Computational studies on the binding of β-sheet breaker (BSB) peptides on amyloid βA(1–42)

RRY Inhibits Amyloid-β1-42 Peptide Aggregation and Neurotoxicity

BACKGROUND

Current understanding of amyloid-β protein (Aβ) aggregation and toxicity provides an extensive list of drugs for treating Alzheimer's disease (AD); however, one of the most promising strategies for its treatment has been tri-peptides.

OBJECTIVE

The aim of this study is to examine those tri-peptides, such as Arg-Arg-Try (RRY), which have the potential of Aβ1-42 aggregating inhibition and Aβ clearance.

METHODS

In the present study, in silico, in vitro, and in vivo studies were integrated for screening tri-peptides binding to Aβ, then evaluating its inhibition of aggregation of Aβ, and finally its rescuing cognitive deficit.

RESULTS

In the in silico simulations, molecular docking and molecular dynamics determined that seven top-ranking tri-peptides could bind to Aβ1-42 and form stable complexes. Circular dichroism, ThT assay, and transmission electron microscope indicated the seven tri-peptides might inhibit the aggregation of Aβ1-42 in vitro. In the in vivo studies, Morris water maze, ELISA, and Diolistic staining were used, and data showed that RRY was capable of rescuing the Aβ1-42-induced cognitive deficit, reducing the Aβ1-42 load and increasing the dendritic spines in the transgenic mouse model.

CONCLUSION

Such converging outcomes from three consecutive studies lead us to conclude that RRY is a preferred inhibitor of Aβ1-42 aggregation and treatment for Aβ-induced cognitive deficit.

Exploration of the mechanism for LPFFD inhibiting the formation of beta-sheet conformation of A beta(1-42) in water

The main component of senile plaques found in AD brain is amyloid beta-peptide (A beta), and the neurotoxicity and aggregation of A beta are associated with the formation of beta-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp (LPFFD) can combine with A beta, which can inhibit the aggregation of A beta. In order to explore why LPFFD can inhibit the formation of beta-sheet conformation of A beta at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD on the A beta(1-42) (LPFFD/A beta(1-42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/A beta(1-42) in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from alpha-helix to beta-sheet structure for the C-terminus of A beta(1-42), which may be attributed to the hydrophobicity decreasing of C-terminus residues of A beta(1-42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD.

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.

Pentapeptide amides interfere with the aggregation of beta-amyloid peptide of Alzheimer's disease

Amyloid peptides (Abeta) play a central role in the pathogenesis of Alzheimer's disease (AD). The aggregation of Abeta molecules leads to fibril and plaque formation. Fibrillogenesis is at the same time a marker and an indirect cause of AD. Inhibition of the aggregation of Abeta could be a realistic therapy for the illness. Beta sheet breakers (BSBs) are one type of fibrillogenesis inhibitors. The first BSB peptides were designed by Tjernberg et al. (1996) and Soto et al. (1998). These pentapeptides have proved their efficiency in vitro and in vivo. In the present study, the effects of two pentapeptide amides are reported. These compounds were designed by using the C-terminal sequence of the amyloid peptide as a template. Biological assays were applied to demonstrate efficiency. Modes of action were studied by FT-IR spectroscopy and molecular modeling methods.