Target deconvolution techniques in modern phenotypic profiling

Current Opinion in Chemical Biology

Volumn 17, Issue 1, 2013, Pages 118-126

  Lee, Jiyoun ^a   Bogyo, Matthew ^b  

^a Sungshin Women's University   (South Korea)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVITY BASED PROTEIN; BENZOPHENONE; COMPLEMENTARY DNA; CYCLOSPORIN A; DIDEMNIN B; DIPEPTIDYL PEPTIDASE I; MESSENGER RNA; PHOSPHOTRANSFERASE INHIBITOR; PROTEIN; RADIOISOTOPE; RAPAMYCIN; RESVERATROL; RETINOBLASTOMA BINDING PROTEIN; SCAFFOLD PROTEIN; TACROLIMUS; THALIDOMIDE; UNCLASSIFIED DRUG;

CHEMICAL LABELING; COMPUTER MODEL; DRUG DESIGN; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC SCREENING; GENOME; HUMAN; LEPROSY; MAMMAL CELL; MOLECULAR CLONING; MOLECULAR LIBRARY; MULTIPLE MYELOMA; PHENOTYPE; PROTEIN DENATURATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; SEQUENCE ANALYSIS; TERATOGENICITY;

ANIMALS; CHROMATOGRAPHY, AFFINITY; CLONING, MOLECULAR; DRUG DISCOVERY; HUMANS; PROTEINS; PROTEOMICS;

EID: 84875241586     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2012.12.022     Document Type: Review

References (77)

