SAR by (Protein-Observed) ¹⁹F NMR

Area of Science:

• Structural Biology
• Chemical Biology
• Biophysics

Background:

• Protein-protein interactions (PPIs) are crucial in cellular processes but challenging to target with inhibitors due to large, dynamic interfaces.
• Existing structural biology methods like X-ray crystallography and NMR spectroscopy have advanced inhibitor discovery, exemplified by Venetoclax.
• Targeting transcription factor-PPIs and epigenetic regulators requires novel ligand discovery approaches.

Purpose of the Study:

• To introduce and validate protein-observed 19F NMR (PrOF NMR) as a sensitive and efficient tool for fragment-based ligand discovery (FBLD).
• To demonstrate the application of PrOF NMR for characterizing native PPIs and screening for small molecule ligands.
• To explore the utility of PrOF NMR in medicinal chemistry for SAR studies and inhibitor deconstruction.

Main Methods:

• Metabolic labeling of proteins with fluorinated aromatic amino acids for 19F NMR.
• Utilizing the high sensitivity and environmental responsiveness of the 19F nucleus.
• Applying PrOF NMR to study transcription factor-coactivator interactions (KIX domain) and epigenetic targets (BRD4, BPTF bromodomains).
• Simultaneous labeling with dual fluorinated aromatic amino acids for enhanced PrOF NMR experiments.

Main Results:

• PrOF NMR successfully characterized native PPIs and identified ligands for challenging targets.
• Demonstrated medicinal chemistry applications including FBLD, selectivity screening, and SAR studies.
• Discovered novel inhibitors for BPTF and a new class of inhibitors for BRD4 bromodomains.

Conclusions:

• PrOF NMR is a rapid, sensitive, and interpretable structural biology method for discovering and characterizing ligands for PPIs.
• The technique is particularly valuable for fragment-based ligand discovery and studying epigenetic proteins and transcription factors.
• PrOF NMR offers a complementary approach to existing methods, accelerating the development of small molecule therapeutics.