraarticular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques.
• the compositions are administered orally, intraperitoneally or intravenously.
• Sterile injectable forms of the compositions of this invention include aqueous or oleaginous suspension. These suspensions are formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents.
• the sterile injectable preparation is also be a sterile injectable solution or suspension in a nontoxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol.
• a nontoxic parenterally acceptable diluent or solvent for example as a solution in 1,3-butanediol.
• the acceptable vehicles and solvents that are employed are water, Ringer's solution and isotonic sodium chloride solution.
• sterile, fixed oils are conventionally employed as a solvent or suspending medium.
• any bland fixed oil employed includes synthetic mono- or di- glycerides.
• Fatty acids such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions.
• These oil solutions or suspensions also contain a long-chain alcohol diluent or dispersant, such as carboxymethyl cellulose or similar dispersing agents that are commonly used in the formulation of pharmaceutically acceptable dosage forms including emulsions and suspensions.
• Other commonly used surfactants such as Tweens, Spans and other emulsifying agents or bioavailability enhancers which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms are also be used for the purposes of formulation.
• compositions of this invention are orally administered in any orally acceptable dosage form.
• Exemplary oral dosage forms are capsules, tablets, aqueous suspensions or solutions.
• carriers commonly used include lactose and corn starch.
• Lubricating agents such as magnesium stearate, are also typically added.
• useful diluents include lactose and dried cornstarch.
• aqueous suspensions are required for oral use, the active ingredient is combined with emulsifying and suspending agents. If desired, certain sweetening, flavoring or coloring agents are optionally also added.
• pharmaceutically acceptable compositions of this invention are administered in the form of suppositories for rectal administration.
• These can be prepared by mixing the agent with a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature and therefore will melt in the rectum to release the drug.
• suitable non-irritating excipient include cocoa butter, beeswax and polyethylene glycols.
• compositions of this invention are also administered topically, especially when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin, or the lower intestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.
• Topical application for the lower intestinal tract can be effected in a rectal suppository formulation (see above) or in a suitable enema formulation. Topically-transdermal patches are also used.
• compositions are formulated in a suitable ointment containing the active component suspended or dissolved in one or more carriers.
• exemplary carriers for topical administration of compounds of this aremineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, polyoxypropylene compound, emulsifying wax and water.
• provided pharmaceutically acceptable compositions can be formulated in a suitable lotion or cream containing the active components suspended or dissolved in one or more pharmaceutically acceptable carriers.
• Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and water.
• compositions are optionally formulated as micronized suspensions in isotonic, pH adjusted sterile saline, or, preferably, as solutions in isotonic, pH adjusted sterile saline, either with or without a preservative such as benzylalkonium chloride.
• the pharmaceutically acceptable compositions are formulated in an ointment such as petrolatum.
• compositions of this invention are optionally administered by nasal aerosol or inhalation.
• Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and are prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other conventional solubilizing or dispersing agents.
• compositions of this invention are formulated for oral administration. Such formulations may be administered with or without food. In some embodiments, pharmaceutically acceptable compositions of this invention are administered without food. In other embodiments, pharmaceutically acceptable compositions of this invention are administered with food.
• compositions of the present invention that are optionally combined with the carrier materials to produce a composition in a single dosage form will vary depending upon the host treated, the particular mode of administration.
• provided compositions should be formulated so that a dosage of between 0.01 - 100 mg/kg body weight/day of the inhibitor can be administered to a patient receiving these compositions.
• a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, and the judgment of the treating physician and the severity of the particular disease being treated.
• the amount of a compound of the present invention in the composition will also depend upon the particular compound in the composition.
• Compounds and compositions described herein are generally useful for the inhibition of protein kinase activity of one or more enzymes.
• Drug resistance is emerging as a significant challenge for targeted therapies.
• drug resistance has been reported for Gleevec ® and Iressa ® , as well as several other kinase inhibitors in development.
• drug resistance has been reported for the cKit and PDGFR receptors. It has been reported that irreversible inhibitors may be effective against drug resistant forms of protein kinases (Kwak, E. L., R. Sordella, et al. (2005).
• Examples of kinases that are inhibited by the compounds and compositions described herein and against which the methods described herein are useful include FGFR4, or a mutant thereof.
• a provided compound inhibits FGFR4 selectively as compared to other FGFR kinases.
• the activity of a compound utilized in this invention as a test compound of FGFR4, or a mutant thereof may be assayed in vitro, in vivo or in a cell line.
