Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2

Most ligands targeting RNA are identified through screening a therapeutic target for binding members of a ligand library. A potential alternative way to construct RNA binders is through rational design using information about the RNA motifs ligands prefer to bind. Herein, we describe such an approach to design modularly assembled ligands targeting the RNA that causes myotonic dystrophy type 2 (DM2), a currently untreatable disease. A previous study identified that 6'-N-5-hexynoate kanamycin A (1) prefers to bind 2x2 nucleotide, pyrimidine-rich RNA internal loops. Multiple copies of such loops are found in the RNA hairpin that causes DM2. The 1 ligand was then modularly displayed on a peptoid scaffold with varied number and spacing to target several internal loops simultaneously. Modularly assembled ligands were tested for binding to a series of RNAs and for inhibiting the formation of the toxic DM2 RNA-muscleblind protein (MBNL-1) interaction. The most potent ligand displays three 1 modules, each separated by four spacing submonomers, and inhibits the formation of the RNA-protein complex with an IC(50) of 25 nM. This ligand has higher affinity and is more specific for binding the DM2 RNA than MBNL-1. It binds the DM2 RNA at least 30 times more tightly than related RNAs and 15-fold more tightly than MBNL-1. A related control peptoid displaying 6'-N-5-hexynoate neamine (2) is >100-fold less potent at inhibiting the RNA-protein interaction and binds to DM2 RNA >125-fold more weakly. Uptake studies into a mouse myoblast cell line also show that the most potent ligand is cell permeable.