Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM/MM computational methods.

Chemical Science
Katarzyna Swiderek, Vicent Moliner

Abstract

SARS-CoV-2 Mpro is one of the enzymes essential for the replication process of the virus responsible for the COVID-19 pandemic. This work is focused on exploring its proteolysis reaction by means of QM/MM methods. The resulting free energy landscape of the process provides valuable information on the species appearing along the reaction path and suggests that the mechanism of action of this enzyme, taking place in four steps, slightly differs from that of other cysteine proteases. Our predictions, which are in agreement with some recently published experimental data, can be used to guide the design of COVID-19 antiviral compounds with clinical potential.

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Citations

Jan 5, 2021·Medicinal Research Reviews·Yinuo WuHai-Bin Luo
Jan 14, 2021·The Biochemical Journal·George M Burslem
Mar 13, 2021·Physical Chemistry Chemical Physics : PCCP·Ernest Awoonor-Williams, Abd Al-Aziz A Abu-Saleh
Mar 20, 2021·ChemMedChem·Angelo SpinelloAlessandra Magistrato
Apr 4, 2021·International Journal of Molecular Sciences·Brigitta Elsässer, Peter Goettig
Apr 15, 2021·Chemistry : a European Journal·Kemel ArafetVicent Moliner
Apr 18, 2021·Journal of Molecular Modeling·Debarati PaulShubhra Ghosh Dastidar
Apr 27, 2021·The Journal of Physical Chemistry Letters·Laura Zanetti-PolziIsabella Daidone
Oct 3, 2020·Frontiers in Molecular Biosciences·Giulia PalermoValentina Tozzini
Jun 2, 2021·Journal of Biomolecular Structure & Dynamics·Sayantan PradhanProsenjit Sen
May 5, 2021·Chemical Communications : Chem Comm·Natalia Díaz, Dimas Suárez
Jun 15, 2021·Journal of Chemical Information and Modeling·Eunice ChoShozeb Haider
Jun 26, 2021·Molecular Diversity·Henrique S FernandesNuno M F S A Cerqueira
Jul 20, 2021·Journal of Chemical Information and Modeling·Jingyi YangWeiwei Xue
Aug 12, 2021·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Mina ZareSeeram Ramakrishna
Dec 17, 2020·Journal of Chemical Information and Modeling·A AcharyaL Zanetti-Polzi
Jan 1, 2020·ACS Catalysis·Carlos A Ramos-GuzmánIñaki Tuñón
Aug 31, 2021·Journal of Chemical Information and Modeling·Vinícius BonattoCarlos A Montanari
Sep 3, 2021·Journal of Chemical Information and Modeling·Santiago MovillaVicent Moliner
Oct 13, 2021·Physical Chemistry Chemical Physics : PCCP·Antonio Francés-MonerrisMarco Marazzi
Nov 25, 2021·Future Medicinal Chemistry·Abdulrahim R HakamiMohammed Y Ghazwani

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Methods Mentioned

BETA
X-ray
acylation
deacylation
diacylation

Software Mentioned

Discovery Studio Visualizer
M06
AMBER

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