EP1670422A2 - Identification d'inhibiteurs de kinase - Google Patents

Identification d'inhibiteurs de kinase

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Publication number
EP1670422A2
EP1670422A2 EP03752561A EP03752561A EP1670422A2 EP 1670422 A2 EP1670422 A2 EP 1670422A2 EP 03752561 A EP03752561 A EP 03752561A EP 03752561 A EP03752561 A EP 03752561A EP 1670422 A2 EP1670422 A2 EP 1670422A2
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EP
European Patent Office
Prior art keywords
kinase
ligand
group
target protein
protein kinase
Prior art date
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Withdrawn
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EP03752561A
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German (de)
English (en)
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EP1670422A4 (fr
Inventor
John C. Prescott
Andrew Braisted
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Viracta Therapeutics Inc
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Sunesis Pharmaceuticals Inc
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Publication of EP1670422A2 publication Critical patent/EP1670422A2/fr
Publication of EP1670422A4 publication Critical patent/EP1670422A4/fr
Withdrawn legal-status Critical Current

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6842—Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
    • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6806—Determination of free amino acids
    • G01N33/6812—Assays for specific amino acids
    • G01N33/6815—Assays for specific amino acids containing sulfur, e.g. cysteine, cystine, methionine, homocysteine
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/91—Transferases (2.)
    • G01N2333/912—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)

Definitions

  • protein kinases enzymes that catalyze the transfer of the ⁇ -phosphatase group of ATP to the oxygen atom of the hydroxyl group of serine, threonine or tyrosine residues in peptides and polypeptides, comprise one of the largest protein superfamilies. Indeed, with the complete sequencing of the human genome, it has been asserted that there are exactly 508 genes encoding human protein kinases, including 58 receptor tyrosine kinases and 32 nonreceptor tyrosine kinases.
  • Kinases and cancer Cancer consists of a variety of diseases characterized by abnormal cell growth. Cancer is caused by both internal and external factors that cause mutations in the genetic material of the cells.
  • Cancer causing genetic mutations can be grouped into two categories, those that act in a positive manner to increase the rate of cell growth, and those that act in a negative manner by removing natural barriers to cell growth and differentiation. Mutated genes that increase the rate of cell growth and differentiation are called oncogenes, while those that remove natural barriers to growth are called tumor suppressor genes.
  • the first oncogene identified encoded the Src tyrosine kinase. Src is a key regulator of signal transduction in many different cell types. Present inside nearly all human cells in an inactive state, Src is poised to respond to extracellular signals from a variety of sources.
  • Src Once triggered by a stimulus, Src is transformed into an active state in which it phosphorylates tyrosine residues on a number of effector proteins. While the tyrosine kinase activity of Src is tightly regulated in normal cells, mutations can occur which transform the enzyme into a constitutively active state. It was one such mutation, identified over 25 years ago, that gave Src the dubious honor of being known as the first oncogene. There are now about 30 tumor suppressor genes and over 100 oncogenes known, about 20% of which encode tyrosine kinases. The disregulation of such central regulators of cell growth and differentiation has disastrous consequences for the cell.
  • ATP which is used by thousands of cellular enzymes, is present in cells in very high concentration. Therefore, kinase inhibitors that act in a strictly ATP competitive manner must bind to their target kinase with extremely high affinity.
  • the high structural conservation surrounding the ATP binding pocket also known as the purine binding pocket
  • GleevecTM small molecule kinase inhibitors
  • GleevecTM Novartis
  • a phenylamino-pyrimidine derivative which binds the purine pocket of Abl tyrosine kinase.
  • This compound shows unique properties that suggest that its mode of action is somewhat unusual. While this compound was approximately a thousand fold less potent than most kinase inhibitor clinical candidates when assayed in biochemical assays, it did not lose as much potency as most inhibitors did when tested in cells, suggesting that it is not competing directly with cellular ATP for binding to Abl.
  • GleevecTM does indeed occupy the purine pocket of the Abl kinase, but it does so only when the kinase is in an inactive conformation, with the amino-terminal and carboxy-terminal lobes twisted such that the catalytic triad of lysine and two aspartic acids is not properly aligned to accept ATP or to catalyze the phosphate transfer reaction. Therefore, GleevecTM makes use of the proven small molecule druggability of the purine pocket without directly competing against ATP, which binds to the inactive conformation with much lower affinity.
  • the invention concerns a method for identifying a ligand binding to an inactive conformation of a target protein kinase, comprising (a) contacting the inactive conformation of the target protein kinase, which contains or is modified to contain a reactive group at or near a binding site of interest, with one or more ligand candidates capable of covalently bonding to the reactive group thereby fonxiing a kinase-ligand conjugate; and (b) detecting the formation of the kinase-ligand conjugate and identifying the ligand present in the kinase-ligand conjugate.
  • the kinase and the ligand candidate preferably form a disulfide bond to yield a kinase- ligand conjugate.
  • the kinase and the ligand candidate(s) can be contacted in the presence of a reducing agent, such as 2-mercaptoethanol or cysteamine.
  • the ligand candidates may be small molecules, and may be less than 1500 daltons, preferably less than 1000 daltons, more preferably less than 750 daltons, even more preferably less than 500 daltons, most preferably less than 250 daltons in size.
  • the invention concerns a method for identifying a ligand that binds to the inactive conformation of a target protein kinase, comprising (a) obtaining the inactive conformation of the target protein kinase comprising an
  • the invention concerns a method for identifying a ligand that binds to the inactive conformation of a target protein kinase, comprising (a) obtaining the inactive conformation of the target protein kinase comprising an -SH group, masked -SH group, or activated -SH group; (b) combining in a mixture the inactive conformation of the target protein kinase with a plurality of ligand candidates that are each capable of forming a disulfide bond with the -SH group, masked -SH group, or activated -SH group thereby forming at least one kinase-ligand conjugate; (c) analyzing the mixture by mass spectrometry; and (d) detecting the most abundant kinase-ligand conjugate that is formed and identifying the ligand thereon.
  • the invention concerns a method for identifying ligands binding to an inactive conformation of a target protein kinase, comprising (a) contacting the inactive conformation of the protein kinase having a first and a second binding site of interest and containing or modified to contain a nucleophile at or near the first site of interest with a plurality of ligand candidates, the candidates having a functional group reactive with the nucleophile, under conditions such that a reversible covalent bond is formed between the nucleophile and a candidate that has affinity for the first site of interest, to form a kinase-first ligand complex; (b) identifying the first ligand from the complex of (a); (c) designing a derivative of the first ligand identified in (b) to provide a small molecule extender (SME) having a first functional group reactive with the nucleophile on the kinase and a second functional group reactive with a second ligand having affinity for the binding second site
  • SME
  • the invention concerns a method for identifying ligands binding to an inactive conformation of a target protein kinase, comprising (a) screening a library of ligand candidates with a kinase-ligand conjugate formed by the covalent bonding of the inactive conformation of a kinase comprising a first reactive functionality with a compound that comprises (1) a second reactive functionality and (2) a chemically reactive group, wherein the second reactive functionality of the compound reacts with the first reactive functionality of the inactive conformation of the target protein kinase to form a first covalent bond such that the kinase-ligand conjugate contains a free chemically reactive group, under conditions wherein at least one member of the library forms a second covalent bond with the kinase-ligand conjugate; and (b) identifying a further ligand that binds covalently to the chemically reactive group of the kinase-ligand conjugate.
  • FIG. 1 A is a schematic illustration of one embodiment of Tethering.
  • a thiol-containing protein is reacted with a plurality of ligand candidates.
  • a ligand candidate that possesses an inherent binding affinity for the target is identified and a ligand is made comprising the identified binding determinant (represented by the circle) that does not include the disulfide moiety.
  • Figure IB is a schematic representation of one embodiment of Tethering where an extender comprising a first and second functionality is used.
  • a target that includes a thiol is contacted with an extender comprising a first functionality -LG that is capable of forming a covalent bond with the reactive thiol and a second functionality second functionality -SPG that is capable of forming a disulfide bond.
  • a target-extender covalent complex is formed which is then contacted with a plurality of ligand candidates.
  • the extender provides one binding determinant (circle) and the ligand candidate provides the second binding determinant (square) and the resulting binding determinants are linked together to form a conjugate compound.
  • Figure 2 illustrates the mass spectrometer profile of purified EGFR1 kinase domain.
  • Figure 2 A is purified EGFR1 in the active conformation.
  • Figure 2B is purified EGFR1 in the inactive conformation.
  • Figures 2C-E) are purified EGFR1 in the inactive conformation following incubation with C) cystamine, D) a quinazoline extender, and E) the quinazoline extender and cystamine.
  • Figure 3 is a schematic depicting the progression from the design and synthesis of a purine pocket extender, through a library screen, and ending with a soluble MEKl inhibitor. The portion of the molecule that binds to the adaptive binding pocket is indicated by a circle.
  • MEKl construct used in each of these successive steps either the S150C screening mutant or wild type, are indicated on the left.
  • Figure 4 is a specificity profile of three inhibitors that were derived from Tethering that inhibit MEKl with ICso's of 80 nM, 50 nM, and 10 nM respectively.
  • ATP concentrations were varied such that the assays were run at or near the K m for ATP for the various kinases: lOmM ATP (IKKb, MEKl, MKK4); 15mM ATP (Aurora-A, CaMKII, CSK, FGFR3, Zap-70); 45mM ATP (CDK2/cyclinA, c-RAF, JNKlal, PKCa, Yes); 50mM ATP (MEKl inactive conformation); 90mM ATP (SAPK2a); 155mM ATP (MAPK2, PKBa); and 200mM ATP (cSRC, IR).
  • protein kinase is used to refer to an enzyme that catalyzes the transfer of the ⁇ -phosphoryl group of ATP (ATP-Mg 2+ complex) to the oxygen atom of the hydroxyl group of serine, threonine or tyrosine residues in peptides and polypeptides (substrates).
  • tyrosine kinase is used to refer to an enzyme that catalyzes the transfer of the ⁇ -phosphoryl group from an ATP-Mg 2+ complex to the oxygen atom of the hydroxyl group of tyrosine residues in another protein (substrate).
  • serine-threonine kinase is used to refer to an enzyme that catalyzes the transfer of the ⁇ -phosphoryl group from an ATP-Mg 2+ complex to the oxygen atom of the hydroxyl group of serine/threonine residues in another protein (substrate).
  • dual specificity kinase is used to refer to kinases that have the unusual ability to phosphorylate both tyrosine and serine/threonine residues of targeted protein substrates, and typically function at pivotal positions in signal transduction pathways.
  • phosphoryl donor refers to an ATP-Mg 2+ complex, where the divalent Mg 2+ ion helps orient the nucleotide and shields the negative charges on its ⁇ - and ⁇ phosphoryl groups, reducing electrostatic repulsion of attacking nucleophiles.
  • phosphoacceptor is used to refer to an atom with a free electron pair that serves as the nucleophile to attack ATP-Mg 2+ (e.g., the oxygen atom of the deprotonated hydroxyl groups of the side chains of Ser, Thr, or Tyr residues in a protein).
  • the phosphoacceptor is the oxygen atom of the deprotonated hydroxyl group of the side chain of a tyrosine (Tyr) residue.
  • activation loop is used to a highly variable segment in protein kinases, situated between the DFG motif and the APE motif that contains the sites of activating phosphorylation in nearly all protein kinases.
  • catalytic loop and “catalytic domain” are used interchangeably and refer to residues in conserved protein kinase motif VIb, which contains an invariant aspartic acid (Asp) residue that serves as the catalytic base in phosphotransfer and a nearly invariant arginine (Arg) residue, that makes electrostatic contact with phosphorylated residues in the activation loop, leading to the catalytically active state of the kinase.
  • APE motif is used to refer to the residues in conserved protein kinase motif VIII, which contains an invariant glutamic acid (Glu) residue that caps a small helix and an invariant proline (Pro) residue that terminates the same helix.
  • DFG motif is used to refer to the residues in conserved protein kinase motif VII, which contains an invariant aspartic acid (Asp) residue that helps mold the active site by forming hydrogen-bonds with the invariant lysine (Lys) in motif II and an invariant asparagine (Asn) residue in motif VIb, thus helping stabilize the conformation of the catalytic loop.
  • inactive conformation refers to a catalytically inactive state of the protein. For example, a protein kinase is in an inactive conformation when, the activation loop is not phosphorylated.
  • a kinase is said to be locked in an inactive conformation when the kinase assumes the inactive conformation and does not phosphorylate its intended substrate.
  • An "inactivation site" on a protein kinase as used herein is any site on the kinase that, when occupied by a ligand, adversely affects the formation of the active conformation or otherwise impairs the kinase's ability to phosphorylate its intended substrate.
  • an inactivation site when referring to an amino acid residue on the kinase is a residue that is directly or indirectly involved in the phosphorylation of the activation loop, and/or in the presentation or transfer of the ⁇ -phosphoryl group of ATP (ATP-Mg 2+ complex) to the substrate of the protein kinase, and/or in any other interaction between the protein kinase and its substrate.
