Collagen hydrogel confinement of Amyloid-β (Aβ) accelerates aggregation and reduces cytotoxic effects

Targeting amyloidogenic proteins through cyclic peptides - A medicinal chemistry perspective

Alzheimer's Disease (AD) is characterized by the formation of amyloid-β (Aβ) in the extracellular region, neurofibrillary tangles (NFTs) in the intracellular region accompanied with neuroinflammation and decreased neurotransmitters in various regions of brain leading to neuroinflammation and neurodegeneration. Of the various bioactive molecules, Cyclic Peptides (CPs) are small circular chains of amino acids that can alter the structure and function of the proteins they interact with. They can be synthesized using chemical or genetic approach leading to the generation of diverse libraries of CPs that are screened for binding with desired target proteins. In AD, CPs can interfere at various levels, by either imitating the structure or altering the conformation of amyloidogenic proteins. They can also interfere with signal transduction by competing with amyloid proteins for various receptors which are involved in AD pathology. This review highlights the application of CPs as scaffolds for the identification of novel small molecules that can interfere with amyloid aggregation or for the formulation of vaccination against AD. Other proteins involved in the pathophysiological pathways of AD that can potentially be targeted for CP design have also been discussed.

Decoding Alzheimer's Disease: Single-Cell Sequencing Uncovers Brain Cell Heterogeneity and Pathogenesis

Alzheimer's disease (AD) is a complex neurodegenerative disorder marked by progressive cognitive decline and diverse neuropathological features. Recent advances in single-cell sequencing technologies have provided unprecedented insights into the cellular and molecular heterogeneity of the AD brain. This review systematically summarizes the applications of single-cell transcriptomic and epigenomic approaches in AD research, with a focus on the characterization of cell type- and subtype-specific transcriptomic alterations. This review highlights key discoveries related to selectively vulnerable neuronal and glial subpopulations, as well as transcriptional dysregulation associated with genetic risk loci such as APOE and TREM2. This review also discusses how the integration of single-cell RNA sequencing (scRNA-seq), assays for transposase-accessible chromatin using sequencing (ATAC-seq), and spatial transcriptomics elucidates disease trajectories and cellular communication networks across pathological stages. These insights not only enhance the understanding of the pathogenesis of AD but also pave the way for precision medicine through the identification of novel therapeutic targets and biomarkers.

A study of alpha-synuclein and poly(N-isopropylacrylamide) complex formation through detailed atomistic simulations

This work presents an investigation of the influence of poly(N-isopropylacrylamide) (PNIPAM) polymer on the structural dynamics of intrinsically disordered alpha-synuclein (α-syn) protein, exploring the formation and intricate features of the resulting α-syn/PNIPAM complexes. Using atomistic molecular dynamics (MD) simulations, our study analyzes the impact of initial configuration, polymer molecular weight, and protein mutations on the α-syn and the α-syn/PNIPAM complex. Atomistic simulations, of a few μs, of the protein/polymer complex reveal crucial insights into molecular interactions within the complex, emphasizing a delicate balance of forces governing its stability and structural evolution. Our findings indicate that PNIPAM polymer engages in significant non-polar interactions with the non-amyloid component (NAC) region of α-syn, which plays a crucial role in fibril formation, under various conditions such as the mutations in the protein structure and polymer chain length. Especially the PNIPAM polymer with a 40mer monomer exhibits a stabilizing effect on the structural properties of the protein, reducing intramolecular interactions that contribute to misfolding. These findings, which delve into protein/polymer interactions, hold promise as potential guidance for therapeutic strategies in various neurodegenerative disorders.

Understanding the protein conformation transition within polymer hydrogels using a near-infrared water spectroscopy probe

For understanding the behavior of the active substance in vivo, the near-infrared (NIR) spectral variations of ovalbumin (OVA) loaded in poly(N, N-dimethyl acrylamide) (PDMAA) hydrogel with temperature were investigated. Analyzing the spectra with improved resolution by continuous wavelet transform (CWT), the absorption variation of the peak at 4851 cm-1 arising from the α-helix of OVA with temperature was studied. The results show that a sharp decrease occurs at a lower temperature in PDMAA hydrogel, indicating that the unfolding of OVA in PDMAA hydrogel is facilitated. On the other hand, the intensity changes for the hydrogen-bonded water were consistent with that for the protein, providing evidence for facilitating the unfolding. Furthermore, the spectral feature of a new water structure with two hydrogen bonds was obtained from the spectra of OVA loaded hydrogel by independent component analysis (ICA). By analyzing the difference of the water structure with temperature and the side chain of hydrogels, it is demonstrated that the water structure may be a double hydration water surrounding both the protein and the methyl groups of the hydrogel. The easy dissociation of the double hydration water may be a crucial factor in facilitating the unfolding of proteins within hydrogels.

