Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid ß Peptide 1-42 Polymerization.

The major pathological feature of Alzheimer's disease (AD) is the aggregation of amyloid ß peptide (Aß) in the brain. Inhibition of Aß42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aß with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aß42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a ß-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 Aß42 aggregation the most. The ThT assay and EM revealed that RR reduced Aß42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in ß-sheet conformation and a 39.3% increase in random coiling of Aß42 in the presence of RR. RR also significantly reduced the toxicity of Aß42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aß42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.

Molecular integrative study on interaction domains of nuclear factor erythroid 2-related factor 2 with sirtuin 6.

Oxidative stress is one of the elements causing aging and related diseases. Inhibiting Nrf2 activity or increasing oxidative pressure can replicate the deficits of premature aging. SIRT6 is one of the few proteins that can regulate both life span and aging. Deletion of SIRT6 in human cells impairs the antioxidant capacity of cells, which results in the accumulation of intracellular reactive oxygen species and DNA oxidation products. Characterization of the binding of Nrf2 with SIRT6 is critical for understanding the modulation of Nrf2-correlated cell activities by SIRT6. The yeast two-hybrid experiments showed that the binding of Nrf2 with SIRT6 is mediated by Neh1 and Neh3 domains. The elimination of the Neh1 and Neh3 domains decreased the binding stability and free energy, according to the molecular dynamic analysis. The roles of theses domains in mediating the binding were confirmed by co-immunoprecipitation. In cells transfected with the small interfering RNA (siRNA) targeting the Nrf2 Neh1 domain and plasmids overexpressing domain-mutant Nrf2, it was discovered that Nrf2 lost its activity to stimulate the transcription of antioxidant genes in the absence of Neh1 and Neh3 domains.