Graphene quantum dots rescue protein dysregulation of pancreatic β-cells exposed to human islet amyloid polypeptide

In silico study on graphene quantum dots modified with various functional groups inhibiting α‑synuclein dimerization

HYPOTHESIS

Graphene quantum dots (GQDs) with various functional groups are hypothesized to inhibit the α-synuclein (αS) dimerization, a crucial step in Parkinson's disease pathogenesis. The potential of differently functionalized GQDs is systematically explored.

EXPERIMENTS

All-atom replica-exchange molecular dynamics simulations (accumulating to 75.6 μs) in explicit water were performed to study the dimerization of the αS non-amyloid component region and the influence of GQDs modified with various functional groups. Conformation ensemble, binding behavior, and free energy analysis were conducted.

FINDINGS

All studied GQDs inhibit β-sheet and backbone hydrogen bond formation in αS dimers, leading to looser oligomeric conformations. Charged GQDs severely impede the growth of extended β-sheets by providing extra contact surface. GQD binding primarily disrupts αS inter-peptide interactions through π-π stacking, CH-π interactions, and for charged GQDs, additionally through salt-bridge and hydrogen bonding interactions. GQD-COO- showed the most optimal inhibitory effect, binding mode, and intensity, which holds promise for the development of nanomedicines targeting amyloid aggregation in neurodegenerative diseases.

Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth

Rapid growth of amyloid fibrils via a seeded conformational conversion of monomers is a critical step of fibrillization and important for disease transmission and progression. Amyloid fibrils often display diverse morphologies with distinct populations, and yet the molecular mechanisms of fibril elongation and their corresponding morphological dependence remain poorly understood. Here, we computationally investigated the single-molecular growth of two experimentally resolved human islet amyloid polypeptide fibrils of different morphologies. In both cases, the incorporation of monomers into preformed fibrils was observed. The conformational conversion dynamics was characterized by a small number of fibril growth intermediates. Fibril morphology affected monomer binding at fibril elongation and lateral surfaces as well as the seeded conformational conversion dynamics at the fibril ends, resulting in different fibril elongation rates and populations. We also observed an asymmetric fibril growth as in our prior experiments, attributing to differences of two fibril ends in terms of their local surface curvatures and exposed hydrogen-bond donors and acceptors. Together, our mechanistic findings afforded a theoretical basis for delineating different amyloid strains-entailed divergent disease progression.

SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges

Inhibiting the aggregation of amyloid peptides with endogenous peptides has broad interest due to their intrinsically high biocompatibility and low immunogenicity. Here, we investigated the inhibition mechanism of the prostatic acidic phosphatase fragment SEVI (semen-derived enhancer of viral infection) against Aβ42 fibrillization using atomistic discrete molecular dynamic simulations. Our result revealed that SEVI was intrinsically disordered with dynamic formation of residual helices. With a high positive net charge, the self-aggregation tendency of SEVI was weak. Aβ42 had a strong aggregation propensity by readily self-assembling into β-sheet-rich aggregates. SEVI preferred to interact with Aβ42, rather than SEVI themselves. In the heteroaggregates, Aβ42 mainly adopted β-sheets buried inside and capped by SEVI in the outer layer. SEVI could bind to various Aβ aggregation species─including monomers, dimers, and proto-fibrils─by capping the exposed β-sheet elongation edges. The aggregation processes Aβ42 from the formation of oligomers to conformational nucleation into fibrils and fibril growth should be inhibited as their β-sheet elongation edges are being occupied by the highly charged SEVI. Overall, our computational study uncovered the molecular mechanism of experimentally observed inhibition of SEVI against Aβ42 aggregation, providing novel insights into the development of therapeutic strategies against Alzheimer's disease.

Evaluation of pancreatic δ- cells as a potential target site of graphene oxide toxicity in Japanese medaka (Oryzias latipes) fish

