combining molecular docking and molecular dynamics to predict the binding modes of flavonoid derivatives with the neuraminidase of the 2009 h1n1 influenza a virus结合分子对接和分子动力学预测的绑定模式类黄酮衍生品与2009年h1n1流感病毒的神经氨酸酶.pdf

Int. J. Mol. Sci. 2012, 13, 4496-4507; doi:10.3390/ijm OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 /journal/ijms Article Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus Shih-Jen Lu 1,2,* and Fok-Ching Chong 1 1 Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan; E-Mail: fcchong931@ 2 Department of Research and Development, BroadMaster Biotech Co., Ltd. : 7F., No.168-2, Liancheng Rd., Zhonghe Dist., New Taipei City 23553, Taiwan * Author to whom correspondence should be addressed; E-Mail: .tw; Tel.: +886-266375859; Fax: +886-222428332. Received: 9 January 2012; in revised form: 22 March 2012 / Accepted: 29 March 2012 / Published: 10 April 2012 Abstract: Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models