• In vitro assays include assays that determine inhibition of either the phosphorylation activity and/or the subsequent functional consequences, or ATPase activity of activated FGFR4, or a mutant thereof. Alternate in vitro assays quantitate the ability of the test compound to bind to FGFR4. Inhibitor binding may be measured by radiolabeling the inhibitor prior to binding, isolating the test compound /FGFR4 complex and determining the amount of radiolabel bound.
• test compound binding may be determined by running a competition experiment where new test compounds are incubated with FGFR4 bound to known radioligands.
• Detailed conditions for assaying a compound utilized in this invention as a test compound of FGFR4, or a mutant thereof, are set forth in the Examples below.
• Protein tyrosine kinases are a class of enzymes that catalyze the transfer of a phosphate group from ATP or GTP to a tyrosine residue located on a protein substrate. Receptor tyrosine kinases act to transmit signals from the outside of a cell to the inside by activating secondary messaging effectors via a phosphorylation event. A variety of cellular processes are promoted by these signals, including proliferation, carbohydrate utilization, protein synthesis, angiogenesis, cell growth, and cell survival,
• FGF fibroblast growth factor
• PTK protein tyrosine kinase receptors regulates a diverse array of physiologic functions including mitogenesis, wound healing, cell differentiation and angiogenesis, and development. Both normal and malignant cell growth as well as proliferation are affected by changes in local concentration of FGFs, extracellular signalling molecules which act as autocrine as well as paracrine factors. Autocrine FGF signalling may be particularly important in the progression of steroid hormone-dependent cancers to a hormone independent state (Powers, et al. (2000) Endocr. Relat. Cancer, 7, 165- 197).
• FGFs and their receptors are expressed at increased levels in several tissues and cell lines and overexpression is believed to contribute to the malignant phenotype.
• the two prototypic members are acidic fibroblast growth factor (aFGF or FGF1) and basic fibroblast growth factor (bFGF or FGF2), and to date, at least twenty distinct FGF family members have been identified.
• the cellular response to FGFs is transmitted via four types of high affinity transmembrane protein tyrosine-kinase fibroblast growth factor receptors (FGFR) numbered 1 to 4 (FGFR1 to FGFR4).
• FGFR high affinity transmembrane protein tyrosine-kinase fibroblast growth factor receptors
• the receptors dimerize and auto- or trans-phosphorylate specific cytoplasmic tyrosine residues to transmit an intracellular signal that ultimately regulates nuclear transcription factor effectors.
• Compounds which inhibit FGFR will be useful in providing a means of preventing the growth or inducing apoptosis in tumors, particularly by inhibiting angiogenesis. It is therefore anticipated that the compounds will prove useful in treating or preventing proliferative disorders such as cancers. In particular tumours with activating mutants of receptor tyrosine kinases or upregulation of receptor tyrosine kinases may be particularly sensitive to the inhibitors.
• the invention provides a method for inhibiting FGFR4, or a mutant thereof, activity in a patient or in a biological sample comprising the step of administering to said patient or contacting said biological sample with a compound according to the invention.
• the FGFR4, or a mutant thereof activity is inhibited irreversibly. In certain embodiments, FGFR4, or a mutant thereof, activity is inhibited irreversibly by covalently modifying Cys 552 of FGFR4.
• the invention provides a method for treating a FGFR4- mediated disorder in a patient in need thereof, comprising the step of administering to said patient a compound according to the invention, or a pharmaceutically acceptable composition thereof.
• the present invention provides a method for treating hepatocellular carcinoma in a patient in need thereof, comprising the step of administering to said patient a compound according to the invention, or a pharmaceutically acceptable composition thereof.
• the present invention provides a method for treating Rhabdomyosarcoma, esophageal cancer, breast cancer, or cancer of a head or neck, in a patient in need thereof, comprising the step of administering to said patient a compound according to the invention, or a pharmaceutically acceptable composition thereof.
• clinical drug resistance refers to the loss of susceptibility of a drug target to drug treatment as a consequence of mutations in the drug target.
• the term “resistance” refers to changes in the wild-type nucleic acid sequence coding a target protein, and/or the protein sequence of the target, which changes decrease or abolish the inhibitory effect of the inhibitor on the target protein.
• treatment refers to reversing, alleviating, delaying the onset of, or inhibiting the progress of a disease or disorder, or one or more symptoms thereof, as described herein.
• treatment is administered after one or more symptoms have developed.
• treatment is administered in the absence of symptoms.
• treatment is administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment is also continued after symptoms have resolved, for example to prevent or delay their recurrence.
• the compounds and compositions, according to the method of the present invention are administered using any amount and any route of administration effective for treating or lessening the severity of a disorder provided above.
