Network pharmacology: A new approach for Chinese herbal medicine research

Evidence-based Complementary and Alternative Medicine

Volumn 2013, Issue , 2013, Pages

  Zhang, Gui Biao ^a   Li, Qing Ya ^a,b   Chen, Qi Long ^a   Su, Shi Bing ^a  

^a SHANGHAI UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

^b HENAN UNIVERSITY OF CHINESE MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HERBACEOUS AGENT;

CHINESE MEDICINE; DRUG RESEARCH; DRUG TARGETING; HERBAL MEDICINE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PUBLIC HEALTH; REVIEW; TOXICOLOGY;

EID: 84878701071     PISSN: 1741427X     EISSN: 17414288     Source Type: Journal    
DOI: 10.1155/2013/621423     Document Type: Review

References (87)

1. Sams-Dodd F., Target-based drug discovery: is something wrong? Drug Discovery Today 2005 10 2 139 147 2-s2.0-13844276627 10.1016/S1359-6446(04) 03316-1 (Pubitemid 40247812)
2. Kola I., Landis J., Can the pharmaceutical industry reduce attrition rates? Nature Reviews Drug Discovery 2004 3 8 711 715 2-s2.0-4344645978 (Pubitemid 39173511)
3. Zambrowicz B. P., Sands A. T., Modeling drug action in the mouse with knockouts and RNA interference. Drug Discovery Today 2004 3 5 198 207 2-s2.0-4644229134 10.1016/S1741-8372(04)02454-5 (Pubitemid 39298775)
4. Hillenmeyer M. E., Fung E., Wildenhain J., Pierce S. E., Hoon S., Lee W., Proctor M., Onge R. P. S., Tyers M., Koller D., Altman R. B., Davis R. W., Nislow C., Giaever G., The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 2008 320 5874 362 365 2-s2.0-42349100173 10.1126/science.1150021 (Pubitemid 351555656)
5. Kitano H., Systems biology: a brief overview. Science 2002 295 5560 1662 1664 2-s2.0-0036500993 10.1126/science.1069492 (Pubitemid 34202893)
6. Sauer U., Heinemann M., Zamboni N., Getting closer to the whole picture. Science 2007 316 5824 550 551 2-s2.0-34247587012 10.1126/science.1142502 (Pubitemid 46683128)
7. Hopkins A. L., Network pharmacology. Nature Biotechnology 2007 25 10 1110 1111 2-s2.0-35148824614 10.1038/nbt1007-1110 (Pubitemid 47538107)
8. Hopkins A. L., Network pharmacology: the next paradigm in drug discovery. Nature Chemical Biology 2008 4 11 682 690 2-s2.0-54249155522 10.1038/nchembio.118
9. Roth B. L., Sheffer D. J., Kroeze W. K., Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nature Reviews Drug Discovery 2004 3 4 353 359 2-s2.0-4644271084 (Pubitemid 38499762)
10. Csermely P., Ágoston V., Pongor S., The efficiency of multi-target drugs: the network approach might help drug design. Trends in Pharmacological Sciences 2005 26 4 178 182 2-s2.0-15044349115 10.1016/j.tips.2005.02.007 (Pubitemid 40432652)
11. Wermuth C. G., Multitargeted drugs: the end of the "one-target-one- disease" philosophy? Drug Discovery Today 2004 9 19 826 827 2-s2.0-4644289587 10.1016/S1359-6446(04)03213-1 (Pubitemid 39286093)
12. Keith C. T., Borisy A. A., Stockwell B. R., Multicomponent therapeutics for networked systems. Nature Reviews Drug Discovery 2005 4 1 71 78 2-s2.0-12144258457 10.1038/nrd1609 (Pubitemid 40109591)
13. Luo G. A., Liang Q. L., Zhang R. L., Study of chemical matteromics and prescription of traditional Chinese medicine-and an analysis of material foundation of compound prescription Qingkailing. World Science and Technology 2006 8 1 6 15
14. Liu Z. H., Sun X. B., Network pharmacology: new opportunity for the modernization of traditional Chinese medicine. Acta Pharmaceutica Sinica 2012 47 6 696 703
15. Friboulet A., Thomas D., Systems biology-an interdisciplinary approach. Biosensors and Bioelectronics 2005 20 12 2404 2407 2-s2.0-18044365052 10.1016/j.bios.2004.11.014 (Pubitemid 40602180)
