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

Hattori, Shin-ichiro; Higashi-Kuwata, Nobuyo; Hayashi, Hironori; Allu, Srinivasa Rao; Raghavaiah, Jakka; Bulut, Haydar; Das, Debananda; Anson, Brandon J.; Lendy, Emma K.; Takamatsu, Yuki; Takamune, Nobutoki; Kishimoto, Naoki; Murayama, Kazutaka; Hasegawa, Kazuya; Li, Mi; Davis, David A.; Kodama, Eiichi N.; Yarchoan, Robert; Wlodawer, Alexander; Misumi, Shogo; Mesecar, Andrew D.; Ghosh, Arun K.; Mitsuya, Hiroaki

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 EC(50) values of 15 ± 4 and 4.2 ± 0.7 μM 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.