Computational approaches in chemogenomics and chemical biology: Current and future impact on drug discovery

Expert Opinion on Drug Discovery

Volumn 3, Issue 12, 2008, Pages 1371-1376

  Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

Chemical biology; Chemogenomics; Computational methods; Drug target networks; Ligand selectivity; Ligand target interactions; Pharmacological space; Polypharmacology; Small molecules; Target families

Indexed keywords

DRUG;

ARTICLE; BAYES THEOREM; BIOINFORMATICS; BIOLOGY; CHEMICAL BIOLOGY; CHEMOGENOMICS; COMPUTER ANALYSIS; DRUG BINDING; DRUG DESIGN; DRUG RESEARCH; DRUG SELECTIVITY; DRUG TARGETING; GENOMICS; LIGAND BINDING; MOLECULAR INTERACTION; MOLECULAR PROBE; POLYPHARMACY; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; SUPPORT VECTOR MACHINE;

EID: 58049191116     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460440802536496     Document Type: Article

References (32)

1. Stockwell BR. Exploring biology with small organic molecules. Nature 2004;432:846-54
2. Tan DS. Diversity-oriented synthesis: exploring the intersections between chemistry and biology. Nat Chem Biol 2005;1:74-84
3. Caron PR, Mullican MD, Mashal RD, et al. Chemogenomic approaches to drug discovery. Curr Opin Chem Biol 2001;5:464-70
4. Bredel M, Jacoby E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat Rev Drug Genet 2004;5:262-75
5. Maréchal E. Chemogenomics: a discipline at the crossroad of high throughput technologies, biomarker research, combinatorial chemistry, genomics, cheminformatics, bioinformatics and artificial intelligence. Comb Chem High Throughput Screen 2008;11:583-6
6. Bajorath J. Computational analysis of ligand relationships within target families. Curr Opin Chem Biol 2008;12:352-8
7. Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov 2002;1:727-30
8. Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov 2006;5:993-6
9. Paolini GV, Shapland RHB, van Hoorn WP, et al. Global mapping of pharmacological space. Nat Biotechnol 2006;24:805-15
10. Mestres J, Martin-Couce L, Gregori-Puigjane E, et al. Ligand-based approaches to in silico pharmacology: nuclear receptor profiling. J Chem Inf Model 2006;46:2725-36
11. Keiser MJ, Roth BL, Armbuster BN, et al. Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007;25:197-206
12. Yildirim MA, Goh KI, Cusick ME, et al. Drug-target network. Nat Biotechnol 2007;25:1119-26
13. Hert J, Keiser MJ, Irwin JJ, et al. Quantifying the relationships among drug classes. J Chem Inf Model 2008;48:755-65
14. Campillos M, Kuhn M, Gavin AC, et al. Drug target identification using side-effect similarity. Science 2008;321:262-6
15. Bender A, Scheiber J, Glick M, et al. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. ChemMedChem 2007;2:861-73
16. Karaman MW, Herrgards S, Treiber DK, et al. A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol 2008;26:127-32
17. MDL Drug Data Report (MDDR), Symyx Software, San Ramon, USA, 2008
18. Olah M, Mracec M, Ostopovici L, et al. WOMBAT: world of molecular bioactivity, in Chemoinformatics in Drug Discovery. Oprea TI edition. New York: Wiley-VCH, 2004;223-39
19. Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34:D668-72
20. Nidhi, Glick M, Davies JW, et al. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J Chem Inf Model 2006;46:1124-33
21. Fliri AF, Loging WT, Thadeio PF, et al. Biospectra analysis: model proteome characterizations for linking molecular structure and biological response. J Med Chem 2005;48:6918-25
22. Fliri AF, Loging WT, Volkmann RA. Analysis of system structure-function relationships. ChemMedChem 2007;2:1774-82
23. Bock JR, Gough DA. Virtual screens for ligands of orphan G protein-coupled receptors. J Chem Inf Model 2005;45:1402-14
24. Cleves AN, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem 2006;49:2921-38
25. Young DW, Bender A, Hoyt J, et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 2008;4:59-68
26. Oprea TI, Tropsha A, Faulon JL, et al. Systems chemical biology. Nat Chem Biol 2007;3:47-50
27. Houlton S. Wellcome boost for open-access chemistry. Nat Rev Drug Discov 2008;7:789-90
28. Stumpfe D, Ahmed HEA, Vogt I, et al. Methods for computer-aided chemical biology. Part 1: design of a benchmark system for the evaluation of compound selectivity. Chem Biol Drug Des 2007;70:182-94
29. Vogt I, Stumpfe D, Ahmed HEA, et al. Methods for computer-aided chemical biology. Part 2: evaluation of compound selectivity using 2D molecular fingerprints. Chem Biol Drug Des 2007;70:195-205
30. Stumpfe D, Geppert H, Bajorath J. Methods for computer-aided chemical biology. Part 3: analysis of structure-selectivity relationships through single- or dual-step selectivity searching and Bayesian classification. Chem Biol Drug Des 2008;71:518-28
31. Peltason L, Bajorath J. Molecular similarity analysis uncovers heterogeneous structure-activity relationships and variable activity landscapes. Chem Biol 2007;14:489-97
32. Wawer M, Peltason L, Weskamp N, et al. Structure-activity relationship anatomy by network-like similarity graphs and local structure-activity indices. J Med Chem 2008;51:6075-84