Molecular dynamics-based methodological approach to clarify PFOA binding on Human Serum Albumin

Abstract

Perfluorooctanoic acid (PFOA) is a persistent environmental contaminant that binds strongly to human serum albumin (HSA), influencing its distribution and toxicokinetics. While crystallographic studies in the presence of myristic acid have identified a limited number of high-affinity binding sites, additional sites may remain undetected due to competitive binding. Here, we combined molecular docking with extensive molecular dynamics (MD) simulations to comprehensively characterize PFOA–HSA interactions. A tiled docking approach revealed twelve non-overlapping binding poses, including six not previously reported. Ligand–residue interaction mapping, RMSD analysis, and MM/PBSA free energy calculations identified four sites, FA3, FA1, FA4, and FA6, as the most stable PFOA binding positions in the absence of competing ligands. Among all examined sites, FA3 displayed the most favorable calculated binding energy. Furthermore, ligands at both FA1 and FA3 sites exhibited over 23 and 85 kJ/mol more favorable binding energy, respectively as calculated by MM/PBSA than the ligand at well-characterized FA4 site under other ligand-free conditions. Persistent salt bridges, hydrogen bonds, and halogen contacts were identified as key stabilizing interactions. Free-energy landscapes further confirmed the stability of PFOA binding at these sites. These findings provide a more complete understanding of the PFOA binding landscape on HSA, offering insights that may inform the design of biomimetic capture agents and strategies for environmental remediation.