Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-Throughput Screening

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C-like protease (3CL^pro), or main protease (M^pro) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high-throughput screening (qHTS) of 10 755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CL^pro assay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CL^pro have been identified with IC₅₀s ranging from 0.26 to 28.85 μM. Walrycin B (IC₅₀ = 0.26 μM), hydroxocobalamin (IC₅₀ = 3.29 μM), suramin sodium (IC₅₀ = 6.5 μM), Z-DEVD-FMK (IC₅₀ = 6.81 μM), LLL-12 (IC₅₀ = 9.84 μM), and Z-FA-FMK (IC₅₀ = 11.39 μM) are the most potent 3CL^pro inhibitors. The activity of the anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CL^pro inhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients and as starting points for chemistry optimization for new drug development.