Identifying potential drugs for inhibition the M2 protein channel of influenza A by steered molecular dynamics
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Abstract
Combining Lipinski’s rule and docking method were used as a virtual screening tool to find out top hits from the large data base CHEMSPIDER with more than 1,4 million compounds. The lowest binding energy ΔEbind obtained in the best docking mode was chosen as a scoring function for selecting top ligands. Virtual screening has obtained top-leads compounds with binding energy less than -11.0 kcal.mol-1 for inhibition the M2 protein channels of influenza A virus H5N1. Since the predictive power of the docking method is limited, top-leads were selected for further study by the more precise steered molecular dynamics method. The main idea of this method is that instead of the binding free energy, the rupture force needed to unbind a ligand from a receptor used as a measure of binding affinity. The higher is rupture force, and the stronger is binding.
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References
Bright, R. A., Medina, M. J., Xu, X., Perez-Oronoz, G., Wallis, T. R., Davis, X. M., Povinelli, N. J., Cox., & Klimov, A. I. (2005). Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern. The Lancet, 366(9492), 1175-1181.
Bright, R. A., Shay, D. K., Shu, B., Cox, N. J., & Klimov, A. I. (2006). Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States. Jama, 295(8), 891-894.
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., & Damborsky, J. (2012). CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol, 8(10), e1002708.
Das, K. (2012). Antivirals targeting influenza A virus. Journal of Medicinal Chemistry, 55(14), 6263-6277.
Grubmüller, H., Heymann, B., & Tavan, P. (1996). Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science, 271(5251), 997-999.
Isralewitz, B., Gao, M., & Schulten, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural biology, 11(2), 224-230.
Kumar, S., & Li, M. S. (2010). Biomolecules under mechanical force. Physics Reports, 486(1), 1-74.
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings¶. Advanced Drug Delivery Reviews, 64, 4-17.
Mai, B. K., & Li, M. S. (2011). Neuraminidase inhibitor R-125489-a promising drug for treating influenza virus: steered molecular dynamics approach. Biochemical and Biophysical Research Communications, 410(3), 688-691.
Pielak, R. M., & Chou, J. J. (2011). Influenza M2 proton channels. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1808(2), 522-529.
Sanner, M. F. (1999). Python: a programming language for software integration and development. J. Mol Graph Model, 17(1), 57-61.
Schnell, J. R., & Chou, J. J. (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 451(7178), 591-595.
Sugrue, R., & Hay, A. (1991). Structural characteristics of the M2 protein of influenza a viruses: Evidence that it forms a tetrameric channe. Virology, 180(2), 617-624.
Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.
Vuong, Q. V., Nguyen, T. T., & Li, M. S. (2015). A new method for navigating optimal direction for pulling ligand from binding pocket: application to ranking binding affinity by steered molecular dynamics. Journal of Chemical Information and Modeling, 55(12), 2731-2738.
Bright, R. A., Shay, D. K., Shu, B., Cox, N. J., & Klimov, A. I. (2006). Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States. Jama, 295(8), 891-894.
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., & Damborsky, J. (2012). CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol, 8(10), e1002708.
Das, K. (2012). Antivirals targeting influenza A virus. Journal of Medicinal Chemistry, 55(14), 6263-6277.
Grubmüller, H., Heymann, B., & Tavan, P. (1996). Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science, 271(5251), 997-999.
Isralewitz, B., Gao, M., & Schulten, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural biology, 11(2), 224-230.
Kumar, S., & Li, M. S. (2010). Biomolecules under mechanical force. Physics Reports, 486(1), 1-74.
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings¶. Advanced Drug Delivery Reviews, 64, 4-17.
Mai, B. K., & Li, M. S. (2011). Neuraminidase inhibitor R-125489-a promising drug for treating influenza virus: steered molecular dynamics approach. Biochemical and Biophysical Research Communications, 410(3), 688-691.
Pielak, R. M., & Chou, J. J. (2011). Influenza M2 proton channels. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1808(2), 522-529.
Sanner, M. F. (1999). Python: a programming language for software integration and development. J. Mol Graph Model, 17(1), 57-61.
Schnell, J. R., & Chou, J. J. (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 451(7178), 591-595.
Sugrue, R., & Hay, A. (1991). Structural characteristics of the M2 protein of influenza a viruses: Evidence that it forms a tetrameric channe. Virology, 180(2), 617-624.
Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.
Vuong, Q. V., Nguyen, T. T., & Li, M. S. (2015). A new method for navigating optimal direction for pulling ligand from binding pocket: application to ranking binding affinity by steered molecular dynamics. Journal of Chemical Information and Modeling, 55(12), 2731-2738.
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