• the exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like.
• Compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage.
• dosage unit form refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
• the specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts.
• compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated.
• the compounds of the invention are administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
• Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
• the liquid dosage forms optionally contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
• the oral compositions can also include
• Injectable preparations for example, sterile injectable aqueous or oleaginous suspensions are formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
• the sterile injectable preparation are also a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
• acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution.
• sterile, fixed oils are conventionally employed as a solvent or suspending medium.
• any bland fixed oil can be employed including synthetic mono- or diglycerides.
• fatty acids such as oleic acid are used in the preparation of injectables.
• Injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
• the rate of compound release can be controlled.
• biodegradable polymers include poly(orthoesters) and poly(anhydrides).
• Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.
• compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
• suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
• Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
• the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar—agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol
• Solid compositions of a similar type are also employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
• the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.
• Solid compositions of a similar type are also employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
• the active compounds can also be in micro-encapsulated form with one or more excipients as noted above.
• the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art.
• the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch.
• Such dosage forms also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose.
• the dosage forms optionally also comprise buffering agents. They optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
• buffering agents optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
• embedding compositions that can be used include polymeric substances and waxes.
• Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
• the active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as required.
• Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention.
• the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body.
• Such dosage forms can be made by dissolving or dispensing the compound in the proper medium.
• Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
• the invention relates to a method of inhibiting protein kinase activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound.
• the invention relates to a method of inhibiting FGFR4, or a mutant thereof, activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound.
• the invention relates to a method of irreversibly inhibiting FGFR4, or a mutant thereof, activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound.
• biological sample includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
• Inhibition of FGFR4, or a mutant thereof, activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, blood transfusion, organ transplantation, biological specimen storage, and biological assays.
• Another embodiment of the present invention relates to a method of inhibiting protein kinase activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound.
• the invention relates to a method of inhibiting FGFR4, or a mutant thereof, activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound.
• the invention relates to a method of irreversibly inhibiting FGFR4, or a mutant thereof, activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound.
• the present invention provides a method for treating a disorder mediated by FGFR4, or a mutant thereof, in a patient in need thereof, comprising the step of administering to said patient a compound according to the present invention or pharmaceutically acceptable composition thereof. Such disorders are described in detail herein.
• the compounds of this invention, or pharmaceutical compositions thereof, are optionally incorporated into compositions for coating an implantable medical device, such as prostheses, artificial valves, vascular grafts, stents and catheters.
• an implantable medical device such as prostheses, artificial valves, vascular grafts, stents and catheters.
• Vascular stents for example, have been used to overcome restenosis (re-narrowing of the vessel wall after injury).
• patients using stents or other implantable devices risk clot formation or platelet activation. These unwanted effects are prevented or mitigated by pre-coating the device with a pharmaceutically acceptable composition comprising a kinase inhibitor.
• Implantable devices coated with a compound of this invention are another embodiment of the present invention.
• a compound of the present invention is tethered to a detectable moiety to form a probe compound.
• a probe compound of the invention comprises an irreversible protein kinase inhibitor of any formulae as described herein, a detectable moiety, and a tethering moiety that attaches the inhibitor to the detectable moiety.
• such probe compounds of the present invention comprise a provided compound of any formulae as described herein, tethered to a detectable moiety, R l , by a bivalent tethering moiety, -T 1 -.
• the tethering moiety is attached to a compound of the invention via Ring A, Ring B, or R 1 .
• R 1 is a bivalent warhead group denoted as R 1 .
• a provided probe compound is selected from any of formula I-t:
• Ring A, R 1 , R2% , and q is as defined above, and described in classes and subclasses herein, R 2 is a bivalent R 2 ; T 1 is a bivalent tethering moiety; and R l is a detectable moiety.
• R l is a detectable moiety selected from a primary label or a secondary label.
• R l is a detectable moiety selected from a fluorescent label (e.g., a fluorescent dye or a fluorophore), a mass-tag, a chemiluminescent group, a chromophore, an electron dense group, or an energy transfer agent.
• R l is biotin, biotin sulfoxide, a radioisotope, or a fluorescent label.
• detectable moiety is used interchangeably with the term “label” and “reporter” and relates to any moiety capable of being detected, e.g., primary labels and secondary labels.
• a presence of a detectable moiety can be measured using methods for quantifying (in absolute, approximate or relative terms) the detectable moiety in a system under study.
