Pseudo-peptide amyloid-ß blocking inhibitors: molecular dynamics and single molecule force spectroscopy study.

By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-ß (Aß) inhibitors that bind to the Aß peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aß (13-23). The binding affinities between the inhibitor and Aß as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aß-Aß binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aß toxicity in Alzheimer's disease.

Amyloid-ß (1-40) restores adhesion properties of pulmonary surfactant, counteracting the effect of cholesterol.

A pulmonary surfactant (PS) is a thin lipid-protein film covering the surface of the lung alveoli at the air/liquid interface. The primary purpose of a PS is to control the surface tension of the air/liquid interface and to reduce the work of breathing. High levels of cholesterol in a PS are associated with life-threatening acute respiratory distress syndrome (ARDS) and acute lung injury (ALI). Finding therapeutics to counteract the effect of cholesterol in a PS is a matter of contemporary research. In our earlier work, we showed that the addition of amyloid-ß (1-40) (Aß40), the protein implicated in Alzheimer's disease, can reverse the detrimental effects of cholesterol in surfactants by improving multilayer formation and restoring PS surface active properties. We hypothesized that this phenomenon was due to Aß40 improving adhesion properties of a surfactant. In this work we used atomic force spectroscopy to demonstrate that Aß40 counteracts the adhesive properties of a PS compromised by high levels of cholesterol in a PS and helps to restore the functionality of a PS.

Comparison of three competing dynamic force spectroscopy models to study binding forces of amyloid-ß (1-42).

We performed single molecule dynamic force spectroscopy experiments to study the dimerization of two amyloid-ß (1-42) peptides and compared three different theoretical models used to fit experimental data: Bell-Evans, Dudko-Hummer-Szabo, and Friddle-De Yoreo. Using these models we extracted values of the dissociation rate at zero force, k0, and height and the width of the energy barrier, ΔG and xß. We show the importance of including the effect of the linker molecule. All three models corrected for the linker effect give comparable results for xß and show more discrepancy for k0 and ΔG values, ΔG parameter correlates well between Dudko-Hummer-Szabo and Friddle-De Yoreo models but differs for the Bell-Evans model.