1. Drews J. Drug discovery: a historical perspective. Science 2000, 287:1960-1964.
2. Swinney D.C., Anthony J. How were new medicines discovered?. Nat Rev Drug Discov 2011, 10:507-519.
3. Mestres J., Gregori-Puigjane E., Valverde S., Sole R.V. The topology of drug-target interaction networks: implicit dependence on drug properties and target families. Mol Biosyst 2009, 5:1051-1057.
4. Roemer T., Davies J., Giaever G., Nislow C. Bugs, drugs and chemical genomics. Nat Chem Biol 2012, 8:46-56.
5. Feng Y., Mitchison T.J., Bender A., Young D.W., Tallarico J.A. Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nat Rev Drug Discov 2009, 8:567-578.
6. Schirle M., Bantscheff M., Kuster B. Mass spectrometry-based proteomics in preclinical drug discovery. Chem Biol 2012, 19:72-84.
7. Rix U., Superti-Furga G. Target profiling of small molecules by chemical proteomics. Nat Chem Biol 2009, 5:616-624.
8. Bantscheff M., Scholten A., Heck A.J. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov Today 2009, 14:1021-1029.
9. Raida M. Drug target deconvolution by chemical proteomics. Curr Opin Chem Biol 2011, 15:570-575.
10. Sato S., Murata A., Shirakawa T., Uesugi M. Biochemical target isolation for novices: affinity-based strategies. Chem Biol 2010, 17:616-623.
11. Mamidyala S.K., Finn M.G. In situ click chemistry: probing the binding landscapes of biological molecules. Chem Soc Rev 2010, 39:1252-1261.
12. Shi H., Cheng X., Sze S.K., Yao S.Q. Proteome profiling reveals potential cellular targets of staurosporine using a clickable cell-permeable probe. Chem Commun (Camb) 2011, 47:11306-11308.
13. Shi H., Zhang C.J., Chen G.Y., Yao S.Q. Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J Am Chem Soc 2012, 134:3001-3014.
14. He G., Luo W., Li P., Remmers C., Netzer W.J., Hendrick J., Bettayeb K., Flajolet M., Gorelick F., Wennogle L.P., et al. Gamma-secretase activating protein is a therapeutic target for Alzheimer's disease. Nature 2010, 467:95-98.
15. Tapper E.B., Knowles D., Heffron T., Lawrence E.C., Csete M. Portopulmonary hypertension: imatinib as a novel treatment and the Emory experience with this condition. Transplant Proc 2009, 41:1969-1971.
16. Netzer W.J., Dou F., Cai D., Veach D., Jean S., Li Y., Bornmann W.G., Clarkson B., Xu H., Greengard P. Gleevec inhibits beta-amyloid production but not Notch cleavage. Proc Natl Acad Sci U S A 2003, 100:12444-12449.
17. Kumar N.S., Young R.N. Design and synthesis of an all-in-one 3-(1,1-difluoroprop-2-ynyl)-3H-diazirin-3-yl functional group for photo-affinity labeling. Bioorg Med Chem 2009, 17:5388-5395.
18. Cisar J.S., Cravatt B.F. Fully functionalized small-molecule probes for integrated phenotypic screening and target identification. J Am Chem Soc 2012, 134:10385-10388.
19. Ito T., Ando H., Suzuki T., Ogura T., Hotta K., Imamura Y., Yamaguchi Y., Handa H. Identification of a primary target of thalidomide teratogenicity. Science 2010, 327:1345-1350.
20. Hu L., Iliuk A., Galan J., Hans M., Tao W.A. Identification of drug targets in vitro and in living cells by soluble-nanopolymer-based proteomics. Angew Chem Int Ed Engl 2011, 50:4133-4136.
21. Evans M.J., Cravatt B.F. Mechanism-based profiling of enzyme families. Chem Rev 2006, 106:3279-3301.
22. Sadaghiani A.M., Verhelst S.H., Bogyo M. Tagging and detection strategies for activity-based proteomics. Curr Opin Chem Biol 2007, 11:20-28.
23. Deu E., Verdoes M., Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 2012, 19:9-16.
24. Nomura D.K., Dix M.M., Cravatt B.F. Activity-based protein profiling for biochemical pathway discovery in cancer. Nat Rev Cancer 2010, 10:630-638.
25. Puri A.W., Bogyo M. Using small molecules to dissect mechanisms of microbial pathogenesis. ACS Chem Biol 2009, 4:603-616.
26. Li H., Child M.A., Bogyo M. Proteases as regulators of pathogenesis: examples from the Apicomplexa. Biochim Biophys Acta 2012, 1824:177-185.
27. Long J.Z., Cravatt B.F. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev 2011, 111:6022-6063.
28. Puri A.W., Lupardus P.J., Deu E., Albrow V.E., Garcia K.C., Bogyo M., Shen A. Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem Biol 2010, 17:1201-1211.
29. Deu E., Leyva M.J., Albrow V.E., Rice M.J., Ellman J.A., Bogyo M. Functional studies of Plasmodium falciparum dipeptidyl aminopeptidase I using small molecule inhibitors and active site probes. Chem Biol 2010, 17:808-819.
30. Arastu-Kapur S., Ponder E.L., Fonovic U.P., Yeoh S., Yuan F., Fonovic M., Grainger M., Phillips C.I., Powers J.C., Bogyo M. Identification of proteases that regulate erythrocyte rupture by the malaria parasite Plasmodium falciparum. Nat Chem Biol 2008, 4:203-213.
