Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV-2

J Phys Chem Lett. 2022 Jun 30;13(25):5776-5786. doi: 10.1021/acs.jpclett.2c01193. Epub 2022 Jun 21.

Abstract

The COVID-19 outbreak has been devastating, with hundreds of millions of infections and millions of deaths reported worldwide. In response, the application of structure-activity relationships (SAR) upon experimentally validated inhibitors of SARS-CoV-2 main protease (Mpro) may provide an avenue for the identification of new lead compounds active against COVID-19. Upon the basis of information gleaned from a combination of reported crystal structures and the docking of experimentally validated inhibitors, four "rules" for designing potent Mpro inhibitors have been proposed. The aim here is to guide medicinal chemists toward the most probable hits and to provide guidance on repurposing available structures as Mpro inhibitors. Experimental examination of our own previously reported inhibitors using the four "rules" identified a potential lead compound, the cathepsin inhibitor GB111-NH2, that was 2.3 times more potent than SARS-CoV-2 Mpro inhibitor N3.

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • COVID-19 Drug Treatment*
  • Cysteine Endopeptidases / metabolism
  • Humans
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Peptide Hydrolases
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology
  • SARS-CoV-2*
  • Viral Nonstructural Proteins

Substances

  • Antiviral Agents
  • Protease Inhibitors
  • Viral Nonstructural Proteins
  • Peptide Hydrolases
  • Cysteine Endopeptidases