Amyloid oligomers as on-pathway precursors or off-pathway competitors of fibrils

Amyloid β fragments that suppress oligomers but not fibrils are cytoprotective

Neurotoxic aggregates of amyloid beta (Aβ) peptide contribute to the etiology of Alzheimer's disease (AD). In this work, we examined how seven overlapping fragments derived from Aβ1-42 affect the oligomerization and toxicity of the full-length peptide. Four fragments inhibited the toxicity of oligomeric Aβ1-42 to various degrees, two others conferred no cellular protection against Aβ1-42 toxicity, and one fragment enhanced both Aβ1-42 oligomerization and toxicity. The structural and aggregation propensities of the peptides that support strong inhibition of Aβ1-42 toxicity have been identified. Data analysis allowed elucidation of the mechanisms of action of each of the seven peptide fragments on Aβ1-42 cytotoxicity. Our work establishes the potential therapeutic value of four Aβ fragments and supports the notion that agents directed to disruption of Aβ oligomers may be more effective AD drug candidates than those targeting Aβ fibrils.

Mechanism of flavonoid myricetin modulated aggregation in α-Synuclein and its familial mutants E46K and A30P

Inhibiting the aggregation of α-Synuclein (α-Syn) and its familial mutants E46K and A30P has emerged as one of the effective therapeutic strategies against Parkinson's disease (PD). The inhibition and modulation of α-Syn/E46K/A30P fibrillation as well as disaggregation of their pre-formed fibrils by a natural flavonoid myricetin (Myr) is studied. The binding of Myr with α-Syn and its mutants with the affinity ranging 104-105 M-1. The isothermal titration calorimetry (ITC) results indicate the involvement of hydrogen binding/ionic and hydrophobic interactions in the binding process. The aggregation kinetics studies demonstrate that Myr inhibits aggregation of α-Syn/E46K/A30P in a concentration dependent manner. Seeding experiments demonstrate that the protein aggregates formed in the presence of Myr do not further instigates aggregation in healthy proteins. Myr also modulates the aggregation process of protein when added after the onset of aggregation. Circular dichroism (CD) show that Myr delays the structural transition of native α-Syn/E46K/A30P into β-sheets rich fibrillar structures. Myr also disassemble the pre-formed fibrillar structures of α-Syn its mutants. These outcomes offer profound insight into the modulatory mechanism of aggregation of α-Syn, E46K and A30P by Myr, thereby suggesting its potential role in designing combination therapies against protein fibrillation related disorders.

Off-pathway oligomers of α-synuclein and Aβ inhibit secondary nucleation of α-synuclein amyloid fibrils

α-Synuclein (αSyn) is a key culprit in the pathogenesis of synucleinopathies such as Parkinson's Disease (PD), in which it forms not only insoluble aggregates called amyloid fibrils but also smaller, likely more detrimental species termed oligomers. This property is shared with other amyloidogenic proteins such as the Alzheimer's Disease-associated amyloid-β (Aβ). We previously found an intriguing interplay between off-pathway Aβ oligomers and Aβ fibrils, in which the oligomers interfere with fibril formation via inhibition of secondary nucleation by blocking secondary nucleation sites on the fibril surface. Here, using ThT aggregation kinetics and atomic force microscopy (AFM), we tested if the same interplay applies to αSyn fibrils. Both homotypic (i.e. αSyn) and heterotypic (i.e. Aβ) off-pathway oligomers inhibited αSyn aggregation in kinetic assays of secondary nucleation. Initially soluble, kinetically trapped Aβ oligomers co-precipitated with αSyn(1-108) fibrils. The resulting co-assemblies were imaged as clusters of curvilinear oligomers by AFM. The results indicate that off-pathway oligomers have a general tendency to bind amyloid fibril surfaces, also in the absence of sequence homology between fibril and oligomer. The interplay between off-pathway oligomers and amyloid fibrils adds another level of complexity to the homo- and hetero-assembly processes of amyloidogenic proteins.

