Discovery of small molecules that target a tertiary-structured RNA

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Growing interest exists in developing therapeutic interventions targeting disease-relevant RNAs with small molecules.
• Understanding structure-activity relationships for RNA-targeted small molecules remains a challenge.
• The theophylline aptamer, a well-characterized RNA, binds theophylline with high affinity.

Purpose of the Study:

• To identify novel small molecules that bind the theophylline aptamer with higher affinity than theophylline.
• To investigate the binding modes of these novel ligands using X-ray crystallography.
• To explore the potential of applying protein drug discovery approaches to RNA targets.

Main Methods:

• High-throughput screening of low-molecular-weight compounds.
• Affinity determination of identified compounds.
• Atomic-resolution X-ray crystallography to elucidate binding modes.

Main Results:

• Several unique small molecules, distinct from theophylline, were identified with up to 340-fold greater binding affinity.
• X-ray crystal structures revealed the rigidity of the theophylline aptamer binding pocket.
• Structures indicated opportunities for enhanced binding through additional hydrogen-bonding interactions.

Conclusions:

• Novel small molecules can bind the theophylline aptamer with significantly higher affinity than its natural ligand.
• The theophylline aptamer's binding pocket allows for tighter binding through specific interactions.
• These findings support the application of established drug discovery methodologies to RNA targets.