In continuation to our previous investigations on graphene oxide (GO) as an endocrine disrupting chemical (EDC), in the present experiment, we have investigated endocrine pancreas of Japanese medaka adults focusing on δ-cells in the islet organs as an endpoint. Breeding pairs of adult male and female fish were exposed to 0 mg/L (control) or 20 mg/L GO by continuous immersion (IMR) for 96 h, or to 0 µg/g or 100 µg/g GO by a single intraperitoneal (IP) administration and depurated 21 days in a GO-free environment. Histological investigations indicated that the endocrine cells are concentrated in one large principal islet, and several small secondary islets scattered within the mesentery near the liver and intestine. The cells of the islet organ are in various shapes with basophilic nuclei and eosinophilic cytoplasm. Immunohistochemical evaluation using rabbit polyclonal antisomatostatin antibody indicated that immunoreactivity is localized either at the periphery or at the central region in principal islets, and throughout the secondary islets, and found to be enhanced in fish exposed to GO than controls. The soma of δ-cells exhibits neuron-like morphology and have filopodia like processes. Cell sorting as non-communicating δ-cells (NCDC), communicating cells (CC), and non- δ-cells (NDC) indicated that within an islet organ, the population of NDCC is found to be the least and NDC is the highest. Our data further indicated that GO-induced impairments in the islet organs of medaka pancreas are inconsistent and could be affected by the exposure roots as well as the sex of the fish.

Recent advances of graphene-biomacromolecule nanocomposites in medical applications

In recent years, graphene-based composites have received increasing attention due to their high biocompatibility, large specific surface area, high electrical conductivity and unique mechanical properties. The combination of biomacromolecules and graphene provides a promising route for the preparation of novel graphene-based nanocomposites. Novel graphene-based nanocomposites with unique functions could be applied to medicine, biology, biosensors, environmental science, energy storage and other fields. Graphene-biomacromolecule nanocomposites have excellent biocompatibility, outstanding biofunctionality and low cytotoxicity, and have more advantages and development prospects than other traditional graphene-based materials in biological and biomedical fields. In this work, we summarize the research on the covalent and non-covalent interactions between different biomacromolecules (peptides, DNA/RNA, proteins and enzymes) and graphene, as well as the synthesis methods of novel functionalized graphene-biomacromolecule composites in recent years. We mainly introduce the recent advances (last 5 years) of graphene-biomacromolecule nanocomposites in medical applications, such as medical detection and disease treatment. We hope that this review will help readers to understand the methods and mechanisms of biomolecules modifying the surface of graphene, as well as the synthesis and application of graphene-based nanocomposites, which will promote the future developments of graphene-biomolecule composites in biomedicine, tissue engineering, materials engineering, and so on.

Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics simulations

The amyloid aggregation of human islet amyloid polypeptide (hIAPP) is associated with pancreatic β-cell death in type 2 diabetes. The S20G substitution of hIAPP (hIAPP(S20G)), found in Japanese and Chinese people, is more amyloidogenic and cytotoxic than wild-type hIAPP. Rat amylin (rIAPP) does not have aggregation propensity or cytotoxicity. Mounting evidence suggests that soluble low-molecular-weight amyloid oligomers formed during early aggregation are more cytotoxic than mature fibrils. The self-assembly dynamics and oligomeric conformations remain unknown because the oligomers are heterogeneous and transient. The molecular mechanism of sequence-variation rendering dramatically different aggregation propensity and cytotoxicity is also elusive. Here, we investigate the oligomerization dynamics and conformations of amyloidogenic hIAPP, hIAPP(S20G), and non-amyloidogenic rIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our simulation results demonstrated that all three monomeric amylin peptides mainly adopted an unstructured formation with partial dynamical helices near the N-terminus. Relatively transient β-hairpins were more abundant in hIAPP and hIAPP(S20G) than in rIAPP. The S20G-substituting mutant of hIAPP altered the turn region of the β-hairpin motif, resulting in more hydrophobic residue-pairwise contacts within the β-hairpin. Oligomerization dynamic investigation revealed that all three peptides spontaneously accumulated into helix-populated oligomers. The conformational conversion to form β-sheet-rich oligomers was only observed in hIAPP and hIAPP(S20G). The population of high-β-sheet-content oligomers was enhanced by S20G substitution. Interestingly, both hIAPP and hIAPP(S20G) could form β-barrel formations, and the β-barrel propensity of hIAPP(S20G) was three times larger than that of hIAPP. No β-sheet-rich or β-barrel formations were observed in rIAPP. Our direct observation of the correlation between β-barrel oligomer formation and cytotoxicity suggests that β-barrels might play a critically important role in the cytotoxicity of amyloidosis.

