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 IC(50)s ranging from 0.26 to 28.85 μM. Walrycin B (IC(50) = 0.26 μM), Hydroxocobalamin (IC(50) = 3.29 μM), Suramin sodium (IC(50) = 6.5 μM), Z-DEVD-FMK (IC(50) = 6.81 μM), LLL-12 (IC(50) = 9.84 μM), and Z-FA-FMK (IC(50) = 11.39 μM) are the most potent 3CL(pro) inhibitors. The activities of 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.