• such methods are well known to one of ordinary skill in the art and include any methods that quantify a reporter moiety (e.g., a label, a dye, a photocrosslinker, a cytotoxic compound, a drug, an affinity label, a photoaffmity label, a reactive compound, an antibody or antibody fragment, a biomaterial, a nanoparticle, a spin label, a fluorophore, a metal- containing moiety, a radioactive moiety, quantum dot(s), a novel functional group, a group that covalently or noncovalently interacts with other molecules, a photocaged moiety, an actinic radiation excitable moiety, a ligand, a photoisomerizable moiety, biotin, a biotin analog (e.g., biotin sulfoxide), a moiety incorporating a heavy atom, a chemically cleavable group, a photocleavable group, a redox-active agent,
• Primary labels such as radioisotopes (e.g., tritium, 32 P, 33 P, 35 S, 14 C, 123 I, 124 I, 125 I, or 131 I), mass-tags are stable isotopes (e.g., 13 C, 2 H, 17 0, 18 0, 15 N, 19 F, and 127 I), positron emitting isotopes (e.g., U C, 18 F, 13 N, 124 I, and 15 0), and fluorescent labels, which are signal generating reporter groups which can be detected without further modifications. Detectable moities are analyzed by methods.
• radioisotopes e.g., tritium, 32 P, 33 P, 35 S, 14 C, 123 I, 124 I, 125 I, or 131 I
• mass-tags are stable isotopes (e.g., 13 C, 2 H, 17 0, 18 0, 15 N, 19 F, and 127 I), positron emitting isotopes (e.g., U C,
• Exemplary methods are fluorescence, positron emission tomography, SPECT medical imaging, chemiluminescence, electron-spin resonance, ultraviolet/visible absorbance spectroscopy, mass spectrometry, nuclear magnetic resonance, magnetic resonance, flow cytometry, autoradiography, scintillation counting, phosphoimaging, and electrochemical methods.
• secondary label refers to moieties such as biotin and various protein antigens that require the presence of a second intermediate for production of a detectable signal.
• the secondary intermediate includes streptavidin-enzyme conjugates.
• antigen labels include antibody-enzyme conjugates.
• fluorescent label refers to moieties that absorb light energy at a defined excitation wavelength and emit light energy at a different wavelength.
• fluorescent labels include, but are not limited to: Alexa Fluor dyes (Alexa Fluor 350, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660 and Alexa Fluor 680), AMCA, AMCA-S, BODIPY dyes (BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 493/503, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665), Carboxyr
• Carboxytetramethylrhodamine (TAMRA), Texas Red, Texas Red-X, 5(6)-Carboxyfluorescein, 2,7-Dichlorofluorescein, N,N-Bis(2,4,6-trimethylphenyl)-3,4:9,10-perylenebis(dicarboximide, HPTS, Ethyl Eosin, DY-490XL MegaStokes, DY-485XL MegaStokes, Adirondack Green 520, ATTO 465, ATTO 488, ATTO 495, YOYO-l,5-FAM, BCECF, dichlorofluorescein, rhodamine 110, rhodamine 123, YO-PRO-1, SYTOX Green, Sodium Green, SYBR Green I, Alexa Fluor 500, FITC, Fluo-3, Fluo-4, fluoro-emerald, YoYo-1 ssDNA, YoYo-1 dsDNA, YoYo
• mass-tag refers to any moiety that is capable of being uniquely detected by virtue of its mass using mass spectrometry (MS) detection techniques.
• mass-tags include electrophore release tags such as N-[3-[4'-[(p- Methoxytetrafluorobenzyl)oxy]phenyl]-3-methylglyceronyl]isonipecotic Acid, 4 ' -[2,3 ,5 ,6- Tetrafluoro-4-(pentafluorophenoxyl)]methyl acetophenone, and their derivatives.
• mass-tags include, but are not limited to, nucleotides, dideoxynucleotides, oligonucleotides of varying length and base composition, oligopeptides, oligosaccharides, and other synthetic polymers of varying length and monomer composition.
• nucleotides dideoxynucleotides
• oligonucleotides of varying length and base composition oligopeptides, oligosaccharides
• other synthetic polymers of varying length and monomer composition.
• a large variety of organic molecules, both neutral and charged (biomolecules or synthetic compounds) of an appropriate mass range (100-2000 Daltons) are also used as mass-tags.
• Stable isotopes e.g., 13 C, 2 H, 17 0, 18 0, and 15 N are also used as mass-tags.
• chemiluminescent group refers to a group which emits light as a result of a chemical reaction without the addition of heat.
