Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils

Noble Metal Nanoparticles with Nanogel Coatings: Coinage Metal Thiolate-Stabilized Glutathione Hydrogel Shells

Developing biocompatible nanocoatings is crucial for biomedical applications. Noble metal colloidal nanoparticles with biomolecular shells are thought to combine diverse chemical and optothermal functionalities with biocompatibility. Herein, we present nanoparticles with peptide hydrogel shells that feature an unusual combination of properties: the metal core possesses localized plasmon resonance, whereas a few-nanometer-thick shells open opportunities to employ their soft framework for loading and scaffolding. We demonstrate this concept with gold and silver nanoparticles capped by glutathione peptides stacked into parallel β-sheets as they aggregate on the surface. A key role in the formation of the ordered structure is played by coinage metal(I) thiolates, i.e., Ag(I), Cu(I), and Au(I). The shell thickness can be controlled via the concentration of either metal ions or peptides. Theoretical modeling of the shell's molecular structure suggests that the thiolates have a similar conformation for all the metals and that the parallel β-sheet-like structure is a kinetic product of the peptide aggregation. Using third-order nonlinear two-dimensional infrared spectroscopy, we revealed that the ordered secondary structure is similar to the bulk hydrogels of the coinage metal thiolates of glutathione, which also consist of aggregated stacked parallel β-sheets. We expect that nanoparticles with hydrogel shells will be useful additions to the nanomaterial toolbox. The present method of nanogel coating can be applied to arbitrary surfaces where the initial deposition of the seed glutathione monolayer is possible.

Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases

Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.

Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters

Monolayer-protected atomically precise metal nanoclusters (MPCs) have potential applications in catalysis, imaging, and drug delivery. Understanding their interactions with biomolecules such as peptides is of paramount interest for their use in cell imaging and drug delivery. Here we have carried out atomistic molecular dynamics simulations to investigate the interactions between MPCs and an anticancer peptide, melittin. Melittin gets attached to the MPCs surface by the formation of multiple hydrogen bonds between its amino acid residues with MPCs ligands. Additionally, the positively charged Lys, Arg, and peptide's N-terminal strongly anchor the peptide to the MPC metal surface, providing extra stabilization.

A review on nanotechnological perspective of "the amyloid cascade hypothesis" for neurodegenerative diseases

Neurodegenerative diseases (NDs) are characterized by progressive degeneration of neurons which deteriorates the brain functions. An early detection of the onset of NDs is utmost important, as it will provide the fast treatment strategies to prevent further progression of the disease. Conventionally, accurate diagnosis of the brain related disorders is difficult in their early phase. To solve this problem, nanotechnology based neurofunctional imaging and biomarker detection techniques have been developed which allows high specificity and sensitivity towards screening and diagnosis of NDs. Another challenge to treat the brain related disorders is to overcome the complex integrity of blood-brain-barrier (BBB) for the delivery of theranostic agents. Fortunately, utilization of nanomaterials has been pursued as promising strategy to address this challenge. Herein, we critically highlighted the recent improvements in the field of neurodiagnostic and therapeutic approaches involving innovative strategies for diagnosis, and inhibition of protein aggregates. We have provided particular emphasis on the use of nanotechnology which can push forward the blooming research growth in this field to win the battle against devastating NDs.

Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters

Monolayer-protected atomically precise nanoclusters (MPCs) are an important class of molecules due to their unique structural features and diverse applications, including bioimaging, sensors, and drug carriers. Understanding the atomistic and dynamical details of their self-assembly process is crucial for designing system-specific applications. Here, we applied molecular dynamics and on-the-fly probability-based enhanced sampling simulations to study the aggregation of Au₂₅(pMBA)₁₈ MPCs in aqueous and methanol solutions. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and crystals. The dimerization free energy profiles reveal a pivotal role of the ligand charged state and solvent mediating the molecular aggregation. Furthermore, MPCs' ligands exhibit suppressed conformational flexibility in the solid phase due to facile intercluster hydrogen bonds and π-stacks. Our work provides unprecedented molecular-level dynamical details of the aggregation process and conformational dynamics of MPCs ligands in solution and crystalline phases.

Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging

The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.

Advanced nanomaterials for modulating Alzheimer's related amyloid aggregation

Alzheimer's disease (AD) is a common neurodegenerative disease that brings about enormous economic pressure to families and society. Inhibiting abnormal aggregation of Aβ and accelerating the dissociation of aggregates is treated as an effective method to prevent and treat AD. Recently, nanomaterials have been applied in AD treatment due to their excellent physicochemical properties and drug activity. As a drug delivery platform or inhibitor, various excellent nanomaterials have exhibited potential in inhibiting Aβ fibrillation, disaggregating, and clearing mature amyloid plaques by enhancing the performance of drugs. This review comprehensively summarizes the advantages and disadvantages of nanomaterials in modulating amyloid aggregation and AD treatment. The design of various functional nanomaterials is discussed, and the strategies for improved properties toward AD treatment are analyzed. Finally, the challenges faced by nanomaterials with different dimensions in AD-related amyloid aggregate modulation are expounded, and the prospects of nanomaterials are proposed.

Reversible assembly of nanoparticles: theory, strategies and computational simulations

The significant advances in synthesis and functionalization have enabled the preparation of high-quality nanoparticles that have found a plethora of successful applications. The unique physicochemical properties of nanoparticles can be manipulated through the control of size, shape, composition, and surface chemistry, but their technological application possibilities can be further expanded by exploiting the properties that emerge from their assembly. The ability to control the assembly of nanoparticles not only is required for many real technological applications, but allows the combination of the intrinsic properties of nanoparticles and opens the way to the exploitation of their complex interplay, giving access to collective properties. Significant advances and knowledge gained over the past few decades on nanoparticle assembly have made it possible to implement a growing number of strategies for reversible assembly of nanoparticles. In addition to being of interest for basic studies, such advances further broaden the range of applications and the possibility of developing innovative devices using nanoparticles. This review focuses on the reversible assembly of nanoparticles and includes the theoretical aspects related to the concept of reversibility, an up-to-date assessment of the experimental approaches applied to this field and the advanced computational schemes that offer key insights into the assembly mechanisms. We aim to provide readers with a comprehensive guide to address the challenges in assembling reversible nanoparticles and promote their applications.

Copper oxide nanoparticles promote amyloid-β-triggered neurotoxicity through formation of oligomeric species as a prelude to Alzheimer's diseases

Protein oligomerization is involved in the progression of Alzheimer's disease (AD). In general, a particle that can accelerate protein oligomerization should be considered a toxic material. Several studies reported the progress of nanoparticles (NPs) such as copper oxide (CuO) in biomedical platforms, however, they may have the ability to promote the protein oligomerization process. Here, we aimed to study the effect of CuO NPs on amyloid β_1-42 (Aβ_1-42) oligomerization and relevant neurotoxicity. CuO NPs were synthesized by precipitation technique and characterized by several methods such as ThT, Congo red, CD spectroscopic methods, and TEM imaging. The outcomes indicated that the fabricated CuO NPs with a size of around 50 nm led to a remarkable acceleration in Aβ_1-42 oligomerization in a concentration-dependent manner through shortening the nucleation step and promoting the fibrillization rate. Moreover, cellular assays revealed that Aβ_1-42 oligomers aged with CuO NPs were more toxic than Aβ_1-42 oligomers untreated against SH-SY5Y cells in triggering cell mortality, membrane leakage, oxidative stress, and apoptosis. In conclusion, this study provides important information about the adverse effects of CuO NPs against proteins in the central nervous system to promote the formation of cytotoxic oligomers.

Engineered Nanoparticle-Protein Interactions Influence Protein Structural Integrity and Biological Significance

Engineered nanoparticles (ENPs) are artificially synthesized particles with unique physicochemical properties. ENPs are being extensively used in several consumer items, elevating the probability of ENP exposure to biological systems. ENPs interact with various biomolecules like lipids, proteins, nucleic acids, where proteins are most susceptible. The ENP-protein interactions are mostly studied for corona formation and its effect on the bio-reactivity of ENPs, however, an in-depth understanding of subsequent interactive effects on proteins, such as alterations in their structure, conformation, free energy, and folding is still required. The present review focuses on ENP-protein interactions and the subsequent effects on protein structure and function followed by the therapeutic potential of ENPs for protein misfolding diseases.

Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing

Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP–GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold–sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry.

A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2

Cadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and L-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd²⁺ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd²⁺ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd²⁺ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd²⁺ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor-acceptor analyses show that molecular orbital interactions between the functional groups and Cd²⁺ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.

Biogenic Synthesis and Characterization of Antioxidant and Antimicrobial Silver Nanoparticles Using Flower Extract of Couroupita guianensis Aubl

Couroupita guianensis Aubl. is an important medicinal tree. This tree is rich in various phytochemicals, and is therefore used as a potent antioxidant and antibacterial agent. This plant is also used for the treatment of various diseases. Here, we have improved its medicinal usage with the biosynthesis of silver nanoparticles (AgNPs) using Couroupita guianensis Aubl. flower extract as a reducing and capping agent. The biosynthesis of the AgNPs reaction was carried out using 1 mM of silver nitrate and flower extract. The effect of the temperature on the biosynthesis of AgNPs was premeditated by room temperature (25 °C) and 60 °C. The continuous stirring of the reaction mixture at room temperature for approximately one hour resulted in the successful formation of AgNPs. A development of a yellowish brown color confirmed the formation of AgNPs. The efficacious development of AgNPs was confirmed by the characteristic peaks of UV-Vis, X-ray diffraction (XRD) and Fourier transform infrared (FT-IR) spectroscopy spectra. The biosynthesized AgNPs exhibited significant free radical scavenging activity through a DPPH antioxidant assay. These AgNPs also showed potent antibacterial activity against many pathogenic bacterial species. The results of molecular dynamics simulations also proved the average size of NPs and antibacterial potential of the flower extract. The observations clearly recommended that the green biosynthesized AgNPs can serve as effective antioxidants and antibacterial agents over the plant extract.

Adsorption on Ligand-Tethered Nanoparticles

We use coarse-grained molecular dynamics simulations to study adsorption on ligand-tethered particles. Nanoparticles with attached flexible and stiff ligands are considered. We discuss how the excess adsorption isotherm, the thickness of the polymer corona, and its morphology depend on the number of ligands, their length, the size of the core, and the interaction parameters. We investigate the adsorption-induced structural transitions of polymer coatings. The behavior of systems involving curved and flat "brushes" is compared.

Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles

Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems.

Multifunctional Gold Nanoparticle-Conjugated Cellulose Nanoonions Alleviate Aβ42 Fibrillation-Induced Toxicity via Regulation of Oxidative Stress and Ion Homeostasis

Inhibition of hen egg white lysozyme (HEWL) and Aβ42 fibrillation have been established as the main models for the treatment of systemic lysozyme amyloidosis and Alzheimer's disease (AD), respectively. Several antiamyloidogenic nanomaterials have been developed over the period; however, their intracellular mechanism of action is still not well understood. In this context, plant-based, gold-conjugated, injectable, hydrophilic cellulose nanoonions (CNOs), viz., DH-CNO (∼60 ± 5 nm) and LC-CNO (∼55 ± 12 nm), were developed from their respective hydrophobic cellulose nanocrystals (DH-CNC and LC-CNC) using a single-step chemical template-mediated process. This unique nanocellulose architecture was chemically and morphologically characterized by various spectroscopic and microscopic techniques. Further, the different biophysical studies documented marked the inhibition/disintegration potential of gold-conjugated LC-CNO against HEWL and Aβ42 peptide aggregation. It was further observed that inhibition of protein fibrillation could be achieved within ∼10 min when the same materials were used under photoirradiation conditions. In vitro protein aggregation studies using HEK293 cells suggested that gold-conjugated LC-CNO could effectively reduce the cellular toxicity via regulation of oxidative stress and ion homeostasis. The outcome of the present study will help in designing cellulose-based novel functional nanochaperones against various neurodegenerative diseases.

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide-nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure-function relationship, for technological and nanomedical applications.

Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations

Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming β-sheets secondary structures that are characteristics of mature amyloid fibrils.