  • a kinase inhibitor binds "preferentially" to an inactive conformation of a target kinase, if its binding affinity to the inactive conformation is at least two fold of its binding affinity to the active conformation.
  • a "ligand" as defined herein is an entity which has an intrinsic binding affinity for the target.
  • the ligand can be a molecule, or a portion of a molecule which binds the target.
  • the ligands are typically small organic molecules which have an intrinsic binding affinity for the target molecule, but may also be other sequence-specific binding molecules, such as peptides (D- , L- or a mixture of D- and L-), peptidomimetics, complex carbohydrates or other oligomers of individual units or monomers which bind specifically to the target.
  • the term also includes various derivatives and modifications that are introduced in order to enhance binding to the target.
  • Ligands that inhibit a biological activity of a target molecule are called "inhibitors" of the target.
  • a “ligand candidate” is a compound that has a moiety that is capable of forming a covalent bond with a reactive group on a target kinase or with a reactive group on a target- kinase-SME covalent complex.
  • a ligand candidate becomes a ligand of a target once it is determined that it has an intrinisc binding affinity for the target.
  • the term "inhibitor” is used in the broadest sense and includes any ligand that partially or fully blocks, inhibits or neutralizes a biological activity exhibited by a target protein kinase.
  • the term "agonist” is used in the broadest sense and includes any ligand that mimics a biological activity exhibited by a target protein kinase.
  • a "binding site of interest" on a target protein kinase as used herein is a site to which a specific ligand binds.
  • the molecular interactions between the ligand and the binding site of interest on the target are non-covalent, and include hydrogen bonds, van der Waals interactions and electrostatic interactions.
  • the binding site of interest broadly includes the amino acid residues involved in binding of the target to a molecule with which it forms a natural complex in vivo or in vitro.
  • “Small molecules” are usually less than about 10 kDa molecular weight, and include but are not limited to synthetic organic or inorganic compounds, peptides, (poly)nucleotides,
  • Small molecules specifically include small non-polymeric (i.e. not peptide or polypeptide) organic and inorganic molecules. Many pharmaceutical companies have extensive libraries of such molecules, which can be conveniently screened by using the extended tethering approach of the present invention.
  • Preferred small molecules have molecular weights of less than about 1000 Da, more preferably about 500 Da, and most preferably about
  • SME Small Molecule Extender
  • the first functional group on one end of the SME is reactive with a nucleophile on a protein kinase (capable of forming an irreversible or reversible covalent bond with such nucleophile), and the reactive group at the other end of the SME is a free or protected thiol or a group that is a precursor of a free or protected thiol.
  • reversible covalent bond refers to a covalent bond which can be broken, preferably under conditions that do not denature the target. Examples include, without limitation, disulfides, Schiff-bases, thioesters, and the like.
  • reactive group with reference to a ligand is used to describe a chemical group or moiety providing a site at which a covalent bond with the ligand candidates (e.g. members of a library or small organic compounds) may be formed.
  • the reactive group is chosen such that it is capable of forming a covalent bond with members of the library against which it is screened.
  • modified to contain and “modified to possess” are used interchangeably, and refer to making a mutant, variant or derivative of the target, or the reactive nucleophile or electrophile, including but not limited to chemical modifications. For example, in a protein one can substitute an amino acid residue having a side chain containing a nucleophile or electrophile for a wild-type residue.
  • reactive nucleophile refers to a nucleophile that is capable of forming a covalent bond with a compatible functional group on another molecule under conditions that do not denature or damage the target.
  • the most relevant nucleophiles are thiols, alcohols, and amines.
  • reactive electrophile refers to an electrophile that is capable of forming a covalent bond with a compatible functional group on another molecule, preferably under conditions that do not denature or otherwise damage the target.
  • a "first binding site of interest" on a target protein kinase refers to a site that can be contacted by at least a portion of the SME when it is covalently bound to the reactive nucleophile or electrophile.
  • the first binding site of interest may, but does not have to possess the ability to form a bond with the SME.
  • group reactive with the nucleophile refers to a functional group, e.g.
  • protected thiol refers to a thiol that has been reacted with a group or molecule to form a covalent bond that renders it less reactive and which may be deprotected to regenerate a free thiol.
  • adjusting the conditions refers to subjecting a target protein kinase, such as a tyrosine kinase, to any individual, combination or series of reaction conditions or reagents necessary to cause a covalent bond to form between the ligand and the target, such as a nucleophile and the group reactive with the nucleophile on the SME, or to break a covalent bond already formed.
  • a target protein kinase such as a tyrosine kinase
  • covalent complex refers to the combination of the SME and the target, e.g.
  • exchangeable disulfide linking group refers to the library of molecules screened with the covalent complex displaying the thiol-containing small molecule extender, where each member of the library contains a disulfide group that can react with the thiol or protected thiol displayed on the covalent complex to form a new disulfide bond when the reaction conditions are adjusted to favor such thiol exchange.
  • phase "highest affinity for the second binding site of interest” as used herein refers to the molecule having the greater thermodynamic stability toward the second site of interest on the target protein kinase that is preferentially selected from the library of disulfide-containing library members.
  • “Functional variants” of a molecule herein are variants having an activity in common with the reference molecule.
  • Activity or “activity” means a qualitative biological and/or immunological property.
  • amino acid "alteration” includes amino acid substitutions, deletions, and/or insertions.
  • the present invention provides a method for locking a protein kinase in an inactive conformation.
  • the invention concerns the identification of inhibitors that preferentially bind to the inactive conformation of a target protein kinase.
  • Protein Kinases Protein kinases are enzymes that catalyze the transfer of the ⁇ -phosphoryl group of ATP
  • Protein kinases play a crucial role in signal transduction, cellular proliferation, differentiation, and various regulatory mechanisms. About 3% of the total coding sequences within the human genome encode protein kinases. While there are many different subfamilies within the broad grouping of protein kinases, they all share a common feature; they all act as ATP phosphotransferases. It is, therefore, not surprising that protein kinases share a very high degree of structural similarity in the region where the ATP is bound, the ATP binding pocket (which is also known as the purine binding pocket).
  • the lysine of this catalytic triad is responsible for properly positioning the ⁇ -phosphate of ATP with the hydroxyl group of the residue in the substrate to which it is transferred (phosphoacceptor residue), while the first aspartic acid acts as a general base catalyst in the phosphotransfer reaction. Strikingly, these three crucial residues span the two lobes of the catalytic domain. Furthermore, the two aspartic acid .residues within the catalytic triad are separated from each other by a second flexible region called the activation loop. To allow the phosphotransfer reaction, the structure of a substrate must conform to the geometric constraints, surface electrostatics, and other features of the active site of the corresponding protein kinase.
  • substrate binding can induce structural changes in a kinase that stimulate its catalytic activity.
  • residues within the activation loop and the catalytic loop need to be made available to make contacts with side chains in a substrate.
  • conserved motifs crucial for catalytic activity such as the ATP binding site
  • kinases in a resting cell generally exist in an inactive conformation.
  • the catalytic triad may be oriented in a manner that will not catalyze phosphate transfer, the substrate binding cleft may be occluded by the flexible activation loop, or both.
  • the amino- and carboxy-terminal lobes in the inactive conformation may be opened up with resultant widening the active site cleft, twisted with resultant tortioning of the active site cleft, or both.
  • Gleevec binds to the adaptive binding pocket that is only revealed when Abl kinase is in the inactive form.
  • specifically targeting the inactive form of the kinase provides a path for mitigating many of the difficulties in developing kinase inhibitors as drugs.
  • An important protein kinase target for drug development is the Tyr kinase EGFRl (Ullrich et al, Nature 309:418-425 (1984); SwissProt accession code P00533).
  • EGFRl a validated target for chemotherapeutics, is a cell surface receptor that contains an extracellular ligand binding domain and an intracellular tyrosine kinase domain.
  • EGFRl including EGF, TGF- ⁇ , amphiregulin, ⁇ -cellulin, and epiregulin.
  • Ligand binding leads to receptor dimerization, autophosphorylatioii at a number of tyrosine residues including Tyr845 in the activation loop, and subsequent recruitment pf substrate proteins and stabilization of the active conformation of the kinase domain.
  • EGFRl, -in this activated state phosphorylates a variety of downstream targets to propagate the extracellular stimulus of ligand binding to the eventual transcriptional upregulation of a variety of growth regulatory genes and resultant cell proliferation.
  • EGFRl In normal cells, EGFRl regulates cell growth in a tightly controlled manner. However, overexpression of EGFRl has been observed in a large number of tumor types, including breast, bladder, colon, lung, squamous cell head and neck, ovarian, and pancreatic cancers. A clear role for EGFRl upregulation in the initiation and progression of a variety of cancers has lead to an intense search for therapeutics that inhibit signal transduction via EGFRl .
  • Another important protein kinase target for drug development is the dual specificity kinase MEKl (Seger et al, J. Biol. Chem. 267: 25628-31 (1992); Swiss Prot accession code Q02750).
  • MEK ⁇ ERK pathway It is the central kinase in the mitogen activated Ras ⁇ Raf ⁇ MEK ⁇ ERK signal transduction cascase (also referred to as the MEK ⁇ ERK pathway). Conditional activation of this pathway transmits mitogenic and cell survival signals from a number of growth factors and receptors, including EGFR, VEGFR, PDGFR and FGFR. Overexpression or consitutive activation of these same growth factors and receptors in tumors correlates with a poor prognosis in cancer patients. Further validation of MEKl as a general cancer therapeutic target comes from the development of two specific MEKl inhibitors. The first, PD98059, is a specific, albeit relatively insoluble, MEKl inhibitor.
  • this compound has been used in over 2,500 publications validating the Ras->Raf- ⁇ MEK- ERK pathway as a critical pathway in transformed cells, and confirming that inhibition of this pathway is sufficient to reverse the transformed phenotype of cells that have upregulated this pathway (e.g., cells transformed with an activated Ras mutant).
  • the second, PD184352 (also known as CI-1040), is a specific MEKl inhibitor currently in Phase II trials for use as a therapeutic in a variety of solid tumors.
  • MEK- ERK pathway can be inhibited in vivo, that inhibition of this pathway does not cause general toxicity, and that inhibition of this pathway correlates with tumor regression in multiple mouse xenograft cancer models.
  • MEK->ERK pathway generally confers resistance to apoptosis.
  • cancers with increased MEK- ERK signaling will be more resistant to chemotherapy-induced apoptosis, and inhibition of MEKl activity will increase the sensitivity of these cancers to traditional chemotherapeutics.
  • the MEKl inhibitors PD98059 and PD 184352 induced apoptosis in tumor cell lines in a manner that directly correlated with the level of ERK activation. As predicted, these MEKl inhibitors acted synergistically with a variety of chemotherapeutic cytotoxins, including ara-C, cisplatin, and paclitaxel.
  • Another important family of protein kinases is the Src family.
  • Src family kinases are well validated casual agents in a variety of cancers. Second, no current small molecule therapeutics effectively targets Src kinases in humans.
  • Src family kinases are the best structurally characterized of all tyrosine kinases.
  • a representative member of this family, the Tyr kinase Lck (Perlmutter et al, J. Cell. Biochem. 38:117-126 (1988); Swiss Prot acession code P06239), is a cytosolic tyrosine kinase, which is expressed primarily in T-cells where it is centrally involved in transducing a signal from the T-cell receptor (TCR).
  • Lck is found associated when the inner plasma membrane where it phosphorylates the CD3 and zeta chains of the TCR in response to antigenic stimulation, initiating a cascade of signal transduction events that eventually result in a clonal proliferation of the stimulated T-cell.
  • Lck is well known as a tiierapeutic target for immunological disorders, such as graft versus host disease.
  • Lck is also validated cancer therapeutic target. In humans, some neuroblastomas and non-Hodgkin's lymphomas show chromosomal abnormalities and translocations in the region of the Lck gene.
  • the "derivative I chromosome" translocation focuses the transcriptional regulatory region of the beta T-cell receptor gene with the coding sequence of Lck, resulting in increased levels of Lck kinase in patients with T-cell acute lymphoblastic leukemia, much like the Philadelphia Chromosome translocation which upregulates Abl expression causing CML.
  • Src family kinases are extremely well characterized structurally. Crystal coordinates are publicly available for three family members, hematopoietic cell kinase (Hck), Src, and Lck, covering both the active and the inactive conformational.
  • Lck is known to express well in baculovirus and to crystallize readily.
  • Other illustrative examples of kinase targets include but are not limited to: Ser/Thr kinase AKT1 (Jones et al, PNAS 88: 4171-4175 (1991); Swiss Prot accession code P31749); Ser/Thr kinase AKT2 (Jones et al, Cell Regul. 2(12): 1001-1009 (1991); Swiss Prot accession code P31751); Ser/Thr kinase AKT3 (Brodbeck et al, J. Biol. Che .
