Despite the success of SARS-CoV-2 vaccines in curbing viral transmission and severe disease, infections in unvaccinated and immune deficient patients continue to drive significant morbidity and mortality globally. To address the needs of this patient population, multiple antiviral drugs must be developed to expand on the protection currently offered by convalescent plasma, monoclonal antibodies, remdesivir, and other next generation SARS-CoV-2 antivirals which may be contraindicated for some patient groups. To this end, we employed a machine-learning based virtual ligand screening algorithm, FRAGSITE, to screen a library of FDA approved compounds for binding to the SARS-CoV-2 endoribonuclease (nsp15), a structurally conserved and demonstrated coronavirus virulence factor in SARS-CoV-1, HCoV-229E, IBV, MHV, and PEDV. Using recombinant SARS-CoV-2 nsp15, we identified the inhibition of nuclease activity by 11 drugs in vitro; 6 also restrict infection by the related human OC43 coronavirus in human A549 airway epithelial cells as measured by a focus forming assay. Among these 6 candidates, pibrentasvir remained active against HCoV-OC43 at the lowest concentration (IC50 < 0.625μM). Consistent with previous findings, HCoV-OC43 infection of A549 cells did not provoke an innate response to the viral dsRNA as quantified by IFNB1 mRNA production, antiviral stress granule formation, or RNase L activation. Our preliminary results suggest that antiviral stress granule formation is partially restored by nsp15 inhibitor treatment in HCoV-OC43 infected cells, although IFNβ production and RNase L activation remain unchanged.

Supported by grants from the Emory School of Medicine