Citation: HU Yan-Bao, PENG Jing-Bo, GU Shuo, PEI Jian-Feng, ZOU Zhong-Mei. Molecular Docking in Xin-Ke-Shu Preparation's Multi-Target Effect on Coronary Heart Disease[J]. Acta Physico-Chimica Sinica, ;2012, 28(05): 1257-1264. doi: 10.3866/PKU.WHXB201202212 shu

Molecular Docking in Xin-Ke-Shu Preparation's Multi-Target Effect on Coronary Heart Disease

1.
1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China;
2. Center for Theoretical Biology, Peking University, Beijing 100871, P. R. China

Received Date: 22 November 2011
Available Online: 21 February 2012
Fund Project: 国家自然科学基金(81073021) (81073021)科技重大专项(2009ZX09501-002, 2012ZX09301002-001)资助项目 (2009ZX09501-002, 2012ZX09301002-001)

Xin-Ke-Shu (XKS), a traditional Chinese medicine (TCM) preparation, has been widely used for treatment of coronary heart disease (CHD) in China. However, the active constituents of XKS and their interactions with targets remain unclear. In this study, we assessed two docking programs, LibDock and AutoDock, by calculating the root-mean-square deviation (RMSD) of X-ray structure reproduction and the enrichment factor (EF) in virtual screening; both proved to be practical in our protein-ligand complex systems. Moreover, the combined use of the two programs yielded better EFs for each target. We therefore used a combination of the two programs to investigate the interactions of the 51 chemical constituents identified from XKS with five CHD targets, namely peroxisome proliferator activated receptor γ (PPAR-γ), angiotensin-converting enzyme (ACE), hydroxymethylglutaryl coenzyme A receptor (HMGR), cyclooxygenase-2 (COX2), and thrombin. The docking results suggest that pueroside A, pueroside B, salvianolic acid A, and salvianolic acid C can interact with two or more targets, and the other eight compounds may be potent for at least one of the five targets. In this research, we propose a strategy for studying TCM preparations, and suggest that XKS has a multi-target effect on CHD.
- Docking,
- Xin-Ke-Shu,
- Traditional Chinese medicine,
- Coronary heart disease,
- Multi-target effect,
- Enrichment factor
1. [1]
  (1) Mozaffarian, D.; Micha, R.;Wallace, S. PLoS Med. 2010, 7 (3), e1000252.
2. [2]
  (2) Zhang, X. H.; Lu, Z. L.; Liu, L. Heart (London, U. K.) 2008, 94, 1126.
3. [3]
  (3) Liu,W. D.; Yuan, Q. Shaanxi Journal of Traditional Chinese Medicine 2007, 28, 1527. [刘卫东, 袁琦. 陕西中医, 2007, 28, 1527.]
4. [4]
  (4) Zhang, Q.; Yu, X. H.; Sun, N. L. Chinese Journal of Practical Internal Medicine 2007, 27, 1301. [张前, 于晓红, 孙宁玲. 中国实用内科杂志, 2007, 27, 1301.]
5. [5]
  (5) Ji, B. Z.; Zhang, J. H.; Ji, J. J. Shandong Journal of Traditional Chinese Medicine 2005, 24, 150. [纪宝佐, 张经华, 纪军军. 山东中医杂志, 2005, 24, 150.]
6. [6]
  (6) Zhao, Z. M.; Zhao,W.W. Traditional Chinese Drug Research & Clinical Pharmacology 2005, 16, 106. [赵自明, 赵玮玮. 中药新药与临床药理, 2005, 16, 106.]
7. [7]
  (7) Lu, J. P.; Ouyang, J. P. Liaoning Journal of Traditional Chinese Medicine 2002, 29, 302. [卢金萍, 欧阳静萍. 辽宁中医杂志, 2002, 29, 302.]
8. [8]
  (8) Lu, J. P.; Ouyang, J. P. Medical Journal of Wuhan University 2003, 24, 254. [卢金萍, 欧阳静萍. 武汉大学学报(医学版), 2003, 24, 254.]
