BPS2026 – Redistribution of structural ensembles shapes free and bound states of HIV TAR RNA

RNA-based drug discovery has historically relied on static RNA structures, failing to capture the dynamic conformational ensembles that exist under cellular conditions. This limitation overlooks states critical for molecular function and therapeutic intervention. Our study focuses on the HIV-1 transactivation response (TAR) element RNA, a well-studied viral regulatory motif and validated small-molecule target. Using the FARFAR-based ensemble refinement with NMR (FERN) pipeline, we generated physiologically relevant ensembles of TAR. Comparing free and bound states revealed a striking redistribution of structural populations, providing a quantitative view of how RNA dynamics drive function. These refined ensembles enable enhanced ensemble-based irtual screening (EBVS)—a computational strategy that leverages multiple conformations to identify small molecules capable of selectively stabilizing functional states. By incorporating both free and bound RNA ensembles, EBVS offers more druggable and physiologically relevant predictions than traditional static structure-based or free-only screening approaches. This integrative framework can be broadly applied to other high-priority RNA targets, establishing a generalizable strategy for RNA-targeted drug discovery. Our results demonstrate that the redistribution of RNA structural ensembles between free and bound states not only governs molecular function but also opens new avenues for targeting RNAs therapeutically.