Amyloid peptide Aβ40 inhibits aggregation of Aβ42: evidence from molecular dynamics simulations

Effects of amyloid beta (Aβ) peptide Aβ(40) on secondary structures of Aβ(42) are studied by all-atom simulations using the GROMOS96 43a1 force field with explicit water. It is shown that in the presence of Aβ(40) the beta-content of monomer Aβ(42) is reduced. Since the fibril-prone conformation N? of full-length Aβ peptides has the shape of beta strand-loop-beta strand this result suggests that Aβ(40) decreases the probability of observing N? of Aβ(42) in monomer state. Based on this and the hypothesis that the higher is the population of N? the higher fibril formation rates, one can expect that, in agreement with the recent experiment, Aβ(40) inhibit fibril formation of Aβ(42). It is shown that the presence of Aβ(40) makes the salt bridge D23-K28 and fragment 18-33 of Aβ(42) more flexible providing additional support for this experimental fact. Our estimation of the binding free energy by the molecular mechanics-Poisson-Boltzmann surface area method reveals the inhibition mechanism that Aβ(40) binds to Aβ(42) modifying its morphology.     

Electrochemical analysis Aβ42 peptide adsorption and aggregation on spectroscopic graphite

Monatshefte für Chemie - Chemical Monthly - Formation of pathological amyloid fibrils in brain accompanies a number of neurodegenerative disorders, including Alzheimer’s disease (AD)...     

Bifunctional metal-free photo-organocatalysts for enantioselective aerobic oxidation of β-dicarbonyl compounds

A series of bifunctional metal-free photo-organocatalysts have been developed by grafting the photosensitizer to cinchona-derived phase-transfer catalysts. Using air as a green oxidant and visible light as the driving force, these catalysts are applied to the oxidation of a range of β-dicarbonyl compounds in good yields (up to 97%) and enantioselectivities (up to 93:7 er).     

Taylor dispersion analysis discloses the impairment of Aβ peptide aggregation by the presence of a fluorescent tag

The use of fluorescently tagged amyloid peptides, implicated in Alzheimer's disease, to study their aggregation at low concentrations is a common method; however, the fluorescent tag should not introduce a bias in the aggregation process. In this work, native amyloid peptides Aβ(1–40) and Aβ(1–42) and fluorescein-5-isothiocyanate (FITC), tagged ones, were studied using Taylor dispersion analysis coupled with a simultaneous UV and light-emitting diode-induced fluorescence detection, to unravel the effect of FITC on the aggregation process. For that, a total concentration of 100 µM of peptides consisting of a mixture of native and tagged ones (up to 10% in moles) was applied. Results demonstrated that FITC had a strong inhibition effect upon the aggregation behaviour of Aβ(1–42), whereas for Aβ(1–40), only a retardation in kinetics was observed. It was also shown that when mixed solutions of Aβ(1–40) and Aβ(1–42) are used, the Aβ(1–42) alloform was the leading peptide in the aggregation process, and when the latter was tagged, the aggregation kinetics decreased but the lifetime of potentially toxic oligomers was drastically increased. These results confirmed that the hydrophilicity of the N-terminus part of the peptide plays a major role in the aggregation process.     

An enzyme-linked immunosorbent assay to compare the affinity of chemical compounds for β-amyloid peptide as a monomer

Aβ_1–42 is the proteolytic cleavage product of cleavage of the amyloid precursor protein by β- and γ-secretases. The aggregation of Aβ_1–42 plays a causative role in the development of Alzheimer’s disease. To lock Aβ_1–42 in a homogenous state, we embedded the Aβ_1–42 sequence in an unstructured region of Bcl-x_L. Both the N-terminus and the C-terminus of Aβ_1–42 were constrained in the disordered region, whereas the conjunction did not introduce any folding to Aβ_1–42 but maintained the sequence as a monomer in solution. With Bcl-x_L-Aβ₄₂, we developed an enzyme-linked immunosorbent assay to compare the affinity of compounds for monomeric Aβ_1–42. Bcl-x_L-Aβ₄₂ was coated on a microplate and this was followed by incubation with different concentrations of compounds. Compounds binding to Leu17-Val24 of Aβ_1–42 inhibited the interaction between Bcl-x_L-Aβ₄₂ and antibody 4G8. The method can not only reproduce the activities of the reported Aβ_1–42 inhibitors such as dopamine, tannin, and morin but can also differentiate decoy compounds that do not bind to Aβ_1–42. Remarkably, using this method, we discovered a new inhibitor that binds to monomeric Aβ_1–42 and inhibits Aβ_1–42 fibril formation. As the structure of Bcl-x_L-Aβ₄₂ monomer is stable in solution, the assay could be adapted for high-throughput screening with a series of antibodies that bind the different epitopes of Aβ_1–42. In addition, the monomeric form of the Aβ_1–42 sequence in Bcl-x_L-Aβ₄₂ would also facilitate the identification of Aβ_1–42 binding partners by coimmunoprecipitation, cocrystallization, surface plasmon resonance technology, or the assay as described here.     

Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ42 peptide

The growth of amyloid fibrils is studied by replica exchange molecular dynamics in an implicit solvent. Our data indicate that extremely long simulation times (at least a few hundred ns) are necessary to study the thermodynamics of fibril elongation in detail. However some aspects of the aggregation process are already accessible on the time scales available in the present study. A peak in the specific heat indicates a docking temperature of T(dock) ≈ 320 K. Irreversible locking requires lower temperatures with the locking temperature estimated as T(lock) ≈ 280 K. In our simulation the fibril grows from both sides with the C-terminal of the incoming monomer attaching to the C-terminal of the peptides in the fibril forming a β-sheet on the fibril edge. Our simulation indicates that the C-terminal is crucial for aggregation.     

Promoting the Activity of Bifunctional Catalysts for Autoxidation of 1-Octanethiol

Mercaptans in petroleum products wreck the quality of finished products, so it is necessary to remove them in petroleum refining industry. Merox fixed-bed process is widely used in which mercaptans are converted by contacting feedstock with a metal phthalocyanine catalyst in the presence of air and an alkaline agent. However, use of caustic brings a spent caustic disposal problem so that novel caustic-free catalysts are highly desired to meet environment requirements1-3. It is not just simply …     

Optimized method for the recombinant production of a sea anemone’s peptide

The production of the analgesic peptide HCRG21 for medical use is restricted by a number of limitations in the technology. The optimal biotechnological method scalable to industrial has been developed based on the production of a fusion protein containing a special leader, His-tag, and Smt3 sequence upstream in the peptide sequence. The resulting peptide shared its inhibitory activity to TRPV1 ion channel identical to the published early.     

Methodology for the synthesis of mimetics of peptide β-turns

This letter describes a scenario which provides for the stereospecific introduction of both the amino and carboxyl termini portion of a designed β-turn mimetic.     

KLVFF peptide functionalized nanoparticles capture Aβ42 by co-assembly for decreasing cytotoxicity

The bis(pyrene)-Lys-Leu-Val-Phe-Phe-Gly-poly ethylene glycol (BP-KLVFFG-PEG) based nanoparticles capture Aβ₄₂ by recognition and co-assembly, the length of PEG chain in which leads to different morphologies of coassemblies and capture efficiency. The co-assembly strategy shows a decrease of cytotoxicity, potentially for Alzheimer's disease treatment.     

Solution-Based Determination of Dissociation Constants for the Binding of Aβ42 to Antibodies

Amyloid β-peptides (Aβ) play a major role in the pathogenesis of Alzheimer's disease. Therefore, numerous monoclonal antibodies against Aβ have been developed for basic and clinical research. The present study applied fluorescence based analytical ultracentrifugation and microscale thermophoresis to characterize the interaction between Aβ42 monomers and three popular, commercially available antibodies, namely 6E10, 4G8 and 12F4. Both methods allowed us to analyze the interactions at low nanomolar concentrations of analytes close to their dissociation constants (K_D) as required for the study of high affinity interactions. Furthermore, the low concentrations minimized the unwanted self-aggregation of Aβ. Our study demonstrates that all three antibodies bind to Aβ42 monomers with comparable affinities in the low nanomolar range. K_D values for Aβ42 binding to 6E10 and 4G8 are in good agreement with formerly reported values from SPR studies, while the K_D for 12F4 binding to Aβ42 monomer is reported for the first time.     

The electrostatic probe: a tool for the investigation of the Aβ(1-16) peptide deformations using the static modes

We investigate the conformational changes of the Amyloid β(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.     

Study of the aggregation behavior of a π-conjugated dendrimer with a twisted core

A dendrimer having phenylene vinylene and phenylene ethynylene moieties, a twisted core, and eighteen chiral centers on the periphery has been prepared in high yield by using Sonogashira and Horner–Wadsworth–Emmons reactions. UV–visible and fluorescence spectra and circular dichroism measurements have been envisaged to study the aggregation behavior.     

