Recent Studies on Mechanisms of New Drug Candidates for Alzheimer’s Disease Interacting with Amyloid-β Protofibrils Using Molecular Dynamics Simulations

Abstract

Alzheimer’s disease (AD) is the most common form of dementia. The aggregation and deposition of amyloid-β (Aβ) peptide in the brain is one of its characteristic hallmarks. In order to inhibit or even destabilize Aβ fibrils, a number of candidate molecules have been proposed in recent years. Although experiments have suggested their interactions with Aβ peptides, the molecular details are generally unclear. The determination of a three-dimensional model of Aβ protofibril boosted the exploration of the details at the atomic level, such as the binding sites, the critical residues, and the key interactions for such compounds to bind or to degrade Aβ protofibril using molecular dynamics (MD) simulations. Focused on this emerging strategy, this review looks through a bunch of Aβ-interacting compounds. In particular, the MD simulations on one of the novel drug candidates, wgx-50, identified by our group recently are described in more details so as to show a typical work flow of these studies. The structural features of these compounds revealed by MD simulations may provide new macroscopic translational information for the structure-based drug design for Alzheimer’s disease.