Activity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry

The hallmarks of cancer

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PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

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The protein kinase complement of the human genome

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Large-scale analysis of the yeast proteome by multidimensional protein identification technology

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Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

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Cancer genes and the pathways they control

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The growing impact of click chemistry on drug discovery

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Genes that mediate breast cancer metastasis to lung

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Anticancer activities of histone deacetylase inhibitors

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A novel heterodimeric cysteine protease is required for interleukin-1βprocessing in monocytes

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A multigenic program mediating breast cancer metastasis to bone

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Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification.

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The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1

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Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase

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Modulation of anxiety through blockade of anandamide hydrolysis

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Structural Determinants of Phosphoinositide 3-Kinase Inhibition by Wortmannin, LY294002, Quercetin, Myricetin, and Staurosporine

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Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug

Marks, P. A., & Breslow, R. (2007) · Nature Biotechnology · doi:10.1038/nbt1272 · Cited by 1,198 · see citing works

Activity-based protein profiling: The serine hydrolases

Liu, Y., Patricelli, M. P., & Cravatt, B. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.26.14694 · Cited by 1,133 · see citing works

Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases

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L-trans-Epoxysuccinyl-leucylamido(4-guanidino)butane (E-64) and its analogues as inhibitors of cysteine proteinases including cathepsins B, H and L

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Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine.

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Design and Therapeutic Application of Matrix Metalloproteinase Inhibitors

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Activity-Based Protein Profiling in Vivo Using a Copper(I)-Catalyzed Azide-Alkyne [3 + 2] Cycloaddition

Speers, A. E., Adam, G. C., & Cravatt, B. F. (2003) · Journal of the American Chemical Society · doi:10.1021/ja034490h · Cited by 955 · see citing works

Photoactivated γ-secretase inhibitors directed to the active site covalently label presenilin 1

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Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1

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Protein microarrays and proteomics

MacBeath, G. (2002) · Nature Genetics · doi:10.1038/ng1037 · Cited by 847 · see citing works

Profiling Enzyme Activities In Vivo Using Click Chemistry Methods

Speers, A. E., & Cravatt, B. F. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.03.012 · Cited by 774 · see citing works

Structure and function of fatty acid amide hydrolase

McKinney, M. K., & Cravatt, B. F. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133450 · Cited by 680 · see citing works

Wortmannin Inactivates Phosphoinositide 3-Kinase by Covalent Modification of Lys-802, a Residue Involved in the Phosphate Transfer Reaction

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Cathepsin cysteine proteases are effectors of invasive growth and angiogenesis during multistage tumorigenesis

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Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with magnesium-ATP and peptide inhibitor

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Chemistry-Based Functional Proteomics Reveals Novel Members of the Deubiquitinating Enzyme Family

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Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools

Greenbaum, D. C., Medzihradszky, K. F., Burlingame, A. L., & Bogyo, M. S. (2000) · Chemistry & Biology · doi:10.1016/s1074-5521(00)00014-4 · Cited by 581 · see citing works

Mechanism-Based Profiling of Enzyme Families

Evans, M. J., & Cravatt, B. F. (2006) · Chemical Reviews · doi:10.1021/cr050288g · Cited by 568 · see citing works

Structural Bioinformatics-Based Design of Selective, Irreversible Kinase Inhibitors

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Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes

Khan, A. R., & James, M. N. G. (1998) · Protein Science · doi:10.1002/pro.5560070401 · Cited by 469 · see citing works

Activity-based probes for the proteomic profiling of metalloproteases

Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., & Cravatt, B. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402784101 · Cited by 456 · see citing works

Functional Interrogation of the Kinome Using Nucleotide Acyl Phosphates

Patricelli, M. P., Szardenings, A. K., Liyanage, M., Nomanbhoy, T. K., Wu, M., Weissig, H., Aban, A., Chun, D., Tanner, S. W., & Kozarich, J. W. (2006) · Biochemistry · doi:10.1021/bi062142x · Cited by 426 · see citing works

Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor

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Discovering potent and selective reversible inhibitors of enzymes in complex proteomes

Leung, D., Hardouin, C., Boger, D. L., & Cravatt, B. F. (2003) · Nature Biotechnology · doi:10.1038/nbt826 · Cited by 387 · see citing works

Profiling Serine Hydrolase Activities in Complex Proteomes

Kidd, D., Liu, Y., & Cravatt, B. F. (2001) · Biochemistry · doi:10.1021/bi002579j · Cited by 369 · see citing works

Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness

Jessani, N., Liu, Y., Humphrey, M., & Cravatt, B. F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162187599 · Cited by 359 · see citing works

Multiple species of CPP32 and Mch2 are the major active caspases present in apoptotic cells

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Activity-based probes that target diverse cysteine protease families

Kato, D., Boatright, K. M., Berger, A. B., Nazif, T. M., Blum, G., Ryan, C., Chehade, K. A. H., Salvesen, G. S., & Bogyo, M. S. (2005) · Nature Chemical Biology · doi:10.1038/nchembio707 · Cited by 356 · see citing works

Reversible Inhibitors of Fatty Acid Amide Hydrolase That Promote Analgesia: Evidence for an Unprecedented Combination of Potency and Selectivity

Lichtman, A. H., Leung, D., Shelton, C. C., Saghatelian, A., Hardouin, C., Boger, D. L., & Cravatt, B. F. (2004) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.104.069401 · Cited by 329 · see citing works

The Plasmodium falciparum sexual development transcriptome: A microarray analysis using ontology-based pattern identification

Young, J. A., Fivelman, Q. L., Blair, P. L., Vega, P. D. L., Roch, K. G. L., Zhou, Y., Carucci, D. J., Baker, D. A., & Winzeler, E. A. (2005) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2005.05.007 · Cited by 329 · see citing works

Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling

Saghatelian, A., Trauger, S. A., Want, E. J., Hawkins, E. G., Siuzdak, G. E., & Cravatt, B. F. (2004) · Biochemistry · doi:10.1021/bi0480335 · Cited by 318 · see citing works

Chemical Approaches for Functionally Probing the Proteome

Greenbaum, D. C., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A. L., Medzihradszky, K. F., & Bogyo, M. S. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t100003-mcp200 · Cited by 291 · see citing works

A Role for the Protease Falcipain 1 in Host Cell Invasion by the Human Malaria Parasite

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Inactivation of Interleukin-1.beta. Converting Enzyme by Peptide (Acyloxy)methyl Ketones

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Chemical Strategies for Activity‐Based Proteomics

Speers, A. E., & Cravatt, B. F. (2003) · ChemBioChem · doi:10.1002/cbic.200300721 · Cited by 259 · see citing works

A Deubiquitinating Enzyme Encoded by HSV-1 Belongs to a Family of Cysteine Proteases that Is Conserved across the Family Herpesviridae

Kattenhorn, L. M., Korbel, G. A., Kessler, B. M., Spooner, E., & Ploegh, H. L. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.003 · Cited by 248 · see citing works

Proteomic profiling of metalloprotease activities with cocktails of active-site probes

Sieber, S. A., Niessen, S., Hoover, H. S., & Cravatt, B. F. (2006) · Nature Chemical Biology · doi:10.1038/nchembio781 · Cited by 247 · see citing works

Activity-based probes for proteomic profiling of histone deacetylase complexes

Salisbury, C. M., & Cravatt, B. F. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608659104 · Cited by 243 · see citing works

Dap1/PGRMC1 Binds and Regulates Cytochrome P450 Enzymes

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A streamlined platform for high-content functional proteomics of primary human specimens

Jessani, N., Niessen, S., Wei, B. Q., Nicolau, M. M., Humphrey, M., Ji, Y., Han, W., Noh, D., Yates, J. R., Jeffrey, S. S., et al. (2005) · Nature Methods · doi:10.1038/nmeth778 · Cited by 240 · see citing works

Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling

Evans, M. J., Saghatelian, A., Sorensen, E. J., & Cravatt, B. F. (2005) · Nature Biotechnology · doi:10.1038/nbt1149 · Cited by 230 · see citing works

Mechanism of Carbamate Inactivation of FAAH: Implications for the Design of Covalent Inhibitors and In Vivo Functional Probes for Enzymes

Alexander, J. P., & Cravatt, B. F. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2005.08.011 · Cited by 226 · see citing works

Developing Photoactive Affinity Probes for Proteomic Profiling: Hydroxamate-based Probes for Metalloproteases

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Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype

Adam, G. C., Sorensen, E. J., & Cravatt, B. F. (2002) · Nature Biotechnology · doi:10.1038/nbt714 · Cited by 224 · see citing works

AFFINITY LABELING OF PURINE NUCLEOTIDE SITES IN PROTEINS

Colman, R. F. (1983) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.52.070183.000435 · Cited by 218 · see citing works

Novel Mechanistic Class of Fatty Acid Amide Hydrolase Inhibitors with Remarkable Selectivity

