Targeting Riboswitches with Beta-Axial-Substituted Cobalamins

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• RNA-ligand interactions are key to RNA-targeting therapeutics but poorly understood.
• Riboswitches, like the cobalamin-sensing riboswitch, are excellent model systems for studying RNA-ligand binding due to their high affinity and selectivity.
• The cobalamin riboswitch is a potential antibiotic target, and its interaction with synthetic cobalamin forms remains unexplored.

Purpose of the Study:

• To characterize the interactions between 11 synthetic cobalamin derivatives and three representative cobalamin riboswitches.
• To investigate the plasticity and selectivity of these RNA-ligand interactions.
• To assess the potential of these derivatives as lead compounds for antibiotic development.

Main Methods:

• In vitro binding experiments, including chemical footprinting and fluorescence-based assays.
• Cell-based reporter assays to evaluate in vivo functionality.
• Structural analysis of ligand binding pocket rearrangements.

Main Results:

• Eleven cobalamin derivatives were tested against three cobalamin riboswitches.
• Productive interactions were observed with two of the three riboswitches, indicating RNA plasticity and selectivity.
• A novel structural rearrangement in the ligand binding pocket was identified.
• In vivo functionality was confirmed for some derivatives.

Conclusions:

• Cobalamin riboswitches exhibit plasticity and selectivity in binding synthetic cobalamin derivatives.
• Novel structural mechanisms contribute to RNA-ligand recognition.
• The tested cobalamin derivatives show potential as starting points for developing novel RNA-targeting antibiotics.