Integrated in silico and experimental screening identifies novel ligands that target precursor microRNA-31 at the...

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• MicroRNAs (miRNAs) regulate gene expression, and their dysregulation is linked to various diseases, including cancer.
• Altered levels of microRNA-31 (miR-31) are specifically associated with several types of cancer.
• Targeting the precursor structure (pre-miR-31) with small molecules presents a strategy to control miR-31 maturation.

Purpose of the Study:

• To explore the druggability of the pre-miR-31 structure using a virtual screening approach.
• To identify small molecules that can bind to pre-miR-31 and potentially modulate its function.
• To establish a generalizable method for discovering RNA-binding ligands from chemical databases.

Main Methods:

• Structure-guided virtual screening of a fragment library against pre-miR-31.
• Experimental characterization of top-ranking virtual screening candidates.
• Heteronuclear single quantum coherence (HSQC) NMR spectroscopy to analyze RNA-ligand complexes.
• Chemical structure similarity searches to identify additional binders.

Main Results:

• Several compounds were identified that bind to pre-miR-31.
• Three compounds were found to bind at the Dicer cleavage site of pre-miR-31, suggesting potential inhibition of Dicer processing.
• Additional pre-miR-31 binders with comparable or improved binding affinity were identified through similarity searches.

Conclusions:

• The study demonstrates a viable approach for identifying RNA-binding ligands using virtual screening and subsequent experimental validation.
• The identified compounds targeting pre-miR-31 offer potential therapeutic strategies for cancers associated with miR-31 dysregulation.
• The developed methodology can be applied to discover ligands for other RNA targets.