A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication

Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (M-pro). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC50 values of 154 and 4.2 +/- 0.7 mu M for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with M-pro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead M-pro inhibitor for the development of therapeutics for SARS-CoV-2 infection.Here, using in vitro assays and structural analysis, the authors characterize the anti-SARS-CoV-2 properties of two small molcules, showing these to bind and target the virus main protease (M-pro), and to exhibit a synergistic antiviral effect when combined with remdesivir in vitro.