• luminol 5-amino-2,3-dihydro-l,4-phthalazinedione
• oxidants like hydrogen peroxide (H 2 0 2 ) in the presence of a base and a metal catalyst to produce an excited state product (3- aminophthalate, 3-APA).
• chromophore refers to a molecule which absorbs light of visible wavelengths, UV wavelengths or IR wavelengths.
• die refers to a soluble, coloring substance which contains a chromophore.
• electrostatic dense group refers to a group which scatters electrons when irradiated with an electron beam.
• groups include, but are not limited to, ammonium molybdate, bismuth subnitrate, cadmium iodide, carbohydrazide, ferric chloride hexahydrate, hexamethylene tetramine, indium trichloride anhydrous, lanthanum nitrate, lead acetate trihydrate, lead citrate trihydrate, lead nitrate, periodic acid, phosphomolybdic acid, phosphotungstic acid, potassium ferricyanide, potassium ferrocyanide, ruthenium red, silver nitrate, silver proteinate (Ag Assay: 8.0-8.5%) "Strong", silver tetraphenylporphin (S-TPPS), sodium chloroaurate, sodium tungstate, thallium nitrate, thiosemicarbazide (TSC), ur
• FRET fluorescence resonance energy transfer
• molecular incorporating a heavy atom refers to a group which incorporates an ion of atom which is usually heavier than carbon.
• ions or atoms include, but are not limited to, silicon, tungsten, gold, lead, and uranium.
• photoaffinity label refers to a label with a group, which, upon exposure to light, forms a linkage with a molecule for which the label has an affinity.
• photocaged moiety refers to a group which, upon illumination at certain wavelengths, covalently or non-covalently binds other ions or molecules.
• photoisomerizable moiety refers to a group wherein upon illumination with light changes from one isomeric form to another.
• radioactive moiety refers to a group whose nuclei spontaneously give off nuclear radiation, such as alpha, beta, or gamma particles; wherein, alpha particles are helium nuclei, beta particles are electrons, and gamma particles are high energy photons.
• spin label refers to molecules which contain an atom or a group of atoms exhibiting an unpaired electron spin (i.e. a stable paramagnetic group) that in some embodiments are detected by electron spin resonance spectroscopy and in other embodiments are attached to another molecule.
• spin-label molecules include, but are not limited to, nitryl radicals and nitroxides, and in some embodiments are single spin-labels or double spin-labels.
• quantum dots refers to colloidal semiconductor nanocrystals that in some embodiments are detected in the near-infrared and have extremely high quantum yields (i.e., very bright upon modest illumination).
• a detectable moiety is attached to a provided compound via a suitable substituent.
• suitable substituent refers to a moiety that is capable of covalent attachment to a detectable moiety.
• moieties are well known to one of ordinary skill in the art and include groups containing, e.g., a carboxylate moiety, an amino moiety, a thiol moiety, or a hydroxyl moiety, to name but a few. It will be appreciated that such moieties are directly attached to a provided compound or via a tethering moiety, such as a bivalent saturated or unsaturated hydrocarbon chain.
• detectable moieties are attached to a provided compound via click chemistry.
• such moieties are attached via a 1,3-cycloaddition of an azide with an alkyne, optionally in the presence of a copper catalyst.
• Methods of using click chemistry are known in the art and include those described by Rostovtsev et al. , Angew. Chem. Int. Ed. 2002, 41, 2596-99 and Sun et al., Bioconjugate Chem., 2006, 17, 52-57.
• a click ready inhibitor moiety is provided and reacted with a click ready -T-R 1 moiety.
• click ready refers to a moiety containing an azide or alkyne for use in a click chemistry reaction.
• the click ready inhibitor moiety comprises an azide.
• the click ready -T-R 1 moiety comprises a strained cyclooctyne for use in a copper-free click chemistry reaction (for example, using methods described in Baskin et al., Proc. Natl. Acad. Sci. USA 2007, 104, 16793-16797).
• the detectable moiety, R l is selected from a label, a dye, a photocrosslinker, a cytotoxic compound, a drug, an affinity label, a photoaffinity label, a reactive compound, an antibody or antibody fragment, a biomaterial, a nanoparticle, a spin label, a fluorophore, a metal-containing moiety, a radioactive moiety, quantum dot(s), a novel functional group, a group that covalently or noncovalently interacts with other molecules, a photocaged moiety, an actinic radiation excitable moiety, a ligand, a photoisomerizable moiety, biotin, a biotin analog (e.g., biotin sulfoxide), a moiety incorporating a heavy atom, a chemically cleavable group, a photocleavable group, a redox-active agent, an isotopically labeled moiety, a
• R l is biotin or an analog thereof. In certain embodiments, R l is biotin. In certain other embodiments, R l is biotin sulfoxide.
