Insights into the development of chemical probes for RNA

Morgan, Brittany S; Forte, Jordan E; Hargrove, Amanda E

Multivalent chemical probes targeted fewer distinct RNA elements, with 27/41 unique ligands targeting nucleotide repeat expansions [ Figure 1B ]. There are several advantages to targeting these RNA repeats: (i) long repeat stretches are typically not present elsewhere in the human genome; (ii) nuclear localization minimizes competition with ribosomal RNA and (iii) targetable motifs are separated by a specific distance (32) . Another target of interest was the heat shock response element of the 32 factor mRNA in E. coli. This RNA element contains a rare, perfectly paired three-way junction that can be stabilized by symmetrical triptycenebased molecules, forming a distinct shape-selective fit (33) . This stabilization resulted in an ∼60% reduction in translation of an 32 -GFP fusion protein and could potentially lead to antimicrobial activity (34) . In addition, 7/41 chemical probes showed efficacy in animal models, targeting two RNA elements: r(CUG) exp repeats and pri-miRNA-96. Pri-miRNA-96 is an oncogenic RNA that suppresses the translation of a pro-apoptotic protein, FOXO1. In a mouse model of triple negative breast cancer, a modular ligand designed to target the Drosha processing site on the RNA led to a statistically significant reduction in tumor size and to changes in RNA and protein levels consistent with the proposed mode of action (17) . Notably, examination of this list further exposes the RNA-driven processes and diseases that still lack functional chemical probes. Ideal RNA targets have defined functional sites and/or clear phenotypes while also being of high abundance, and several untargeted RNAs, ranging from archaeal ncRNA to oncogenic lncR-NAs, meet these criteria.