In-silico studies in Chinese herbal medicines' research: Evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date

Journal of Ethnopharmacology

Volumn 140, Issue 3, 2012, Pages 526-534

  Barlow, D J ^a   Buriani, A ^a,b,c   Ehrman, T ^a   Bosisio, E ^d   Eberini, I ^d   Hylands, P J ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF PADOVA   (Italy)

^c Data Medica   (Italy)

^d UNIVERSITY OF MILAN   (Italy)

Author keywords

Chinese Herbal medicine; GP TCM; In silico studies; Traditional Chinese Medicine

Indexed keywords

ALGORITHM; BIOINFORMATICS; CHINESE HERB; CHINESE MEDICINE; EVALUATION; HERBAL MEDICINE; MEDICAL RESEARCH; METHODOLOGY; MOLECULAR DOCKING; NERVE CELL NETWORK; PHYTOCHEMISTRY; REVIEW; SCREENING; SUPPORT VECTOR MACHINE;

EID: 84859005497     PISSN: 03788741     EISSN: 18727573     Source Type: Journal    
DOI: 10.1016/j.jep.2012.01.041     Document Type: Article

References (77)

1. Auffray, C., Chen, Z., Hood, L., 2009. Systems medicine: the future of medical genomics and healthcare. Genome Medicine 1, 2.
2. Becker, K.G., Barnes, K.C., Bright, T.J., Wang, S.A., 2004. The genetic association database. Nature Genetics 36, 431-432.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., 2000. The protein data bank. Nucleic Acids Research 28, 235-242. (Pubitemid 30047768)
4. Buriani, A., Garcia-Bermejo, M.L., Bosisio, E., Xu, Q., Li, H., Dong, X., Simmonds, M.S.J., Carrara, M., Tejedor, N., Lucio-Cazana, J., Hylands, P.J., 2012. Omic techniques in systems biology approaches to traditional Chinese medicine research: present and future. Journal of Ethnopharmacology 140, 535-544.
5. Chadeau-Hyam, M., Ebbels, T.M.D., Brown, I.J., Chan, Q., Stamler, J., Huang, C.C., Daviglus, M.L., Ueshima, H., Zhao, L., Holmes, E., Nicholson, J.K., Elliott, P., De Iorio, M., 2010. Metabolic profiling and the metabolome-wide association study: significance level for biomarker identification. Journal of Proteome Research 9, 4620-4627.
6. Cai, J.H., Han, C., Hu, T.C., Zhang, J., Wu, D.L., Wang, F.D., Liu, Y.Q., Ding, J.P., Chen, K.X., Yue, J.M., Shen, X., Jiang, H.L., 2006. Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Science 15, 2071-2081. (Pubitemid 44316010)
7. Chen, C.Y.-C., 2011. TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico. PLoS One 6, e15939, doi:10.1371/journal.pone.0015939.
8. Chen, Y.Z., Zhi, D.G., 2001. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43, 217-226.
9. Chen, X., Zhou, H., Liu, Y.B., Wang, J.F., Li, H., Ung, C.Y., Han, L.Y., Cao, Z.W., Chen, Y.Z., Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. British Journal of Pharmacology 149, 1092-1103.
10. Chen, C.Y., Chang, Y.H., Bau, D.T., Huang, H.J., Tsai, F.J., Tsai, C.H., Chen, C.Y.C., 2009. Discovery of potent inhibitors for phosphodiesterase 5 by virtual screening and pharmacophore analysis. Acta Pharmacologica Sinica 30, 1186-1194.
11. Chen, Y.Z., Ung, C.Y., 2002. Computer automated prediction of potential therapeutic and toxicity protein targets of bioactive compounds from Chinese medicinal plants. American Journal of Chinese Medicine 30, 139-154. (Pubitemid 41758929)
12. Chen, X., Ung, C.Y., Chen, Y.Z., 2003. Can an in silico drug-target search method be used to probe potential mechanisms of medicinal plant ingredients? Natural Products Reports 20, 432-444. (Pubitemid 37007966)
13. Choi, H., Ghosh, D., Nesvizhskii, A.I., 2008. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. Journal of Proteome Research 7, 286-292. (Pubitemid 351171141)