The Role of Reactive Oxygen Species in Alzheimer's Disease: From Mechanism to Biomaterials Therapy

Alzheimer's disease (AD) is a chronic, insidious, and progressive neurodegenerative disease that remains a clinical challenge for society. The fully approved drug lecanemab exhibits the prospect of therapy against the pathological processes, while debatable adverse events conflict with the drug concentration required for the anticipated therapeutic effects. Reactive oxygen species (ROS) are involved in the pathological progression of AD, as has been demonstrated in much research regarding oxidative stress (OS). The contradiction between anticipated dosage and adverse event may be resolved through targeted transport by biomaterials and get therapeutic effects through pathological progression via regulation of ROS. Besides, biomaterials fix delivery issues by promoting the penetration of drugs across the blood-brain barrier (BBB), protecting the drug from peripheral degradation, and elevating bioavailability. The goal is to comprehensively understand the mechanisms of ROS in the progression of AD disease and the potential of ROS-related biomaterials in the treatment of AD. This review focuses on OS and its connection with AD and novel biomaterials in recent years against AD via OS to inspire novel biomaterial development. Revisiting these biomaterials and mechanisms associated with OS in AD via thorough investigations presents a considerable potential and bright future for improving effective interventions for AD.

Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis

Systemic light chain (LC) amyloidosis (AL) is a disease where organs are damaged by an overload of a misfolded patient-specific antibody-derived LC, secreted by an abnormal B cell clone. The high LC concentration in the blood leads to amyloid deposition at organ sites. Indeed, cryogenic electron microscopy (cryo-EM) has revealed unique amyloid folds for heart-derived fibrils taken from different patients. Here, we present the cryo-EM structure of heart-derived AL amyloid (AL59) from another patient with severe cardiac involvement. The double-layered structure displays a u-shaped core that is closed by a β-arc lid and extended by a straight tail. Noteworthy, the fibril harbours an extended constant domain fragment, thus ruling out the variable domain as sole amyloid building block. Surprisingly, the fibrils were abundantly concatenated with a proteinaceous polymer, here identified as collagen VI (COLVI) by immuno-electron microscopy (IEM) and mass-spectrometry. Cryogenic electron tomography (cryo-ET) showed how COLVI wraps around the amyloid forming a helical superstructure, likely stabilizing and protecting the fibrils from clearance. Thus, here we report structural evidence of interactions between amyloid and collagen, potentially signifying a distinct pathophysiological mechanism of amyloid deposits.

sAPPα Peptide Promotes Damaged Microglia to Clear Alzheimer's Amyloid-β via Restoring Mitochondrial Function

Alzheimer's disease (AD) is an age-related neurodegenerative disease with amyloid-β (Aβ) deposition as the main pathological feature. It's an important challenge to find new ways to clear Aβ from the brain. The soluble amyloid precursor protein α (sAPPα) is a neuroprotective protein and can attenuate neuronal damage, including toxic Aβ. However, the regulatory role of sAPPα in non-neuronal cells, such as microglia, is less reported and controversial. Here, we showed that sAPPα promoted the phagocytosis and degradation of Aβ in both normal and damaged microglia. Moreover, the function of damaged microglia was improved by the sAPPα through normalizing mitochondrial function. Furthermore, the results of molecular docking simulation showed that sAPPα had a good affinity with Aβ. We preliminarily reveal that sAPPα is similar to antibodies and can participate in the regulation of microglia phagocytosis and degradation of Aβ after binding to Aβ. sAPPα is expected to be a mild and safe peptide drug or drug carrier for AD.

