In Silico Analysis of the Antagonist Effect of Enoxaparin on the ApoE4–Amyloid-Beta (Aβ) Complex at Different pH Conditions

Apolipoprotein E4 (ApoE4) is thought to increase the risk of developing Alzheimer’s disease. Several studies have shown that ApoE4-Amyloid β (Aβ) interactions can increment amyloid depositions in the brain and that this can be augmented at low pH values. On the other hand, experimental studies in transgenic mouse models have shown that treatment with enoxaparin significantly reduces cortical Aβ levels, as well as decreases the number of activated astrocytes around Aβ plaques. However, the interactions between enoxaparin and the ApoE4-Aβ proteins have been poorly explored. In this work, we combine molecular dynamics simulations, molecular docking, and binding free energy calculations to elucidate the molecular properties of the ApoE4-Aβ interactions and the competitive binding affinity of the enoxaparin on the ApoE4 binding sites. In addition, we investigated the effect of the environmental pH levels on those interactions. Our results showed that under different pH conditions, the closed form of the ApoE4 protein, in which the C-terminal domain folds into the protein, remains stabilized by a network of hydrogen bonds. This closed conformation allowed the generation of six different ApoE4-Aβ interaction sites, which were energetically favorable. Systems at pH5 and 6 showed the highest energetic affinity. The enoxaparin molecule was found to have a strong energetic affinity for ApoE4-interacting sites and thus can neutralize or disrupt ApoE4-Aβ complex formation.

Exploring Amyloid-β Dimer Structure Using Molecular Dynamics Simulations

A major hallmark of Alzheimer's disease (AD) is the aggregation of amyloid-β peptides in the brains of people afflicted by the disease. The exact pathway to this catastrophic event is unknown. In this work, a total of 9.5 μs molecular dynamics simulations have been performed to investigate the structure and dynamics of the smallest form of toxic Aβ oligomers, i.e., the Aβ dimers. This study suggests that specific hydrophobic regions are vital in the aggregation process. Different possible structures for Aβ dimers are reported along with their relative binding affinity. These data may be used to design better Aβ-aggregation inhibitors. The diversity of the dimer structures suggests several aggregation pathways.

The combined force field-sampling problem in simulations of disordered amyloid-β peptides

Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm. The force field and sampling combinations are used to characterize the structural ensembles of the amyloid-beta peptides Aβ42 and Aβ43, which both should be random coils as shown recently by experimental nuclear magnetic resonance (NMR) and 2D Förster resonance energy transfer (FRET) experiments. The results illustrate the key importance of the sampling algorithm: while the standard force field using TREx is in poor agreement with the NMR J-coupling and nuclear Overhauser effect and 2D FRET data, when using the TCW method, the standard and optimized protein-water force field combinations are in very good agreement with the same experimental data since the TCW sampling method produces qualitatively different ensembles than TREx. We also discuss the relative merit of the 2D FRET data when validating structural ensembles using the different force fields and sampling protocols investigated in this work for small IDPs such as the Aβ42 and Aβ43 peptides.