Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity

The COVID-19 pandemic continues to disrupt everyday life, with constantly emerging SARS-CoV-2 variants threatening to render current vaccines ineffective. Small-molecule antivirals can provide an important therapeutic treatment option that is subject to challenges caused by the virus variants. The viral main Protease (M ^pro ) is critical for the virus replication and thus is considered an attractive drug target for specific Protease Inhibitors. We performed the design and characterization of three reversible covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2, whose structures were derived from those of hepatitis C Protease Inhibitors boceprevir and narlaprevir. A joint X-ray/neutron structure of the M ^pro /BBH-1 complex demonstrated that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion, similar to that proposed for the M ^pro -catalyzed peptide bond hydrolysis. Protonation states of the ionizable residues in the M ^pro active site adapt to the inhibitor, which appears to be an intrinsic property of M ^pro . Structural comparisons of the hybrid inhibitors with PF-07321332 revealed unconventional interactions of PF-07321332 with M ^pro which may explain its more favorable enthalpy of binding and consequently higher potency. BBH-1, BBH-2 and NBH-2 demonstrated comparable Antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.