Chemical proteomics and its impact on the drug discovery process

Expert Review of Proteomics

Volumn 9, Issue 3, 2012, Pages 281-291

  Miao, Qing ^a   Zhang, Cheng Cheng ^a   Kast, Juergen ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

activity or affinity based protein profiling; chemical proteomics; compound centric chemical proteomics; drug target identification; global proteomics; mass spectrometry; quantitation

Indexed keywords

4 [N (7 BROMO 3,4 DIHYDRO 2 METHYL 4 OXO 6 QUINAZOLINYLMETHYL) N (2 PROPYNYL)AMINO] N (3 PYRIDYLMETHYL)BENZAMIDE; 5 CHLORO 1 (2,6 DIMETHYLPIPERIDIN 1 YL) N TOSYLPENTAN 1 IMINE; ANTIINFLAMMATORY AGENT; BAFETINIB; BISINDOLYLMALEIMIDE; BOSUTINIB; CARBAMIC ACID DERIVATIVE; DASATINIB; DONEPEZIL; IMATINIB; JW 480; NILOTINIB; PETROSASPONGIOLIDE M; PIPERAZINE DERIVATIVE; PIPERIDINE DERIVATIVE; RHODAMINE; RUFOCROMOMYCIN; TERPENOID DERIVATIVE; TETRAHYDROLIPSTATIN; UNCLASSIFIED DRUG;

ALZHEIMER DISEASE; ANTIINFLAMMATORY ACTIVITY; ANTINEOPLASTIC ACTIVITY; ANTIPROLIFERATIVE ACTIVITY; CHRONIC MYELOID LEUKEMIA; CLICK CHEMISTRY; COVALENT BOND; DRUG DESIGN; DRUG PROTEIN BINDING; DRUG STRUCTURE; DRUG TARGETING; ENZYME ACTIVITY; HUMAN; NONHUMAN; OBESITY; OSTEOLYSIS; PROTEIN DEPLETION; PROTEIN PHOSPHORYLATION; PROTEIN TARGETING; PROTEOMICS; REVIEW;

CLICK CHEMISTRY; DRUG DISCOVERY; ENZYMES; FLUORESCENT DYES; HUMANS; MASS SPECTROMETRY; MOLECULAR PROBES; PROTEIN BINDING; PROTEINS; PROTEOMICS; SMALL MOLECULE LIBRARIES;

EID: 84864213648     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.12.22     Document Type: Review

References (83)

