Open Access
Supercomputing Frontiers and Innovations, volume 7, issue 3
Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease
Publication type: Journal Article
Publication date: 2020-09-01
Quartile SCImago
Q3
Quartile WOS
—
Impact factor: —
ISSN: 24096008, 23138734
Computer Science Applications
Hardware and Architecture
Computational Theory and Mathematics
Information Systems
Computer Networks and Communications
Software
Abstract
Molecular dynamics simulations with the QM(DFT)/MM potentials are utilized to discriminate between reactive and nonreactive complexes of the SARS-CoV-2 main protease and its substrates. Classification of frames along the molecular dynamic trajectories is utilized by analysis of the 2D maps of the Laplacian of electron density. Those are calculated in the plane formed by the carbonyl group of the substrate and a nucleophilic sulfur atom of the cysteine residue that initiates enzymatic reaction. Utilization of the GPU-based DFT code allows fast and accurate simulations with the hybrid functional PBE0 and double-zeta basis set. Exclusion of the polarization functions accelerates the calculations 2-fold, however this does not describe the substrate activation. Larger basis set with d-functions on heavy atoms and p-functions on hydrogen atoms enables to disclose equilibrium between the reactive and nonreactive species along the MD trajectory. The suggested approach can be utilized to choose covalent inhibitors that will readily interact with the catalytic residue of the selected enzyme.
Citations by journals
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Molecules
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Molecules
1 publication, 100%
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Citations by publishers
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
1 publication, 100%
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