Nanomaterials in targeting amyloid-β oligomers: current advances and future directions for Alzheimer's disease diagnosis and therapy

The amyloid cascade hypothesis posits that amyloid-β oligomers (AβOs) are the most neurotoxic species in Alzheimer's disease (AD). These oligomers, characterized by their high β-sheet content, have been shown to significantly disrupt cell membranes, induce local inflammation, and impair autophagy processes, which collectively contribute to neuronal loss. As such, targeting AβOs specifically, rather than solely focusing on amyloid-β fibrils (AβFs), may offer a more effective therapeutic approach for AD. Recent advances in detection and diagnosis have emphasized the importance of accurately identifying AβOs in patient samples, enhancing the potential for timely intervention. In recent years, nanomaterials (NMs) have emerged as promising agents for addressing AβOs regarding their multivalent interactions, which can more effectively detect and inhibit AβO formation. This review provides an in-depth analysis of various nanochaperones developed to target AβOs, detailing their mechanisms of action and therapeutic potential via focusing on two main strategies, namely, disruption of AβOs through direct interaction and the inhibition of AβO nucleation by binding to intermediates of the oligomerization process. Evidence from in vivo studies indicate that NMs hold promise for ameliorating AD symptoms. Additionally, the review explores the different interaction mechanisms through which nanoparticles exhibit their inhibitory effects on AβOs, providing insights into their potential for clinical application. This comprehensive overview highlights the current advancements in NM-based therapies for AD and outlines future research directions aimed at optimizing these innovative treatments.

Detection of non-native species formed during fibrillization of the myocilin olfactomedin domain

Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin-associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C-terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid-like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X-ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non-native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo-EM imaging shows two-dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X-ray crystallography. In summary, after incubating OLF under fibrillization-promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid-like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non-model amyloidogenic proteins.

The Impact of Single Amino Acid Insertion on the Supramolecular Assembly Pathway of Aromatic Peptide Amphiphiles

Understanding the mechanism of self-assembly driven by non-covalent interactions is crucial for designing supramolecular materials with desired properties. Here we investigate the self-assembly of aromatic peptide amphiphiles, Fmoc-L2QG and Fmoc-L3QG using a combination of spectroscopic, transmission electron and superresolution optical microscopy techniques. Our results show that Fmoc-L2QG leads to concentration-dependent assembly, forming fibrous assemblies at low concentrations and supramolecular droplets via liquid-liquid phase separation (LLPS) at higher concentrations. Mechanical activation using for example ultrasonication triggered the transition from metastable droplets to fibre morphologies of Fmoc-L2QG. In contrast, Fmoc-L3QG followed both on-pathway and off-pathway routes, resulting in the formation of fibrous morphologies regardless of concentration. Seeding experiments revealed that homo-seeds of the same peptide sequence accelerated the on-pathway process, while hetero-seeds of a mismatched peptide sequences accelerated the off-pathway process, highlighting the competing nature of the complex assembly profile. These findings demonstrate the significant impact of single amino acid insertion on the supramolecular assembly process of oligopeptide monomers, and highlight the potential for controlling the structure and dynamics of peptide materials. Pathway engineering of oligopeptide building blocks and multidomain supramolecular monomers will open new avenues in tailor-made and customizable supramolecular biomaterials.

ALZ-801 prevents amyloid β-protein assembly and reduces cytotoxicity: A preclinical experimental study

Alzheimer's disease (AD) is the most prevalent age-related neurodegenerative disorder, mainly characterized by amyloid β (Aβ) accumulation in the brain. Numerous new agents are currently undergoing clinical trials as disease-modifying therapies (DMTs) targeting Aβ. ALZ-801 is a promising candidate DMT for AD, with a phase 3 trial of ALZ-801 ongoing specifically for apolipoprotein E (APOE) ε4 homozygous patients with early-stage AD. This study aimed to examine the effects of ALZ-801 on Aβ assembly and explore its toxicological profile. Thioflavin T (ThT) assays and two imaging modalities-transmission electron microscopy (TEM) and high-speed atomic force microscopy (HS-AFM)-were used to evaluate ALZ-801's effects on Aβ assembly. To assess the effect of ALZ-801 on Aβ42-induced cytotoxicity, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays and lactate dehydrogenase (LDH) assays were performed. ThT assays revealed increased lag time and decreased fluorescence in the presence of ALZ-801, confirming inhibition of Aβ42 fibril formation, as confirmed by TEM. Real-time observation using HS-AFM revealed that ALZ-801 inhibited the formation of Aβ42 fibril from low-molecular-weight (LMW)-Aβ42 in the presence of Aβ42 seeds. HS-AFM also revealed that globular aggregates from LMW-Aβ42 were significantly larger with ALZ-801, with few fibrils noted. MTT and LDH assays indicated that ALZ-801 prevented LMW-Aβ42-induced cytotoxicity but did not reduce cytotoxicity induced by high-molecular-weight-Aβ42. ALZ-801 can inhibit Aβ42 aggregation by preventing both nucleus formation and fibril elongation, while promoting large globular oligomer formation, and can significantly reduce LMW-Aβ42-induced cytotoxicity. These findings underscore the potential of ALZ-801 as an effective DMT for APOE ε4 homozygous patients with AD.

