Discovery of RNA-binding fragments using biolayer interferometry.

Area of Science:

• Biochemistry
• Pharmacology
• Molecular Biology

Background:

• Structured RNAs are emerging as key pharmacological targets for various diseases.
• Developing efficient RNA-focused hit discovery methods is essential for therapeutic development.
• Biolayer Interferometry (BLI) is a label-free, high-throughput technique for biomolecular interaction analysis, primarily used for protein screening.

Purpose of the Study:

• To evaluate and demonstrate the utility of Biolayer Interferometry (BLI) for RNA-small molecule interaction studies.
• To explore BLI's application in identifying drug-like fragments that bind to RNA targets.
• To establish BLI as a viable method for RNA-targeted drug discovery.

Main Methods:

• Utilized Biolayer Interferometry (BLI) to investigate interactions between small molecules and three distinct riboswitches.
• Employed BLI for high-throughput screening to identify fragment binders for RNA targets.
• Integrated ligand-based Nuclear Magnetic Resonance (NMR) spectroscopy as an orthogonal validation technique.

Main Results:

• Successfully demonstrated the application of BLI for characterizing RNA-small molecule binding.
• Identified fragment binders for riboswitches, potential targets for novel antibiotics.
• Discovered seven competitive fragment binders for the flavin mononucleotide (FMN) riboswitch using BLI and NMR, with novel chemical scaffolds.

Conclusions:

• Biolayer Interferometry (BLI) is an effective and scalable method for RNA-targeted drug discovery.
• BLI facilitates the identification of novel small molecules and fragments binding to RNA targets.
• The combination of BLI and NMR provides a robust approach for validating RNA-small molecule interactions and discovering new chemical matter.