16. Metz J. T., Hajduk P. J., Rational approaches to targeted polypharmacology: creating and navigating protein-ligand interaction networks. Current Opinion in Chemical Biology 2010 14 4 498 504 2-s2.0-77955333346 10.1016/j.cbpa.2010.06.166
17. Pan J. H., New paradigm for drug discovery based on network pharmacology. Chinese Journal of New Drugs and Clinical Remedies 2009 28 10 721 726
18. Wu X., Jiang R., Zhang M. Q., Network-based global inference of human disease genes. Molecular Systems Biology 2008 4 1 11
19. Chen Y., Zhu J., Lum P. Y., Yang X., Pinto S., MacNeil D. J., Zhang C., Lamb J., Edwards S., Sieberts S. K., Leonardson A., Castellini L. W., Wang S., Champy M. F., Zhang B., Emilsson V., Doss S., Ghazalpour A., Horvath S., Drake T. A., Lusis A. J., Schadt E. E., Variations in DNA elucidate molecular networks that cause disease. Nature 2008 452 7186 429 435 2-s2.0-40749105508 10.1038/nature06757 (Pubitemid 351450844)
20. Yildirim M. A., Goh K. I., Cusick M. E., Barabási A. L., Vidal M., Drug-target network. Nature Biotechnology 2007 25 10 1119 1126 2-s2.0-35148838537 10.1038/nbt1338 (Pubitemid 47538114)
21. Barabási A. L., Gulbahce N., Loscalzo J., Network medicine: a network-based approach to human disease. Nature Reviews Genetics 2011 12 1 56 68 2-s2.0-78650373804 10.1038/nrg2918
22. Gu J., Zhang H., Chen L., Drug-target network and polypharmacology studies of a Traditional Chinese Medicine for type II diabetes mellitus. Computational Biology and Chemistry 2011 35 5 293 297 10.1016/j.compbiolchem. 2011.07.003
23. Yan J., Wang Y., Luo S. J., TCM grammar systems: an approach to aid the interpretation of the molecular interactions in Chinese herbal medicine. Journal of Ethnopharmacology 2011 137 1 77 84 10.1016/j.jep.2011.04.057
24. Li S., Zhang B., Jiang D., Wei Y., Zhang N., Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics 2010 11 11, article S6 2-s2.0-78650832745 10.1186/1471-2105-11-S11-S6
25. Li X., Wu L., Fan X., Network pharmacology study on major active compounds of Fufang Danshen formula. China Journal of Chinese Materia Medica 2011 36 21 2911 2914
26. Ma C., Yao Y., Yue Q. X., Zhou X. W., Yang P. Y., Wu W. Y., Guan S. H., Jiang B. H., Yang M., Liu X., Guo D. A., Differential proteomic analysis of platelets suggested possible signal cascades network in platelets treated with Salvianolic acid B. PLoS ONE 2011 6 2 2-s2.0-79951883850 10.1371/journal.pone. 0014692 e14692
27. Cheng X. R., Zhou W. X., Zhang Y. X., Experimental techniques in network pharmacology. Chinese Journal of Pharmacology and Toxicology 2012 26 2 131 137
28. Edwards B. S., Oprea T., Prossnitz E. R., Sklar L. A., Flow cytometry for high-throughput, high-content screening. Current Opinion in Chemical Biology 2004 8 4 392 398 2-s2.0-3342898403 10.1016/j.cbpa.2004.06.007 (Pubitemid 38993732)
29. Miscevic F., Rotstein O., Wen X. Y., Advances in zebrafish high content and high throughput technologies. Combinatorial Chemistry & High Throughput Screening 2012 15 7 515 521
30. Fakhari F. D., Dittmer D. P., Charting latency transcripts in Kaposi's sarcoma-associated herpesvirus by whole-genome real-time quantitative PCR. Journal of Virology 2002 76 12 6213 6223 2-s2.0-0036100266 10.1128/JVI.76.12. 6213-6223.2002 (Pubitemid 34556317)
31. Guo X., Surface plasmon resonance based biosensor technique: a review. Journal of Biophotonics 2012 5 7 483 501 10.1002/jbio.201200015
32. Wartchow C. A., Podlaski F., Li S., Biosensor-based small molecule fragment screening with biolayer interferometry. Journal of Computer-Aided Molecular Design 2011 25 7 669 676 10.1007/s10822-011-9439-8
