个人简介

Associate Professor, Born 1964; B.A. Reed College (1986); Ph.D. UC Berkeley (1991);Life Sciences Research Foundation Fellow, Stanford University (1991-94); Assistant Professor of Chemistry, Princeton University (1994-98); Associate Professor of Chemistry, Princeton University (1998-99); NSF Early Career Development Award (1995-97); Pew Scholar in the Biomedical Sciences (1996-00); Searle Scholar (1997-00); Cottrell Scholar (1997-00); Glaxo-Wellcome Scholar in Organic Chemistry (1997-98); Alfred P. Sloan Research Fellow (1999-2001); Associate Professor of Cellular and Molecular Pharmacology, UC San Francisco (99-current).

研究领域

Bio-organic Chemistry — Organic chemistry is used to probe fundamental signal transduction pathways in cells and whole organisms. Research in our laboratory is focussed on the development of novel chemical tools to decipher signal transduction pathways on a genome-wide scale. The cellular machinery responsible for integrating complex extracellular signals from other cells is very complex. Protein phosphorylation is at the heart of these signaling cascades and is thus the most common on/off switch used in our bodies. The enzymes that catalyze protein phosphorylation are protein kinases. The major focus of our laboratory is to understand in detail the role of each kinase in the body, and determine which kinases would be good candidates for drug development to cure a wide range of human diseases. Specific examples of diseases we are currently working on are: asthma, multiple forms of cancer, neurological disorders, bacterial infections, drug addiction, and chronic pain. The main advantage of our chemical approach to these problems is that the small organic molecules we make to inhibit single kinases in whole animals are much better models of how potential drugs which target the same proteins might actually work, hopefully saving time in avoiding failed clinical trials. We believe that small-molecule based methods for decoding cell-biology could provide information not currently accessible through solely genetic and biochemical techniques. The key problem with using small-molecules to control processes inside cells is that most often these reagents inhibit closely related enzymes with equal potency, making dissection of each individual protein impossible. Currently, small-molecules which alter the enzymatic activity or cellular localization of key biological macromolecules are derived from two sources: natural product screening (eg. Taxol, FK506, staurosporine, and others) and drug development efforts (eg. Aspirin, Raloxifine, SKB203580, and others). These two approaches require large commitments of time and resources to find even one specific inhibitor. Our lab has developed a third method for producing these valuable reagents using an approach combining protein design and chemical synthesis. We use protein design to engineer a functionally silent yet structurally significant mutation into the active site of the protein of interest. This mutation could be the substitution of a conserved large residue in the wild-type enzyme for a smaller residue thus creating a new "pocket" in the active site. The mutant enzyme is then tested in a relevant cellular system to ensure that it functions in all aspects like the wild-type enzyme. The next step is the initiation of a chemical design and synthesis project to modify a non-specific inhibitor of the wild-type enzyme with substituents which specifically complement the mutation introduced into the active site of the protein of interest. Substituents with the appropriate chemical functionality that bind to the newly introduced pocket are chemically appended to the origininal inhibitor structure. Importantly, the new substituent is designed to preclude binding of the inhibitor to any wild-type enzymes because they would "bump" into the large residue in the wild-type enzyme. This makes choosing a residue which is conserved in the entire protein family critical for the success of the method. A pyrazolopyrimidine based kinase inhibitor we have identified satisfies the criteria for an inhibitor which only inhibits mutated kinases and does not inhibit any wild-type kinases we have assayed. We have most clearly demonstrated the utility of our approach in several studies of the yeast kinases CDC28 (cyclin dependent kinase 1: cell cycle), Fus3 (Map Kinase: involved in mating), Ipl1 (centrosome associate kinase), CDC15 (kinase involved in the exit from mitosis), Cla4 (Pak kinase, bud emergence), Elm1 (control of bud emergence), Ark1 (actin associated kinase 1, vescicle fusion), and a number of others are currently in progress. The variety of kinases that our approach has been applied to already suggests to us that over 70% of the protein kinase superfamily can be suitably engineered to be sensitive to the pyrazolopyrimidine based inhibitor we have identified. The exciting aspect of this is that the pyrazolopyrimidine has ideal pharmacological properties, including good bioavailability in mice, is able to cross the blood brain barrier, crosses the yeast cell wall, and is easy to synthesize in large amounts. The inhibitor is quite potent, in that it is a <5 nM inhibitor of every mutant kinase we have made. These features make our chemical genetic system very portable for studies of protein kinases in multiple model organisms including yeast, mouse, and soon C. Elegans, and the fly.

