Structure-based lead optimization of peptide-based vinyl methyl ketones as SARS-CoV-2 main protease inhibitors

Eur J Med Chem. 2023 Feb 5;247:115021. doi: 10.1016/j.ejmech.2022.115021. Epub 2022 Dec 15.


Despite several major achievements in the development of vaccines and antivirals, the fight against SARS-CoV-2 and the health problems accompanying COVID-19 are still ongoing. SARS-CoV-2 main protease (Mpro), an essential viral cysteine protease, is a crucial target for the development of antiviral agents. A virtual screening analysis of in-house cysteine protease inhibitors against SARS-CoV-2 Mpro allowed us to identify two hits (i.e., 1 and 2) bearing a methyl vinyl ketone warhead. Starting from these compounds, we herein report the development of Michael acceptors targeting SARS-CoV-2 Mpro, which differ from each other for the warhead and for the amino acids at the P2 site. The most promising vinyl methyl ketone-containing analogs showed sub-micromolar activity against the viral protease. SPR38, SPR39, and SPR41 were fully characterized, and additional inhibitory properties towards hCatL, which plays a key role in the virus entry into host cells, were observed. SPR39 and SPR41 exhibited single-digit micromolar EC50 values in a SARS-CoV-2 infection model in cell culture.

Keywords: Antiviral activity; COVID-19; Michael acceptors; Peptide-based inhibitors; SARS-CoV-2 M(pro) inhibition.

MeSH terms

  • Antiviral Agents / chemistry
  • COVID-19*
  • Humans
  • Ketones / pharmacology
  • Molecular Docking Simulation
  • Peptides
  • Protease Inhibitors / chemistry
  • SARS-CoV-2 / metabolism
  • Viral Nonstructural Proteins


  • 3C-like proteinase, SARS-CoV-2
  • Protease Inhibitors
  • Viral Nonstructural Proteins
  • Antiviral Agents
  • Peptides
  • Ketones