Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

(2022) Nat Commun 13: 2268

• PubMed: 35477935 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/s41467-022-29915-z
• Primary Citation of Related Structures:  
  7SI9,7TDU,7TEH,7TFR


• PubMed Abstract: 
  

  Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (M^pro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the M^pro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor's keto-warhead creates a negatively charged oxyanion. 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 reveal unconventional F···O interactions of PF-07321332 with M^pro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.

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Organizational Affiliation: 

Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.