Chemical Proteomics pp 15-21 | Cite as
Chemical Proteomics in Drug Discovery
Abstract
Real-world drug discovery and development remains a notoriously unproductive and increasingly uneconomical process even in the Omics era. The dominating paradigm in the industry continues to be target-based drug design, with an increased perception of the role of signaling pathways in homeostasis and in disease. Since proteins represent the major type of drug targets, proteomics-based approaches, which study proteins under relatively physiological conditions, have great potential if they can be reduced to practice such that they successfully complement the arsenal of drug discovery techniques. This chapter discusses examples of drug discovery processes where chemical proteomics-based assays using native endogenous proteins should have substantial impact.
Key words
Chemical Proteomics Drug target Target deconvolution Target validation Drug discovery Selectivity profilingReferences
- 1.Brown, D. (2007) Unfinished business: target-based drug discovery. Drug Discov. Today 12, 1007–1012.PubMedCrossRefGoogle Scholar
- 2.Kola, I., and Landis, J. (2004) Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. 3, 711–715.PubMedCrossRefGoogle Scholar
- 3.Fishman, M. C., and Porter, J. A. (2005) Pharmaceuticals: a new grammar for drug discovery. Nature 437, 491–493.PubMedCrossRefGoogle Scholar
- 4.Hall, S. E. (2006) Chemoproteomics-driven drug discovery: addressing high attrition rates. Drug Discov. Today 11, 495–502.PubMedCrossRefGoogle Scholar
- 5.Overington, J. P., Al-Lazikani, B., and Hopkins, A. L. (2006) How many drug targets are there? Nat. Rev. Drug Discov. 5, 993–996.PubMedCrossRefGoogle Scholar
- 6.Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., and Lander, E. S. (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. USA 104, 19428–19433.PubMedCrossRefGoogle Scholar
- 7.Hopkins, A. L., and Groom, C. R. (2002) The druggable genome. Nat. Rev. Drug Discov. 1, 727–730.PubMedCrossRefGoogle Scholar
- 8.Brown, E. J., Albers, M. W., Shin, T. B., Ichikawa, K., Keith, C. T., Lane, W. S., and Schreiber, S. L. (1994) A mammalian protein targeted by G1-arresting rapamycin-receptor complex. Nature 369, 756–758.PubMedCrossRefGoogle Scholar
- 9.Harding, M. W., Galat, A., Uehling, D. E., and Schreiber, S. L. (1989) A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature 341, 758–760.PubMedCrossRefGoogle Scholar
- 10.Huang, S. M., Mishina, Y. M., Liu, S., Cheung, A., Stegmeier, F., Michaud, G. A., Charlat, O., Wiellette, E., Zhang, Y., Wiessner, S., Hild, M., Shi, X., Wilson, C. J., Mickanin, C., Myer, V., Fazal, A., Tomlinson, R., Serluca, F., Shao, W., Cheng, H., Shultz, M., Rau, C., Schirle, M., Schlegl, J., Ghidelli, S., Fawell, S., Lu, C., Curtis, D., Kirschner, M. W., Lengauer, C., Finan, P. M., Tallarico, J. A., Bouwmeester, T., Porter, J. A., Bauer, A., and Cong, F. (2009) Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature 461, 614–620.PubMedCrossRefGoogle Scholar
- 11.Fleischer, T. C., Murphy, B. R., Flick, J. S., Terry-Lorenzo, R. T., Gao, Z. H., Davis, T., McKinnon, R., Ostanin, K., Willardsen, J. A., and Boniface, J. J. (2010) Chemical proteomics identifies Nampt as the target of CB30865, an orphan cytotoxic compound. Chem. Biol. 17, 659–664.PubMedCrossRefGoogle Scholar
