Capturing structure-activity relationships from chemogenomic spaces

Journal of Chemical Information and Modeling

Volumn 51, Issue 4, 2011, Pages 843-851

  Wendt, Bernd ^a,c   Uhrig, Ulrike ^b   Bös, Fabian ^b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b Tripos GmbH   (Germany)

^c Elara Pharmaceuticals   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; EXTRACTION; OUTSOURCING; QUERY PROCESSING;

CHEMICAL BIOLOGY; ITS APPLICATIONS; LIGAND STRUCTURE; QUERY STRUCTURES; STRUCTURAL SIMILARITY; STRUCTURAL TRENDS; STRUCTURE ACTIVITY RELATIONSHIPS; STRUCTURE AND ACTIVITIES;

SPACE-BASED RADAR;

DRUG; LIGAND;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DEVELOPMENT; FACTUAL DATABASE; INFORMATION SCIENCE; METHODOLOGY; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DISCOVERY; INFORMATICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79955437617     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100270x     Document Type: Article

References (46)

1. Sams-Dodd, F. Target-based drug discovery: Is something wrong? Drug Discovery Today 2005, 10, 139-137
2. Cheung, C. H.; Coumar, M. S.; Hsieh, H. P.; Chang, J. Y. Aurora kinase inhibitors in preclinical and clinical testing Expert Opin. Invest. Drugs 2009, 18, 379-398
3. Paolini, G. V.; Shapland, R. H.; van Hoorn, W. P.; Mason, J. S.; Hopkins, A. L. Global mapping of pharmacological space Nat. Biotechnol. 2006, 24, 805-815 (Pubitemid 44086621)
4. Hopkins, A. L. Network pharmacology: The next paradigm in drug discovery Nat. Chem. Biol. 2008, 4, 682-690
5. Hart, C. P. Finding the target after screening the phenotype Drug Discovery Today 2005, 10, 513-519
6. Terstappen, G. C.; Schlüpen, C.; Raggiaschi, R.; Gaviraghi, G. Target deconvolution strategies in drug discovery Nat. Rev. Drug Discovery 2007, 6, 891-903 (Pubitemid 350042397)
7. Huang, S. M. A.; 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.; Cong, F. Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling Nature 2009, 461, 614-20
8. Hopkins, A. L.; Mason, J. S.; Overington, J. P. Can we rationally design promiscuous drugs? Curr. Opin. Struct. Biol. 2006, 16, 127-136 (Pubitemid 43221881)
9. Cleves, A. E.; Jain, A. N. Robust ligand-based modeling of the biological targets of known drugs J. Med. Chem. 2006, 49, 2921-2938
10. 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.; Whaley, R.; Glennon, R. A.; Hert, J.; Thomas, K. L. H.; Edwards, D. D.; Shoichet, B. K.; Roth, B. L. Predicting new molecular targets for known drugs Nature 2009, 462, 175-181
11. Bender, A.; Scheiber, J.; Glick, M.; Davies, J. W.; Azzaoui, K.; Hamon, J.; Urban, L.; Whitebread, S.; Jenkins, J. L. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure ChemMedChem 2007, 2, 861-873
12. Kuhn, M.; Campillos, M.; González, P.; Jensen, L. J.; Bork, P. Large-scale prediction of drug-target relationships FEBS Lett. 2008, 582, 1283-1290
13. Campillo, M.; Kuhn, M.; Gavin, A. C.; Jensen, L. J.; Bork, P. Drug target identification using side-effect similarity Science 2008, 321, 263-266 (Pubitemid 351989100)
14. Jenkins, J.; Bender, A.; Davies, J. W. In silico target fishing: Predicting biological targets from chemical structure Drug Discovery Today: Technol. 2006, 3, 413-421 (Pubitemid 46158395)
15. Garcia-Serna, R.; Mestres, J. Anticipating drug side effects by comparative pharmacology Expert Opin. Drug Metab. Toxicol. 2010, 6, 1253-1263
16. Nettles, J. H.; Jenkins, J. L.; Bender, A.; Deng, Z.; Davies, J. W.; Glick, M. Bridging chemical and biological space: "Target fishing" using 2D and 3D molecular descriptors J. Med. Chem. 2006, 49, 6802-6810 (Pubitemid 44749747)
17. Peterson, R. T. Chemical biology and the limits of reductionism Nat. Chem. Biol. 2008, 4, 635-638
18. Senger, S.; Leach, A. SAR Knowledge Bases in Drug Discovery Ann. Rep. Comp. Chem. 2008, 4, 203-216
19. Bolton, E. E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H. PubChem: Integrated platform of small molecules and biological activities Ann. Rep. Comp. Chem. 2008, 4, 217-241
20. 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.; Ferraiolo, P.; Tolliday, N. J.; Schreiber, S. L.; Clemons, P. A. ChemBank: a small-molecule screening and cheminformatics resource database Nucl. Acid. Res. 2008, 36, 351-359
