About this Journal Submit a Manuscript Table of Contents
Evidence-Based Complementary and Alternative Medicine
Volume 2013 (2013), Article ID 456747, 12 pages
http://dx.doi.org/10.1155/2013/456747
Research Article

An Integrative Platform of TCM Network Pharmacology and Its Application on a Herbal Formula, Qing-Luo-Yin

Bo Zhang,1,2 Xu Wang,1 and Shao Li1

1Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Room 1-107, FIT Building, Beijing 100084, China
2Joint Computational Center of Drug Discovery, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin 300457, China

Received 6 January 2013; Accepted 4 February 2013

Academic Editor: Aiping Lu

Copyright © 2013 Bo Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. M. Barnes, E. Powell-Griner, K. McFann, and R. L. Nahin, “Complementary and alternative medicine use among adults: United States, 2002,” Advance Data, no. 343, pp. 1–19, 2004. View at Scopus
  2. US Food and Drug Administration, Guidance for industry on complementary and alternative medicine products and their regulation by the Food and Drug Administration, 2006.
  3. J. Qiu, “Traditional medicine: a culture in the balance,” Nature, vol. 448, no. 7150, pp. 126–128, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. T. W. Corson and C. M. Crews, “Molecular understanding and modern application of traditional medicines: triumphs and trials,” Cell, vol. 130, no. 5, pp. 769–774, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. D. K. W. Mok and F. T. Chau, “Chemical information of Chinese medicines: a challenge to chemist,” Chemometrics and Intelligent Laboratory Systems, vol. 82, no. 1-2, pp. 210–217, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. J. L. Zhang, M. Cui, Y. He, H. L. Yu, and D. A. Guo, “Chemical fingerprint and metabolic fingerprint analysis of Danshen injection by HPLC-UV and HPLC-MS methods,” Journal of Pharmaceutical and Biomedical Analysis, vol. 36, no. 5, pp. 1029–1035, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. L. Zhou, Z. Zuo, and M. S. S. Chow, “Danshen: an overview of its chemistry, pharmacology, pharmacokinetics, and clinical use,” Journal of Clinical Pharmacology, vol. 45, no. 12, pp. 1345–1359, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Kamei, A. Saitoh, T. Asano et al., “Pharmacokinetic and pharmacodynamic profiles of the antitussive principles of Glycyrrhizae radix (licorice), a main component of the Kampo preparation Bakumondo-to (Mai-men-dong-tang),” European Journal of Pharmacology, vol. 507, no. 1–3, pp. 163–168, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. T. Efferth, Y. J. Fu, Y. G. Zu, G. Schwarz, V. S. B. Konkimalla, and M. Wink, “Molecular target-guided tumour therapy with natural products derived from traditional Chinese medicine,” Current Medicinal Chemistry, vol. 14, no. 19, pp. 2024–2032, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. W. C. S. Cho, “Application of proteomics in Chinese medicine research,” The American Journal of Chinese Medicine, vol. 35, no. 6, pp. 911–922, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Wang, R. J. A. N. Lamers, H. A. A. J. Korthout et al., “Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology,” Phytotherapy Research, vol. 19, no. 3, pp. 173–182, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. Z. Xu, “Modernization: one step at a time,” Nature, vol. 480, no. 7378, pp. S90–S92, 2011. View at Publisher · View at Google Scholar
  13. S. Li, “Possible relationship between traditional Chinese medicine ZHENG and molecular networks,” in Proceedings of the 1st Academic Annual Meeting of the China Association for Science and Technology, 1999.
  14. S. Li, Z. Q. Zhang, L. J. Wu, X. G. Zhang, Y. D. Li, and Y. Y. Wang, “Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network,” IET Systems Biology, vol. 1, no. 1, pp. 51–60, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Li, “Framework and practice of network-based studies for Chinese herbal formula,” Journal of Chinese Integrative Medicine, vol. 5, no. 5, pp. 489–493, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. A. L. Hopkins, “Network pharmacology: the next paradigm in drug discovery,” Nature Chemical Biology, vol. 4, no. 11, pp. 682–690, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. A. L. Hopkins, “Network pharmacology,” Nature Biotechnology, vol. 25, no. 10, pp. 1110–1111, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. S. Li, “Network systems underlying traditional Chinese medicine syndrome and herb formula,” Current Bioinformatics, vol. 4, no. 3, pp. 188–196, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Li, “Network target: a starting point for traditional Chinese medicine network pharmacology,” Zhongguo Zhong Yao Za Zhi, vol. 36, pp. 2017–2020, 2011.