  • the present invention provides methods for identifying protein kinase inhibitors that specifically target kinases in the inactive conformation.
  • Traditional high throughput screening techniques detect phosphoryl transfer to a substrate molecule by an activated kinase.
  • the present invention provides an efficient, high- throughput method to identify kinase inhibitors that bind preferentially to the inactive confonnation of protein kinases. This method includes the step of locking the protein kinase in its inactive conformation, and using Tethering to identify inhibitors specifically targeting the inactive kinase conformation. a.
  • a target protein kinase is locked in a catalytically inactive conformation by introducing one or more amino acid alterations at an inactivating site such that the kinase cannot exert its kinase activity, in most cases because the alteration inhibits the phosphorylation of the activation loop.
  • the alteration may target any site participating (directly or indirectly) in the formation of a catalytically active state of the kinase.
  • the alteration may take place at or near amino acid residues participating in the phosphorylation of the activation loop, and/or in the presentation or transfer of the ⁇ -phosphoryl group of ATP to the substrate of the protein kinase, and/or in any other interaction between the protein kinase and its substrate.
  • Alterations within or in the vicinity of the catalytic loop e.g. the ATP binding site including the catalytic triad, the substrate binding channel, a cofactor binding site, if any, residues involved in hydrogen bond/acceptor interactions, and/or docking of the substrate on the tyrosine kinase are particularly preferred.
  • the number refers to the amino acid position where the amino acid substitution is being made, and the second (right-hand) letter designates the amino acid that is used to replace the wild-type amino acid at that position.
  • the designation for an insertion variant consists of the letter i followed by a number designating the position of the residue in wild-type protein kinase before which the insertion starts, followed by one or more capital letters indicating, inclusively, the insertion to be made.
  • the designation for a deletion variant consists of the letter d followed by the number of the start position of the deletion to the number of the end position of the deletion, with the positions being based on the wild-type protem kinase. Multiple alterations are separated by a comma in the notation for ease of reading them.
  • the kinase is locked in an inactive conformation by mutating one or more residues selected from the group consisting of the invariant aspartic acid in the catalytic loop; the arginine in the catalytic loop; the invariant aspartic acid in the DFG motif; and the invariant lysine in motif II.
  • one or more of these residues are substituted by an alanine residue.
  • Illustrative examples of kinase mutants where the invariant aspartic acid residue in the catalytic loop is mutated to X include any combination of the following: D274X AKT1; D275X AKT2; D271X AKT3; D359X BLK; D521X BTK; D128X
  • CDK1 D127X CDK2; D127X CDK3; D140X CDK4; D126X CDK5; D145X CDK6; D137X
  • kinase mutants where the arginine residue in the catalytic loop is mutated to X (wherein X denotes any amino acid residue other than arginine) include any combination of the following: R273X AKT1; R274X AKT2; R270X AKT3; R358X BLK; R520X BTK; R127X
  • MAPK MAPK; R189X MEKl; R514X NIK; R388X PAK1; R367X PAK2; R386X PAK3; R439X PAK4; R567X PAK5; R817X PDGFR-a; R825X PDGFR-b; R166X PM1; R428X A-Raf;
  • Illustrative examples of kinase mutants where the invariant aspartic acid in the DFG motif is mutated to X include any combination of the following: D292X AKT1; D293X AKT2; D289X AKT3; D377X BLK; D539X BTK; D146X
  • CDK1 D145X CDK2; D145X CDK3; D158X CDK4; D144X CDK5; D163X CDK6; D155X
  • kinase mutants where the invariant lysine in motif II is mutated to X (wherein X denotes any amino acid residue other than lysine) include: K179X AKT1; K181X AKT2; K177X AKT3; K268X BLK; K430X BTK; K33X CDK1;
  • K514X FGFRl K517X FGFR2; K508X FGFR3; K503X FGFR4; K298X FYN; K290X HCK; K44X IKK-a; K44X IKK-b; K38X. IKK-e; K896X JAK1; K882X JAK2; K855X JAK3; K55X
  • K429X NIK K299X PAK1; K228X PAK2; K297X PAK3; K350X PAK4; K478X PAK5;
  • Amino acid sequence variants with more than one amino acid substitution may be generated in one of several ways. If the amino acids are located close together in the polypeptide chain, they may be mutated simultaneously, using one oligonucleotide that codes for all of the desired amino acid substitutions. If, however, the amino acids are located some distance from one another (e.g. separated by more than ten amino acids), it is more difficult to generate a single oligonucleotide that encodes all of the desired changes. Instead, one of two alternative methods may be employed. In the first method, a separate oligonucleotide is generated for each amino acid to be substituted.
  • the oligonucleotides are then annealed to the single-stranded template DNA simultaneously, and the second strand of DNA that is synthesized from the template will encode all of the desired amino acid substitutions.
  • the alternative method involves two or more rounds of mutagenesis to produce the desired mutant.
  • the nucleic acid encoding the desired kinase mutant is then inserted into a replicable expression vector for further cloning or expression.
  • Expression and cloning vectors are well known in the art and contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells.
  • an appropriate vector will depend on 1) whether it is to be used for DNA amplification or for DNA expression, 2) the size of the DNA to be inserted into the vector, and 3) the host cell to be transformed with the vector.
  • Each vector contains various components depending on its function (amplification of DNA or expression of DNA) and the host cell for which it is compatible.
  • the vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
  • Suitable expression vectors, for use in combination with a variety of host cells are well known in the art and are commercially available.
  • the protein kinase mutants can be produced in prokaryotic or eukaryotic host cells, including bacterial hosts, such as E. coli, eukaryotic microbes, such as filamentous fungi or yeast, and host cells derived from multicellular orgamsms.
  • bacterial hosts such as E. coli
  • eukaryotic microbes such as filamentous fungi or yeast
  • host cells derived from multicellular orgamsms examples include invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells, such as cell cultures of cotton, corn, potato, soybean, petunia, tomato, and tobacco.
  • Numerous baculoviral strains and corresponding permissive insect host cells e.g.
  • Suitable mammalin host cell lines include, without limitation, human embryonic kidney cell line 293, Chinese hamster ovary (CHO) cells, etc.
  • Host cells are transformed with the expression or cloning vectors encoding the desired protem kinase mutants, and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • Tethering the protein kinases locked in inactive conformation are used to screen for inhibitors preferentially binding to the inactive conformation by using Tethering. This approach differs significantly from the conventional drug discovery route that is based on the synthesis of large organic compound libraries, and subsequent screening, usually for inhibitory activity against the target protein kinase.
  • small, drug-like fragments containing or modified to contain a moiety capable of forming a disulfide bond are tested for binding activity to the desired kinase. These monophores are then used to synthesize conjugates of fragments that bind in non-overlapping sites to generate molecules that no longer require the disulfide for binding.
  • the linking or merging of multiple fragments effectively results in the combination of individual binding energies, plus a favorable entropic term due to the high local concentration of the second fragment once the first fragment is bound, yielding dissociation constants at levels similar to a typical medicinal chemistry starting point.
  • a library of disulfide-containing molecules is allowed to react with a cysteine-containing target protein under partially reducing conditions that promote rapid thiol exchange. If a molecule has even weak affinity for the target protein, the disulfide bond linking the molecule to the target protein will be entropically stabilized.
  • the disulfide-bonded fragments can then be identified by a variety of methods, including mass spectrometry (MS), and their affinity improved by traditional approaches upon removal of the disulfide tether. See also PCT Publication Nos. WO 00/00823 and WO 03/046200, the entire disclosures of which are hereby expressly incorporated by reference.
  • a disulfide bond is formed between the target protein kinase molecule locked in inactive configuration and a ligand candidate to yield a target protein-ligand conjugate, and the ligand present in the conjugate is identified.
  • the target protein is contacted with a ligand candidate (preferably a library of ligand candidates) in the presence of a reducing agent, such as 2-mercaptoethanol, or cysteamine.
  • a ligand candidate preferably a library of ligand candidates
  • Most of the library members will have little or no intrinsic affinity for the target molecule, and thus by mass action the equilibrium will lie toward the unbound target molecule.
  • the target contains, or is modified to contain, free or protected thiol groups, preferably not more than about 5 thiol groups, more preferably not more than about 2 thiol groups, more preferably not more than one free thiol group.
  • the target protein kinase of interest may be initially obtained or selected such that it already possesses the desired number of thiol groups, or may be modified to possess the desired number of thiol groups.
  • the kinase of interest possesses at least one naturally occurring cysteine that is amenable to Tethering.
  • Illustrative examples of kinases that include naturally occurring cysteines that are amenable to Tethering include: CDK5 (C53) ERKl (C183); ERK2 (C166); ERK3 (C28); FGFRl (C488); FGFR2 (C491); FGFR3 (C482) FGFR4 (C477); MEKl (C207); NIK (C533); PDGFR-a (C835); PDGFR-b (C843); SRC (C279) SRC2 (C273); STK1 (C828); TGFR2 (C396); VEGFRl (C1039); VEGFR2 (C1045); VEGFR3 (C1054); YES (C287); ZAP-70 (C346).
  • one or more amino acids are mutated into a cysteine.
  • cysteine mutants are made using the following guidelines.
  • the "binding site of interest" on a particular target such as a target protein kinase, is defined by the residues that are involved in binding of the target to a molecule with which it forms a natural complex in vivo or in vitro. If the target is a peptide, polypeptide, or protein, the site of interest is defined by the amino acid residues that participate in binding to (usually by non-covalent association) to a ligand of the target.
  • the binding site of interest can include amino acids that make contact with, or lie within, about 4 angstroms of a bound substrate, inhibitor, activator, cofactor or allosteric modulator of the enzyme.
  • the binding site of interest includes the substrate-binding channel and the ATP binding site.
  • the target protein kinases either contain, or are modified to contain, a reactive residue at or near a binding site of interest.
  • the target kinases contain or are modified to contain a thiol-containing amino acid residue at or near a binding site of interest. In this case, after a protein kinase is selected, the binding site of interest is calculated.
  • a process of determining which amino acid residue within, or near, the binding site of interest to modify is undertaken. For example, one preferred modification results in substituting a cysteine residue for another amino acid residue located near the binding site of interest.
  • the choice of which residue within, or near, the binding site of interest to modify is detemiined based on the following selection criteria.
  • a three dimensional description of the target protein kinase is obtained from one of several well-known sources. For example, the tertiary structure of many protein kinases has been determined through x-ray crystallography experiments.
  • x-ray structures are available from a wide variety of sources, such as the Protem Databank (PDB) which can be found on the Internet at http://www.rcsb.org. Tertiary structures can also be found in the Protein Structure Database (PSdb) which is located at the Pittsburg Supercomputer Center at http://www.psc.com.
  • PDB Protem Databank
  • PSdb Protein Structure Database
  • the tertiary structure of many proteins, and protein complexes, including protein kinases has been determined through computer-based modeling approaches. Thus, models of protein three-dimensional conformations are now widely available.
  • a measurement is made based on a structural model of the wild-type, or a variant form locked in an inactive configuration, from any atom of an amino acid within the site of interest across the surface of the protein for a distance of approximately 10 angstroms. Since the goal is to identify protein kinase inhibitors that preferentially bind to an inactive conformation of the target protein kinase, preferably the site(s) of interest is/are identified base upon a structural model of the protein kinase locked in an inactive conformation.
  • binding sites (pockets) presented by such inactive conformations are often significantly different from the binding sites (pockets) present on the wild-type structure.
  • Variants of the inactive protein kinases which have been modified to contain the desired reactive groups (e.g. thiol groups, or thiol-containing residues) are based on the identification of one or more wild- type amino acid(s) on the surface of the target protein kinase that fall within that approximate 10- angstrom radius from the binding site of interest (which may have been first revealed as a result of the alteration resulting the stabilization of an inactive conformation).
  • any amino acid having at least one atom falling within the about 10 angstrom radius from any atom of an amino acid within the binding site of interest is a potential residue to be modified to a thiol containing residue.
  • Preferred residues for modification are those that are solvent-accessible. Solvent accessibility may be calculated from structural models using standard numeric (Lee, B. & Richards, F. M. J Mol. Biol 55:379-400 (1971); Slirake, A. & Rupley, J. A. J Mol Biol 79:351- 371 (1973)) or analytical (Connolly, M. L. Science 221:709-713 (1983); Richmond, T. J. J Mol. Biol.
  • a potential cysteine variant is considered solvent-accessible if the combined surface area of the carbon- ⁇ et (CB), or sulfur-gamma (SG) is greater than 21 A 2 when calculated by the method of Lee and Richards (Lee, B. & Richards, F. M. J. Mol. Biol 55:379-400 (1971)). This value represents approximately 33% of the theoretical surface area accessible to a cysteine side-chain as described by Creamer et al (Creamer, T. P. et al. Biochemistry 34:16245-16250 (1995)).
