Determination of Ligand Binding Epitope Structures Using Polarization Transfer from Hyperpolarized Ligands

Area of Science:

• Biochemistry
• Structural Biology
• Chemical Physics

Background:

• Protein binding site structure determination is crucial for drug discovery.
• Traditional Nuclear Magnetic Resonance (NMR) spectroscopy has limitations in sensitivity.
• Hyperpolarization techniques significantly enhance NMR signal sensitivity.

Purpose of the Study:

• To investigate the application of dissolution dynamic nuclear polarization (D-DNP) NMR for determining protein-ligand binding site structures.
• To compare experimental D-DNP NMR data with predictions from docking-derived structures.
• To develop and validate a scoring function based on experimental data for improved structure ranking.

Main Methods:

• Hyperpolarization of folic acid using dissolution dynamic nuclear polarization (D-DNP).
• Measurement of NMR signal evolution and polarization transfer to dihydrofolate reductase.
• Comparison of experimental data with signal evolution predicted for docking-derived structures.
• Development of a scoring function based on experimental NMR data.

Main Results:

• A scoring function derived from D-DNP NMR experimental data significantly improved the ranking of protein-ligand binding site structures compared to docking alone.
• Spearman's correlation coefficient for the experimental scoring function was 0.88 for five individually addressed ligand protons and 0.59 for the entire ligand.
• Docking energy alone yielded a correlation coefficient of 0.49.
• Accurate ligand structure determination was achieved using data from a small number of individually addressed source spins.

Conclusions:

• D-DNP NMR is a powerful technique for enhancing NMR sensitivity in structural biology.
• The developed D-DNP NMR-derived scoring function effectively ranks protein-ligand binding site structures.
• This method offers a sensitive and accurate approach for determining ligand structures in drug discovery, even with limited data.