14. Cheng, W.Y., Wu, S.L., Hsiang, C.Y., Li, C.C., Lai, T.Y., Lo, H.Y., Shen, W.S., Lee, C.H., Chen, J.C., Wu, H.C., Ho, T.Y., 2008. Relationship between San-Huang-Xie-Xin- Tang and its herbal components on the gene expression profiles in HepG2 cells. American Journal of Chinese Medicine 36, 783-797.
15. Deng, X.Q., Wang, H.Y., Zhao, Y.L., Xiang, M.L., Jiang, P.D., Cao, Z.X., Zheng, Y.Z., Luo, S.D., Yu, L.T., Wei, Y.Q., Yang, S.Y., 2008. Pharmacophore modelling and virtual screening for identification of new Aurora-A kinase inhibitors. Chemical Biology & Drug Design 71, 533-539.
16. Ding, Y., Choi, H., Nesvizhskii, A.I., 2008. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. Journal of Proteome Research 7, 4878-4889.
17. Dixon, S.L., Smondyrev, A.M., Rao, S.N., 2006. PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chemical Biology & Drug Design 67, 370-372.
18. Do, Q.T., Bernard, P., 2006. Reverse pharmacognosy: a new concept for accelerating natural drug discovery. In: Khan, M.T.H., Ather, A. (Eds.), Lead Molecules from Natural Products. Elsevier, pp. 1-20.
19. Duke, J.A., 1992. Handbook of Phytochemical Constituents of GRAS Herbs and Other Economic Plants. CRC Press, Boca Raton.
20. Ehrman, T.M., Barlow, D.J., Hylands, P.J., 2007a. Phytochemical databases of Chinese herbal constituents and bioactive plant compounds with known target specificities. Journal of Chemical Information & Modeling 47, 254-263. (Pubitemid 46615931)
21. Ehrman, T.M., Barlow, D.J., Hylands, P.J., 2007b. Virtual screening of Chinese herbs with Random Forest. Journal of Chemical Information & Modeling 47, 264-278. (Pubitemid 46615932)
22. Ehrman, T.M., Barlow, D.J., Hylands, P.J., 2010a. In-silico search for multi-target anti-inflammatories in Chinese herbs and formulas. Bio-organic & Medicinal Chemistry 18, 2204-2218.
23. Ehrman, T.M., Barlow, D.J., Hylands, P.J., 2010b. Phytochemical informatics & virtual screening of herbs used in Chinese medicine. Current Pharmaceutical Design 16, 1785-1798.
24. Fang, X., Shao, L., Zhang, H., Wang, S., 2005. CHMIS-C: a comprehensive herbal medicine information system for cancer. Journal of Medicinal Chemistry 48, 1481-1488. (Pubitemid 40364555)
25. Fang, Y.C., Huang, H.C., Chen, H.H., Juan, H.F., 2008. TCMGeneDIT: a database for associated traditional Chinese medicine gene and disease information using text mining. BMC Complementary & Alternative Medicine 14, 8-18.
26. Feher, M., Schmidt, J.M., 2003. Property distributions: differences between drugs natural products and molecules from combinatorial chemistry. Journal of Chemical Information & Computer Science 43, 218-227.
27. Fiehn, O., Barupal, D.K., Kind, T., 2011. Extending biochemical databases by metabolomic surveys. Journal of Biological Chemistry 286, 23637-23643.
28. Frolkis, A., Knox, C., Lim, E., Jewison, T., Law, V., Hau, D.D., Liu, P., Gautam, B., Ly, S., Guo, A.C., Xia, J., Liang, Y., Shrivastava, S., Wishart, D.S., 2010. SMPDB: the small molecule pathway database. Nucleic Acids Research 38, D480-D487.
29. Griss, J., Haudek-Prinz, V., Gerner, C., 2011. GPDE: a biological proteomic database for biomarker discovery and evaluation. Proteomics 11, 1000-1004.
30. Gao, W.N., Li, Y., Zhang, R., Gao, H., Xu, W.R., Li, A.X., Du, Q.S., Zhang, X., Wei, D.Q., 2007. Screening of new HIV inhibitors based on the database of traditional Chinese medicine. Yaoxue Xuebao 2006, 241-246.
31. Gao, Z., Li, H., Zhang, H., Liu, X., Kang, L., Luo, X., Zhu, W., Chen, K., Wang, X., Jiang, H., 2008. PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics 9, 104-110.
