Background. Traditional Chinese medicine encompasses a well established alternate system of medicine based on a broad range of herbal formulations and is practiced extensively in the region for the treatment of a wide variety of diseases. In recent years, several reports describe in depth studies of the molecular ingredients of traditional Chinese medicines on the biological activities including anti-bacterial activities. The availability of a well-curated dataset of molecular ingredients of traditional Chinese medicines and accurate in-silico cheminformatics models for data mining for antitubercular agents and computational filters to prioritize molecules has prompted us to search for potential hits from these datasets.
References
[1]
Baell JB, Holloway GA. 2010. New substructure filters for removal of Pan Assay Interference Compounds (PAINS) from screening libraries and for their exclusion in bioassays. Journal of Medicinal Chemistry 53:2719-2740
[2]
Bouckaert RR, Frank E, Hall MA, Holmes G, Pfahringer B, Reutemann P. 2010. WEKA—experiences with a Java Open-Source Project. Journal of Machine Learning Research 11:2533-2541
[3]
Chang HM, Paul PHB. 2001. Pharmacology and applications of Chinese materia Medica. Hong Kong: World Scientific Publishing. 1061-1077
[4]
Chen CYC. 2011. TCM Database@Taiwan: the world’s largest traditional Chinese medicine database for drug screening in silico. PLoS ONE 6:e15939
[5]
Chen JJ, Wu HM, Peng CF, Chen IS, Chu SD. 2009. seco-Abietane diterpenoids, a phenylethanoid derivative, and antitubercular constituents from Callicarpa pilosissima. Journal of Natural Products 72(2):223-228
[6]
Chen X, Zhou H, Liu YB, Wang JF, Li H, Ung CY, Han LY, Cao ZW, Chen YZ. 2006. Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. British Journal of Pharmacology 149:1092-1103
[7]
Cheng HM, Li CC, Chen CY, Lo HY, Cheng WY, Lee CH, Yang SZ, Wu SL, Hsiang CY, Ho TY. 2010. Application of bioactivity database of Chinese herbal medicine on the therapeutic prediction, drug development, and safety evaluation. Journal of Ethnopharmacology 132(2):429-437
[8]
Choi TA, Czerwonka R, Frhner W, Krahl MP, Reddy KR, Franzblau SG, Knlker HJ. 2006. Synthesis and activity of carbazole derivatives against Mycobacterium tuberculosis. ChemMedChem 1(8):812-815
[9]
DiMasi JA, Hansen RW, Grabowski HG. 2003. The price of innovation: new estimates of drug development costs. Journal of Health Economics 22:151-185
[10]
Fang YC, Huang HC, Chen HH, Juan HF. 2008. TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. BMC Complementary and Alternative Medicine 8:58
[11]
Han C, Guo J. 2012. Antibacterial and anti-inflammatory activity of traditional Chinese herb pairs, Angelica sinensis and Sophora flavescens. Inflammation 35(3):913-919
[12]
Hann M, Hudson B, Lewell X, Lifely R, Miller L, Ramsden N. 2009. Strategic pooling of compounds for high-throughput screening. Journal of Chemical Information and Computer Sciences 39(5):897-902
[13]
Hu Y, Wang S, Wu X, Zhang J, Chen R, Chen M, Wang Y. 2013. Chinese herbal medicine-derived compounds for cancer therapy: a focus on hepatocellular carcinoma. Journal of Ethnopharmacology 149(3):601-612
[14]
Huth JR, Mendoza R, Olejniczak ET, Johnson RW, Cothron DA, Liu Y, Lerner CG, Chen J, Hajduk PJ. 2005. ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. Journal of the American Chemical Society 127:217-224
[15]
Iinuma M, Tosa H, Tanaka T, Kanamaru S, Asai F, Kobayashi Y, Miyauchi K, Shimano R. 1996. Antibacterial activity of some Garcinia benzophenone derivatives against methicillin-resistant Staphylococcus aureus. Biological and Pharmaceutical Bulletin 19(2):311-314
[16]
Issabeagloo E, Taghizadieh M. 2012. Hepatomodulatory action of camellia sinensis aqueous extract against isoniazid-rifampicin combination induced oxidative stress in rat. Advances in Bioresearch 3:18-27
[17]
Jaiswal R, Beuria TK, Mohan R, Mahajan SK, Panda D. 2007. Totarol inhibits bacterial cytokinesis by perturbing the assembly dynamics of FtsZ. Biochemistry 46(14):4211-4220
[18]
Jamal S, Periwal V, Scaria V. 2012. Computational analysis and predictive modeling of small molecule modulators of microRNA. Journal of Cheminformatics 4:16
[19]
Jamal S, Periwal V, Scaria V. 2013. Predictive modeling of anti-malarial molecules inhibiting apicoplast formation. BMC Bioinformatics 14:55
[20]
Jiang L, Deng L, Wu T. 2013. Chinese medicinal herbs for influenza. Cochrane Database Systems Reviews 3:CD004559
[21]
John EF (Translator). 1977. A barefoot doctors manual: the American translation of the official Chinese paramedical manual. Philadelphia, PA: Running Press Book Publishers.
