Molecular Mechanism of Beta-Amyloid Aggregation Inhibition by KLVFF

The accumulation of β-amyloid (Aβ) oligomers is a critical hallmark for different neurodegenerative conditions, including Alzheimer's disease. The short peptide KLVFF, derived from the central hydrophobic domain of Aβ, binds to Aβ oligomers and interferes with Aβ aggregation. However, the underlying molecular mechanism of action of this peptide remains to be elucidated. This work addresses this question by studying the interaction between an Aβ hexamer model and randomly positioned KLVFF peptides (n = 1, 3, 6) from triplicate microsecond-scale molecular dynamics (MD) simulations. Our findings revealed that KLVFF peptides engage in highly dynamic interactions with the oligomer's lateral face and terminal monomers, preferentially targeting the hydrophobic regions of the CHD and SHD domains. We observed no evidence of KLVFF peptide aggregation or the formation of amyloid-like interactions at fibril ends, contradicting the previously postulated mechanism of action for KLVFF. Instead, we found that KLVFF binding at the oligomer ends induces conformational changes and the gradual detachment of terminal monomers from the fibril, suggesting an inhibitory mechanism based on the loss of structural integrity and the prevention of ordered Aβ addition at the fibril ends. Our computational findings were validated by circular dichroism and thioflavin T aggregation assays. The experiments confirmed that KLVFF reduces the formation of β-sheet secondary structures in Aβ solutions, with a concentration- and incubation-time-dependent effect and negligible self-aggregation when isolated. These results provide key insights for the rational design of novel Aβ aggregation inhibitors mimicking KLVFF as fibril-end destabilizers and inhibitors of oligomer elongation.