  • residue to be mutated to cysteine, or another thiol-containing amino acid residue for tethering purposes not participate in hydrogen-bonding with backbone atoms or, that at most, it interacts with the backbone through only one hydrogen bond.
  • Wild- type residues where the side-chain participates in multiple (>1) hydrogen bonds with other side- chains are also less preferred.
  • Variants for which all standard rotamers (chil angle of -60°, 60°, or 180°) can introduce unfavorable steric contacts with the N, CA, C, O, or CB atoms of any other residue are also less preferred.
  • Unfavorable contacts are defined as interatomic distances that are less than 80% of the sum of the van der Waals radii of the participating atoms. Additionally, residues found on convex "ridge" regions adjacent to concave surfaces are more preferred while those within concave regions are less preferred cysteine residues to be modified. Convexity and concavity can be calculated based on surface vectors (Duncan, B. S. & Olson, A. J. Biopolymers 33:219-229 (1993)) or by determining the accessibility of water probes placed along the molecular surface (NichoUs, A. et al. Proteins 11:281-296 (1991); Brady, G. P., Jr. & Stouten, P. F. J.
  • Residues possessing a backbone conformation that is nominally forbidden for L-amino acids are less preferred targets for modification to a cysteine. Forbidden conformations commonly feature a positive value of the phi angle.
  • preferred variants are those which, when mutated to cysteine and linked via a disulfide bond to an alkyl tether, would possess a conformation that directs the atoms of that tether towards the binding site of interest.
  • Two general procedures can be used to identify these preferred variants. In the first procedure, a search is made of unique structures (Hobohm, U. et al. Protein Science 1:409-417 (1992)) in the Protein Databank (Berman, H. M. et al.
  • the residue at position i is computationally "mutated” to a cysteine and capped with an S-Methyl group via a disulfide bond.
  • one or more naturally occurring cysteines outside of the site of interest can be mutated to a non-cysteine residue (such as alanine or serine) to prevent unwanted labeling.
  • those naturally occurring cysteines outside of the site of interest and are reactive to cystamine are candidates for being "scrubbed" (mutated to a non- cysteine residue).
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L156C AKT1; K158C AKT1; T160C AKT1; F161C AKT1; K194C AKT1; E198C AKT1; M227C AKT1; E278C AKT1; T291C AKT1; K297C AKT1.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: K158C AKT2; K160C AKT2; T162C AKT2; F163C AKT2; H196C AKT2; E200C AKT2; M229C AKT2; E279C AKT2; T292C AKT2; K298C AKT2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L154C AKT3; K156C AKT3; T158C AKT3; F159C AKT3; H192C AKT3; E196C AKT3; M225C AKT3;-E274C AKT3; T288C AKT3; K294C AKT3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L246C BLK; S248C BLK; Q151C BLK; F251C BLK; A279C BLK; E283C BLK; T311C BLK; A363C BLK; A376C BLK; R382C BLK.
  • cysteine mutants are illustrative examples of mutants that re used for Tethering: L408C BTK; T410C BTK; Q313C BTK; F413C BTK; E441C BTK; E445C BTK; T474C BTK; R525C BTK; S538C BTK; R544C BTK.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: HOC CDK1; E12C CDK1; T14C CDK1; Y15C CDK1; S53C CDK1; E57C CDK1; F80C CDK1; Q432C CDK1; A145C CDK1; R151C CDK1.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: HOC CDK2; E12C CDK2; T14C CDK2; Y15C CDK2; S53C CDK2; E57C CDK2; F80C CDK2; Q431C CDK2; A144C CDK2; R150C CDK2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: HOC CDK3; E12C CDK3; T14C CDK3; Y15C CDK3; S53C CDK3; E57C CDK3; F80C CDK3; Q431C CDK3; A144C CDK3; R150C CDK3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I12C CDK4; V14C CDK4; A16C CDK4; Y17C CDK4; R55C CDK4; L59C CDK4; F93C CDK4; E153C CDK4; A157C CDK4; R163C CDK4.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: HOC CDK5; E12C CDK5; T14C CDK5; Y15C CDK5; E57C CDK5; F80C CDK5; Q430C CDK5; A143C CDK5; R149C CDK5.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I19C CDK6; E21C CDK6; A23C CDK6; Y24C CDK6; A63C
  • the following cysteine mutants are illustrative examples of mutants that are used for Tethering: L18C CDK7; E20C CDK7; Q22C CDK7; F23C CDK7; R61C CDK7; L65C CDK7; F91C CDK7; N141C CDK7; A154C CDK7; K161C CDK7.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: V27C CDK8; R29C CDK8; T31C CDK8; Y32C CDK8; R65C CDK8; L69C CDK8; F97C CDK8; A155C CDK8; A172C CDK8; H178C CDK8.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I25C CDK9; Q27C CDK9; T29C CDK9; F30C CDK9; R65C CDK9; I69C CDK9; F103C CDK9; A153C CDK9; A166C CDK9; R172C CDK9.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: 1201 C CSK; K203C CSK; E205C CSK; F206C CSK; A232C CSK; E236C CSK; T266C CSK; R318C CSK; S331C CSK; K337C CSK.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L718C EGFRl; S720C EGFRl; A722C EGFRl; F723C EGFRl; E758C EGFRl; E762C EGFRl; T790C EGFRl; R841C EGFRl; T854C EGFRl; K860C EGFRl.
  • ERB2 also referred to as ErbB2
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L726C ERB2; S728C ERB2; A730C ERB2; F731C ERB2; E766C ERB2; E770C ERB2; T798C ERB2; R849C ERB2; T862C ERB2; R868C ERB2.
  • ERB4 also referred to as ErbB4
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L724C ERB4; S726C ERB4; A728C ERB4; F729C ERB4; E764C ERB4; E768C ERB4; T796C ERB4; R847C ERB4; T860C ERB4; R864C ERB4.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I48C ERKl; E50C ERKl; A52C ERKl; Y53C ERKl; R84C ERKl; E88C ERKl; Q122C ERKl; S170C ERKl; R189C ERKl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: 131C ERK2; E33C ERK2; A35C ERK2; Y36C ERK2; R67C ERK2; E71C ERK2; Q105C ERK2; S153C ERK2; R172C ERK2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L26C ERK3; G30C ERK3; N31C ERK3; H61C ERK3; E65C ERK3; Q108C ERK3; A156C ERK3; G170C ERK3; R176C ERK3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L26C ERK4; F28C ERK4; V30C ERK4; N31C ERK4; H61C ERK4; E65C ERK4; Q105C ERK4; A153C ERK4; G167C ERK4; R173C ERK4.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I60C ERK5; N62C ERK5; A64C ERK5; Y65C ERK5; R97C ERK5; E101C ERK5; L136C ERK5; S185C ERK5; G198C ERK5; R204C ERK5.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: V33C ERK6; S35C ERK6; A37C ERK6; Y38C ERK6; R70C ERK6; E74C ERK6; M109C ERK6; G157C ERK6; L170C ERK6; R176C ERK6.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I428C FAKl; E430C FAK2; Q333C FAKl; F433C FAKl; K467C FAKl; E471C FAKl; M499C FAKl; R550C FAKl; G563C FAKl; R569C FAKl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L484C FGFRl; E486C FGFRl; F489C FGFRl; L528C FGFRl; M532C FGFRl; V561C FGFRl; R627C FGFRl; A640C FGFRl; R646C FGFRl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L487C FGFR2; E489C FGFR2; F492C FGFR2; L531C FGFR2; M535C FGFR2; V564C FGFR2; R630C FGFR2; A643C FGFR2; R649C FGFR2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L478C FGFR3; E480C FGFR3; F483C FGFR3; L522C FGFR3; M526C FGFR3; V555C FGFR3; R621C FGFR3; A634C FGFR3; R640C FGFR3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L473C FGFR4;.
  • the following cysteine mutants are illustrative examples of mutants that are used for Tethering: L276C FYN; N278C FYN; Q181C FYN; F281C FYN; S309C FYN; E313C FYN; T341C FYN; A393C FYN; A406C FYN; R412C FYN.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L268C HCK; A270C HCK; Q173C HCK; F273C HCK; A301C HCK; E305C HCK; T333C HCK; A385C HCK; A398C HCK; R404C HCK.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L21C IKK-a; T23C IKK-a; G25C IKK-a; F26C IKK-a; R57C IKK- a; E61C IKK-a; M95C IKK-a; E148C IKK-a; I164C IKK-a; K170C IKK-a.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L21C IKK-b; T23C IKK-b; G25C IKK-b; F26C IKK-b; R57C IKK- b; E61C IKK-b; M96C IKK-b; E149C IKK-b; I165C IKK-b; K171C IKK-b.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L15C IKK-e; Q17C IKK-e; A19C IKK-e; T20C IKK-e; V51C IKK- e; E55C IKK-e; M86C IKK-e; G139C IKK-e; T156C IKK-e; R163C IKK-e.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L870C JAK1; E872C JAK1; H874C JAK1; F875C JAK1; D909C JAK1; E913C JAK1; M944C JAK1; R995C JAK1; G1008C JAK1; K1014C JAK1.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L855C JAK2; L857C JAK2; N859C JAK2; F860C JAK2; D894C JAK2; E898C JAK2; M929C JAK2; R980C JAK2; G993C JAK2; K999C JAK2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L828C JAK3; K830C JAK3; N832C JAK3; F833C JAK3; D867C JAK3; E871C JAK3; M902C JAK3; R953C JAK3; A966C JAK3; K972C JAK3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I32C JNKl; S34C JNKl; A36C JNKl; Q37C JNKl; R69C JNKl; E73C JNKl; M108C JNKl; S155C JNKl; L168C JNKl; R174C JNKl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I32C JNK2; S34C JNK2; A36C JNK2; Q37C JNK2; R69C JNK2; E73C JNK2; M108C JNK2; S155C JNK2; L168C JNK2; R174C JNK2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I70C JNK3; S72C JNK3; A74C JNK3; Q75C JNK3; R107C JNK3; Ell 1C JNK3; M146C JNK3; S193C JNK3; L206C JNK3; R212C JNK3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L250C Lck; A252C Lck; Q155C Lck; F255C Lck; A283C Lck; E287C Lck; T315C Lck; A367C Lck; A380C Lck; R386C Lck.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L252C LYN; A254C LYN; Q157C LYN; F257C LYN; A285C LYN; E289C LYN; T318C LYN; A370C LYN; A383C LYN; D389C LYN.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: V30C MAPK; S32C MAPK; A34C MAPK; Y35C MAPK; R67C MAPK; E71C MAPK; T106C MAPK; S154C MAPK; L167C MAPK; R173C MAPK.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L406C NIK; R408C NIK; S410C NIK; F411C NIK; F436C NIK; E439C NIK; M469C NIK; D519C NIK; V540C NIK.
  • cysteine mutants are illustrative examples of mutants that are used for tethering: I276C PAK1; Q179C PAK1; A280C PAK1; S281C PAK1; N314C PAK1; V318C PAK1; M344C PAK1; D393C PAK1; T406C PAK1; A412C PAK1.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I255C PAK2; Q158C PAK2; A259C PAK2; S260C PAK2; N293C PAK2; V297C PAK2; M323C PAK2; D372C PAK2; T385C PAK2; A391C PAK2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I274C PAK3; Q177C PAK3; A278C PAK3; S279C PAK3; N312C PAK3; V316C PAK3; M342C PAK3; D391C PAK3; T404C PAK3; A410C PAK3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I327C PAK4; E329C PAK4; S331C PAK4; R332C PAK4; N365C PAK4; I369C PAK4; M395C PAK4; D444C PAK4; S457C PAK4; A463C PAK4.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I455C PAK5; E457C PAK5; S459C PAK5; T460C PAK5; N492C PAK5; I496C PAK5; M523C PAK5; D572C PAK5; D585C PAK5; A591C PAK5.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L599C PDGFR-a; S601C PDGFR-a; A603C PDGFR-a; F604C PDGFR-a; L641C PDGFR-a; L645C PDGFR-a; T674C PDGR-a; R822C PDGFR-a; R841C PDGFR-a.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L606C PDGFR-b; S608C PDGFR-b; A700C PDGFR-b; F701C PDGFR-b; L648C PDGFR-b; L652C PDGFR-b; T681C PDGFR-b; R830C PDGFR-b; R849C PDGFR-b.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L44C PIM1; S46C PIM1; G48C PIM1; F49C PIM1; M87C PIM1; L91C PIM1; E121C PIM1; E171C PIM1; E171C PIM1; I185C PIM1; A192C PIM1.