9. [9]
  (9) Zeng, M. G.; Chen, L.W.; Zheng, C. S.; Du, J. Chinese Journal of New Drugs and Clinical Remedies 2007, 26, 892. [曾茂贵, 陈立武, 郑春松, 杜建. 中国新药与临床杂志, 2007, 26, 892.]
10. [10]
  (10) Zheng, C. S.; Chen, L.W.; Du, J.; Ye, H. Z. Chinese Journal of Clinical Pharmacology and Therapeutics 2007, 12, 892. [郑春松, 陈立武, 杜建, 叶蕻芝. 中国临床药理学与治疗学, 2007, 12, 892.]
11. [11]
  (11) Ma, S. T.; Liu, P. X.; Long,W.; Yu, J.; Xu, Y. Acta Phys. -Chim. Sin. 2009, 25, 2080. [马世堂, 刘培勋, 龙伟, 禹洁, 徐阳. 物理化学学报, 2009, 25, 2080.]
12. [12]
  (12) Huang, Q.; Qiao, X. B.; Xu, X. J. Bioorg. Med. Chem. Lett. 2007, 17, 1779.
13. [13]
  (13) Gu, J. Y.; Yuan, G.; Zhu, Y. H.; Xu, X. J. Sciencein China Series B: Chemistry 2009, 39, 1415. [古江勇, 袁谷, 朱永宏, 徐筱杰. 中国科学B 辑: 化学, 2009, 39, 1415.]
14. [14]
  (14) Zheng, C. S.; Huang, Q.; Li, X. D.; Liu, X. X.; Xu, X. J. Comput. Appl. Chem. 2009, 26, 9. [郑春松, 黄钦, 李旭东, 刘献祥, 徐筱杰. 计算机与应用化学, 2009, 26, 9.]
15. [15]
  (15) Li, H. L.; Gao, Z. T.; Kang, L.; Zhang, H. L.; Yang, K.; Yu, K. Q.; Luo, X. M.; Zhu,W. L.; Chen, K. X.; Shen, J. H.;Wang, X. C.; Jiang, H. L. Nucleic Acids Res. 2006, 34 (Suppl.2),W219.
16. [16]
  (16) Zhang, S. D.; Lu,W. Q.; Liu, X. F.; Diao, Y. Y.; Bai, F.;Wang, L. Y.; Shan, L.; Huang, J.; Li, H. L.; Zhang,W. D. Med. Chem. Commun. 2011, 2, 471.
17. [17]
  (17) Warren, G. L.; Andrews, C.W.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.;Wall, I. D.;Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912.
18. [18]
  (18) Diller, D. J.; Merz, K. M., Jr. Proteins: Struct. Funct. Genet. 2001, 43, 113.
19. [19]
  (19) Morris, G. M.; Huey, R.; Lindstrom,W.; Sanner, M. F.; Belew, R. K.; odsell, D. S.; Olson, A. J. J. Comput. Chem. 2009, 30, 2785.
20. [20]
  (20) Chen, R. J.; Chung, T. Y.; Li, F. Y.; Yang,W. H.; Jinn, T. R.; Tzen, J. T. Acta Pharmacol. Sin. 2010, 31, 696.
21. [21]
  (21) Chen, R. J.; Chung, T. Y.; Li, F. Y.; Lin, N. H.; Tzen, J. T. Acta Pharmacol. Sin. 2009, 30, 61.
22. [22]
  (22) Khan, I.; Nisar, M.; Ebad, F.; Nadeem, S.; Saeed, M.; Khan, H.; Samiullah; Khuda, F.; Karim, N.; Ahmad, Z. J. Ethnopharmacol. 2009, 121, 175.
23. [23]
  (23) Konkimalla, V. B.; Efferth, T. Biochem. Pharmacol. 2010, 80, 39.
24. [24]
  (24) Smellie, A.; Teig, S. L.; Towbin, P. J. Comput. Chem. 1995, 16, 171.
25. [25]
  (25) odford, P. J. J. Med. Chem. 1985, 28, 849.
