26 results on '"Limbocker, R."'
Search Results
2. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease
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Benedetta Mannini, Roberta Pierattelli, Thomas Löhr, Massimiliano Bonomi, Carlo Camilloni, Thomas C. T. Michaels, Francesco Simone Ruggeri, Gabriella T. Heller, Alfonso De Simone, Michele Vendruscolo, Francesco A. Aprile, Christopher M. Dobson, Ryan Limbocker, Michele Perni, Isabella C. Felli, Tuomas P. J. Knowles, Heller, Gabriella T [0000-0002-5672-0467], Aprile, Francesco A [0000-0002-5040-4420], Perni, Michele [0000-0001-7593-8376], Ruggeri, Francesco Simone [0000-0002-1232-1907], Mannini, Benedetta [0000-0001-6812-7348], Löhr, Thomas [0000-0003-2969-810X], Bonomi, Massimiliano [0000-0002-7321-0004], Camilloni, Carlo [0000-0002-9923-8590], De Simone, Alfonso [0000-0001-8789-9546], Felli, Isabella C [0000-0002-6018-9090], Pierattelli, Roberta [0000-0001-7755-0885], Knowles, Tuomas PJ [0000-0002-7879-0140], Dobson, Christopher M [0000-0002-5445-680X], Vendruscolo, Michele [0000-0002-3616-1610], Apollo - University of Cambridge Repository, Heller, G. T., Aprile, F. A., Michaels, T. C. T., Limbocker, R., Perni, M., Ruggeri, F. S., Mannini, B., Lohr, T., Bonomi, M., Camilloni, C., de Simone, A., Felli, I. C., Pierattelli, R., Knowles, T. P. J., Dobson, C. M., Vendruscolo, M., University of Cambridge [UK] (CAM), Imperial College London, Harvard University, Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano = University of Milan (UNIMI), University of Naples Federico II = Università degli studi di Napoli Federico II, Università degli Studi di Firenze = University of Florence (UniFI), Funding: G.T.H. is supported by the Gates Cambridge Trust and the Rosalind Franklin Research Fellowship at Newnham College, Cambridge, F.A.A. is supported by UK Research and Innovation (Future Leaders Fellowship MR/S033947/1) and the Alzheimer’s Society, UK (317, 511), R.L. is supported by the Gates Cambridge Trust, TCTM by Peterhouse, Cambridge and the Swiss National Science Foundation, and F.S.R. is supported by Darwin College and the Swiss National Foundation (grant numbers P300P2_171219 and P2ELP2_162116, respectively). We acknowledge ARCHER UK National Supercomputing Service under ARCHER Leadership project (grant number e510) and PRACE for awarding us access to MareNostrum at Barcelona Supercomputing Center (BSC), Spain for metadynamic metainference simulations. Parameterization of 10074-G5 was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/P020259/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). MALDI mass spectrometry measurements were performed by L. Packman at the Protein and Nucleic Acid Chemistry Facility (PNAC) at the Department of Biochemistry, University of Cambridge. The NMR measurements were supported by the iNEXT H2020 Programme (EC contract no. 653706). OW450 C. elegans were donated by E. Nollen. BLI measurements were performed in the Biophysics facility at the Department of Biochemistry, University of Cambridge. The work was also supported by the Centre for Misfolding Diseases and the INCEPTION project ANR-16-CONV-0005., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Harvard University [Cambridge], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano [Milano] (UNIMI), University of Naples Federico II, and Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI)
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Amyloid beta ,In silico ,Biophysics ,Intrinsically disordered proteins ,03 medical and health sciences ,0302 clinical medicine ,Alzheimer Disease ,Drug Discovery ,medicine ,Humans ,Life Science ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Molecular Biology ,Research Articles ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Amyloid beta-Peptides ,biology ,Drug discovery ,Chemistry ,SciAdv r-articles ,Conformational entropy ,Small molecule ,Peptide Fragments ,3. Good health ,Mechanism of action ,biology.protein ,Small molecule binding ,medicine.symptom ,Hydrophobic and Hydrophilic Interactions ,030217 neurology & neurosurgery ,Research Article - Abstract
A small molecule binds to a disordered protein in its monomeric form, preventing its aggregation linked to Alzheimer’s disease., Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