  • cysteine mutants are illustrative examples of mutants that are used for tethering: 1316C A-Raf; T318C A-Raf; S320C A-Raf; F321C A-Raf; A350C A- Raf; E354C A-Raf; T382C A-Raf; N433C A-Raf; G446C A-Raf; T452C A-Raf.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I462C B-Raf; S464C B-Raf; S466C B-Raf; F467C B-Raf; A496C B- Raf; E500C B-Raf; T528C B-Raf; N579C B-Raf; G592C B-Raf; T598C B-Raf.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I355C C-Raf; S357C C-Raf; S359C C-Raf; F-360C C-Raf; A389C C-Raf; E393C C-Raf; T421C C-Raf; N472C C-Raf; G485C C-Raf; T491C C-Raf.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L275C SRC; Q178C SRC; F280C SRC; A308C SRC; E402C SRC; T340C SRC; A392C SRC; A405C SRC; R411C SRC.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L269C SRC2; T271C SRC2; F274C SRC2; A302C SRC2; E306C SRC2; T334C SRC2; A386C SRC2; A399C SRC2; R405C SRC2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L616C STKl; S618C STKl; A620C STKl; F621C STKl; L658C STKl; L662C STKl; F691C STKl; R815C STKl, R834C STKl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L377C SYK; S379C SYK; N381C SYK; F382C SYK; E416C SYK; E420C SYK; M448C SYK; R498C SYK; S511C SYK; K518C SYK.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L376C TEC; S378C TEC; L380C TEC; F381C TEC; D409C TEC; E413C TEC; T442C TEC; R493C TEC; S506C TEC; R513C TEC.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: 1211C TGFRl; K213C TGFRl; R215C TGFRl; F216C TGFRl; F243C TGFRl; E247C TGFRl; S280C TGFRl; K337C TGFRl; A350C TGFRl; V357C TGFRl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: V250C TGFR2; K252C TGFR2; R254C TGFR2; F255C TGFR2; K288C TGFR2; D292C TGFR2; T325C TGFR2; S383C TGFR2; L403C TGFR2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I845C TIEl ; E847C TIEl ; N849C TIEl ; F850C TIEl ; F884C TIEl ; L888C TIEl; I917C TIEl; R983C TIEl; A996C TIE 1; R1002C TIEl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: I830C TIE2; E832C TIE2; N834C TIE2; F835C TIE2; F869C TIE2; L873C TIE2; I902C TIE2; R968C TIE2; A981C TIE2; R987C TIE2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L834C VEGFRl; R836C VEGFRl; A838C VEGFRl; F839C VEGFRl; L876C VEGFRl; L880C VEGFRl; V910C VEGFRl; R1026C VEGFRl; R1045C VEGFRl.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L840C VEGFR2; R842C VEGFR2; A844C VEGFR2; F845C VEGFR2; L882C VEGFR2; L886C VEGFR2; V916C VEGFR2; R1032C VEGFR2; R1051C VEGFR2.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L851C VEGFR3; Y853C VEGFR3; A855C VEGFR3; F856C VEGFR3; L893C VEGFR3; L987C VEGFR3; V927C VEGFR3; R1041C VEGFR3; R1060C VEGFR3.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L283C YES; Q286C YES; C287C YES; F288C YES; A316C YES; E320C YES; T348C YES; A400C YES; A413C YES; R419C YES.
  • cysteine mutants are illustrative examples of mutants that are used for Tethering: L344C ZAP-70; N348C ZAP-70; F349C ZAP-70; E382C ZAP-70; E386C ZAP-70; M414C ZAP-70; R465C ZAP-70; S478C ZAP-70; and K485C ZAP- 70.
  • this approach is typically exemplified with reference to a protein kinase target havmg a thiol functionality to screen a disulfide-containing library, other chemistries are also available and are readily used.
  • Tethering with extenders is a variation of Tethering described above that uses a Small Molecule Extender (SME) to form a target kinase-SME covalent complex.
  • SME Small Molecule Extender
  • the SME has a first reactive functionality that is capable of forming a reversible or irreversible covalent bond with the target kinase and a second reactive functionality that is capable of forming a reversible or irreversible covalent bond with a ligand candidate.
  • the SME forms a first covalent bond with the target kinase thereby forming a target kinase-SME covalent complex.
  • the SME also includes a binding element that has an affinity for the SME binding site or a first site of interest.
  • the second reactive functionality on the SME on the target kinase- SME covalent complex is used in Tethering to identify ligands that have an affinity for a site on the kinase that is adjacent to the SME binding site. This adjacent site is referred to as the second site of interest.
  • the first reactive functionality on a SME forms a irreversible covalent bond through the nucleophile or electrophile, preferably nucleophile, on the protein kinase target, thereby forming an irreversible protein kinase-SME complex.
  • Preferred nucleophiles on the target protein kinase suitable for forming an irreversible kinase-SME complex include -SH, -OH, -NH 2 and -COOH usually arising from side chains of Cys, Ser or Thr, Lys and Asp or Glu respectively.
  • Protein kinases may be modified (e.g. mutants or derivatives) to contain these nucleophiles or may contain them naturally.
  • BLK, BTK, EGFRl, ERB2, ERB4, ERKl, ERK2, FGFRl, FGFR2, FGFR3, FGFR4, etc. are examples of kinases containing suitable naturally occurring cysteine thiol nucleophiles.
  • the second reactive functionality is a group capable of forming a disulfide bond.
  • a group capable of forming a disulfide bond.
  • Illustrative examples of such a group include a free thiol (-SH) , protected thiol (-SR where R' is a thiol protecting group), and a disulfide (-SSR" where R" is a substituted or unsubstituted aliphatic or substituted or unsubstituted aryl).
  • the SME may, but does not have to, include a portion that has binding affinity (i.e. is capable of bonding to) a first site of interest on the target kinase.
  • FIG. IB is a schematic illustration of one embodiment of Tethering with extenders.
  • a target that includes a thiol is contacted with an extender comprising a first functionality -LG that is capable of forming a covalent bond with the reactive thiol and a second functionality second functionality -SPG that is capable of forming a disulfide bond.
  • the extender binds to the first site of interest and forms a target-extender covalent complex which is then contacted with a plurality of ligand candidates to identify a ligand for a second site of interest.
  • the SME includes a binding element that has affinity for the SME binding site.
  • compounds having known affinity for kinases can be modified to be SME's by adding the first reactive functionality (-LG in Figure IB) and the second reactive functionality (-SPG in Figure IB).
  • Suitable first reactive functionalities include groups that are capable of undergoing SN2- like or Michael-type addition and thus forming an irreversible covalent bond with the target kinase. Examples of SME's having such groups are further described below.
  • I — I optionally includes a binding element for the intended SME binding site and -S is the second reactive functionality that is capable of forming a disulfide bond.
  • ⁇ -halo acids F, CI and Br substituted ⁇ to a COOH, PO 3 H 2 or P(OR)O 2 H acid that is part of the SME can form a thioether with the thiol of the target kinase.
  • Illustrative examples of generic ⁇ -halo acids are shown below.
  • R is C1-C20 unsubstituted aliphatic, C1-C20 substituted aliphatic, unsubstituted aryl or substituted aryl
  • R' is H, SCH 3 , S(CH 2 ) conflictA, where A is OH, COOH, SO 3 H, CONH 2 or NH 2 and n is 1 to 5, preferably n is 2 to 4.
  • Fluorophosph(on)ates are Sarin-like compounds which react readily with both SH and OH nucleophiles. Illustrative examples of general fluorophosph(on)ates are shown below. where R and R' are as defined above.
  • Epoxides, aziridines and thiiranes SME's containing these reactive functional groups are capable of undergoing SN2 ring opening reactions with -SH, -OH and -COOH nucleophiles. Preferred examples of the latter are aspartyl proteases like ⁇ -secretase (BASE). Preferred generic examples of epoxides, aziridines and thiiranes are shown below.
  • R' is as defined above, R is usually H or lower alkyl and R" is lower alkyl, lower alkoxy, OH, NH 2 or SR'.
  • R is usually H or lower alkyl and R" is lower alkyl, lower alkoxy, OH, NH 2 or SR'.
  • SR' is optionally present because upon nucleophilic attack and ring opening a free thiol is produced which may be used in the subsequent extended tethering reaction.
  • 'RS- x o Fluromethylketones are simple examples of this class of activated ketones which result in the formation of a thioether when reacted with a thiol containing protein.
  • Electrophilic aromatic systems examples include 7-halo-2,l,3-benzoxadiazoles and ortho/para nitro substituted halobenzenes.
  • SN2 like reactions suitable for formation of covalent bonds with protein kinase nucleophiles include formation of a Schiff base between an aldehyde and the amine group of lysine of enzymes like DNA repair proteins followed by reduction with for example NaCNBH 4 .
  • SR where R is H, glutathione or S -lower alkyl substituted with NH or OH
  • the first site of interest is the ATP binding pocket.
  • known compounds that target the ATP binding pocket of kinases can be modified to be an SME by adding first and second reactive functionalities.
  • SME's include those that contain purine or purine mimetics such as the following:
  • R' is -S(CH 2 ) n NH 2 , -S(CH 2 ) n OH or -S(CH 2 ) n COOH where n is 1-5, preferably 2-4.
  • Michael acceptors include
  • Suitable SME's containg quinazolines include:
  • Figure 2 illustrates the use of a quinazoline extender to form a kinase-extender covalent complex.
  • Figure 2A is the mass spectrometer profile of purified EGFRl kinase domain in the active conformation.
  • Figure 2B is purified EGFRl kinase domain in the inactive conformation.
  • Figures 2C-E) are purified EGFRl in the inactive conformation following incubation with C) cystamine, D) the quinazoline extender shown, and E) the quinazoline extender and cystamine.
  • Tethering can be used to identify novel ligands that bind to the ATP- binding pocket. For example, Tethering off the naturally occurring cysteine at the bottom of the ATP binding pocket in EGFRl (C797), identified the expected purine and purine mimetic containing ligands along with several novel scaffolds.
  • Representative ligand candidates with novel scaffolds include:
  • SME's that can be made using such scaffolds by adding first and second functionalities include but are not limited to:
  • cysteines As described above, certain kinases already possess a naturally occurring cysteine within the ATP binding pocket that can be used to identify ligands that bind to this site.
  • other examples of kinases that include a naturally occurring cysteine within the ATP binding pocket include: BLK (C318); BTK (C481); ERB2 (C805); ERB4 (C803); JAK3 (C909); TEC (C449).
  • BLK C318
  • BTK C481
  • ERB2 C805
  • ERB4 C803
  • JAK3 C909
  • TEC C449
  • the resulting kinase-SME complex can be used to identify ligands to the adaptive binding region adjacent to the ATP binding site.
  • Tethering with extenders has been primarily described with target kinases having reactive thiols and extenders having a group capable of forming a covalent bond with the thiol, other chemistries can be used.
  • the amino group of lysines are alternative nucleophiles on the target kinases.
  • the following extender is an exemplary extender that is capable of forming a covalent bond with a lysine
  • the 5'-(p- fluorosulfonylbenzoyl)adenosine-based extender can be used with any kinase without the need for making a cysteine mutation in this site.
  • the precursor for installing a masked thiol onto the adenosine-containing compound is made by reacting reacting commercially available N-Boc- cysteamine with commercially available methanethiosulfonic acid S-methyl ester, followed by deprotection of the Boc group to generate the hydrochloride salt. The resulting compound is reacted with commercially available 6-chloroadenosine.
  • the kinase-SME complex can then be used in Tethering as described above. While it is usually preferred that the attachment of the SME does not denature the target, the kinase-SME complex may also be formed under denaturing conditions, followed by refolding the complex by methods known in the art.
  • the SME and the covalent bond should not substantially alter the three-dimensional structure of the target protein kinase, so that the ligands will recognize and bind to a binding site of interest on the target with useful site specificity.
  • the SME should be substantially unreactive with other sites on the target under the reaction and assay conditions.
  • the monophores fragments are also broadly representative of recognized and unique drug-like pharmacophores and fragments thereof.
  • candidate fragments satisfy two primary criteria. First, they contain a functional group that will permit the installation of a disulfide linker. Suitable functional groups include a free amine, carboxylate, sulfonyl chloride, isocyanate, aldehyde, ketone, etc.
  • Reductive aminations between aldehydes and ketones and amines are described, for example, in March et al, supra, at pp. 898-900; alternative methods for preparing amines at page 1276; reactions between aldehydes and ketones and hydrazide derivatives to give hydrazones and hydrazone derivatives such as semicarbazones at pp. 904-906; amide bond formation at p. 1275; formation of ureas at p. 1299; formation of thiocarbamates at p. 892; formation of carbamates at p. 1280; formation of sulfonamides at p. 1296; formation of thioethers at p.
  • transition metal-catalyzed couplings of aryl halides and sulfonates with alkanes and acetylenes e.g. Heck reactions, at pp. 717-178
  • organometallic reagents such as organoboron, reagents, at p. 662
  • organotin, and organozinc reagents formation of oxazolidines
  • disulfide-containing small molecule libraries may be made from commercially available carboxylic acids and protected cysteamine (e.g. mono-BOC-cysteamine) by adapting the method of Parlow et al, Mol. Diversity 1:266-269 (1995), and can be screened for binding to polypeptides that contain, or have been modified to contain, reactive cysteines.
