LAUSR

Significance There have been increased efforts recently to “drug” RNA using orally bioavailable, low-molecular-weight compounds. This study combines two of the most powerful tools of modern drug discovery, high-throughput screening and structure-based design, to target the theophylline aptamer, a tertiary-structured RNA that binds theophylline with high affinity and selectivity. These efforts led to the discovery of compounds that bind the RNA with up to 340-fold greater affinity compared to theophylline. X-ray crystal structures were determined for the aptamer, both in isolation and in complex with various ligands, revealing the molecular basis for ligand binding. The results give encouragement that tertiary-structured RNAs are indeed druggable if one makes an effort similar to that used to address the most challenging protein targets.