Citation: DING Xin-Qiang, WU Zhi-Yin, JIN Hong-Wei, LIU Zhen-Ming. Characterization and Comparative Analysis of Chemical Libraries for Drug Discovery[J]. Acta Physico-Chimica Sinica, ;2012, 28(10): 2401-2410. doi: 10.3866/PKU.WHXB201208241
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With the development of computer technology and software for molecular modeling, virtual screening plays an important role in drug discovery. In the flow of virtual screening, high quality compound libraries used are essential for success. In this paper, we analyzed two known drug libraries, a natural product library, compounds from plants used for traditional Chinese medicines (TCM), two frequently used commercial libraries, and a compound library in home. Features of these libraries were extracted and compared for molecular diversity, chemical space, and molecular scaffolds. We found similarities between drugs and the compounds used for TCM, which indicates TCM could be useful for virtual screening. These results aid understand of the chemical characteristics used in virtual screening libraries.
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-
[1]
(1) Shoichet, B. K. Nature 2004, 432 (7019), 862. doi: 10.1038/nature03197
-
[2]
(2) Jorgensen,W. L. Science 2004, 303 (5665), 1813. doi: 10.1126/science.1096361
-
[3]
(3) Böhm, H. J.; Schneider, G. Virtual Screening for Bioactive Molecules;Wiley-VCH:Weinheim, 2000; pp 1-14.
-
[4]
(4) Schneider, G. Nat. Rev. Drug Discov. 2010, 9 (4), 273. doi: 10.1038/nrd3139
-
[5]
(5) Dobson, C. M. Nature 2004, 432 (7019), 824. doi: 10.1038/nature03192
-
[6]
(6) Khanna, V.; Ranganathan, S. J. Cheminformatics 2011, 3, 30.doi: 10.1186/1758-2946-3-30
-
[7]
(7) Bemis, G.W.; Murcko, M. A. J. Med. Chem. 1996, 39 (15),2887. doi: 10.1021/jm9602928
-
[8]
(8) Dobson, P. D.; Patel, Y.; Kell, D. B. Drug Discov. Today 2009,14 (1-2), 31.
-
[9]
(9) Feher, M.; Schmidt, J. M. J. Chem. Inf. Comp. Sci. 2002, 43 (1),218.
-
[10]
(10) Singh, N.; Guha, R.; Giulianotti, M. A.; Pinilla, C.; Houghten,R. A.; Medina-Franco, J. L. J. Chem. Inf. Model. 2009, 49 (4),1010. doi: 10.1021/ci800426u
-
[11]
(11) Knox, C.; Law, V.; Jewison, T.; Liu, P.; Ly, S.; Frolkis, A.; Pon,A.; Banco, K.; Mak, C.; Neveu, V.; Djoumbou, Y.; Eisner, R.;Guo, A. C.;Wishart, D. S. Nucleic Acids Res. 2011, 39 (Database issue), D1035.
-
[12]
(12) Wishart, D. S.; Knox, C.; Guo, A. C.; Cheng, D.; Shrivastava,S.; Tzur, D.; Gautam, B.; Hassanali, M. Nucleic Acids Res.2008, 36 (Database issue), D901.
-
[13]
(13) Wishart, D. S.; Knox, C.; Guo, A. C.; Shrivastava, S.; Hassanali,M.; Stothard, P.; Chang, Z.;Woolsey, J. Nucleic Acids Res.2006, 34 (Database issue), D668.
-
[14]
(14) http://thomsonreuters.com/products_services/science/science_products/a-z/world_drug_i ndex/.(accessed June 30,2012)
-
[15]
(15) Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.;Coleman, R. G. J. Chem. Inf. Model. 2012, 52 (7), 1757. doi: 10.1021/ci3001277
-
[16]
(16) http://www.inno-chem.com.cn/maybridge/ (accessed June 30,2012).
-
[17]
(17) http://us.chemdiv.com/index.php/discovery-tools-chemistry/screening-libraries (accessed June 30, 2012).
-
[18]
(18) Zhou, J. J.; Xie, G. R.; Yan, X. J. Traditional Chinese Medicines: Molecular Structures, Natural Sources and Applications;Chemistry Industry Press: Beijing, 2004. [周家驹, 谢桂荣, 严新建. 中药原植物化学成分手册. 北京: 化学工业出版社, 2004.]
-
[19]
(19) Rogers, D.; Hahn, M. J. Chem. Inf. Model. 2010, 50 (5), 742.doi: 10.1021/ci100050t
-
[20]
(20) Team, R. D. C. R: A Language and Environment for StatisticalComputing, In: Computing RFfS; Viena: Austria, 2008; pp100-121.
-
[21]
(21) Sarkar, D. Lattice: Multivariate Data Visualization with R;Springer: Heidelberg, 2008; p 1
-
[22]
(22) Ertl, P.; Rohde, B.; Selzer, P. J. Med. Chem. 2000, 43 (20),3714. doi: 10.1021/jm000942e
-
[23]
(23) Ghose, A. K.; Crippen, G. M. J. Comput. Chem. 1986, 7 (4),565. doi: 10.1002/(ISSN)1096-987X
-
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