  • the monophores library can be derived from commercially available compounds that satisfy the above criteria. However, many motifs common in biologically active compounds are rare or absent in commercial sources of chemicals. Therefore, the fragment collection is preferably supplemented by synthesizing monophores fragments that help fill these gaps.
  • a typical library can contain 10,000 or more compounds. e. Detection and identification of ligands bound to a target The ligands bound to a target (or to a target-SME complex) can be readily detected and identified by mass spectroscopy (MS).
  • MS detects molecules based on mass-to-charge ratio (m/z) and thus can resolve molecules based on their sizes (reviewed in Yates, Trends Genet. 16: 5-8 [2000]).
  • a mass spectrometer first converts molecules into gas-phase ions, then individual ions are separated on the basis of m z ratios and are finally detected.
  • a mass analyzer which is an integral part of a mass spectrometer, uses a physical property (e.g. electric or magnetic fields, or time-of-flight [TOF]) to separate ions of a particular m/z value that then strikes the ion detector.
  • Mass spectrometers are capable of generating data quickly and thus have a great potential for high-throughput analysis.
  • MS offers a very versatile tool that can be used for drug discovery.
  • Mass spectroscopy may be employed either alone or in combination with other means for detection or identifying the organic compound ligand bound to the target.
  • Techniques employing mass spectroscopy are well known in the art and have been employed for a variety of applications (see, e.g., Fitzgerald and Siuzdak, Chemistry & Biology 3: 707-715 [1996]; Chu et al, J. Am. Chem. Soc. 118: 7827-7835 [1996]; Siudzak, Proc. Natl Acad. Sci. USA 91: 11290- 11297 [1994]; Burlingame et al, Anal Chem.
  • any other suitable technique for the detection of the adduct formed between the protein kinase target molecule and the library member can be used.
  • chromatographic techniques such as liquid chromatography, thin layer chromatography and likes for separation of the components of the reaction mixture so as to enhance the ability to identify the covalently bound organic molecule.
  • Such chromatographic techniques may be employed in combination with mass spectroscopy or separate from mass spectroscopy.
  • a labeled probe fluorescently, radioactively, or otherwise
  • the formation of the new bonds liberates a labeled probe, which can then be monitored.
  • Other techniques that may find use for identifying the organic compound bound to the target molecule include, for example, nuclear magnetic resonance (NMR), capillary electrophoresis, X-ray crystallography, and the like, all of which will be well known to those skilled in the art.
  • pools containing compounds that covalently modify the kinase or the kinase-extender covalent complex are identified by mass spectrometry (MS) analysis. From the deconvoluted MS profile, the molecular weight of the bound compound can be precisely calculated, and thus its identity in the pool determined. The discrete compound is then tested alone to determine if it can covalently modify the kinase or the kinase-extender complex. Each screen is likely to identify multiple hits. Hits are prioritized according to their relative binding affinities and according to their relative preference for the inactive enzyme conformation.
  • Relative enzyme binding affinities expressed as a BME 50
  • BME titration curve to determine the concentration that allows 50% modification while using a constant concentration of compound. From this one can easily rank the compounds, 5 based upon their binding affinities.
  • additional valuable information can be gained from analyzing the structure-activity relationship (SAR) between hit compounds and their relatives in the monophores library. For example, if several hit molecules for a particular kinase or kinase-extender pair fall into a closely related family, one may then go back to theO monophores library and find structurally similar compounds that were not selected in the initial screen.
  • SAR structure-activity relationship
  • the identified ligands can be advanced into lead compounds by any number of methods known in the art.
  • compound libraries are made based upon the identified fragments.
  • traditional medicinal chemistry approaches are used.5
  • the binding determinant from the extender can be merged with the identified fragment to make a conjugate compound that is equivalent or better than a lead compound derived from traditional high-throughput screening.
  • Figure 3 illustrates one example of such a conjugate compound in which subsequent optimization led to a nanomolar kinase inhibitor.
  • a cysteine mutant of MEKl0 S150C was made that placed a thiol at the bottom of the ATP binding pocket.
  • a pyrimidine extender that had been previously been identified as a fragment that had binding affinity for ATP binding pocket of kinases was used to form a MEKl -extender covalent complex. This complex was then used to identify a fragment that binds to the adaptive binding site that was then merged with the binding determinant from the pyrimidine extender to yield a 33 ⁇ M MEKl inhibitor (compound 1). Acylation of the amine resulted in a 170 nM MEKl inhibitor (compound 2).
  • Other potent inhibitors that resulted from simple modification of compound 1 include the following compounds which inhibits MEKl with ICso's of 80 nM, 50 nM, 30 nM, and 10 nM respectively.
  • the resulting submicromolar MEKl inhibitors all preferentially inhibit the inactive form.
  • No inhibition of the active form of MEKl was observed at concentrations of compounds 2-6 at 10 ⁇ M (and ATP concentrations of 50 ⁇ M).
  • these compounds also showed remarkable specificity for compounds that have yet to be optimized. For example, neither compounds 1 nor 2 inhibit Raf kinase at concentrations that inhibit MEKl completely.
  • the most potent of the above compounds (3, 4 and 6) were tested in a panel of kinases, as shown in Figure 4, these compounds were also very specific for the inactive conformation of MEKl. Only RAF showed any significant inhibition.
  • Example 1 Construction and Expression of EGFRl and Lck variants Wild-type human Lck and wild-type human EGFRl were cloned by RT-PCR from poly(A)+ enriched mRNA from Jurkat cells and A431 cells, respectively.
  • Jurkat cells were grown in suspension in 30 mL of medium containing 10% fetal bovine serum (FBS), at a concentration of 8.4 x 107 cells/mL. Approximately 40% of the Jurkat cells were put into an Eppendorf tube and pelleted.
  • FBS fetal bovine serum
  • Adherent A431 cells were grown in DMEM containing 4 mM glutamine, 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, and 10% FBS. A T75 monolayer was trypsinized and resuspended in IX phosphate buffered saline. 28 mL of A431 cells at 5.6 x 106 cells/mL were pelleted into a second Eppendorf tube. The RNA was isolated from each type of cells as follows. The pelleted cells were lysed with 1 mL Tri Reagent, microfuged atl5K rpm for 10 min at 4 °C, and the supernatant was transferred into a new tube.
  • Chloroform 400 ⁇ L was added to the tube, which was vortexed, allowed to stay at room temperature for 5 min, and then microfuged for 15 min at 4 °C.
  • the aqueous phase was transferred to a new tube, to which a half- volume of 2-propanol was added. The tube was vortexed, allowed to stay at room temperature for 5 min, and then microfuged for
  • RNA pellet was resuspended in 200 ⁇ L deionized water.
  • Poly(A)+ mRNA was purified using an Oligotex purification kit (QIAgen), and stored at -20 °C.
  • the first strand of cDNA was obtained by reverse transcription from the poly(A)+ mRNA as follows. Oligonucleotides corresponding to SEQ ID NO:l and SEQ ID NO:2 were used as a reverse transcriptase primer for Lck and EGFR, respectively.
  • Oligonucleotides SEQ ID NO:3 and SEQ ID NO:4 were used as 5' and 3' PCR primers for Lck, respectively, and oligonucleotides SEQ ID NO:5 and SEQ ID NO:6 were used as 5' and 3' PCR primers for EGFR, respectively.
  • PCR products were purified on a QIAgen miniprep column, digested in a 80 ⁇ L volume with Xhol and Hindlll in IX Buffer2/BSA (New England Biolabs) for 2 hr at 37 °C. Five micrograms of pRSETB were also digested by Xhol and Hindlll in the same manner. The resulting digestion products were also purified on a QIAgen miniprep column, and then used in ligation reactions. All ligation reactions (Boehringer Rapid Ligation kit) contained 1 ⁇ L of purified vector, and 1-2 ⁇ L of insert, and were performed according to the manufacturer's instructions.
  • NO:9 was altered to express a mutant Lck construct having S323 mutated to cysteine.
  • the mutation was designed to allow covalent attachment of a small molecule extender by introducing a cysteine residue into the target kinase in a position analogous to EGFRl C797 of SEQ ID NO:9
  • APQSSEFIGA Mutagenesis of the Lck pRSETB construct was performed by PCR using sense and antisense oligonucleotide of SEQ ID NO:l 1 and SEQ ID NO: 12, respectively.
  • the mutagenesis PCR reactions contained 1 ⁇ L (approximately 300 ng) of methylated pRSETB plasmid isolated from bacteria transformed by pRSETB encoding wild-type Lck (residues 231-496), 2.5 ⁇ L each of sense and antisense primers (10 ⁇ M stock concentration), 1 ⁇ L dNTPs (12.5 mM stock concentration), 5 ⁇ L Pfu-turbo buffer, 37 ⁇ L deionized water, and 1 ⁇ L Pfu-turbo polymerase.
  • PCR reactions were heated to 95 °C for 1 min, and then cycled three times through 95 °C for 30 sec, 55 °C for 1 min, and 68 °C for 3 min. Finally the reactions were allowed to remain at 68 °C for 10 min.
  • Dpnl (1 mL) was used to digest the methylated parent plasmid, and 1 ⁇ L of the digest containing the in vitro synthesized, unmethylated, intact linear PCR product, including the introduced mutation, was transformed into ToplOF' cells, where the PCR product was ligated to produce the pRSETB plasmid encoding mutant Lck.
  • the pRSETB constructs expressing wild-type EGFRl residues 698-970 and the Lck mutant were subcloned into a pFastbacHTa vector (GIBCO-BRL), such that the resulting encoded proteins contained a (His) 6 tag on their N-termini.
  • 5' PCR primers SEQ ID NO: 13 and SEQ ID NO: 14 were used to amplify Lck and EGFRl from the corresponding pRSETB constructs, respectively; each contain an Ncol site.
  • the region spanning BamHI-Hindlll was removed from the polylinker of the plasmid pFastBacl, and replaced with an annealed oligonucleotide duplex of SEQ ID NO:15 and SEQ ID NO:16 encoding for a (His) 6 tag.
  • This replacement into the pFastBacl vector obliterates the BamHI and Hindlll sites, and introduces an Ncol site and a new Hindlll site to produce the plasmid pFastBacl C-termHis.
  • the primers used for this purpose correspond to SEQ ID NO: 17 and SEQ ID NO: 18.
  • the resulting DNA was inserted into the pFastBacl C-termHis plasmid so as to replace the Ncol- Hindlll segment.
  • the resulting construct encoded for residues 670-988 of SEQ ID NO:10, and contained a (His) 6 tag only on the C-terminus.
  • the cells were allowed to sit for 15 min at 4 °C, and then for 10 min at room temperature. SOC (900 ⁇ L) was then added to the cells, which were shaken 4 hr at 37 °C. Two hundred microliters of the cell mixture was plated onto LB-agar plates containing 50 ⁇ g/mL kanamycin, 7 ⁇ g/mL gentamycin, 10 ⁇ g/mL tetracyclin, 100 ⁇ g/mL Bluo-Gal, and 40 ⁇ g/mL IPTG. Plates were grown for 2 d at 37 °C, after which white colonies were picked for sequence verification.
  • the resulting recombinant bacmids expressing the Lck S323 mutant and EGFRl residues 670-988 were transfected into Sf9 cells for preparation of recombinant baculovirus. Transfection of the bacmids, and harvest and storage of the recombinant baculovirus were performed according to the manufacturer's instructions (GibcoBRL).
  • High Five insect cells (Invitrogen) were grown to 2 X 106 cells/mL, and then 50 mL of High Five cells were infected with 0.5 mL virus. Standard time and temperature of induction variation was used to optimize expression conditions. Typically, the infected High Five cells were grown for 2 d at 27 °C.
  • Insect cells were pelleted and washed with 5 mL PBS; cells were then lysed with 1 mL mammalian protein extraction reagent (MPER) solution (23.5 mL MPER (Pierce), 1.5 mL 5M NaCl, 35 ⁇ L 14.3 M ⁇ -mercaptoethanol, 250 mL protease inhibitor-EDTA), rocking end over end for 20 min at 4 °C. Lysate was placed in a tube and spun for 15 min at 4 °C (15K, Sorval SS-34 rotor).
  • MPER mammalian protein extraction reagent
  • N-terminally (His) 6 -tagged Lck S323C mutant protein was purified from cell lysates using standard protein chromatography techniques. Specifically, the Lck S323C was purified on a 6 mL Ni-NTA-agarose column. The column was rinsed in deionized water at 2 mL/ min, and then equilibrated in binding buffer (pH 8.0) containing 50 mM NaH PO 4 , 0.5 M NaCl, and 5 mM ⁇ -mercaptoethanol.
  • binding buffer pH 8.0
  • Buffer B (20 mM Tris pH 7.5, 1.0 M NaCl, 5 mM ⁇ -mercaptoethanol) was run in 45 min, and the eluate collected in fractions.
