Aβ Trimer Research Articles

Development of Triphenylmethane Dyes for In Vivo Fluorescence Imaging of Aβ Oligomers.

Detection of amyloid β (Aβ) oligomers, regarded as the most toxic aggregated forms of Aβ, can contribute to the diagnosis and treatment of Alzheimer's disease (AD). Thus, the development of imaging probes for in vivo visualization of Aβ oligomers is crucial. However, the structural uncertainty regarding Aβ oligomers makes it difficult to design imaging probes with high sensitivity to Aβ oligomers against highly aggregated Aβ fibrils. In this study, we developed Aβ oligomer-selective fluorescent probes based on triphenylmethane dyes through screening of commercially available compounds followed by structure-activity relationship (SAR) studies on cyclic or acyclic 4-dialkylamino groups. We synthesized 11 triarylmethane-based Aβ oligomer probe (TAMAOP) derivatives. In vitro evaluation of fluorescence properties, TAMAOP-9, which had bulky 4-diisobutylamino groups introduced into three benzenes of a twisted triphenylmethane backbone, showed marked fluorescence enhancement in the presence of Aβ oligomers and demonstrated high selectivity for Aβ oligomers against Aβ fibrils. In docking studies using the Aβ trimer model, TAMAOP-9 bound to the hydrophobic surface and interacted with the side chain of Phe20. In vitro section staining revealed that TAMAOP-9 could visualize Aβ oligomers in the brains of AD model mice. An in vivo fluorescence imaging study using TAMAOP-9 showed significantly higher fluorescence signals from the brains of AD model mice than those of age-matched wild-type mice, confirmed by ex vivo section observation. These results suggest that TAMAOP-9 is a promising Aβ oligomer-targeting fluorescent probe applicable to in vivo imaging.

Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study.

Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer’s disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer’s disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers’ structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1–42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1–42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.

Effects of Boron Nitride Nanotube on the Secondary Structure of Aβ(1-42) Trimer: Possible Inhibitory Effect on Amyloid Formation.

Aggregation of amyloid-β (Aβ) peptides into prefibrillar toxic oligomers is responsible for Alzheimer's disease, which is one of the most commonly known forms of neurodegenerative diseases. It has been reported that the low-molecular weight Aβ(1-42) trimer and its higher order oligomers are responsible for the cytotoxicity in the neuronal cells, leading to their death. Various experimental studies have shown that boron nitride nanotube (BNNTs) are noncytotoxic for health and environment and biocompatible in living cells and can be used as delivery vehicles for brain anticancer drugs. Here, we investigate the effects of BNNT on the secondary structure of Aβ(1-42) in the amyloid oligomerization process. We have performed long atomistic molecular dynamics simulations of 4.0 μs in total to study the structural stability of Aβ(1-42) trimer both in presence and absence of BNNT in explicit solvent. It is found that in the absence of BNNT, Aβ(1-42) trimer aggregates, leading to α-helix to β-sheet transition, whereas BNNT provides structural stability to the peptides by keeping them separated and preserving the initial monomeric helical conformation of the Aβ(1-42) trimer. It is found through a free-energy decomposition analysis that the key residues (Lys28, Ile31, Ile32, Leu34, Val40, and Ile41) from the C-terminal that are more responsible for β-sheet fibril formation bind with the BNNT surface and block their structural conversion. Due to the presence of polar B-N bonds, BNNT is less hydrophobic as compared with the carbonaceous nanomaterials where large hydrophobicity of these carbonaceous nanomaterials mostly destabilizes the secondary structure of peptides. The current study reveals that the less hydrophobicity of BNNT provides stability of the initial secondary structure of the Aβ(1-42) trimer and hinders their aggregation. Hence, the secondary structure stabilization in presence of BNNT provides new possibilities for the design of different nanoparticles as therapeutic agents for different types of amyloidogenesis by tuning their hydrophobicity.

Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study

Increasing evidence shows that the formation of misfolded aggregates amyloid-β (Aβ) peptide is associated with the Alzheimer’s disease (AD). Recent experiments reveal a significant correlation of the amount of trimer species bound to neurons with increasing neuro-toxicity. Our previous computational study demonstrated that carbon nanotubes (CNT) can inhibit effectively the formation of β-sheet-rich oligomers of Aβ(16-22) – a hydrophobic peptide essential for Aβ fibrillization. However, the influence of CNT on the oligomers formed by full-length Aβ remains elusive. In this study, we have investigated the conformational dynamics of Aβ(1-42) trimer, built from an NMR structure of α-helical monomer, in the absence and presence of a single-walled carbon nanotube (SWCNT). Our simulations demonstrate that SWCNT can significantly hinder the trimerisation and prevents the secondary structure formation of Aβ(1-42) peptide. Hydrophobic and aromatic stacking interactions between SWCNT and Aβ play important roles in the secondary structure formation of the Aβ trimer. This study reveals a complete picture of the detailed preventable mechanism of full-length Aβ(1-42) by SWCNT, providing theoretical insights into the development of drug candidates of AD.