32. Goodsell, D.S., Morris, G.M., Olson, A.J., 1996. Automated docking of flexible ligands: applications of AutoDock. Journal of Molecular Recognition 9, 1-5. (Pubitemid 126565462)
33. Guo, L., Mei, N., Liao, W., Chan, P.C., Fu, P.P., 2010. Ginkgo biloba extract induces gene expression changes in xenobiotics metabolism and the Myc-centered network. OMICS 14, 75-90.
34. Halgren, T.A., Murphy, R.B., Friesner, R.A., Beard, H.S., Frye, L.L., Pollard, W.T., Banks, J.L., 2004. Glide: a new approach for rapid, accurate docking and scoring: 1. Method assessment of docking accuracy. Journal of Medicinal Chemistry 47, 1739-1749. (Pubitemid 38380917)
35. Hayes, K.R., Vollrath, A.L., Zastrow, G.M., McMillan, B.J., Craven, M., Jovanovich, S., Rank, D.R., Penn, S., Walisser, J.A., Reddy, J.K., Thomas, R.S., Bradfield, C.A., 2005. EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information. Molecular Pharmacology 67, 1360-1368. (Pubitemid 40410437)
36. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y., Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, M., Nakanishi, Y., Ikeda, H., Akimoto, K., Maoka, N., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K.i., Nishioka, T., 2010. Mass- Bank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry 45, 703-714.
37. Huang, Q., Qiao, X.B., Xu, X.J., 2007. Potential synergism and inhibitors to multiple target enzymes of Xuefu Zhuyu decocotion in cardiac disease therapeutics: a computational approach. Bioorganic & Medicinal Chemistry Letters 17, 1779-1783. (Pubitemid 46274333)
38. Hung, Y.-C., Wang, P.-W., Pan, T.-L., 2010. Functional proteomics reveal the effect of Salvia miltiorrhiza aqueous extract against vascular atherosclerotic lesions. Biochimica et Biophysica Acta 1804, 1310-1321.
39. Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor, R., 1997. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology 267, 727-748. (Pubitemid 27170693)
40. Kamath, K.S., Vasavada, M.S., Srivastava, S., 2011. Proteomic databases and tools to decipher post-translational modifications. Journal of Proteomics 75, 127-144.
41. Khan, I., Nisar, M., Ebad, F., Nadeem, S., Saeed, M., Khan, H., Ullah, S., Khuda, F., Karim, N., Ahmad, Z., 2009. Anti-inflammatory activities of sieboldigenin from Smilax china Linn.: experimental and computational studies. Journal of Ethnopharmacology 121, 175-177.
42. Klimek, J., Eddes, J.S., Hohmann, L., Jackson, J., Peterson, A., Letarte, S., Gafken, P.R., Katz, J.E., Mallick, P., Lee, H., Schmidt, A., Ossola, R., Eng, J.K., Aebersold, R., Martin, D.B., 2008. The standard protein mix database: a diverse dataset to assist in the production of improved peptide and protein identification software tools. Journal of Proteome Research 7, 96-103. (Pubitemid 351171120)
43. Kouskoumvekaki, I., Panagiotou, G., 2011. Navigating the human metabolome for biomarker identification and design of pharmaceutical molecules. Journal of Biomedicine and Biotechnology 2011, 19, Article ID 525497. Lamb, J., 2007. The connectivity map: a new tool for biomedical research. Nature Reviews 7, 54-60.
44. 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., 2006. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Research 34, 219-224.
45. Li, C.Y., Hou, Y.C., Lee Chao, P.D., Shia, C.S., Hsu, I.C., Fang, S.H., 2010. Potential ex vivo immunomodulatory effects of San-Huang-Xie-Xin-Tang and its component herbs on mice and humans. Journal of Ethnopharmacology 127, 292-298.
46. Lim, E., Pon, A., Djoumbou, Y., Knox, C., Shrivastava, S., Guo, A.C., Neveu, V., Wishart, D.S., 2010. T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Research 38, D781-D786.
