Target identification and validation in drug discovery: The role of proteomics

Biochemical Pharmacology

Volumn 69, Issue 8, 2005, Pages 1133-1139

  Kopec, Karla K ^a   Bozyczko Coyne, Donna ^a   Williams, Michael ^a  

^a CEPHALON INC   (United States)

Author keywords

Drug discovery; Proteomics; Target confidence building; Target validation

Indexed keywords

4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; CELL PROTEIN; G PROTEIN COUPLED RECEPTOR; INDISULAM; ION CHANNEL; NIMESULIDE; PROTEOME;

ACCURACY; ALGORITHM; BIOINFORMATICS; BIOPROCESS; BIOTECHNOLOGY; COMPLEX FORMATION; DRUG PURIFICATION; GENE MAPPING; HUMAN; HYDROPHOBICITY; HYPOTHESIS; MASS SPECTROMETRY; MEDICAL INFORMATICS; MEDICAL RESEARCH; MEDICAL TECHNOLOGY; NONHUMAN; OUTCOMES RESEARCH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REPRODUCIBILITY; REVIEW; SAMPLE; SIGNAL TRANSDUCTION; TARGET CELL; TECHNIQUE; THEORY; TIME; TWO DIMENSIONAL GEL ELECTROPHORESIS; VALIDATION PROCESS; VELOCITY; WHEAT;

EID: 15744388954     PISSN: 00062952     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bcp.2005.01.004     Document Type: Note

References (52)

