Inhibition mechanism and antiviral activity of an α-ketoamide based SARS-CoV-2 main protease inhibitor

Abstract

SARS-CoV-2 has demonstrated extraordinary ability to evade antibody immunity by antigenic drift. Small molecule drugs may provide effective therapy while being part of a solution to circumvent SARS-CoV-2 immune escape. In this study we report an α-ketoamide based peptidomimetic inhibitor of SARS-CoV-2 main protease (Mpro), RAY1216. Enzyme inhibition kinetic analysis established that RAY1216 is a slow-tight inhibitor with a Ki of 8.6 nM; RAY1216 has a drug-target residence time of 104 min compared to 9 min of PF-07321332 (nirmatrelvir), the antiviral component in Paxlovid, suggesting that RAY1216 is approximately 12 times slower to dissociate from the protease:inhibitor complex compared to PF-07321332. Crystal structure of SARS-CoV-2 Mpro:RAY1216 complex demonstrates that RAY1216 is covalently attached to the catalytic Cys145 through the α-ketoamide warhead; more extensive interactions are identified between bound RAY1216 and Mpro active site compared to PF-07321332, consistent with a more stable acyl-enzyme inhibition complex for RAY1216. In cell culture and human ACE2 transgenic mouse models, RAY1216 demonstrates comparable antiviral activities towards different SARS-CoV-2 virus variants compared to PF-07321332. Improvement in pharmacokinetics has been observed for RAY1216 over PF-07321332 in various animal models, which may allow RAY1216 to be used without ritonavir. RAY1216 is currently undergoing phase III clinical trials to test real-world therapeutic efficacy against COVID-19.

A potent and broad‐spectrum neutralizing nanobody for SARS‐CoV‐2 viruses, including all major Omicron strains

“…Although with reduced protection efficiency of most antibodies and vaccines for new Omicron variants, 9–13 neutralizing antibody treatment still protects many infected people from severe symptoms and death. Although efficacious drugs have been developed to treat COVID‐19, 14–19 developing new broad‐spectrum antibodies against emerging coronavirus strains remains urgent and necessary 20 …”

Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity

“…6,7 Nirmatrelvir, a peptidomimetic inhibitor of the SARS-CoV-2 main protease (M pro ), is commercialized under the brand name Paxlovid in combination with ritonavir to prevent its fast metabolic degradation. 8 Simnotrelvir 9 and leritrelvir 10 are SARS-CoV-2 M pro inhibitors, out of which simnotrelvir is used in combination with ritonavir, similar to nirmatrelvir, while leritrelvir is a single agent. S-217622 (ensitrelvir) is a noncovalent, orally available SARS-CoV-2 M pro inhibitor.…”