Exploring PfDHFR reaction surface: A combined molecular dynamics and QM/MM analysis

Area of Science:

• Biochemistry
• Enzymology
• Computational Biology

Background:

• Plasmodium falciparum Dihydrofolate Reductase (PfDHFR) is a key enzyme in folate metabolism.
• Understanding PfDHFR's catalytic mechanism is crucial for antimalarial drug development.

Purpose of the Study:

• To investigate the binding affinities and molecular interactions of substrate (DHF/DHFP) and product (THF) in the wild-type PfDHFR active site.
• To evaluate the binding of the cofactor (NADPH/NADP+) and its role in the catalytic process.

Main Methods:

• Molecular Dynamics (MD) simulations were employed to analyze atomic-level interactions.
• Quantum Mechanics/Molecular Mechanics (QM/MM) analysis was used to calculate binding energies.
• Hydride ion donor-acceptor distance (DAD) analysis was performed.

Main Results:

• DHFP exhibits stronger binding to the PfDHFR active site compared to DHF and THF.
• Protonation of DHF to DHFP enhances the proximity between the substrate and the NADPH cofactor.
• Calculated binding energies indicate DHFP-NADPH and DHF-NADPH complexes are more stable than THF-NADP+.

Conclusions:

• The protonation step is critical for facilitating the PfDHFR catalytic reaction.
• Stronger binding of DHFP promotes efficient hydride transfer from NADPH.
• These findings provide insights into PfDHFR's mechanism and potential drug targets.