Characterizing the Binding and Function of Transcription-Inhibiting Compounds Designed to Target Nucleotide Repeat Expansions

Targeting nucleic acids with small molecules has shown strong potential as a therapeutic strategy. However, before this potential can be realized, the interactions between the small molecule and the nucleic acid target must be fully characterized. Trinucleotide repeat diseases provide a good model system for studying the interactions between small molecules and target nucleic acids. The d(CTG·CAG)exp repeat that causes myotonic dystrophy type 1 and Huntington’s Disease is one such target. Herein, we used an interdisciplinary approach that combined solution-phase stability assays, native mass spectrometry, and enzymatic transcription assays to study the interactions between three unique compounds and disease-associated repeat expansion DNA. Stability assays and native mass spectrometry measurements evaluated the nature of interactions occurring between the compounds studied and DNA and determined that two of the compounds are highly prone to interacting with DNA, with one compound demonstrating some degree of specificity to repeating d(CTG) sequences. Transcription assays indicated that only one of the three compounds studied herein effectively inhibits bidirectional transcription of only repeat expansion containing DNA. The data supports that the lead compound interacts with the disease-relevant repeat DNA and shows promise as a potential therapeutic agent.