Physiochemical property space distribution among human metabolites, drugs and toxins

BMC Bioinformatics

Volumn 10, Issue SUPPL. 15, 2009, Pages

  Khanna, Varun ^a   Ranganathan, Shoba ^a,b  

^a MACQUARIE UNIVERSITY   (Australia)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; CHEMICAL COMPOUNDS; LIGANDS; MOLECULES; TOXIC MATERIALS; BIOINFORMATICS; FUNCTIONAL GROUPS; LEAD COMPOUNDS;

BIOCHEMICAL PROPERTIES; BIOPHYSICAL PROPERTIES; FUNCTIONAL GROUP ANALYSIS; HUMAN METABOLITES; MOLECULAR DESCRIPTORS; PHYSICOCHEMICAL CHARACTERISTICS; PHYSIO-CHEMICAL PROPERTIES; THERAPEUTIC APPLICATION; AS-LIGANDS; DATA SETS; DRUG MOLECULES; PHYSICOCHEMICAL PROPERTY; REDUCED TOXICITY; SEARCH SPACES; SMALL MOLECULES; SPACE DISTRIBUTION; TOXIC COMPOUNDS;

METABOLITES;

CARBON; NATURAL PRODUCT; NITROGEN; OXYGEN; TOXIN; DRUG;

ARTICLE; ARTIFICIAL NEURAL NETWORK; ATOMIC PARTICLE; BIOINFORMATICS; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CHIRALITY; DATA BASE; HYDROGEN BOND; LIPOPHILICITY; METABOLITE; METABOLOME; MOLECULAR WEIGHT; PHYSICAL CHEMISTRY; PROCESS OPTIMIZATION; SOLUBILITY; SUPPORT VECTOR MACHINE; SURFACE PROPERTY; BIOLOGY; CHEMISTRY; DRUG DESIGN; FACTUAL DATABASE; HUMAN; METABOLISM; METHODOLOGY; STRUCTURE ACTIVITY RELATION; TISSUE DISTRIBUTION;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DESIGN; HUMANS; METABOLOME; PHARMACEUTICAL PREPARATIONS; SOLUBILITY; STRUCTURE-ACTIVITY RELATIONSHIP; TISSUE DISTRIBUTION; TOXINS, BIOLOGICAL;

EID: 71549138352     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S15-S10     Document Type: Article

References (38)

