Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV‑2 to Low-Nanomolar Antiviral Potency

Non-covalent inhibitors of the main protease (M^pro) of SARS-CoV-2 having a pyridinone core were previously reported with IC₅₀ values as low as 0.018 μM for inhibition of enzymatic activity and EC₅₀ values as low as 0.8 μM for inhibition of viral replication in Vero E6 cells. The series has now been further advanced by consideration of placement of substituted five-membered-ring heterocycles in the S4 pocket of M^pro and N-methylation of a uracil ring. Free energy perturbation calculations provided guidance on the choice of the heterocycles, and protein crystallography confirmed the desired S4 placement. Here we report inhibitors with EC₅₀ values as low as 0.080 μM, while remdesivir yields values of 0.5–2 μM in side-by-side testing with infectious SARS-CoV-2. A key factor in the improvement is enhanced cell permeability, as reflected in PAMPA measurements. Compounds 19 and 21 are particularly promising as potential therapies for COVID-19, featuring IC₅₀ values of 0.044–0.061 μM, EC₅₀ values of ca. 0.1 μM, good aqueous solubility, and no cytotoxicity.