Dynamic Covalent Template-Guided Screen for Nucleic Acid-Targeting Agents.

Area of Science:

• Molecular Biology
• Medicinal Chemistry
• Genetics

Background:

• Trinucleotide repeat diseases, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD), are caused by expanded DNA repeats.
• These expanded repeats can serve as templates for synthesizing specific inhibitors.
• Developing agents that can reversibly assemble in situ to target multiple nucleic acids is highly desirable.

Purpose of the Study:

• To develop a target-guided screening approach utilizing dynamic covalent chemistry.
• To identify multitarget inhibitors for trinucleotide repeat diseases.
• To synthesize and evaluate amine- or aldehyde-containing fragments for inhibitor development.

Main Methods:

• Synthesis of a diverse library of amine- and aldehyde-containing chemical fragments.
• Target-guided screening employing dynamic covalent chemistry for fragment assembly.
• Confirmation of hit combinations using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) with DM1 and HD repeat sequences.
• In vitro assessment of transcriptional inhibition and cooperativity.

Main Results:

• A diverse set of hit combinations was successfully assembled from the fragment library.
• Hit combinations were confirmed to bind to DM1 and HD repeat sequences via MALDI-MS.
• The identified compounds selectively inhibited transcription in a cooperative manner in vitro.
• Inhibitory concentration (IC50) values for the hit compounds were in the micromolar range.

Conclusions:

• The dynamic covalent library and screening approach is effective for identifying inhibitors of trinucleotide repeat sequences.
• This method successfully yielded compounds that selectively and cooperatively inhibit transcription in vitro.
• The strategy holds potential for developing reversible, multivalent nucleic acid-targeting agents for various diseases.