bims-proned 2024-04-21 papers

bims-proned

Biomed News

on Proteostasis in neurodegeneration

Issue of 2024–04–21
twenty-one papers selected by
Verena Kohler, Umeå University

In vitro inhibition of α-Synuclein aggregation and disaggregation of preformed fibers by polyphenol hybrids with 2-conjugated benzothiazole.
Macrophages and Natural Killers Degrade α-Synuclein Aggregates.
Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning.
Yeast Prion Protein Sup35 Initiates α-Synuclein Pathology in Parkinson's Disease.
A crazy trio in Parkinson's disease: metabolism alteration, α-synuclein aggregation, and oxidative stress.
Cyclic-NDGA Effectively Inhibits Human γ-Synuclein Fibrillation, Forms Nontoxic Off-Pathway Species, and Disintegrates Preformed Mature Fibrils.
The Ability of DNAJB6b to Suppress Amyloid Formation Depends on the Chaperone Aggregation State.
Plasminogen degrades α-synuclein, Tau and TDP-43 and decreases dopaminergic neurodegeneration in mouse models of Parkinson's disease.
Proteasome hyperactivation rewires the proteome enhancing stress resistance, proteostasis, lipid metabolism and ERAD in C. elegans.
Post-Translational Modifications in Tau and Their Roles in Alzheimer's Pathology.
14-3-3τ as a Modulator of Early α-Synuclein Multimerization and Amyloid Formation.
Formation of Calprotectin Inhibits Amyloid Aggregation of S100A8 and S100A9 Proteins.
Seeding competent TDP-43 persists in human patient and mouse muscle.
The detection methods currently available for protein aggregation in neurological diseases.
An α-helical peptide-based plasmonic biosensor for highly specific detection of α-synuclein toxic oligomers.
Selection of lansoprazole from an FDA-approved drug library to inhibit the Alzheimer's disease seed-dependent formation of tau aggregates.
A turn for the worse: Aβ β-hairpins in Alzheimer's disease.
Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43370-375 fragment.
Novel multifunctional nanoliposomes inhibit α-synuclein fibrillization, attenuate microglial activation, and silence the expression of SNCA gene.
In silico study on graphene quantum dots modified with various functional groups inhibiting α‑synuclein dimerization.
Sensitive detection of pathological seeds of α-synuclein, tau and prion protein on solid surfaces.

Bioorg Med Chem Lett. 2024 Apr 15. pii: S0960-894X(24)00154-9. [Epub ahead of print]105 129752

In vitro inhibition of α-Synuclein aggregation and disaggregation of preformed fibers by polyphenol hybrids with 2-conjugated benzothiazole.

Ya-Dong Zhao, Wei Zhang, Li-Zi Xing, Ji Xu, Wei-Min Shi, Yun-Xiao Zhang.

  The misfolding and aggregation of α-Syn play a pivotal role in connecting diverse pathological pathways in Parkinson's disease (PD). Preserving α-Syn proteostasis and functionality by inhibiting its aggregation or disaggregating existing aggregates using suitable inhibitors represents a promising strategy for PD prevention and treatment. In this study, a series of benzothiazole-polyphenol hybrids was designed and synthesized. Three identified compounds exhibited notable inhibitory activities against α-Syn aggregation in vitro, with IC50 values in the low micromolar range. These inhibitors demonstrated sustained inhibitory effects throughout the entire aggregation process, stabilizing α-Syn proteostasis conformation. Moreover, the compounds effectively disintegrated preformed α-Syn oligomers and fibers, potentially by binding to specific domains within the fibers, inducing fibril instability, collapse, and ultimately resulting in smaller-sized aggregates and monomers. These findings offer valuable insights into the therapeutic potential of polyphenol hybrids with 2-conjugated benzothiazole targeting α-Syn aggregation in the treatment of PD.

Keywords:  Disaggregation of preformed α-Syn fibers; Mechanism; Polyphenol hybrids with benzothiazole; Synthesis; α-Syn aggregation inhibition

DOI:  https://doi.org/10.1016/j.bmcl.2024.129752
Mol Pharm. 2024 Apr 18.

Macrophages and Natural Killers Degrade α-Synuclein Aggregates.

Mikhail Matveyenka, Kiryl Zhaliazka, Dmitry Kurouski.