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- 2020
3. Editorial: Promising therapeutic strategies for Alzheimer's disease: a focus on amyloid-β targeting.
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Bigi A, Limbocker R, and Cecchi C
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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- 2024
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4. A Relationship between the Structures and Neurotoxic Effects of Aβ Oligomers Stabilized by Different Metal Ions.
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Chia S, Cataldi RL, Ruggeri FS, Limbocker R, Condado-Morales I, Pisani K, Possenti A, Linse S, Knowles TPJ, Habchi J, Mannini B, and Vendruscolo M
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- Humans, Metals, Ions, Peptide Fragments chemistry, Amyloid beta-Peptides chemistry, Alzheimer Disease
- Abstract
Oligomeric assemblies of the amyloid β peptide (Aβ) have been investigated for over two decades as possible neurotoxic agents in Alzheimer's disease. However, due to their heterogeneous and transient nature, it is not yet fully established which of the structural features of these oligomers may generate cellular damage. Here, we study distinct oligomer species formed by Aβ40 (the 40-residue form of Aβ) in the presence of four different metal ions (Al
3+ , Cu2+ , Fe2+ , and Zn2+ ) and show that they differ in their structure and toxicity in human neuroblastoma cells. We then describe a correlation between the size of the oligomers and their neurotoxic activity, which provides a type of structure-toxicity relationship for these Aβ40 oligomer species. These results provide insight into the possible role of metal ions in Alzheimer's disease by the stabilization of Aβ oligomers.- Published
- 2024
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5. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases.
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Rinauro DJ, Chiti F, Vendruscolo M, and Limbocker R
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- Humans, Amyloid metabolism, Amyloid beta-Peptides, Parkinson Disease metabolism, Proteostasis Deficiencies
- Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
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- 2024
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6. Quantitative Attribution of the Protective Effects of Aminosterols against Protein Aggregates to Their Chemical Structures and Ability to Modulate Biological Membranes.
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Errico S, Lucchesi G, Odino D, Osman EY, Cascella R, Neri L, Capitini C, Calamai M, Bemporad F, Cecchi C, Kinney WA, Barbut D, Relini A, Canale C, Caminati G, Limbocker R, Vendruscolo M, Zasloff M, and Chiti F
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- Humans, Cell Membrane metabolism, Amyloidogenic Proteins chemistry, Lipids, Lipid Bilayers metabolism, Amyloid beta-Peptides metabolism, Protein Aggregates, Neurodegenerative Diseases metabolism
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Natural aminosterols are promising drug candidates against neurodegenerative diseases, like Alzheimer and Parkinson, and one relevant protective mechanism occurs via their binding to biological membranes and displacement or binding inhibition of amyloidogenic proteins and their cytotoxic oligomers. We compared three chemically different aminosterols, finding that they exhibited different (i) binding affinities, (ii) charge neutralizations, (iii) mechanical reinforcements, and (iv) key lipid redistributions within membranes of reconstituted liposomes. They also had different potencies (EC
50 ) in protecting cultured cell membranes against amyloid-β oligomers. A global fitting analysis led to an analytical equation describing quantitatively the protective effects of aminosterols as a function of their concentration and relevant membrane effects. The analysis correlates aminosterol-mediated protection with well-defined chemical moieties, including the polyamine group inducing a partial membrane-neutralizing effect (79 ± 7%) and the cholestane-like tail causing lipid redistribution and bilayer mechanical resistance (21 ± 7%), linking quantitatively their chemistry to their protective effects on biological membranes.- Published
- 2023
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7. Characterization of Pairs of Toxic and Nontoxic Misfolded Protein Oligomers Elucidates the Structural Determinants of Oligomer Toxicity in Protein Misfolding Diseases.
