The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)

Area of Science:

• Immunology
• Structural Biology
• Computational Biology

Background:

• Programmed Cell Death protein 1 (PD-1) is a critical immune checkpoint molecule involved in immune escape.
• Blocking the PD-1/PD-L1 interaction offers therapeutic potential in cancer immunotherapy.
• Understanding the PD-1 ligand binding mechanism is essential for designing effective modulators.

Purpose of the Study:

• To investigate the structural dynamics of PD-1 in apo and ligand-bound states using molecular dynamics simulations.
• To identify key residues and structural features influencing PD-1 and PD-L1 interactions.
• To guide the rational design of engineered PD-1 mutants with enhanced ligand-binding properties.

Main Methods:

• Utilized 50 ns molecular dynamics (MD) simulations to analyze PD-1 structure in human and mouse, in both apo and PD-L1 bound states.
• Performed in silico mutagenesis to predict potential functional gains in ligand binding.
• Conducted in vitro binding experiments to validate the efficacy of engineered PD-1 mutants.

Main Results:

• Apo human PD-1 (hPD-1) exhibited greater flexibility compared to its PD-L1 bound state.
• Residue K135 was identified as crucial for binding energy, despite not being at the direct binding interface.
• Mutants M70I, S87W, A129L, A132L, and K135M demonstrated improved ligand binding compared to wild-type PD-1.

Conclusions:

• MD simulations and in silico mutagenesis provide valuable insights into PD-1 structural dynamics and ligand interactions.
• Identified specific mutations that enhance PD-1's affinity for its ligand.
• The findings offer a foundation for designing engineered PD-1 mutants to modulate the PD-1/PD-L1 pathway for therapeutic benefit.