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.]
1. [1]
  Weiliang Wang , Zijing Yu , Jingyuan Li , Hong Shang . The Debate between Traditional Chinese Medicine and Western Medicine. University Chemistry, 2024, 39(9): 109-114. doi: 10.12461/PKU.DXHX202402001
2. [2]
  Junjie Zhang , Yue Wang , Qiuhan Wu , Ruquan Shen , Han Liu , Xinhua Duan . Preparation and Selective Separation of Lightweight Magnetic Molecularly Imprinted Polymers for Trace Tetracycline Detection in Milk. University Chemistry, 2024, 39(5): 251-257. doi: 10.3866/PKU.DXHX202311084
3. [3]
  Tiancheng Yang , Yang Yang , Chunhua Qu , Rui Chu , Yue Xia . Wandering through the Kingdom of Chinese Mineral Medicines. University Chemistry, 2024, 39(9): 94-101. doi: 10.12461/PKU.DXHX202403015
4. [4]
  Shuang Meng , Haixin Long , Zhou Zhou , Meizhu Rong . Inorganic Chemistry Curriculum Design and Implementation of Based on “Stepped-Task Driven + Multi-Dimensional Output” Model: A Case Study on Intermolecular Forces. University Chemistry, 2024, 39(3): 122-131. doi: 10.3866/PKU.DXHX202309008
5. [5]
  Wenliang Wang , Weina Wang , Sufan Wang , Tian Sheng , Tao Zhou , Nan Wei . “Schrödinger Equation – Approximate Models – Core Concepts – Simple Applications”: Constructing a Logical Framework and Knowledge Graph of Atom and Molecule Structures. University Chemistry, 2024, 39(8): 338-343. doi: 10.3866/PKU.DXHX202312084
6. [6]
  Manman Jin , Zhiguo Lv , Qingtao Niu . Teaching Reformation and Case Study for “Chemical Process Development and Design” Based on “Just-in-Time” Dynamic and Accurate Matching Industrial Needs. University Chemistry, 2024, 39(11): 108-116. doi: 10.12461/PKU.DXHX202403030
7. [7]
  Kejie Li , Dongmei Qi . Exploration and Practice of Traditional Chinese Medicine Chemistry Laboratory Management Based on the “Smart Laboratory”. University Chemistry, 2024, 39(10): 353-360. doi: 10.12461/PKU.DXHX202406080
8. [8]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
9. [9]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
10. [10]
  Siyu Zhang , Kunhong Gu , Bing'an Lu , Junwei Han , Jiang Zhou . Hydrometallurgical Processes on Recycling of Spent Lithium-lon Battery Cathode: Advances and Applications in Sustainable Technologies. Acta Physico-Chimica Sinica, 2024, 40(10): 2309028-. doi: 10.3866/PKU.WHXB202309028
11. [11]
  Laiying Zhang , Yinghuan Wu , Yazi Yu , Yecheng Xu , Haojie Zhang , Weitai Wu . Innovation and Practice of Polymer Chemistry Experiment Teaching for Non-Polymer Major Students of Chemistry: Taking the Synthesis, Solution Property, Optical Performance and Application of Thermo-Sensitive Polymers as an Example. University Chemistry, 2024, 39(4): 213-220. doi: 10.3866/PKU.DXHX202310126
12. [12]
  Miaomiao He , Zhiqing Ge , Qiang Zhou , Jiaqing He , Hong Gong , Lingling Li , Pingping Zhu , Wei Shao . Exploring the Fascinating Realm of Quantum Dots. University Chemistry, 2024, 39(6): 231-237. doi: 10.3866/PKU.DXHX202310040
13. [13]
  Yang YANG , Pengcheng LI , Zhan SHU , Nengrong TU , Zonghua WANG . Plasmon-enhanced upconversion luminescence and application of molecular detection. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 877-884. doi: 10.11862/CJIC.20230440
14. [14]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169
15. [15]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
16. [16]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
17. [17]
  Rui Gao , Ying Zhou , Yifan Hu , Siyuan Chen , Shouhong Xu , Qianfu Luo , Wenqing Zhang . Design, Synthesis and Performance Experiment of Novel Photoswitchable Hybrid Tetraarylethenes. University Chemistry, 2024, 39(5): 125-133. doi: 10.3866/PKU.DXHX202310050
18. [18]
  Wenbing Hu , Jin Zhu . Flipped Classroom Approach in Teaching Professional English Reading and Writing to Polymer Graduates. University Chemistry, 2024, 39(6): 128-131. doi: 10.3866/PKU.DXHX202310015
19. [19]
  Shicheng Yan . Experimental Teaching Design for the Integration of Scientific Research and Teaching: A Case Study on Organic Electrooxidation. University Chemistry, 2024, 39(11): 350-358. doi: 10.12461/PKU.DXHX202408036
20. [20]
  Linhan Tian , Changsheng Lu . Discussion on Sextuple Bonding in Diatomic Motifs of Chromium Family Elements. University Chemistry, 2024, 39(8): 395-402. doi: 10.3866/PKU.DXHX202401056

Get Citation

PDF

XML

Metrics

PDF Downloads(885)
Abstract views(2916)
HTML views(90)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142