Article Sidebar

PDF
Date Published: 24/06/2023
Online Published: 23/06/2023
Abstract Views: 82
Views PDF: 31
DOI: https://doi.org/10.52714/dthu.12.5.2023.1070
Issue
Vol. 12 No. 5 (2023): Natural Sciences Issue (English)
Section
Natural Sciences Issue
How to Cite
Huynh, T. N. T., Tran, T. T. T., Pham, T. M. H., & Quach, K. Q. (2023). Study on the interaction mechanism of penciclovir drug on 3CLpro of SAR-CoV-2 by simulation methods. Dong Thap University Journal of Science, 12(5), 42-47. https://doi.org/10.52714/dthu.12.5.2023.1070

Study on the interaction mechanism of penciclovir drug on 3CLpro of SAR-CoV-2 by simulation methods

Thi Ngoc Thanh Huynh1, Thi Thanh Thu Tran2, Thi My Hanh Pham2, Kha Quang Quach3,
1 Center for Practice - Experiments, Dong Thap University, Vietnam
2 Department of Natural Sciences Teacher Education, Dong Thap University, Vietnam
3 International Affairs Office, Dong Thap University, Vietnam

Main Article Content

Abstract

Since the outbreak of SAR-CoV-2 infections in Wuhan (China), researched communication is on race to investigate the specific antiviral drug for Covid-19 treatment. 3CLpro main protease is chosen as a protein target because of its high value in preventing the SAR-CoV-2 viral replications. In this study, we hereby aim to clarify the efficiency of Penciclovir in inhibiting the mechanic of 3CLpro target of SAR-CoV-2. Using docking simulation and molecular dynamic simulation (SMD), the interaction of Penciclovir with 3CLpro target was investigated. The results show that Penciclovir strongly interacts with 3CLpro target, and the non-binding interaction plays a more important role than hydrogen bonding in the steady state of the receptor-ligand conformation.

Article Details

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Keywords

3CLpro, SAR-CoV-2, Penciclovir, docking method, SMD method

References

Bright, R. A., Medina, M. J., Xu, X., Perez-Oronoz, G., Wallis, T. R., Davis, X. M., Povinelli, L., Cox, N. J., & 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 Computational Biology, 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. Journal of Molecular Graphics and Modelling, 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. J., & Hay, A. J. (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.
Nguyen, H. L., Thai, N. Q., & Li, M. S. (2023). Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases. Journal of Biomolecular Structure and Dynamics, 41(15), 7045-7054.