Constructing conformational library for amyloid-β42 dimers as the smallest toxic oligomers using two CHARMM force fields

Dimerization of the Aβ42 under the Influence of the Gold Nanoparticle: A REMD Study

Advances in Alzheimer's disease (AD) are related to the oligomerization of Amyloid β (Aβ) peptides. Therefore, alteration of the process can prevent AD. We investigated the Aβ42 dimerization under the effects of gold nanoparticles using temperature replica-exchange molecular dynamics (REMD) simulations. The structural change of dimers in the presence and absence of the gold nanoparticle, Au55, was monitored over stable intervals. Physical insights into the oligomerization of Aβ were thus clarified. The computed metrics indicate that Au55 affects the progress of oligomerization. Specifically, the presence of the gold nanoparticle significantly modifies the structure of dimeric Aβ42. The β-content experienced a substantial decrease with the induction of Au55. The turn and coil-contents are also decreased under the effects of the gold nanoparticle. However, the α-content of the dimer exhibited a rigid increase. The influence of gold nanoparticles on the dimeric Aβ42 differs significantly from that of silver nanoparticles, which reduce β-content but increase coil-, turn-, and α-contents. The nature of inhibition will be discussed, in which the vdW interaction plays a driving force for the interaction between the Aβ42 dimer and the gold nanoparticle.

Silver nanoparticles alter the dimerization of Aβ42 studied by REMD simulations

The aggregation of amyloid beta (Aβ) peptides is associated with the development of Alzheimer's disease (AD). However, there has been a growing belief that the oligomerization of Aβ species in different environments has a neurotoxic effect on the patient's brain, causing damage. It is necessary to comprehend the compositions of Aβ oligomers in order to develop medications that may effectively inhibit these neurotoxic forms that affect the nervous system of AD patients. Thus, dissociation or inhibition of Aβ aggregation may be able to prevent AD. To date, the search for traditional agents and biomolecules has largely been unsuccessful. In this context, nanoparticles have emerged as potential candidates to directly inhibit the formation of Aβ oligomers. The oligomerization of the dimeric Aβ peptides with or without the influence of a silver nanoparticle was thus investigated using temperature replica-exchange molecular dynamics (REMD) simulations. The physical insights into the dimeric Aβ oligomerization were clarified by analyzing intermolecular contact maps, the free energy landscape of the dimeric oligomer, secondary structure terms, etc. The difference in obtained metrics between Aβ with or without a silver nanoparticle provides a picture of the influence of silver nanoparticles on the oligomerization process. The underlying mechanisms that are involved in altering Aβ oligomerization will be discussed. The obtained results may play an important role in searching for Aβ inhibitor pathways.

Disrupting Dimeric β-Amyloid by Electric Fields

The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer's disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids in vitro and eventually in vivo.

Identification of Catechins' Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

The assembly of the amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline-in the framework of the ensemble docking strategy-to identify catechins' binding sites in monomeric Aβ₄₂. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ₄₂. Additionally, it has been found that all the studied ligands, especially EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.

Interactions of Curcumin's Degradation Products with the Aβ42 Dimer: A Computational Study

Amyloid-β (Aβ) dimers are the smallest toxic species along the amyloid-aggregation pathway and among the most populated oligomeric accumulations present in the brain affected by Alzheimer's disease (AD). A proposed therapeutic strategy to avoid the aggregation of Aβ into higher-order structures is to develop molecules that inhibit the early stages of aggregation, i.e., dimerization. Under physiological conditions, the Aβ dimer is highly dynamic and does not attain a single well-defined structure but is rather characterized by an ensemble of conformations. In a recent study, a highly heterogeneous library of conformers of the Aβ dimer was generated by an efficient sampling method with constraints based on ion mobility mass spectrometry data. Here, we make use of the Aβ dimer library to study the interaction with two curcumin degradation products, ferulic aldehyde and vanillin, by molecular dynamics (MD) simulations. Ensemble docking and MD simulations are used to provide atomistic detail of the interactions between the curcumin degradation products and the Aβ dimer. The simulations show that the aromatic residues of Aβ, and in particular ¹⁹FF²⁰, interact with ferulic aldehyde and vanillin through π-π stacking. The binding of these small molecules induces significant changes on the ¹⁶KLVFF²⁰ region.