Traditional Chinese medicine network pharmacology: Theory, methodology and application

Chinese Journal of Natural Medicines

Volumn 11, Issue 2, 2013, Pages 110-120

  Li, Shao ^a   Zhang, Bo ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

Application; Methodology; Network pharmacology; Network target; Theory; Traditional Chinese medicine

Indexed keywords

BERBERINE; BI XIE; CHUAN XIONG; DIOSCOREA COLLETTII; DIOSGENIN; HERBACEOUS AGENT; KURARINONE; LIU WEI DI HUANG PILL; MATRINE; MAXINGSHIGAN YINQIAOSAN; QING FENG TENG; QING LUO YIN PILL; SINOMENINE; UNCLASSIFIED DRUG; WEN LUO YIN;

ARTICLE; CHINESE HERB; CHINESE MEDICINE; DRUG FORMULATION; DRUG TARGETING; EVIDENCE BASED MEDICINE; GENE TARGETING; GENOMICS; PHELLODENDRON CHINENSIS; PREDICTION; SINOMENIUM ACUTUM;

EID: 84879147636     PISSN: 20956975     EISSN: 18755364     Source Type: Journal    
DOI: 10.1016/S1875-5364(13)60037-0     Document Type: Article

References (73)

1. Corson TW, Crews CM Molecular understanding and modern application of traditional medicines: triumphs and trials [J]. Cell 2007, 130(5):769-774.
2. Chan K Progress in traditional Chinese medicine [J]. Trends Pharmacol Sci 1995, 16(6):182-187.
3. Qiu J Traditional medicine: a culture in the balance [J]. Nature 2007, 448(7150):126-128.
4. Stone R Lifting the veil on traditional Chinese medicine [J. Science 2008, 319(5864):709-710.
5. Wang L, Zhou GB, Liu P, et al. Dissection of mechanisms of Chinese medicinal formula Realgar-Indigo naturalis as an effective treatment for promyelocytic leukemia [J]. Proc Natl Acad Sci USA 2008, 105(12):4826-4831.
6. Lam W, Bussom S, Guan F, et al. The four-herb Chinese medicine PHY906 reduces chemotherapy-induced gastro- intestinal toxicity [J]. Sci Transl Med 2010, 2(45):45ra59.
7. Hoessel R, Leclerc S, Endicott JA, et al. Indirubin, the active constituent of a Chinese antileukaemia medicine, inhibits cyclin-dependent kinases [J]. Nat Cell Biol 1999, 1(1):60-67.
8. Yue QX, Cao ZW, Guan SH, et al. Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network [J]. Mol Cell Proteomics 2008, 7(5):949-961.
9. Park SJ, Ahmad F, Philp A, et al. Resveratrol ameliorates aging-related metabolic phenotypes by inhibiting cAMP phosphodiesterases [J]. Cell 2012, 148(3):421-433.
10. Zhou H, Sun L, Yang XL, et al. ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase [J]. Nature 2013, 494(7435):121-124.
11. Titov DV, Gilman B, He QL, et al. A subunit of TFIIH, is a target of the natural product triptolide [J]. Nat Chem Biol 2011, 7(3):182-188.
12. Xu Z Modernization: One step at a time [J]. Nature 2011, 480(7378):S90-S92.
13. Keith CT, Borisy AA, Stockwell BR Multicomponent therapeutics for networked systems [J]. Nat Rev Drug Discov 2005, 4(1):71-78.
14. Jia J, Zhu F, Ma X, et al. Mechanisms of drug combinations: interaction and network perspectives [J]. Nat Rev Drug Discov 2009, 8(2):111-128.
15. Schadt EE, Friend SH, Shaywitz DA A network view of disease and compound screening [J]. Nat Rev Drug Discov 2009, 8(4):286-295.
16. Levinson AD Cancer therapy reform [J]. Science 2010, 328(5975):137.
17. Li S. Possible relationship between traditional Chinese medicine ZHENG and molecular networks. The First Academic Annual Meeting of the China Association for Science and Technology. 1999.
18. Li S Framework and practice of network-based studies for Chinese herbal formula [J]. J Chin Integrat Med 2007, 5(5):489-493.
19. Li S, Zhang Z, Wu L, et al. Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network [J]. IET Syst Biol 2007, 1(1):51-60.
20. Li S Network systems underlying traditional Chinese medicine syndrome and herb formula [J]. Curr Bioinformat 2009, 4(3):188-196.