1. Hodgson J. ADMET - turning chemicals into drugs. Nat Biotechnol 2001, 19(8):722-726. 10.1038/90761, 11479558.
2. Lipinski C, Hopkins A. Navigating chemical space for biology and medicine. Nature 2004, 432(7019):855-861. 10.1038/nature03193, 15602551.
3. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001, 46(1-3):3-26. 10.1016/S0169-409X(00)00129-0, 11259830.
4. Leeson PD, Davis AM. Time-related differences in the physical property profiles of oral drugs. J Med Chem 2004, 47(25):6338-6348. 10.1021/jm049717d, 15566303.
5. Frimurer TM, Bywater R, Naerum L, Lauritsen LN, Brunak S. Improving the odds in discriminating "drug-like" from "non drug-like" compounds. J Chem Inf Comput Sci 2000, 40(6):1315-1324.
6. Ajay A, Walters WP, Murcko MA. Can we learn to distinguish between "drug-like" and "nondrug-like" molecules?. J Med Chem 1998, 41(18):3314-3324. 10.1021/jm970666c, 9719583.
7. Sadowski J, Kubinyi H. A scoring scheme for discriminating between drugs and nondrugs. J Med Chem 1998, 41(18):3325-3329. 10.1021/jm9706776, 9719584.
8. Brustle M, Beck B, Schindler T, King W, Mitchell T, Clark T. Descriptors, physical properties, and drug-likeness. J Med Chem 2002, 45(16):3345-3355. 10.1021/jm011027b, 12139446.
9. Oprea TI. Property distribution of drug-related chemical databases. J Comput Aided Mol Des 1999, 14:251-264. 10.1023/A:1008130001697.
10. Congreve M, Carr R, Murray C, Jhoti H. A 'rule of three' for fragment-based lead discovery?. Drug Discov Today 2003, 8(19):876-877. 10.1016/S1359-6446(03)02831-9, 14554012.
11. Ertl P, Roggo S, Schuffenhauer A. Natural product-likeness score and its application for prioritization of compound libraries. J Chem Inf Model 2008, 48(1):68-74. 10.1021/ci700286x, 18034468.
12. Gupta S, Aires-de-Sousa J. Comparing the chemical spaces of metabolites and available chemicals: models of metabolite-likeness. Mol Divers 2007, 11(1):23-36. 10.1007/s11030-006-9054-0, 17447158.
13. Eckert H, Bajorath J. Exploring peptide-likeness of active molecules using 2D fingerprint methods. J Chem Inf Model 2007, 47(4):1366-1378. 10.1021/ci700086m, 17539624.
14. Oprea T. Cheminformatics and the quest for leads in drug discovery. Handbook of Chemoinformatics 2003, 1508-1531. Wiley-VCH, J Gasteiger, Weinheim.
15. Oprea TI. Current trends in lead discovery: are we looking for the appropriate properties?. J Comput Aided Mol Des 2002, 16(5-6):325-334. 10.1023/A:1020877402759, 12489682.
16. Oprea TI, Davis AM, Teague SJ, Leeson PD. Is there a difference between leads and drugs? A historical perspective. J Chem Inf Comput Sci 2001, 41(5):1308-1315.
17. Jorissen RN, Gilson MK. Virtual screening of molecular databases using a support vector machine. J Chem Inf Model 2005, 45(3):549-561. 10.1021/ci049641u, 15921445.
18. Henkel T, Brunne RM, Muller H, Reichel F. Statistical investigation into the structural complementarity of natural products and synthetic compounds. Angewandte Chemie-International Edition 1999, 38(5):643-647.
19. Stahura FL, Godden JW, Xue L, Bajorath J. Distinguishing between natural products and synthetic molecules by descriptor Shannon entropy analysis and binary QSAR calculations. J Chem Inf Comput Sci 2000, 40(5):1245-1252.
20. Feher M, Schmidt JM. Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry. J Chem Inf Comput Sci 2003, 43(1):218-227.
21. Lee ML, Schneider G. Scaffold architecture and pharmacophoric properties of natural products and trade drugs: application in the design of natural product-based combinatorial libraries. J Comb Chem 2001, 3(3):284-289. 10.1021/cc000097l, 11350252.
22. Hattori M, Okuno Y, Goto S, Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc 2003, 125(39):11853-11865. 10.1021/ja036030u, 14505407.
23. Nobeli I, Ponstingl H, Krissinel EB, Thornton JM. A structure-based anatomy of the E. coli metabolome. J Mol Biol 2003, 334(4):697-719. 10.1016/j.jmb.2003.10.008, 14636597.
24. Karakoc E, Sahinalp SC, Cherkasov A. Comparative QSAR- and fragments distribution analysis of drugs, druglikes, metabolic substances, and antimicrobial compounds. J Chem Inf Model 2006, 46(5):2167-2182. 10.1021/ci0601517, 16995747.
25. Dobson PD, Patel Y, Kell DB. 'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug libraries. Drug Discov Today 2009, 14(1-2):31-40. 10.1016/j.drudis.2008.10.011, 19049901.
26. Gleeson MP. Generation of a set of simple, interpretable ADMET rules of thumb. J Med Chem 2008, 51(4):817-834. 10.1021/jm701122q, 18232648.
27. Schuster D, Laggner C, Langer T. Why drugs fail--a study on side effects in new chemical entities. Curr Pharm Des 2005, 11(27):3545-3559. 10.2174/138161205774414510, 16248807.
28. Gut J, Bagatto D. Theragenomic knowledge management for individualised safety of drugs, chemicals, pollutants and dietary ingredients. Expert Opin Drug Metab Toxicol 2005, 1(3):537-554. 10.1517/17425255.1.3.537, 16863460.
29. Hansch C, Bjorkroth JP, Leo A. Hydrophobicity and central nervous system agents: on the principle of minimal hydrophobicity in drug design. J Pharm Sci 1987, 76(9):663-687. 10.1002/jps.2600760902, 11002801.
30. Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD. Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 2002, 45(12):2615-2623. 10.1021/jm020017n, 12036371.
31. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S. HMDB: the Human Metabolome Database. Nucleic Acids Res 2007, (35 Database):D521-526. 10.1093/nar/gkl923, 1899095, 17202168.
32. Wishart DS, Knox C, Guo AC, 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 Database):D668-672. 10.1093/nar/gkj067, 1347430, 16381955.
33. Shin JM, Cho DH. PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Res 2005, (33 Database):D238-241. 540013, 15608186.
34. Gold LS, Sawyer CB, Magaw R, Backman GM, de Veciana M, Levinson R, Hooper NK, Havender WR, Bernstein L, Peto R. A carcinogenic potency database of the standardized results of animal bioassays. Environ Health Perspect 1984, 58:9-319. 10.2307/3429857, 1569423, 6525996.
35. SciTegic Pipeline Pilot. Accelrys, Inc., San Diego, CA, USA., http://accelrys.com/products/scitegic/
36. Zhou D, Alelyunas Y, Liu R. Scores of extended connectivity fingerprint as descriptors in QSPR study of melting point and aqueous solubility. J Chem Inf Model 2008, 48(5):981-987. 10.1021/ci800024c, 18465850.
37. Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org Biomol Chem 2004, 2(22):3256-3266. 10.1039/b409865j, 15534703.
38. Ghose AK, Crippen GM. Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions. J Chem Inf Comput Sci 1987, 27(1):21-35.