Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA

Area of Science:

• Medicinal Chemistry
• Molecular Biology
• Drug Discovery

Background:

• DNA-encoded library (DEL) technology is a key method for small molecule identification.
• Current DEL strategies are mainly applied to protein targets, limiting broader applications.
• DEL selection on RNA targets, like HIV-1 TAR, often yields false-positive DNA-RNA binding signals.

Purpose of the Study:

• To develop and validate an optimized DEL selection strategy for RNA targets.
• To minimize non-specific DNA-RNA interactions and improve signal accuracy.
• To demonstrate the feasibility of identifying potent small molecules against RNA targets.

Main Methods:

• Developed an optimized DEL selection strategy using RNA patches and competitive elution.
• Implemented k-mer analysis and motif search for differentiating false-positive signals.
• Applied the strategy to screen for ligands against the Escherichia coli FMN Riboswitch.

Main Results:

• The optimized strategy significantly reduced background noise and false positives.
• Enriched compounds against the FMN Riboswitch exhibited double-digit nanomolar binding affinity.
• Identified compounds showed functional potency in FMN competition assays.

Conclusions:

• Small molecule identification against RNA targets using DEL selection is feasible.
• The developed experimental and computational approach enhances RNA ligand screening.
• This work expands the application scope of DEL selection in drug discovery.