Single Molecule Studies of Early Stages of Amyloid Aggregation an Effect of pH

The deposition of amyloid fibrils in senile plaques of the brain is the hallmark for many neurodegenerative diseases including Alzheimer's disease (AD). The normal pH in the neuron is neutral, which may decrease due to the mental depression or other environmental factors that may affect amyloid aggregation inside the brain. Moreover, liposomes in the brain are acidic. In vitro studies indicate that acidic pH accelerates amyloid aggregation but the molecular mechanism underlying this effect is unknown. In this work, we probed a Aβ(14-23) trimer and tetramer using our previously developed flexible nano array (FNA) technique to characterize the assembly of this peptide in trimers and tetramers depending on pH. Using atomic force microscopy-single molecule force spectroscopy, and fluorescence based tethered approach for probing intermolecular interactions (TAPIN) approach, we found that pH affects the pathways of oligomers assembly. If at neural pH there is primarily one assembly pathway, at acidic pH three different pathways with different stabilities were identified. Models for the assembly of Aβ(14-23) trimers and tetramers are proposed. We posit that the highly stable oligomers found at acidic pH lead to acceleration of aggregation process suggesting that acidic pH may be a risk factor in development of AD.Acknowledgements. The work was supported by NIH grants R01 GM096039 and R01GM118006 to YLL.

Oligomeric Amyloid-β Toxicity Can Be Inhibited by Blocking Its Cellular Binding in Cortical Neuronal Cultures with Addition of the Triphenylmethane Dye Brilliant Blue G.

Accumulation of soluble amyloid β (Aβ) oligomers in the brain has been suggested to cause neurodegeneration associated with Alzheimer's disease (AD). Our previous findings showed that the binding of Aβ trimer and tetramer to neurons is significantly correlated with Aβ-induced neuronal cell death. We propose blocking of neuronal binding of these neurotoxic Aβ oligomers as a therapeutic strategy for preventing this disease. To test this, a nontoxic triphenylmethane dye, Brilliant Blue G (BBG), which has been reported to modulate Aβ aggregation and neurotoxicity, was investigated using mouse primary cortical neuronal cultures treated with photoinduced cross-linked toxic Aβ40 oligomers as well as soluble Aβ40 and Aβ42 peptides. We found that the BBG-induced decrease in Aβ binding resulted in a significant decrease in its neurotoxicity. These findings support our hypothesis that disruption of cellular Aβ binding is a promising therapeutic strategy for combating AD.

Membrane-bound tetramer and trimer Aβ oligomeric species correlate with toxicity towards cultured neurons.

Amyloid beta (Aβ) peptide is the major constituent of the extracellular amyloid plaques deposited in the brains of Alzheimer's disease patients and is central to the pathogenic pathway causing this disease. The identity of the neurotoxic Aβ species remains elusive. We previously reported that Aβ toxicity correlates strongly with its neuronal cell binding leading us to hypothesize that neuronal cell death is caused by the binding of a specific oligomeric Aβ species. To identify the specific oligomeric Aβ species that is associated with cell death, we treated mouse cortical neuronal cultures with synthetic Aβ40 and Aβ42 peptides and identified that the cellular Aβ binding and neurotoxicity were time and concentration dependent. We found a significant correlation between the amount of trimer and tetramer species bound to neurons with increasing neurotoxicity. We prepared Aβ40 oligomers (up to tetramers) using photo-induced cross-linking of unmodified peptides to confirm this oligomer-specific neurotoxic activity. Our results identify the Aβ tetramer, followed by the trimer, as the most toxic low-order oligomers Aβ species. Our findings suggested that binding of amyloid-β (Aβ) tetramer and trimer, not monomer or dimer, to neurons is critical to induce neuronal cell death associated with Alzheimer's Disease. We proposed that Aβ trimer and tetramer are the potential neurotoxic Aβ species. This would provide more specific therapeutic target for Alzheimer's Disease.

Atomic-level study of the effects of O4 molecules on the structural properties of protofibrillar Aβ trimer: β-sheet stabilization, salt bridge protection, and binding mechanism.

Alzheimer's disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic prefibrillar aggregates. Recent experiments reported that small organic molecule O4 decreases the concentration of toxic oligomers by promoting fibrillation and thus reduces Aβ toxicity. However, the atomic-level details of O4-Aβ-oligomer interaction are largely unknown. In this work, we studied the structural stability of the fibrillike Aβ(17-42) trimer by performing atomistic molecular dynamics simulations of 1.5 μs in total on the trimer with and without O4. We found that the Aβ(17-42) trimer is unstable without O4, whereas its structural stability is greatly enhanced with O4. Four binding sites were found around residues F20, S26, and M35, namely the central hydrophobic core (CHC) site, the turn site, and two hydrophobic-groove sites. The two hydrophobic grooves near M35 facilitate O4 to bind through hydrophobic interaction and geometry match. The binding of O4 at the CHC site is mostly stabilized by hydrophobic and π-π stacking interactions. Hydrogen-bonding interaction between O4 and S26 plays a role in the binding of O4 to the turn site. Our work reveals the detailed stabilization mechanism of protofibrillar Aβ oligomers by O4 and may provide novel insight into the development of drug candidates against AD.

Molecular Dynamics Simulations of Low-Ordered Alzheimer β-Amyloid Oligomers from Dimer to Hexamer on Self-Assembled Monolayers

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface.