Structural characterization of HCoV-229E and H163A main protease (Mpro) interactions with the inhibitor narlaprevir.

Narlaprevir, originally developed as a clinical-stage inhibitor of the hepatitis C virus (HCV) NS3/4A protease, has recently demonstrated potent inhibitory activity against the SARS-CoV-2 main protease (Mpro), with its co-crystal structure already resolved. To elucidate the mechanistic basis of its cross-genus inhibition and drug resistance profiles, we determined the crystal structures of narlaprevir in complex with HCoV-229E Mpro and the SARS-CoV-2 Mpro(H163A) mutant at resolutions of 2.01 Å and 2.14 Å, respectively. By integrating these crystallographic data with molecular dynamics (MD) simulations and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) free energy calculations, we systematically compared narlaprevir against clinically approved antivirals, including bofutrelvir, PF-07304814, and pomotrelvir. Structural analysis revealed that narlaprevir forms a conserved covalent C-S bond with the catalytic cysteine residue across all investigated complexes. Thermodynamic evaluations indicated that the SARS-CoV-2 WT-Mpro-narlaprevir complex exhibits the most negative total binding free energy (-66.29 kcal/mol), suggesting a marginally stronger theoretical binding affinity compared to the 229E-narlaprevir (-64.91 kcal/mol) and H163A-narlaprevir (-64.14 kcal/mol) complexes. Notably, distinct from the approved drugs, narlaprevir exclusively occupies protomer A when bound to both HCoV-229E and H163A Mpro. Collectively, these findings establish narlaprevir as a highly promising lead compound with notable broad-spectrum potential. While its overall efficacy parallels that of clinically approved agents, it exhibits distinct binding characteristics. These insights provide a critical structural foundation for the rational design of next-generation antiviral strategies capable of mitigating threats from both circulating and emerging coronaviruses.