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 f ound that specific diphenylfuran derivatives, which are related to compound s 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 o f the diphenylfuran series, we found that a tetracationic heterocycle conta ining a phenyl-furan-benzimidazole unfused aromatic system, DB340, exhibits pronounced selectivity for the RRE RNA stem-loop from HIV-1. We report her e RNA footprinting, spectroscopic analysis, affinity determinations, and in itial NMR structural results of the complex. The results indicate that DB34 0 binds to RRE in a highly structured and cooperative complex at a 2:1 DB34 0 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 R NA minor groove. Additionally, footprinting results and studies with mutant RRE sequences indicate that the internal loop of RRE is required for speci fic binding of DB340 as with the Rev protein. These results provide excitin g new ideas for rational drug design with RNA as is now common with DNA and proteins.