Discovery of small molecules that target a tertiary-structured RNA

There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure-activity relationships in pursuing these targets has remained elusive. One of the best-studied tertiary-structured RNAs is the theophylline aptamer, which binds theophylline with high affinity and selectivity. Although not a drug target, this aptamer has had many applications, especially pertaining to genetic control circuits. Heretofore, no compound has been shown to bind the theophylline aptamer with greater affinity than theophylline itself. However, by carrying out a high-throughput screen of low-molecular-weight compounds, several unique hits were identified that are chemically distinct from theophylline and bind with up to 340-fold greater affinity. Multiple atomic-resolution X-ray crystal structures were determined to investigate the binding mode of theophylline and four of the best hits. These structures reveal both the rigidity of the theophylline aptamer binding pocket and the opportunity for other ligands to bind more tightly in this pocket by forming additional hydrogen-bonding interactions. These results give encouragement that the same approaches to drug discovery that have been applied so successfully to proteins can also be applied to RNAs.

Automated summary

There is growing interest in using small molecules to target disease-relevant RNAs in therapeutic intervention. However, the understanding of structure-activity relationships in pursuing RNA targets is limited. This study identified several unique compounds through high-throughput screening that bind to a well-studied RNA structure, the theophylline aptamer, with significantly higher affinity than theophylline itself. The atomic-resolution X-ray crystal structures of these compounds revealed the rigidity of the RNA binding pocket and the potential for other ligands to bind more tightly. These findings suggest that the same approaches used for protein drug discovery can also be applied to RNA.