Impact of Confinement within a Hydrogel Mesh on Protein Thermodynamic Stability and Aggregation Kinetics

Though protein stability and aggregation have been well characterized in dilute solutions, the influence of a confining environment that exists (e.g., in intercellular and tissue spaces and therapeutic formulations) on the protein structure is largely unknown. Herein, the effects of confinement on stability and aggregation were explored for proteins of different sizes, stability, and hydrophobicity when encapsulated in hydrophilic poly(ethylene glycol) hydrogels. Denaturation curves show linear correlations between confinement size (mesh size) and thermodynamic stability, i.e., unfolding free energy and surface area accessible for solvation (represented by m-value). Two clusters of protein types are identifiable from these correlations; the clusters are defined by differences in protein stability, surface area, and aggregation propensity. Proteins with higher stability, larger surface area, and lower aggregation propensity (e.g., lysozyme and myoglobin) are less affected by the confinement imposed by mesh size than proteins with lower stability, smaller surface area, and higher aggregation propensity (e.g., growth hormone and aldehyde dehydrogenase). According to aggregation kinetics measured by thioflavin T fluorescence, confinement in smaller mesh sizes resulted in slower aggregation rates than that in larger mesh sizes. Compared to that in buffer solution, the confinement of a hydrophobic protein (e.g., human insulin) in the hydrogels accelerates protein aggregation. Conversely, the confinement of a hydrophilic protein (e.g., human amylin) in the hydrogels decelerates or prevents aggregation, with the rates of aggregation inversely proportional to mesh size. These findings provide new insights into protein conformational stability in confined microenvironments relevant to various cellular, tissue, and therapeutics scenarios.

A multi-target theranostic nano-composite against Alzheimer's disease fabricated by conjugating carbon dots and triple-functionalized human serum albumin

The complex pathogenesis of Alzheimer's disease (AD) involves the aggregation and accumulation of amyloid β-protein (Aβ) as well as elevated levels of reactive oxygen species (ROS), which requires the development of comprehensive diagnostic and therapeutic interventions. In this work, a multifunctional theranostic nano-composite (HSA-BFP@CDs) is constructed by conjugating triple-functionalized human serum albumin (HSA-BFP) as a theranostic agent targeting Aβ and carbon dots (CDs) as an ROS scavenger. HSA-BFP@CDs exhibits a fluorescence "off-on" effect at 700 nm upon interaction with Aβ aggregates, showing the capability for detection of Aβ plaques and potential for early diagnosis of AD. Besides, HSA-BFP@CDs effectively inhibits the aggregation of Aβ, increasing the viability of Aβ-treated cells from 74% to over 95% at 100 µg/mL. Moreover, multiple ROS, including hydroxyl radicals, superoxide radicals, hydrogen peroxide, and Aβ-Cu²⁺-induced-ROS, can be scavenged by HSA-BFP@CDs, thus resulting in the mitigation of cellular oxidative damages. Experiments with the AD model of Caenorhabditis elegans further demonstrate the multifunctionality of HSA-BFP@CDs in imaging amyloid plaques, reducing Aβ deposition, and relieving oxidative stress in vivo, showing the prospect for Aβ- and ROS-targeted AD diagnosis and treatment. This work provided new insight into the design of protein-carbon dots conjugate and the development of multi-target therapy of AD. STATEMENT OF SIGNIFICANCE: Alzheimer's disease (AD) is the most common form of dementia, which currently affects over 55 million people worldwide. Due to the complex pathogenesis of AD involving amyloid β-protein (Aβ) aggregation as well as elevated levels of reactive oxygen species (ROS), it is highly desired to develop comprehensive diagnostic and therapeutic interventions. In this paper, we fabricated a multifunctional theranostic nano-composite (HSA-BFP@CDs) via the conjugation of triple-functionalized human serum albumin (HSA-BFP) and carbon dots (CDs). The multifunctionality of HSA-BFP@CDs for efficient detection of Aβ aggregates and inhibition of Aβ aggregation as well as scavenging of ROS was demonstrated, demonstrating the potential of the protein-carbon dots conjugate for the multi-target therapy of AD.

Two statins and cromolyn as possible drugs against the cytotoxicity of Aβ(31-35) and Aβ(25-35) peptides: a comparative study by advanced computer simulation methods

In this work, possible effective mechanisms of cromolyn, atorvastatin and lovastatin on the cytotoxicity of Aβ(31-35) and Aβ(25-35) peptides were investigated by classical molecular dynamics and well-tempered metadynamics simulations. The results demonstrate that all the drugs affect the behavior of the peptides, such as their ability to aggregate, and alter their secondary structures and their affinity to a particular drug. Our findings from the computed properties suggest that the best drug candidate is lovastatin. This medicine inhibits peptide aggregation, adsorbs the peptides on the surface of the drug clusters, changes the secondary structure and binds to MET₃₅, which has been seen as the reason for the toxicity of the studied peptide sequences. Moreover, lovastatin is the drug which previously has demonstrated the strongest ability to penetrate the blood-brain barrier and makes lovastatin the most promising medicine among the three investigated drugs. Atorvastatin is also seen as a potential candidate if its penetration through the blood-brain barrier could be improved. Otherwise, its properties are even better than the ones demonstrated by lovastatin. Cromolyn appears to be less interesting as an anti-aggregant from the computational data, in comparison to the two statins.

