Computational identification of bioactive natural products by structure activity relationship

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 1, 2010, Pages 38-45

  Zhou, Xi ^a   Li, Yongquan ^a   Chen, Xin ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Bioactive natural compound likeness; Drug likeness; Natural product; Statistical learning; Structural activity relationship

Indexed keywords

DRUG-LIKENESS; NATURAL COMPOUNDS; NATURAL PRODUCTS; STATISTICAL LEARNING; STRUCTURAL ACTIVITY RELATIONSHIP;

DRUG PRODUCTS;

NATURAL PRODUCT;

APIALES; ARALIACEAE; ARTICLE; CAPRIFOLIACEAE; HERB; IRIDACEAE; LEGUME; MAGNOLIACEAE; NONHUMAN; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; STRUCTURE ACTIVITY RELATION; TRADITIONAL MEDICINE; VALIDATION PROCESS;

BIOLOGICAL PRODUCTS; COMPUTER SIMULATION; DRUG DESIGN; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; ROC CURVE; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77955772600     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.04.007     Document Type: Article

References (60)

1. Strohl W.R. The role of natural products in a modern drug discovery program. Drug Discov. Today 2000, 5:39-41.
2. Sutter M.C., Wang Y.X. Recent cardiovascular drugs from Chinese medicinal plants. Cardiovasc. Res. 1993, 27:1891-1901.
3. Zhu D.Y.B.D.L., Tang X.C. Recent studies on traditional Chinese medicinal plants. Drug Dev. Res. 1996, 39:147-157.
4. Li F., Sun S., Wang J., Wang D. Chromatography of medicinal plants and Chinese traditional medicines. Biomed. Chromatogr. 1998, 12:78-85.
5. Gong X., Sucher N.J. Stroke therapy in traditional Chinese medicine (TCM): prospects for drug discovery and development. Trends Pharmacol. Sci. 1999, 20:191-196.
6. Lee K.H. Novel antitumor agents from higher plants. Med. Res. Rev. 1999, 19:569-596.
7. Evans F.J. Natural products as probes for new drug target identification. J. Ethnopharmacol. 1991, 32:91-101.
8. Chaudhury R. Herbal Medicine for Human Health 1992, WHO Regional Office for South-East Asia.
9. Chan K. Progress in traditional Chinese medicine. Trends Pharmacol. Sci. 1995, 16:182-187.
10. Henkel J. Attacking AIDS with a 'cocktail' therapy?. FDA Consum. 1999, 33:12-17.
11. Feliu J., Sereno M., Castro J.D., Belda C., Casado E., Gonzalez-Baron M. Chemotherapy for colorectal cancer in the elderly: whom to treat and what to use. Cancer Treat. Rev. 2009, 35:246-254.
12. Borisy A.A., Elliott P.J., Hurst N.W., Lee M.S., Lehar J., Price E.R., et al. Systematic discovery of multicomponent therapeutics. Proc. Natl. Acad. Sci. USA 2003, 100:7977-7982.
13. Xue T., Roy R. Studying traditional Chinese medicine. Science 2003, 300:740-741.
14. Oka H., Yamamoto S., Kuroki T., Harihara S., Marumo T., Kim S.R., et al. Prospective study of chemoprevention of hepatocellular carcinoma with Sho-saiko-to (TJ-9). Cancer 1995, 76:743-749.
15. Sheehan-Dare R., Cotterill J. Experience with the Hexascan in argon laser treatment of vascular skin lesions. Br. J. Dermatol. 1992, 127:33-34.
16. Sheehan M.P., Rustin M.H., Atherton D.J., Buckley C., Harris D.W., Brostoff J., et al. Efficacy of traditional Chinese herbal therapy in adult atopic dermatitis. Lancet 1992, 340:13-17.
17. Sengupta S., Toh S.A., Sellers L.A., Skepper J.N., Koolwijk P., Leung H.W., et al. Modulating angiogenesis: the yin and the yang in ginseng. Circulation 2004, 110:1219-1225.
18. Wang L., Zhou G.B., Liu P., Song J.H., Liang Y., Yan X.J., et al. Dissection of mechanisms of Chinese medicinal formula Realgar-Indigo naturalis as an effective treatment for promyelocytic leukemia. Proc. Natl. Acad. Sci. USA 2008, 105:4826-4831.
19. Balandrin M.F.K.A.D., Farnsworth N.R. In Human Medicinal Agents from Plants 1993, American Chemical Society, Washington, DC.
20. Butler M.S. The role of natural product chemistry in drug discovery. J. Nat. Prod. 2004, 67:2141-2153.
21. Singh B., Kaur P., Gopichand, Singh R.D., Ahuja P.S. Biology and chemistry of Ginkgo biloba. Fitoterapia 2008, 79:401-418.
22. Vistoli G., Pedretti A., Testa B. Assessing drug-likeness - what are we missing?. Drug Discov Today 2008, 13:285-294.
23. Brown R.D., Hassan M., Waldman M. Combinatorial library design for diversity, cost efficiency, and drug-like character. J. Mol. Graph. Model 2000, 18. 427-437, 537.
24. Lipinski C.A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 2000, 44:235-249.
25. Li Q., Bender A., Pei J., Lai L. A large descriptor set and a probabilistic kernel-based classifier significantly improve druglikeness classification. J. Chem. Inf. Model 2007, 47:1776-1786.
26. Schneider N., Jackels C., Andres C., Hutter M.C. Gradual in silico filtering for druglike substances. J. Chem. Inf. Model 2008, 48:613-628.
27. Koch M.A., Schuffenhauer A., Scheck M., Wetzel S., Casaulta M., Odermatt A., et al. Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc. Natl. Acad. Sci. USA 2005, 102:17272-17277.