21. Li S Network target: a starting point for traditional Chinese medicine network pharmacology [J]. China J Chin Mater Med 2011, 36(15):2017-2020.
22. Li S, Zhang B, Zhang NB Network target for screening synergistic drug combinations with application to traditional Chinese medicine [J]. BMC Syst Biol 2011, 5(S1):S10.
23. Zhao S, Li S Network-based relating pharmacological and genomic spaces for drug target identification [J]. PLoS ONE 2010, 5(7):e11764.
24. Wu X, Jiang R, Zhang MQ, et al. Network-based global inference of human disease genes [J]. Mol Syst Biol 2008, 4:189.
25. Yao X, Hao H, Li Y, et al. Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network [J]. BMC Syst Biol 2011, 5:79.
26. Li S, Wu LJ, Zhang ZQ Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach [J]. Bioinformatics 2006, 22(17):2143-2150.
27. Huang Y, Li S Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network [J]. BMC Bioinformatics 2010, 11(S1):S32.
28. Gu J, Chen Y, Li S, et al. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis [J]. BMC Syst Biol 2010, 4:47.
29. Gu J, Li S Towards integrative annotating of the cell-type specific gene functional and signaling map in vascular endothelial cells [J]. Mol Biosyst 2012, 8(8):2041-2049.
30. Chen Y, Gu J, Li D, et al. Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells [J]. Bioinformatics 2012, 28(1):1-4.
31. Li S, Zhang B, Jiang D, et al. Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae [J]. BMC Bioinformatics 2010, 11(S11):S6.
32. Li LS, Zhang NB, Li S Ranking effects of candidate drugs on biological process by integrating network analysis and Gene Ontology [J]. Chin Sci Bull 2010, 55(26):2974-2980.
33. Yan H, Zhang B, Li S, et al. A formal model for analyzing drug combination effects and its application in TNF-alpha-induced NFkappaB pathway [J]. BMC Syst Biol 2010, 4:50.
34. Zhao S, Li S A co-module approach for elucidating drug- disease associations and revealing their molecular basis [J]. Bioinformatics 2012, 28:955-961.
35. Li S, Zhao S. Network-based identification of drug target and drug action: China, 201010218468.X [P]. 2010-10-21.
36. Li S, Zhang NB, Zhang B. Method of network-based identification of multicomponent synergy and compositions for use as effective component of anti-angiogenesis medicines: US, 8112230 B2[P].
37. Li S, Zhang N, Zhang B. Network-based identification of synergistic drug combination: China, ZL200810239284.4 [P]. 2008-10-23.
38. Zhuang YL, Li S, Li YD dbNEI: a specific database for neuro-endocrine-immune interactions [J]. Neuro Endocrinol Lett 2006, 27(1-2):53-59.
39. Zhang J, Ma T, Li Y, et al. dbNEI2.0: building multilayer network for drug-NEI-disease [J]. Bioinformatics 2008, 24(20):2409-2411.
40. Li S, Zhang B, Yuan J. A HerbBioMap database. China Software Copyright: 2011SR076502.
41. Zhang B, Liu L, Zhao S, et al. Vitexicarpin acts as a novel angiogenesis inhibitor and its target network [J]. Evid Based Complement Alternat Med 2013, 278405.
42. Zhang B, Wang X, Li S An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo- Yin [J]. Evid Based Complement Alternat Med 2013, 456747.
43. Ma T, Tan C, Zhang H, et al. Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network [J]. Mol Bio Syst 2010, 6(4):613-619.
44. Jiang B, Liang X, Chen Y, et al. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome [J]. Sci Rep 2012, 2:936.
45. Hopkins AL Network pharmacology [J]. Nature Biotechnol 2007, 25(10):1110-1111.
46. Hopkins AL Network pharmacology: the next paradigm in drug discovery [J]. Nature Chem Biol 2008, 4(11):682-690.
47. Schadt EE Molecular networks as sensors and drivers of common human diseases [J]. Nature 2009, 461(7261):218-223.
48. Barabási AL, Gulbahce N, Loscalzo J Network medicine: a network-based approach to human disease [J]. Nat Rev Genet 2011, 12(1):56-68.
