Discovery and Crystallographic Studies of Trisubstituted Piperazine Derivatives as Non-Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity and Low Toxicity

J Med Chem. 2022 Oct 13;65(19):13343-13364. doi: 10.1021/acs.jmedchem.2c01146. Epub 2022 Sep 15.


The continuous spread of SARS-CoV-2 calls for more direct-acting antiviral agents to combat the highly infectious variants. The main protease (Mpro) is an promising target for anti-SARS-CoV-2 drug design. Here, we report the discovery of potent non-covalent non-peptide Mpro inhibitors featuring a 1,2,4-trisubstituted piperazine scaffold. We systematically modified the non-covalent hit MCULE-5948770040 by structure-based rational design combined with multi-site binding and privileged structure assembly strategies. The optimized compound GC-14 inhibits Mpro with high potency (IC50 = 0.40 μM) and displays excellent antiviral activity (EC50 = 1.1 μM), being more potent than Remdesivir. Notably, GC-14 exhibits low cytotoxicity (CC50 > 100 μM) and excellent target selectivity for SARS-CoV-2 Mpro (IC50 > 50 μM for cathepsins B, F, K, L, and caspase 3). X-ray co-crystal structures prove that the inhibitors occupy multiple subpockets by critical non-covalent interactions. These studies may provide a basis for developing a more efficient and safer therapy for COVID-19.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • COVID-19*
  • Caspase 3
  • Cathepsins
  • Coronavirus 3C Proteases
  • Cysteine Endopeptidases / metabolism
  • Hepatitis C, Chronic*
  • Humans
  • Molecular Docking Simulation
  • Orotic Acid / analogs & derivatives
  • Piperazines / pharmacology
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology
  • SARS-CoV-2


  • 6-(4-(3,4-dichlorophenyl)piperazine-1-carbonyl)-1H-pyrimidine-2,4-dione
  • Antiviral Agents
  • Piperazines
  • Protease Inhibitors
  • Orotic Acid
  • Cathepsins
  • 3C-like proteinase, SARS-CoV-2
  • Caspase 3
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases