Discovery of synthetic G-quadruplex DNA as SARS-CoV-2 helicase inhibitor with antiviral, anti-inflammatory and antioxidative properties

SARS-CoV-2 RNA contains guanine-rich sequences that form secondary structures known as G quadruplexes (G4s). The SARS-CoV-2 nonstructural protein (NSP13) resolves G4s due to its helicase and ATPase activity, a process essential for viral replication. Here, we tested the effects of synthetic G4s on SARS-CoV-2 replication. In agreement, a synthetic G4 DNA 20 mer, consisting exclusively of guanines linked by a phosphorothioate backbone (designated GQ20-PTO), inhibited the replication of various SARS-CoV-2 variants in human lung cell cultures. Mechanistically, GQ20-PTO bound to NSP13 and inhibited its helicase and ATPase activity. Independent of its antiviral effects, GQ20-PTO additionally suppressed IFNβ and IL-6 (but not TNFα) signaling and the formation of reactive oxygen species, processes known to contribute to hyperinflammation in severe COVID-19. Hence, G4 quadruplexes like GQ20-PTO represent a novel class of DNA-based compounds for COVID-19 treatment with the potential to interfere with both SARS-CoV-2 replication and the uncontrolled inflammation associated with life-threatening COVID-19.