  Amyloid oligomers and fibrils are protein aggregates that exert a high cell toxicity. Efficient degradation of these protein aggregates can minimize the spread and progression of neurodegeneration. In this study, we investigate the properties of natural killer (NK) cells and macrophages in the degradation of α-synuclein (α-Syn) aggregates grown in a lipid-free environment and in the presence of phosphatidylserine and cholesterol (PS/Cho), which are lipids that are directly associated with the onset and progression of Parkinson's disease. We found that both types of α-Syn aggregates were endocytosed by neurons, which caused strong damage to cell endosomes. Our results also indicated that PS/Cho vesicles drastically increased the toxicity of α-Syn fibrils formed in their presence compared to the toxicity of α-Syn aggregates grown in a lipid-free environment. Both NK cells and macrophages were able to degrade α-Syn and α-Syn/Cho monomers, oligomers, and fibrils. Quantitative analysis of protein degradation showed that macrophages demonstrated substantially more efficient internalization and degradation of amyloid aggregates in comparison to NK cells. We also found that amyloid aggregates induced the proliferation of macrophages and NK cells and significantly changed the expression of their cytokines and chemokines.

Keywords:  amyloids; cholesterol; macrophages; natural killers; phospholipids; α-synuclein

DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c00160
Nat Chem Biol. 2024 Apr 17.

Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning.

Robert I Horne, Ewa A Andrzejewska, Parvez Alam, Z Faidon Brotzakis, Ankit Srivastava, Alice Aubert, Magdalena Nowinska, Rebecca C Gregory, Roxine Staats, Andrea Possenti, Sean Chia, Pietro Sormanni, Bernardino Ghetti, Byron Caughey, Tuomas P J Knowles, Michele Vendruscolo.

Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been particularly challenging. To address this problem, we describe here a machine learning approach to identify small molecule inhibitors of α-synuclein aggregation, a process implicated in Parkinson's disease and other synucleinopathies. Because the proliferation of α-synuclein aggregates takes place through autocatalytic secondary nucleation, we aim to identify compounds that bind the catalytic sites on the surface of the aggregates. To achieve this goal, we use structure-based machine learning in an iterative manner to first identify and then progressively optimize secondary nucleation inhibitors. Our results demonstrate that this approach leads to the facile identification of compounds two orders of magnitude more potent than previously reported ones.

DOI: https://doi.org/10.1038/s41589-024-01580-x
Mov Disord. 2024 Apr 16.

Yeast Prion Protein Sup35 Initiates α-Synuclein Pathology in Parkinson's Disease.

Youcui Wang, Hui Li, Ning Song, Junxia Xie.

Sinus infection of Saccharomyces cerevisiae accelerates the aggregation of α-synuclein (α-syn) in A53T mice, which was caused by prion protein Sup35. Sup35 promotes α-syn aggregation in vitro and in vivo and leads to Parkinson's disease (PD)-like motor impairment in wildtype mice, suggesting that the yeast Sup35 triggers α-syn pathology in PD.

DOI: https://doi.org/10.1002/mds.29810
Mol Cell Biochem. 2024 Apr 16.

A crazy trio in Parkinson's disease: metabolism alteration, α-synuclein aggregation, and oxidative stress.

Sheng Li, Yanbing Liu, Sen Lu, Jiayi Xu, Xiaokun Liu, Di Yang, Yuxuan Yang, Lin Hou, Ning Li.

  Parkinson's disease (PD) is an aging-associated neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons in the pars compacta of the substantia nigra and the presence of Lewy bodies containing α-synuclein within these neurons. Oligomeric α-synuclein exerts neurotoxic effects through mitochondrial dysfunction, glial cell inflammatory response, lysosomal dysfunction and so on. α-synuclein aggregation, often accompanied by oxidative stress, is generally considered to be a key factor in PD pathology. At present, emerging evidences suggest that metabolism alteration is closely associated with α-synuclein aggregation and PD progression, and improvement of key molecules in metabolism might be potentially beneficial in PD treatment. In this review, we highlight the tripartite relationship among metabolic changes, α-synuclein aggregation, and oxidative stress in PD, and offer updated insights into the treatments of PD, aiming to deepen our understanding of PD pathogenesis and explore new therapeutic strategies for the disease.

Keywords:  Amino acid; Glycolysis; Lipid; Metabolism; Oxidative stress; Parkinson's disease; α-Synuclein

DOI:  https://doi.org/10.1007/s11010-024-04985-3
ACS Chem Neurosci. 2024 Apr 18.