  • the EGFRl elutes at about 50% buffer B, corresponding to 0.5 M NaCl.
  • Example 2 Construction and Expression of MEKl variants
  • the amino acid sequence of MEKl is shown here as SEQ ID NO: 19.
  • MEKl DLKQLMVHAF IKRSDAEEVD FAGWLCSTIG LNQPSTPTHA AGV
  • the entire coding sequence of MEKl was subcloned into the expression plasmid pGEX- 6P-1 (Invitrogen) using 5' and 3' PCR primers (SEQ ID NO:20 and SEQ ID NO:21, respectively), along with a commercially available MEKl cDNA (Mekl cDNA in pUSEamp, Upstate #21-106) as a PCR template.
  • the resulting plasmid, pMekl-001 encodes a GST-MEK1 fusion protein in which the MEKl portion contains a 14 amino acid insertion between residues Ml and P2 of the GenBank reported sequence, as well as tliree single amino acid substitutions from the GenBank reported sequence: M274L G392S, and V393T, numbering relative to SEQ ID NO:l.
  • the liberated MEKl protein contains an additional five non-native amino (GPLGS) acids at the amino terminus.
  • MEKl Constructs The surface accessibility of native cysteines was assessed by mass spectrometry, according to their reactivity with cystine in the presence of 0-16 mM ⁇ -mercaptoethanol. Of the six naturally occurring cysteines, C207, C277, and C341 were determined to be reactive cysteines and were "scrubbed". In addition, a cysteine was introduced in a location (S150C) analogous to that of C797 of EGFRl. All mutations have been introduced using long-range PCR with a pair of complementary oligonucleotides containing the desired mutation. The oligos for making the constructs were:
  • a frozen glycerol stock of E. coli (Rosetta DE3 competent cells from Novagen) containing the desired pGEX-MEKl construct is used to inoculate 50 mL 2xYT media containing 150 ⁇ g/mL ampicillin and 30 ⁇ g/mL chloramphenicol; the resulting culture is grown overnight at 37 °C. A portion of the overnight culture (10-15 mL) is then used to inoculate 1.5 L 2xYT media containing 150 ⁇ g/mL ampicillin and 30 ⁇ g/mL chloramphenicol, and the culture is grown at 37 °C until OD 6 oo * 0.7-1.0.
  • the cultures are chilled at 4 °C for 30-60 min; after chilling, IPTG is added to 0.2 mM, and cultures are incubated overnight at room temperature with shaking at 225 rpm (20-22 °C).
  • Cells are harvested by centrifugation at 5000 rpm, media is discarded, and the pellet is resuspended in 50 mL freshly made lysis buffer (lx phosphate buffered saline (PBS), 400 mM KCl, 1 M urea, 1 tablet Complete Protease Inhibitor Cocktail, 1% (v/v) aprotinin, DNase I (100 units/mL)).
  • lysis buffer lx phosphate buffered saline (PBS), 400 mM KCl, 1 M urea, 1 tablet Complete Protease Inhibitor Cocktail, 1% (v/v) aprotinin, DNase I (100 units/mL)
  • phenylmethyl sulfonyl fluoride (PMSF) is added to a final concentration of 2 mM.
  • Cells are lysed by passing through a micro-fluidizer four separate times. Lysate is kept on ice, and immediately spun at 16,000 rpm at 4 °C for 30 min. While the lysate is spinning, a glutathione agarose column is equilibrated with Wash Buffer #1 (lx PBS, 400 mM KCl, 1 M urea). Supernatant is removed from the spun lysate, and immediately loaded onto the equilibrated column at 2-3 mL/min.
  • Wash Buffer #1 lx PBS, 400 mM KCl, 1 M urea
  • the column is washed first with Wash Buffer #1 until the OD 28 o drops to a baseline absorbance level, and then with Wash Buffer #2 (lx PBS, 400 mM KCl) for several minutes to remove the urea.
  • Wash Buffer #2 (lx PBS, 400 mM KCl) for several minutes to remove the urea.
  • the bound GST-MEK1 fusion protein is eluted with Elution Buffer (20 mM HEPES pH 8.4, 100 mM KCl, 10 mM glutathione, 1 mM DTT).
  • Elution Buffer (20 mM HEPES pH 8.4, 100 mM KCl, 10 mM glutathione, 1 mM DTT).
  • the column can be regenerated by stripping with 6 M guanidine-HCl and washing with DI water after stripping.
  • GST is cleaved off the fusion protein by addition 60 ⁇ L Prescission Protease (Amersham Biosciences); the digest reaction is transferred into 10,000-14,000 mwco dialysis tubing and dialyzed against 4 L of 20 mM HEPES pH 7.4, 150 mM NaCl, 1 mM DTT overnight at 4 °C. Subsequently the digest reaction is removed from the dialysis tubing, and spun at 16,000 rpm at 4 °C for 30 min. While the digest reaction is spinning, a glutathione agarose column is washed with Wash Buffer #3 (20 mM HEPES pH 7.4, 150 mM NaCl, 1 mM DTT).
  • the supernatant is loaded onto the equilibrated column at 1-3 mL/min, and then the column is washed with Wash Buffer #3 until the OD 280 drops to baseline. Flow-through is collected until baseline is reached. The flowthrough is then mixed 1 : 1 with Dilution buffer (20 mM HEPES pH 8.4, 1 mM DTT), to make a solution that is 20 mM HEPES pH 8.0, 75 mM NaCl.
  • Dilution buffer (20 mM HEPES pH 8.4, 1 mM DTT)
  • a Q- Sepharose column connected in series with a prepacked 5 mL glutathione agarose column is equilibrated with Low Salt Buffer #1 (20 mM HEPES pH 8.0, 75 mM NaCl, 1 mM DTT).
  • the diluted flowthrough is loaded onto the equilibrated Q-Sepharose column at 1-3 mL/min, and the resulting flowthrough is collected. After the entire sample is loaded, the column is washed with Low Salt buffer #1 (20 mM HEPES pH 8.0, 75 mM NaCl, 1 mM DTT), and the flowthrough containing MEKl is collected until the OD 28 o reaches baseline. Bound protein (GST and impurities) is eluted by washing the column with High Salt buffer #1 (20 mM HEPES pH 8.0, 750 mM NaCl, 1 mM DTT), and collected for analysis.
  • Low Salt buffer #1 (20 mM HEPES pH 8.0, 75 mM NaCl, 1 mM DTT
  • Bound protein (GST and impurities) is eluted by washing the column with High Salt buffer #1 (20 mM HEPES pH 8.0, 750 mM NaCl, 1 mM DTT), and collected for analysis.
  • the flowthrough containing MEKl is then mixed with saturated ammonium sulfate solution (3.9 M), to a final concentration of 1.2 M ammonium sulfate.
  • the resulting solution is then loaded at 2-3 mL/min onto an HIC phenyl-Sepharose column that has been equilibrated with High Salt Buffer #2 (20 mM HEPES pH 7.4, 1.2 M ammonium sulfate). After loading, the column is washed with High Salt Buffer #2 until the OD 280 drops to baseline.
  • a linear gradient is run from 20 mM HEPES pH 7.4, 1.2 M ammonium sulfate to 20 mM HEPES pH 7.4 with no ammonium sulfate over 30 min, and 4 mL fractions are collected.
  • the fractions are run on a gel to determine which fractions to pool.
  • the pooled fractions are then dialyzed overnight at 4 °C against 4 L of 20 mM HEPES pH 7.4, 150 mM NaCl, in the absence of DTT. Finally, the pooled fractions are dialyzed again against 2 L of 20 mM HEPES pH 7.4, 150 mM NaCl for 2-4 hr.
  • the dialyzed protein is quantitated, divided into aliquots and stored frozen at -80 °C.
  • One absorbance unit at 280 nm is equivalent to a concentration of 1.86 mg/mL, and 1 ⁇ g of MEKl is equivalent to 22.8 pmol, as MEKl has a MW of 43,832.
  • Example 3 Activity Assays MEKl ELISA Assay Phosphorylation of ERK2 by MEKl is measured for two reaction formats.
  • the first reaction format is a Raf- ⁇ MEK1- ⁇ ERK2 cascade where constitutively active truncated Rafl, inactive MEKl , inactive biotinylated ERK2, and dephosphorylated MBP (Myelin Basic Protein) are present.
  • the second reaction format uses activated MEKl, biotinylated ERK2, and dephosphorylated MBP in the absence of Raf. Results can be compared to determine whether a compound preferentially inhibits the inactive conformation of MEKl over the active conformation of MEKl .
  • Both reaction formats are run in the presence and absence of compounds, and use ELISA as a readout of the extent of phosphorylation of the biotinylated ERK2.
  • tliree final concentrations of compound are used, e.g., 50 ⁇ M, 10 ⁇ M and 2 ⁇ M.
  • concentrations of the compound with 2 fold dilutions are used to determine the IC 50 for the compound; the concentrations of the compound used depend on the activity observed in the three-point experiment.
  • Typical stock concentrations of a moderately active compound in a 9-point experiment are 1 mM, 0.5 mM, 0.25 mM, 0.125 mM, 62.5 ⁇ M, 31.2 ⁇ M, 15.6 ⁇ M, 7.8 ⁇ M and 3.9 ⁇ M.
  • the corresponding final concentrations of compound in the phosphorylation reaction are 20 ⁇ M, 10 ⁇ M, 5 ⁇ M, 2.5 ⁇ M, 1.25 ⁇ M, 0.625 ⁇ M, 0.312 ⁇ M, 0.156 ⁇ M, and 0.078 ⁇ M.
  • the most concentrated final concentration of compound would be 200 ⁇ M, and for more active compounds, the most concentrated final concentration of compound would be 2 ⁇ M.
  • Inactive ERK2 (Cell Signaling #6082) is biotinylated as follows. Twenty-five microliters of 10X PBS and 200 ⁇ L of 50 mM carbonate buffer pH 9.0 are added to 250 ⁇ L of ERK2 at 2 mg/mL; the resulting solution is kept on ice for 10 min. Next, sulfo-NHS-LC-LC- biotin (Pierce) is freshly dissolved in solution to a final concentration of 2 mg/mL, and 10 ⁇ L of the biotin solution is added immediately to the ERK2 solution.
  • the resulting reaction is incubated at room temperature for 1 hr, after which 100 ⁇ L of 3 M ethanolamine is added to quench the reaction. Five hundred microliters of the quenched reaction are loaded onto a Nap5 column, discarding the flowthrough. The remaining 85 ⁇ L of the quenched reaction are then loaded onto the same column, while collecting the flowthrough, followed by 715 ⁇ L Tris- buffered saline (IX TBS: 10 mM Tris pH 7.5, 150 mM NaCl), while continuing to collect the flowthrough.
  • IX TBS 10 mM Tris pH 7.5, 150 mM NaCl
  • Biotin-ERK2 is stored at -20 °C in IX TBS containing 10% glycerol.
  • Avidin-coated capture plates are prepared by adding 100 ⁇ L of NeutrAvidin (Pierce #31000) in PBS at 0.040 mg/mL to each well of 96- well polystyrene plates (NUNC brand maxisorp, VWR #442404). After addition of the NeutrAvidin, the plates are covered and allowed to sit at room temperature for 2-4 hr, or overnight at 4 °C.
  • BLOCK solution 0.05 g/mL BSA, IX TBS, 0.1% Tween-20
  • the plates are allowed to sit at room temperature for 0.5-2 hr, until the phosphorylation reactions are ready to be transferred to the capture plate.
  • phosphorylation Cascade Reactions Using Inactive MEKl Typical phosphorylation reactions are performed in either eppendorf tubes or 96-well plates with conical bottoms (Costar #3363).
  • the phosphorylation reactions in this reaction format contain in a 50 ⁇ L total volume the following components: 20 ⁇ g/mL MBP (Upstate #13-110), 150 nM biotin-ERK2, 0.7 nM Rafl (residues 306-648, N-terminally GST-tagged, Upstate # 14-352), 10 nM MEKl, 4.5 mM MgCl 2 , 100 ⁇ M NaOV0 3 , 30 mM Tris HC1 (pH 7.5), 120 mM NaCl, 6 mM DTT, 0.0067% Triton X-100 (vol/vol) and 50 ⁇ M ATP; all concentrations are final.
  • phosphorylation reactions are performed in either eppendorf tubes or 96-well plates with conical bottoms (Costar #3363).
  • the phosphorylation reactions in this format contain in a 50 ⁇ L total volume the following components: 20 ⁇ g/mL MBP (Upstate #13-110), 150 nM biotin-ERK2, 1 nM active MEKl (Upstate #14-429), 4.5 mM MgCl 2 , 100 ⁇ M NaOVO 3 , 30 mM Tris HCl (pH 7.5), 120 mM NaCl, 6 mM DTT, 0.0067% Triton X-100 (vol/vol) and 50 ⁇ M ATP; all concentrations are final.
