Insights into the development of chemical probes for RNA

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

One notable exception to the aforementioned design strategies is the use of dynamic combinatorial chemistry (DCC) [ Figure 5B ] (69) . Several multivalent ligands were derived from a library of resin-bound, cysteine-containing monomers, which were allowed to incubate with the RNA of interest, probing thousands of multivalent ligand combinations by forming covalent yet reversible disulfide linkages. The binders with highest affinity were thus enriched and then isolated, characterized, and validated for RNAbinding. After replacing the disulfide linkage with more sta-ble bioisosteres, the method yielded bioactive ligands for two RNAs of known structure: DM1 r(CUG) exp , where statistically significant improvements in splicing were observed in mouse models (70) , and HIV-1 frameshift-stimulating RNA, (71, 72) where in one example the decrease in viral infectivity (EC 50 values of 3.9 and 26 M) correlated to frame-shifting activity (>50% at 50 M) in cell culture (73) . A powerful advantage of DCC is that multivalent ligands can be constructed without knowledge of the RNA structure, including larger and complex tertiary folds. In general, both rational design and DCC yield multivalent probes with significantly increased affinity and specificity for RNA targets relative to small molecules. While achieving high potency in biological systems with larger molecules may require more development than with traditional small molecules, the examples identified support the possibility of success.