Dimensionality of carbon nanomaterial impacting on the modulation of amyloid peptide assembly

2D nanostructures: Potential in diagnosis and treatment of Alzheimer's disease

Two-dimensional (2D) nanomaterials have garnered enormous attention seemingly due to their unusual architecture and properties. Graphene and graphene oxide based 2D nanomaterials remained the most sought after for several years but the quest to design superior 2D nanomaterials which can find wider application gave rise to development of non-graphene 2D materials as well. Consequently, in addition to graphene based 2D nanomaterials, 2D nanostructures designed using macromolecules (such as DNAs, proteins, peptides and peptoids), transition metal dichalcogenides, transition-metal carbides and/or nitrides (MXene), black phosphorous, chitosan, hexagonal boron nitrides, and graphitic carbon nitride, and covalent organic frameworks have been developed. Interestingly, these 2D nanomaterials have found applications in diagnosis and treatment of various diseases including Alzheimer's disease (AD). Although AD is one of the most debilitating neurodegenerative conditions across the globe; unfortunately, there remains a paucity of effective diagnostic and/or therapeutic intervention for it till date. In this scenario, nanomaterial-based biosensors, or therapeutics especially 2D nanostructures are emerging to be promising in this regard. This review summarizes the diagnostic and therapeutic platforms developed for AD using 2D nanostructures. Collectively, it is worth mentioning that these 2D nanomaterials would seemingly provide an alternative and intriguing platform for biomedical interventions.

Interactions of the Aβ(1-42) Peptide with Boron Nitride Nanoparticles of Varying Curvature in an Aqueous Medium: Different Pathways to Inhibit β-Sheet Formation

The aggregation of amyloid β (Aβ) peptide triggered by its conformational changes leads to the commonly known neurodegenerative disease of Alzheimer's. It is believed that the formation of β sheets of the peptide plays a key role in its aggregation and subsequent fibrillization. In the current study, we have investigated the interactions of the Aβ(1-42) peptide with boron nitride nanoparticles and the effects of the latter on conformational transitions of the peptide through a series of molecular dynamics simulations. In particular, the effects of curvature of the nanoparticle surface are studied by considering boron nitride nanotubes (BNNTs) of varying diameter and also a planar boron nitride nanosheet (BNNS). Altogether, the current study involves the generation and analysis of 9.5 μs of dynamical trajectories of peptide-BNNT/BNNS pairs in an aqueous medium. It is found that BN nanoparticles of different curvatures that are studied in the present work inhibit the conformational transition of the peptide to its β-sheet form. However, such an inhibition effect follows different pathways for BN nanoparticles of different curvatures. For the BNNT with the highest surface curvature, i.e., (3,3) BNNT, the nanoparticle is found to inhibit β-sheet formation by stabilizing the helical structure of the peptide, whereas for planar BNNS, the β-sheet formation is prevented by making more favorable pathways available for transitions of the peptide to conformations of random coils and turns. The BNNTs with intermediate curvatures are found to exhibit diverse pathways of their interactions with the peptide, but in all cases, essentially no formation of the β sheet is found whereas substantial β-sheet formation is observed for Aβ(1-42) in water in the absence of any nanoparticle. The current study shows that BN nanoparticles have the potential to act as effective tools to prevent amyloid formation from Aβ peptides.

Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications

Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Effects of Dissolved Gases on the Amyloid Fibril Morphology

The onset or progression of numerous neurodegenerative diseases occurs due to aggregation of proteins that ultimately form fibrils. The assembly and morphology of fibrils are susceptible to environmental factors. In this work, we used atomic force microscopy (AFM) to investigate the effects of dissolved nitrogen and oxygen molecules on the morphology of fibrils formed by a hydrophobic amyloid peptide implicated in amyotrophic lateral sclerosis, 15 repeats of glycine-alanine, on a highly oriented pyrolytic graphite substrate. We started with preformed fibril solutions that were then diluted with buffers of different gas conditions, resulting in the aggregation of the fibrils into different morphologies that were revealed by AFM after adsorption on the substrate. Straight fibrils were observed in both degassed and ambient buffers, but a stronger lateral association was seen in degassed buffers. Smaller and softer fibrils were observed in O₂-supersaturated buffers, and plaque-like fibril aggregates of considerably large size were evident in N₂-supersaturated buffers. In overnight incubation experiments, we observed changes in both the morphology and height of the fibril aggregates, and their evolution varied with different gas conditions. These findings indicate that the gas type and concentration affect the aggregation of amyloid fibrils and may facilitate the development of biomaterial applications and treatments for amyloid-related diseases.