33. Wu L. H., Wang Y., Fan X., Tools for network pharmacology study: network visualization and network analysis. China Journal of Chinese Materia Medica 2011 36 21 2923 2925
34. Cagnolo L., Salvo A., Valladares G., Network topology: patterns and mechanisms in plant-herbivore and host-parasitoid food webs. Journal of Animal Ecology 2011 80 2 342 351 2-s2.0-79551594948 10.1111/j.1365-2656.2010.01778.x
35. Brinda K. V., Vishveshwara S., Vishveshwara S., Random network behaviour of protein structures. Molecular Biosystems 2010 6 2 391 398 2-s2.0-75749155822 10.1039/b903019k
36. Hou L., Wang L., Berg A., Comparison and evaluation of network clustering algorithms applied to genetic interaction networks. Frontiers in Bioscience 2012 4 2150 2161
37. Lopes C. T., Franz M., Kazi F., Donaldson S. L., Morris Q., Bader G. D., Cytoscape web: an interactive web-based network browser. Bioinformatics 2010 26 18 2347 2348 2-s2.0-77956548953 10.1093/bioinformatics/btq430 btq430
38. Adar E., Kim M., Soft GUESS: visualization and exploration of code clones in context. Proceedings of the 29th International Conference on Software Engineering (ICSE '07) May 2007 762 765 2-s2.0-34548765475 10.1109/ICSE.2007.76
39. Wouter D. N., Andrej M., Vladimir B., Exploratory Social Network Analysis With Pajek 2005 Cambridge, Mass, USA Cambridge University Press
40. Xu J., Yang Y., Traditional Chinese medicine in the Chinese health care system. Health Policy 2009 90 2-3 133 139 2-s2.0-63949088173 10.1016/j.healthpol.2008.09.003
41. Cheung F., TCM: made in China. Nature 2011 480 S82 S83 10.1038/480S82a
42. Chen X., Zhou H., Liu Y. B., Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. British Journal of Pharmacology 2006 149 8 1092 1103 (Pubitemid 44950812)
43. Ye H., Ye L., Kang H., HIT: linking herbal active ingredients to targets. Nucleic Acids Research 2011 39 supplement 1 D1055 D1059 10.1093/nar/gkq1165
44. Fang Y. C., Huang H. C., Chen H. H., TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. BMC Complementary and Alternative Medicine 2008 8 58 10.1186/1472-6882-8-58
45. Chen C. Y., TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening In Silico. PLoS ONE 2011 6 1 2-s2.0-79251561193 10.1371/journal.pone.0015939 e15939
46. Gunther S., Kuhn M., Dunkel M., SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research 2008 36 D919 D922 (Pubitemid 351149845)
47. Knox C., Law V., Jewison T., DrugBank 3. 0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Research 2011 39 1 D1035 D1041 10.1093/nar/gkq1126
48. Zhu F., Han B., Kumar P., Liu X., Ma X., Wei X., Huang L., Guo Y., Han L., Zheng C., Chen Y., Update of TTD: therapeutic target database. Nucleic Acids Research 2009 38 1 D787 D791 2-s2.0-75549090848 10.1093/nar/gkp1014
49. Li S., Network target: a starting point for traditional Chinese medicine network pharmacology. China Journal of Chinese Materia Medica 2011 36 15 2017 2020
50. Wu L., Gao X., Wang L., Prediction of multi-target of aconiti lateralis radix praeparata and its network pharmacology. China Journal of Chinese Materia Medica 2011 36 21 2907 2910
51. Yu S., Guo Z., Guan Y., Combining ZHENG theory and high-throughout expression data to predict new effects of Chinese herbal formulae. Evidence-Based Complementary and Alternative Medicine 2012 2012 8 986427 10.1155/2012/986427
52. Lamb J., Crawford E. D., Peck D., Modell J. W., Blat I. C., Wrobel M. J., Lerner J., Brunet J. P., Subramanian A., Ross K. N., Reich M., Hieronymus H., Wei G., Armstrong S. A., Haggarty S. J., Clemons P. A., Wei R., Carr S. A., Lander E. S., Golub T. R., The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006 313 5795 1929 1935 2-s2.0-33749335282 10.1126/science.1132939 (Pubitemid 44497995)
