Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD

Genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), collectively named c9ALS/FTD, are triggered by hexanucleotide GGGGCC repeat expansions [r(G(4)C(2))(exp)] within the C9orf 72 gene. In these diseases, neuronal loss occurs through an interplay of deleterious phenotypes, including r(G(4)C(2))(exp) RNA gain-of-function mechanisms. Herein, we identified a benzimidazole derivative, CB096, that specifically binds to a repeating 1 x 1 GG internal loop structure, 5'CGG/3'GGC, that is formed when r(G(4)C(2))(exp) folds. Structure-activity relationship (SAR) studies and molecular dynamics (MD) simulations were used to define the molecular interactions formed between CB096 and r(G(4)C(2))(exp) that results in the rescue of disease-associated pathways. Overall, this study reveals a unique structural feature within r(G(4)C(2))(exp) that can be exploited for the development of lead medicines and chemical probes.