Insight into the stability of protein in confined environment through analyzing the structure of water by temperature-dependent near-infrared spectroscopy

To understand the stability of protein in confined environment, the near-infrared (NIR) spectra of aqueous solutions and reverse micelles (RMs) containing bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) were measured at different temperature. With the resolution enhanced spectra calculated by continuous wavelet transform (CWT), the intensity change of the α-helix band at 4617 cm^-1 with temperature shows a clear denaturation of the protein in aqueous solution but not in RMs. The effect of the confined environment on the stability of the proteins is indicated. More importantly, the intensity change of the spectral bands of water around 6956 and 6842 cm^-1 provide an evidence for the denaturation, suggesting that water can be a probe exhibiting the structural change of proteins. Furthermore, comparing the spectral features of different water structures obtained by principal component analysis (PCA) from the spectra of RM with and without BSA, it is demonstrated that the bridging water connecting NH in protein and SO in the inner surface of RM may be the reason for the stabilization.

Polyphenol-Peptide Interactions in Mitigation of Alzheimer's Disease: Role of Biosurface-Induced Aggregation

Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder, responsible for nearly two-thirds of all dementia cases. In this review, we report the potential AD treatment strategies focusing on natural polyphenol molecules (green chemistry) and more specifically on the inhibition of polyphenol-induced amyloid aggregation/disaggregation pathways: in bulk and on biosurfaces. We discuss how these pathways can potentially alter the structure at the early stages of AD, hence delaying the aggregation of amyloid-β (Aβ) and tau. We also discuss multidisciplinary approaches, combining experimental and modelling methods, that can better characterize the biochemical and biophysical interactions between proteins and phenolic ligands. In addition to the surface-induced aggregation, which can occur on surfaces where protein can interact with other proteins and polyphenols, we suggest a new concept referred as "confinement stability". Here, on the contrary, the adsorption of Aβ and tau on biosurfaces other than Aβ- and tau-fibrils, e.g., red blood cells, can lead to confinement stability that minimizes the aggregation of Aβ and tau. Overall, these mechanisms may participate directly or indirectly in mitigating neurodegenerative diseases, by preventing protein self-association, slowing down the aggregation processes, and delaying the progression of AD.

Biomaterials in treatment of Alzheimer's disease

Alzheimer's disease (AD) is a non-recoverable progressive neurodegenerative disorder most prevalent but not limited to the old age population. After all the scientific efforts, there are still many unmet criteria and loopholes in available treatment and diagnostic strategies, limiting their efficacy. The poor drug efficacy is attributed to various biological hurdles, including blood-brain barrier (BBB) and peripheral side effects as most prominent ones and the lack of promising carriers to precisely deliver the drug to the brain by conserving its therapeutic potency. The increasing disease prevalence and unavailability of effective therapy calls for developing a more innovative, convenient and affordable way to treat AD. To fulfill such need, researchers explored various biomaterials to develop potential vectors or other forms to target the bioactives in the brain by preserving their inherent properties, improving the existing lacuna like poor solubility, permeability and bioavailability etc. and minimize the side effect. The unique characteristic properties of biomaterials are used to develop different drug carriers, surface modifying target active ligands, functional carriers, drug conjugate, biosensing probe, diagnostic tool and many more. The nanoparticulate system and other colloidal carriers like hydrogel and biodegradable scaffold can effectively target the drug moieties to the brain. Also, the use of different target-acting ligands and stimuli-responsive carriers assures the site-specificity and controlled release at the desired site by interaction with receptors and various exo- and endogenous stimuli. This review article has highlighted the application of biomaterials for targeting the drug to the brain and as promising diagnostic tools to detect the markers for better AD management. The work particularly focuses on the use of biomaterials as smart drug carriers including pH, thermo, photo, electro and magnetically triggered system; novel drug carriers for brain targeting including polymeric carriers (polymeric nanoparticle, dendrimer and polymeric micelle); lipid carrier (liposome, nanoemulsion, NLC and SLN); inorganic nanoparticles (quantum dots, gold nanoparticles etc.); and other drug vectors (hydrogel, biodegradable scaffold, and carbon nanotube) in treatment of AD. It also highlighted the application of some novel carrier systems and biomaterials as biosensor and other diagnostic tools for early and precise AD diagnosis.