1. Krogsgaard-Larsen P, Liljefors T, Madsen U. Textbook of Drug Design and Discovery. (Third Edition). CRC Press, Taylor & rancis Inc, NY, USA (2002).
2. Landry Y, Gies JP. Drugs and their molecular targets: An updated overview. Fundam. Clin. Pharmacol. 22(1), 1-18 (2008).
3. Anderson NL, Anderson NG. Proteome and proteomics: New technologies, new concepts, and new words. Electrophoresis 19(11), 1853-1861 (1998).
4. Blackstock WP, Weir MP. Proteomics: Quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17(3), 121-127 (1999).
5. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312(5771), 212-217 (2006).
6. Zhang CC, Kast J. Applications of current proteomics techniques in modern drug design. Curr. Comput. Aided. Drug Des. 6(3), 147-164 (2010).
7. Carrette O, Burkhard PR, Sanchez JC, Hochstrasser DF. State-of-the-art two-dimensional gel electrophoresis: A key tool of proteomics research. Nat. Protoc. 1(2), 812-823 (2006).
8. Alban A, David SO, Bjorkesten L et al. A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3(1), 36-44 (2003).
9. Schubert P, Thon JN, Walsh GM et al. A signaling pathway contributing to platelet storage lesion development: Targeting PI3-kinase-dependent Rap1 activation slows storage-induced platelet deterioration. Transfusion 49(9), 1944-1955 (2009).
10. Soares HD, Williams SA, Snyder PJ et al. Proteomic approaches in drug discovery and development. Int. Rev. Neurobiol. 61, 97-126 (2004).
11. Sleno L, Emili A. Proteomic methods for drug target discovery. Curr. Opin. Chem. Biol. 12(1), 46-54 (2008).
12. Jeffery DA, Bogyo M. Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. 14(1), 87-95 (2003).
13. Oda Y, Owa T, Sato T et al. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75(9), 2159-2165 (2003).
14. Piggott AM, Karuso P. Quality, not quantity: The role of natural products and chemical proteomics in modern drug discovery. Comb. Chem. High Throughput Screen. 7(7), 607-630 (2004).
15. Heal WP, Dang TH, Tate EW. Activitybased probes: Discovering new biology and new drug targets. Chem. Soc. Rev. 40(1), 246-257 (2011).
16. Barglow KT, Cravatt BF. Activity-based protein profiling for the functional annotation of enzymes. Nat. Methods 4(10), 822-827 (2007).
17. Tate EW. Recent advances in chemical proteomics: Exploring the post-translational proteome. J. Chem. Biol. 1(1-4), 17-26 (2008).
18. Uttamchandani M, Li J, Sun H, Yao SQ. Activity-based protein profiling: New developments and directions in functional proteomics. Chembiochem 9(5), 667-675 (2008).
19. Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77, 383-414 (2008).
20. Nomura DK, Dix MM, Cravatt BF. Activity-based protein profiling for biochemical pathway discovery in cancer. Nat. Rev. Cancer 10(9), 630-638 (2010).
21. Katayama H, Oda Y. Chemical proteomics for drug discovery based on compoundimmobilized affinity chromatography. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 855(1), 21-27 (2007).
22. Bantscheff M, Scholten A, Heck AJ. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov. Today 14(21-22), 1021-1029 (2009).
23. Rix U, Superti-Furga G. Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol. 5(9), 616-624 (2009).
24. Han SY, Hwan Kim S. Introduction to chemical proteomics for drug discovery and development. Arch. Pharm. (Weinheim) 340(4), 169-177 (2007).
25. Kearney P, Currier NL, Chelsky D et al. Global proteomics: Pharmacodynamic decision making via geometric interpretations of proteomic analyses. J. Proteomics Bioinf. 1(7), 315-328 (2008).
26. Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R. The Orbitrap: A new mass spectrometer. J. Mass Spectrom. 40(4), 430-443 (2005).
27. Olsen JV, Blagoev B, Gnad F et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127(3), 635-648 (2006).
28. Dang THT, De La Riva L, Fagan RP et al. Chemical probes of surface layer biogenesis in Clostridium difficile. ACS Chem. Biol. 5(3), 279-285 (2010).
29. Sadaghiani AM, Verhelst SH, Bogyo M. Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol. 11(1), 20-28 (2007).
30. Mitsopoulos G, Walsh DP, Chang YT. Tagged library approach to chemical genomics and proteomics. Curr. Opin. Chem. Biol. 8(1), 26-32 (2004).