1. L.A. Huber Is proteomics heading in the wrong direction? Nat Rev Mol Cell Biol 4 2003 74 80
2. V.C. Wasinger, S.J. Cordwell, A. Cerpa-Poljak, J.X. Yan, A.A. Gooley, and M.R. Wilkins Progress with gene-product mapping for the Mollicutes: Mycoplasma genitalium Electrophoresis 16 7 1995 1090 1094
3. C. Southan Has the yo-yo stopped? An assessment of human protein-coding gene number Proteomics 4 6 2004 1712 1726
4. S.I. Kim, H. Voshol, J. van Oostrum, T.G. Hastings, M. Cascio, and M.J. Glucksman Neuroproteomics: expression profiling of the brain's proteomes in health and disease Neurochem. Res. 29 6 2004 1317 1331
5. J. Drews Strategic trends in drug discovery Drug Disov Today 8 9 2003 411 420
6. A.L. Hopkins, and C.R. Groom The druggable genome Nat Rev Drug Discov 1 2003 727 730
7. M.A. Lindsay Target discovery Nat Rev Drug Discov 2 2003 831 838
8. D.F. Horrobin Realism in drug discovery-could Cassandra be right? Nat Biotechnol 19 2001 1099 1100
9. G.M. Milne Pharmaceutical productivity - the imperative for new paradigms Ann Rep Med Chem 38 2003 383 396
10. M. Williams Target validation Curr Opin Pharmacol 3 2003 571 577
11. E.F. Petricoin, and L.A. Liotta Clinical applications of proteomics J Nutr 133 2003 2476S 2484S
12. Collins FS, Green ED, Guttmacher AE, Guyer MS, USNHGRI. A vision for the future of genomics research. Nature 2003;422:835-47.
13. S.D. Patterson Data analysis - the Achilles heel of proteomics Nat Biotech 21 2003 221 222
14. P.L. Ferguson, and R.D. Smith Proteome analysis by mass spectrometry Ann Rev Biophys Biomol Struct 32 2003 399 424
15. M. Fountoulakis, N. Cairns, and G. Lubec Increased levels of 14-3-3 gamma and epsilon proteins in brain of patients with Alzheimer's disease and Down syndrome J Neural Transm Suppl 57 1999 323 335
16. Bridges D, Moorhead GB. 14-3-3 proteins: a number of functions for a numbered protein. Sci. STKE 242: re20, 2004.
17. C.C. Wu, and J.R. Yates III The application of mass spectrometry to membrane proteomics Nat Biotechnol 21 3 2003 262 267
18. A. Krogh, B. Larsson, G. von Heijne, and E.L. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J Mol Biol 305 3 2001 567 580
19. E. Wallin, and G. von Heijne Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms Protein Sci 7 4 1998 1029 1038
20. R. Schwartz, C.S. Ting, and J. King Whole proteome pI values correlate with subcellular localization of proteins for organisms within the the three domains of life Genome Res 11 5 2001 703 709
21. M. Ferro, D. Seigneurin-Berny, D. Rolland, A. Chapel, D. Salvi, and J. Garin Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins Electrophoresis 21 16 2000 3517 3526
22. R. Henningsen, B.L. Gale, K.M. Straub, and D.C. DeNagel Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry Proteomics 2 2002 1479 1488
23. D.A. Jeffery, and M. Bogyo Chemical proteomics and its application to drug discovery Curr Opin Biotechnol 14 2003 87 95
24. Y. Oda, T. Owa, T. Sato, B. Boucher, S. Daniels, and H. Yamanaka Quantitative chemical proteomics for identifying candidate trug targets Anal Chem 75 2003 2159 2165
25. S.M. Stevens, A.D. Zharikova, and L. Prokai Proteomic analysis of the synaptic membrane fraction isolated from rat forebrain Brain Res Mol Brain Res 117 2 2003 116 128
26. M.B. Goshe, J. Blonder, and R.D. Smith Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis J Proteome Res 2 2003 153 161
27. H. Husi, M.A. Ward, J.S. Choudhary, W.P. Blackstock, and S.G.N. Grant Proteomic analysis of NMDA receptor-adhesion protein signaling complexes Nat Neurosci 3 7 2000 661 669
28. J. Klose, C. Nock, M. Herrmann, K. Stuhler, K. Marcus, and M. Bluggel Genetic analysis of the mouse brain proteome Nat Genet 30 4 2002 385 393
29. M. Fountoulakis, J.F. Juranville, M. Dierssen, and G. Lubec Proteomic analysis of the fetal brain Proteomics 2 11 2002 1547 1576
30. J.H. Shin, J.W. Yang, J.F. Juranville, M. Fountoulakis, and G. Lubec Evidence for existence of thirty hypothetical proteins in rat brain Proteome Sci 2 1 2004 1 8
31. P.J. Legrain, J. Wojcik, and J.M. Gauthier Protein-protein interactive maps: leads towards cellular function Trends Genet 17 6 2001 346 352
32. J. Bockaert, P. Marin, A. Dumuis, and L. Fagni The 'magic tail' of G protein-coupled receptors: an anchorage for functional protein networks FEBS Lett 546 2003 65 72
33. J. Huang, H. Zhu, S.L. Haggarty, D.R. Spring, H. Hwang, and F. Jin Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips Proc Natl Acad Sci USA 101 2004 16594 16599
34. K. Godl, J. Wissing, A. Kurtenbach, P. Habenberger, S. Blencke, and H. Gutbrod An efficient proteomics method to identify the cellular targets of protein kinase inhibitors Proc Natl Acad Sci 100 26 2003 15434 15439
35. M. Merchant, and S.R. Weinberger Recent advancements in surface-enhanced laser desorption/ionization-timeof flight-mass spectrometry Electrophoresis 21 6 2000 1164 1177
36. C. Gineste, L. Ho, P. Pompl, M. Bianci, and G.M. Pasinetti High-throughput proteomics and protein biomarker discovery in an experimental model of inflammatory hyperalgesia: effects of nimesulide Drugs 63 Suppl. 1 2003 23 29
37. Z.E. Perlman, M.D. Slack, Y. Feng, T.J. Mitchison, L.F. Wu, and S.J. Altschuler Multidimensional drug profiling by automated microscopy Science 306 2004 1194 1198
38. R. Kramer, and D. Cohen Functional genomics to new drug targets Nat Rev Drug Discov 3 2004 965 972
39. G.S. Firestein, and D.S. Pisetsky DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology Arthritis Rheum 46 2002 859 861
40. J.S. Choudhary, and S.G.N. Grant Proteomics in postgenomic neuroscience: the end of the beginning Nat Neurosci 7 2004 440 445
41. E.C. Butcher, E.L. Berg, and E.J. Kunkel Systems biology in drug discovery Nat Biotechnol 22 10 2004 1253 1259
42. L. Hood, J.R. Heath, M.E. Phelps, and B. Lin Systems biology and new technologies enable predictive and preventative medicine Science 306 2004 640 643
43. M. Williams A return to the fundamentals of drug discovery Curr Opin Investigational Drugs 5 1 2004 29 33
44. E.F. Petricoin, K.C. Zoon, E.C. Kohn, J.C. Barrett, and L.A. Liotta Clinical proteomics: translating benchside promise to bedside reality Nat Rev Drug Discov 1 2002 683 695
45. E.F. Petricoin, D.A. Fishman, T.P. Conrads, T.D. Veenstra, and L.A. Liotta Lessons from Kitty Hawk: from feasibility to routine clinical use for the field of proteomic pattern diagnostics Proteomics 4 2004 2357 2360
46. J.S. Lazo, A.P. Ducruet, and R.P. Koldamova Sleuthful pharmacology Mol Pharmacol 64 2 2003 199 201
47. T. Kenakin Pharmacologic analysis of drug-receptor interaction second ed. 1997 Raven New York p. 344-346
48. D.F. Horrobin Modern biomedical research: an internally self consistent universe with little contact with medical reality Nat Rev Drug Discov 2 2003 151 154
49. R.S. Hauptschein, B.K. Eustace, and D.G. Jay Global high-throughput screens for cellular function Exp Hematol 30 2002 381 387
50. B.P. Zambrowicz, and A.T. Sands Knockouts model the 100 best-selling drugs - will they model the next 100 Nat Rev Drug Discov 2 2003 38 51
51. G. Duyk Attrition and translation Science 302 2003 603 605
52. Horton R. AIDS: the elusive vaccine. New York Rev. Books, vol. 51, 2004. p. 53-8.