Mechanistic Insights into the Disaggregation of Amyloid-β Fibrils by EPPS via Replica-Exchange Molecular Dynamics Simulations

Amyloid-β (Aβ) fibrils are considered key pathological agents in the progression of Alzheimer’s disease. Recent studies demonstrated that N-(2-hydroxyethyl)piperazine-N'-(3-propane-sulfonic acid) (EPPS) effectively disaggregates Aβ oligomers and plaques in the brains of APP/PS1 transgenic mice, though its molecular mechanism remains unclear. In this study, we investigated the disaggregation mechanism of Aβ fibrils by EPPS using replica-exchange molecular dynamics (REMD) simulations. Our results showed that EPPS preferentially binds to the exterior strands of Aβ fibrils, particularly interacting with Glu22 residues via ionic interactions. This binding induced significant structural fluctuations, which propagated to neighboring strands in a time-dependent manner. Clustering analysis revealed that EPPS disrupts intermolecular hydrogen bonding at the fibril edge, destabilizing the β-strand structure. Secondary structure analysis further confirmed a decrease in β-sheet content in the exterior segments. These findings provide molecular-level insights into the dissociation mechanism of Aβ fibrils by EPPS and suggest potential strategies for developing anti-amyloid therapeutics.