NMR analysis of interaction between RNA structure elements and small molecules: evaluation of RNA libraries and confirmation by two more molecules

Abstract

RNA-targeted small molecule drug discovery is widely recognized as an important modality. We have demonstrated that NMR spectroscopy is useful for screening small molecules that bind to specific RNA structures (J. Biochem. 2025). In the previous work, we analyzed the changes in the imino proton signals of 47 RNAs with different structural it was clearly indicated s upon addition of three well-known small molecules, risdiplam, NCD, and CPFX, and found several combinations of small molecules and RNA structures which showed specific changes. In this study, the structural characteristics of the model RNAs were further analyzed by measuring the Tm values. Then, to demonstrate the importance of the NMR-based method, we applied the method to two additional small molecules. In addition to the imino proton signals, the H5-H6 signals were also used to detect the interaction between small molecules and single stranded regions of RNAs. As a result, two additional examples of specific RNA–small molecule interactions were identified.