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 shu

Characterization and Comparative Analysis of Chemical Libraries for Drug Discovery

1.
1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China;
2. Center for Theoretical Biology, Peking University, Beijing, 100871, P. R. China;
3. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences-Peking Union Medical College, Beijing 100094, P. R. China

Received Date: 2 July 2012
Available Online: 24 August 2012
Fund Project: 国家高技术研究发展计划(863)(2012AA020308) (863)(2012AA020308)国家自然科学基金(20972010)资助项目 (20972010)

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.
- Virtual screening,
- Chemical library,
- Molecular diversity,
- Chemical space,
- Molecular scaffold
1. [1]
  
  (1) Shoichet, B. K. Nature 2004, 432 (7019), 862. doi: 10.1038/nature03197
2. [2]
  (2) Jorgensen,W. L. Science 2004, 303 (5665), 1813. doi: 10.1126/science.1096361
3. [3]
  (3) Böhm, H. J.; Schneider, G. Virtual Screening for Bioactive Molecules;Wiley-VCH:Weinheim, 2000; pp 1-14.
4. [4]
  (4) Schneider, G. Nat. Rev. Drug Discov. 2010, 9 (4), 273. doi: 10.1038/nrd3139
5. [5]
  (5) Dobson, C. M. Nature 2004, 432 (7019), 824. doi: 10.1038/nature03192
6. [6]
  (6) Khanna, V.; Ranganathan, S. J. Cheminformatics 2011, 3, 30.doi: 10.1186/1758-2946-3-30
7. [7]
  (7) Bemis, G.W.; Murcko, M. A. J. Med. Chem. 1996, 39 (15),2887. doi: 10.1021/jm9602928
8. [8]
  (8) Dobson, P. D.; Patel, Y.; Kell, D. B. Drug Discov. Today 2009,14 (1-2), 31.
9. [9]
  (9) Feher, M.; Schmidt, J. M. J. Chem. Inf. Comp. Sci. 2002, 43 (1),218.
10. [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]
  (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]
  (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]
  (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]
  (14) http://thomsonreuters.com/products_services/science/science_products/a-z/world_drug_i ndex/.(accessed June 30,2012)
15. [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]
  (16) http://www.inno-chem.com.cn/maybridge/ (accessed June 30,2012).
17. [17]
  (17) http://us.chemdiv.com/index.php/discovery-tools-chemistry/screening-libraries (accessed June 30, 2012).
18. [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]
  (19) Rogers, D.; Hahn, M. J. Chem. Inf. Model. 2010, 50 (5), 742.doi: 10.1021/ci100050t
20. [20]
  (20) Team, R. D. C. R: A Language and Environment for StatisticalComputing, In: Computing RFfS; Viena: Austria, 2008; pp100-121.
21. [21]
  (21) Sarkar, D. Lattice: Multivariate Data Visualization with R;Springer: Heidelberg, 2008; p 1
22. [22]
  (22) Ertl, P.; Rohde, B.; Selzer, P. J. Med. Chem. 2000, 43 (20),3714. doi: 10.1021/jm000942e
23. [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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