Three-dimensional model of a selective theophylline-binding RNA molecule

A three-dimensional (3D) model for an RNA molecule that selectively binds theophylline but not caffeine is proposed. This RNA, which was found using SELEX (Jenison et al., 1994), is 10 000 times more specific for theophylline (KD = 320 nM) than for caffeine (KD = 3.5 mM), although the two ligands are identical except for a methyl group substituted at N7 (present only in caffeine). The binding affinity for ten xanthine-based ligands was used to derive a comparative molecular field analysis model (R2 = 0.93 for three components, with cross-validated R2 of 0.73), using the SYBYL and GOLPE programs. A pharmacophoric map was generated to locate steric and electrostatic interactions between theophylline and the RNA binding site. This information was used to identify putative functional groups of the binding pocket and to generate distance constraints. On the basis of a model for the secondary structure (Jenison et al., 1994), the 3D structure of this RNA was then generated using the following method: each helical region of the RNA molecule was treated as a rigid body; single-stranded loops with specific end-to-end distances were generated. The structures of RNA-xanthine complexes were studied using a modified Monte Carlo algorithm. The detailed structure of an RNA–ligand complex model, as well as possible explanations for the theophylline selectivity are discussed