31. Speers AE, Cravatt BF. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11(4), 535-546 (2004).
32. Uttamchandani M, Lu CH, Yao SQ. Next generation chemical proteomic tools for rapid enzyme profiling. Acc. Chem. Res. 42(8), 1183-1192 (2009).
33. Kalesh KA, Shi H, Ge J, Yao SQ. The use of click chemistry in the emerging field of catalomics. Org. Biomol. Chem. 8(8), 1749-1762 (2010).
34. Salisbury CM, Cravatt BF. Click chemistry-led advances in high content functional proteomics. QSAR Comb. Sci. 26(11-12), 1229-1238 (2007).
35. Singaravelu R, Blais DR, McKay CS, Pezacki JP. Activity-based protein profiling of the hepatitis C virus replication in Huh-7 hepatoma cells using a non-directed active site probe. Proteome Sci. 8, 5 (2010).
36. Dolai S, Xu Q, Liu F, Molloy MP. Quantitative chemical proteomics in small-scale culture of phorbol ester stimulated basal breast cancer cells. Proteomics 11(13), 2683-2692 (2011).
37. Yang PY, Liu K, Ngai MH, Lear MJ, Wenk MR, Yao SQ. Activity-based proteome profiling of potential cellular targets of Orlistat-an FDA-approved drug with anti-tumor activities. J. Am. Chem. Soc. 132(2), 656-666 (2010).
38. Ngai MH, Yang PY, Liu K et al. Clickbased synthesis and proteomic profiling of lipstatin analogues. Chem. Commun. (Camb.) 46(44), 8335-8337 (2010).
39. Knuckley B, Jones JE, Bachovchin DA et al. A fluopol-ABPP HTS assay to identify PAD inhibitors. Chem. Commun. (Camb.) 46(38), 7175-7177 (2010).
40. Luo Y, Knuckley B, Lee YH, Stallcup MR, Thompson PR. A fluoroacetamidine-based inactivator of protein arginine deiminase 4: Design, synthesis, and in vitro and in vivo evaluation. J. Am. Chem. Soc. 128(4), 1092-1093 (2006).
41. Knuckley B, Causey CP, Pellechia PJ, Cook PF, Thompson PR. Haloacetamidine-based inactivators of protein arginine deiminase 4 (PAD4): Evidence that general acid catalysis promotes efficient inactivation. Chembiochem 11(2), 161-165 (2010).
42. Bachovchin DA, Ji T, Li W et al. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc. Natl Acad. Sci. USA 107(49), 20941-20946 (2010).
43. Li W, Blankman JL, Cravatt BF. A functional proteomic strategy to discover inhibitors for uncharacterized hydrolases. J. Am. Chem. Soc. 129(31), 9594-9595 (2007).
44. Long JZ, Li W, Booker L et al. Selective blockade of 2- arachidonoylglycerol hydrolysis produces cannabinoid behavioral effects. Nat. Chem. Biol. 5(1), 37-44 (2009).
45. Chiang KP, Niessen S, Saghatelian A, Cravatt BF. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem. Biol. 13(10), 1041-1050 (2006).
46. Chang JW, Nomura DK, Cravatt BF. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. Chem. Biol. 18(4), 476-484 (2011).
47. Lone AM, Bachovchin DA, Westwood DB et al. A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. J. Am. Chem. Soc. 133(30), 11665-11674 (2011).
48. Beatty KE. Chemical strategies for tagging and imaging the proteome. Mol. Biosyst. 7(8), 2360-2367 (2011).
49. Yang YY, Hang HC. Chemical approaches for the detection and synthesis of acetylated proteins. Chembiochem 12(2), 314-322 (2011).
50. Wang G, Shang L, Burgett AW, Harran PG, Wang X. Diazonamide toxins reveal an unexpected function for ornithine delta-amino transferase in mitotic cell division. Proc. Natl Acad. Sci. USA 104(7), 2068-2073 (2007).
51. Shiyama T, Furuya M, Yamazaki A, Terada T, Tanaka A. Design and synthesis of novel hydrophilic spacers for the reduction of nonspecific binding proteins on affinity resins. Bioorg. Med. Chem. 12(11), 2831-2841 (2004).
52. Speers AE, Cravatt BF. A tandem orthogonal proteolysis strategy for high-content chemical proteomics. J. Am. Chem. Soc. 127(28), 10018-10019 (2005).
53. Verhelst SH, Fonovic M, Bogyo M. A mild chemically cleavable linker system for functional proteomic applications. Angew. Chem. Int. Ed. 46(8), 1284-1286 (2007).
54. Yamamoto K, Yamazaki A, Takeuchi M, Tanaka A. A versatile method of identifying specific binding proteins on affinity resins. Anal. Biochem. 352(1), 15-23 (2006).
55. Patricelli MP, Szardenings AK, Liyanage M et al. Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry 46(2), 350-358 (2007).