Carbon Nanodots from an In Silico Perspective

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

Optical Fluorescence Imaging of Native Proteins Using a Fluorescent Probe with a Cell-Membrane-Permeable Carboxyl Group

Although various methods for selective protein tagging have been established, their ap plications are limited by the low fluorescent tagging efficiency of specific terminal regions of the native proteins of interest (NPIs). In this study, the highly sensitive fluorescence imaging of single NPIs was demonstrated using a eukaryotic translation mechanism involving a free carboxyl group of a cell-permeable fluorescent dye. In living cells, the carboxyl group of cell-permeable fluorescent dyes reacted with the lysine residues of acceptor peptides (AP or AVI-Tag). Genetically encoded recognition demonstrated that the efficiency of fluorescence labeling was nearly 100%. Nickel-nitrilotriacetic acid (Ni-NTA) beads bound efficiently to a single NPI for detection in a cell without purification. Our labeling approach satisfied the necessary conditions for measuring fluorescently labeled NPI using universal carboxyl fluorescent dyes. This approach is expected to be useful for resolving complex biological/ecological issues and robust single-molecule analyses of dynamic processes, in addition to applications in ultra-sensitive NPIs detection using nanotechnology.

Human islet amyloid polypeptide: A therapeutic target for the management of type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) and other metabolic disorders are often silent and go unnoticed in patients because of the lack of suitable prognostic and diagnostic markers. The current therapeutic regimens available for managing T2DM do not reverse diabetes; instead, they delay the progression of diabetes. Their efficacy (in principle) may be significantly improved if implemented at earlier stages. The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) or amylin has been associated with a gradual decrease in pancreatic β-cell function and mass in patients with T2DM. Hence, hIAPP has been recognized as a therapeutic target for managing T2DM. This review summarizes hIAPP's role in mediating dysfunction and apoptosis in pancreatic β-cells via induction of endoplasmic reticulum stress, oxidative stress, mitochondrial dysfunction, inflammatory cytokine secretion, autophagy blockade, etc. Furthermore, it explores the possibility of using intermediates of the hIAPP aggregation pathway as potential drug targets for T2DM management. Finally, the effects of common antidiabetic molecules and repurposed drugs; other hIAPP mimetics and peptides; small organic molecules and natural compounds; nanoparticles, nanobodies, and quantum dots; metals and metal complexes; and chaperones that have demonstrated potential to inhibit and/or reverse hIAPP aggregation and can, therefore, be further developed for managing T2DM have been discussed.

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Misfolded species of hIAPP form toxic oligomers in pancreatic β-cells.

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hIAPP amyloids has been detected in the pancreas of about 90% subjects with T2DM.

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Inhibitors of hIAPP aggregation can help manage T2DM.

Unifying structural descriptors for biological and bioinspired nanoscale complexes

Biomimetic nanoparticles are known to serve as nanoscale adjuvants, enzyme mimics and amyloid fibrillation inhibitors. Their further development requires better understanding of their interactions with proteins. The abundant knowledge about protein-protein interactions can serve as a guide for designing protein-nanoparticle assemblies, but the chemical and biological inputs used in computational packages for protein-protein interactions are not applicable to inorganic nanoparticles. Analysing chemical, geometrical and graph-theoretical descriptors for protein complexes, we found that geometrical and graph-theoretical descriptors are uniformly applicable to biological and inorganic nanostructures and can predict interaction sites in protein pairs with accuracy >80% and classification probability ~90%. We extended the machine-learning algorithms trained on protein-protein interactions to inorganic nanoparticles and found a nearly exact match between experimental and predicted interaction sites with proteins. These findings can be extended to other organic and inorganic nanoparticles to predict their assemblies with biomolecules and other chemical structures forming lock-and-key complexes.

Inhibiting protein aggregation with nanomaterials: The underlying mechanisms and impact factors

Protein aggregation is correlated with the onset and progression of protein misfolding diseases (PMDs). Inhibiting the generation of toxic aggregates of misfolded proteins has been proposed as a therapeutic approach for PMDs. Due to their unique properties, nanomaterials have been extensively investigated for their ability to inhibit protein aggregation and have shown great potential in the diagnosis and treatment of PMDs. However, the precise mechanisms by which nanomaterials interact with amyloidogenic proteins and the factors influencing these interactions remain poorly understood. Consequently, developing a rational design strategy for nanomaterials that target specific proteins in PMDs has been challenging. In this review, we elucidate the effects of nanomaterials on protein aggregation and describe the mechanisms through which nanomaterials interfere with protein aggregation. The major factors impacting protein-nanomaterial interaction such as size, charge, concentration, surface modification and morphology that can be rationally addressed to achieve the desired effects of nanomaterials on protein aggregation are summarized. The prospects and challenges to the clinical application of nanomaterials for the treatment of PMDs are also discussed.

