SARS-CoV-2 Nsp13 Helicase Resolves G-Quadruplexes and is Inhibited by G4 Ligands or an Anti-Viral Regulator: Implications for G4 Anti-Coronavirus Therapies

ABSTRACT The COVID-19 pandemic is often viewed as a once-in-a-century event. However, the rise of new variants and the potential for infections from related coronaviruses continues to be a significant concern. Vaccines were a successful deterrent to COVID-19, but anti-coronavirus drugs to treat individuals with COVID-19 or Long COVID are not robust. Efforts to identify novel coronavirus and host targets for drug therapies are highly valued. We determined that the SARS-CoV-2 Nsp13 helicase resolves G-quadruplexes (G4) of various topologies in an ATP-stimulated manner. Additionally, the requirement for a 5ʹ-single-stranded tail flanking DNA-G4 indicates its 5ʹ-to-3ʹ translocation directionality. G4 ligands were tested for inhibition of Nsp13 G4 resolvase. PhenDC3 inhibited Nsp13 resolution of four-stranded parallel G4 (IC50 = 0.06 nM), 150-fold more potent than two-stranded anti-parallel G4 (IC50 = 9 nM) and 680-fold more potent than the prominent human G4 resolvase FANCJ on the four-stranded parallel substrate (IC50 = 41 nM). Nsp13 is also capable of resolving uni-molecular RNA-G4 substrates, including a SARS-CoV-2-derived RNA-G4-forming sequence, strongly stimulated by its intrinsic ATPase activity. Nsp13-catalyzed resolution of a RNA-G4 substrate is inhibited by the G4 ligand PhenDC3 in a dose-dependent manner. Consistent with the biochemical studies that Nsp13 resolves RNA G-quadruplexes, Nsp13-transfected human cells treated with several G4 ligands displayed reduced RNA-G4 accumulation. The anti-viral regulator Cellular Nucleic Acid Binding Protein (CNBP) interacts with Nsp13 and inhibits Nsp13 G4 resolvase in vitro, suggesting a host mechanism to modulate Nsp13-dependent SARS-CoV-2 replication, which may have implications for G4-based coronavirus therapies.