56. Bantscheff M, Eberhard D, Abraham Y et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25(9), 1035-1044 (2007).
57. Bantscheff M, Hopf C, Savitski MM et al. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat. Biotechnol. 29(3), 255-265 (2011).
58. Lee MY, Kim MH, Kim J et al. Synthesis and SAR of sulfonyl- and phosphoryl amidine compounds as anti-resorptive agents. Bioorg. Med. Chem. Lett. 20(2), 541-545 (2010).
59. Chang SY, Bae SJ, Lee MY, Baek SH, Chang S, Kim SH. Chemical affinity matrix-based identification of prohibitin as a binding protein to anti-resorptive sulfonyl amidine compounds. Bioorg. Med. Chem. Lett. 21(2), 727-729 (2011).
60. Fleischer TC, Murphy BR, Flick JS et al. Chemical proteomics identifies Nampt as the target of CB30865, an orphan cytotoxic compound. Chem. Biol. 17(6), 659-664 (2010).
61. Cheng KW, Wong CC, Wang M, He QY, Chen F. Identification and characterization of molecular targets of natural products by mass spectrometry. Mass Spectrom. Rev. 29(1), 126-155 (2010).
62. Margarucci L, Monti MC, Tosco A, Riccio R, Casapullo A. Chemical proteomics discloses petrosapongiolide M, an antiinflammatory marine sesterterpene, as a proteasome inhibitor. Angew. Chem. Int. Ed. Engl. 49(23), 3960-3963 (2010).
63. Blanchard E, Belouzard S, Goueslain L et al. Hepatitis C virus entry depends on clathrin-mediated endocytosis. J. Virol. 80(14), 6964-6972 (2006).
64. Margarucci L, Monti MC, Fontanella B, Riccio R, Casapullo A. Chemical proteomics reveals bolinaquinone as a clathrin-mediated endocytosis inhibitor. Mol. Biosyst. 7(2), 480-485 (2011).
65. Capdeville R, Buchdunger E, Zimmermann J, Matter A. Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nat. Rev. Drug Discov. 1(7), 493-502 (2002).
66. Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem. Pharmacol. 80(5), 739-747 (2010).
67. Piersma SR, Labots M, Verheul HM, Jiménez CR. Strategies for kinome profiling in cancer and potential clinical applications: Chemical proteomics and array-based methods. Anal. Bioanal. Chem. 397(8), 3163-3171 (2010).
68. Rix U, Remsing Rix LL, Terker AS et al. A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells. Leukemia 24(1), 44-50 (2010).
69. Karaman MW, Herrgard S, Treiber DK et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26(1), 127-132 (2008).
70. Li J, Rix U, Fang B et al. A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Nat. Chem. Biol. 6(4), 291-299 (2010).
71. Missner E, Bahr I, Badock V, Lücking U, Siemeister G, Donner P. Off-target decoding of a multitarget kinase inhibitor by chemical proteomics. Chembiochem 10(7), 1163-1174 (2009).
72. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: A critical review. Anal. Bioanal. Chem. 389(4), 1017-1031 (2007).
73. Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1(5), 376-386 (2002).
74. Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents. Mol. Cell Proteomics 3(12), 1154-1169 (2004).
75. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17(10), 994-999 (1999).
76. Daub H, Olsen JV, Bairlein M et al. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol. Cell 31(3), 438-448 (2008).
77. Oppermann FS, Gnad F, Olsen JV et al. Large-scale proteomics analysis of the human kinome. Mol. Cell Proteomics 8(7), 1751-1764 (2009).
78. Breitkopf SB, Oppermann FS, Keri G, Grammel M, Daub H. Proteomics analysis of cellular imatinib targets and their candidate downstream effectors. J. Proteome Res. 9(11), 6033-6043 (2010).
79. Pan C, Olsen JV, Daub H, Mann M. Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics. Mol. Cell Proteomics 8(12), 2796-2808 (2009).
80. Ong SE, Schenone M, Margolin AA et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl Acad. Sci. USA 106(12), 4617-4622 (2009).
81. Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 4, 222 (2008).
82. Becker F, Murthi K, Smith C et al. A three-hybrid approach to scanning the proteome for targets of small molecule kinase inhibitors. Chem. Biol. 11(2), 211-223 (2004).
83. Caligiuri M, Molz L, Liu Q et al. MASPIT: Three-hybrid trap for quantitative proteome fingerprinting of small molecule-protein interactions in mammalian cells. Chem. Biol. 13(7), 711-722 (2006).