Design, synthesis and activity of light deactivatable microRNA inhibitor

Abstract

miRNAs are key cellular regulators and their dysregulation is associated with many human diseases. They are usually produced locally in a spatiotemporally controlled manner to target mRNAs and regulate gene expression. Thus, developing chemical tools for manipulating miRNA with spatiotemporal precise is critical for studying miRNA. Herein, we designed a strategy to control miRNA biogenesis with light controllable inhibitor targeting the pre-miRNA processing by Dicer. By conjugating two non-inhibiting units, a low affinity Dicer inhibitor and a pre-miRNA binder, through a photocleavable linker, the bifunctional molecule obtained could inhibit miRNA production. Taking advantage of the photocleavable property of the linker, the bifunctional inhibitor can be fragmented into separate non-inhibiting units and therefore be deactivated by light. We expect that this strategy could be applied to generate chemical biological tools that allow light-mediated spatiotemporal control of miRNA maturation and contribute to the study of miRNA function.

Precise Small Molecule Degradation of a Noncoding RNA Identifies Cellular Binding Sites and Modulates an Oncogenic Phenotype

“…These RNAs, particularly those that are noncoding, have diverse functions . Small molecule targeting of RNA, however, has been challenging, except for RNAs that fold into globally ordered, highly defined three-dimensional structures such as ribosomes and riboswitches. − More recently, it has been shown that pre-mRNAs in complexes can be targeted and stabilized with small molecules. , Most RNAs, however, do not have highly complex long-range folds but do have extensive two-dimensional (secondary) structures including motifs such as hairpins, internal loops, and bulges that could be targeted with small molecules. , Indeed, small molecules have been discovered that target biological RNAs that contain these folds such as microRNA precursors (miRNAs). − Furthermore, approaches to study the cellular binding of small molecules to RNA targets are needed to support mechanism of action studies.…”

Noncoding RNA therapeutics — challenges and potential solutions

“…A similar approach consists of linkage of a miRNA binding molecule to a weak Dicer inhibitor, a method termed ‘proximity-enabled Dicer inhibition’. This system was used to successfully inhibit miR-21 biogenesis in vitro, and the use of a photocleavable linker enabled inactivation of the reaction by light 120 , 121 .…”

Targeting Ribonucleases with Small Molecules and Bifunctional Molecules

“…Aminoglycosides neomycin and kanamycin were employed as the RNA-binding molecules to target the oncogenic miRNA miR-21. , The specificity of such bifunctional Dicer inhibitors was increased using antisense oligonucleotides, which alone did not inhibit the processing of pre-miR-21 by Dicer . A following study showed the possibility of incorporating a light-cleavable linker in the bifunctional molecule to deactivate the inhibitory activity by light …”