Alzheimer's Therapeutic Strategy: Photoactive Platforms for Suppressing the Aggregation of Amyloid β Protein

Neurodegenerative diseases such as Alzheimer's disease (AD) have become a public health problem. Progressive cerebral accumulation of amyloid protein (Aβ) was widely considered as the cause of AD. One promising strategy for AD preclinical study is to degrade and clear the deposited amyloid aggregates with β-sheet-rich secondary structure in the brain. Based on the requirement, photo-active materials with the specific excitation and the standardization of the photosensitizer preparation and application in clinics, have attracted increased attention in the study and treatment of neurodegenerative disease as a novel method termed as photodynamic therapy (PDT). This review will focus on the new photosensitizing materials and discuss the trend of PDT techniques for the possible application in the treatment strategy of amyloid-related diseases.

Destabilization of amyloid fibrils on interaction with MoS2-based nanomaterials

The present work is motivated by the established concept that the structure and energetics of biomacromolecules can be modulated by confining their dimensions in the nanoscale. In particular, here we use force-field methods to understand the stability of amyloid fibrils at nanostructured interfaces, which can be useful for the development of new therapeutics for Alzheimer's disease. We explore the binding modes and structural properties of fibrils at the interface of molybdenum disulphide nanotubes and the nanosurface using classical molecular dynamics simulations. We find that in general the MoS2 materials induces disruptions in the structure of the amyloid fibrils where the beta sheet conformation of the fibrils changes to a turned conformation, and it is large in the case of nanotubes in comparison to the nanosurfaces. The intermolecular hydrogen bonds, hydrophilic and hydrophobic contacts between the monomer peptides in the fibril are reduced due to their adsorption onto the MoS2 materials, which results in a destabilization of the fibril. The destabilization of fibril is to some extent compensated for by the van der Waals interactions between the fibril and MoS2. Overall the results indicate that MoS2-based materials can be useful in inhibiting the aggregation of smaller protofibrils to matured fibrils and to bust the already formed fibrils. Therapeutic materials should not exhibit any cross interaction with other off-targets compounds. In order to test whether the MoS2 nanomaterial has any such effect we have studied its interaction with two additional biomacromolecules, the human serum albumin and p53 protein, and we report no significant changes in the secondary structure of these biomolecules. Through molecular docking studies we also established that the drug binding ability of HSA is not altered by its surface binding to MoS2 nanosurface.

Advances in Molecularly Imprinting Technology for Bioanalytical Applications

In recent years, along with the rapid development of relevant biological fields, there has been a tremendous motivation to combine molecular imprinting technology (MIT) with biosensing. In this situation, bioprobes and biosensors based on molecularly imprinted polymers (MIPs) have emerged as a reliable candidate for a comprehensive range of applications, from biomolecule detection to drug tracking. Unlike their precursors such as classic immunosensors based on antibody binding and natural receptor elements, MIPs create complementary cavities with stronger binding affinity, while their intrinsic artificial polymers facilitate their use in harsh environments. The major objective of this work is to review recent MIP bioprobes and biosensors, especially those used for biomolecules and drugs. In this review, MIP bioprobes and biosensors are categorized by sensing method, including optical sensing, electrochemical sensing, gravimetric sensing and magnetic sensing, respectively. The working mechanism(s) of each sensing method are thoroughly discussed. Moreover, this work aims to present the cutting-edge structures and modifiers offering higher properties and performances, and clearly point out recent efforts dedicated to introduce multi-sensing and multi-functional MIP bioprobes and biosensors applicable to interdisciplinary fields.

Molecular dynamics simulations reveal the mechanism of graphene oxide nanosheet inhibition of Aβ1–42 peptide aggregation

Graphene oxide nanosheets inhibit Aβ1–42 aggregation by weakening inter-peptide interactions and reducing β-sheet contents mostly via salt bridge, hydrogen bonding and cation–π interactions with charged residues.

Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement

Understanding the mechanism of fibrillization of amyloid forming peptides could be useful for the development of therapeutics for Alzheimer's disease (AD). Taking this standpoint, we have explored in this work the free energy profile for the interconversion of monomeric and dimeric forms of amyloid forming peptides into different secondary structures namely beta-sheet, helix, and random coil in aqueous solution using umbrella sampling simulations and density functional theory calculations. We show that the helical structures of amyloid peptides can form β sheet rich aggregates through random coil conformations in aqueous condition. Recent experiments ( Chem. Eur. J. 2018, 24, 3397-3402 and ACS Appl. Mater. Interfaces 2017, 9, 21116-21123) show that molybdenum disulfide nanosurface and nanoparticles can reduce the fibrillization process of amyloid beta peptides. We have unravelled the free energy profile for the interconversion of helical forms of amyloid forming peptides into beta-sheet and random coil in the presence of a two-dimensional nanosurface of MoS₂. Results indicate that the monomer and dimeric forms of the peptides adopt the random coil conformation in the presence of MoS₂ while the helical form is preferable for the monomeric form and that the beta-sheet and helix forms are the preferable forms for dimers in aqueous solution. This is due to strong interaction with MoS₂ and intramolecular hydrogen bonds of random coil conformation. The stabilization of random coil conformation does not lead to a β sheet like secondary structure for the aggregate. Thus, the confinement of MoS₂ promotes deaggregation of amyloid beta peptides rather than aggregation, something that could be useful for the development of therapeutics for AD.

