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

Exploring the Curvature-Dependence of Boron Nitride Nanoparticles on the Inhibition of hIAPP Aggregation

Nanoparticles, particularly carbon nanoparticles, have gathered significant interest in the field of anti-aggregation research. However, due to their cytotoxicity, the exploration of biocompatible nanoparticles has become a new frontier in the quest for drugs against human amyloid diseases. The application of non-cytotoxic and biocompatible boron nitride (BN) nanoparticles against amyloid aggregation has been probed to tackle this issue. BN nanoparticles displayed inhibitory activity against the aggregation of Aβ and α-syn peptides. In this work, the effect of BN nanoparticles on the dimerization of hIAPP, which is associated with the pathogenesis of type 2 diabetes, is studied. BN nanoparticles prevent the misfolding of hIAPP into β-sheet-rich aggregates. On varying the curvature, the nanoparticles display variation in the interaction preference with hIAPP. Interestingly, as the hydrophobicity of the nanoparticles increases from (5,5) BN nanotube to BN nanosheet, the interaction propensity shifts from N-terminal to the amyloid prone C-terminal of hIAPP. The hydrophobic and aromatic stacking interactions are a contributing factor toward the binding between hIAPP and BN. Due to this, the flat surface of the nanosheet shows better interaction potential toward hIAPP, compared to the nanotubes. Further, the nanoparticles can also disassemble preformed hIAPP fibrils, and the effect is more pronounced for (5,5) nanotube and the nanosheet. This study provides insight into the inhibitory mechanism of hIAPP aggregation by boron nitride nanoparticles and also an understanding of the significance of the curvature of nanoparticles in their interaction with amyloid peptides, which is valuable for the design of antiamyloid drugs.

Dissecting the Molecular Mechanisms of the Co-Aggregation of Aβ40 and Aβ42 Peptides: A REMD Simulation Study

The aggregation of amyloid-β protein (Aβ) into oligomers and amyloid fibrils is closely related to Alzheimer's disease (AD). Aβ40 and Aβ42, as two most prominent isoforms of Aβ peptides, can cross-interact with each other and form co-aggregates, which affect the progression of the disease. However, the molecular determinants underlying Aβ40 and Aβ42 cross-interaction and the structural details of their co-oligomers remain elusive. Herein, we performed all-atom explicit-solvent replica exchange molecular dynamics simulations on Aβ40-Aβ42 heterogeneous and Aβ40/Aβ42 homogeneous dimer systems to dissect the co-aggregation mechanisms of the two isoforms. Our results show that the interpeptide main-chain interaction of Aβ40-Aβ42 is stronger than that of Aβ40-Aβ40 and Aβ42-Aβ42. The positions of hotspot residues in heterodimers and homodimers display high similarity, implying similar molecular recognition sites for both cross-interaction and self-interaction. Contact maps of Aβ40-Aβ42 heterodimers reveal that residue pairs crucial for cross-interaction are mostly located in the C-terminal hydrophobic regions of Aβ40 and Aβ42 peptides. Conformational analysis shows that Aβ40 and Aβ42 monomers can co-assemble into β-sheet-rich heterodimers with shorter β-sheets than those in homodimers, which is decremental to monomer addition. Similar molecular recognition sites and β-sheet distribution of Aβ40 and Aβ42 peptides are observed in heterodimers and homodimers, which may provide the molecular basis for the two isoforms' co-aggregation and cross-seeding. Our work dissects the co-aggregation mechanisms of Aβ40 and Aβ42 peptides at the atomic level, which will help for in-depth understanding of the cross-talk between the two Aβ isoforms and the pathogenesis of AD.

Self-Therapeutic Nanomaterials: Applications in Biology and Medicine

Over past decades, nanotechnology has contributed to the biomedical field in areas including detection, diagnosis, and drug delivery via opto-electronic properties or enhancement of biological effects. Though generally considered inert delivery vehicles, a plethora of past and present evidence demonstrates that nanomaterials also exude unique intrinsic biological activity based on composition, shape, and surface functionalization. These intrinsic biological activities, termed self-therapeutic properties, take several forms, including mediation of cell-cell interactions, modulation of interactions between biomolecules, catalytic amplification of biochemical reactions, and alteration of biological signal transduction events. Moreover, study of biomolecule-nanomaterial interactions offers a promising avenue for uncovering the molecular mechanisms of biology and the evolution of disease. In this review, we observe the historical development, synthesis, and characterization of self-therapeutic nanomaterials. Next, we discuss nanomaterial interactions with biological systems, starting with administration and concluding with elimination. Finally, we apply this materials perspective to advances in intrinsic nanotherapies across the biomedical field, from cancer therapy to treatment of microbial infections and tissue regeneration. We conclude with a description of self-therapeutic nanomaterials in clinical trials and share our perspective on the direction of the field in upcoming years.

