Broad-spectrum inhibitors targeting the viral replication promoter conserved in dengue and Zika viruses

Project Summary Zika virus (ZIKV) and dengue virus (DENV) are mosquito-borne flaviviruses that cause disease ranging in severity from mild symptoms to deadly hemorrhagic dengue fever. ZIKV was rapidly spreading five years ago to over 20 countries in South and Central America, where infections by ZIKV reached pandemic levels and threatened to expand to the southern US. The threat by DENV has increased dramatically over the last two decades as one of the worst mosquito-borne pathogens in tropical regions. To treat outbreaks of DENV in ZIKV-endemic regions, and vice versa, broad-spectrum inhibitor drugs against mosquito-borne flaviviruses would provide an efficient therapeutic approach that reduces the risk of immuno-associated exacerbation, for example in previously infected or vaccinated patients. Sequence alignment of DENV and ZIKV clinical isolates in combination with secondary structure prediction have led us to identify a conserved RNA three-way junction that serves as the replication promoter in flaviviruses. Here, we propose to identify compounds that inhibit viral replication by targeting the promoter RNA as lead candidates for the future development of DENV and ZIKV broad-spectrum therapeutics. The Specific Aims of this proposal are to 1) develop a FRET-based binding assay to assess small molecules as selective ligands of the DENV and ZIKV replication promoter RNA, 2) establish an in vitro replication initiation assay to identify promoter RNA-binding ligands as inhibitors of ZIKV replication, and 3) discover small molecules that inhibit DENV and ZIKV in cell culture by targeting the RNA 3WJ motif that serves as the viral replication promoter.