Cyclic-NDGA Effectively Inhibits Human γ-Synuclein Fibrillation, Forms Nontoxic Off-Pathway Species, and Disintegrates Preformed Mature Fibrils.

Sneh Lata Singh, Rajiv Bhat.

  Parkinson's disease arises from protein misfolding, aggregation, and fibrillation and is characterized by LB (Lewy body) deposits, which contain the protein α-synuclein (α-syn) as their major component. Another synuclein, γ-synuclein (γ-syn), coexists with α-syn in Lewy bodies and is also implicated in various types of cancers, especially breast cancer. It is known to seed α-syn fibrillation after its oxidation at methionine residue, thereby contributing in synucleinopathy. Despite its involvement in synucleinopathy, the search for small molecule inhibitors and modulators of γ-syn fibrillation remains largely unexplored. This work reveals the modulatory properties of cyclic-nordihydroguaiaretic acid (cNDGA), a natural polyphenol, on the structural and aggregational properties of human γ-syn employing various biophysical and structural tools, namely, thioflavin T (ThT) fluorescence, Rayleigh light scattering, 8-anilinonaphthalene-1-sulfonic acid binding, far-UV circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR) spectroscopy, atomic force microscopy, ITC, molecular docking, and MTT-toxicity assay. cNDGA was observed to modulate the fibrillation of γ-syn to form off-pathway amorphous species that are nontoxic in nature at as low as 75 μM concentration. The modulation is dependent on oxidizing conditions, with cNDGA weakly interacting (Kd ∼10-5 M) with the residues at the N-terminal of γ-syn protein as investigated by isothermal titration calorimetry and molecular docking, respectively. Increasing cNDGA concentration results in an increased recovery of monomeric γ-syn as shown by sodium dodecyl sulfate and native-polyacrylamide gel electrophoresis. The retention of native structural properties of γ-syn in the presence of cNDGA was further confirmed by far-UV CD and FTIR. In addition, cNDGA is most effective in suppression of fibrillation when added at the beginning of the fibrillation kinetics and is also capable of disintegrating the preformed mature fibrils. These findings could, therefore, pave the ways for further exploring cNDGA as a potential therapeutic against γ-synucleinopathies.

Keywords:  IDP; amorphous aggregates; amyloid; cNDGA; fibrillation; γ-synuclein

DOI:  https://doi.org/10.1021/acschemneuro.3c00793
ACS Chem Neurosci. 2024 Apr 19.

The Ability of DNAJB6b to Suppress Amyloid Formation Depends on the Chaperone Aggregation State.

Andreas Carlsson, Emil Axell, Cecilia Emanuelsson, Ulf Olsson, Sara Linse.

  For many chaperones, a propensity to self-assemble correlates with function. The highly efficient amyloid suppressing chaperone DNAJB6b has been reported to oligomerize. A key question is whether the DNAJB6b self-assemblies or their subunits are active units in the suppression of amyloid formation. Here, we address this question using a nonmodified chaperone. We use the well-established aggregation kinetics of the amyloid β 42 peptide (Aβ42) as a readout of the amyloid suppression efficiency. The experimental setup relies on the slow dissociation of DNAJB6b assemblies upon dilution. We find that the dissociation of the chaperone assemblies correlates with its ability to suppress fibril formation. Thus, the data show that the subunits of DNAJB6b assemblies rather than the large oligomers are the active forms in amyloid suppression. Our results provide insights into how DNAJB6b operates as a chaperone and illustrate the importance of established assembly equilibria and dissociation rates for the design of kinetic experiments.

Keywords:  Amyloid beta peptides; Amyloid inhibition; Chaperone activity; Oligomer dissociation; Protein aggregation; Self-assembly

DOI:  https://doi.org/10.1021/acschemneuro.4c00120
Sci Rep. 2024 04 13. 14(1): 8581

Plasminogen degrades α-synuclein, Tau and TDP-43 and decreases dopaminergic neurodegeneration in mouse models of Parkinson's disease.

Chunying Guo, Ting Wang, Haiyan Huang, Xiaolu Wang, Yugui Jiang, Jinan Li.