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Limbocker R, Cremades N, Cascella R, Tessier PM, Vendruscolo M, and Chiti F
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- Animals, Escherichia coli metabolism, Amyloid beta-Peptides metabolism, Amyloid chemistry, Alzheimer Disease drug therapy, Proteostasis Deficiencies
- Abstract
The aberrant misfolding and aggregation of peptides and proteins into amyloid aggregates occurs in over 50 largely incurable protein misfolding diseases. These pathologies include Alzheimer's and Parkinson's diseases, which are global medical emergencies owing to their prevalence in increasingly aging populations worldwide. Although the presence of mature amyloid aggregates is a hallmark of such neurodegenerative diseases, misfolded protein oligomers are increasingly recognized as of central importance in the pathogenesis of many of these maladies. These oligomers are small, diffusible species that can form as intermediates in the amyloid fibril formation process or be released by mature fibrils after they are formed. They have been closely associated with the induction of neuronal dysfunction and cell death. It has proven rather challenging to study these oligomeric species because of their short lifetimes, low concentrations, extensive structural heterogeneity, and challenges associated with producing stable, homogeneous, and reproducible populations. Despite these difficulties, investigators have developed protocols to produce kinetically, chemically, or structurally stabilized homogeneous populations of protein misfolded oligomers from several amyloidogenic peptides and proteins at experimentally ameneable concentrations. Furthermore, procedures have been established to produce morphologically similar but structurally distinct oligomers from the same protein sequence that are either toxic or nontoxic to cells. These tools offer unique opportunities to identify and investigate the structural determinants of oligomer toxicity by a close comparative inspection of their structures and the mechanisms of action through which they cause cell dysfunction.This Account reviews multidisciplinary results, including from our own groups, obtained by combining chemistry, physics, biochemistry, cell biology, and animal models for pairs of toxic and nontoxic oligomers. We describe oligomers comprised of the amyloid-β peptide, which underlie Alzheimer's disease, and α-synuclein, which are associated with Parkinson's disease and other related neurodegenerative pathologies, collectively known as synucleinopathies. Furthermore, we also discuss oligomers formed by the 91-residue N-terminal domain of [NiFe]-hydrogenase maturation factor from E. coli , which we use as a model non-disease-related protein, and by an amyloid stretch of Sup35 prion protein from yeast. These oligomeric pairs have become highly useful experimental tools for studying the molecular determinants of toxicity characteristic of protein misfolding diseases. Key properties have been identified that differentiate toxic from nontoxic oligomers in their ability to induce cellular dysfunction. These characteristics include solvent-exposed hydrophobic regions, interactions with membranes, insertion into lipid bilayers, and disruption of plasma membrane integrity. By using these properties, it has been possible to rationalize in model systems the responses to pairs of toxic and nontoxic oligomers. Collectively, these studies provide guidance for the development of efficacious therapeutic strategies to target rationally the cytotoxicity of misfolded protein oligomers in neurodegenerative conditions.
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- 2023
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8. Combinations of Vitamin A and Vitamin E Metabolites Confer Resilience against Amyloid-β Aggregation.
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Joshi P, Chia S, Yang X, Perni M, Gabriel JM, Gilmer M, Limbocker R, Habchi J, and Vendruscolo M
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- Animals, Vitamin E pharmacology, Vitamin E metabolism, Protein Aggregates, Amyloid beta-Peptides metabolism, Vitamins pharmacology, Vitamins metabolism, Vitamin K metabolism, Caenorhabditis elegans, Vitamin A, Alzheimer Disease metabolism
- Abstract
Alzheimer's disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-β peptide (Aβ). Since many vitamins are dysregulated in this disease, we explored whether these molecules contribute to the protein homeostasis system by modulating Aβ aggregation. By screening 18 fat-soluble and water-soluble vitamin metabolites, we found that retinoic acid and α-tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect Aβ aggregation both in vitro and in a Caenorhabditis elegans model of Aβ toxicity. We then show that the effects of these two vitamin metabolites in specific combinations cancel each other out, consistent with the "resilience in complexity" hypothesis, according to which the complex composition of the cellular environment could have an overall protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins can be added to the list of components of the protein homeostasis system that regulate protein aggregation.
