A Small Molecule Exploits Hidden Structural Features within the RNA Repeat Expansion That Causes c9ALS/FTD and...

Area of Science:

• Neuroscience
• RNA Biology
• Drug Discovery

Background:

• The GGGGCC hexanucleotide repeat expansion in C9orf72 is a primary genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD).
• Pathogenic mechanisms involve RNA gain- and loss-of-function, with the repeat RNA forming hairpin and G-quadruplex structures.

Purpose of the Study:

• To identify small molecules that selectively bind and modulate the structure of the pathogenic r(G₄C₂)^exp RNA.
• To investigate the structural basis of small molecule binding and its impact on RNA conformation and disease-related pathways.

Main Methods:

• Small molecule screening to identify binders of r(G₄C₂)^exp RNA.
• Nuclear Magnetic Resonance (NMR) spectroscopy and molecular dynamics (MD) simulations to determine binding modes and structural changes.
• Cellular assays to assess the impact of the small molecule on c9ALS/FTD pathobiology.

Main Results:

• Identification of CB253, a small molecule that selectively binds the hairpin form of r(G₄C₂)^exp RNA.
• CB253 binds to a novel 2 × 2 GG internal loop conformation, distinct from the native 1 × 1 loop.
• Binding of CB253 shifts the RNA hairpin equilibrium towards the 2 × 2 loop conformation, inhibiting stress granule formation and nucleocytoplasmic transport defects in cellular models.

Conclusions:

• CB253 effectively targets the pathogenic r(G₄C₂)^exp RNA by stabilizing a unique structural conformation.
• This targeted structural modulation inhibits critical pathogenic mechanisms in c9ALS/FTD.
• CB253 represents a promising therapeutic lead for c9ALS/FTD by directly interfering with the RNA-mediated disease process.