53. Zhu W., Yao L. M., Potential targets and molecular mechanisms of, "Xiaochaihu Decoction" by Metadrug software. Shanghai Journal of Traditional Chinese Medicine 2011 45 1 79 82
54. Zhang A. H., Hui S., Bo Y., Predicting new molecular targets for rhein using network pharmacology. BMC Systems Biology 2012 6 20 10.1186/1752-0509-6-20
55. Witten I. H., Frank E., Data Mining Practical Machine Learning Tools and Techniques 2005 Beijing, China China Machine
56. Li S., Wu L., Zhang Z., Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 2006 22 17 2143 2150 2-s2.0-33748669610 10.1093/bioinformatics/btl363 (Pubitemid 44390906)
57. Wu L., Gao X., Cheng Y., Symptom-based traditional Chinese medicine slices relationship network and its network pharmacology study. China Journal of Chinese Materia Medica 2011 36 21 2916 2919
58. Zhang P., Li J., Wang Y., Bayesian belief network and its application in predicting the five flavors of Chinese medicinal components. Modernization of Traditional Chinese Medicine and Materia Materia-World Science and Technology 2008 10 5 114 117
59. Montironi R., Whimster W. F., Collan Y., Hamilton P. W., Thompson D., Bartels P. H., How to develop and use a Bayesian belief network. Journal of Clinical Pathology 1996 49 3 194 201 2-s2.0-0029925198 (Pubitemid 26101513)
60. Li S., Zhang B., Zhang N., Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology 2011 5 1, article S10 2-s2.0-79959199033 10.1186/1752-0509-5-S1-S10
61. Zheng C. S., Lin Z. C., Xu H. F., Pharmacological research on osteoarthritis treated by tougu xiaotong capsule. Journal of Fujian University of TCM 2011 21 1 43 47
62. Zhu Y. F., Xu Z. W., Ao H. Q., Pharmacodynamic research of spleen-regulating and heart-nourishing formula based on network features. Traditional Chinese Drug Research & Clinical Pharmacology 2012 23 1 25 29
63. Wang X., Xu X., Tao W., A systems biology approach to uncovering pharmacological synergy in herbal medicines with applications to cardiovascular disease. Evidence-Based Complementary and Alternative Medicine 2012 2012 15 10.1155/2012/519031
64. Li B., Xu X., Wang X., A systems biology approach to understanding the mechanisms of action of Chinese herbs for treatment of cardiovascular disease. International Journal of Molecular Sciences 2012 13 10 13501 13520 10.3390/ijms131013501
65. Liu Q., Zhang Z., Fang L., Application of network pharmacology and high through-put technology on active compounds screening from traditional Chinese medicine. China Journal of Chinese Materia Medica 2012 37 2 134 137
66. Fan X., Zhao X., Jin Y., Network toxicology and its application to traditional Chinese medicine. China Journal of Chinese Materia Medica 2011 36 21 2920 2922
67. Zhou M. M., Liu P., Jia W., Evaluation of therapeutic effects of TCM based on metabolic variation. Modernization of Traditional Chinese Medicine and Materia Materia-World Science and Technology 2006 8 6 113 119
68. Davis A. P., King B. L., Mockus S., Murphy C. G., Saraceni-Richards C., Rosenstein M., Wiegers T., Mattingly C. J., The comparative toxicogenomics database: update 2011. Nucleic Acids Research 2011 39 1 D1067 D1072 2-s2.0-78651317084 10.1093/nar/gkq813
69. Wolfgang G. H. I., Johnson D. E., Web resources for drug toxicity. Toxicology 2002 173 1-2 67 74 2-s2.0-0037171691 10.1016/S0300-483X(02)00022-7 (Pubitemid 34304289)
70. Lagunin A., Filimonov D., Zakharov A., Xie W., Huang Y., Zhu F., Shen T., Yao J., Poroikov V., Computer-aided prediction of rodent carcinogenicity by PASS and CISOC-PSCT. QSAR and Combinatorial Science 2009 28 8 806 810 2-s2.0-70350380202 10.1002/qsar.200860192
