Sequence-based design of bioactive small molecules that target precursor microRNAs

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Oligonucleotides target RNA but face challenges in cellular delivery and immune stimulation.
• Small molecules are preferred drug leads but designing them from sequence is difficult.

Purpose of the Study:

• To develop a method (Inforna) for designing sequence-specific small molecules targeting RNA.
• To identify bioactive small molecules that inhibit microRNA hairpin precursor processing.

Main Methods:

• Applied the Inforna approach to all human microRNA hairpin precursors.
• Screened for small molecules binding to nuclease-processing sites.
• Validated compound selectivity using siRNA knockdown of target mRNA.

Main Results:

• Inforna identified bioactive small molecules inhibiting microRNA biogenesis with a 44% hit rate.
• A benzimidazole compound (1) selectively inhibited precursor microRNA-96 biogenesis.
• Compound 1 upregulated FOXO1 protein and induced cancer cell apoptosis, which was reversed by FOXO1 knockdown.

Conclusions:

• Inforna enables sequence-based design of small molecules for RNA targeting.
• Compound 1 demonstrates selective inhibition of microRNA-96 and therapeutic potential in cancer.
• The identified small molecule is as selective as oligonucleotide inhibitors.