  Parkinson's disease (PD) is the second most frequently diagnosed neurodegenerative disease, and it is characterized by the intracellular and extracellular accumulation of α-synuclein (α-syn) and Tau, which are major components of cytosolic protein inclusions called Lewy bodies, in the brain. Currently, there is a lack of effective methods that preventing PD progression. It has been suggested that the plasminogen activation system, which is a major extracellular proteolysis system, is involved in PD pathogenesis. We investigated the functional roles of plasminogen in vitro in an okadaic acid-induced Tau hyperphosphorylation NSC34 cell model, ex vivo using brains from normal controls and methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice, and in vivo in a widely used MPTP-induced PD mouse model and an α-syn overexpression mouse model. The in vitro, ex vivo and in vivo results showed that the administered plasminogen crossed the blood‒brain barrier (BBB), entered cells, and migrated to the nucleus, increased plasmin activity intracellularly, bound to α-syn through lysine binding sites, significantly promoted α-syn, Tau and TDP-43 clearance intracellularly and even intranuclearly in the brain, decreased dopaminergic neurodegeneration and increased the tyrosine hydroxylase levels in the substantia nigra and striatum, and improved motor function in PD mouse models. These findings indicate that plasminogen plays a wide range of pivotal protective roles in PD and therefore may be a promising drug candidate for PD treatment.

Keywords:  Dopaminergic neuron; PD; Plasminogen; TDP-43; Tau; α-syn

DOI:  https://doi.org/10.1038/s41598-024-59090-8
bioRxiv. 2024 Apr 06. pii: 2024.04.04.588128. [Epub ahead of print]

Proteasome hyperactivation rewires the proteome enhancing stress resistance, proteostasis, lipid metabolism and ERAD in C. elegans.

David Salcedo-Tacuma, Nadeeem Asad, Giovanni Howells, Raymond Anderson, David M Smith.

Proteasome dysfunction is implicated in the pathogenesis of neurodegenerative diseases and age-related proteinopathies. Using a C. elegans model, we demonstrate that 20S proteasome hyperactivation, facilitated by 20S gate-opening, accelerates the targeting of intrinsically disordered proteins. This leads to increased protein synthesis, extensive rewiring of the proteome and transcriptome, enhanced oxidative stress defense, accelerated lipid metabolism, and peroxisome proliferation. It also promotes ER-associated degradation (ERAD) of aggregation-prone proteins, such as alpha-1 antitrypsin (ATZ) and various lipoproteins. Notably, our results reveal that 20S proteasome hyperactivation suggests a novel role in ERAD with broad implications for proteostasis-related disorders, simultaneously affecting lipid homeostasis and peroxisome proliferation. Furthermore, the enhanced cellular capacity to mitigate proteostasis challenges, alongside unanticipated acceleration of lipid metabolism is expected to contribute to the longevity phenotype of this mutant. Remarkably, the mechanism of longevity induced by 20S gate opening appears unique, independent of known longevity and stress-resistance pathways. These results support the therapeutic potential of 20S proteasome activation in mitigating proteostasis-related disorders broadly and provide new insights into the complex interplay between proteasome activity, cellular health, and aging.

DOI: https://doi.org/10.1101/2024.04.04.588128
Curr Alzheimer Res. 2024 Apr 15.

Post-Translational Modifications in Tau and Their Roles in Alzheimer's Pathology.

Subha Kalyaanamoorthy, Stanley Kojo Opare, Xiaoxiao Xu, Aravindhan Ganesan, Praveen P N Rao.

  Microtubule-Associated Protein Tau (also known as tau) has been shown to accumulate into paired helical filaments and neurofibrillary tangles, which are known hallmarks of Alzheimer's disease (AD) pathology. Decades of research have shown that tau protein undergoes extensive post-translational modifications (PTMs), which can alter the protein's structure, function, and dynamics and impact the various properties such as solubility, aggregation, localization, and homeostasis. There is a vast amount of information describing the impact and role of different PTMs in AD pathology and neuroprotection. However, the complex interplay between these PTMs remains elusive. Therefore, in this review, we aim to comprehend the key post-translational modifications occurring in tau and summarize potential connections to clarify their impact on the physiology and pathophysiology of tau. Further, we describe how different computational modeling methods have helped in understanding the impact of PTMs on the structure and functions of the tau protein. Finally, we highlight the tau PTM-related therapeutics strategies that are explored for the development of AD therapy.

Keywords:  Alzheimer’s disease; acetylation; computational modeling; deamidation; glycation; glycosylation; methylation; nitration; phosphorylation; post-translational modifications; sumoylation; tau protein; therapeutic approaches.; truncation; ubiquitination

DOI:  https://doi.org/10.2174/0115672050301407240408033046
ACS Chem Neurosci. 2024 Apr 18.