• R l is a fluorophore.
• the fluorophore is selected from Alexa Fluor dyes (Alexa Fluor 350, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660 and Alexa Fluor 680), AMCA, AMCA-S, BODIPY dyes (BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 493/503, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665), Carboxyrhodamine 6G, carboxy-X-rhodamine (ROX), Cascade Blue, Cascade Yellow, Coumarin 34
• Alexa Fluor dyes Alexa Flu
• a provided probe compound comprises a tethering moiety, -T-, that attaches the irreversible inhibitor to the detectable moiety.
• tether or “tethering moiety” refers to any bivalent chemical spacer.
• Exemplary tethers are a covalent bond, a polymer, a water soluble polymer, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyl, optionally substituted cycloalkyl, optionally substituted heterocyclyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocycloalkylalkenyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocycloalkylalkenylalkyl, an optionally substituted amide moiety, an ether moiety, an ketone moiety, an ester moiety, an optionally substituted carbamate moiety, an optionally substituted hydrazone moiety, an optionally substituted hydrazine moiety, an optionally substituted oxime moiety, a disulfide moiety, an optionally substituted imine moiety, an optionally substituted sulfonamide moiety, a sulfone mo
• the tethering moiety, - T 1 - is selected from a covalent bond, a polymer, a water soluble polymer, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocycloalkylalkenyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocycloalkylalkenylalkyl.
• the tethering moiety is an optionally substituted heterocycle.
• the heterocycle is selected from aziridine, oxirane, episulfide, azetidine, oxetane, pyrroline, tetrahydrofuran, tetrahydrothiophene, pyrrolidine, pyrazole, pyrrole, imidazole, triazole, tetrazole, oxazole, isoxazole, oxirene, thiazole, isothiazole, dithiolane, furan, thiophene, piperidine, tetrahydropyran, thiane, pyridine, pyran, thiapyrane, pyridazine, pyrimidine, pyrazine, piperazine, oxazine, thiazine, dithiane, and dioxane.
• the heterocycle is piperazine.
• the tethering moiety is optionally substituted with halogen, -CN, -OH, -N0 2 , alkyl, S(O), and S(0) 2 .
• the water soluble polymer is a PEG group.
• the tethering moiety provides sufficient spatial separation between the detectable moiety and the protein kinase inhibitor moiety. In further embodiments, the tethering moiety is stable. In yet a further embodiment, the tethering moiety does not substantially affect the response of the detectable moiety. In other embodiments, the tethering moiety provides chemical stability to the probe compound. In further embodiments, the tethering moiety provides sufficient solubility to the probe compound.
• a tethering moiety, - T 1 - such as a water soluble polymer is coupled at one end to a provided irreversible inhibitor and to a detectable moiety, R l , at the other end.
• a water soluble polymer is coupled via a functional group or substituent of the provided irreversible inhibitor.
• a water soluble polymer is coupled via a functional group or substituent of the reporter moiety.
• examples of hydrophilic polymers for use in tethering moiety - T 1 -, include, but are not limited to: polyalkyl ethers and alkoxy-capped analogs thereof (e.g., polyoxyethylene glycol, polyoxyethylene/propylene glycol, and methoxy or ethoxy-capped analogs thereof, polyoxyethylene glycol, the latter is also known as polyethylene glycol or PEG); polyvinylpyrrolidones; polyvinylalkyl ethers; polyoxazolines, polyalkyl oxazolines and polyhydroxyalkyl oxazolines; polyacrylamides, polyalkyl acrylamides, and polyhydroxyalkyl acrylamides (e.g., polyhydroxypropylmethacrylamide and derivatives thereof); polyhydroxyalkyl acrylates; polysialic acids and analogs thereof, hydrophilic peptide sequences; polysaccharides and their derivatives, including dextran and dextran
• a water soluble polymer is any structural form.
• Exemplary forms are linear, forked or branched.
• multifunctional polymer derivatives include, but are not limited to, linear polymers having two termini, each terminus being bonded to a functional group which is the same or different.
• a water polymer comprises a poly(ethylene glycol) moiety.
• the molecular weight of the polymer is of a wide range. Exemlary ranges are between about 100 Da and about 100,000 Da or more.
