Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination,...

M^pro of SARS-CoV-2 plays a vital role in the replication and pathogenesis of virus. Additionally, its high conservation within the Coronaviridae family makes it an attractive therapeutic target for developing broad-spectrum agents. This study describes the design, synthesis, and structure-activity relationships of azapeptide-based SARS-CoV-2 M^pro inhibitors, leading to several compounds with nanomolar IC₅₀ values. Examples include 14r (IC₅₀ = 13.3 nM), 14s (IC₅₀ = 30.6 nM), 20a (TPG-20a, IC₅₀ = 28.0 nM), and 20g (IC₅₀ = 30.4 nM). Some compounds inhibit MERS-CoV and SARS-CoV-1 M^pro but not the human protease cathepsin L. Several inhibitors, such as 20a and 20f, exhibit antiviral activity with potencies comparable to nirmatrelvir and activity against the E166V-carrying SARS-CoV-2 variant (SARS-CoV-2^E166V). An M^pro cocrystal structure with 20a shows a covalent adduct with the catalytic Cys145. Overall, these new inhibitors are promising chemical tools that may contribute to the identification of future pan-anticoronaviral drugs.