Publication date: Feb 10, 2025

Main protease (M) is a cysteine protease enzyme crucial for the replication of SARS-CoV-2, the etiological agent of COVID-19 and thus considered as a viable target for antiviral development. The GC373 compound, an aldehyde-containing inhibitor, is one of the most effective inhibitors that retards the catalytic function of M. A deeper understanding of the inhibitory action of GC373 by providing precise mechanistic details, is pivotal toward developing more potent inhibitors against M. In this work, we provide novel insights into the inhibition mechanism considering different models and possible pathways using a combination of molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) methodologies. Our study reveals the impact of key residues on both the binding of the GC373 inhibitor and its inhibition mechanism. Together with the oxyanion hole residues, G143, S144 and C145, we note that H163, and E166 residues play a crucial role in the binding of the inhibitor. Further, our exploration of two pathways namely, water-assisted and direct inhibition mechanisms, using three differently sized QM/MM models shows consistent and distinguishable trends in catalytic pathways and rate-limiting steps, respectively. Our results highlight the importance of treating more representative active site residues in the QM layer enabling a more accurate description of the inhibition mechanism. More importantly, we propose that designing novel inhibitors that could afford stronger interaction with the underlying essential residues is a promising strategy to guide the efforts toward optimizing efficient inhibitors against M.

Semantics

Original Article