Mechanistic insights into the inhibition and size effects of graphene oxide nanosheets on the aggregation of an amyloid-β peptide fragment

The aggregation of amyloid-β (Aβ), which involves the formation of small oligomers and mature fibrils, has received considerable attention in the past few decades due to its close link with Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. In this respect, graphene oxide (GO) has gained significant attention because of its high solubility, good biocompatibility and inhibitory effect on the aggregation of Aβ and the 33-42 fragment (Aβ33-42). However, the inhibitory mechanism at the atomic level remains elusive. Herein, we investigated the oligomerization of Aβ33-42 by performing replica exchange molecular dynamics simulations on four Aβ33-42 peptide chains in the absence and presence of two different sizes of GO. Our simulations show that isolated Aβ33-42 can form fibril-prone extended β-sheets and barrel-like structures, whereas they are suppressed in the presence of GO nanosheets. Our data reveal that GO inhibits Aβ33-42 oligomerization by making Aβ33-42 peptides separate from each other through strong interactions with M35. With the same total number of atoms, GO120 displays better inhibitory effect than GO60 by providing a larger effective contact surface area. This study provides the molecular mechanism of GO in inhibiting the aggregation of Aβ33-42, which might offer a theoretical insight into the design of drugs against AD at the atomic level.

Differential Modulating Effect of MoS2 on Amyloid Peptide Assemblies

The abnormal fibrillogenesis of amyloid peptides such as amyloid fibril and senior amyloid plaques, is associated with the pathogenesis of many amyloid diseases. Hence, modulation of amyloid assemblies is related to the possible pathogenesis of some diseases. Some two-dimensional nanomaterials, that is, graphene oxide, tungsten disulfide, exhibit strong modulation effects on the amyloid fibrillogenesis. Herein, the modulation effect of molybdenum disulfide on two amyloid peptide assemblies based on the label-free techniques is presented, including quartz crystal microbalance (QCM), AFM, and CD spectroscopy. MoS₂ presents different modulating effects on the assembly of amyloid-β peptide (33-42) [Aβ (33-42)] and amylin (20-29), mainly owing to the distinct affinity between amyloid peptides and MoS₂ . This is to our knowledge the first report of MoS₂ as a modulator for amyloid aggregation. It enriches the variety of 2D nanomodulators of amyloid fibrillogenesis and explains the mechanism for the self-assembly of amyloid peptides, and expands the applications of MoS₂ in biology.

Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces

Amyloid aggregates are associated with a range of human neurodegenerative disorders, and it has been shown that neurotoxicity is dependent on aggregate size. Combining molecular simulation with analytical theory, a predictive model is proposed for the adsorption of amyloid aggregates onto oppositely charged surfaces, where the interaction is governed by an interplay between electrostatic attraction and entropic repulsion. Predictions are experimentally validated against quartz crystal microbalance-dissipation experiments of amyloid beta peptides and fragmented fibrils in the presence of a supported lipid bilayer. Assuming amyloids as rigid, elongated particles, we observe nonmonotonic trends for the extent of adsorption with respect to aggregate size and preferential adsorption of smaller aggregates over larger ones. Our findings describe a general phenomenon with implications for stiff polyions and rodlike particles that are electrostatically attracted to a surface.

Fluorine Functionalized Graphene Quantum Dots as Inhibitor against hIAPP Amyloid Aggregation

Fibrillar deposits of the human islet amyloid polypeptide (hIAPP) are considered as a root of Type II diabetes mellitus. Fluorinated graphene quantum dots (FGQDs) are new carbon nanomaterials with unique physicochemical properties containing highly electronegative F atoms. Herein we report a single step synthesis method of FGQDs with an inhibitory effect on aggregation and cytotoxicity of hIAPP in vitro. Highly fluorescent and water dispersible FGQDs, less than 3 nm in size, were synthesized by the microwave-assisted hydrothermal method. Efficient inhibition capability of FGQDs to amyloid aggregation was demonstrated. The morphologies of hIAPP aggregates were observed to change from the entangled long fibrils to short thin fibrils and amorphous aggregates in the presence of FGQDs. In thioflavin T fluorescence analysis, inhibited aggregation with prolonged lag time and reduced fluorescence intensity at equilibrium were observed when hIAPP was incubated together with FGQDs. Circular dichroism spectrum results reveal that FGQDs could inhibit conformational transition of the peptide from native structure to β-sheets. FGQDs could also rescue the cytotoxicity of INS-1 cells induced by hIAPP in a dose dependent manner. This study could be beneficial for design and preparation of inhibitors for amyloids, which is important for prevention and treatment of amyloidosis.