Development of Graphene-Based Materials in Bone Tissue Engineaering

Bone regeneration-related graphene-based materials (bGBMs) are increasingly attracting attention in tissue engineering due to their special physical and chemical properties. The purpose of this review is to quantitatively analyze mass academic literature in the field of bGBMs through scientometrics software CiteSpace, to demonstrate the rules and trends of bGBMs, thus to analyze and summarize the mechanisms behind the rules, and to provide clues for future research. First, the research status, hotspots, and frontiers of bGBMs are analyzed in an intuitively and vividly visualized way. Next, the extracted important subjects such as fabrication techniques, cytotoxicity, biodegradability, and osteoinductivity of bGBMs are presented, and the different mechanisms, in turn, are also discussed. Finally, photothermal therapy, which is considered an emerging area of application of bGBMs, is also presented. Based on this approach, this work finds that different studies report differing opinions on the biological properties of bGBMS due to the lack of consistency of GBMs preparation. Therefore, it is necessary to establish more standards in fabrication, characterization, and testing for bGBMs to further promote scientific progress and clinical translation.

Emerging Theranostic Nanomaterials in Diabetes and Its Complications

Diabetes mellitus (DM) refers to a group of metabolic disorders that are characterized by hyperglycemia. Oral subcutaneously administered antidiabetic drugs such as insulin, glipalamide, and metformin can temporarily balance blood sugar levels, however, long-term administration of these therapies is associated with undesirable side effects on the kidney and liver. In addition, due to overproduction of reactive oxygen species and hyperglycemia-induced macrovascular system damage, diabetics have an increased risk of complications. Fortunately, recent advances in nanomaterials have provided new opportunities for diabetes therapy and diagnosis. This review provides a panoramic overview of the current nanomaterials for the detection of diabetic biomarkers and diabetes treatment. Apart from diabetic sensing mechanisms and antidiabetic activities, the applications of these bioengineered nanoparticles for preventing several diabetic complications are elucidated. This review provides an overall perspective in this field, including current challenges and future trends, which may be helpful in informing the development of novel nanomaterials with new functions and properties for diabetes diagnosis and therapy.

Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta

Soluble low-molecular-weight oligomers formed during the early aggregation of amyloid peptides have been hypothesized as a major toxic species of amyloidogenesis. Herein, we performed the first synergic in silico, in vitro and in vivo validations of the structure, dynamics and toxicity of Aβ42 oligomers. Aβ peptides readily assembled into β-rich oligomers comprised of extended β-hairpins and β-strands. Nanosized β-barrels were observed with certainty with simulations, transmission electron microscopy and Fourier transform infrared spectroscopy, corroborated by immunohistochemistry, cell viability, apoptosis, inflammation, autophagy and animal behavior assays. Secondary and tertiary structural proprieties of these oligomers, such as the sequence regions with high β-sheet propensities and inter-residue contact frequency patterns, were similar to the properties known for Aβ fibrils. The unambiguous spontaneous formation of β-barrels in the early aggregation of Aβ42 supports their roles as the common toxic intermediates in Alzheimer's pathobiology and a target for Alzheimer's therapeutics.

Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau

Pathological aggregation of intrinsically disordered tau protein, driven by the interactions between microtubule-binding (MTB) domains, is associated with Alzheimer's disease. The MTB domain contains either three or four repeats with sequence similarities. Compared to amyloid β, many aspects of the misfolding and aggregation mechanisms of tau are largely unknown. In this study, we systematically investigated the dynamics of monomer misfolding and dimerization of each MTB repeat using atomistic discrete molecular dynamic simulations. Our results revealed that all the four repeat monomers (R1-R4) were very dynamic, featuring frequent conformational conversion and lacking stable conformations. While R1, R2, and R4 monomers occasionally adopted partially helical conformations, R3 monomers frequently formed β-sheets. In dimerization simulations, R3 displayed the strongest aggregation propensity with high β-sheet contents, while R1 was the least prone to aggregation. The R2 and R4 dimers contained both helix and β-sheet structures. The β-sheets in R4 assemblies were dominant with β-hairpin conformation. In R2 and R3 dimers, intermolecular β-sheets were mainly driven by residues around the paired helical filament (PHF) regions. Residues around the PHF6* in R2 and PHF6 in R3 had significantly higher intermolecular contacts than other regions, suggesting that these residues play a key role in the amyloid aggregation of tau. Our results on the structural ensembles and early aggregation dynamics of each tau MTB repeat will help understand the nucleation and fibrillization of tau.

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.