71. Niu X. Y., Li J., Lu C., The molecular mechanism of 'Herbs-Pattern Correspondence' in RA with heat pattern based on network pharmacology. Chinese Journal of Experimental Traditional Medical Formulae 2012 18 8 299 303
72. Li S., Zhang Z. Q., Wu L. J., Zhang X. G., Li Y. D., Wang Y. Y., Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Systems Biology 2007 1 1 51 60 2-s2.0-34249037449 10.1049/iet-syb:20060032 (Pubitemid 46779218)
73. Guo Z., Yu S., Guan Y., Molecular mechanisms of 'Same TCM Syndrome for Different Diseases' and 'Different TCM Syndrome for Same Disease' in chronic hepatitis B and liver cirrhosis. Evidence-Based Complementary and Alternative Medicine 2012 2012 9 10.1155/2012/120350
74. Shi Q., Zhao H. H., Chen J. X., Study on TCM syndrome identification modes of coronary heart disease based on data mining. Evidence-Based Complementary and Alternative Medicine 2012 2012 697028 10.1155/2012/697028
75. Du G. H., Wang Y. H., Zhang R., Multi-target and multi-component pattern, a superficial understanding of the action mechanism of Traditional Chinese Medicine. Modernization of Traditional Chinese Medicine and Materia Materia-World Science and Technology 2009 11 4 480 484
76. He F. Y., Deng K. W., Liu W. L., Study on theoretical and technologic key problems of network pharmacology and pharmacodynamics for the Chinese Materia Medica Formula. Pharmacology and Clinics of Chinese Materia Medica 2012 28 5 256 259
77. He F. Y., Zhou H. H., Luo J. Y., Establishment of a network pharmacokinetic model for multiple component drugs and parameter analyses. Chinese Journal of Clinical Pharmacology and Therapeutics 2007 12 12 1321 1331
78. He F., Deng K., Zou H., Qiu Y., Chen F., Zhou H., Study on differences between pharmacokintics and chromatopharmacodynamics for Chinese materia medica formulae. China Journal of Chinese Materia Medica 2011 36 2 136 141 2-s2.0-79955952405 10.4268/cjcmm20110210
79. Tal W. Y., Xu X., Wang X., Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease. Journal of Ethnopharmacology 2013 145 1 1 10 10.1016/j.jep.2012.09.051
80. Li B. H., Xu X., Wang X., A systems biology approach to understanding the mechanisms of action of Chinese herbs for treatment of cardiovascular disease. International Journal of Molecular Sciences 2012 13 10 13501 13520 10.3390/ijms131013501
81. Wang M., Zhang X., Xiong X., Efficacy of the Chinese traditional medicinal herb Celastrus orbiculatus Thunb on human hepatocellular carcinoma in an orthothopic fluorescent nude mouse model. Anticancer Research 2012 32 4 1213 1220
82. Hu M., Zhao M., An C., Real-time imaging of apoptosis induction of human breast cancer cells by the traditional Chinese medicinal herb tubeimu. Anticancer Research 2012 32 7 2509 2514
83. Zhao B., Liu L., Zhao S., Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-Based Complementary and Alternative Medicine 2013 2013 13 278405 10.1155/2013/278405
84. Albert R., Jeong H., Barabási A. L., Error and attack tolerance of complex networks. Nature 2000 406 6794 378 382 2-s2.0-0034721164 10.1038/35019019 (Pubitemid 30625551)
85. Yu H., Kim P. M., Sprecher E., Trifonov V., Gerstein M., The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Computational Biology 2007 3 4 713 720 2-s2.0-34247622363 10.1371/journal.pcbi.0030059 (Pubitemid 46683453)
86. Hwang W. C., Zhang A., Ramanathan M., Identification of information flow-modulating drug targets: a novel bridging paradigm for drug discovery. Clinical Pharmacology and Therapeutics 2008 84 5 563 572 2-s2.0-54349093738 10.1038/clpt.2008.129
87. Farkas I. J., Korcsmáros T., Kovács I. A., Network-based tools for the identification of novel drug targets. Science Signaling 2011 4 173 10.1126/scisignal.2001950