- 12.Nicodeme, E., Jeffrey, K. L., Schaefer, U., Beinke, S., Dewell, S., Chung, C. W., Chandwani, R., Marazzi, I., Wilson, P., Coste, H., White, J., Kirilovsky, J., Rice, C. M., Lora, J. M., Prinjha, R. K., Lee, K., and Tarakhovsky, A. (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468, 1119–1123.PubMedCrossRefGoogle Scholar
- 13.Fadden, P., Huang, K. H., Veal, J. M., Steed, P. M., Barabasz, A. F., Foley, B., Hu, M., Partridge, J. M., Rice, J., Scott, A., Dubois, L. G., Freed, T. A., Silinski, M. A., Barta, T. E., Hughes, P. F., Ommen, A., Ma, W., Smith, E. D., Spangenberg, A. W., Eaves, J., Hanson, G. J., Hinkley, L., Jenks, M., Lewis, M., Otto, J., Pronk, G. J., Verleysen, K., Haystead, T. A., and Hall, S. E. (2010) Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting hsp90. Chem. Biol. 17, 686–694.PubMedCrossRefGoogle Scholar
- 14.Bantscheff, M., Hopf, C., Savitzki, M. M., Dittmann, A., Grandi, P., Michon, A. M. M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., Boesche, M., Delling, M., Dümpelfeld, B., Eberhard, D., Huthmacher, C., Mathieson, T., Poeckel, D., Strunk, K., Sweetman, G., Kruse, U., Neubauer, G., Ramsden, N., and Drewes, G. (2011) Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat. Biotechnol. 29, 255–265.Google Scholar
- 15.Morphy, R., Kay, C., and Rankovic, Z. (2004) From magic bullets to designed multiple ligands. Drug Discov. Today 9, 641–651.PubMedCrossRefGoogle Scholar
- 16.Kruse, U., Bantscheff, M., Drewes, G., and Hopf, C. (2008) Chemical and pathway proteomics: powerful tools for oncology drug discovery and personalized health care. Mol. Cell Proteomics. 7, 1887–1901.PubMedCrossRefGoogle Scholar
- 17.Ito, T., Ando, H., Suzuki, T., Ogura, T., Hotta, K., Imamura, Y., Yamaguchi, Y., and Handa H. (2010) Identification of a primary target of thalidomide teratogenicity. Science. 327, 1345–1350.PubMedCrossRefGoogle Scholar
- 18.Fliri, A. F., Loging, W. T., Thadeio, P. F., and Volkmann, R. A. (2005) Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat. Chem. Biol. 1, 389–397.PubMedCrossRefGoogle Scholar
- 19.Ong, S. E., Schenone, M., Margolin, A. A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L., and Carr, S. A. (2009) Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA 106, 4617–4622.PubMedCrossRefGoogle Scholar
- 20.Rix, U., and Superti-Furga, G. (2009) Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol. 5, 616–624.PubMedCrossRefGoogle Scholar
- 21.Sharma, K., Weber, C., Bairlein, M., Greff, Z., Keri, G., Cox, J., Olsen, J. V., and Daub, H. (2009) Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nat. Methods 6, 741–744.PubMedCrossRefGoogle Scholar
- 22.Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Boesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., Reader, V., Sweetman, G., Bauer, A., Bouwmeester, T., Hopf, C., Kruse, U., Neubauer, G., Ramsden, N., Rick, J., Kuster, B., and Drewes, G. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035–1044.PubMedCrossRefGoogle Scholar
- 23.Cravatt, B. F., Wright, A. T., and Kozarich, J. W. (2008) Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77, 383–414.PubMedCrossRefGoogle Scholar
- 24.Paulick, M. G., and Bogyo, M. (2008) Application of activity-based probes to the study of enzymes involved in cancer progression. Curr. Opin. Genet. Dev. 18, 97–106.PubMedCrossRefGoogle Scholar
- 25.Haystead, T. A. (2006) The purinome, a complex mix of drug and toxicity targets. Curr. Top. Med. Chem. 6, 1117–1127.PubMedCrossRefGoogle Scholar
