Discovery and structure-activity relationship studies of novel α-ketoamide derivatives targeting the SARS-CoV-2 main protease

The SARS-CoV-2 main protease (M^pro, also named 3CL^pro) is a promising antiviral target against COVID-19 due to its functional importance in viral replication and transcription. Herein, we report the discovery of a series of α-ketoamide derivatives as a new class of SARS-CoV-2 M^pro inhibitors. Structure-activity relationship (SAR) of these compounds was analyzed, which led to the identification of a potent M^pro inhibitor (27h) with an IC₅₀ value of 10.9 nM. The crystal structure of M^pro in complex with 27h revealed that α-ketoamide warhead covalently bound to Cys145s of the protease. In an in vitro antiviral assay, 27h showed excellent activity with an EC₅₀ value of 43.6 nM, comparable to the positive control, Nirmatrelvir. This compound displayed high target specificity for M^pro against human proteases and low toxicity. It also possesses favorable pharmacokinetic properties. Overall, compound 27h could be a promising lead compound for drug discovery targeting SARS-CoV-2 M^pro and deserves further in-depth studies.