Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography

J Med Chem. 2021 Apr 22;64(8):4991-5000. doi: 10.1021/acs.jmedchem.1c00058. Epub 2021 Mar 23.


The main protease (3CL Mpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. To date, no small-molecule clinical drugs are available that specifically inhibit SARS-CoV-2 Mpro. To aid rational drug design, we determined a neutron structure of Mpro in complex with the α-ketoamide inhibitor telaprevir at near-physiological (22 °C) temperature. We directly observed protonation states in the inhibitor complex and compared them with those in the ligand-free Mpro, revealing modulation of the active-site protonation states upon telaprevir binding. We suggest that binding of other α-ketoamide covalent inhibitors can lead to the same protonation state changes in the Mpro active site. Thus, by studying the protonation state changes induced by inhibitors, we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 Mpro.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Coronavirus 3C Proteases / antagonists & inhibitors*
  • Coronavirus 3C Proteases / chemistry*
  • Coronavirus 3C Proteases / metabolism
  • Crystallography / methods
  • Crystallography, X-Ray
  • Cysteine Proteinase Inhibitors / chemistry
  • Cysteine Proteinase Inhibitors / metabolism
  • Models, Molecular
  • Neutrons
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Protein Conformation
  • Protons


  • Cysteine Proteinase Inhibitors
  • Oligopeptides
  • Protons
  • telaprevir
  • 3C-like proteinase, SARS-CoV-2
  • Coronavirus 3C Proteases