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

Int J Mol Sci. 2020 Apr 28;21(9):3099. doi: 10.3390/ijms21093099.


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.

Keywords: COVID-19; SARS-CoV; SARS-CoV-2; coronavirus; drug design; evolutionary analysis; ligand tracking approach; molecular dynamics simulations; small-molecule inhibitors.

MeSH terms

  • Antiviral Agents / pharmacology
  • Betacoronavirus / drug effects
  • Betacoronavirus / enzymology*
  • Betacoronavirus / genetics
  • Binding Sites
  • COVID-19
  • Catalytic Domain
  • Coronavirus 3C Proteases
  • Coronavirus Infections
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / chemistry*
  • Cysteine Endopeptidases / genetics
  • Drug Design*
  • Drug Evaluation, Preclinical
  • Evolution, Molecular
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Mutation
  • Pandemics
  • Pneumonia, Viral
  • Protease Inhibitors / pharmacology*
  • SARS Virus / enzymology
  • SARS-CoV-2
  • Small Molecule Libraries*
  • Solvents
  • Thermodynamics
  • Viral Nonstructural Proteins / antagonists & inhibitors*
  • Viral Nonstructural Proteins / chemistry*
  • Viral Nonstructural Proteins / genetics


  • Antiviral Agents
  • Protease Inhibitors
  • Small Molecule Libraries
  • Solvents
  • Viral Nonstructural Proteins
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases