Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor

Abstract

The RNA motifs that bind guanidinylated kanamycin A (G Kan A) and guanidinylated neomycin B (G Neo B) were identified via two-dimensional combinatorial screening (2DCS). The results of these studies enabled the “bottom-up” design of a small molecule inhibitor of oncogenic microRNA-10b.

Ribosome-targeting antibiotics as inhibitors of oncogenic microRNAs biogenesis: Old scaffolds for new perspectives in RNA targeting

“…This step of the biogenesis process is particularly well-suited for targeting with small molecules thanks to RNA accessibility and some examples of the efficacy of this approach have already been reported in the literature. [14][15][16]18 Furthermore, pre-miRNAs are organized in a three-dimensional structure containing double-stranded regions (stems) and single-stranded regions (bulges and loops) that induce the distortion of RNA double helix thus offering the possibility for small molecules to fix specific binding sites. 30 Concerning the RNA sequences, antibiotics were screened on pre-miR-372 and premiR-373, precursors of two oncogenic miRNAs that are overexpressed in various cancers such as gastric tumors, while they are undetectable in normal cells.…”

“…5,[8][9][10] Most of them were discovered after the screening of libraries containing thousands of compounds [11][12][13] or after the evaluation of focused libraries containing fewer compounds known to act as general RNA binders. [14][15][16] Disney and coworkers also described a very efficient lead identification strategy for RNA motif/small molecule interactions, named Inforna, and they applied it to human pre-miRNAs. 17 Recently, we contributed to this field with the first example of focused design of RNA ligands targeting oncogenic pre-miRNAs processing by Dicer.…”

Small-Molecule Approaches Toward the Targeting of Oncogenic Mirnas: Roadmap for the Discovery of Rna Modulators

“…Our experiments demonstrated that the biological activity is correlated to the inhibition of the production of these oncogenic miRNAs, thus leading to the restoration of normal mRNA transla- This work further demonstrated that it is possible to greatly improve the activity of a minoglycosides by chemical modification. Finally, in the field of the design of specific RNA binders, the works reported by Disney and co-workers represent outstanding and elegant approaches leading to excellent results in terms of specificity and biological activity [64,[73][74]. In fact, this research group developed a lead identification strategy called Inforna [75] allowing for the discovery of highly specific and efficient ligands of pre-miRNAs precursors that are able to inhibit miRNAs biogenesis inside cells.…”

“…One of the most original approaches toward the discovery of miRNAs inhibitors is the one reported by Disney and co-workers in 2014 [64]. The authors applied a particularly clever screening methodology called 2D combinatorial screening (2DCS) [65][66][67].…”

“…Non-specific Binding to pre-miRNA and inhibition of Dicer cleavage Cell-free screening (FRET-based assay) [59] 16,20 miR-27a Binding to pre-miRNA and inhibition of Dicer cleavage Cell-free screening (FRET-based assay) [62] 23,24 miR-10b Binding to pri-miRNA and inhibition of Drosha cleavage Cell-free screening (2-DCS) [64] 25 miR-21 -Design based on 2 [75] 26 miR-122 Binding to Ago2 and inhibition of miRNA/Ago2 interaction Design based on in silico HTS [76] 27 miR-372 and miR-373…”