How is the Amyloid Fold Built? Polymorphism and the Microscopic Mechanisms of Fibril Assembly

For a given protein sequence, many, up to sometimes hundreds of different amyloid fibril folds, can be formed in vitro. Yet, fibrils extracted from, or found in, human tissue, usually at the end of a long disease process, are often structurally homogeneous. Through monitoring of amyloid assembly reactions in vitro, the scientific community has gained a detailed understanding of the kinetic mechanisms of fibril assembly and the rates at which the different processes involved occur. However, how this kinetic information relates to the structural changes as a protein transforms from its initial, native structure to the canonical cross-β structure of amyloid remain obscure. While cryoEM has yielded a plethora of high-resolution information that portray a vast variety of fibril structures, there remains little knowledge of how and why each particular structure resulted. Recent work has demonstrated that fibril structures can change over an assembly time course, despite the different fibril types having similar thermodynamic stability. This points to kinetic control of the fibrils formed, with structures that initiate or elongate faster becoming the dominant products of assembly. Annotating kinetic assembly mechanisms alongside structural analysis of the fibrils formed is required to truly understand the molecular mechanisms of amyloid formation. However, this is a complicated task. In this review, we discuss how embracing this challenge could open new frontiers in amyloid research and new opportunities for therapy.

Globular-shaped Aβ oligomers have diverse mechanisms for promoting Aβ aggregations with the facilitation of fibril elongation

The accumulation of amyloid β-proteins (Aβ) in the extracellular space, forming insoluble plaques, is a primary pathological process underlying Alzheimer's disease (AD). Among the various Aβ species that appear during Aβ aggregation, Aβ oligomers are considered the most neurotoxic form. However, the precise mechanisms of their molecular functions within the Aβ aggregation cascade have not been clarified so far. This research aimed to uncover the structural and functional characteristics of globular-shaped Aβ oligomers (gAβO) under in vitro conditions. We performed thioflavin T (ThT) assays on low-molecular-weight (LMW) Aβ42, testing different concentrations of Aβ42 mature fibril (MF) seeds and gAβO. Fibril formation was continuously observed using high-speed atomic force microscopy (HS-AFM) in LMW Aβ42 with different sample conditions. Conformational changes of Aβ42 aggregates in the presence of gAβO was also evaluated using circular dichroism spectroscopy. The results of the ThT analysis and HS-AFM observation indicated that gAβO promoted fibril formation of LMW Aβ42 while gAβO itself did not form fibrous aggregates, indicating that gAβO would have a catalytic effects on LMW Aβ42 aggregation. We also showed that the molecular interaction of gAβO was altered by the presence and amount of MF seeds in the reaction buffers, indicating that complex interactions would exist among different Aβ species. The results of our present research demonstrated that gAβO would have significant roles to accelerate Aβ aggregation in AD pathogenesis. 225 < 250 words.

Multimer Detection System: A Universal Assay System for Differentiating Protein Oligomers from Monomers

Depositions of protein aggregates are typical pathological hallmarks of various neurodegenerative diseases (NDs). For example, amyloid-beta (Aβ) and tau aggregates are present in the brain and plasma of patients with Alzheimer's disease (AD); α-synuclein in Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA); mutant huntingtin protein (Htt) in Huntington's disease (HD); and DNA-binding protein 43 kD (TDP-43) in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43 encephalopathy (LATE). The same misfolded proteins can be present in multiple diseases in the form of mixed proteinopathies. Since there is no cure for all these diseases, understanding the mechanisms of protein aggregation becomes imperative in modern medicine, especially for developing diagnostics and therapeutics. A Multimer Detection System (MDS) was designed to distinguish and quantify the multimeric/oligomeric forms from the monomeric form of aggregated proteins. As the unique epitope of the monomer is already occupied by capturing or detecting antibodies, the aggregated proteins with multiple epitopes would be accessible to both capturing and detecting antibodies simultaneously, and signals will be generated from the oligomers rather than the monomers. Hence, MDS could present a simple solution for measuring various conformations of aggregated proteins with high sensitivity and specificity, which may help to explore diagnostic and treatment strategies for developing anti-aggregation therapeutics.