- 26.Graves, P. R., Kwiek, J. J., Fadden, P., Ray, R., Hardeman, K., Coley, A. M., Foley, M., and Haystead, T. A. (2002) Discovery of novel targets of quinoline drugs in the human purine binding proteome. Mol. Pharmacol. 62, 1364–1372.PubMedCrossRefGoogle Scholar
- 27.Borawski, J., Troke, P., Puyang, X., Gibaja, V., Zhao, S., Mickanin, C., Leighton-Davies, J., Wilson, C. J., Myer, V., Cornellataracido, I., Baryza, J., Tallarico, J., Joberty, G., Bantscheff, M., Schirle, M., Bouwmeester, T., Mathy, J. E., Lin, K., Compton, T., Labow, M., Wiedmann, B., and Gaither, L. A. (2009) Class III phosphatidylinositol 4-kinase alpha and beta are novel host factor regulators of hepatitis C virus replication. J. Virol. 83, 10058–10074.PubMedCrossRefGoogle Scholar
- 28.Gharbi, S. I., Zvelebil, M. J., Shuttleworth, S. J., Hancox, T., Saghir, N., Timms, J. F., and Waterfield, M. D. (2007) Exploring the specificity of the PI3K family inhibitor LY294002. Biochem. J. 404, 15–21.PubMedCrossRefGoogle Scholar
- 29.Raijmakers, R., Dadvar, P., Pelletier, S., Gouw, J., Rumpel, K., and Heck, A. J. (2010) Target profiling of a small library of phosphodiesterase 5 (PDE5) inhibitors using chemical proteomics. ChemMedChem. 5, 1927–1936.PubMedCrossRefGoogle Scholar
- 30.Patricelli, M. P., Szardenings, A. K., Liyanage, M., Nomanbhoy, T. K., Wu, M., Weissig, H., Aban, A., Chun, D., Tanner, S., and Kozarich, J. W. (2007) Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry 46, 350–358.PubMedCrossRefGoogle Scholar
- 31.Luo, Y., Fischer, J. J., Baessler, O. Y., Schrey, A. K., Ungewiss, J., Glinski, M., Sefkow, M., Dreger, M., and Koester, H. (2010) GDP-capture compound – a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS). J. Proteomics. 73, 815–819.PubMedCrossRefGoogle Scholar
- 32.Dalhoff, C., Huben, M., Lenz, T., Poot, P., Nordhoff, E., Koster, H., and Weinhold, E. (2010) Synthesis of S-adenosyl-L-homocysteine capture compounds for selective photoinduced isolation of methyltransferases. Chembiochem. 11, 256–265.PubMedCrossRefGoogle Scholar
- 33.Ge, X., Wakim, B., and Sem, D. S. (2008) Chemical proteomics-based drug design: target and antitarget fishing with a catechol-rhodanine privileged scaffold for NAD(P)(H) binding proteins. J. Med. Chem. 51, 4571–4580.PubMedCrossRefGoogle Scholar
- 34.Kato, D., Boatright, K. M., Berger, A. B., Nazif, T., Blum, G., Ryan, C., Chehade, K. A., Salvesen, G. S., and Bogyo, M. (2005) Activity-based probes that target diverse cysteine protease families. Nat. Chem. Biol. 1, 33–38.PubMedCrossRefGoogle Scholar
- 35.Berkers, C. R., Verdoes, M., Lichtman, E., Fiebiger, E., Kessler, B. M., Anderson, K. C., Ploegh, H. L., Ovaa, H., and Galardy, P. J. (2005) Activity probe for in vivo profiling of the specificity of proteasome inhibitor bortezomib. Nat. Methods 2, 357–362.PubMedCrossRefGoogle Scholar
- 36.Salisbury, C. M., and Cravatt, B. F. (2007) Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc. Natl. Acad. Sci. USA 104, 1171–1176.PubMedCrossRefGoogle Scholar
- 37.Nomura, D. K., Dix, M. M., and Cravatt, B. F. (2010) Activity-based protein profiling for biochemical pathway discovery in cancer. Nat. Rev. Cancer 10, 630–638.PubMedCrossRefGoogle Scholar
- 38.Edgington, L. E., Berger, A. B., Blum, G., Albrow, V. E., Paulick, M. G., Lineberry, N., and Bogyo, M. (2009) Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes. Nat. Med. 15, 967–973.PubMedCrossRefGoogle Scholar