14-3-3τ as a Modulator of Early α-Synuclein Multimerization and Amyloid Formation.

Gobert Heesink, Maxime C M van den Oetelaar, Slav A Semerdzhiev, Christian Ottmann, Luc Brunsveld, Christian Blum, Mireille M A E Claessens.

  The aggregation of α-synuclein (αS) plays a key role in Parkinson's disease (PD) etiology. While the onset of PD is age-related, the cellular quality control system appears to regulate αS aggregation throughout most human life. Intriguingly, the protein 14-3-3τ has been demonstrated to delay αS aggregation and the onset of PD in various models. However, the molecular mechanisms behind this delay remain elusive. Our study confirms the delay in αS aggregation by 14-3-3τ, unveiling a concentration-dependent relation. Utilizing microscale thermophoresis (MST) and single-molecule burst analysis, we quantified the early αS multimers and concluded that these multimers exhibit properties that classify them as nanoscale condensates that form in a cooperative process, preceding the critical nucleus for fibril formation. Significantly, the αS multimer formation mechanism changes dramatically in the presence of scaffold protein 14-3-3τ. Our data modeling suggests that 14-3-3τ modulates the multimerization process, leading to the creation of mixed multimers or co-condensates, comprising both αS and 14-3-3τ. These mixed multimers form in a noncooperative process. They are smaller, more numerous, and distinctively not on the pathway to amyloid formation. Importantly, 14-3-3τ thus acts in the very early stage of αS multimerization, ensuring that αS does not aggregate but remains soluble and functional. This offers long-sought novel entries for the pharmacological modulation of PD.

Keywords:  14-3-3 chaperone; IDP multimerization; modulation of multimerization; protein co-condensation; protein-protein interactions; α-synuclein aggregation

DOI:  https://doi.org/10.1021/acschemneuro.4c00100
ACS Chem Neurosci. 2024 Apr 18.

Formation of Calprotectin Inhibits Amyloid Aggregation of S100A8 and S100A9 Proteins.

Ieva Baronaitė, Darius Šulskis, Aurimas Kopu Stas, Marijonas Tutkus, Vytautas Smirnovas.

  Calcium-binding S100A8 and S100A9 proteins play a significant role in various disorders due to their pro-inflammatory functions. Substantially, they are also relevant in neurodegenerative disorders via the delivery of signals for the immune response. However, at the same time, they can aggregate and accelerate the progression of diseases. Natively, S100A8 and S100A9 exist as homo- and heterodimers, but upon aggregation, they form amyloid-like oligomers, fibrils, or amorphous aggregates. In this study, we aimed to elucidate the aggregation propensities of S100A8, S100A9, and their heterodimer calprotectin by investigating aggregation kinetics, secondary structures, and morphologies of the aggregates. For the first time, we followed the in vitro aggregation of S100A8, which formed spherical aggregates, unlike the fibrillar structures of S100A9 under the same conditions. The aggregates were sensitive to amyloid-specific ThT and ThS dyes and had a secondary structure composed of β-sheets. Similarly to S100A9, S100A8 protein was stabilized by calcium ions, resulting in aggregation inhibition. Finally, the formation of S100A8 and S100A9 heterodimers stabilized the proteins in the absence of calcium ions and prevented their aggregation.

Keywords:  S100; aggregation; amyloid; inflammation

DOI:  https://doi.org/10.1021/acschemneuro.4c00093
bioRxiv. 2024 Apr 04. pii: 2024.04.03.587918. [Epub ahead of print]

Seeding competent TDP-43 persists in human patient and mouse muscle.

Eileen M Lynch, Sara Pittman, Jil Daw, Chiseko Ikenaga, Sheng Chen, Dhruva D Dhavale, Meredith E Jackrel, Yuna M Ayala, Paul Kotzbauer, Cindy V Ly, Alan Pestronk, Thomas E Lloyd, Conrad C Weihl.