Bio-organic Chemistry — Organic chemistry is used to probe fundamental signal transduction pathways in cells and whole organisms. Research in our laboratory is focussed on the development of novel chemical tools to decipher signal transduction pathways on a genome-wide scale. The cellular machinery responsible for integrating complex extracellular signals from other cells is very complex. Protein phosphorylation is at the heart of these signaling cascades and is thus the most common on/off switch used in our bodies. The enzymes that catalyze protein phosphorylation are protein kinases. The major focus of our laboratory is to understand in detail the role of each kinase in the body, and determine which kinases would be good candidates for drug development to cure a wide range of human diseases. Specific examples of diseases we are currently working on are: asthma, multiple forms of cancer, neurological disorders, bacterial infections, drug addiction, and chronic pain. The main advantage of our chemical approach to these problems is that the small organic molecules we make to inhibit single kinases in whole animals are much better models of how potential drugs which target the same proteins might actually work, hopefully saving time in avoiding failed clinical trials. We believe that small-molecule based methods for decoding cell-biology could provide information not currently accessible through solely genetic and biochemical techniques. The key problem with using small-molecules to control processes inside cells is that most often these reagents inhibit closely related enzymes with equal potency, making dissection of each individual protein impossible. Currently, small-molecules which alter the enzymatic activity or cellular localization of key biological macromolecules are derived from two sources: natural product screening (eg. Taxol, FK506, staurosporine, and others) and drug development efforts (eg. Aspirin, Raloxifine, SKB203580, and others). These two approaches require large commitments of time and resources to find even one specific inhibitor. Our lab has developed a third method for producing these valuable reagents using an approach combining protein design and chemical synthesis. We use protein design to engineer a functionally silent yet structurally significant mutation into the active site of the protein of interest. This mutation could be the substitution of a conserved large residue in the wild-type enzyme for a smaller residue thus creating a new "pocket" in the active site. The mutant enzyme is then tested in a relevant cellular system to ensure that it functions in all aspects like the wild-type enzyme. The next step is the initiation of a chemical design and synthesis project to modify a non-specific inhibitor of the wild-type enzyme with substituents which specifically complement the mutation introduced into the active site of the protein of interest. Substituents with the appropriate chemical functionality that bind to the newly introduced pocket are chemically appended to the origininal inhibitor structure. Importantly, the new substituent is designed to preclude binding of the inhibitor to any wild-type enzymes because they would "bump" into the large residue in the wild-type enzyme. This makes choosing a residue which is conserved in the entire protein family critical for the success of the method. A pyrazolopyrimidine based kinase inhibitor we have identified satisfies the criteria for an inhibitor which only inhibits mutated kinases and does not inhibit any wild-type kinases we have assayed. We have most clearly demonstrated the utility of our approach in several studies of the yeast kinases CDC28 (cyclin dependent kinase 1: cell cycle), Fus3 (Map Kinase: involved in mating), Ipl1 (centrosome associate kinase), CDC15 (kinase involved in the exit from mitosis), Cla4 (Pak kinase, bud emergence), Elm1 (control of bud emergence), Ark1 (actin associated kinase 1, vescicle fusion), and a number of others are currently in progress. The variety of kinases that our approach has been applied to already suggests to us that over 70% of the protein kinase superfamily can be suitably engineered to be sensitive to the pyrazolopyrimidine based inhibitor we have identified. The exciting aspect of this is that the pyrazolopyrimidine has ideal pharmacological properties, including good bioavailability in mice, is able to cross the blood brain barrier, crosses the yeast cell wall, and is easy to synthesize in large amounts. The inhibitor is quite potent, in that it is a <5 nM inhibitor of every mutant kinase we have made. These features make our chemical genetic system very portable for studies of protein kinases in multiple model organisms including yeast, mouse, and soon C. Elegans, and the fly.

