Structural and molecular dynamics insights into the competitive inhibition of the platelet-activating factor receptor by acyl-PAF

Platelet-activating factor (PAF) promotes cellular activation, inflammation, and platelet aggregation, leading to acute thrombosis. The remodeling pathway swiftly produces PAF upon activation, establishing intracellular signaling via the PAF receptor (PAFR). Alkyl-PAF exhibits the aforementioned inflammatory properties; conversely, its structural analog acyl-PAF elicits a diminished response and functions as an endogenous PAFR antagonist. The underlying mechanism remains undefined. We conducted the molecular dynamics simulation to elucidate the interactions of acyl-PAF or alkyl-PAF on PAFR. Results showed that alkyl-PAF and acyl-PAF share the same binding pocket. However, acyl-PAF increases the radius of gyration and root-mean-square deviation of PAFR, resulting in structural instability. Root-mean-square fluctuation and solvent-accessible surface area analysis indicated that acyl-PAF reduces flexibility at the PAFR-G protein interface and interaction with key residues involved in signaling, suggesting impaired G protein dissociation and downstream transduction. Acyl-PAF forms stronger interaction with PAFR by increasing hydrogen bonds and favorable Gibbs free energy (ΔG) changes. The Markov state model analysis confirmed these findings, showing that acyl-PAF attaches to PAFR with a lower equilibrium dissociation constant, greater association rate, and lower dissociation rate. In conclusion, acyl-PAF induces structural instability and diminishes signaling effectiveness despite a high binding affinity. This study dissects the intricate interactions within PAFR signaling pathway and offers new insights into potential therapeutic interventions.