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Ngày xuất bản: 24/06/2023
Ngày xuất bản Online: 23/06/2023
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DOI: https://doi.org/10.52714/dthu.12.5.2023.1070
Số xuất bản
Tập 12 Số 5 (2023): Chuyên san Khoa học Tự nhiên (Tiếng Anh)
Chuyên mục
Khoa học Tự nhiên (Tiếng Anh)
Trích dẫn bài báo
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. Tạp chí Khoa học Đại học Đồng Tháp, 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

Huynh Thi Ngoc Thanh1, Tran Thi Thanh Thu2, Pham Thi My Hanh2, Quach Kha Quang3,
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

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Tóm tắt

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.

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Creative Commons License

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

Từ khóa

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

Tài liệu tham khảo

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.

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