  • the concentration of active MEKl used is lower than the concentration of inactive MEKl in the format above, in order to keep readout in the linear range. Forty-five microliters of all reagents except the ATP, MgCl and NaOVO 3 are added to 1 ⁇ L of stock concentrations of compound in DMSO; thus the phosphorylation reactions using active MEKl also contain a final amount of DMSO that is 2% by volume. Addition of 5 ⁇ L of a solution of ATP, MgCl 2 , and NaOVO 3 , each 10 fold higher in concentration than their respective final concentrations, starts the phosphorylation reaction. Reactions are allowed to proceed 30 min at room temperature with gentle shaking.
  • Post-reaction treatment is the same for both reaction formats.
  • the solution phase phosphate-transfer reactions are stopped by addition of 75 ⁇ L stop buffer containing 0.4 M EDTA pH 7.5, 1% BSA, IX TBS and 0.1% Tween-20.
  • the BLOCK is removed from the prepared avidin-coated capture plates, and a 100 ⁇ L portion of each stopped reaction is transferred to a well of the plate.
  • Biotinylated ERK2 is captured on the surface of the avidin- coated polystyrene plate by incubation of the plate at room temperature with gentle shaking for 1-2 hr.
  • the reaction mixture is aspirated and the plate is incubated with a primary polyclonal antibody (Cell Signaling #9101) that recognizes the activation loop of ERK2 phosphorylated on T202 and Y204, the antibody diluted 1000 fold in a solution containing final concentrations of 1% BSA, IX TBS and 0.1% Tween-20 by volume.
  • a primary polyclonal antibody Cell Signaling #9101
  • the capture plate is incubated with the primary antibody solution at room temperature with gentle shaking for 2-3 hr prior to aspiration and addition of 100 ⁇ L of the secondary antibody, which is horseradish peroxidase (HRP)-conjugated Goat anti Rabbit IgG, (Zymed #62-6120) that has been diluted 1000 fold in 1% BSA, IX TBS, 0.1% Tween 20.
  • HRP horseradish peroxidase
  • Goat anti Rabbit IgG Goat anti Rabbit IgG
  • the secondary antibody is incubated with the plate at room temperature for 1-2 hr with gentle shaking, the solution is aspirated, and the wells are then washed gently 3 times with IX PBS with 0.05% Tween-20.
  • the amount of phosphorylated ERK2 present on the capture plate is quantitated using the ImmunoPure TMB substrate kit (Pierce #34021). After the PBS is aspirated, 100 ⁇ L of a freshly made TMB/H 2 O 2 solution at room temperature containing equal volumes of peroxidase substrate solution (TMB, #1854050) and H 2 O 2 solution (#1854060) is added to the wells, and the plate is incubated at room temperature with gentle shaking for 5-20 min. Color development is stopped by adding 100 ⁇ L of 2.5 M H 2 SO 4 to each well of the capture plate and shaking gently for 1-2 min. Absorbance of the substrate is measured at 450 nm.
  • EGFRl and Lck ELISA Assay The ELISA assay for EGFRl and Lck are generally similar to that described above for MEKl except that biotinylated E4Y substrate is used instead of ERK2.
  • Typical EGFRl or Lck kinase assays contain 0.75% BSA, 30 mM Tris pH 7.5, 30 mM MgCl 2 , 18 mM MnCl 2 , 45 ⁇ M Na 2 VO 3 , 0.5 mM DTT, 100 pM EGFR or Lck kinase, 30 ⁇ g/ml biotinylated E 4 Y, and 60 ⁇ M ATP.
  • Bound substrate/reaction product was reacted with HRP-conjugated anti-phospho-tyrosine antibody instead of sequentially with anti-phospho-p44/42 ERK1/2 antibody and HRP- conjugated anti-rabbit antibody for the MEKl assays.
  • MEKl Western Assay The MEKl ELISA does not distinguish between Raf inhibition and MEKl inhibition. Therefore, a Western assay was established for independently monitoring Raf activity. This assay has a ten fold lower throughput (8-10 compounds per week) than the ELISA, but it allows for independent analyses of both MEKl and Raf inhibition in the same assay. Briefly, assays are carried out as described for the ELISA format with the exception that ERK2 is used in place of biotinylated ERK2 and reactions are terminated with the addition of SDS-PAGE gel loading buffer.
  • transfer membranes are incubated overnight with primary antibody in either TBST with 5% BSA and anti MEKl, anti phospho MEKl, or anti ERK (Cell Signaling #9122, #9121, and #9102 respectively) or TBST with 5% nonfat dry milk and anti-phospho ERK (Cell Signaling #9101). All transfer membranes are then incubated for two hours in TBST with 5% nonfat dry milk and HRP-conjugated anti- Rabbit antibody (ZyMed #62-6120) and HRP activity quantified using ECL plus (Amersham #RPN2132).
  • Example 4 Tethering EGFRl Tethering was performed on the inactive conformation of EGFRl (not phosphorylated on Y745) using Cys797 as the reactive thiol.
  • the disulfide containing monophore library was screened in pools of 10. Using 2 ⁇ M EGFRl, 500 ⁇ M library pool, and 600 ⁇ M BME, 252 compounds gave >50% conjugation to C97. These 252 compounds were re-tested as isolated compounds using 2 ⁇ M EGFRl, 50 ⁇ M discrete compound, and 600 ⁇ M BME. In this manner, 214 (85%) screening hits were confirmed.
  • the identified ligands showed clear preference for some chemical classes (aromatic 5 and 6 carbon ring systems and aromatic 5,6 carbon heterocycles, separated from the thiol by a single methylene linker) while other chemical classes were not selected (aliphatic chains, aliphatic 5 carbon rings, and aliphatic 6 carbon rings, separated from the thiol by a 2 or 3 methylene linker).
  • these ligands showed clear enrichment for a number of purine-like compounds, including pyrazines, pyridines, quinolines, quinoxalines, pyrazoles, thiazoles, and other substituted benzenes.
  • Example 5 This example describes the synthesis of
  • Example 6 This example describes the synthesis of
  • Example 7 This example describes the synthesis of
  • Example 8 This example describes the synthesis of
  • Example 9 This example describes Tethering with extenders on the inactive conformation of MEKl.
  • a cysteine mutant of MEKl S150C that also included the following mutations C207A, C277S, C376S was used for the following labelling procedure.
  • a frozen aliquot of MEKl (20 mM HEPES pH 7.4 150 mM NaCl) was thawed, and DTT was added to a final concentration of 2 mM.
  • An extender stored at a concentration of 100 mM in DMSO, was added to the protein so that the final concentration of extender was 1 mM.
  • protem, reductant, and extender were incubated at 4 °C overnight, such that greater than 80% of protein was labelled with extender, as detected by mass spectrometry.
  • the samples were injected onto an HP 1100 HPLC and chromatographed on a Protein MicroTrap (Micrhom Bioresources, Inc. # 004/25109/03) attached to a hybrid quadrupole-TOF QSTAR Pulsar i mass spectrometer (PE Sciex Instruments).
  • the QSTAR was outfitted with a MicrolonSpray ESI source, and was operated in the positive ion mode, scanning the range of 800-1400 m/z.
  • the protein-extender covalent complex was dialyzed against 7 L dialysis buffer (20 mM HEPES pH 7.4, 150 mM NaCl) overnight at 4 °C to remove unreacted extender and reductant. After checking for protein labelling again by QSTAR, the protein-extender conjugate was split into 1.1 mL working aliquots at 2 ⁇ M, frozen on dry ice/ethanol, and stored at -80 °C.
  • different reaction conditions e.g., type of reductant, concentration of reductant, reaction time, etc., can be used.
  • a working aliquot of the MEKl -extender covalent complex was thawed and placed on ice.
  • a library of compounds to be screened was distributed across the wells of a 96-well plate, with each well containing a pool of 10 disulfide-containing compounds. The compounds were pooled so that each compound in the pool has a unique molecular weight, thus enabling deconvolution of the various protein-extender-compound conjugates by mass spectrometry.
  • the following reagents were added in order: 0.86 ⁇ L of each library pool, 1 ⁇ L of 13.5 mM ⁇ -mercaptoethanol, and 25 ixL of protein-extender conjugate.
  • the final screening conditions were 400 ⁇ M library pools, 500 ⁇ M ⁇ -mercaptoethanol, and 2 ⁇ M protein-extender covalent complex.
  • the reactions were incubated at room temperature on a shaker for 1-2 hr. After reaction, samples were run on a QSTAR mass spectrometer as described above for the labelling step, in order to determine which of the library compounds reacted with the protein-extender covalent complex.
  • Example 10 This example describes the synthesis of the following compound
  • Example 11 This example describes the synthesis of the following compound
  • Boc-7-aminoheptanoic acid (4.0 g, 16.31 mmol) was dissolved in benzene (60 mL) and methanol (20 mL) was added.
  • (Trimethylsilyl)diazomethane (2.0 M in hexanes) (16.31 mL, 32.61 mmol) was added and the solution stirred at ambient temperature for 30 min at which point the solvent was removed.
  • the crude residue was then dissolved in 4.0 M HCL in dioxane (42 mL) and stirred for 2 h at ambient temperature at which point the solvent was removed, yielding 7-amino-heptanoic acid methyl ester (3.04 g, 15.53 mmol, 95%).
  • the titled compound was prepared according to Example lOc-d except starting with 7- amino-heptanoic acid methyl ester instead of methyl 6-aminohexanoate hydrochloride.
  • Example 12 This example describes the synthesis of
  • Example 13 This example describes the synthesis of
  • Example 14 This example describes the synthesis of
  • Example 15 This example describes the synthesis of the following compounds
  • Compound 25 was made using 7-amino-heptanoic acid methyl ester hydrochloride instead of methyl 6-aminohexanoate hydrochloride.
  • Compound 26 was made using 8-amino-octanoic acid methyl ester hydrochloride instead of methyl 6-aminohexanoate hydrochloride.
  • Example 16 This example describes the synthesis of the following compounds
  • Example 17 This example describes the synthesis of
  • Example 18 This example describes the synthesis of
  • Example 19 This example describes the synthesis of
  • Example 21 This example describes the synthesis of
  • Example 22 This example describes the synthesis of
  • Example 24 This example describes the synthesis of

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Abstract

L'invention se rapporte à l'identification d'inhibiteurs de protéines kinases qui se lient de manière préférentielle à la conformation inactive d'une protéine kinase cible. Ces inhibiteurs sont identifiés par verrouillage de la protéine kinase cible dans une conformation inactive, et par un ancrage permettant d'identifier les inhibiteurs ciblant de manière préférentielle la conformation inactive.
EP03752561A 2003-09-17 2003-09-17 Identification d'inhibiteurs de kinase Withdrawn EP1670422A4 (fr)

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EA200970361A1 (ru) 2006-10-09 2010-02-26 Такеда Фармасьютикал Компани Лимитед Ингибиторы киназы
WO2011034907A2 (fr) 2009-09-16 2011-03-24 Avila Therapeutics, Inc. Conjugués et inhibiteurs de protéine kinase
CA2785738A1 (fr) 2009-12-30 2011-07-07 Avila Therapeutics, Inc. Modification covalente de proteine, dirigee sur un ligand
CN103097526B (zh) 2010-06-09 2015-09-16 达纳－法伯癌症研究所公司 赋予针对raf和mek抑制剂的抗性的mek1突变
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US20220265669A1 (en) * 2019-02-25 2022-08-25 Albert Einstein College Of Medicine Compounds useful for inhibiting raf dimers
CN116434828B (zh) * 2023-04-17 2024-03-26 深圳新锐基因科技有限公司 基于计算结构生物学的蛋白分子动态二硫键的引入方法及装置

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WO2003014308A2 (fr) * 2001-08-07 2003-02-20 Sunesis Pharmaceuticals, Inc. Mutants de cysteine et procedes de detection de liaison de ligands a des molecules biologiques
WO2003081210A2 (fr) * 2002-03-21 2003-10-02 Sunesis Pharmaceuticals, Inc. Identification d'inhibiteurs de kinase

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WO2002042773A2 (fr) * 2000-11-21 2002-05-30 Sunesis Pharmaceuticals, Inc. Methode de fixation etendue pour l'identification rapide de ligands
WO2003014308A2 (fr) * 2001-08-07 2003-02-20 Sunesis Pharmaceuticals, Inc. Mutants de cysteine et procedes de detection de liaison de ligands a des molecules biologiques
WO2003081210A2 (fr) * 2002-03-21 2003-10-02 Sunesis Pharmaceuticals, Inc. Identification d'inhibiteurs de kinase

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MALY D J ET AL: "Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src inhibitors" PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 14 MAR 2000 UNITED STATES, vol. 97, no. 6, 14 March 2000 (2000-03-14), pages 2419-2424, XP002199108 ISSN: 0027-8424 *
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