近期论文

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Davies JM, Robinson AE, Cowdrey C, Mummaneni PV, Ducker GS, Shokat KM, Bollen A, Hann B, Phillips JJ. (2014) Generation of a patient-derived chordoma xenograft and characterization of the phosphoproteome in a recurrent chordoma. J Neurosurg. Feb;120(2):331-6. doi: 10.3171/2013.10.JNS13598. Epub 2013 Nov 29. PMID: 24286145 Tan YX, Manz BN, Freedman TS, Zhang C, Shokat KM, Weiss A. (2014) Inhibition of the kinase Csk in thymocytes reveals a requirement for actin remodeling in the initiation of full TCR signaling., Nat Immunol. Feb;15(2):186-94. doi: 10.1038/ni.2772. Epub 2013 Dec 8. PMID: 24317039 Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM. (2013) Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. Cell Rep. Dec 26;5(6):1725-36. doi: 10.1016/j.celrep.2013.11.040. Epub 2013 Dec 19. PMID: 24360963 Lopez MS, Choy JW, Peters U, Sos ML, Morgan DO, Shokat KM. (2013) Staurosporine-derived inhibitors broaden the scope of analog-sensitive kinase technology. J Am Chem Soc. Dec 4;135(48):18153-9. doi: 10.1021/ja408704u. Epub 2013 Nov 20. PMID: 24171479 Ostrem JM, Peters U, Sos ML, Wells JA, Shokat KM. (2013) K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature. Nov 28;503(7477):548-51. doi: 10.1038/nature12796. Epub 2013 Nov 20. PMID: 24256730 Fan QW, Cheng CK, Gustafson WC, Charron E, Zipper P, Wong RA, Chen J, Lau J, Knobbe-Thomsen C, Weller M, Jura N, Reifenberger G, Shokat KM, Weiss WA. (2013) EGFR phosphorylates tumor-derived EGFRvIII driving STAT3/5 and progression in glioblastoma. Cancer Cell. Oct 14;24(4):438-49. doi:10.1016/j.ccr.2013.09.004. PMID: 24135280 Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. (2013) A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell. Aug 15;154(4):737-47. doi: 10.1016/j.cell.2013.07.030. PMID: 23953109 Zhang C, Lopez MS, Dar AC, Ladow E, Finkbeiner S, Yun CH, Eck MJ, Shokat KM. (2013) Structure-guided inhibitor design expands the scope of analog-sensitive kinase technology. ACS Chem Biol. Sep 20;8(9):1931-8. doi: 10.1021/cb400376p. Epub 2013 Jul 23. PMID: 23841803 Pourdehnad M, Truitt ML, Siddiqi IN, Ducker GS, Shokat KM, Ruggero D. (2013) Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers. Proc Natl Acad Sci U S A. Jul 16;110(29):11988-93. doi: 10.1073/pnas.1310230110. Epub 2013 Jun 26. Erratum in: Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):1760. PMID: 23803853 Atreya CE, Sangale Z, Xu N, Matli MR, Tikishvili E, Welbourn W, Stone S, Shokat KM, Warren RS. (2013) PTEN expression is consistent in colorectal cancer primaries and metastases and associates with patient survival. Cancer Med. Aug;2(4):496-506. doi: 10.1002/cam4.97. Epub 2013 Jun 10. PMID: 24156022 Schachter MM, Merrick KA, Larochelle S, Hirschi A, Zhang C, Shokat KM, Rubin SM, Fisher RP. (2013) A Cdk7-Cdk4 T-loop phosphorylation cascade promotes G1 progression. Mol Cell. Apr 25;50(2):250-60. doi: 10.1016/j.molcel.2013.04.003. PMID: 23622515 Lourido S, Zhang C, Lopez MS, Tang K, Barks J, Wang Q, Wildman SA, Shokat KM, Sibley LD. (2013) Optimizing small molecule inhibitors of calcium-dependent protein kinase 1 to prevent infection by Toxoplasma gondii. J Med Chem. Apr 11;56(7):3068-77. doi: 10.1021/jm4001314. Epub 2013 Mar 26. PMID: 23470217 Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptáček LJ, Fu YH. (2013) Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock. Cell Metab. Feb 5;17(2):291-302. doi: 10.1016/j.cmet.2012.12.017. PMID: 23395175 Statsuk AV, Shokat KM. (2012) Covalent cross-linking of kinases with their corresponding peptide substrates. Methods Mol Biol. 795:179-90. Atreya CE, Ducker GS, Feldman ME, Bergsland EK, Warren RS, Shokat KM. (2012) Combination of ATP-competitive mammalian target of rapamycin inhibitors with standard chemotherapy for colorectal cancer. Invest New Drugs. Dec;30(6):2219-25. doi: 10.1007/s10637-012-9793-y. Epub 2012 Jan 24. PMID: 22270257 Soskis MJ, Ho HY, Bloodgood BL, Robichaux MA, Malik AN, Ataman B, Rubin AA, Zieg J, Zhang C, Shokat KM, Sharma N, Cowan CW, Greenberg ME. (2012) A chemical genetic approach reveals distinct EphB signaling mechanisms during brain development. Nat Neurosci. Dec 15(12):1645-54. doi: 10.1038/nn.3249. Epub Nov 11. PMID: 23143520 Larochelle S, Amat R, Glover-Cutter K, Sansó M, Zhang C, Allen JJ, Shokat KM, Bentley DL, Fisher RP. (2012) Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II. Nat Struct Mol Biol. Nov 19(11):1108-15. doi: 10.1038/nsmb.2399. Epub 2012 Oct 14. PMID: 23064645