Efficient NMR Screening Approach to Discover Small Molecule Fragments Binding Structured RNA

Area of Science:

• Biochemistry
• Chemical Biology
• Drug Discovery

Background:

• Structured RNAs play crucial roles in cellular processes and disease.
• Identifying small molecules that bind to RNA is challenging but essential for therapeutic development.
• Current methods for RNA-targeted small molecule discovery are often limited in scope or scalability.

Purpose of the Study:

• To present a scalable nuclear magnetic resonance (NMR) screening approach for identifying and prioritizing small molecule fragments that bind to structured RNAs.
• To demonstrate the utility of this target-agnostic method using the pre-miR-21 stem-loop as a model system.
• To provide initial hits for further synthetic elaboration and structure-based drug discovery.

Main Methods:

• Development of a scalable nuclear magnetic resonance (NMR) screening approach.
• Screening of a 420-compound commercially available fragment library against the pre-miR-21 hairpin.
• Application of a screening cascade to refine initial hits.
• Validation of fragment binding using target-detected NMR experiments and Nuclear Overhauser Effect (NOE) spectroscopy.

Main Results:

• The NMR screening approach was successfully applied to the pre-miR-21 stem-loop.
• 18 initial fragment hits were identified from a library of 420 compounds.
• The hits were refined to four fragments that passed all screening filters.
• A thiadiazole fragment was confirmed to bind the Dicer cleavage site of pre-miR-21.

Conclusions:

• The described NMR screening approach is scalable and target-agnostic, suitable for diverse RNA structures and compound libraries.
• This method effectively identifies and prioritizes small molecule fragments for RNA-targeted drug discovery.
• The identified thiadiazole fragment provides a promising starting point for developing therapeutics against pre-miR-21 related diseases.