It is widely believed that Alzheimer's disease pathogenesis is driven by the production and deposition of the
amyloid-β peptide (Aβ) in the brain. In this study, we employ a combination of in silico and in vitro approaches to investigate
the inhibitory properties of selected arginine-rich D-enantiomeric peptides (D-peptides) against amyloid aggregation.
The D-peptides include D3, a 12-residue peptide with anti-amyloid potencies demonstrated in vitro and in vivo, RD2,
a scrambled sequence of D3, as well as truncated RD2 variants. Using a global optimization method together with binding
free energy calculations followed by molecular dynamics simulations, we perform a detailed analysis of D-peptide binding
to Aβ monomer and a fibrillar Aβ structure. Results obtained from both molecular simulations and surface plasmon
resonance experiments reveal a strong binding of D3 and RD2 to Aβ, leading to a significant reduction in the amount of β
structures in both monomer and fibril, which was also demonstrated in Thioflavin T assays. The binding of the D-peptides
to Aβ is driven by electrostatic interactions, mostly involving the D-arginine residues and Glu11, Glu22 and Asp23 of Aβ.
Furthermore, we show that the anti-amyloid activities of the D-peptides depend on the length and sequence of the Dpeptide,
its ability to form multiple weak hydrophobic interactions with Aβ, as well as the Aβ oligomer size.