A review on the cytotoxicity of graphene quantum dots: from experiment to simulation

Graphene quantum dots (GQDs) generate intrinsic fluorescence and improve the aqueous stability of graphene oxide (GO) while maintaining wide chemical adaptability and high adsorption capacity. Despite GO's remarkable advantages in bio-imaging, bio-sensing, and other biomedical applications, many experiments and simulations have focused on the biosafety of GQDs. Here, we review the findings on the biosafety of GQDs from experiments; then, we review the results from simulated interactions with biological membranes, DNA molecules, and proteins; finally, we examine the intersection between experiments and simulations. The biosafety results from simulations are explained in detail. Based on the literature and our experiments, we also discuss the trends toward GQDs with better biosafety.

Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes

The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.

Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants

Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature of these aggregation intermediates. To uncover the structural characteristics of toxic oligomeric intermediates, we compared the self-assembly dynamics and structures of SOD1_28-38, a cytotoxic fragment of the superoxide dismutase 1 (SOD1) associated with the amyotrophic lateral sclerosis, with its two nontoxic mutants G33V and G33W using molecular dynamics simulations. Single-point glycine substitutions in SOD1_28-38 have been reported to abolish the amyloid toxicity. Our simulation results showed that the toxic SOD1_28-38 and its nontoxic mutants followed different aggregation pathways featuring distinct aggregation intermediates. Specifically, wild-type SOD1_28-38 initially self-assembled into random-coil-rich oligomers, among which fibrillar aggregates composed of well-defined curved single-layer β-sheets were nucleated via coil-to-sheet conversions and the formation of β-barrels as intermediates. In contrast, the nontoxic G33V/G33W mutants readily assembled into small β-sheet-rich oligomers and then coagulated with each other into cross-β fibrils formed by two-layer β-sheets without forming β-barrels as the intermediates. The direct observation of β-barrel oligomers during the assembly of toxic SOD1_28-38 fragments but not the nontoxic glycine-substitution mutants strongly supports β-barrels as the toxic oligomers in amyloidosis, probably via interactions with the cell membrane and forming amyloid pores. With well-defined structures, the β-barrel might serve as a novel therapeutic target against amyloid-related diseases.

Novel Strategies to Protect and Visualize Pancreatic β Cells in Diabetes

A common feature in the pathophysiology of different types of diabetes is the reduction of β cell mass and/or impairment of β cell function. Diagnosis and treatment of type 1 and type 2 diabetes is currently hampered by a lack of reliable techniques to restore β cell survival, to improve insulin secretion, and to quantify β cell mass in patients. Current new approaches may allow us to precisely and specifically visualize β cells in vivo and provide viable therapeutic strategies to preserve, recover, and regenerate β cells. In this review, we discuss recent protective approaches for β cells and the advantages and limitations of current imaging probes in the field.

Amyloidosis Inhibition, a New Frontier of the Protein Corona

The protein corona has served as a central dogma and a nuisance to the applications of nanomedicine and nanobiotechnology for well over a decade. Here we introduce the emerging field of amyloidosis inhibition, which aims to understand and harness the interfacial phenomena associated with a nanoparticle interacting with pathogenic amyloid proteins. Much of this interaction correlates with our understanding of the protein corona, and yet much differs, as elaborated for the first time in this Perspective. Specifically, we examine the in vitro, in silico and in vivo features of the new class of "amyloid protein corona", and discuss how the interactions with nanoparticles may halt the self-assembly of amyloid proteins. As amyloidosis is driven off pathway by the nanoparticles, the oligomeric and protofibrillar populations are suppressed to ameliorate their cytotoxicity. Furthermore, as amyloid proteins spread via the transport of bodily fluids or cross seeding, amyloidosis is inherently associated with dynamic proteins and ligands to evoke the immune system. Accordingly, we ponder the structural and medical implications of the amyloid protein corona in the presence of their stimulated cytokines. Understanding and exploiting the amyloid protein corona may facilitate the development of new theranostics against a range of debilitating amyloid diseases.

Implications of the Human Gut-Brain and Gut-Cancer Axes for Future Nanomedicine

Recent clinical and pathological evidence have implicated the gut microbiota as a nexus for modulating the homeostasis of the human body, impacting conditions from cancer and dementia to obesity and social behavior. The connections between microbiota and human diseases offer numerous opportunities in medicine, most of which have limited or no therapeutic solutions available. In light of this paradigm-setting trend in science, this review aims to provide a comprehensive and timely summary of the mechanistic pathways governing the gut microbiota and their implications for nanomedicines targeting cancer and neurodegenerative diseases. Specifically, we discuss in parallel the beneficial and pathogenic relationship of the gut microbiota along the gut-brain and gut-cancer axes, elaborate on the impact of dysbiosis and the gastrointestinal corona on the efficacy of nanomedicines, and highlight a molecular mimicry that manipulates the universal cross-β backbone of bacterial amyloid to accelerate neurological disorders. This review further offers a forward-looking section on the rational design of cancer and dementia nanomedicines exploiting the gut-brain and gut-cancer axes.

