Mapping of possible binding sequences of two beta-sheet breaker peptides on beta amyloid peptide of Alzheimer's disease.

Aggregation of amyloid peptide (Abeta) has been identified as a major feature of the pathogenesis of Alzheimer's disease. Increased risk for disease is associated with increased formation of polymerized Abeta. Inhibition of formation of toxic (aggregated) form of Abeta is one of the therapeutic possibilities. Beta sheet breaker peptides (BSBs) fulfill the requirements of an effective inhibitor. After having attached to the Abeta molecules, BSBs can prevent aggregation of Abeta to polymeric forms (aggregates). In the present study, we performed molecular modelling of complex formation between Abeta and two BSB peptides. Our aim was to find proper binding sequences for the BSB peptides on Abeta and characterize them. A dimeric model of Abeta was also used to study the interaction of BSBs with the aggregated forms of Abeta and find the sequences responsible for the polymerization process. A fast and efficient computational method: molecular docking was used for the afore-mentioned purposes.