• the molecular weight of the polymer is between about 100 Da and about 100,000 Da, about 100,000 Da, about 95,000 Da, about 90,000 Da, about 85,000 Da, about 80,000 Da, about 75,000 Da, about 70,000 Da, about 65,000 Da, about 60,000 Da, about 55,000 Da, about 50,000 Da, about 45,000 Da, about 40,000 Da, about 35,000 Da, 30,000 Da, about 25,000 Da, about 20,000 Da, about 15,000 Da, about 10,000 Da, about 9,000 Da, about 8,000 Da, about 7,000 Da, about 6,000 Da, about 5,000 Da, about 4,000 Da, about 3,000 Da, about 2,000 Da, about 1,000 Da, about 900 Da, about 800 Da, about 700 Da, about 600 Da, about 500 Da, about 400 Da, about 300 Da, about 200 Da, and about 100 Da.
• the molecular weight of the polymer is between about 100 Da and 50,000 Da. In some embodiments, the molecular weight of the polymer is between about 100 Da and 40,000 Da. In some embodiments, the molecular weight of the polymer is between about 1,000 Da and 40,000 Da. In some embodiments, the molecular weight of the polymer is between about 5,000 Da and 40,000 Da. In some embodiments, the molecular weight of the polymer is between about 10,000 Da and 40,000 Da. In some embodiments, the poly(ethylene glycol) molecule is a branched polymer. In further embodiments, the molecular weight of the branched chain PEG is between about 1,000 Da and about 100,000 Da.
• Exemplary ranges are about 100,000 Da, about 95,000 Da, about 90,000 Da, about 85,000 Da, about 80,000 Da, about 75,000 Da, about 70,000 Da, about 65,000 Da, about 60,000 Da, about 55,000 Da, about 50,000 Da, about 45,000 Da, about 40,000 Da, about 35,000 Da, about 30,000 Da, about 25,000 Da, about 20,000 Da, about 15,000 Da, about 10,000 Da, about 9,000 Da, about 8,000 Da, about 7,000 Da, about 6,000 Da, about 5,000 Da, about 4,000 Da, about 3,000 Da, about 2,000 Da, and about 1,000 Da.
• the molecular weight of a branched chain PEG is between about 1,000 Da and about 50,000 Da.
• the molecular weight of a branched chain PEG is between about 1,000 Da and about 40,000 Da. In some embodiments, the molecular weight of a branched chain PEG is between about 5,000 Da and about 40,000 Da. In some embodiments, the molecular weight of a branched chain PEG is between about 5,000 Da and about 20,000 Da.
• the foregoing list for substantially water soluble backbones is by no means exhaustive and is merely illustrative, and in some embodiments, polymeric materials having the qualities described above are suitable for use in methods and compositions described herein.
• the tethering moiety, -T 1 - has one of the following structures:
• the tethering moiety, - T 1 - has the following structure:
• the tethering moiety, - T 1 - has the following structure:
• the tethering moiety, - T 1 - has the following structure:
• the tethering moiety, - T 1 - has the following structure [00324] :
• - T ⁇ -R 1 is of the following structure:
• - T ⁇ -R 1 is of the following structure:
• - T ⁇ -R* is of the following structure:
• - T ⁇ -R* is of the following structure:
• a probe compound of formula I-t is derived from any compound described herein.
• the probe compound is one of the following structures:
• T ⁇ -R 1 reagents are commercially available.
• biotinylating reagents are available from, e.g., Thermo Scientific having varying tether lengths.
• Such reagents include NHS-PEG 4 -Biotin and NHS-PEGi 2 -Biotin.
• analogous probe structures to the ones exemplified above are prepared using click-ready inhibitor moieties and click-ready - T ⁇ R 1 moieties, as described herein.
• a provided probe compound covalently modifies a phosphorylated conformation of a protein kinase.
• the phosphorylated conformation of the protein kinase is either an active or inactive form of the protein kinase.
• the phosphorylated conformation of the protein kinase is an active form of said kinase.
• the probe compound is cell permeable.
• the present invention provides a method for determining occupancy of a protein kinase by a provided irreversible inhibitor (i.e., a compound of any of the formulae presented herein) in a patient, comprising providing one or more tissues, cell types, or a lysate thereof, obtained from a patient administered at least one dose of a compound of said irreversible inhibitor, contacting said tissue, cell type or lysate thereof with a probe compound (i.e., a compound of formula I-t) to covalent modify at least one protein kinase present in said lysate, and measuring the amount of said protein kinase covalently modified by the probe compound to determine occupancy of said protein kinase by said compound as compared to occupancy of said protein kinase by said probe compound.
• a probe compound i.e., a compound of formula I-t
• the method further comprises the step of adjusting the dose of the compound of formulae presented herein to increase occupancy of the protein kinase. In certain other embodiments, the method further comprises the step of adjusting the dose of the compound of formulae presented herein to decrease occupancy of the protein kinase.