31. Hall C.I., Reese M.L., Weerapana E., Child M.A., Bowyer P.W., Albrow V.E., Haraldsen J.D., Phillips M.R., Sandoval E.D., Ward G.E., et al. Chemical genetic screen identifies Toxoplasma DJ-1 as a regulator of parasite secretion, attachment, and invasion. Proc Natl Acad Sci U S A 2011, 108:10568-10573.
32. Crump C.J., am Ende C.W., Ballard T.E., Pozdnyakov N., Pettersson M., Chau D.M., Bales K.R., Li Y.M., Johnson D.S. Development of clickable active site-directed photoaffinity probes for gamma-secretase. Bioorg Med Chem Lett 2012, 22:2997-3000.
33. Sieber S.A., Niessen S., Hoover H.S., Cravatt B.F. Proteomic profiling of metalloprotease activities with cocktails of active-site probes. Nat Chem Biol 2006, 2:274-281.
34. Geurink P.P., Florea B.I., Van der Marel G.A., Kessler B.M., Overkleeft H.S. Probing the proteasome cavity in three steps: bio-orthogonal photo-reactive suicide substrates. Chem Commun (Camb) 2010, 46:9052-9054.
35. Barglow K.T., Saikatendu K.S., Bracey M.H., Huey R., Morris G.M., Olson A.J., Stevens R.C., Cravatt B.F. Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes. Biochemistry 2008, 47:13514-13523.
36. Pace N.J., Pimental D.R., Weerapana E. An inhibitor of glutathione S-transferase omega 1 that selectively targets apoptotic cells. Angew Chem Int Ed Engl 2012, 51:8365-8368.
37. Wright A.T., Song J.D., Cravatt B.F. A suite of activity-based probes for human cytochrome P450 enzymes. J Am Chem Soc 2009, 131:10692-10700.
38. Saario S.M., McKinney M.K., Speers A.E., Wang C., Cravatt B.F. Clickable, photoreactive inhibitors to probe the active site microenvironment of fatty acid amide hydrolase. Chem Sci 2012, 3:77-83.
39. van der Linden W.A., Li N., Hoogendoorn S., Ruben M., Verdoes M., Guo J., Boons G.J., van der Marel G.A., Florea B.I., Overkleeft H.S. Two-step bioorthogonal activity-based proteasome profiling using copper-free click reagents: a comparative study. Bioorg Med Chem 2012, 20:662-666.
40. Kulkarni S.S., Hu X., Doi K., Wang H.G., Manetsch R. Screening of protein-protein interaction modulators via sulfo-click kinetic target-guided synthesis. ACS Chem Biol 2011, 6:724-732.
41. Berry A.F., Heal W.P., Tarafder A.K., Tolmachova T., Baron R.A., Seabra M.C., Tate E.W. Rapid multilabel detection of geranylgeranylated proteins by using bioorthogonal ligation chemistry. Chembiochem 2010, 11:771-773.
42. Willems L.I., Verdoes M., Florea B.I., van der Marel G.A., Overkleeft H.S. Two-step labeling of endogenous enzymatic activities by Diels-Alder ligation. Chembiochem 2010, 11:1769-1781.
43. Shields D.J., Niessen S., Murphy E.A., Mielgo A., Desgrosellier J.S., Lau S.K., Barnes L.A., Lesperance J., Bouvet M., Tarin D., et al. RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia. Proc Natl Acad Sci U S A 2010, 107:2189-2194.
44. Chiang K.P., Niessen S., Saghatelian A., Cravatt B.F. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem Biol 2006, 13:1041-1050.
45. Nomura D.K., Long J.Z., Niessen S., Hoover H.S., Ng S.W., Cravatt B.F. Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. Cell 2010, 140:49-61.
46. Bachovchin D.A., Brown S.J., Rosen H., Cravatt B.F. Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. Nat Biotechnol 2009, 27:387-394.
47. Deu E., Yang Z., Wang F., Klemba M., Bogyo M. Use of activity-based probes to develop high throughput screening assays that can be performed in complex cell extracts. PLoS ONE 2010, 5:e11985.
48. Bachovchin D.A., Mohr J.T., Speers A.E., Wang C., Berlin J.M., Spicer T.P., Fernandez-Vega V., Chase P., Hodder P.S., Schurer S.C., et al. Academic cross-fertilization by public screening yields a remarkable class of protein phosphatase methylesterase-1 inhibitors. Proc Natl Acad Sci U S A 2011, 108:6811-6816.
49. Fontana A., de Laureto P.P., Spolaore B., Frare E., Picotti P., Zambonin M. Probing protein structure by limited proteolysis. Acta Biochim Pol 2004, 51:299-321.
50. Lomenick B., Hao R., Jonai N., Chin R.M., Aghajan M., Warburton S., Wang J., Wu R.P., Gomez F., Loo J.A., et al. Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci U S A 2009, 106:21984-21989.
51. Chang Y., Schlebach J.P., Verheul R.A., Park C. Simplified proteomics approach to discover protein-ligand interactions. Protein Sci 2012, 21:1280-1287.
52. West G.M., Tang L., Fitzgerald M.C. Thermodynamic analysis of protein stability and ligand binding using a chemical modification- and mass spectrometry-based strategy. Anal Chem 2008, 80:4175-4185.
53. West G.M., Tucker C.L., Xu T., Park S.K., Han X., Yates J.R., Fitzgerald M.C. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements. Proc Natl Acad Sci U S A 2010, 107:9078-9082.
54. Dearmond P.D., Xu Y., Strickland E.C., Daniels K.G., Fitzgerald M.C. Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. J Proteome Res 2011, 10:4948-4958.