The Search for a Universal Treatment for Defined and Mixed Pathology Neurodegenerative Diseases

The predominant neurodegenerative diseases, Alzheimer's disease, Parkinson's disease, dementia with Lewy Bodies, Huntington's disease, amyotrophic lateral sclerosis, and frontotemporal dementia, are rarely pure diseases but, instead, show a diversity of mixed pathologies. At some level, all of them share a combination of one or more different toxic biomarker proteins: amyloid beta (Aβ), phosphorylated Tau (pTau), alpha-synuclein (αSyn), mutant huntingtin (mHtt), fused in sarcoma, superoxide dismutase 1, and TAR DNA-binding protein 43. These toxic proteins share some common attributes, making them potentially universal and simultaneous targets for therapeutic intervention. First, they all form toxic aggregates prior to taking on their final forms as contributors to plaques, neurofibrillary tangles, Lewy bodies, and other protein deposits. Second, the primary enzyme that directs their aggregation is transglutaminase 2 (TGM2), a brain-localized enzyme involved in neurodegeneration. Third, TGM2 binds to calmodulin, a regulatory event that can increase the activity of this enzyme threefold. Fourth, the most common mixed pathology toxic biomarkers (Aβ, pTau, αSyn, nHtt) also bind calmodulin, which can affect their ability to aggregate. This review examines the potential therapeutic routes opened up by this knowledge. The end goal reveals multiple opportunities that are immediately available for universal therapeutic treatment of the most devastating neurodegenerative diseases facing humankind.

Structures of Oligomeric States of Tau Protein, Amyloid-β, α-Synuclein and Prion Protein Implicated in Alzheimer's Disease, Parkinson's Disease and Prionopathies

In this review, we focus on the biophysical and structural aspects of the oligomeric states of physiologically intrinsically disordered proteins and peptides tau, amyloid-β and α-synuclein and partly disordered prion protein and their isolations from animal models and human brains. These protein states may be the most toxic agents in the pathogenesis of Alzheimer's and Parkinson's disease. It was shown that oligomers are important players in the aggregation cascade of these proteins. The structural information about these structural states has been provided by methods such as solution and solid-state NMR, cryo-EM, crosslinking mass spectrometry, AFM, TEM, etc., as well as from hybrid structural biology approaches combining experiments with computational modelling and simulations. The reliable structural models of these protein states may provide valuable information for future drug design and therapies.

Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches

Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.

Tau Protein and Tauopathies: Exploring Tau Protein-Protein and Microtubule Interactions, Cross-Interactions and Therapeutic Strategies

Tau, a microtubule-associated protein (MAP), is essential to maintaining neuronal stability and function in the healthy brain. However, aberrant modifications and pathological aggregations of Tau are implicated in various neurodegenerative disorders, collectively known as tauopathies. The most common Tauopathy is Alzheimer's Disease (AD) counting nowadays more than 60 million patients worldwide. This comprehensive review delves into the multifaceted realm of Tau protein, puzzling out its intricate involvement in both physiological and pathological roles. Emphasis is put on Tau Protein-Protein Interactions (PPIs), depicting its interaction with tubulin, microtubules and its cross-interaction with other proteins such as Aβ1-42, α-synuclein, and the chaperone machinery. In the realm of therapeutic strategies, an overview of diverse possibilities is presented with their relative clinical progresses. The focus is mostly addressed to Tau protein aggregation inhibitors including recent small molecules, short peptides and peptidomimetics with specific focus on compounds that showed a double anti aggregative activity on both Tau protein and Aβ amyloid peptide. This review amalgamates current knowledge on Tau protein and evolving therapeutic strategies, providing a comprehensive resource for researchers seeking to deepen their understanding of the Tau protein and for scientists involved in the development of new peptide-based anti-aggregative Tau compounds.

