Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M^pro

Abstract

A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (M pro ), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of M pro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant M pro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, R g , averaged betweenness centrality, and geometry calculations. The results showed that SARS-CoV-2 M pro essentially behaves in a similar manner to its SAR-CoV homolog. However, we report the following new findings from the variants: (1) Residues GLY15, VAL157, and PRO184 have mutated more than once in SARS CoV-2; (2) the D48E variant has lead to a novel “TSEEMLN”” loop at the binding pocket; (3) inactive apo M pro does not show signs of dissociation in 100 ns MD; (4) a non-canonical pose for PHE140 widens the substrate binding surface; (5) dual allosteric pockets coinciding with various stabilizing and functional components of the substrate binding pocket were found to display correlated compaction dynamics; (6) high betweenness centrality values for residues 17 and 128 in all M pro samples suggest their high importance in dimer stability—one such consequence has been observed for the M17I mutation whereby one of the N-fingers was highly unstable. (7) Independent coarse-grained Monte Carlo simulations suggest a relationship between the rigidity/mutability and enzymatic function. Our entire approach combining database preparation, variant retrieval, homology modeling, dynamic residue network (DRN), relevant conformation retrieval from 1-D kernel density estimates from reaction coordinates to other existing approaches of structural analysis, and data visualization within the coronaviral M pro is also novel and is applicable to other coronaviral proteins.

Identification of SARS-CoV2 Main Protease Coldspots Suitable for Drug Targeting

“…The observed mutational frequencies in the hotspots at the active site and dimer interface indicate that the virus may be developing protective strategies against inhibitors. This correlates with the findings described in recent reports, which show the positions are changing the shape of the sites via mutations and plasticity 17,33 . However, coldspots that are identified here might be good areas to target.…”

“…However, based on our data analysis, the other pocketforming residues in the structures undergo mutations, which may modify the shape of the binding pocket. This prediction is supported by a recent study 17 , in which the structures of the mutants Met49Ile, Pro184Leu/Ser, and Ala191Val were shown to substantially deviate from the wildtype. Thus, the residues were assumed to belong within the mobile regions of the active site, which control the conformational changes that may be required for catalysis.…”

Identification of SARS-CoV2 Main Protease Coldspots Suitable for Drug Targeting

“…The observed mutational frequencies in the hotspots at the active site and dimer interface indicate that the virus may be developing protective strategies against inhibitors. This correlates with the ndings described in recent reports, which show the positions are changing the shape of the sites via mutations and plasticity 17,32 . However, coldspots that are identi ed here might be good areas to target.…”

“…However, based on our data analysis, the other pocket-forming residues in the structures undergo mutations, which may modify the shape of the binding pocket. This prediction is supported by a recent study 17 , in which the structures of the mutants Met49Ile, Pro184Leu/Ser, and Ala191Val were shown to substantially deviate from the wildtype. Thus, the residues were assumed to belong within the mobile regions of the active site, which control the conformational changes that may be required for catalysis.…”

Dynamic Community Composition Unravels Allosteric Communication in PDZ3

“…[27][28][29] In an RN, centrality of nodes reveals the residues that manipulate information flow, and identifying residues with high centrality provides a profile of biological function and evolutionarily conservation. 26,[30][31][32][33] On the other hand, focusing on edge centrality in order to detect 'communities' has been put forth as an approach to distinguish modular units with interdependent functions for any network, [34][35][36] and these ideas have been applied to residue networks to shed light on communication patterns between structural segments. [34][35][36] Here, we analyze molecular dynamics (MD) simulations to gather a range of conformations sampled by PDZ3 with a novel approach ( Figure 1b).…”