A general fragment-based approach to identify and optimize bioactive ligands targeting RNA

Area of Science:

• Biochemistry
• Molecular Biology
• Medicinal Chemistry

Background:

• RNA structure dictates function, making RNA a target for small molecule drugs.
• Developing small molecules that specifically bind RNA is challenging.
• Existing methods for RNA-small molecule interaction mapping have limitations.

Purpose of the Study:

• To develop a fragment-based approach for discovering and optimizing bioactive small molecules targeting RNA.
• To establish a novel method, Chem-CLIP-Frag-Map, for identifying and mapping RNA-binding small molecule fragments.
• To identify and characterize small molecules that inhibit the oncogenic microRNA-21 (miR-21).

Main Methods:

• Extension of chemical cross-linking and isolation by pull-down (Chem-CLIP) to Chem-CLIP fragment mapping (Chem-CLIP-Frag-Map).
• Application of Chem-CLIP-Frag-Map to identify fragments binding to precursor miR-21 (pre-miR-21).
• Assembly of identified fragments into a potent bioactive compound inhibiting pre-miR-21 processing.

Main Results:

• Chem-CLIP-Frag-Map successfully identified fragments binding to pre-miR-21.
• A novel compound was synthesized by assembling fragments, demonstrating improved potency.
• The compound inhibited pre-miR-21 processing, reducing mature miR-21 levels and selectively affecting the transcriptome.
• The compound mitigated a miR-21-associated invasive phenotype in triple-negative breast cancer cells.

Conclusions:

• The Chem-CLIP-Frag-Map approach is effective for identifying and optimizing small molecules targeting RNA.
• This method accelerates the discovery of RNA-targeting therapeutics.
• The developed compound shows potential for treating miR-21-associated cancers.