Structural Insight into Melatonin's Influence on the Conformation of Aβ42 Dimer Studied by Molecular Dynamics Simulation

The accumulation of amyloid-beta (Aβ) oligomers is recognized as a potential culprit in Alzheimer's disease (AD). Experimental studies show that melatonin, a hormone that mainly regulates circadian rhythm and sleep, can interact with Aβ peptides and disrupt the formation of oligomers. However, how melatonin inhibits the oligomerization of soluble Aβ is unclear. Here, by computational simulations, we investigate the effect of different levels of melatonin on the conformation of the Aβ42 dimer. We find that the conformation of the Aβ42 dimer is dependent on melatonin levels. When melatonin is absent, the dimer mainly forms a parallel β-sheet in the CHC region. When one melatonin molecule is present, the overall conformation of the dimer does not change much, but the N-terminal of the dimer tends to adopt antiparallel β-sheets. When two melatoinin molecules are present, the Aβ42 dimer exhibits significant structural change, especially in its central region, resulting in a more compact conformation, and forms parallel β-sheets in the C-terminal. This conformational difference induced by different levels of melatoinin can shed light on the protective role of melatonin.

Natural products targeting amyloid-β oligomer neurotoxicity in Alzheimer's disease

Alzheimer's disease (AD) constitutes a major global health issue, characterized by progressive neurodegeneration and cognitive impairment, for which no curative treatment is currently available. Current therapeutic approaches are focused on symptom management, highlighting the critical need for disease-modifying therapy. The hallmark pathology of AD involves the aggregation and accumulation of amyloid-β (Aβ) peptides in the brain. Consequently, drug discovery efforts in recent decades have centered on the Aβ aggregation cascade, which includes the transition of monomeric Aβ peptides into toxic oligomers and, ultimately, mature fibrils. Historically, anti-Aβ strategies focused on the clearance of amyloid fibrils using monoclonal antibodies. However, substantial evidence has highlighted the critical role of Aβ oligomers (AβOs) in AD pathogenesis. Soluble AβOs are now recognized as more toxic than fibrils, directly contributing to synaptic impairment, neuronal damage, and the onset of AD. Targeting AβOs has emerged as a promising therapeutic approach to mitigate cognitive decline in AD. Natural products (NPs) have demonstrated promise against AβO neurotoxicity through various mechanisms, including preventing AβO formation, enhancing clearance mechanisms, or converting AβOs into non-toxic species. Understanding the mechanisms by which anti-AβO NPs operate is useful for developing disease-modifying treatments for AD. In this review, we explore the role of NPs in mitigating AβO neurotoxicity for AD drug discovery, summarizing key evidence from biophysical methods, cellular assays, and animal models. By discussing how NPs modulate AβO neurotoxicity across various experimental systems, we aim to provide valuable insights into novel therapeutic strategies targeting AβOs in AD.

Fluorescence of Aggregated Aromatic Peptides for Studying the Kinetics of Aggregation and Hardening of Amyloid-like Structures

The capability of amyloid-like peptide fibers to emit intrinsic-fluorescence enables the study of their formation, stability and hardening through time-resolved fluorescence analysis, without the need for additional intercalating dyes. This approach allows the monitoring of amyloid-like peptides aggregation kinetics using minimal sample volumes, and the simultaneous testing of numerous experimental conditions and analytes, offering rapid and reproducible results. The analytical procedure applied to the aromatic hexapeptide F6, alone or derivatized with PEG (polyethylene glycol) moiety of different lengths, suggests that aggregation into large anisotropic structures negatively correlates with initial monomer concentration and relies on the presence of charged N- and C-termini. PEGylation reduces the extent of aggregates hardening, possibly by retaining water, and overall impacts the final structural properties of the aggregates.

Preparation and Characterization of Zn(II)-Stabilized Aβ42 Oligomers

Aβ oligomers are being investigated as cytotoxic agents in Alzheimer's disease (AD). Because of their transient nature and conformational heterogeneity, the relationship between the structure and activity of these oligomers is still poorly understood. Hence, methods for stabilizing Aβ oligomeric species relevant to AD are needed to uncover the structural determinants of their cytotoxicity. Here, we build on the observation that metal ions and metabolites have been shown to interact with Aβ, influencing its aggregation and stabilizing its oligomeric species. We thus developed a method that uses zinc ions, Zn(II), to stabilize oligomers produced by the 42-residue form of Aβ (Aβ42), which is dysregulated in AD. These Aβ42-Zn(II) oligomers are small in size, spanning the 10-30 nm range, stable at physiological temperature, and with a broad toxic profile in human neuroblastoma cells. These oligomers offer a tool to study the mechanisms of toxicity of Aβ oligomers in cellular and animal AD models.

