Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

Science. 2020 Apr 24;368(6489):409-412. doi: 10.1126/science.abb3405. Epub 2020 Mar 20.

Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. On the basis of the unliganded structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 Mpro The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry*
  • Amides / metabolism
  • Amides / pharmacology*
  • Animals
  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism
  • Antiviral Agents / pharmacokinetics
  • Antiviral Agents / pharmacology
  • Betacoronavirus / drug effects*
  • Betacoronavirus / enzymology*
  • Binding Sites
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / chemistry*
  • Cysteine Endopeptidases / metabolism
  • Drug Design
  • Half-Life
  • Humans
  • Lung / metabolism
  • Mice
  • Models, Molecular
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / metabolism
  • Protease Inhibitors / pharmacokinetics
  • Protease Inhibitors / pharmacology*
  • Protein Domains
  • Protein Multimerization
  • Pyridones / chemistry
  • Viral Nonstructural Proteins / chemistry*
  • Viral Nonstructural Proteins / metabolism
  • Virus Replication / drug effects

Substances

  • Amides
  • Antiviral Agents
  • Protease Inhibitors
  • Pyridones
  • Viral Nonstructural Proteins
  • 3C-like proteinase, Coronavirus
  • Cysteine Endopeptidases

Supplementary concepts

  • severe acute respiratory syndrome coronavirus 2