Designing small molecules targeting a cryptic RNA binding site through base displacement.

Area of Science:

• Medicinal Chemistry
• Molecular Biology
• Drug Discovery

Background:

• Small molecules targeting RNA often suffer from poor solubility, weak affinity, and lack of specificity, hindering drug development.
• Conjugating 'guest' ligands to a 'host' molecule can improve solubility and enable site-specific delivery to RNA targets.

Purpose of the Study:

• To design and discover novel small molecules that effectively target the cobalamin (Cbl) riboswitch.
• To overcome limitations of traditional RNA-binding small molecules through a host-guest conjugation strategy.

Main Methods:

• Designed a small-molecule library hosted by cobalamin (Cbl) for Cbl riboswitch interaction.
• Employed in vitro binding assays, cell-based assays, chemoinformatic modeling, and structure-based design.
• Utilized a base displacement mechanism for ligand interaction with the riboswitch.

Main Results:

• Unmasked a cryptic binding site within the Cbl riboswitch.
• Discovered compounds with affinity exceeding the native ligand.
• Identified compounds that antagonize riboswitch function and are structurally distinct from Cbl.
• Demonstrated the efficacy of a biphenyl-like scaffold targeting RNA via π-stacking interactions.

Conclusions:

• Host-guest molecular conjugation is a viable strategy to enhance RNA-binding small molecule properties.
• The Cbl riboswitch possesses a druggable cryptic site amenable to small-molecule targeting.
• Optimized π-stacking interactions within the binding pocket are key for effective RNA targeting.