[22]
Kurti V, Uldrich J. 1958. Effect of azulenes on Mycobacterium tuberculosis & their use in the local treatment of tuberculous cystitis. Casopis Lekaru Ceskych 97(3):67-71
[23]
Li SZ. 1984. Combined traditional Chinese medicine and western medicine in the treatment of 356 cases of scrofula of the neck and axilla. Zhong Xi Yi Jie He Za Zhi 4(2):90-92
[24]
Li XM, Brown L. 2009. Efficacy and mechanisms of action of traditional Chinese medicines for treating asthma and allergy. Journal of Allergy and Clinical Immunology 123(2):297-306
[25]
Li XJ, Kong DX, Zhang HY. 2010. Chemoinformatics approaches for traditional Chinese medicine research and case application in anticancer drug discovery. Current Drug Discovery Technologies 7(1):22-31
[26]
Liu K, Feng J, Young SS. 2005. PowerMV: a software environment for molecular viewing, descriptor generation, data analysis and hit evaluation. Journal of Chemical Information and Modeling 45:515-522
[27]
Liu Q, Garner P, Wang Y, Huang B, Smith H. 2008. Drugs and herbs given to prevent hepatotoxicity of tuberculosis therapy: systematic review of ingredients and evaluation studies. BMC Public Health 21(8):365
[28]
Lu J, Ye S, Qin R, Deng Y, Li CP. 2013. Effect of Chinese herbal medicine extracts on cell-mediated immunity in a rat model of tuberculosis induced by multiple drug-resistant bacilli. Molecular Medicine Reports 8(1):227-232
[29]
Melville JL, Burke EK, Hirst JD. 2009. Machine learning in virtual screening. Combinatorial Chemistry High Throughput Screen 12:332-343
[30]
Merget B, Zilian D, Müller T, Sotriffer CA. 2013. MycPermCheck: the mycobacterium tuberculosis permeability prediction tool for small molecules. Bioinformatics 29(1):62-68
[31]
Mohamed Saleem TS, Christina AJM, Chidambaranathan N, Ravi V, Gauthaman K. 2008. Hepatoprotective activity of Annona squamosa Linn. on experimental animal model. International Journal of Applied Research in Natural Products 1(3):1-7
[32]
Nader LA, de Mattos AA, Picon PD, Bassanesi SL, De Mattos AZ, Pineiro Rodriguez M. 2010. Hepatotoxicity due to rifampicin, isoniazid and pyrazinamide in patients with tuberculosis: is anti-HCV a risk factor? Annals of Hepatology 9(1):70-74
[33]
Nair RR, Abraham RS. 2008. Integrating the science of pharmacology and bio informatics phyllanthus “The wonder plant”. Advanced Biotech 2008:28
[34]
Normile D. 2003. The new face of traditional Chinese medicine. Science 299:188-190
[35]
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. 2011. Open babel: an open chemical toolbox. Journal of Cheminformatics 7(3):33
[36]
Ooi GL. 1993. Chinese medicine in Malaysia and Singapore: the business of healing. American Journal of Chinese Medicine 21(3–4):197-212
[37]
Periwal V, Kishtapuram S, Scaria V. 2012. Computational models for in-vitro antitubercular activity of molecules based on high-throughput chemical biology screening datasets. BMC Pharmacology 12:1
[38]
Periwal V, Rajappan JK, Jaleel AU, Scaria V. 2011. Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets. BMC Research Notes 4:504
[39]
Qiu J. 2007. Traditional medicine—a culture in the balance. Nature 448:126-128
[40]
Rani SM, Dayanand CD, Shetty J, Vegi PK, Kutty AVM. 2013. Evaluation of antibacterial activity of pongamia pinnata linn on pathogens of clinical isolates. American Journal of Phytomedicine and Clinical Therapeutics 1(8):645-651
[41]
Sato M, Tanaka H, Tani N, Nagayama M, Yamaguchi R. 2006. Different antibacterial actions of isoflavones isolated from Erythrina poeppigiana against methicillin-resistant Staphylococcus aureus. Letters in Applied Microbiology 43(3):243-248
[42]
Schierz AC. 2009. Virtual screening of bioassay data. Journal of Cheminformatics 1:21
[43]
Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. 2008. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Research 36:W223-W228
[44]
Shah NS, Wright A, Bai G-H, Barrera L, Boulahbal F, Martín-Casabona N, Drobniewski F, Gilpin C, Havelková M, Lepe R, Lumb R, Metchock B, Portaels F, Rodrigues MF, Rüsch-Gerdes S, Van Deun A, Vincent V, Laserson K, Wells C, Cegielski JP. 2007. Worldwide emergence of extensively drug-resistant tuberculosis. Emerging Infectious Diseases 13(3):380-387
[45]
Silva KN, Silva RC, Coelho VPM, Agra M. 2011. A pharmacobotanical study of vegetative organs of Solanum torvum. Brazilian Journal of Pharmacognosy 21(4):568-574
[46]
Singla D, Tewari R, Kumar A, Raghava GP. 2013. Open source drug discovery consortium. Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv) Chemistry Central Journal 7(1):49
[47]
Sucher NJ. 2006. Insights from molecular investigations of traditional Chinese herbal stroke medicines: implications for neuroprotective epilepsy therapy. Epilepsy Behavior 8(2):350-362
[48]
Su SY, Hsieh CL. 2011. Anti-inflammatory effects of Chinese medicinal herbs on cerebral ischemia. Chinese Medicine 6:26
[49]
Thattakudian Sheik Uduman MS, Sundarapandian R, Muthumanikkam A, Kalimuthu G, Parameswari SA, Vasanthi Srinivas TR, Karunakaran G. 2011. Protective effect of methanolic extract of Annona squamosa Linn in isoniazid rifampicin induced hepatotoxicity in rats. Pakistan Journal of Pharmaceutical Sciences 24(2):129-134
[50]
Udino L, Abaul J, Bourgeois P, Gorrichon L, Duran H, Zedde C. 1999. Lignans from the Seeds of Hernandia sonora. Planta Medica 65(3):279-281
[51]
Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NP, Olsen L, Jorgensen FS. 2009. Classification of cytochrome P450 1A2 inhibitors and non-inhibitors by machine learning techniques. Drug Metabolism and Disposition 37:658-664
[52]
Vert JP, Jacob L. 2008. Machine learning for in silico virtual screening and chemical genomics: new strategies. Combinatorial Chemistry High Throughput Screen 11:677-685
[53]
Wagner H, Wolff P. 1977. New natural products and plant drugs with pharmacological, biological or therapeutical activity. Berlin: Springer-Verlag. 212
[54]
Wang MW, Hao X, Chen K. 2007. Biological screening of natural products and drug innovation in China. Philosophical Transactions of the Royal Society B: Biological Sciences 362:1093-1105
[55]
Wang L, Qiu XM, Hao Q, Li DJ. 2013. Anti-inflammatory effects of a Chinese herbal medicine in atherosclerosis via estrogen receptor β mediating nitric oxide production and NF-κB suppression in endothelial cells. Cell Death and Disease 4:e551
[56]
Wen Z, Wang Z, Wang S, Ravula R, Yang L, Xu J, Wang C, Zuo Z, Chow MSS, 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(3):e18278
[57]
World Health Organization. 2012. Global tubercolosis report 2012. Available at http://apps.who.int/iris/bitstream/10665/75938/1/9789241564502_eng.pdf
[58]
Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. 2013. TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Research 41:D1089-D1095
[59]
Yantao H, Zeng L-F, Zhang Z-Y. 2012. Tyrosine phosphatase inhibitors and uses thereof to modulate the activity of enzymes involved in the pathology of mycobacterium tuberculosis, WIPO Patent Application PCT/US2012/035039
[60]
Yew WW, Leung CC. 2006. Antituberculosis drugs and hepatotoxicity. Respirology 11(6):699-707
[61]
Zhang K, Li Y, Zhang ZR, Guan WH, Pu YC. 2013. Chemoinformatics study on antibacterial activity of traditional Chinese medicine compounds. Zhongguo Zhong Yao Za Zhi 38(5):777-780
[62]
2011. Zhou J, Xie G, Yan X, eds. Encyclopedia of traditional Chinese medicines—molecular structures, pharmacological activities, natural sources and applications. New York: Springer.
