Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization

Area of Science:

• Biochemistry
• Structural Biology
• Chemical Biology

Background:

• Understanding small molecule-protein interactions is crucial for biological process elucidation and drug discovery.
• Identifying the precise binding epitope of ligands is essential for rational drug design.

Purpose of the Study:

• To determine the binding epitope of folic acid complexed with dihydrofolate reductase.
• To showcase the utility of multi-dimensional NMR with dissolution dynamic nuclear polarization (D-DNP) for this purpose.

Main Methods:

• Utilized multi-dimensional NMR with sensitivity enhancement via D-DNP.
• Employed polarization transfer from hyperpolarized folic acid to dihydrofolate reductase.
• Implemented pseudo 3D data acquisition with Hadamard encoding for intermolecular NOE information.

Main Results:

• Successfully determined the binding epitope of folic acid on dihydrofolate reductase.
• Achieved high accuracy in ligand pose selection, with top poses within 0.76 Å RMSD.
• Demonstrated superior performance compared to traditional energy-based scoring functions.

Conclusions:

• D-DNP enhanced multi-dimensional NMR significantly improves the speed and selectivity of ligand binding epitope structure elucidation.
• This technique offers a powerful tool for advancing rational drug development and understanding molecular interactions.