Events MOL2NET'21, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 7th ed.

Event submissions

Published

10.3390/mol2net-07-12118 (registering DOI)

This submission belongs to the session 01. CHEMBIO.INFO-07: Cheminfo., Chemom., Comput. Chem. & Bioinfo. Congress München, GR-Cambridge, UK-Ch. Hill, USA, 2021. of the event MOL2NET'21, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 7th ed.

Published date

28 Dec, 2021

Academic Editor

Humbert G. Díaz

Citation

Henrique Fernandes, Sérgio F Sousa, Nuno Cerqueira, The Catalytic Mechanism of the SARS-Cov-2 Main Protease, in Proceedings of MOL2NET'21, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 7th ed., 25 January–30 December 2021, MDPI: Basel, Switzerland, doi: 10.3390/mol2net-07-12118

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The Catalytic Mechanism of the SARS-Cov-2 Main Protease

Henrique Fernandes ^1,2

Sérgio F Sousa ^2,3

Nuno Cerqueira ^2,3

1. Associate Laboratory i4HB - Institute for Health and Bioeconomy, BioSIM, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal, Portugal

2. UCIBIO – Applied Molecular Biosciences Unit, BioSIM, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal

3. Associate Laboratory i4HB - Institute for Health and Bioeconomy, BioSIM, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal

Abstract

SARS-CoV-2 Main Protease (M^pro), also known as 3C-like protease, is a key enzyme involved in the replication process of the virus that is causing the COVID-19 pandemic. It is also the most promising antiviral drug target targeting the SARS-CoV-2 virus. In this work ^[1], the catalytic mechanism of M^pro was studied using the full model of the enzyme and a computational QM/MM methodology ^[2] with 69/72-atoms included in the QM region treated at DLPNO-CCSD(T)^[3]^[4]/CBS//B3LYP/6-31G(d,p):AMBER level, containing the catalytic important oxyanion-hole residues. The transition state of each step was fully characterized and described together with the related reactants and products. The rate-limiting step of the catalytic process is the hydrolysis of the thioester-enzyme adduct, and the calculated barrier closely agrees with the available kinetic data. Our simulations have disclosed important aspects of the mechanism, namely: (1) the role of the interaction between the P2 residue of the substrate and the catalytic His; (2) the important role of P1’ residue of the substrate in the stabilization of the ion pair intermediate; (3) the critical role of Gly143, Ser144, and Cys145 in the stabilization of the substrate’s oxo group.

The obtained Gibbs free energy profile, together with the full atomistic detail of the structures involved in catalysis, can be helpful for the rational drug design of transition state analogs as new inhibitors targeting the SARS-CoV-2 virus.

References:

[1] H. S. Fernandes, S. F. Sousa, N. M. F. S. A. Cerqueira, Mol. Divers. 2021, DOI 10.1007/s11030-021-10259-7.
[2] H. S. Fernandes, M. J. Ramos, N. M. F. S. A. Cerqueira, J. Comput. Chem. 2018, 39, 1344–1353.
[3] Y. Guo, C. Riplinger, U. Becker, D. G. Liakos, Y. Minenkov, L. Cavallo, F. Neese, J. Chem. Phys. 2018, 148, 011101.
[4] F. Neese, F. Wennmohs, U. Becker, C. Riplinger, J. Chem. Phys. 2020, 152, 224108.

Acknowledgments:

This work was supported by the Applied Molecular Biosciences Unit—UCIBIO (UIDP/04378/2020 and UIDB/04378/2020).

Keywords

SARS-CoV-2

COVID19

protease

QM/MM

computational

Manuscript

henrique_fernandes.pdf

Extension of the stochastic CpHMD method to the CHARMM36m force field

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