49. Hoeng J, Deehan R, Pratt D, et al. A network-based approach to quantifying the impact of biologically active substances [J]. Drug Discov Today 2012, 17(9-10):413-418.
50. Li S, Lu A, Wang Y, et al. Suppressive effects of a Chinese herbal medicine Qing-Luo-Yin extract on the angiogenesis of collagen induced arthritis in rats [J]. Am J Chinese Med 2003, 31(5):713-720.
51. van der Greef Jan Perspective: All systems go [J]. Nature 2011, 480:S87.
52. Ji ZL, Zhou H, Wang JF, et al. Traditional Chinese medicine information database [J]. J Ethnopharmacol 2006, 103(3):501.
53. Chen CY TCM DatabaseTaiwan: the world's largest traditional Chinese medicine database for drug screening in silico [J]. PLoS One 2011, 6(1):e15939.
54. Fang YC, Huang HC, Chen HH, et al. TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining [J]. BMC Complement Altern Med 2008, 8:58.
55. Fang X, Shao L, Zhang H, et al. CHMIS-C: a comprehensive herbal medicine information system for cancer [J]. J Med Chem 2005, 48(5):1481-1488.
56. Xue R, Fang Z, Zhang M, et al. TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis [J]. Nucleic Acids Res 2013, 41:D1089-D1095.
57. Goel R, Harsha HC, Pandey A, et al. Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis [J]. Mol Biosyst 2012, 8(2):453-463.
58. Licata L, Briganti L, Peluso D, et al. MINT, the molecular interaction database: 2012 update [J]. Nucleic Acids Res 2012, 40:D857-D861.
59. Franceschini A, Szklarczyk D, Frankild S, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration [J]. Nucleic Acids Res 2013, 41:D808-D815.
60. Xenarios I, Salwínski L, Duan XJ, et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions [J]. Nucleic Acids Res 2002, 30(1):303-305.
61. Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, et al. The BioGRID interaction database [J]. Nucleic Acids Res 2013, 41:D816-D823.
62. Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders [J]. Nucleic Acids Res 2005, 33:D514-D517.
63. Bodenreider O The Unified Medical Language System (UMLS): integrating biomedical terminology [J]. Nucleic Acids Res 2004, 32:D267-D270.
64. Robinson PN, Mundlos S The Human Phenotype Ontology [J]. Clin Genet 2010, 77:525-534.
65. Yue QX, Cao ZW, Guan SH, et al. Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network [J]. Mol Cell Proteomics 2008, 7(5):949-961.
66. Zhao J, Jiang P, Zhang W Molecular networks for the study of TCM pharmacology [J]. Brief Bioinform 2010, 11(4):417-430.
67. Wang Y, Liu Z, Li C, et al. Drug target prediction based on the herbs components: the study on the multitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease [J]. Evid Based Complement Alternat Med 2012, 698531.
68. Jiang M, Lu C, Chen G, et al. Understanding the molecular mechanism of interventions in treating rheumatoid arthritis patients with corresponding traditional Chinese medicine patterns based on bioinformatics approach [J]. Evid Based Complement Alternat Med 2012, 129452.
69. Zhang A, Sun H, Yang B, et al. Predicting new molecular targets for rhein using network pharmacology [J]. BMC Syst Biol 2012, 6:20.
70. Sun Y, Zhu R, Ye H, et al. Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective [J]. Brief Bioinform 2012 Aug 11.
71. Li X, Xu X, Wang J, et al. A system-level investigation into the mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for cardiovascular disease treatment [J]. PLoS One 2012, 7(9):e43918.
72. Dai W, Chen JX, Lu P, et al. Pathway pattern-based prediction of active drug components and gene targets from H1N1 influenza's treatment with Maxingshigan-Yinqiaosan Formula [J]. Mol Biosyst 2013, 9(3):375-385.
73. Tao W, Xu X, Wang X, et al. Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease [J]. J Ethnopharmacol 2013, 145(1):1-10.