47. Lu, X., Xiong, Z., Li, J., Zheng, S., Huo, T., Li, F., 2011. Metabonomic study on 'Kidney-Yang Deficiency syndrome' and intervention effects of Rhizoma drynariae extracts in rats using ultra performance liquid chromatography coupled with mass spectrometry. Talanta 83, 700-708.
48. Ma, I., Bi, K., Zhang, M., Su, D., Fan, X., Ji, W., Wang, C., Chen, X., 2010. Metabonomic study of biochemical changes in the urine of Morning Glory seed treated rat. Journal of Pharmaceutical and Biomedical Analysis 53, 559-566.
49. Naylor, S., Chen, J.Y., 2010. Unraveling human complexity and disease with systems biology and personalized medicine. Personalized Medicine 7, 275-289.
50. Paoletta, S., Steventon, G.B., Wildeboer, D., Ehrman, T.M., Hylands, P.J., Barlow, D.J., 2008. Screening of herbal constituents for aromatase inhibitory activity. Bioorganic & Medicinal Chemistry 16, 8466-8470.
51. Qiao, X., Hou, T.J., Zhang, W., Guo, S.L., Xu, X.J., 2002. A 3D structure database of components from Chinese traditional medicinal herbs. Journal of Chemical Information & Computer Science 42, 481-489. (Pubitemid 35355253)
52. Rarey, M., Wefing, S., Lengauer, T., 1996. Placement of medium-sized molecular fragments in active sites of proteins. Journal of Computer-aided Molecular Design 10, 41-54. (Pubitemid 126712801)
53. Rollinger, J.M., Hornick, A., Langer, T., Stuppner, H., Prast, H., 2004. Acetylcholinesterase inhibitory activity of scoploin and scopoletin discovered by virtual screening of natural products. Journal of Medicinal Chemistry 47, 6248-6254. (Pubitemid 39587249)
54. Rollinger, J.M., Bodensieck, A., Seger, C., Ellmerer, E.P., Bauer, R., Langer, T., Stuppner, H., 2005. Discovering COX-inhibiting constituents of Morus root bark: activity-guided versus computer-aided methods. Planta Medica 71, 399-405. (Pubitemid 40839770)
55. Rollinger, J.M., Schuster, D., Danzl, B., Schwaiger, S., Markt, P., Schmidtke, M., Gertsch, J., Raduner, S., Wolber, G., Langer, T., Stuppner, H., 2009. In silico target fishing for rationalized ligand discovery exemplified on constituents of Ruta graveolens. Planta Medica 75, 195-204.
56. Sana, T.R., Roark, J.C., Li, X., Waddell, K., Fischer, S.M., 2008. Molecular formula and METLIN personal metabolite database matching applied to the identification of compounds generated by LC/TOF-MS. Journal of Biomolecular Techniques 19, 258-266.
57. Schellenberger, J., Park, J.O., Conrad, T.M., Palsson, B.Ø., 2010. BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11, 213.
58. Shen, J.H., Xu, X.Y., Cheng, F., Liu, H., Luo, X.M., Shen, J.K., Chen, K.X., Zhao, W.M., Shen, X., Jiang, H.L., 2003. Virtual screening on natural products for discovering active compounds and target information. Current Medicinal Chemistry 10, 1241-1253.
59. Shinde, K., Phatak, M., Johannes, F.M., Chen, J., Li, Q., Vineet, J.K., Hu, Z., Ghosh, K., Meller, J., Medvedovic, M., 2010. Genomics portals: integrative web-platform for mining genomics data. BMC Genomics 11, 27.
60. Shoichet, B.K., Kuntz, I.D., 1993. Matching chemistry and shape in molecular docking. Protein Engineering 6, 723-732. (Pubitemid 23293201)
61. Smith, J.G., Newton-Cheh, C., 2009. Genome-wide association study in humans. Methods in Molecular Biology 573, 231-258.
62. Thomsen, R., Christensen, M.H., 2006. MolDock: a new technique for high-accuracy molecular docking. Journal of Medicinal Chemistry 49, 3315-3321. (Pubitemid 43830529)
63. Venkatachalam, C.M., Jiang, X., Oldfield, T., Waldman, M., 2003. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. Journal of Molecular Graphics & Modeling 21, 289-307. (Pubitemid 35441326)