In vitro electrochemical detection of the degradation of amyloid-β oligomers

The clearance of overloaded amyloid β (Aβ) oligomers is thought to be an attractive and potential strategy for the therapy of Alzheimer's disease (AD). A variety of strategies have already been utilized to study Aβ degradation in vitro. Here, the electrochemical detection based on direct electrooxidation of specific Tyr residues within Aβ peptide has been developed as a simple and robust approach for monitoring the oligomers' degradation. C60 was employed for photodegrading Aβ oligomers due to the generated ROS under light irradiation. The oxidation current of Tyr residues by square wave voltammetry (SWV) increased upon the Aβ degradation, confirming that the structure variation of Aβ peptide indeed influenced the exposure of those redox species to the electrode surface and final signal output. Chronoamperometric assay also found the electrooxidation of Tyr undergone an irreversible process. Additionally, the direct electrochemistry was capable of detecting the aggregation with rapid test and better sensitivity in compared with dynamic light scattering (DLS), atomic force microscopy (AFM) and thioflavin T (ThT) based fluorescence assay. Thus, this work indicated the potential application of direct electrochemistry in the in vitro measurement of Aβ degradation and clearance, providing new insights and a complementary means into the AD theranostics.

Disparate Effect of Hybrid Peptidomimetics Containing Isomers of Aminobenzoic Acid on hIAPP Aggregation

The abnormal misfolding of human islet amyloid polypeptide (hIAPP) in pancreatic β-cells is implicated in the progression of type II diabetes (T2D). With the prevalence of T2D increasing worldwide, preventing the aggregation of hIAPP has been recognized as a promising therapeutic strategy to control this disease. Recently, a class of novel conformationally restricted β-sheet breaker hybrid peptidomimetics (BSBHps) was found to demonstrate efficient inhibitory ability toward amyloid formation of hIAPP. One (Ile26) or more (Gly24 and Ile26) residues in these six-membered peptide sequences, which have been extracted from the amyloidogenic core of hIAPP, N₂₂FGAIL₂₇, are substituted by three different isomers of the conformationally restricted aromatic amino acid, i.e., aminobenzoic acid (β, γ, and δ), to generate these BSBHps. The presence of the nonproteinogenic aminobenzoic acid moiety renders the BSBHps to be more stable toward proteolytic degradation. The different isomeric BSBHps exhibit contrasting influence on the self-assembly of hIAPP. The BSBHps containing β- and γ-aminobenzoic acid can sufficiently prevent hIAPP aggregation, but those with the δ-aminobenzoic group stabilize the β-sheet-rich aggregate of hIAPP. The difference in the angle between the amino and carboxyl groups in the isomers of the aminobenzoic moiety causes the BSBHps to attain discrete conformation and hence leads to variation in their binding preference with hIAPP and ultimately their inhibitory potency. This guides the pathway for the dissimilar effect of BSBHps on peptide aggregation and, therefore, provides insights into the design considerations for novel drugs against T2D.

Recent Advances in the Discovery of Therapeutics to Curtail Islet Amyloid Polypeptide Aggregation for Type 2 Diabetes Treatment

In humans with type 2 diabetes, at least 70% of patients exhibit islet amyloid plaques formed by misfolding islet amyloid polypeptides (IAPP). The oligomeric conformation and accumulation of the IAPP plaques lead to a panoply of cytotoxic effects on the islet β-cells. Currently, no marketed therapies for the prevention or elimination of these amyloid deposits exist, and therefore significant efforts are required to address this gap. To date, most of the experimental treatments are limited to only in vitro stages of testing. In general, the proposed therapeutics use various targeting strategies, such as binding to the N-terminal region of islet amyloid polypeptide on residues 1-19 or the hydrophobic region of IAPP. Other strategies include targeting the peptide self-assembly through π-stacking. These methods are realized by using several different families of compounds, four of which are highlighted in this review: naturally occurring products, small molecules, organometallic compounds, and nanoparticles. Each of these categories holds immense potential to optimize and develop inhibitor(s) of pancreatic amyloidosis in the near future.

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.