TAR DNA-binding protein 43 (TDP-43) is an RNA binding protein that accumulates as aggregates in the central nervous system of some neurodegenerative diseases. However, TDP-43 aggregation is also a sensitive and specific pathologic feature found in a family of degenerative muscle diseases termed inclusion body myopathy (IBM). TDP-43 aggregates from ALS and FTD brain lysates may serve as self-templating aggregate seeds in vitro and in vivo, supporting a prion-like spread from cell to cell. Whether a similar process occurs in IBM patient muscle is not clear. We developed a mouse model of inducible, muscle-specific cytoplasmic localized TDP-43. These mice develop muscle weakness with robust accumulation of insoluble and phosphorylated sarcoplasmic TDP-43, leading to eosinophilic inclusions, altered proteostasis and changes in TDP-43-related RNA processing that resolve with the removal of doxycycline. Skeletal muscle lysates from these mice also have seeding competent TDP-43, as determined by a FRET-based biosensor, that persists for weeks upon resolution of TDP-43 aggregate pathology. Human muscle biopsies with TDP-43 pathology also contain TDP-43 aggregate seeds. Using lysates from muscle biopsies of patients with IBM, IMNM and ALS we found that TDP-43 seeding capacity was specific to IBM. Surprisingly, TDP-43 seeding capacity anti-correlated with TDP-43 aggregate and vacuole abundance. These data support that TDP-43 aggregate seeds are present in IBM skeletal muscle and represent a unique TDP-43 pathogenic species not previously appreciated in human muscle disease.
Summary: TDP-43 aggregate seeds persist in mouse and human skeletal muscle independent of large TDP-43 inclusions.

DOI: https://doi.org/10.1101/2024.04.03.587918
J Chem Neuroanat. 2024 Apr 16. pii: S0891-0618(24)00033-4. [Epub ahead of print]138 102420

The detection methods currently available for protein aggregation in neurological diseases.

Jing-Yi Li, Cheng-Mei Zhou, Rui-Lin Jin, Jia-Hui Song, Ke-Chao Yang, Shu-Lei Li, Bai-Hong Tan, Yan-Chao Li.

  Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.

Keywords:  Detection; Neurodegenerative diseases; Neurological; Protein aggregation; Stain

DOI:  https://doi.org/10.1016/j.jchemneu.2024.102420
Anal Chim Acta. 2024 May 22. pii: S0003-2670(24)00360-X. [Epub ahead of print]1304 342559

An α-helical peptide-based plasmonic biosensor for highly specific detection of α-synuclein toxic oligomers.

Juliana Fátima Giarola, Jaime Santos, M-Carmen Estevez, Salvador Ventura, Irantzu Pallarès, Laura M Lechuga.

   BACKGROUND: α-Synuclein (αS) aggregation is the main neurological hallmark of a group of neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease (PD) is the most prevalent. αS oligomers are elevated in the cerebrospinal fluid (CSF) of PD patients, standing as a biomarker for disease diagnosis. However, methods for early PD detection are still lacking. We have recently identified the amphipathic 22-residue peptide PSMα3 as a high-affinity binder of αS toxic oligomers. PSMα3 displayed excellent selectivity and reproducibility, binding to αS toxic oligomers with affinities in the low nanomolar range and without detectable cross-reactivity with functional monomeric αS.
RESULTS: In this work, we leveraged these PSMα3 unique properties to design a plasmonic-based biosensor for the direct detection of toxic oligomers under label-free conditions.
SIGNIFICANCE AND NOVELTY: We describe the integration of the peptide in a lab-on-a-chip plasmonic platform suitable for point-of-care measurements of αS toxic oligomers in CSF samples in real-time and at an affordable cost, providing an innovative biosensor for PD early diagnosis in the clinic.

Keywords:  Oligomers; Parkinson's disease; Plasmonic biosensor; Synucleinopathies diagnosis; α-synuclein

DOI:  https://doi.org/10.1016/j.aca.2024.342559
Front Aging Neurosci. 2024 ;16 1368291

Selection of lansoprazole from an FDA-approved drug library to inhibit the Alzheimer's disease seed-dependent formation of tau aggregates.

Ahmed Imtiaz, Shotaro Shimonaka, Mohammad Nasir Uddin, Montasir Elahi, Koichi Ishiguro, Masato Hasegawa, Nobutaka Hattori, Yumiko Motoi.

