Viruses are a global human health burden, however, few have targeted antiviral therapies. The current “one drug, one bug” approach is unsuitable given the increasing incidence of emerging viral pathogens, instead, broad-spectrum strategies are required. Viral RNA-dependent RNA polymerases (RdRps) are attractive drug targets due to their lack of mammalian homologues and conservation across RNA viruses. For example, recent studies repurposing hepatitis C virus (HCV) antivirals have identified an alternative allosteric binding site (Site-B) conserved throughout Caliciviridae RdRps.
We aimed to utilise Site-B to develop broad-spectrum antivirals against Caliciviridae. Pharmacophore models were constructed using docking configurations of two antivirals predicted to bind within Site-B (JTK-109 and TMC647055) within calicivirus RdRp crystal structures. These models were used to virtually screen ~200,000 commercially available compounds. Resulting structures were filtered based on molecular properties to identify “drug-like” candidates and 33 “hit” compounds were selected for further study.
These 33 compounds were initially tested for inhibition of human norovirus (NoV) RdRp, and one promising compound (NCS-013) was trialled against feline calicivirus (FCV) RdRp to assess cross-genera inhibition. NCS-013 inhibited both RdRps at 50 µM (NoV: 55.9±3.8%, FCV: 51.3±5.4%).
Since the pharmacophore models were based on HCV-targeting molecules, compounds were also examined against the RdRp of Zika virus (Flaviviridae). Additionally, eight promising candidates were trialled against replicons of HCV (Flaviviridae) and hepatitis A virus (HAV: Picornaviridae) to explore inter-family inhibition. NCS-013 demonstrated inhibition of Zika virus RdRp at 100 µM (58.4±22.6%) and HCV/HAV replicons at 10 µM (62.5±23.6%, 45.6±10.1% respectively).
Due to the broad-spectrum inhibition displayed by NCS-013, it was used as a scaffold for derivative searching, which identified a further 11 compounds for assessment. Of these, NCS-013A demonstrated cross-family inhibition of HAV (58.9±17.7% at 10 µM) and Zika virus (42.1±22.6% at 50 µM).
In summary, we identified two structures, NCS-013 and NCS-013A, with potential broad-spectrum activity. As these compounds target three viral families, they could be useful as scaffolds for future broad-spectrum antiviral discovery.