Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

Abstract

The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mixed-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar severe acute respiratory syndrome (SARS) Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins showed major differences in both shape and size, indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding site's conformational changes during the simulation time indicated its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicated that the virus' mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design.

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.…”

Virtual prediction of antiviral potential of ginger (Zingiber officinale) bioactive compounds against spike and MPro of SARS-CoV2 protein

“…Several drugs used the MPro enzyme as a target to inhibit polyprotein processing during viral RNA translation (Bzówka et al, 2020;Dai et al, 2020;Joshi et al, 2020;Zhang et al, 2020). MPro of SARS-CoV2 has three domains with an active site in the middle of domain I and domain II.…”

“…This protein is accountable for processing the poly-proteins pp1a and pp1ab into established nonstructural protein as a part of the replication/transcription complex (Hilgenfeld, 2014). Thus, targeting MPro also promising to combat COVID-19 (Bzówka et al, 2020).…”

In Silico Analysis of Sea Urchin Pigments as Potential Therapeutic Agents Against SARS-CoV-2: Main Protease (Mpro) as a Target.

“…The viral replication can be inhibited in the active site in Mpro of SARS-CoV (Jin et al, 2020), which is located in the same position in SARS-CoV and SARS-CoV-2 between domain I (8-99 aa) and domain II (100-183 aa). Mpro presents flexibility in the binding site conformation constituting a good target for small drugs (Bzowka et al, 2020;Bzówka et al, 2020).…”