A Small Molecule That Targets r(CGG)^exp and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome

Abstract

The development of small molecule chemical probes or therapeutics that target RNA remains a significant challenge despite the great interest in such compounds. The most significant barrier to compound development is a lack of knowledge of the chemical and RNA motif spaces that interact specifically. Herein, we describe a bioactive small molecule probe that targets expanded r(CGG) repeats, or r(CGG)exp , that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS). The compound was identified by using information on the chemotypes and RNA motifs that interact. Specifically, 9-hydroxy-5,11-dimethyl-2-(2-(piperidin-1-yl)ethyl)-6H-pyrido[4,3-b]carbazol-2-ium, binds the 5’CGG/3’GGC motifs in r(CGG)exp and disrupts a toxic r(CGG)exp -protein complex in vitro. Structure-activity relationships (SAR) studies determined that the alkylated pyridyl and phenolic side chains are important chemotypes that drive molecular recognition to r(CGG)exp . Importantly, the compound is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTAS-associated pre-mRNA splicing defects and to reduce the size and number of r(CGG)exp -protein aggregates. This approach may establish a general strategy to identify lead ligands that target RNA while also providing a chemical probe to dissect the varied mechanisms by which r(CGG)exp promotes toxicity.

Discovery of a Biomarker and Lead Small Molecules to Target r(GGGGCC)-Associated Defects in c9FTD/ALS

“…2I ). In contrast, we reported that 1a does reduce foci in r(CGG) 60 -expressing cells (Disney et al, 2012), and we show here that 1a also inhibits RAN translation in cells expressing (CGG) 88 placed in the 5'UTR of GFP, but does not affect downstream canonical translation ( Fig. 2J ).…”

“…Small molecule leads can be further optimized by chemical similarity searching, which identifies compounds that are chemically similar to the leads. We reported that small molecule 1a binds 1×1 GG internal loops present in r(CGG) exp and improves fragile X-associated tremor/ataxia syndrome (FXTAS)-associated defects (Disney et al, 2012). Given the structural similarity between r(CGG) exp and r(GGGGCC) exp , we hypothesized that 1a and compounds chemically similar to it might bind r(GGGGCC) exp .…”

Fragile X-associated tremor/ataxia syndrome — features, mechanisms and management

“…The GABA A agonist allopregnanolone is currently in clinical trials after it has had beneficial effects in cells and animals, and additional GABA A agonists that might help pain control, anxiety and sleep disturbances in premutation carriers could be tested in the future. Small molecules that can block chronic DNA damage repair or can block the production of FMRpolyG should now be studied, first in the premutation mouse model, then in patient trials 163 . These treatments will need to be used before the onset of FXTAS, however, as brain atrophy and white matter disease begins earlier than the clinical symptoms of FXTAS.…”

RNA Structures as Mediators of Neurological Diseases and as Drug Targets

“…Following the same rational approach to the design of ligands targeting r(CUG) exp and r(CCUG) exp , our group has developed selective compounds that target r(CGG) exp in both FXTAS and FXS (Colak et al, 2014; Disney et al, 2012; Tran et al, 2014). The small molecule 1a was identified to bind 5′CGG3′/3′GGC5′ using chemical similarity searching of a known RNA binder (Disney et al, 2012).…”

“…The small molecule 1a was identified to bind 5′CGG3′/3′GGC5′ using chemical similarity searching of a known RNA binder (Disney et al, 2012). A high-throughput FRET-based screen was used to identify compounds that disrupt the binding of r(CGG) repeats to an RNA-binding protein (DGCR8Δ) (Disney et al, 2012). Small molecule 1a inhibits formation of nuclear foci and improves FXTAS-associated alternative pre-mRNA splicing defects (Disney et al, 2012).…”