Synthesis of ‘difficult’ peptide sequences: application of a depsipeptide technique to the Jung-Redemann 10- and 26-mers and the amyloid peptide Aβ(1-42)

Recently a 26-mer peptide 1 incorporating Ser and Thr was described as a ‘difficult’ sequence that could not be synthesized by standard methods. If the first Ser residue was used to incorporate a depsipeptide unit, the resulting hybrid was readily assembled. The 26-mer ester was then converted to the native peptide by an O→N acyl shift. The technique may be general for other systems containing appropriate Ser and Thr units and was demonstrated here for the case of the amyloid peptide Aβ(1-42).     

Stochastic kinetic study of protein aggregation and molecular crowding effects of Aβ40 and Aβ42

Two isoforms of β-amyloid peptides, Aβ40 and Aβ42, differ from each other only in the last two amino acids, IA, at the end of Aβ42. They, however, differ significantly in their ability in inducing Alzheimer's disease (AD). The rate curves of fibril growth of Aβ40 and Aβ42 and the effects of molecular crowding have been measured in in vitro experiments. These experimental curves, on the other hand, have been fitted in terms of rate constants for elementary reaction steps using rate equation approaches. Several sets of such rate parameters have been reported in the literature. Employing a recently developed stochastic kinetic method, implemented in a browser-based simulator, popsim, we study to reveal the differences in the kinetic behaviors implied by these sets of rate parameters. In particular, the stochastic method is used to distinguish the kinetic behaviors between Aβ40 and Aβ42 isoforms. As a result, we make general comments on the usefulness of these sets of rate parameters.     

Parallel kinetic resolution of racemic mixtures: a new strategy for the preparation of enantiopure compounds?

Kinetic resolution of racemic mixtures is a well-established methodology for the preparation of optically active compounds. However, excellent enantioselectivities are required to obtain them in enantiopure form, due to the decrease in ee when conversion values are close to 50%. To overcome this limitation, a parallel (asymmetric) reaction can remove the disfavored enantiomer. In this review, several examples of this strategy showing its wide range of applicability are described, as well as their mathematical treatment and some new applications in combinatorial chemistry.     

Affinity of Cu+ for the copper-binding domain of the amyloid-β peptide of Alzheimer's disease

The role of metal ions in Alzheimer's disease etiology is unresolved. For the redox-active metal ions iron and copper, the formation of reactive oxygen species by metal amyloid complexes has been proposed to contribute to Alzheimer's disease neurodegeneration. For copper, reactive oxygen species are generated by copper redox cycling between its 1+ and 2+ oxidation states. Thus, the AβCu(I) complex is potentially a critical reactant associated with Alzheimer's disease etiology. Through competitive chelation, we have measured the affinity of the soluble copper-binding domain of the amyloid-β peptide for Cu(I). The dissociation constants are in the femtomolar range for both wild-type and histidine-to-alanine mutants. These results indicate that Cu(I) binds more tightly to monomeric amyloid-β than Cu(II) does, which leads us to propose that Cu(I) is a relevant in vivo oxidation state.     

1,2,4-trihydroxynaphthalene-2-O-β-D-glucopyranoside: A new powerful antioxidant and inhibitor of Aβ42 aggregation isolated from the leaves of Lawsonia inermis

Mounting evidence indicates free radicals as toxic species causing damage to human cells leading to the pathogenesis of many diseases such as neurodegenerative disease. Plant derived antioxidants are considered as promising strategy to prevent free radical toxicity. In this study, the crude extract (CE), 50%MeOH, Petroleum Ether (PE) and Ethyl acetate (EA) fractions of Lawsonia inermis leaves were investigated for their antioxidant activity and their ability to counteract amyloid-β₄₂ (Aβ₄₂) aggregation. Elution of the most bioactive fraction (EA) on silica gel column chromatography led to six sub-fractions. The most active sub-fraction (1) was further resolved on silica gel column chromatography. A new compound with powerful antioxidant and anti-Aβ₄₂ aggregation properties was purified and characterised by spectroscopic methods as 1,2,4-trihydroxynaphthalene-2-O-β-D-glucopyranoside (THNG). This finding suggests that the antioxidant and anti-Aβ₄₂ aggregation activities of L. inermis leaves are strongly correlated to this compound.