• occupancy refers to the extent to which a protein kinase is modified by a provided covalent inhibitor compound.
• a protein kinase is modified by a provided covalent inhibitor compound.
• One of ordinary skill in the art would appreciate that it is desirable to administer the lowest dose possible to achieve the desired efficacious occupancy of the protein kinase.
• the protein kinase to be modified is FGFR4.
• the probe compound comprises the irreversible inhibitor for which occupancy is being determined.
• the present invention provides a method for assessing the efficacy of a provided irreversible inhibitor in a mammal, comprising administering a provided irreversible inhibitor to the mammal, administering a provided probe compound to tissues or cells isolated from the mammal, or a lysate thereof, measuring the activity of the detectable moiety of the probe compound, and comparing the activity of the detectable moiety to a standard.
• the present invention provides a method for assessing the pharmacodynamics of a provided irreversible inhibitor in a mammal, comprising administering a provided irreversible inhibitor to the mammal, administering a probe compound presented herein to one or more cell types, or a lysate thereof, isolated from the mammal, and measuring the activity of the detectable moiety of the probe compound at different time points following the administration of the inhibitor.
• the present invention provides a method for in vitro labeling of a protein kinase comprising contacting said protein kinase with a probe compound described herein.
• the contacting step comprises incubating the protein kinase with a probe compound presented herein.
• the present invention provides a method for in vitro labeling of a protein kinase comprising contacting one or more cells or tissues, or a lysate thereof, expressing the protein kinase with a probe compound described herein.
• the present invention provides a method for detecting a labeled protein kinase comprising separating proteins, the proteins comprising a protein kinase labeled by probe compound described herein, by electrophoresis and detecting the probe compound by fluorescence.
• the present invention provides a method for assessing the pharmacodynamics of a provided irreversible inhibitor in vitro, comprising incubating the provided irreversible inhibitor with the target protein kinase, adding the probe compound presented herein to the target protein kinase, and determining the amount of target modified by the probe compound.
• the probe compound is detected by binding to avidin, streptavidin, neutravidin, or captavidin.
• the probe is detected by Western blot. In other embodiments, the probe is detected by ELISA. In certain embodiments, the probe is detected by flow cytometry.
• the present invention provides a method for probing the kinome with irreversible inhibitors comprising incubating one or more cell types, or a lysate thereof, with a biotinylated probe compound to generate proteins modified with a biotin moiety, digesting the proteins, capturing with avidin or an analog thereof, and performing multidimensional LC-MS-MS to identify protein kinases modified by the probe compound and the adduction sites of said kinases.
• the present invention provides a method for measuring protein synthesis in cells comprising incubating cells with an irreversible inhibitor of the target protein, forming lysates of the cells at specific time points, and incubating said cell lysates with an inventive probe compound to measure the appearance of free protein over an extended period of time.
• the present invention provides a method for determining a dosing schedule in a mammal for maximizing occupancy of a target protein kinase comprising assaying a one or more cell types, or a lysate thereof, isolated from the mammal, (derived from, e.g., splenocytes, peripheral B cells, whole blood, lymph nodes, intestinal tissue, or other tissues) from a mammal administered a provided irreversible inhibitor of any of the formulae presented herein, wherein the assaying step comprises contacting said one or more tissues, cell types, or a lysate thereof, with a provided probe compound and measuring the amount of protein kinase covalently modified by the probe compound.
• the assaying step comprises contacting said one or more tissues, cell types, or a lysate thereof, with a provided probe compound and measuring the amount of protein kinase covalently modified by the probe compound.
• TBDPSC1 tert-butyl(chloro)diphenylsilane
• Step 2 Intermediate 2 [00354] A 500-mL, three-necked flask equipped with a mechanical stirrer was charged with Intermediate 1 (25.0 g, 176 mmol), toluene (30 mL), and phosphorous oxychloride (125 mL). DIPEA (130 mL) was added dropwise over 10 min. The resulting mixture was heated at reflux overnight. The solution was concentrated and the resulting residue was slowly poured onto cooled (0 °C) 1.5 M HC1 and extracted with EtOAc. The organic phase was washed with water, saturated aqueous NaHC0 3 , brine, dried over anhydrous Na 2 S0 4 and concentrated to afford the title compound (32.0 g) which was used in the next step without further purification.
• Compound 1-16 was prepared as described in Example 5, using (4- methoxyphenyl)methanamine in place of methylamine to prepare the starting material. MS m/z: 635.4 (M+H + ).

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