Crystal Violet Selectively Detects Aβ Oligomers but Not Fibrils In Vitro and in Alzheimer's Disease Brain Tissue

Deposition of extracellular Amyloid Beta (Aβ) and intracellular tau fibrils in post-mortem brains remains the only way to conclusively confirm cases of Alzheimer's Disease (AD). Substantial evidence, though, implicates small globular oligomers instead of fibrils as relevant biomarkers of, and critical contributors to, the clinical symptoms of AD. Efforts to verify and utilize amyloid oligomers as AD biomarkers in vivo have been limited by the near-exclusive dependence on conformation-selective antibodies for oligomer detection. While antibodies have yielded critical evidence for the role of both Aβ and tau oligomers in AD, they are not suitable for imaging amyloid oligomers in vivo. Therefore, it would be desirable to identify a set of oligomer-selective small molecules for subsequent development into Positron Emission Tomography (PET) probes. Using a kinetics-based screening assay, we confirm that the triarylmethane dye Crystal Violet (CV) is oligomer-selective for Aβ42 oligomers (AβOs) grown under near-physiological solution conditions in vitro. In postmortem brains of an AD mouse model and human AD patients, we demonstrate that A11 antibody-positive oligomers but not Thioflavin S (ThioS)-positive fibrils colocalize with CV staining, confirming in vitro results. Therefore, our kinetic screen represents a robust approach for identifying new classes of small molecules as candidates for oligomer-selective dyes (OSDs). Such OSDs, in turn, provide promising starting points for the development of PET probes for pre-mortem imaging of oligomer deposits in humans.

Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations

Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.

Each big journey starts with a first step: Importance of oligomerization

Protein oligomers, widely found in nature, have significant physiological and pathological functions. They are classified into three groups based on their function and toxicity. Significant advancements are being achieved in the development of functional oligomers, with a focus on various applications and their engineering. The antimicrobial peptides oligomers play roles in death of bacterial and cancer cells. The predominant pathogenic species in neurodegenerative disorders, as shown by recent results, are amyloid oligomers, which are the main subject of this chapter. They are generated throughout the aggregation process, serving as both intermediates in the subsequent aggregation pathways and ultimate products. Some of them may possess potent cytotoxic properties and through diverse mechanisms cause cellular impairment, and ultimately, the death of cells and disease progression. Information regarding their structure, formation mechanism, and toxicity is limited due to their inherent instability and structural variability. This chapter aims to provide a concise overview of the current knowledge regarding amyloid oligomers.

Conformation of Pyroglutamated Amyloid β (3-40) and (11-40) Fibrils - Extended or Hairpin?

Amyloid β (Aβ) is a hallmark protein of Alzheimer's disease. One physiologically important Aβ variant is formed by initial N-terminal truncation at a glutamic acid position (either E3 or E11), which is subsequently cyclized to a pyroglutamate (either pE3 or pE11). Both forms have been found in high concentrations in the core of amyloid plaques and are likely of high importance in the pathology of Alzheimer's disease. However, the molecular structure of the fibrils of these variants is not entirely clear. Solid-state NMR spectroscopy studies have reported a molecular contact between Gly25 and Ile31, which would disagree with the conventional hairpin model of wildtype (WT-)Aβ1-40 fibrils, most often described in the literature. We investigated the conformation of the monomeric unit of pE3-Aβ3-40 and pE11-Aβ11-40 (and for comparison also wildtype (WT)-Aβ1-40) fibrils to find out whether the hairpin or a newly suggested extended structure dominates the structure of the Aβ monomers in these fibrils. To this end, solid-state NMR spectroscopy was applied probing the inter-residual contacts between Phe19/Leu34, Ala21/Leu34, and especially Gly25/Ile31 using suitable isotopic labeling schemes. In the second part, the flexible turn of the Aβ40 peptides was replaced by a (3-(3-aminomethyl)phenylazo)phenylacetic acid (AMPP)-based photoswitch, which can predefine the peptide conformation to either an extended (trans) or hairpin (cis) conformation. This enables simultaneous spectroscopic assessment of the conformation of the AMPP-photoswitch, allowing in situ structural investigations during fibrillation in contrast to structural techniques such as NMR spectroscopy or cryo-EM, which can only be applied to stable conformers. Both methods confirm an extended structure for the peptidic monomers in fibrils of all investigated Aβ variants. Especially the Gly25/Ile31 contact is a decisive indicator for the extended structure along with the characteristic absorption spectra of trans-AMPP-Aβ.

