Targeting Viral Suppressor of RNAi for Combating SARS-CoV-2 Variants

The ongoing SARS-CoV-2 pandemic underscores the persistent threat viruses pose to human health, necessitating the development of innovative antiviral therapies. RNA interference (RNAi) is a conserved cell-intrinsic antiviral mechanism in diverse eukaryotic organisms, including mammals, while many viruses encode viral suppressors of RNAi (VSRs) to evade the RNAi response, suggesting that targeting VSRs is a novel strategy to develop antiviral therapies. In this study, we demonstrated that the dimerization is crucial or the VSR activity of SARS-CoV-2 nucleocapsid (N) protein. We designed a series of peptides specifically targeting the dimerization interface of N protein. Among them, a peptide designated GL directly interacted with the N protein, inhibiting its dimerization and thereby inactivating its VSR activity. This unleased the RNAi response and reduced SARS-CoV-2 replication both in vitro and in vivo. Moreover, GL exhibited potent antiviral effects not only against various SARS-CoV-2 variants, including Delta, Omicron BA.5, XBB and JN.1, but also against other coronaviruses such as 229E, OC43 and MHV. The in vivo anti-MHV activity of GL was also confirmed. Our findings demonstrate that the strategy of VSR-targeting drug development could be inspiring for developing broad-spectrum antiviral agents against coronaviruses.