Libraries used in high-throughput screening (HTS) are optimized for the deep, hydrophobic pockets of protein targets and not the more polar and solvent exposed pockets typical of RNA targets 7. There are, however, fundamental challenges in targeting RNA using small molecules 4– 7. Much attention has been directed towards targeting ncRNAs with small molecules, which do not suffer from the inherent delivery limitations associated with oligonucleotide-based therapeutics, and which can be tailored to specifically target the diverse 3D structures of RNA 2– 5. The growing list of ncRNA targets now includes microRNAs, long ncRNAs, repetitive RNA transcripts, riboswitches, and viral RNAs. These results demonstrate that experimentally determined ensembles can significantly enrich libraries with structure-specific RNA binders as well as motivate the continued development of methods for improving ensemble accuracy.Īccompanying the non-coding RNA (ncRNA) revolution has been growing interest in RNA as a drug target, particularly for diseases that do not have suitable protein targets 1– 6. The prediction accuracy decreased significantly with decreasing accuracy of the target ensemble or when docking against a single RNA structure. Ensemble-based VS (EBVS) scores molecules with an area under the receiver operator characteristic curve (ROC AUC) of 0.87 with ~50% of all hits falling within the top 2% of scored molecules, and also correctly predicts the different TAR inter-helical structures when bound to six molecules. We used this dataset, along with 240 known hit molecules, to evaluate virtual screening (VS) against a high-resolution TAR ensemble determined by combining NMR spectroscopy and molecular dynamics (MD) simulations.

Here, we experimentally screened the transactivation response element (TAR) RNA from human immunodeficiency virus type-1 (HIV-1) against ~100,000 small molecules. Dynamic ensembles that capture the flexibility of RNA three-dimensional (3D) structures hold great promise in advancing RNA-targeted drug discovery.

Chemdoodle on high resolution screen