21. Bender, A. Compound bioactivities go public Nat. Chem. Biol. 2010, 6, 309
22. Liu, T.; Lin, Y.; Wen, X.; Jorrisen, R. N.; Gilson, M. K. BindingDB: A Web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 2007, 35, 198-201
23. Hu, L.; Benson, M. L.; Smith, R. D.; Lerner, M. G.; Carlson, H. A. Binding MOAD (Mother Of All Databases) Proteins 2005, 60, 333-340 (Pubitemid 41061630)
24. Data was generously provided by the National Institute of Mental Health's Psychoactive Drug Screening Program, Contract HHSN-271-2008-00025-C (NIMH PDSP).
25. Oprea, T.; Tropsha, A.; Faulon, J.-L.; Rintoul, M. D. Systems chemical biology Nat. Chem. Biol. 2007, 3, 447-450 (Pubitemid 47080379)
26. Wendt, B.; Cramer, R. D. Quantitative Series Enrichment Analysis (QSEA): A novel procedure for 3D-QSAR analysis J. Comput.- Aided Mol. Des. 2008, 22, 541-551
27. Cramer, R. D.; Jilek, R. J.; Andrews, K. M. dbtop: Topomer similarity searching of conventional structure databases J. Mol. Graphics Modell. 2002, 20, 447-462 (Pubitemid 34312060)
28. Cramer, R. D.; Topomer CoMFA, A. Design methodology for rapid lead optimization J. Med. Chem. 2003, 46, 374-388 (Pubitemid 36139790)
29. SYBYL, Tripos International, 1699 South Hanley Rd., St. Louis, Missouri 63144, USA.
30. csp-standard.defs contains a set of SLN-rules (SYBYL Line Notation) to convert ionized structures into their neutral forms.
31. Jilek, R. J.; Cramer, R. D. Topomers: A validated protocol for their self-consistent generation J. Chem. Inf. Comput. Sci. 2004, 44, 1221-1227
32. Pearlman, R. S. Concord; Tripos International, St. Louis, MO.
33. Hert, J.; Willett, P.; Wilton, D. J. Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures J. Chem. Inf. Comput. Sci. 2004, 44, 1177-1185
34. Matter, H. Selecting optimally diverse compounds from structure databases: A validation study of two-dimensional and three-dimensional molecular descriptors J. Med. Chem. 1997, 40, 1219-1229 (Pubitemid 27175101)
35. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45, 4350-4358 (Pubitemid 35025581)
36. Boecker, A. Toward an improved clustering of large data sets using maximum common substructures and tolological fingerprints J. Chem. Inf. Model. 2008, 48, 2097-2107
37. Xie, X. Q.; Chen, J. Z. Data mining a small molecule drug screening representative subset from NIH PubChem J. Chem. Inf. Model. 2008, 48, 465-475
38. Sheridan, R. P.; Feuston, B. P.; Maiorov, V. N.; Kearsley, S. K. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR J. Chem. Inf. Comput. Sci. 2004, 44, 1912-1928
39. Xue, L.; Stahura, F. L.; Godden, J. W.; Bajorath, J. Mini-fingerprints detect similar activity of receptor ligands previously recognized only by three-dimensional pharmacophore-based methods J. Chem. Inf. Comput. Sci. 2001, 41, 394-401 (Pubitemid 32408656)
40. Kogej, T.; Engkvist, O.; Blomberg, N.; Muresan, S. Multifingerprint based similarity searches for targeted class compound selection J. Chem. Inf. Model. 2006, 46, 1201-1213 (Pubitemid 43999164)
41. Freitas, R. F.; Bauab, R. L.; Montanari, C. A. Novel application of 2D and 3D-similarity searches to identify substrates among cytochrome P450 2C9, 2D6, and 3A4 J. Chem. Inf. Model. 2010, 50, 97-109
42. Nicholls, A.; McGaughey, G. B.; Sheridan, R. P.; Good, A. C.; Warren, G.; Mathieu, M.; Muchmore, S. W.; Brown, S. P.; Grant, J. A.; Haigh, J. A.; Nevins, N.; Jain, A. N.; Kelley, B. Molecular shape and medicinal chemistry: A perspective J. Med. Chem. 2010, 53, 3862-3886
43. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors J. Med. Chem. 1996, 39, 3049-3059 (Pubitemid 26260310)
44. Olah, M.; Bologa, C.; Oprea, T. I. An automated PLS search for biologically relevant QSAR descriptors J. Comput.- Aided Mol. Des. 2004, 18, 437-449
45. Olah, M.; Mracec, M.; Ostopovici, L.; Rad, R.; Bora, A.; Hadaruga, N.; Olah, I.; Banda, M.; Simon, Z.; Mracec, M.; Oprea., T. I. WOMBAT: World of Molecular Bioactivity. In Chemoinformatics in Drug Discovery; Oprea, T.I., Ed.; Wiley-VCH: New York, 2004, pp 223 - 239.
46. Tobita, M.; Nishikawaa, T.; Nagashimaa, R. A discriminant model constructed by the support vector machine method for HERG potassium channel inhibitors Bioorg. Med. Chem. Lett. 2005, 15, 2886-2890 (Pubitemid 40732240)