  20. S. Li, B. Zhang, and N. B. Zhang, “Network target for screening synergistic drug combinations with application to traditional Chinese medicine,” BMC Systems Biology, vol. 5, supplement 1, article S10, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Sun, R. Zhu, H. Ye et al., “Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective,” Briefings in Bioinformatics, vol. 8, pp. 1–17, 2012. View at Publisher · View at Google Scholar
  22. X. Wang, X. Xu, W. Y. Tao, Y. Li, Y. H. Wang, and L. Yang, “A systems biology approach to uncovering pharmacological synergy in herbal medicines with applications to cardiovascular disease,” Evidence-Based Complementary and Alternative Medicine, vol. 2012, Article ID 519031, 15 pages, 2012. View at Publisher · View at Google Scholar
  23. Y. Wang, Z. Liu, C. Li 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,” Evidence-Based Complementary and Alternative Medicine, vol. 2012, Article ID 698531, 10 pages, 2012. View at Publisher · View at Google Scholar
  24. J. Zhao, P. Jiang, and W. Zhang, “Molecular networks for the study of TCM pharmacology,” Briefings in Bioinformatics, vol. 11, no. 4, Article ID bbp063, pp. 417–430, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. S. Li, B. Zhang, D. Jiang, Y. Wei, and N. Zhang, “Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae,” BMC Bioinformatics, vol. 11, supplement 11, article S6, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Zhao and S. Li, “Network-based relating pharmacological and genomic spaces for drug target identification,” PLoS ONE, vol. 5, no. 7, Article ID e11764, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. X. Wu, R. Jiang, M. Zhang, and S. Li, “Network-based global inference of human disease genes,” Molecular Systems Biology, vol. 4, article 189, 2008.
  28. S. Li, L. Wu, and Z. Zhang, “Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach,” Bioinformatics, vol. 22, no. 17, pp. 2143–2150, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. Y. Huang and S. Li, “Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network,” BMC Bioinformatics, vol. 11, supplement 1, article S32, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. L. S. Li, N. B. Zhang, and S. Li, “Ranking effects of candidate drugs on biological process by integrating network analysis and gene ontology,” Chinese Science Bulletin, vol. 55, no. 26, pp. 2974–2980, 2010. View at Publisher · View at Google Scholar · View at Scopus
  31. S. Zhao and S. Li, “A co-module approach for elucidating drug-disease associations and revealing their molecular basis,” Bioinformatics, vol. 28, no. 7, pp. 955–961, 2012. View at Publisher · View at Google Scholar
  32. B. Zhang, L. Liu, S. Zhao, X. Wang, L. Liu, and S. Li, “Vitexicarpin acts as a novel angiogenesis inhibitor and its target network,” Evidence-Based Complementary and Alternative Medicine, vol. 2012, Article ID 278405, 13 pages, 2012. View at Publisher · View at Google Scholar
  33. S. Li, A. P. Lu, Y. Y. Wang, and Y. D. Li, “Suppressive effects of a Chinese herbal medicine Qing-Luo-Yin extract on the angiogenesis of collagen-induced arthritis in rats,” The American Journal of Chinese Medicine, vol. 31, no. 5, pp. 713–720, 2003. View at Publisher · View at Google Scholar · View at Scopus
  34. S. Li, B. Zhang, and J. Yuan, “HerbBioMap database,” China Copyright of Computer Software, 2011SR076502.
  35. X. Chen, C. Yi, X. Yang, and X. Wang, “Liquid chromatography of active principles in Sophora flavescens root,” Journal of Chromatography B, vol. 812, no. 1-2, pp. 149–163, 2004. View at Publisher · View at Google Scholar · View at Scopus
  36. X. X. Zhao, C. Peng, H. Zhang, and L. P. Qin, “Sinomenium acutum: a review of chemistry, pharmacology, pharmacokinetics, and clinical use,” Pharmaceutical Biology, vol. 50, no. 8, pp. 1053–1061, 2012. View at Publisher · View at Google Scholar
  37. J. Zhao, Q. C. Pang, J. Ma, X. W. Zheng, Q. X. Meng, and C. M. Liu, “Main active constituent detection of cortex phellodendri chinensis by spectral imaging technology,” Acta Optica Sinica, vol. 28, no. 12, pp. 2288–2291, 2008. View at Publisher · View at Google Scholar · View at Scopus
