NMR and SPR Fragment-Based Screening Can Produce Novel High Affinity Small Molecule Hits against Structured RNAs

Noncoding RNAs account for up to 98% of the human transcriptome. It has become increasingly clear that noncoding RNAs play diverse and critical roles in many important cellular functions. Although modulation of noncoding RNAs using small molecules is a promising therapeutic strategy, there are relatively few well-characterized RNA-ligand structures. Therefore, the structure-interaction relationships of RNA-targeting small molecules remain underexplored. Here, we present a fragment-based screening approach using biophysical assays to identify and evaluate fragments that bind to the theophylline-binding RNA aptamer, which we use as a model system. We were able to identify high affinity fragment hits and generate models of RNA-ligand complexes using a combination of biophysical data and computational docking. Together, these findings provided insights into the RNA-fragment interactions that underpin binding. This approach demonstrates the feasibility of identifying high-affinity RNA-targeting small molecules with limited structural information.