28. Henkel T., Brunne R., Müller H., Reichel F. Statistical investigation into the structural complementarity of natural products and synthetic compounds. Angew. Chem. Int. Ed. 1999, 38:643-647.
29. Feher M., Schmidt J.M. Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry. J. Chem. Inf. Comput. Sci. 2003, 43:218-227.
30. Singh N., Guha R., Giulianotti M.A., Pinilla C., Houghten R.A., Medina-Franco J.L. Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository. J. Chem. Inf. Model 2009, 49:1010-1024.
31. Lee M.L., 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, 3:284-289.
32. Stahura F.L., Godden J.W., 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, 40:1245-1252.
33. Ertl P., Roggo S., Schuffenhauer A. Natural product-likeness score and its application for prioritization of compound libraries. J. Chem. Inf. Model 2008, 48:68-74.
34. J. Duke, Dr. Duke's Phytochemical and Ethnobotanical Databases, 2006, (accessed October 1, 2009). http://www.ars-grin.gov/duke/.
35. Cragg G.M., Boyd M.R., Hallock Y.F., Newman D.J., Sausville E.A., Wolpert M.K. Natural products drug discovery at the national cancer institute. Past achievements and new defections for the new millennium. Biodiversity: New Leads for the Pharmaceutical and Agrochemical Industries 2000, 22-45. RSC Publishing, Cambridge UK. K.W. Stephen, A.H. Martin, T. Robert, J.T.C. Ewan, N. Neville (Eds.).
36. M.C. Nicklaus, Technical Notes of Structure Files of NCI Open Database Compounds, September 2003 SD File of Combined DTP Releases, 2007, (accessed September 23, 2009). http://129.43.27.140/ncidb2/download-notes_2003-09.htm.
37. DRAGON, version 5.4, Talete srl, Milano, Italy, 2007.
38. Winters-Hilt S., Yelundur A., McChesney C., Landry M. Support vector machine implementations for classification & clustering. BMC Bioinformatics 2006, 7(Suppl. 2):S4.
39. Quinlan J. C4.5: Programs for Machine Learning 2003, Morgan Kaufmann.
40. World Drug Index (WDI), Derwent Information, London, 2007.
41. Hanley J.A., McNeil B.J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982, 143:29-36.
42. Bradley A.P. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognit. 1997, 30:1145-1159.
43. Sadowski J., Kubinyi H. A scoring scheme for discriminating between drugs and nondrugs. J. Med. Chem. 1998, 41:3325-3329.
44. Available Chemicals Directory (ACD), Molecular Design Limited, Calif, 2007.
45. Lloyd S. Least squares quantization in PCM. IEEE Trans. Inf. Theory 1982, 28:129-137.
46. Jia J., Zhu F., Ma X., Cao Z., Li Y., Chen Y.Z. Mechanisms of drug combinations: interaction and network perspectives. Nat. Rev. Drug Discov. 2009, 8:111-128.
47. Chen Y.Z., Zhi D.G. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 2001, 43:217-226.
48. Chen X., Ung C.Y., Chen Y. Can an in silico drug-target search method be used to probe potential mechanisms of medicinal plant ingredients?. Nat. Prod. Rep. 2003, 20:432-444.
49. Chen X., Ji Z.L., Chen Y.Z. TTD: therapeutic target database. Nucleic Acids Res. 2002, 30:412-415.
50. Sun L.Z., Ji Z.L., Chen X., Wang J.F., Chen Y.Z. ADME-AP: a database of ADME associated proteins. Bioinformatics 2002, 18:1699-1700.
51. Ji Z.L., Han L.Y., Yap C.W., Sun L.Z., Chen X., Chen Y.Z. Drug adverse reaction target database (DART): proteins related to adverse drug reactions. Drug Saf. 2003, 26:685-690.
52. Yue Q.X., Cao Z.W., Guan S.H., Liu X.H., Tao L., Wu W.Y., et al. Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Mol. Cell. Proteomics 2008, 7:949-961.
53. Classen-Houben D., Schuster D., Da Cunha T., Odermatt A., Wolber G., Jordis U., et al. Selective inhibition of 11beta-hydroxysteroid dehydrogenase 1 by 18alpha-glycyrrhetinic acid but not 18beta-glycyrrhetinic acid. J. Steroid Biochem. Mol. Biol. 2009, 113:248-252.
54. Kavitha A., Prabhakar P., Narasimhulu M., Vijayalakshmi M., Venkateswarlu Y., Venkateswarlu Rao K., et al. Isolation, characterization and biological evaluation of bioactive metabolites from Nocardia levis MK-VL_113. Microbiol. Res. 2010, 165:199-210.
55. Julsing M.K., Koulman A., Woerdenbag H.J., Quax W.J., Kayser O. Combinatorial biosynthesis of medicinal plant secondary metabolites. Biomol. Eng. 2006, 23:265-279.
56. Guengerich F.P. Cytochrome P450s and other enzymes in drug metabolism and toxicity. AAPS J. 2006, 8:E101-E111.
57. Handbook of Molecular Descriptors 2000, Wiley-VCH, Weinheim. R.V. Todeschini, Consonni (Eds.).
58. Yap C.W., Li H., Ji Z.L., Chen Y.Z. Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties. Mini Rev. Med. Chem. 2007, 7:1097-1107.
59. Vieth M., Siegel M.G., Higgs R.E., Watson I.A., Robertson D.H., Savin K.A., et al. Characteristic physical properties and structural fragments of marketed oral drugs. J. Med. Chem. 2004, 47:224-232.
60. Wishart D.S., Knox C., Guo A.C., Cheng D., Shrivastava S., Tzur D., et al. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008, 36:D901-D906.