Molecular Dynamics Simulations Indicate the SARS-CoV-2 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design

Maria Bzówka; Karolina Mitusinska; Agata Raczynska; Aleksandra Samol; Jack Tuszynski; Artur Góra

The initial analysis of the effect of the 12 amino acid replacements in SARS-CoV-Mpro on the SARS-CoV-2 Mpro structure stability was expected to provide neutral or stabilising contribution to proteins folding. Indeed, all replacements were found to stabilise the protein's folding (e.g., H134F: -0.85 kcal/mol) or have almost neutral character (e.g., R88K, S94A, T285A, I286L). The analysis of the potential risk of further Mpro structure evolution within the binding cavity suggests that mutations of residues that contribute to . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.968008 doi: bioRxiv preprint ligand binding or access to the active site are energetically favourable, and likely to occur. Some of the residues that are prone to mutate would provide the inactive enzyme (e.g., the residues forming the catalytic dyad) and therefore could be considered as a blind alley in enzyme evolution, but others (e.g., amino acids from the C44-P52 loop, T45, S46, E47, L50) could significantly modify the inhibitors binding mode of Mpro. The location of prone to mutate residues on the regulatory loop questions the effort for Mpro active site inhibitors design as a long term strategy. However, our results indicate also residues that are energetically unfavourable to mutate (e.g., P39, R40, P52, G143, G146, or L167), which could provide an anchor for successful drug design that can outlast coronavirus' Mpros variability in future. Alternatively, we would suggest targeting the region between II and III domains, which contributes to the dimer formation.