Self-Fluorescent Lone Tryptophan Nanoparticles as Theranostic Agents Against Alzheimer's Disease

Aggregation of β-amyloid (Aβ42) peptide in the neural extracellular space leads to cellular dysfunction, resulting in Alzheimer's disease (AD). The hydrophobic core of the amyloidogenic Aβ42 peptide contains aromatic residues that play an important role in the self-assembly and subsequent aggregation of the peptide. Hence, targeting these hydrophobic core residues by potent low molecular agents can be a promising therapeutic approach toward AD. In the current work, we have developed self-fluorescent solo tryptophan nanoparticles (TNPs) as nanotheranostic systems against AD. We demonstrated that TNPs could significantly inhibit as well as disrupt the fibrils formed by both Aβ42 peptide and another reductionist approach-based amyloid model dipeptide, phenylalanine-phenylalanine (FF). More importantly, these nanostructures were nontoxic to neural cells and could protect the neurons from Aβ42 peptide and FF aggregate-induced cytotoxicity. In addition, efficacy studies performed in animal model further revealed that the TNPs could rescue spatial and learning memory in intracerebroventricular streptozotocin-administration-induced AD phenotype in rats. Moreover, our pharmacokinetics study further established the BBB permeability and brain delivery potency of TNPs. The inherent excellent fluorescent properties of these nanoparticles could be exploited further to use them as imaging modalities for tagging and detecting FF and Aβ42 peptide fibrils. Overall, our results clearly illustrated that the solo TNPs could serve as promising nanotheranostic agents for AD therapy.

Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation

Amyloid depositions of human islet amyloid polypeptides (hIAPP) are associated with type II diabetes (T2D) impacting millions of people globally. Accordingly, strategies against hIAPP aggregation are essential for the prevention and eventual treatment of the disease. Helix mimetics, which modulate the protein-protein interaction by mimicking the side chain residues of a natural α-helix, were found to be a promising strategy for inhibiting hIAPP aggregation. Here, we applied molecular dynamics simulations to investigate two helix mimetics reported to have opposite effects on hIAPP aggregation in solution, the oligopyridylamide-based scaffold 1e promoted, whereas naphthalimide-appended oligopyridylamide scaffold DM 1 inhibited the aggregation of hIAPP in solution. We found that 1e promoted hIAPP aggregation because of the recruiting effects through binding with the N-termini of hIAPP peptides. In contrast, DM 1 with a higher hydrophobic/hydrophilic ratio effectively inhibited hIAPP aggregation by strongly binding with the C-termini of hIAPP peptides, which competed for the interpeptide contacts between amyloidogenic regions in the C-termini and impaired the fibrillization of hIAPP. Structural analyses revealed that DM 1 formed the core of hIAPP-DM 1 complexes and stabilized the off-pathway oligomers, whereas 1e formed the corona outside the hIAPP-1e complexes and remained active in recruiting free hIAPP peptides. The distinct interaction mechanisms of DM 1 and 1e, together with other reported potent antagonists in the literature, emphasized the effective small molecule-based amyloid inhibitors by disrupting peptide interactions that should reach a balanced hydrophobic/hydrophilic ratio, providing a viable and generic strategy for the rational design of novel anti-amyloid nanomedicine.

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C₆₀. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol⁻¹, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol⁻¹ for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C₆₀ was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C₆₀ binding.

Interactive Mechanism of Potential Inhibitors with Glycosyl for SARS-CoV-2 by Molecular Dynamics Simulation

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a type of Ribonucleic Acid (RNA) coronavirus and it has infected and killed many people around the world. It is reported that the receptor binding domain of the spike protein (S_RBD) of the SARS-CoV-2 virus is responsible for attachment to human angiotensin converting enzyme II (ACE2). Many researchers are attempting to search potential inhibitors for fighting SARS-CoV-2 infection using theoretical or experimental methods. In terms of experimental and theoretical research, Cefuroxime, Erythromycin, Lincomycin and Ofloxacin are the potential inhibitors of SARS-CoV-2. However, the interactive mechanism of the protein SARS-CoV-2 and the inhibitors are still elusive. Here, we investigated the interactions between S_RBD and the inhibitors using molecular dynamics (MD) simulations. Interestingly, we found that there are two binding sites of S_RBD for the four small molecules. In addition, our analysis also illustrated that hydrophobic and π-π stacking interactions play crucial roles in the interactions between S_RBD and the small molecules. In our work, we also found that small molecules with glycosyl group have more effect on the conformation of S_RBD than other inhibitors, and they are also potential inhibitors for the genetic variants of SARS-CoV-2. This study provides in silico-derived mechanistic insights into the interactions of S_RBD and inhibitors, which may provide new clues for fighting SARS-CoV-2 infection.

