Initial study on SARS-CoV-2 main protease inhibition mechanism of some potential drugs using molecular docking simulation

Quan Minh PHAM, Thuy Huong Thi LE, Toan Quoc TRAN, Tung Son NGO, Dan Trong NGUYEN, Thu Thuy Thi TRAN, Cuong Manh NGUYEN, Long Quoc PHAM

Abstract


The infection by the new coronavirus SARS-CoV-2 (called as COVID-19 disease) is a worldwide emergency, however, there is no antiviral treatment or vaccine until now. The crystal structure of SARS-CoV-2 main protease has been made publicity in the Protein Data Bank recently. Many efforts have been conducted by scientists including the use of several commercial medicines, however, understanding at atomic level how these compounds prevent SARS-CoV-2 protease is still lacking. In this context docking protocol was employed to rapidly estimate the binding affinity and binding pose of six drugs on the main protease.


Keywords


COVID-19, SARS-CoV-2, autodock4, protease inhibitor, molecular docking

Full Text:

PDF

References


Zumla A., Chan J. F. W., Azhar E. I., Hui D. S.C., and Yuen K. Y. - Coronaviruses — drug discovery and therapeutic options, Nature Reviews Drug Discovery. 15 (5) (2016) 327-347.

de Wit E., van Doremalen N., Falzarano D., and Munster V. J. - SARS and MERS: recent insights into emerging coronaviruses, Nature Reviews Microbiology. 14 (8) (2016) 523-534.

https://www.who.int/westernpacific/emergencies/pneumonia-in-wuhan-china. Accessed 12th January 2020.

https://abcnews.go.com/Health/coronavirus-map-tracking-spread-us-world/story?id=69415591.

Wang M., Cao R., Zhang L., Yang X., Liu J., Xu M., Shi Z., Hu Z., Zhong W., and Xiao G. - Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro, Cell Research. 30 (3) (2020) 269-271.

Ratia K., Saikatendu K. S., Santarsiero B. D., Barretto N., Baker S. C., Stevens R. C., and Mesecar A. D. - Severe acute respiratory syndrome coronavirus papain-like protease: Structure of a viral deubiquitinating enzyme, Proceedings of the National Academy of Sciences. 103 (15) (2006) 5717-5722.

Chen S., Chen L., Tan J., Chen J., Du L., Sun T., Shen J., Chen K., Jiang H., and Shen X. - Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase N Terminus Is Indispensable for Proteolytic Activity but Not for Enzyme Dimerization, Journal of Biological Chemistry. 280 (1) (2005) 164-173..

Chen Y., Savinov S. N., Mielech A. M., Cao T., Baker S. C., and Mesecar A. D. - X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions, Journal of Biological Chemistry. 290 (42) (2015) 25293-25306.

Liu X., Zhang B., Jin Z., Yang H., and Rao Z. - The crystal structure of COVID-19 main protease in complex with an inhibitor N3. To be published. PDB code 6LU7, https://www.rcsb.org/structure/6LU7.

Marshall G. R. - Computer-aided drug design, Annu Rev Pharmacol Toxicol. 27 (1987) 193-213.

Morris G. M., Huey R., Lindstrom W., Sanner M. F., Belew R. K., Goodsell D. S., and Olson A. J. - AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, Journal of Computational Chemistry. 30 (16) (2009) 2785-2791.

Muchtaridi M., Syahidah H. N., Subarnas A., Yusuf M., Bryant S. D., and Langer T. - Molecular Docking and 3D-Pharmacophore Modeling to Study the Interactions of Chalcone Derivatives with Estrogen Receptor Alpha, Pharmaceuticals. 10 (4) (2017).

Deng L., Li C., Zeng Q., Liu X., Li X., Zhang H., Hong Z., and Xia J. - Arbidol combined with LPV/r versus LPV/r alone against Corona Virus Disease 2019:a retrospective cohort study, Journal of Infection. 2020.

Lai C. C., Shih T. P., Ko W. C., Tang H. J., and Hsueh P. R.. - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges, International Journal of Antimicrobial Agents. 55 (3) (2020).

Sahu K. K., Mishra A. K., and Lal A. - Novel coronavirus (2019-nCoV): Update on 3rd Coronavirus Outbreak of 21st Century, QJM: An International Journal of Medicine. 2020.

Schrodinger, LLC, The PyMOL Molecular Graphics System, Version 1.8. 2015.

Allouche A. R. - Gabedit-A graphical user interface for computational chemistry softwares, Journal of Computational Chemistry. 32 (1) (2011) 174-182.

Tan J., Verchueren K. H. G., Anand K., Shen J., Yang M., Xu Y., Rao Z., Bigalke J., Heisen B., Mesters J. R., Chen K., Shen X., Hualiang J., and Hilgenfeld R. - pH-dependent Conformational Flexibility of the SARS-CoV Main Proteinase (Mpro) Dimer: Molecular Dynamics Simulations and Multiple X-ray Structure Analyses, Journal of Molecular Biology. 354 (1) (2005) 25-40.

Yang H., Yang M., Ding Y., Liu Y., Lou Z., Zhou Z., Sun L., Mo L., Ye S., Pang H., Gao G. F., Anand K., Bartlam M., Hilgenfeld R., and Rao Z. - The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor, Proceedings of the National Academy of Sciences. 100 (23) (2003) 13190-13195.

Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., and Ferrin T. E. - UCSF Chimera - A visualization system for exploratory research and analysis, Journal of Computational Chemistry. 25 (13) (2004) 1605-1612.

Dassault Systèmes BIOVIA, Discovery Studio Visualizer, v17.2.0.16349, San Diego: Dassault Systèmes, 2019.

Laskowski R. A., and Swindells M. B. - LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery, Journal of Chemical Information and Modeling. 51 (10) (2011) 2778-2786.

Maestro, S.R.-. Schrödinger Release 2019-4: Maestro, Schrödinger, LLC, New York, NY, 2019..

Hopkins A. L., Groom C. R., and Alex A. - Ligand efficiency: a useful metric for lead selection, Drug Discovery Today. 9 (10) (2004) 430-431.




DOI: https://doi.org/10.15625/2525-2518/58/5/14914 Display counter: Abstract : 221 views. PDF : 47 views.

Refbacks

  • There are currently no refbacks.


budidaya tani

Index: Google Scholar; Crossref; VCGate; Asean Citation Index

Published by Vietnam Academy of Science and Technology