From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease

The main protease (M-pro) of the betacoronavirus SARS-CoV-2 is an attractive target for the development of treatments for COVID-19. Structure-based design is a successful approach to discovering new inhibitors of the M-pro. Starting from crystal structures of the M-pro in complexes with the Hepatitis C virus NS3/4A protease inhibitors boceprevir and telaprevir, we optimized the potency of the alpha-ketoamide boceprevir against the M-pro by replacing its P1 cyclobutyl moiety by a gamma-lactam as a glutamine surrogate. The resulting compound, MG-78, exhibited an IC50 of 13 nM versus the recombinant M-pro, and similar potency was observed for its P1 ' N-methyl derivative MG-131. Crystal structures confirmed the validity of our design concept. In addition to SARS-CoV-2 M-pro inhibition, we also explored the activity of MG-78 against the M-pro of the alphacoronavirus HCoV NL63 and against enterovirus 3C proteases. The activities were good (0.33 mu M, HCoV-NL63 M-pro), moderate (1.45 mu M, Coxsackievirus 3C(pro)), and relatively poor (6.7 mu M, enterovirus A71 3C(pro)), respectively. The structural basis for the differences in activities was revealed by X-ray crystallo-graphy. We conclude that the modified boceprevir scaffold is suitable for obtaining high-potency inhibitors of the coronavirus M(pro)s but further optimization would be needed to target enterovirus 3C(pro)s efficiently.