Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines

Journal of Cheminformatics

Volumn 5, Issue 1, 2013, Pages

  Tian, Sheng ^a   Li, Youyong ^a   Wang, Junmei ^b   Xu, Xiaojie ^c   Xu, Lei ^a   Wang, Xiaohong ^a   Chen, Lei ^a   Hou, Tingjun ^a  

^a SOOCHOW UNIVERSITY   (China)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c PEKING UNIVERSITY   (China)

Author keywords

Drug likeness; Murcko frameworks; Scaffold; Scaffold tree; Traditional Chinese medicines; Tree maps

Indexed keywords

EID: 84876731496     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-5-5     Document Type: Article

References (32)

1. Lawrence RN: Rediscovering natural product biodiversity. Drug Discov Today 1999, 4:449-451. (Pubitemid 29460836)
2. Newman DJ, Cragg GM, Snader KM: Natural products as sources of new drugs over the period 1981-2002. J Nat Prod 2003, 66:1022-1037. (Pubitemid 36909859)
3. Boldi AM: Libraries from natural product-like scaffolds. Curr Opin Chem Biol 2004, 8:281-286. (Pubitemid 38759403)
4. Wetzel S, Schuffenhauer A, Roggo S, Ertl P, Waldmann H: Cheminformatic analysis of natural products and their chemical space. Chimia 2007, 61:355-360.
5. Newman DJ, Cragg GM: Natural products as sources of new drugs over the last 25 years. J Nat Prod 2007, 70:461-477. (Pubitemid 46595760)
6. Breinbauer R, Manger M, Scheck M, Waldmann H: Natural product guided compound library development. Curr Med Chem 2002, 9:2129-2145. (Pubitemid 35331917)
7. Grabowski K, Schneider G: Properties and architecture of drugs and natural products revisited. Current Chemical Biology 2007, 1:115-127.
8. Krier M, Bret G, Rognan D: Assessing the scaffold diversity of screening libraries. J Chem Inf Model 2006, 46:512-524.
9. 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, 3:284-289. (Pubitemid 33616450)
10. Evans BE, Rittle KE, Bock MG, Dipardo RM, Freidinger RM, Whitter WL, Lundell GF, Veber DF, Anderson PS, Chang RSL, Lotti VJ, Cerino DJ, Chen TB, Kling PJ, Kunkel KA, Springer JP, Hirshfield J: Methods for drug discovery - development of potent, selective, orally effective cholecystokinin antagonists. J Med Chem 1988, 31:2235-2246. (Pubitemid 19001640)
11. Ertl P, Jelfs S, Muhlbacher J, Schuffenhauer A, Selzer P: Quest for the rings. In silico exploration of ring universe to identify novel bioactive heteroaromatic scaffolds. J Med Chem 2006, 49:4568-4573. (Pubitemid 44162682)
12. Bohm HJ, Flohr A, Stahl M: Scaffold hopping. Drug discov today: Technologies 2004, 1:217-224.
13. Bemis GW, Murcko MA: The properties of known drugs.1. Molecular frameworks. J Med Chem 1996, 39:2887-2893. (Pubitemid 26251026)
14. Bemis GW, Murcko MA: Properties of known drugs. 2. Side chains. J Med Chem 1999, 42:5095-5099. (Pubitemid 30020260)
15. Broughton HB, Watson IA: Selection of heterocycles for drug design. J Mol Graph Model 2004, 23:51-58. (Pubitemid 39141245)
16. Koch MA, Schuffenhauer A, Scheck M, Wetzel S, Casaulta M, Odermatt A, Ertl P, Waldmann H: Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc Natl Acad Sci USA 2005, 102:17272-17277. (Pubitemid 41740856)
17. Lipkus AH: Exploring chemical rings in a simple topological-descriptor space. J Chem Inf Comput Sci 2001, 41:430-438. (Pubitemid 32408661)
18. Schuffenhauer A, Ertl P, Roggo S, Wetzel S, Koch MA, Waldmann H: The scaffold tree - Visualization of the scaffold universe by hierarchical scaffold classification. J Chem Inf Model 2007, 47:47-58. (Pubitemid 46225559)
19. Agrafiotis DK, Wiener JJM: Scaffold explorer: an interactive tool for organizing and mining structure-activity data spanning multiple chemotypes. J Med Chem 2010, 53:5002-5011.
20. Wetzel S, Klein K, Renner S, Rauh D, Oprea TI, Mutzel P, Waldmann H: Interactive exploration of chemical space with Scaffold Hunter. Nat Chem Biol 2009, 5:581-583.
21. Wang J, Hou T: Drug and drug candidate building block analysis. J Med Chem 2009, 50:55-67.
22. Qiao XB, Hou TJ, Zhang W, Guo SL, Xu SJ: A 3D structure database of components from Chinese traditional medicinal herbs. J Chem Inf Comput Sci 2002, 42:481-489. (Pubitemid 35355253)
23. Wipke WT, Dyott TM: Use of ring assemblies in a ring perception algorithm. J Chem Inf Comput Sci 1975, 15:140-147.
24. Hou TJ, Qiao XB, Xu XJ: Research and development of 3D molecular structure database of traditional Chinese drugs. Acta Chimica Sinica 2001, 59:1788-1792.
25. Hou TJ, Li YY, Zhang W, Wang JM: Recent Developments of In Silico predictions of intestinal absorption and oral bioavailability. Comb Chem High Throughput Screen 2009, 12:497-506.
26. Hou TJ, Wang JM, Zhang W, Wang W, Xu X: Recent advances in computational prediction of drug absorption and permeability in drug discovery. Curr Med Chem 2006, 13:2653-2667. (Pubitemid 44364143)
27. Shen M, Tian S, Li Y, Li Q, Xu X, Wang J, Hou T: Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines. J Cheminform 2012, 4:31.
28. Langdon SR, Brown N, Blagg J: Scaffold diversity of exemplified medicinal chemistry space. J Chem Inf Model 2011, 51:2174-2185.
29. Sato Y, Hotta N, Sakamoto N, Matsuoka S, Ohishi N, Yagi K: Lipid peroxide level in plasma of diabetic-patients. Biochem Med 1979, 21:104-107. (Pubitemid 9190794)
30. Shneiderman B: Tree Visualization with Tree-Maps - 2-D Space-Filling Approach. Acm Transactions on Graphics 1992, 11:92-99.
31. Nishimura C, Kuriyama K: Alteration of lipid peroxide and endogenous antioxidant contents in retina of Streptozotocin-induced diabetic rats - effect of vitamin - a administration. Jpn J Pharmacol 1985, 37:365-372. (Pubitemid 15107907)
32. Rogers D, Brown RD, Hahn M: Using extended-connectivity fingerprints with Laplacian-modified Bayesian analysis in high-throughput screening follow-up. J Biomol Screen 2005, 10:682-686. (Pubitemid 41476802)