Deriving knowledge through data mining high-throughput screening data

Journal of Medicinal Chemistry

Volumn 47, Issue 25, 2004, Pages 6373-6383

  Diller, David J ^a   Hobbs, Doug W ^a  

^a PHARMACOPEIA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC ACID; FUNCTIONAL GROUP; POLYMER;

ARTICLE; CALCULATION; CHEMICAL BOND; COMBINATORIAL LIBRARY; DATA ANALYSIS; DRUG ABSORPTION; DRUG ACTIVITY; DRUG DETERMINATION; DRUG SCREENING; DRUG SOLUBILITY; DRUG STABILITY; DRUG STRUCTURE; DRUG TARGETING; ENCODED COMBINATORIAL LIBRARY ON POLYMERIC SUPPORT; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; MOLECULAR WEIGHT; PARAMETER; PHYSICAL CHEMISTRY; REDUNDANCY ANALYSIS; RELIABILITY; STATISTICAL ANALYSIS; STATISTICAL MODEL; STRUCTURE ANALYSIS; TECHNIQUE;

ALGORITHMS; DATABASES, FACTUAL; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR WEIGHT; PHARMACEUTICAL PREPARATIONS; PROBABILITY; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 9744264881     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm049902r     Document Type: Article

References (35)

1. Spencer, R. W. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. Biotechnol. Bioeng. 1998, 61, 61-67.
2. Ohlmeyer, M. H.; Swanson, R. N.; Dillard, L. W.; Reader, J. C.; Asouline, G.; et al. Complex synthetic chemical libraries indexed with molecular tags. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 10922-10926.
3. Baldwin, J. J.; Horlbeck, E. G. Direct dividing method for synthesis of combinatorial libraries (Pharmacopeia, Inc.). WO9535503, 1995; p 40.
4. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
5. Oprea, T. I. Property distribution of drug-related chemical databases. J. Comput.-Aided Mol. Des. 2000, 14, 251-264.
6. Veber, D. F.; Johnson, S. R.; Cheng, H. Y.; Smith, B. R.; Ward, K. W.; et al. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 2002, 45, 2615-2623.
7. Vieth, M.; Siegel, M. G.; Higgs, R. E.; Watson, I. A.; Robertson, D. H.; et al. Characteristic physical properties and structural fragments of marketed oral drugs. J. Med. Chem. 2004, 47, 224-232.
8. Gillet, V. J.; Willett, P.; Bradshaw, J. Identification of biological activity profiles using substructural analysis and genetic algorithms. J. Chem. Inf. Comput. Sci. 1998, 38, 165-179.
9. World Drug Index; Daylight Chemical Information Systems: Mission Viejo, CA.
10. SPRESI; Daylight Chemical Information Systems: Mission Viejo, CA.
11. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks. J. Med. Chem. 1996, 39, 2887-2893.
12. Bemis, G. W.; Murcko, M. A. Properties of Known Drugs. 2. Side Chains. J. Med. Chem. 1999, 42, 5095-5099.
13. Yoshida, F.; Topliss, J. G. QSAR model for drug human oral bioavailability. J. Med. Chem. 2000, 43, 2575-2585.
14. Andrews, C. W.; Bennett, L.; Yu, L. X. Predicting human oral bioavailability of a compound: development of a novel quantitative structure-bioavailability relationship. Pharm. Res. 2000, 17, 639-644.
15. Bacha, P. A.; Gruver, H. S.; Den Hartog, B. K.; Tamura, S. Y.; Nutt, R. F. Rule extraction from a mutagenicity data set using adaptively grown phylogenetic-like trees. J. Chem. Inf. Comput. Sci. 2002, 42, 1104-1111.
16. Cramer, R. D., 3rd; Redl, G.; Berkoff, C. E. Substructural analysis. A novel approach to the problem of drug design. J. Med. Chem. 1974, 17, 533-535.
17. Chu, K. C.; Feldmann, R. J.; Shapiro, M. B.; Hazard, G. F., Jr.; Geran, R. I. Pattern recognitiion and structure-activity relationship studies. Computer-assisted prediction of antitumor activity in structurally diverse drugs in an experimental mouse brain tumor system. J. Med. Chem. 1975, 18, 539-545.
18. Adamson, G. W.; Bawden, D. A substructural analysis method for structure-activity correlation of heterocyclic compounds using Wiswesser line notation. J. Chem. Inf. Comput. Sci. 1977, 17, 164-171.
19. Hodes, L.; Hazard, G. F.; Geran, R. I.; Richman, S. A statistical-heuristic methods for automated selection of drugs for screening. J. Med. Chem. 1977, 20, 469-475.
20. Patchett, A. A.; Nargund, R. P. Privileged structures - an update. Ann. Rep. Med. Chem. 2000, 35, 289-298.
21. Hajduk, P. J.; Bures, M.; Praestgaard, J.; Fesik, S. W. Privileged molecules for protein binding identified from NMR-based screening. J. Med. Chem. 2000, 43, 3443-3447.
22. Roche, O.; Schneider, P.; Zuegge, J.; Guba, W.; Kansy, M.; et al. Development of a virtual screening method for identification of "frequent hitters" in compound libraries. J. Med. Chem. 2002, 45, 137-142.
23. Muller, G. Medicinal chemistry of target family-directed masterkeys. Drug Discovery Today 2003, 8, 681-691.
24. Bondensgaard, K.; Ankersen, M.; Thogersen, H.; Hansen, B. S.; Wulff, B. S.; et al. Recognition of privileged structures by G-protein coupled receptors. J. Med. Chem. 2004, 47, 888-899.
25. Press, W. H.; Teulkolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in C, 2nd ed.; Cambridge University Press: Cambridge, 1997; p 994.
26. Ott, R. L.; Longnecker, M. Statistical Methods and Data Analysis, 5th ed.; Duxbury: Pacific Groove, CA, 2001.
27. Cerius2-4.8; Accelrys Inc.: San Diego, CA.
28. Viswanadhan, V. N.; Ghose, A. K.; Wendoloski, J. J. Estimating aqueous solvation and lipophilicity of small organic molecules: A comparative overview of atom/group contribution methods. Perspect. Drug Discovery Des. 2000, 19, 85-98.
29. Ghose, A. K.; Viswanadhan, V. N.; Wendoloski, J. J. Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods. J. Phys. Chem. A 1998, 102, 3762-3772.
30. Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9997-10002.
31. Glick, M.; Klon, A. E.; Acklin, P.; Davies, J. W. Prioritization of high throughput screening data of compound mixtures using molecular similarity. Mol. Phys. 2003, 101, 1325-1328.
32. Glick, M.; Klon, A. E.; Acklin, P.; Davies, J. W. Enrichment of extremely noisy high-throughput screening data using a naive Bayes classifier. J. Biomol. Screening 2004, 9, 32-36.
33. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45, 4350-4358.
34. Comprehsive Medicinal Chemistry; MDL Information Systems: San Leandro, CA.
35. MDL Drug Data Report; MDL Information Systems: San Leandro, CA.