Binding mode characterization of 13b in the monomeric and dimeric states of SARS-CoV-2 main protease using molecular dynamics simulations

The main protease, M-pro/3CL(pro), plays an essential role in processing polyproteins translated from viral RNA to produce functional viral proteins and therefore serve as an attractive target for discovering COVID-19 therapeutics. The availability of both monomer and dimer crystal bound with a common ligand, `13b' (alpha-ketoamide inhibitor), opened up opportunities to understand the M-pro mechanism of action. A comparative analysis of both forms of M-pro was carried out to elucidate the binding site architectural differences in the presence and absence of `13b'. Molecular dynamics simulations suggest that the presence of `13b' enhances the stability of M-pro than the unbound APO form. The N- and C-terminals of both the protomers stabilize each other, and making it's interface essential for the active form of M-pro. In comparison to monomer, the relatively high affinity of `13b' is gained in dimer pocket due to the high stability of the pocket by the interaction of S1 residue of chain B with residues F140, E166 and H172 of chain A, which is absent in monomer. The comprehensive essential dynamics, protein structure network analysis and thermodynamic profiling highlight the hot-spots, pivotal in molecular recognition process at protein-ligand and protein-protein interaction levels, cross-validated through computational alanine scanning study. A comparative description of `13b' binding mechanism in both forms illustrates valuable insights into the inhibition mechanism and the selection of critical residues suitable for the structure-based approaches for the identification of more potent M-pro inhibitors.

Automated summary

The study compared monomer and dimer forms of the main protease M-pro, revealing differences in the mechanism of binding between the potential COVID-19 inhibitor `13b' and the enzyme. Molecular dynamics simulations suggest that the presence of `13b' enhances the stability of M-pro, and protein structure analysis highlights key hot-spots in protein-ligand and protein-protein interactions.