  The efficacy of current treatments is still insufficient for Alzheimer's disease (AD), the most common cause of Dementia. Out of the two pathological hallmarks of AD amyloid-β plaques and neurofibrillary tangles, comprising of tau protein, tau pathology strongly correlates with the symptoms of AD. Previously, screening for inhibitors of tau aggregation that target recombinant tau aggregates have been attempted. Since a recent cryo-EM analysis revealed distinct differences in the folding patterns of heparin-induced recombinant tau filaments and AD tau filaments, this study focused on AD seed-dependent tau aggregation in drug repositioning for AD. We screened 763 compounds from an FDA-approved drug library using an AD seed-induced tau aggregation in SH-SY5Y cell-based assay. In the first screening, 180 compounds were selected, 72 of which were excluded based on the results of lactate dehydrogenase assay. In the third screening with evaluations of soluble and insoluble tau, 38 compounds were selected. In the fourth screening with 3 different AD seeds, 4 compounds, lansoprazole, calcipotriene, desogestrel, and pentamidine isethionate, were selected. After AD seed-induced real-time quaking-induced conversion, lansoprazole was selected as the most suitable drug for repositioning. The intranasal administration of lansoprazole for 4 months to AD seed-injected mice improved locomotor activity and reduced both the amount of insoluble tau and the extent of phosphorylated tau-positive areas. Alanine replacement of the predicted binding site to an AD filament indicated the involvement of Q351, H362, and K369 in lansoprazole and C-shaped tau filaments. These results suggest the potential of lansoprazole as a candidate for drug repositioning to an inhibitor of tau aggregate formation in AD.

Keywords:  Alzheimer’s disease; FDA-approved drug; aggregation; drug reposition; filament; seed; tau

DOI:  https://doi.org/10.3389/fnagi.2024.1368291
Bioorg Med Chem. 2024 Apr 10. pii: S0968-0896(24)00129-9. [Epub ahead of print]105 117715

A turn for the worse: Aβ β-hairpins in Alzheimer's disease.

Sarah M Ruttenberg, James S Nowick.

  Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.

Keywords:  Alzheimer’s disease; Amyloid-β; Oligomers; β-hairpin

DOI:  https://doi.org/10.1016/j.bmc.2024.117715
Biophys Chem. 2024 Mar 29. pii: S0301-4622(24)00059-0. [Epub ahead of print]310 107230

Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43370-375 fragment.

Zhengdong Xu, Jianxin Zhang, Jiaxing Tang, Yehong Gong, Yu Zou, Qingwen Zhang.

  The aggregation of transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43) into ubiquitin-positive inclusions is closely associated with amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and chronic traumatic encephalopathy. The 370-375 fragment of TDP-43 (370GNNSYS375, TDP-43370-375), the amyloidogenic hexapeptides, can be prone to forming pathogenic amyloid fibrils with the characteristic of steric zippers. Previous experiments reported the ALS-associated mutation, serine 375 substituted by glycine (S375G) is linked to early onset disease and protein aggregation of TDP-43. Based on this, it is necessary to explore the underlying molecular mechanisms. By utilizing all-atom molecular dynamics (MD) simulations of 102 μs in total, we investigated the impact of S375G mutation on the conformational ensembles and oligomerization dynamics of TDP-43370-375 peptides. Our replica exchange MD simulations show that S375G mutation could promote the unstructured conformation formation and induce peptides to form a loose packed oligomer, thus inhibiting the aggregation of TDP-43370-375. Further analyses suggest that S375G mutation displays a reduction effect on the number of total hydrogen bonds and contacts among TDP-43370-375 peptides. Hydrogen bonding and polar interactions among TDP-43370-375 peptides, as well as Y374-Y374 π-π stacking interaction, are attenuated by S375G mutation. Additional microsecond MD simulations demonstrate that S375G mutation could prohibit the conformational conversion to β-structure-rich aggregates and possess an inhibitory effect on the oligomerization dynamics of TDP-43370-375. This study offers for the first time of molecular insights into the S375G mutation affecting the aggregation of TDP-43370-375 at the atomic level, and may open new avenues in the development of future site-specific mutation therapeutics.

Keywords:  Aggregation; Amyotrophic lateral sclerosis; Molecular dynamics simulation; Molecular mechanism; S375G mutation; TDP-43

DOI:  https://doi.org/10.1016/j.bpc.2024.107230
Neurologia (Engl Ed). 2024 May;pii: S2173-5808(24)00034-8. [Epub ahead of print]39(4): 321-328

Novel multifunctional nanoliposomes inhibit α-synuclein fibrillization, attenuate microglial activation, and silence the expression of SNCA gene.

A Jebali, M Rashidi, R Keikha, K Daliri, T F Outeiro.