26. [26]
  (26) Morris, G. M.; odsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19, 1639.
27. [27]
  (27) Accelrys Software Inc. Discovery Studio Modeling Environment, Release 2.5.5; Accelrys Software Inc.: San Die , USA, 2010.
28. [28]
  (28) Morris, G. M.; Huey, R.; Lindstrom,W.; et al . AutoDock, Release 4.2.3; The Scripps Research Institute: La Jolla, USA, 2010.
29. [29]
  (29) Peng, J. B.; Jia, H. M.; Liu, Y. T.; Zhang, H.W.; Dong, S.; Zou, Z. M. J. Pharm. Biomed. Anal. 2011, 55, 984.
30. [30]
  (30) CambridgeSoft Corp. ChemDraw Ultra 8.0, Version 8.0; CambridgeSoft Corp.: Cambridge, USA, 2003.
31. [31]
  (31) CambridgeSoft Corp. Chem3D Ultra 8.0, Version 8.0; CambridgeSoft Corp.: Cambridge, USA, 2003.
32. [32]
  (32) Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127.
33. [33]
  (33) Berman, H. M.;Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.;Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235.
34. [34]
  (34) Bekhit, A. A.; Fahmy, H. T. Y.; Rostom, S. A. F.; Bekhit, A. E. A. Eur. J. Med. Chem. 2010, 45, 6027.
35. [35]
  (35) Ghodsi, R.; Zarghi, A.; Daraei, B.; Hedayati, M. Bioorg. Med. Chem. 2010, 18, 1029.
36. [36]
  (36) El-Sayed, M. A. A.; Abdel-Aziz, N. I.; Abdel-Aziz, A. A. M.; El-Azab, A. S.; Asiri, Y. A.; El-Tahir, K. E. H. Bioorg. Med. Chem. 2011, 19, 3416.
37. [37]
  (37) Wu, D. H.; Xu, X. J. Acta Phys. -Chim. Sin. 2009, 25, 446. [吴钉红, 徐筱杰. 物理化学学报, 2009, 25, 446.]
38. [38]
  (38) hlke, H.; Hendlich, M.; Klebe, G. J. Mol. Biol. 2000, 295, 231.
39. [39]
  (39) Huang, N.; Shoichet, B. K.; Irwin, J. J. J. Med. Chem. 2006, 49, 6789.
40. [40]
  (40) DUD-A Directory of Useful Decoys. http://dud.docking.org/; accessed May 24, 2011.
41. [41]
  (41) Gai,W.; Zhang, Y. L.; Ai, L.; Qiao, Y. J. Chin. J. Nat. Med. 2010, 8, 51. [盖伟, 张燕玲, 艾路, 乔延江. 中国天然药物, 2010, 8, 51.]
42. [42]
  (42) Hilpert, K.; Ackermann, J.; Banner, D.W.; Gast, A.; Gubernator, K.; Hadváry, P.; Labler, L.; Müller, K.; Schmid, G.; Tschopp, T. B.; van deWaterbeemd, H. J. Med. Chem. 1994, 37, 3889.
43. [43]
  (43) Delano,W. L. The PyMOL Molecular Graphics System, Version 1.3; Schrödinger, LLC: New York, USA, 2010.
44. [44]
  (44) Fan, H. Y.; Fu, F. H.; Yang, M. Y.; Xu, H.; Zhang, A. H.; Liu, K. Thromb. Res. 2010, 126, e17.
45. [45]
  (45) Sun, A. J.; Liu, H. Y.;Wang, S. J.; Shi, D. Z.; Xu, L.; Cheng, Y.; Wang, K. Q.; Chen, K. J.; Zou, Y. Z.; Ge, J. B. Br. J. Pharmacol. 2011, 164, 2042.
46. [46]
  (46) Duan, A. X.; Chen, J.; Liu, H. D.; Liu, X. H.; Lu, X. Q. J. Anal. Sci. 2009, 25, 473. [段爱霞, 陈晶, 刘宏德, 刘秀辉, 卢小泉. 分析科学学报, 2009, 25, 473.]
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