55. Van Dorst B., Mehta J., Rouah-Martin E., Somers V., De Coen W., Blust R., Robbens J. cDNA phage display as a novel tool to screen for cellular targets of chemical compounds. Toxicol In Vitro 2010, 24:1435-1440.
56. Jung H.J., Shim J.S., Lee J., Song Y.M., Park K.C., Choi S.H., Kim N.D., Yoon J.H., Mungai P.T., Schumacker P.T., et al. Terpestacin inhibits tumor angiogenesis by targeting UQCRB of mitochondrial complex III and suppressing hypoxia-induced reactive oxygen species production and cellular oxygen sensing. J Biol Chem 2010, 285:11584-11595.
57. Takakusagi Y., Takakusagi K., Sugawara F., Sakaguchi K. Use of phage display technology for the determination of the targets for small-molecule therapeutics. Expert Opin Drug Discov 2010, 5:361-389.
58. Van Dorst B., Mehta J., Rouah-Martin E., De Coen W., Blust R., Robbens J. The identification of cellular targets of 17beta estradiol using a lytic (T7) cDNA phage display approach. Toxicol In Vitro 2011, 25:388-393.
59. Roberts R.W., Szostak J.W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 1997, 94:12297-12302.
60. McPherson M., Yang Y., Hammond P.W., Kreider B.L. Drug receptor identification from multiple tissues using cellular-derived mRNA display libraries. Chem Biol 2002, 9:691-698.
61. Licitra E.J., Liu J.O. A three-hybrid system for detecting small ligand-protein receptor interactions. Proc Natl Acad Sci U S A 1996, 93:12817-12821.
62. Becker F., Murthi K., Smith C., Come J., Costa-Roldan N., Kaufmann C., Hanke U., Degenhart C., Baumann S., Wallner W., et al. A three-hybrid approach to scanning the proteome for targets of small molecule kinase inhibitors. Chem Biol 2004, 11:211-223.
63. Chidley C., Haruki H., Pedersen M.G., Muller E., Johnsson K. A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis. Nat Chem Biol 2011, 7:375-383.
64. Gaulton A., Bellis L.J., Bento A.P., Chambers J., Davies M., Hersey A., Light Y., McGlinchey S., Michalovich D., Al-Lazikani B., et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 2012, 40:D1100-D1107.
65. Wishart D.S., Knox C., Guo A.C., Shrivastava S., Hassanali M., Stothard P., Chang Z., Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006, 34:D668-D672.
66. Seiler K.P., George G.A., Happ M.P., Bodycombe N.E., Carrinski H.A., Norton S., Brudz S., Sullivan J.P., Muhlich J., Serrano M., et al. ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res 2008, 36:D351-D359.
67. Koutsoukas A., Simms B., Kirchmair J., Bond P.J., Whitmore A.V., Zimmer S., Young M.P., Jenkins J.L., Glick M., Glen R.C., et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics 2011, 74:2554-2574.
68. Keiser M.J., Setola V., Irwin J.J., Laggner C., Abbas A.I., Hufeisen S.J., Jensen N.H., Kuijer M.B., Matos R.C., Tran T.B., et al. Predicting new molecular targets for known drugs. Nature 2009, 462:175-181.
69. Lounkine E., Keiser M.J., Whitebread S., Mikhailov D., Hamon J., Jenkins J.L., Lavan P., Weber E., Doak A.K., Cote S., et al. Large-scale prediction and testing of drug activity on side-effect targets. Nature 2012, 486:361-367.
70. Dakshanamurthy S., Issa N.T., Assefnia S., Seshasayee A., Peters O.J., Madhavan S., Uren A., Brown M.L., Byers S.W. Predicting new indications for approved drugs using a proteochemometric method. J Med Chem 2012, 55:6832-6848.
71. Areias F.M., Brea J., Gregori-Puigjane E., Zaki M.E., Carvalho M.A., Dominguez E., Gutierrez-de-Teran H., Proenca M.F., Loza M.I., Mestres J. In silico directed chemical probing of the adenosine receptor family. Bioorg Med Chem 2010, 18:3043-3052.
72. Flachner B., Lorincz Z., Carotti A., Nicolotti O., Kuchipudi P., Remez N., Sanz F., Tovari J., Szabo M.J., Bertok B., et al. A chemocentric approach to the identification of cancer targets. PLoS ONE 2012, 7:e35582.
73. Laggner C., Kokel D., Setola V., Tolia A., Lin H., Irwin J.J., Keiser M.J., Cheung C.Y., Minor D.L., Roth B.L., et al. Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol 2012, 8:144-146.
74. Plouffe D., Brinker A., McNamara C., Henson K., Kato N., Kuhen K., Nagle A., Adrian F., Matzen J.T., Anderson P., et al. In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen. Proc Natl Acad Sci U S A 2008, 105:9059-9064.
75. Young D.W., Bender A., Hoyt J., McWhinnie E., Chirn G.W., Tao C.Y., Tallarico J.A., Labow M., Jenkins J.L., Mitchison T.J., et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 2008, 4:59-68.
76. Anastassiadis T., Deacon S.W., Devarajan K., Ma H., Peterson J.R. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nat Biotechnol 2011, 29:1039-1045.
77. Lounkine E., Kutchukian P., Petrone P., Davies J.W., Glick M. Chemotography for multi-target SAR analysis in the context of biological pathways. Bioorg Med Chem 2012, 20:5416-5427.