# Integrated in silico and experimental screening identifies novel ligands that target precursor microRNA-31 at the dicer cleavage site

## TL;DR

Researchers combined computer modeling and lab experiments to find new molecules that bind to a specific part of a microRNA precursor, which could help control its role in diseases like cancer.

## Contribution

A novel structure-guided virtual screening and experimental approach to identify small molecules targeting pre-miR-31's Dicer cleavage site.

## Key findings

- Three compounds were found to bind pre-miR-31 at the Dicer cleavage site.
- Similarity-based searches identified additional compounds with equivalent or improved binding.
- The approach is generalizable for identifying RNA-binding ligands from large chemical databases.

## Abstract

MicroRNAs (miRNAs) regulate gene expression and the dysregulation in mature miRNA levels has been implicated in a wide variety of diseases. In particular, altered levels of mature microRNA-31 (miR-31) has been linked to a variety of different cancers. Targeting functionally relevant sites of the precursor structure of miR-31 with small molecules offer a strategy to regulate miR-31 maturation. Herein we describe a virtual screening approach to explore the druggability of the precursor structure of microRNA-31 (pre-miR-31). We used a structure-guided approach to virtually screen a fragment library and followed up with experimental characterization of top-ranking candidates, leading to the identification of several compounds that bound to pre-miR-31. Further characterization of the RNA-ligand complexes by heteronuclear single quantum coherence (HSQC) NMR spectroscopy revealed three compounds bound pre-miR-31 at the Dicer cleavage site, suggesting that these compounds may function to inhibit Dicer processing. Using these initial hits, we performed chemical structure similarity searches and identified additional binders of pre-miR-31 that had equivalent or enhanced binding relative to the parent compounds. These studies suggest a generalizable approach by which RNA-binding ligands can be identified from large chemical databases. These hits can then be further optimized to improve affinity and specificity for downstream functional assays.

MicroRNAs (miRNAs) regulate gene expression and the dysregulation in mature miRNA levels has been implicated in a wide variety of diseases.