Targeting G-Quadruplex with Bis-thiourea Compounds Inhibits SARS-CoV-2 Replication

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus behind COVID-19, has a single-stranded RNA genome approximately 30 kb long. Due to its continuous mutation and potential for reemergence, identifying new therapeutic targets is crucial. G-quadruplexes (G4s), high-order genome structures, are promising therapeutic targets for various viral diseases due to their ability to inhibit virus replication. To develop new anti-SARS-CoV-2 drugs targeting G4s, identifying G4 structures in the viral genome and finding small molecules that selectively bind to them is essential. Recently, we identified a unique G4-forming sequence (SC-2) in SARS-CoV-2 RNA using our developed G4 prediction tool. We screened our in-house compound library with a Thiazole Orange (TO) displacement assay and found bis-urea/bis-thiourea compounds that bind to the SC-2 G4 motif. Notably, a bis-thiourea compound (BT1) inhibited SARS-CoV-2 replication in a VeroE6/TMPRSS2 infection assay, showing antiviral activity comparable to remdesivir. The displacement efficacy of TO from G4 by synthesized bis-urea/bis-thiourea derivatives to SC-2 G4 correlated strongly with reduced viral RNA levels in infected cells. Fluorescently labeled bis-thiourea compounds accumulated near double-stranded RNA during viral replication, highlighting their potential to target viral RNA G4s. Our study offers a new approach for anti-SARS-CoV-2 drug development.