Three-Dimensional in vitro Models of Healthy and Tumor Brain Microvasculature for Drug and Toxicity Screening

Tissue vascularization is essential for its oxygenation and the homogenous diffusion of nutrients. Cutting-edge studies are focusing on the vascularization of three-dimensional (3D) in vitro models of human tissues. The reproduction of the brain vasculature is particularly challenging as numerous cell types are involved. Moreover, the blood-brain barrier, which acts as a selective filter between the vascular system and the brain, is a complex structure to replicate. Nevertheless, tremendous advances have been made in recent years, and several works have proposed promising 3D in vitro models of the brain microvasculature. They incorporate cell co-cultures organized in 3D scaffolds, often consisting of components of the native extracellular matrix (ECM), to obtain a micro-environment similar to the in vivo physiological state. These models are particularly useful for studying adverse effects on the healthy brain vasculature. They provide insights into the molecular and cellular events involved in the pathological evolutions of this vasculature, such as those supporting the appearance of brain cancers. Glioblastoma multiform (GBM) is the most common form of brain cancer and one of the most vascularized solid tumors. It is characterized by a high aggressiveness and therapy resistance. Current conventional therapies are unable to prevent the high risk of recurrence of the disease. Most of the new drug candidates fail to pass clinical trials, despite the promising results shown in vitro. The conventional in vitro models are unable to efficiently reproduce the specific features of GBM tumors. Recent studies have indeed suggested a high heterogeneity of the tumor brain vasculature, with the coexistence of intact and leaky regions resulting from the constant remodeling of the ECM by glioma cells. In this review paper, after summarizing the advances in 3D in vitro brain vasculature models, we focus on the latest achievements in vascularized GBM modeling, and the potential applications for both healthy and pathological models as platforms for drug screening and toxicological assays. Particular attention will be paid to discuss the relevance of these models in terms of cell-cell, cell-ECM interactions, vascularization and permeability properties, which are crucial parameters for improving in vitro testing accuracy.

Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives

In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.

Human Pluripotent Stem Cell-Derived Neural Cells as a Relevant Platform for Drug Screening in Alzheimer's Disease

Extracellular amyloid-beta deposition and intraneuronal Tau-laden neurofibrillary tangles are prime features of Alzheimer's disease (AD). The pathology of AD is very complex and still not fully understood, since different neural cell types are involved in the disease. Although neuronal function is clearly deteriorated in AD patients, recently, an increasing number of evidences have pointed towards glial cell dysfunction as one of the main causative phenomena implicated in AD pathogenesis. The complex disease pathology together with the lack of reliable disease models have precluded the development of effective therapies able to counteract disease progression. The discovery and implementation of human pluripotent stem cell technology represents an important opportunity in this field, as this system allows the generation of patient-derived cells to be used for disease modeling and therapeutic target identification and as a platform to be employed in drug discovery programs. In this review, we discuss the current studies using human pluripotent stem cells focused on AD, providing convincing evidences that this system is an excellent opportunity to advance in the comprehension of AD pathology, which will be translated to the development of the still missing effective therapies.

Protein folding and assembly in confined environments: Implications for protein aggregation in hydrogels and tissues

In the biological milieu of a cell, soluble crowding molecules and rigid confined environments strongly influence whether the protein is properly folded, intrinsically disordered proteins assemble into distinct phases, or a denatured or aggregated protein species is favored. Such crowding and confinement factors act to exclude solvent volume from the protein molecules, resulting in an increased local protein concentration and decreased protein entropy. A protein's structure is inherently tied to its function. Examples of processes where crowding and confinement may strongly influence protein function include transmembrane protein dimerization, enzymatic activity, assembly of supramolecular structures (e.g., microtubules), nuclear condensates containing transcriptional machinery, protein aggregation in the contexts of disease and protein therapeutics. Historically, most protein structures have been determined from pure, dilute protein solutions or pure crystals. However, these are not the environments in which these proteins function. Thus, there has been an increased emphasis on analyzing protein structure and dynamics in more "in vivo-like" environments. Complex in vitro models using hydrogel scaffolds to study proteins may better mimic features of the in vivo environment. Therefore, analytical techniques need to be optimized for real-time analysis of proteins within hydrogel scaffolds.