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The development and application of methods for activity-based protein profiling

Jessani, N., & Cravatt, B. F. (2003) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2003.11.004 · Cited by 217 · see citing works

Wortmannin, a Widely Used Phosphoinositide 3-Kinase Inhibitor, also Potently Inhibits Mammalian Polo-like Kinase

Liu, Y., Shreder, K. R., Gai, W. Z., Corral, S., Ferris, D. K., & Rosenblum, J. S. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.11.009 · Cited by 210 · see citing works

A Tandem Orthogonal Proteolysis Strategy for High-Content Chemical Proteomics

Speers, A. E., & Cravatt, B. F. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0532842 · Cited by 204 · see citing works

Structure-guided development of affinity probes for tyrosine kinases using chemical genetics

Blair, J. A., Rauh, D., Kung, C. K.-H., Yun, C., Fan, Q.-W., Rode, H. B., Zhang, C., Eck, M. J., Weiss, W. A., & Shokat, K. M. (2007) · Nature Chemical Biology · doi:10.1038/nchembio866 · Cited by 204 · see citing works

An Enzyme that Regulates Ether Lipid Signaling Pathways in Cancer Annotated by Multidimensional Profiling

Chiang, K. P., Niessen, S., Saghatelian, A., & Cravatt, B. F. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.08.008 · Cited by 201 · see citing works

Active site-directed protein regulation

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Chemical modifications of proteins: history and applications

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Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo

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A Functional Proteomic Strategy to Discover Inhibitors for Uncharacterized Hydrolases

Li, W., Blankman, J. L., & Cravatt, B. F. (2007) · Journal of the American Chemical Society · doi:10.1021/ja073650c · Cited by 180 · see citing works

Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors

Nazif, T. M., & Bogyo, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061028898 · Cited by 179 · see citing works

Chemical Strategies for Functional Proteomics

Adam, G. C., Sorensen, E. J., & Cravatt, B. F. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200006-mcp200 · Cited by 176 · see citing works

Chemistry in Living Cells: Detection of Active Proteasomes by a Two‐Step Labeling Strategy

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Targeted covalent inactivation of protein kinases by resorcylic acid lactone polyketides

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Proteomic analysis of Fasciola hepatica excretory-secretory products

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Small Molecule Affinity Fingerprinting

Greenbaum, D. C., Arnold, W. D., Lu, F., Hayrapetian, L., Baruch, A., Krumrine, J. R., Toba, S., Chehade, K. A. H., Brömme, D., Kuntz, I. D., et al. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00238-7 · Cited by 168 · see citing works

Profiling protein function with small molecule microarrays

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A Cell-permeable, Activity-based Probe for Protein and Lipid Kinases

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A Mild Chemically Cleavable Linker System for Functional Proteomic Applications

Verhelst, S. H. L., Fonovič, M., & Bogyo, M. S. (2007) · Angewandte Chemie International Edition · doi:10.1002/anie.200603811 · Cited by 163 · see citing works

A clickable inhibitor reveals context-dependent autoactivation of p90 RSK

Cohen, M. S., Hadjivassiliou, H., & Taunton, J. (2007) · Nature Chemical Biology · doi:10.1038/nchembio859 · Cited by 157 · see citing works

Selective Chemical Functional Probes of Granzymes A and B Reveal Granzyme B Is a Major Effector of Natural Killer Cell-Mediated Lysis of Target Cells

Mahrus, S., & Craik, C. S. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2005.03.006 · Cited by 156 · see citing works

Mechanism and Catalysis of Reactions of Acyl Phosphates. II. Hydrolysis1

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Kinomics: characterizing the therapeutically validated kinase space

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Activity-based probes for protein tyrosine phosphatases

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Profiling the specific reactivity of the proteome with non-directed activity-based probes

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A Strategy for Functional Proteomic Analysis of Glycosidase Activity from Cell Lysates

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Activity-Based Protein Profiling

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The Putative Endocannabinoid Transport Blocker LY2183240 Is a Potent Inhibitor of FAAH and Several Other Brain Serine Hydrolases

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A membrane enzyme from Staphylococcus aureus which catalyzes transpeptidase, carboxypeptidase, and penicillinase activities

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Mechanism and Catalysis of Reactions of Acyl Phosphates. I. Nucleophilic Reactions1

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Function of human cytochrome P450s: Characterization of the orphans

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A Mild Chemically Cleavable Linker System for Functional Proteomic Applications

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