Int. J. Mol. Sci. 2012, 13(4), 4496-4507; doi:10.3390/ijms13044496
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,* email and Fok-Ching Chong 1 email
1 Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan 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.
Received: 9 January 2012; in revised form: 22 March 2012 / Accepted: 29 March 2012 / Published: 10 April 2012
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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 of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R2 = 0.75.
Keywords: molecular dynamics; H1N1; neuraminidase; molecular docking

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MDPI and ACS Style

Lu, S.-J.; Chong, F.-C. Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus. Int. J. Mol. Sci. 2012, 13, 4496-4507.

AMA Style

Lu S-J, Chong F-C. Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus. International Journal of Molecular Sciences. 2012; 13(4):4496-4507.

Chicago/Turabian Style

Lu, Shih-Jen; Chong, Fok-Ching. 2012. "Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus." Int. J. Mol. Sci. 13, no. 4: 4496-4507.

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