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- 2023
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9. EGCG inactivates a pore-forming toxin by promoting its oligomerization and decreasing its solvent-exposed hydrophobicity.
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Gabriel JM, Tan T, Rinauro DJ, Hsu CM, Buettner CJ, Gilmer M, Kaur A, McKenzie TL, Park M, Cohen S, Errico S, Wright AK, Chiti F, Vendruscolo M, and Limbocker R
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- Hydrophobic and Hydrophilic Interactions, Solvents, Bee Venoms, Animals, Catechin pharmacology, Catechin chemistry, Melitten pharmacology
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Natural proteinaceous pore-forming agents can bind and permeabilize cell membranes, leading to ion dyshomeostasis and cell death. In the search for antidotes that can protect cells from peptide toxins, we discovered that the polyphenol epigallocatechin gallate (EGCG) interacts directly with melittin from honeybee venom, resulting in the elimination of its binding to the cell membrane and toxicity by markedly lowering the extent of its solvent-exposed hydrophobicity and promoting its oligomerization into larger species. These physicochemical parameters have also been shown to play a key role in the binding to cells of misfolded protein oligomers in a host of neurodegenerative diseases, where oligomer-membrane binding and associated toxicity have been shown to correlate negatively with oligomer size and positively with solvent-exposed hydrophobicity. For melittin, which is not an amyloid-forming protein and has a very distinct mechanism of toxicity compared to misfolded oligomers, we find that the size-hydrophobicity-toxicity relationship also rationalizes the pharmacological attenuation of melittin toxicity by EGCG. These results highlight the importance of the physicochemical properties of pore forming agents in mediating their interactions with cell membranes and suggest a possible therapeutic approach based on compounds with a similar mechanism of action as EGCG., (Published by Elsevier B.V.)
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- 2023
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10. A Brain-Permeable Aminosterol Regulates Cell Membranes to Mitigate the Toxicity of Diverse Pore-Forming Agents.
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Kreiser RP, Wright AK, Sasser LR, Rinauro DJ, Gabriel JM, Hsu CM, Hurtado JA, McKenzie TL, Errico S, Albright JA, Richardson L, Jaffett VA, Riegner DE, Nguyen LT, LeForte K, Zasloff M, Hollows JE, Chiti F, Vendruscolo M, and Limbocker R
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- Biological Transport, Cell Membrane, Brain
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The molecular composition of the plasma membrane plays a key role in mediating the susceptibility of cells to perturbations induced by toxic molecules. The pharmacological regulation of the properties of the cell membrane has therefore the potential to enhance cellular resilience to a wide variety of chemical and biological compounds. In this study, we investigate the ability of claramine, a blood-brain barrier permeable small molecule in the aminosterol class, to neutralize the toxicity of acute biological threat agents, including melittin from honeybee venom and α-hemolysin from Staphylococcus aureus . Our results show that claramine neutralizes the toxicity of these pore-forming agents by preventing their interactions with cell membranes without perturbing their structures in a detectable manner. We thus demonstrate that the exogenous administration of an aminosterol can tune the properties of lipid membranes and protect cells from diverse biotoxins, including not just misfolded protein oligomers as previously shown but also biological protein-based toxins. Our results indicate that the investigation of regulators of the physicochemical properties of cell membranes offers novel opportunities to develop countermeasures against an extensive set of cytotoxic effects associated with cell membrane disruption.
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- 2022
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11. Squalamine and trodusquemine: two natural products for neurodegenerative diseases, from physical chemistry to the clinic.