64. Uzuner, H., Fan, T.P., Dias, A., Guo, D.A., El-Nezami, H.S., Xu, Q., 2010. Establishing an EU-China consortium on traditional Chinese medicine research. Chinese Medicine 5, 42.
65. Wang, S.Q., Du, Q.S., Zhao, K., Li, A.X., Wei, D.Q., Chou, K.C., 2007. Virtual screening for finding natural inhibitor against cathepsin-L for SARS therapy. Amino Acids 33, 129-137.
66. Wang, E., Bussom, S., Chen, J., Quinn, C., Bedognetti, D., Lam, W., Guan, F., Jiang, Z., Mark, Y., Zhao, Y., Stroncek, D.F., White, J., Marincola, F.M., Cheng, Y.-C., 2011. Interaction of a traditional Chinese medicine (PHY906) and CPT-11 on the inflammatory process in the tumor microenvironment. BMC Medical Genomics 4, 38.
67. Wang, H.Y., Cao, Z.X., Li, L.L., Jiang, P.D., Zhao, Y.L., Luo, S.D., Yang, L., Wei, Y.Q., Yang, S.Y., 2008. Pharmacophore modeling and virtual screening for designing potential PLK1 inhibitors. Bioorganic & Medicinal Chemistry Letters 18, 4972-4977.
68. Wang, R., Fabregat, A., Ríos, D., Ovelleiro, D., Foster, J.M., Côté, R.G., Griss, J., Csordas, A., Perez-Riverol, Y., Reisinger, F., Hermjakob, H., Martens, L., Vizcaíno, J.A., 2012. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nature Biotechnology 30 (2), 135-137.
69. Waters, M., Stasiewicz, S., Merrick, B.A., Tomer, K., Bushel, P., Paules, R., Stegman, N., Nehls, G., Yost, K.J., Johnson, C.H., Gustafson, S.F., Xirasagar, S., Xiao, N., Huang, C.-C., Boyer, P., Chan, D.D., Pan, Q., Gong, H., Taylor, J., Choi, D., Rashid, A., Ahmed, A., Howle, R., Selkirk, J., Tennant, R., Fostel, J., 2008. CEBS - Chemical effects in biological systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Research 36, D892-D900. (Pubitemid 351149841)
70. Wen, Z., Wang, Z., Wang, S., Ravula, R., Yang, L., Xu, J., Wang, C., Zuo, Z., Chow, M.S., Shi, L., Huang, Y., 2011. Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map. PLoS One 6, e18278.
71. Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., Gautam, B., Hau, D.D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J.A., Lim, E., Sobsey, C.A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H.J., Forsythe, I., 2009. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research 37, D603-D610.
72. Wolber, G., Langer, T., 2005. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. Journal of Chemical Information & Modeling 45, 160-169. (Pubitemid 40736968)
73. Wolf, S., Schmidt, S., Müller-Hannemann, M., Neumann, S., 2010. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11, 148.
74. Yu, H., Wang, Z.L., Zhang, L.R., Zhang, J.F., Huang, Q., 2007. Pharmacophore modeling and in silico screening for new KDR kinase inhibitors. Bioorganic & Medicinal Chemistry Letters 17, 2126-2133. (Pubitemid 46484321)
75. Yue, Q.X., Cao, Z.W., Guan, S.H., Liu, X.H., Tao, L., Wu, W.Y., Li, Y.X., Yang, P.Y., Liu, X., Guo, D.A., 2008. Proteomics characterization of the cytotoxicity of mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Molecular & Cellular Proteomics 7, 949-961. (Pubitemid 351737094)
76. Zeng, Z.R., Qian, L., Cao, L.X., Tan, H.M., Huang, Y.L., Xue, X.L., Shen, Y., Zhou, S.N., 2008. Virtual screening for novel quorum sensing inhibitors to eradicate biofilm formation of Pseudomonas aeruginosa. Applied Microbiology & Biotechnology 79, 119-126.
77. Zhu, F., Han, B., Kumar, P., Liu, X., Ma, X., Wei, X., Huang, L., Guo, Y., Han, L., Zheng, C., Chen, Y., 2010. Update of TTD: therapeutic target database. Nucleic Acids Research 38, D787-D791.