Real-time monitoring of the amyloid β1-42 monomer-to-oligomer channel transition using a lipid bilayer system

This study describes the observation of the transformation of monomeric amyloid β1-42 (Aβ42) into oligomers in a lipid membrane utilizing a lipid bilayer system for electrophysiological measurement. The relevance of oligomers and protofibrils in Alzheimer's disease (AD) is underscored given their significant neurotoxicity. By closely monitoring the shift of Aβ42 from its monomeric state to forming oligomeric channels in phospholipid membranes, we noted that this transformation transpired within a 2-h frame. We manipulated the lipid membrane's constitution with components such as glycerophospholipid, porcine brain total lipid extract, sphingomyelin (SM), and cholesterol (Chol.) to effectively imitate nerve cell membranes. Interesting findings showcased Chol.'s ability to foster stable oligomeric channel formation in the lipid membrane, with SM and GM1 lipids potentially enhancing channel formation as well. Additionally, the study identified the potential of a catechin derivative, epigallocatechin gallate (EGCG), in obstructing oligomerization. With EGCG present in the outer solution of the Aβ42-infused membrane, a noteworthy reduction in channel current was observed, suggesting the successful inhibition of oligomerization. This conclusion held true in both, prior and subsequent, stages of oligomerization. Our findings shed light on the toxicity of oligomers, promising invaluable information for future advancements in AD treatment strategies.

A Biomimetic Multiparametric Assay to Characterise Anti-Amyloid Drugs

Alzheimer's disease (AD) is the most widespread form of senile dementia worldwide and represents a leading socioeconomic problem in healthcare. Although it is widely debated, the aggregation of the amyloid β peptide (Aβ) is linked to the onset and progression of this neurodegenerative disease. Molecules capable of interfering with specific steps in the fibrillation process remain of pharmacological interest. To identify such compounds, we have set up a small molecule screening process combining multiple experimental methods (UV and florescence spectrometry, ITC, and ATR-FTIR) to identify and characterise potential modulators of Aβ1-42 fibrillation through the description of the biochemical interactions (molecule-membrane Aβ peptide). Three known modulators, namely bexarotene, Chicago sky blue and indomethacin, have been evaluated through this process, and their modulation mechanism in the presence of a biomembrane has been described. Such a well-adapted physico-chemical approach to drug discovery proves to be an undeniable asset for the rapid characterisation of compounds of therapeutic interest for Alzheimer's disease. This strategy could be adapted and transposed to search for modulators of other amyloids such as tau protein.

Role of NFE2L1 in the Regulation of Proteostasis: Implications for Aging and Neurodegenerative Diseases

A hallmark of aging and neurodegenerative diseases is a disruption of proteome homeostasis ("proteostasis") that is caused to a considerable extent by a decrease in the efficiency of protein degradation systems. The ubiquitin proteasome system (UPS) is the major cellular pathway involved in the clearance of small, short-lived proteins, including amyloidogenic proteins that form aggregates in neurodegenerative diseases. Age-dependent decreases in proteasome subunit expression coupled with the inhibition of proteasome function by aggregated UPS substrates result in a feedforward loop that accelerates disease progression. Nuclear factor erythroid 2- like 1 (NFE2L1) is a transcription factor primarily responsible for the proteasome inhibitor-induced "bounce-back effect" regulating the expression of proteasome subunits. NFE2L1 is localized to the endoplasmic reticulum (ER), where it is rapidly degraded under basal conditions by the ER-associated degradation (ERAD) pathway. Under conditions leading to proteasome impairment, NFE2L1 is cleaved and transported to the nucleus, where it binds to antioxidant response elements (AREs) in the promoter region of proteasome subunit genes, thereby stimulating their transcription. In this review, we summarize the role of UPS impairment in aging and neurodegenerative disease etiology and consider the potential benefit of enhancing NFE2L1 function as a strategy to upregulate proteasome function and alleviate pathology in neurodegenerative diseases.