SARS-CoV-2 Main Protease: A Molecular Dynamics Study

Abstract

Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in explicit solvent. After having performed electrostatic p K a calculations on several X-ray structures, we consider both the native (unbound) configuration of the enzyme and its noncovalent complex with a model peptide, Ace-Ala-Val-Leu-Gln∼Ser-Nme, which mimics the polyprotein sequence recognized at the active site. For each configuration, we also study their monomeric and homodimeric forms. The simulations of the unbound systems show that the relative orientation of domain III is not stable in the monomeric form and provide further details about interdomain motions, protomer–protomer interactions, inter-residue contacts, accessibility at the catalytic site, etc. In the presence of the peptide substrate, the monomeric protease exhibits a stable interdomain arrangement, but the relative orientation between the scissile peptide bond and the catalytic dyad is not favorable for catalysis. By means of comparative analysis, we further assess the catalytic impact of the enzyme dimerization, the actual flexibility of the active site region, and other structural effects induced by substrate binding. Overall, our computational results complement previous crystallographic studies on the SARS-CoV-2 enzyme and, together with other simulation studies, should contribute to outline useful structure–activity relationships.

Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 Main Protease complexes reveal the role of a lateral pocket in enhancing the ligand affinity

“…In order to understand the dynamics of a SARS-CoV-2 M pro in the absence of a bound ligand, we Fig.3c). These observations are consistent with the previous studies 66,67 . In addition, we also identified a critical water-mediated interaction near the active site of Mpro, where a central water-molecule formed a 3-way H-bond network with residues HIS41…”

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

“…Examination of five separate runs shows frequent variations in site RMSD over the course of 250 ns for almost all runs ( Figure S12), suggesting that the active site is more flexible than the overall protein structure, as has been seen in previous MD simulations. 27,28 The RMSF and RMSD per residue ( Figure S13) have similar shapes to those from the shorter apo simulations ( Figures S5 and S9). Large variations in the pocket volumes were also observed, ranging from 0-800Å 3 , indicating high site flexibility.…”

“…Since the release of SARS-CoV-2 M pro structures in apo and inhibitor-bound states, multiple MD simulation and docking studies of this enzyme have already been published. [22][23][24][25][26][27][28] Although a precise determination of the specific protonation states of Cys145 and several histidines in M pro in this pH-sensitive enzyme will be critical to effective and robust computational drug design efforts, these protonation states have not been unequivocally determined.…”

Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches

“…In addition to the screening provided by docking, further studies including dynamic sampling are essential to evaluate the favorable drug–3CLpro interactions and their stability along the simulation time. Indeed, MD studies were performed to first assess the molecular bases of the SARS-CoV-2 3CLpro catalytic function, including the impact of the enzyme dimerization 195 and the definition of the ligand anchor site within its pocket. 183 …”