Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG)^exp Degrader in...

Area of Science:

• Molecular Biology
• RNA Therapeutics
• Genetics

Background:

• Myotonic dystrophy type 1 (DM1) is a genetic disorder caused by a toxic RNA repeat expansion, r(CUG)^exp, in the *DMPK* gene.
• This repeat expansion drives disease through a gain-of-function mechanism, leading to cellular dysfunction.

Purpose of the Study:

• To develop a small molecule that specifically binds to and targets the toxic r(CUG)^exp RNA in DM1 cells.
• To create an RNA degrader capable of eliminating the disease-causing RNA and ameliorating DM1-associated defects.

Main Methods:

• Screening of low-molecular-weight fragments for cross-linking to r(CUG)^exp RNA *in vitro*.
• Characterization of small molecule-RNA interactions using NMR spectroscopy and molecular modeling.
• Transcriptome-wide profiling of small molecule binding in DM1 myotubes and assessment of RNA degrader efficacy using RNA-seq.

Main Results:

• Identified perimidin-2-amine diazirine (1) as a ligand that binds to r(CUG)^exp.
• Developed a chimeric RNA degrader that specifically targets and eliminates r(CUG)^exp.
• The degrader demonstrated broad improvement of DM1-associated defects in myotubes with minimal impact on healthy cells.

Conclusions:

• The study provides a platform for investigating ligand recognition in disease-affected cells.
• RNA degraders can achieve higher specificity than their parent binding molecules.
• Repeating transcripts with multiple ligand binding sites are amenable to selective degradation.