Abstract
The interaction between drug molecules and target proteins is the basis of pharmacological action. The pharmacodynamic mechanism of Chinese medicinal plants for chronic kidney disease (CKD) was studied by molecular docking and complex network analysis. It was found that the interaction network of components-proteins of Chinese medicinal plants is different from the interaction network of components-proteins of drugs. The action mechanism of Chinese medicinal plants is different from that of drugs. We also found the interaction network of components-proteins of tonifying herbs is different from the interaction network of components-proteins of evil expelling herbs using complex network research approach. It illuminates the ancient classification theory of Chinese medicinal plants. This computational approach could identify the pivotal components of Chinese medicinal plants and their key target proteins rapidly. The results provide data for development of multi-component Chinese medicine.
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Coresh J, Selvin E, Stenvens LA, Manzi J, Kusek JW, Eggers P, Lente FV, Levey AS. Prevalence of chronic kidney disease in the United States. JAMA, 2007, 298: 2038–2047
Ye RG. Integration of Chinese and Western Medicine: Nephrology. Beijing: People’s Health Press, 2004. 25
Zhu W, Wang XM, Zhang L, Li XY, Wang BX. Pharmacokinetic of rhein in healthy male volunteers following oral and retention enema administration of rhubarb extract: a single dose study. Am J Chin Med, 2005, 33: 839–850
Jia J, Zhu F, Ma XH, Cao ZW, Li YX, Chen YZ. Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov, 2009, 8: 111–128
Zimmermann GR, Lehár J, Keith CT. Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today, 2007, 12: 34–42
Hippisley CJ, Coupland C. Effect of combinations of two drugs on all cause in patients with ischaemic heart disease: Nested case-control analysis. Brit Med J, 2005, 330: 1059–1063
Hennekens CH, Sacks FM, Tonkin A, Jukema JW, Byington RP, Pitt B, Berry DA, Berry SM, Ford NF, Walker AJ, Natarajan K, Chen SL, Fiedorek FT, Belder R. Additive benefits of pravastain and aspirin to decrease risks of cardiovascular disease. Arch Intern Med, 2003, 164: 40–44
The Indian Polycap Study (TIPS). Effects of a polypill (Polycap) on risk factors in middle-aged individuals without cardiovascular disease (TIPS): A phase II, double-blind, randomised trial. Lancet, 2009, 373: 1341–1351
Zhu W, Ruan XM, Chen KJ. A new insight into application of evidence-based medicine in TCM. J Trad Chin Med, 2006, 47: 333–335
Wang L, Zhou GB, Liu P, Song JH, Liang Y, Yan XJ, Xu F, Wang BS, Mao JH, Shen ZX, Chen SJ, Chen Z. Dissection of mechanisms of Chinese medicinal formula Realgar-Indigo naturalis as an effective treatment for promyelocytic leukemia. Proc Natl Acad Sci USA, 2008, 105, 4826
Editorial Committee of the Pharmacopoeia of People’s Republic of China. The Pharmacopoeia of People’s Republic of China (part 1). Beijing: Chemical Industry Press, 2005
Zhou JJ, Xie GR, Yan JX. Handbook of Chemical Composition in Chinese Herbal Original Plants. Beijing: Chemical Industry Press, 2004
Assenov Y, Ramírez F, Schelhorn SE, Albrecht M. Computing topological parameters of biological networks. Bioinformatics, 2008, 24: 282–284
Xu XJ. Study on computer simulation for Chinese traditional compound medicine. Prog Chem, 11: 202–204
Xu XJ. New concepts and approaches for drug discovery based on traditional Chinese medicine. Drug Discov Today, 2006, 3: 247–253
Huang Q, Qiao XB, Xu XJ. Potential synergism and inhibitors to multiple target enzymes of Xuefu Zhuyu decoction in cardiac disease therapeutics: A computational approach. Bioorg Med Chem Lett, 2007, 17: 1779–1783
Li XD, Huang Q, Xu XJ. Target-ligand space distribution of the compound sets from XuefuZhuyu decoction, a traditional Chinese medicinal recipe. Acta Phys-Chim Sin, 2008, 24: 547–551
Wu DH, Xu XJ. Computational simulation of benefiting Qi and activating blood mechanism of traditional Chinese medicine. Acta Phys-Chim Sin, 2009, 25: 446–450
Gu JY, Yuan G, Zhu YH, Xu XJ. Computational pharmacological studies on cardiovascular disease by Qishen Yiqi Diwan. Sci China Ser B-Chem, 2009, 52: 1879–1884
Watts DJ. The “new” science of networks. Annu Rev Sociol, 2004, 30: 243–270
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature, 2000, 407: 651–654
Yoshie O, Imai T, Nomiyama H. Chemokines in immunity. Adv Immunol, 2001, 78: 57–110
Rousset F, Garcia E, Defrance T, Peronne C, Vezzio N, Hsu DH, Kastelein R, Moore KW, Banchereau J. Interleukin 10 is a potent growth and differentiation factor for activated human B lymphocytes. Proc Natl Acad Sci USA, 1992, 89: 1890–1893
Feng JT, Xu Q, Xue XY, Zhang FF, Xiao YS, Liang XM. Preparation of standard multi-component of traditional Chinese medicine and construction for its library. World Science and Technology-Modernization of Traditional Chinese Medicine and Materia Medica, 2006, 8: 1–7
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science, 2008, 321: 263–266
Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Garcia Urdiales E, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R. SuperTarget and Matador: resources for exploring drug-target relationships. Nucl Acids Res, 2008, 36: 919–922
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, Mering CV, Jensen LJ, Beyer A, Bork P. STITCH 2: An interaction network database for small molecules and proteins. Nucl Acids Res, 2010, 38: 552–556
Keith CT, Borisy AA, Stckwell BR. Multicomponent therapentics for networked system. Nat Rev Drug Discov, 2005, 4: 1–8
Imming P, Sinning C, Meyer A. Drug, their targets and the nature and number of drug targets. Nat Rev Drug Discov, 2006, 5: 821–834
Kitano H. A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov, 2007, 6: 202–210
Watts DJ, Strogatz SH. Collective dynamics of “small-world” networks. Nature, 1998, 393: 440–442
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Zhu, W., Qiu, X., Xu, X. et al. Computational network pharmacological research of Chinese medicinal plants for chronic kidney disease. Sci. China Chem. 53, 2337–2342 (2010). https://doi.org/10.1007/s11426-010-4082-0
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DOI: https://doi.org/10.1007/s11426-010-4082-0