Graphene Quantum Dots as Flourishing Nanomaterials for Bio-Imaging, Therapy Development, and Micro-Supercapacitors

Graphene quantum dots (GQDs) are considerably a new member of the carbon family and shine amongst other members, thanks to their superior electrochemical, optical, and structural properties as well as biocompatibility features that enable us to engage them in various bioengineering purposes. Especially, the quantum confinement and edge effects are giving GQDs their tremendous character, while their heteroatom doping attributes enable us to specifically and meritoriously tune their prospective characteristics for innumerable operations. Considering the substantial role offered by GQDs in the area of biomedicine and nanoscience, through this review paper, we primarily focus on their applications in bio-imaging, micro-supercapacitors, as well as in therapy development. The size-dependent aspects, functionalization, and particular utilization of the GQDs are discussed in detail with respect to their distinct nano-bio-technological applications.

Strategies for the Molecular Imaging of Amyloid and the Value of a Multimodal Approach

Protein aggregation has been widely implicated in neurodegenerative diseases such as Alzheimer's disease, frontotemporal dementia, Parkinson's disease, and Huntington disease, as well as in systemic amyloidoses and conditions associated with localized amyloid deposits, such as type-II diabetes. The pressing need for a better understanding of the factors governing protein assembly has driven research for the development of molecular sensors for amyloidogenic proteins. To date, a number of sensors have been developed that report on the presence of protein aggregates utilizing various modalities, and their utility demonstrated for imaging protein aggregation in vitro and in vivo. Analysis of these sensors highlights the various advantages and disadvantages of the different imaging modalities and makes clear that multimodal sensors with properties amenable to more than one imaging technique need to be developed. This critical review highlights the key molecular scaffolds reported for molecular imaging modalities such as fluorescence, positron emission tomography, single photon emission computed tomography, and magnetic resonance imaging and includes discussion of the advantages and disadvantages of each modality, and future directions for the design of amyloid sensors. We also discuss the recent efforts focused on the design and development of multimodal sensors and the value of cross-validation across multiple modalities.

Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains

Tungsten oxide nanodot (WO_3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO_3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO_3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO_3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO_3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO_3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.

Pristine and Hydroxylated Fullerenes Prevent the Aggregation of Human Islet Amyloid Polypeptide and Display Different Inhibitory Mechanisms

Protein aggregation, involving the formation of dimers, oligomers, and fibrils, is associated with many human diseases. Type 2 diabetes is one of the common amyloidosis and linked with the aggregation of human islet amyloid polypeptide (hIAPP). A series of nanoparticles are reported to be able to interact with proteins and enhance/inhibit protein aggregation. However, the effects of C₆₀ (a model system of hydrophobic nanoparticle) and C₆₀(OH)₈ (a hydroxylated fullerene) on hIAPP aggregation remain unknown. In this study, we investigate the influences of pristine fullerene C₆₀ and hydroxylated C₆₀ on the dimerization of hIAPP using molecular dynamics (MD) simulations. Extensive replica exchange molecular dynamics (REMD) simulations show that isolated hIAPP dimers adopt β-sheet structure containing the amyloid-precursor (β-hairpin). Both C₆₀ and C₆₀(OH)₈ notably inhibit the β-sheet formation of hIAPP dimer and induce the formation of collapsed disordered coil-rich conformations. Protein—nanoparticle interaction analyses reveal that the inhibition of hIAPP aggregation by C₆₀ is mainly via hydrophobic and aromatic-stacking interactions, while the prevention of hIAPP aggregation by C₆₀(OH)₈ is mostly through collective hydrogen bonding and aromatic-stacking interactions. Conventional MD simulations indicate that both C₆₀ and C₆₀(OH)₈ weaken the interactions within hIAPP protofibril and disrupt the β-sheet structure. These results provide mechanistic insights into the possible inhibitory mechanism of C₆₀ and C₆₀(OH)₈ toward hIAPP aggregation, and they are of great reference value for the screening of potent amyloid inhibitors.