Potential of ATP toward Prevention of hIAPP Oligomerization and Destabilization of hIAPP Protofibrils: An In Silico Perspective

The aggregation of an intrinsically disordered protein, human islet amyloid polypeptide (hIAPP), leads to one of the most prevalent endocrine disorders, type II diabetes mellitus (T2DM). Hence inhibition of hIAPP aggregation provides a possible therapeutic approach for the treatment of T2DM. In this regard, a new aspect of adenosine triphosphate (ATP), which is widely known as the energy source for biological reactions, has recently been discovered, where it can inhibit the formation of protein aggregates and simultaneously dissolve preformed aggregates at a millimolar concentration scale. In this work, we investigate the effect of ATP on the aggregation of an amyloidogenic segment of hIAPP, hIAPP_22-28, and also of the full length sequence. Using all-atom classical molecular dynamics simulations, we observe that the tendency of hIAPP to oligomerize into β-sheet conformers is inhibited by ATP, due to which the peptides remain distant, loosely packed random monomers. Moreover, it can also disassemble preformed hIAPP protofibrils. ATP preferentially interacts with the hydrophobic residues of hIAPP_22-28 fragment and the terminal and turn residues of the full length peptide. The hydrogen bonding, hydrophobic, π-π, and N-H-π stacking interactions are the driving forces for the ATP induced inhibition of hIAPP aggregation. Interestingly, the hydrophobic adenosine of ATP is found to be more in contact with the peptide residues than the hydrophilic triphosphate moiety. The insight into the inhibitory mechanism of ATP on hIAPP aggregation can prove to be beneficial for the design of novel amyloid inhibitors in the future.

Mechanistic Insights into the Co-Aggregation of Aβ and hIAPP: An All-Atom Molecular Dynamic Study

Patients with Alzheimer's disease (AD) have a high risk of developing Type II diabetes (T2D). The co-aggregation of the two disease-related proteins, Aβ and hIAPP, has been proposed as a potential molecular mechanism. However, the detailed Aβ-hIAPP interactions and structural characteristics of co-aggregates are mostly unknown at atomic level. Here, we explore the conformational ensembles of the Aβ-hIAPP heterodimer and Aβ or hIAPP homodimer by performing all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations show that the interaction propensity of Aβ-hIAPP in the heterodimer is comparable with that of Aβ-Aβ/hIAPP-hIAPP in the homodimer. Similar hot spot residues of Aβ/hIAPP in the homodimer and heterodimer are identified, indicating that both Aβ and hIAPP have similar molecular recognition sites for self-aggregation and co-aggregation. Aβ in the heterodimer possesses three high β-sheet probability regions: the N-terminal region E3-H6, the central hydrophobic core region K16-E22, and the C-terminal hydrophobic region I31-A41, which is highly similar to Aβ in the homodimer. More importantly, in the heterodimer, the regions E3-H6, F19-E22, and I31-M35 of Aβ and the amyloid core region N20-T30 of hIAPP display higher β-sheet probability than they do in homodimer, implying their crucial roles in the formation of β-sheet-rich co-aggregates. Our study sheds light on the co-aggregation of Aβ and hIAPP at an atomic level, which will be helpful for an in-depth understanding of the molecular mechanism for epidemiological correlation of AD and T2D.

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.

In vitro and in vivo models for anti-amyloidosis nanomedicines

Amyloid diseases are global epidemics characterized by the accumulative deposits of cross-beta amyloid fibrils and plaques. Despite decades of intensive research, few solutions are available for the diagnosis, treatment, and prevention of these debilitating diseases. Since the early work on the interaction of human β₂-microglobulin and nanoparticles by Linse et al. in 2007, the field of amyloidosis inhibition has gradually evolved into a new frontier in nanomedicine offering numerous interdisciplinary research opportunities, especially for materials, chemistry and biophysics. In this review we summarise, for the first time, the in vitro and in vivo models employed thus far in the field of anti-amyloidosis nanomedicines. Based on this systematic summary, we bring forth the notion that, due to the complex and often overlapping physiopathologies of amyloid diseases, there is a crucial need for the appropriate use of in vitro and in vivo models for validating novel anti-amyloidosis nanomedicines, and there is a crucial need for the development of new animal models that reflect the behavioural, symptomatic and cross-talk hallmarks of amyloid diseases such as Alzheimer's (AD), Parkinson's (PD) diseases and type 2 diabetes (T2DM).

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.

Nanomaterial synthesis, an enabler of amyloidosis inhibition against human diseases

Amyloid diseases are global epidemics with no cure currently available. In the past decade, the use of engineered nanomaterials as inhibitors or probes against the pathogenic aggregation of amyloid peptides and proteins has emerged as a new frontier in nanomedicine. In this Minireview, we summarize for the first time the pivotal role of chemical synthesis in enabling the development of this multidisciplinary field.