Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1–42 Polymerization

Abstract

The major pathological feature of Alzheimer’s disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ42 aggregation the most. The ThT assay and EM revealed that RR reduced Aβ42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ42 in the presence of RR. RR also significantly reduced the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.

A Molecular Integrative Study on the Inhibitory Effects of WRR and ERW on Amyloid β Peptide (1–42) Polymerization and Cell Toxicity

“…Polymerized Aβ42 adopts a conformation in which the backbone atoms are distributed almost in a flat plane, while the Aβ42 monomer is a globular protein, in the MD analysis. Previous molecular docking studies have found that a few dipeptides bonded to the polymerization core of Aβ42, and thus inhibited polymerization [15]. In the present study, a molecular docking experiment between Aβ42 and oligopeptides was carried out.…”

“…In this study, a molecular dynamics analysis was used to examine both the binding free energy in protein complexes as well as the time-dependent changes in the locations of the heavy atoms of the ligands attached to Aβ42. We recently published an article [15] in which we proposed thermodynamic mechanisms and a possible pathway for Aβ42 aggregation. Folding and aggregation were driven by a system's free energy.…”

“…However, upon polymerization, more than five Aβ42 strands bind together to form a stable S-shaped structure composed of parallel strands. This structure serves as a frame core for additional polymerization, and the binding free energy between parallel Aβ42 strands in the S-shaped polymer is reduced by arginine dipeptide bound to the hydrophobic regions of an Aβ42 strand [15]. The tripeptides bind to the same hydrophobic regions as those for arginine dipeptide, thereby enabling them to block and reduce the binding free energy between Aβ42 strands.…”

“…The 17th leucine, 19th phenylalanine, 21st alanine, 24th valine, and 31st isoleucine form the second hydrophobic cluster. The third hydrophobic cluster is formed by the 30th alanine, 32nd isoleucine, 35th methionine, 40th valine, and 42nd alanine at the C-terminus [15]. Polymerized Aβ42 adopts a conformation in which the backbone atoms are distributed almost in a flat plane, while the Aβ42 monomer is a globular protein, in the MD analysis.…”

“…In recent years, computer-aided drug design has been successful in designing various medicines [14]. Additionally, based on the results of molecular docking and dynamics analyses, we have found that dipeptides (arginine-arginine, R-R) form hydrogen bonds with the backbone atoms of Aβ42 oligomers to inhibit their elongating into fibrils [15]. Thus, we suspected that arginine tripeptide had inhibitory activity on the formation of Aβ42 aggregates.…”