  38. M. Wu, C. Ma, Y. Wu, and S. Li, “Simultaneous LC analysis of five bioactive alkaloids in an anti-angiogenesis herbal formula, Qing-Luo-Yin,” Chromatographia, vol. 68, no. 7-8, pp. 579–585, 2008. View at Publisher · View at Google Scholar · View at Scopus
  39. S. Yang, K. Li, Y. Zhang, S. Li, and Y. Shi, “Identification and determination of the major constituents in an antiangiogenesis herbal formula, Qing-Luo-Fang, by HPLC-DAD-ESI/MS,” Journal of Liquid Chromatography and Related Technologies, vol. 33, no. 20, pp. 1842–1853, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. Y. Wang, J. Xiao, T. O. Suzek, J. Zhang, J. Wang, and S. H. Bryant, “PubChem: a public information system for analyzing bioactivities of small molecules,” Nucleic Acids Research, vol. 37, supplement 2, pp. W623–W633, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, and V. A. McKusick, “Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders,” Nucleic Acids Research, vol. 33, supplement 1, pp. D514–D517, 2005. View at Publisher · View at Google Scholar · View at Scopus
  42. D. S. Wishart, C. Knox, A. C. Guo et al., “DrugBank: a knowledgebase for drugs, drug actions and drug targets,” Nucleic Acids Research, vol. 36, supplement 1, pp. D901–D906, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. T. S. K. Prasad, R. Goel, K. Kandasamy et al., “Human protein reference database—2009 update,” Nucleic Acids Research, vol. 37, supplement 1, pp. D767–D772, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. U. Rix and G. Superti-Furga, “Target profiling of small molecules by chemical proteomics,” Nature Chemical Biology, vol. 5, no. 9, pp. 616–624, 2009. View at Publisher · View at Google Scholar · View at Scopus
  45. D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar · View at Scopus
  47. S. Li and S. Zhao, “Network-based identification of drug target and drug action,” Invention Patent: 201010218468.X.
  48. S. Li, N. Zhang, and B. Zhang, “Network-based identification of synergistic drug combination,” Invention Patent: ZL200810239284. 4.
  49. Y. Li and Y. Liu, “Experience of Professor Li Ji-Ren in the treatment of Bi-ZHENG,” Journal of Beijing University of Traditional Chinese Medicine (Clinical Medicine), vol. 14, no. 5, pp. 21–23, 2007.
  50. T. P. Fan, J. C. Yeh, K. W. Leung, P. Y. K. Yue, and R. N. S. Wong, “Angiogenesis: from plants to blood vessels,” Trends in Pharmacological Sciences, vol. 27, no. 6, pp. 297–309, 2006. View at Publisher · View at Google Scholar · View at Scopus
  51. S. Li, A. Lu, and H. Jia, “Therapeutic actions of the Chinese herbal formulae with cold and heat properties and their effects on ultrastructures of synoviocytes in rats of the collagen-induced arthritis,” Journal of Traditional Chinese Medicine, vol. 22, no. 4, pp. 296–302, 2002. View at Scopus
  52. H. Yan, B. Zhang, S. Li, and Q. Zhao, “A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway,” BMC Systems Biology, vol. 4, article 50, 2010. View at Publisher · View at Google Scholar
  53. L. G. Darlington and T. W. Stone, “Antioxidants and fatty acids in the amelioration of rheumatoid arthritis and related disorders,” The British Journal of Nutrition, vol. 85, no. 3, pp. 251–269, 2001. View at Scopus
  54. X. L. Piao, X. S. Piao, S. W. Kim, J. H. Park, H. Y. Kim, and S. Q. Cai, “Identification and characterization of antioxidants from Sophora flavescens,” Biological and Pharmaceutical Bulletin, vol. 29, no. 9, pp. 1911–1915, 2006. View at Publisher · View at Google Scholar · View at Scopus
  55. T. Nakahama, A. Kimura, N. T. Nguyen et al., “Aryl hydrocarbon receptor deficiency in T cells suppresses the development of collagen-induced arthritis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 34, pp. 14222–14227, 2011. View at Publisher · View at Google Scholar
  56. E. Lounkine, M. J. Keiser, S. Whitebread et al., “Large-scale prediction and testing of drug activity on side-effect targets,” Nature, vol. 486, no. 7403, pp. 361–367, 2012. View at Publisher · View at Google Scholar