   INTRODUCTION: The aim of this study was to compare the effect of five types of PEGlated nanoliposomes (PNLs) on α-synuclein (α-syn) fibrillization, attenuation of microglial activation, and silence of the SNCA gene, which encodes α-syn.
METHODS: To evaluate the inhibition of α-syn fibrillization, we used standard in vitro assay based on Thioflavin T (ThT) fluorescence. Next, to evaluate the attenuation of microglial activation, the concentration of TNF-a and IL-6 was quantified by ELISA assay in BV2 microglia cells treated with 100nM A53T α-syn and PNLs. In order to determine the silencing of the SNCA, real-time PCR and Western blot analysis was used. Finally, the efficacy of PNLs was confirmed in a transgenic mouse model expressing human α-syn.
RESULTS: ThT assay showed both PNL1 and PNL2 significantly inhibited a-syn fibrillization. ELISA test also showed the production of TNF-a and IL-6 was significantly attenuated when microglial cells treated with PNL1 or PNL2. We also found that SNCA gene, at both mRNA and protein levels, was significantly silenced when BV2 microglia cells were treated with PNL1 or PNL2. Importantly, the efficacy of PNL1 and PNL2 was finally confirmed in vivo in a transgenic mouse model.
CONCLUSIONS: In conclusion, the novel multifunctional nanoliposomes tested in our study inhibit α-syn fibrillization, attenuate microglial activation, and silence SNCA gene. Our findings suggest the therapeutic potential of PNL1 and PNL2 for treating synucleinopathies.

Keywords:  Activación microglial; Fibrilización de sinucleína; Microglial activation; Nanoliposomas; Nanoliposomes; SNCA; Synuclein fibrillization

DOI:  https://doi.org/10.1016/j.nrleng.2021.08.003
J Colloid Interface Sci. 2024 Apr 16. pii: S0021-9797(24)00830-0. [Epub ahead of print]

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

Xiaoxiao Wu, Gang Wang, Ziqian Zhao, Zhenyu Qian.

   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.

Keywords:  Graphene quantum dots; Inhibitory mechanism; Molecular dynamics simulation; Parkinson’s disease; α-synuclein aggregation

DOI:  https://doi.org/10.1016/j.jcis.2024.04.111
PLoS Pathog. 2024 Apr 19. 20(4): e1012175

Sensitive detection of pathological seeds of α-synuclein, tau and prion protein on solid surfaces.

Christina D Orrú, Bradley R Groveman, Andrew G Hughson, Tomás Barrio, Kachi Isiofia, Brent Race, Natalia C Ferreira, Pierluigi Gambetti, David A Schneider, Kentaro Masujin, Kohtaro Miyazawa, Bernardino Ghetti, Gianluigi Zanusso, Byron Caughey.

Prions or prion-like aggregates such as those composed of PrP, α-synuclein, and tau are key features of proteinopathies such as prion, Parkinson's and Alzheimer's diseases, respectively. Their presence on solid surfaces may be biohazardous under some circumstances. PrP prions bound to solids are detectable by ultrasensitive real-time quaking-induced conversion (RT-QuIC) assays if the solids can be immersed in assay wells or transferred to pads. Here we show that PrP prions can remain detectable on steel wires for at least a year, or even after enzymatic cleaning and sterilization. We also show that contamination of larger objects with pathological seeds of α-synuclein, tau, and PrP can be detected by simply assaying a sampling medium that has been transiently applied to the surface. Human α-synuclein seeds in dementia with Lewy bodies brain tissue was detected by α-synuclein RT-QuIC after drying of tissue dilutions with concentrations as low as 10-6 onto stainless steel. Tau RT-QuIC detected tau seeding activity on steel exposed to Alzheimer's disease brain tissue diluted as much as a billion fold. Prion RT-QuIC assays detected seeding activity on plates exposed to brain dilutions as extreme as 10-5-10-8 from prion-affected humans, sheep, cattle and cervids. Sampling medium collected from surgical instruments used in necropsies of sporadic Creutzfeldt-Jakob disease-infected transgenic mice was positive down to 10-6 dilution. Sensitivity for prion detection was not sacrificed by omitting the recombinant PrP substrate from the sampling medium during its application to a surface and subsequent storage as long as the substrate was added prior to performing the assay reaction. Our findings demonstrate practical prototypic surface RT-QuIC protocols for the highly sensitive detection of pathologic seeds of α-synuclein, tau, and PrP on solid objects.

DOI: https://doi.org/10.1371/journal.ppat.1012175