Non-covalent inhibitors targeting SARS-CoV-2 3CLpro: structural insights and developmental landscape

The SARS-CoV-2 3CLpro (or Mpro) is a key antiviral target due to its essential role in viral replication and its high structural conservation across coronaviruses. While covalent inhibitors such as nirmatrelvir have demonstrated clinical success, non-covalent 3CLpro inhibitors offer a complementary strategy for achieving potent inhibition through reversible binding and structurally diverse chemical scaffolds. This review summarizes fifteen representative non-covalent 3CLpro inhibitor series selected based on the availability of structural, biochemical, and antiviral data. Comparative analysis reveals conserved binding features across diverse chemical scaffolds, including hydrogen bonding to His163 and Glu166, hydrophobic occupancy of the S2 pocket, and stabilizing interactions proximal to the catalytic Cys145. Several compounds exhibit potent enzymatic and cellular antiviral activity, with ensitrelvir standing out as a clinically approved example that demonstrates the clinical feasibility of non-covalent 3CLpro inhibition. Despite substantial progress, challenges remain in resistance management, oral bioavailability, and pharmacokinetic optimization. This review provides a comparative framework integrating structural features, medicinal chemistry principles, pharmacological properties, resistance profiles, and developmental considerations to inform future 3CLpro inhibitor design and pandemic preparedness.