Design, Synthesis, Evaluation, and Molecular Dynamics Simulation of SARS-CoV-2 M^pro Inhibitors

COVID-19, caused by SARS-CoV-2, is a highly contagious disease with significant transmissibility and pathogenicity. The main protease of SARS-CoV-2 (M^pro or 3CL^pro) is crucial for viral replication, making it a key therapeutic target. Nirmatrelvir, a promising M^pro inhibitor, contains a trifluoroacetyl group in its P4 fragment, which presents opportunities for further optimization. This study aims to enhance the inhibitory activity of nirmatrelvir through structural modification of the P4 fragment. Using a computer-aided drug design (CADD) approach, 11 novel compounds were identified based on molecular docking scores, binding free energy, predicted ADMET properties, structural diversity, synthetic feasibility, and inhibitory activity. IC₅₀ measurements and molecular dynamics (MD) simulations demonstrated significant inhibitory potential for most compounds, with IC₅₀ values ranging from 0.0435-0.9989 μM. Notably, compounds 2-5a and 2-5f exhibited inhibitory activity against SARS-CoV-2 M^pro comparable to that of nirmatrelvir. These findings offer valuable insights for the development of anti-SARS-CoV-2 therapeutics.