Identification and Characterization of Novel Chikungunya Virus Polymerase Inhibitors

Chikungunya virus (CHIKV) and other alphaviruses in the Togaviridae family (positive-sense RNA viruses) are major human pathogens, causing millions of infections worldwide. In humans, alphaviruses such as CHIKV, Mayaro, and Ross River viruses typically cause arthritogenic disease characterized by debilitating arthralgia, joint inflammation, fever, and rash. Although two vaccines were recently approved for use against CHIKV, no vaccines are licensed against other alphaviruses. No antiviral treatments are licensed to prevent or treat infections by any alphavirus. To address this unmet need, we used a CHIKV nanoluciferase reporter virus to develop a high-throughput screening assay for novel small-molecule inhibitors. From this campaign, we identified several unique inhibitors of CHIKV replication. Mechanistic studies of two inhibitors revealed that both target the nsP4 polymerase, while susceptibility profiling pinpointed unique nsP4 mutations that specifically confer resistance. In silico docking analyses indicated potential binding poses of the inhibitors within the polymerase active site. Collectively, these results define multiple chemotypes for further development and highlight a novel molecular target within nsP4 for CHIKV inhibition.