Abstract
The new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mpro dimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averaged betweenness centrality and geometry calculations. Domains from each Mpro protomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants. A mirrored interprotomer pocket was found to be correlated to the catalytic site using compaction dynamics, and can be a potential allosteric target. The high number of titratable amino acids of Mpro may indicate an important role of pH on enzyme dynamics, as previously reported for SARS-CoV. Independent coarse-grained Monte Carlo simulations suggest a link between rigidity/mutability and enzymatic function.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- BC
- Betweenness centrality
- BLAST
- Basic Local Alignment Search Tool
- CG
- Coarse-grained
- CHPC
- Centre for High Performance Computing
- COM
- Centre of mass
- DCC
- Dynamic Cross Correlation
- GISAID
- Global Initiative on Sharing All Influenza Data
- PDB
- Protein Data Bank
- PME
- Particle Mesh Ewald
- MC
- Monte Carlo
- MD
- Molecular dynamics
- RMSD
- Root mean squared deviation
- RMSF
- Root mean squared fluctuation
- COVID-19
- Coronavirus disease 2019
- SARS-CoV
- Severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- Severe acute respiratory syndrome coronavirus 2