Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting

Sun, Yu; Abriola, Laura; Niederer, Rachel O.; Pedersen, Savannah F.; Alfajaro, Mia M.; Silva Monteiro, Valter; Wilen, Craig B.; Ho, Ya-Chi; Gilbert, Wendy V.; Surovtseva, Yulia V.; Lindenbach, Brett D.; Guo, Junjie U.

Translation of open reading frame 1b (ORF1b) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a programmed −1 ribosomal frameshift (−1 PRF) promoted by an RNA pseudoknot. The extent to which SARS-CoV-2 replication may be sensitive to changes in −1 PRF efficiency is currently unknown. Through an unbiased, reporter-based high-throughput compound screen, we identified merafloxacin, a fluoroquinolone antibacterial, as a −1 PRF inhibitor for SARS-CoV-2. Frameshift inhibition by merafloxacin is robust to mutations within the pseudoknot region and is similarly effective on −1 PRF of other betacoronaviruses. Consistent with the essential role of −1 PRF in viral gene expression, merafloxacin impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing proof-of-principle for targeting −1 PRF as a plausible and effective antiviral strategy for SARS-CoV-2 and other coronaviruses.