Recent discoveries of novel classes of non-coding, regulatory RNAs have provided evidence for a variety of roles for RNA in cancer and other diseases, propelling interest in developing RNA-binding small molecule therapeutics. However, the discovery of molecules that bind RNA with good affinity and specificity is challenging, and new approaches to identify novel RNA-binding motifs are needed. As one approach, we have used a small molecule microarray (SMM) screening platform to broadly search for small molecule binders to a variety of non-coding RNAs. MicroRNAs (miRNAs) are one such class of RNAs, the aberrant expression of which is implicated in the development, metastasis and progression of cancers. Using the SMM platform, we identified druglike compounds that directly bind to a pre-miR-21 hairpin, an overexpressed oncomiR in various cancers. These compounds are not composed of typical RNA binding motifs and exhibit KDs from 0.8 – 2.0 µM. Notably, several of the highest affinity compounds inhibit Dicer-mediated maturation of pre-miR-21. Further, in-line probing indicates that the compounds bind to the apical loop of the miR-21 hairpin, proximal to the Dicer cleavage site. Taken together, this work demonstrates that SMMs can be applied to the identification of miRNA-binding molecules and provides evidence that the goal of inhibiting miR-21 biogenesis using a small molecule may be possible. In a second example, an SMM screen was applied to a PreQ1 riboswitch, a regulatory, metabolite-responsive RNA aptamer in Bacillus subtilis. Several molecules that bind the PreQ1 riboswitch were identified that are structurally distinct from its cognate ligand, and binding was validated through a series of biophysical methods. Further, in-line probing suggests that the compounds induce a riboswitch conformation that is distinct from that of the cognate ligand-bound form. Future studies will focus on evaluating the ability of these ligands to regulate riboswitch function in vivo.

Targeting regulatory non-coding RNAs with druglike small molecules

254th National Meeting (2017)

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