A heterocyclic inhibitor of the REV-RRE complex binds to RRE as a dimer

As part of a search for organic compounds that selectively target RNA, we found that specific diphenylfuran derivatives, which are related to compounds that bind to the DNA minor groove, bind very strongly to RNA in a manner very sensitive to the structure of the compounds. In extended development of the diphenylfuran series, we found that a tetracationic heterocycle containing a phenyl-furan-benzimidazole unfused aromatic system, DB340, exhibits pronounced selectivity for the RRE RNA stem-loop from HIV-1. We report here RNA footprinting, spectroscopic analysis, affinity determinations, and initial NMR structural results of the complex. The results indicate that DB340 binds to RRE in a highly structured and cooperative complex at a 2:1 DB340 to RRE ratio. Overlap in the NMR spectra prevents detailed description of binding interactions at this time, but we are able to place DB340 in the RNA minor groove. Additionally, footprinting results and studies with mutant RRE sequences indicate that the internal loop of RRE is required for specific binding of DB340 as with the Rev protein. These results provide exciting new ideas for rational drug design with RNA as is now common with DNA and proteins.