  57. H. Kitano, “Biological robustness,” Nature Reviews Genetics, vol. 5, no. 11, pp. 826–837, 2004.
  58. H. Kitano, “Cancer as a robust system: implications for anticancer therapy,” Nature Reviews Cancer, vol. 4, no. 3, pp. 227–235, 2004. View at Scopus
  59. J. Lehár, A. Krueger, G. Zimmermann, and A. Borisy, “High-order combination effects and biological robustness,” Molecular Systems Biology, vol. 4, article 215, 2008. View at Publisher · View at Google Scholar
  60. P. Csermely, V. Ágoston, and S. Pongor, “The efficiency of multi-target drugs: the network approach might help drug design,” Trends in Pharmacological Sciences, vol. 26, no. 4, pp. 178–182, 2005. View at Publisher · View at Google Scholar · View at Scopus
  61. A. del Sol, R. Balling, L. Hood, and D. Galas, “Diseases as network perturbations,” Current Opinion in Biotechnology, vol. 21, no. 4, pp. 566–571, 2010. View at Publisher · View at Google Scholar · View at Scopus
  62. R. B. Russell and P. Aloy, “Targeting and tinkering with interaction networks,” Nature Chemical Biology, vol. 4, no. 11, pp. 666–673, 2008. View at Publisher · View at Google Scholar · View at Scopus
  63. A. F. Fliri, W. T. Loging, and R. A. Volkmann, “Cause-effect relationships in medicine: a protein network perspective,” Trends in Pharmacological Sciences, vol. 31, no. 11, pp. 547–555, 2010. View at Publisher · View at Google Scholar · View at Scopus
  64. R. P. Araujo, C. Doran, L. A. Liotta, and E. F. Petricoin, “Network-targeted combination therapy: a new concept in cancer treatment,” Drug Discovery Today: Therapeutic Strategies, vol. 1, no. 4, pp. 425–433, 2004. View at Publisher · View at Google Scholar · View at Scopus
  65. S. Li, N. Zhang, and B. Zhang, “Method of network-based identification of multicomponent synergy and compositions for use as effective component of anti-angiogenesis medicines,” Invention Patent: US, 8112230 B2, 2009.
  66. A. L. Barabási, N. Gulbahce, and J. Loscalzo, “Network medicine: a network-based approach to human disease,” Nature Reviews Genetics, vol. 12, no. 1, pp. 56–68, 2011. View at Publisher · View at Google Scholar · View at Scopus
  67. C. Morel, F1000.com/12166956, 2011.
  68. C. Y. Chuang, J. G. Xiao, and G. C. Y. Chiou, “Ocular anti-inflammatory actions of matrine,” Journal of Ocular Pharmacology, vol. 3, no. 2, pp. 129–134, 1987. View at Scopus
  69. T. W. Kok, P. Y. K. Yue, N. K. Mak, T. P. D. Fan, L. Liu, and R. N. S. Wong, “The anti-angiogenic effect of sinomenine,” Angiogenesis, vol. 8, no. 1, pp. 3–12, 2005. View at Publisher · View at Google Scholar · View at Scopus
  70. X. J. Li, P. Y. K. Yue, W. Y. Ha et al., “Effect of sinomenine on gene expression of the IL-1β-activated human synovial sarcoma,” Life Sciences, vol. 79, no. 7, pp. 665–673, 2006. View at Publisher · View at Google Scholar · View at Scopus
  71. Z. Hu, Q. Jiao, J. Ding et al., “Berberine induces dendritic cell apoptosis and has therapeutic potential for rheumatoid arthritis,” Arthritis and Rheumatism, vol. 63, no. 4, pp. 949–959, 2011. View at Publisher · View at Google Scholar · View at Scopus
  72. P. Lito, C. A. Pratilas, E. W. Joseph et al., “Relief of profound feedback inhibition of mitogenic signaling by RAF inhibitors attenuates their activity in BRAFV600E melanomas,” Cancer Cell, vol. 22, no. 5, pp. 668–682, 2012. View at Publisher · View at Google Scholar
  73. A. Britschgi, R. Andraos, H. Brinkhaus et al., “JAK2/STAT5 inhibition circumvents resistance to PI3K/mTOR blockade: a rationale for cotargeting these pathways in metastatic breast cancer,” Cancer Cell, vol. 22, no. 6, pp. 796–811, 2012. View at Publisher · View at Google Scholar
  74. F. R. Greten, M. C. Arkan, J. Bollrath et al., “NF-κB is a negative regulator of IL-1β secretion as revealed by genetic and pharmacological inhibition of IKKβ,” Cell, vol. 130, no. 5, pp. 918–931, 2007. View at Publisher · View at Google Scholar · View at Scopus
  75. L. C. Hsu, T. Enzler, J. Seita et al., “IL-1β-driven neutrophilia preserves antibacterial defense in the absence of the kinase IKKβ,” Nature Immunology, vol. 12, no. 2, pp. 144–150, 2011. View at Publisher · View at Google Scholar · View at Scopus
  76. Y. Ben-Neriah and M. Karin, “Inflammation meets cancer, with NF-κB as the matchmaker,” Nature Immunology, vol. 12, no. 8, pp. 715–723, 2011. View at Publisher · View at Google Scholar
  77. L. P. Zhang, J. K. Jiang, J. W. O. Tam et al., “Effects of matrine on proliferation and differentiation in K-562 cells,” Leukemia Research, vol. 25, no. 9, pp. 793–800, 2001. View at Publisher · View at Google Scholar · View at Scopus