Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.

Aggregates of amyloid-β (Aβ) peptides are thought to cause Alzheimer's disease. Polyphenolic compounds are known to inhibit Aβ aggregation. We applied replica permutation with solute tempering (RPST) to the system of Aβ fragments, Aβ(16-22), and polyphenols to elucidate the mechanism of inhibition of Aβ aggregation. The RPST molecular dynamics simulations were performed for two polyphenols, myricetin (MYC) and rosmarinic acid (ROA). Two Aβ fragments were distant, and the number of residues forming the intermolecular β-sheet was reduced in the presence of MYC and ROA compared with that in the absence of polyphenols. MYC was found to interact with glutamic acid and phenylalanine of Aβ fragments. These interactions induce helix structure formation of Aβ fragments, making it difficult to form β-sheet. ROA interacted with glutamic acid and lysine, which reduced the hydrophilic interaction between Aβ fragments. These results indicate that these polyphenols inhibit the aggregation of Aβ fragments with different mechanisms.