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Limbocker R, Errico S, Barbut D, Knowles TPJ, Vendruscolo M, Chiti F, and Zasloff M
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- Animals, Chemistry, Physical, Cholestanes, Cholestanols, Humans, Spermine analogs & derivatives, Alzheimer Disease drug therapy, Biological Products pharmacology, Neurodegenerative Diseases drug therapy
- Abstract
Covering: 1993 to 2021 (mainly 2017-2021)Alzheimer's and Parkinson's diseases are neurodegenerative conditions affecting over 50 million people worldwide. Since these disorders are still largely intractable pharmacologically, discovering effective treatments is of great urgency and importance. These conditions are characteristically associated with the aberrant deposition of proteinaceous aggregates in the brain, and with the formation of metastable intermediates known as protein misfolded oligomers that play a central role in their aetiology. In this Highlight article, we review the evidence at the physicochemical, cellular, animal model and clinical levels on how the natural products squalamine and trodusquemine offer promising opportunities for chronic treatments for these progressive conditions by preventing both the formation of neurotoxic oligomers and their interaction with cell membranes.
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- 2022
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12. Publisher Correction: Two human metabolites rescue a C. elegans model of Alzheimer's disease via a cytosolic unfolded protein response.
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Joshi P, Perni M, Limbocker R, Mannini B, Casford S, Chia S, Habchi J, Labbadia J, Dobson CM, and Vendruscolo M
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- 2021
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13. Two human metabolites rescue a C. elegans model of Alzheimer's disease via a cytosolic unfolded protein response.
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Joshi P, Perni M, Limbocker R, Mannini B, Casford S, Chia S, Habchi J, Labbadia J, Dobson CM, and Vendruscolo M
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- Alzheimer Disease prevention & control, Amyloid beta-Peptides chemistry, Amyloid beta-Peptides metabolism, Animals, Caenorhabditis elegans Proteins metabolism, Carnosine pharmacology, Cytosol metabolism, HSP40 Heat-Shock Proteins metabolism, Humans, Kynurenic Acid pharmacology, Protein Aggregates, Protein Aggregation, Pathological prevention & control, Transcription Factors metabolism, Unfolded Protein Response drug effects, Alzheimer Disease metabolism, Caenorhabditis elegans metabolism, Carnosine metabolism, Disease Models, Animal, Kynurenic Acid metabolism, Unfolded Protein Response physiology
- Abstract
Age-related changes in cellular metabolism can affect brain homeostasis, creating conditions that are permissive to the onset and progression of neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Although the roles of metabolites have been extensively studied with regard to cellular signaling pathways, their effects on protein aggregation remain relatively unexplored. By computationally analysing the Human Metabolome Database, we identified two endogenous metabolites, carnosine and kynurenic acid, that inhibit the aggregation of the amyloid beta peptide (Aβ) and rescue a C. elegans model of Alzheimer's disease. We found that these metabolites act by triggering a cytosolic unfolded protein response through the transcription factor HSF-1 and downstream chaperones HSP40/J-proteins DNJ-12 and DNJ-19. These results help rationalise previous observations regarding the possible anti-ageing benefits of these metabolites by providing a mechanism for their action. Taken together, our findings provide a link between metabolite homeostasis and protein homeostasis, which could inspire preventative interventions against neurodegenerative disorders.
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- 2021
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14. Squalamine and Its Derivatives Modulate the Aggregation of Amyloid-β and α-Synuclein and Suppress the Toxicity of Their Oligomers.
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Limbocker R, Staats R, Chia S, Ruggeri FS, Mannini B, Xu CK, Perni M, Cascella R, Bigi A, Sasser LR, Block NR, Wright AK, Kreiser RP, Custy ET, Meisl G, Errico S, Habchi J, Flagmeier P, Kartanas T, Hollows JE, Nguyen LT, LeForte K, Barbut D, Kumita JR, Cecchi C, Zasloff M, Knowles TPJ, Dobson CM, Chiti F, and Vendruscolo M
- Abstract
The aberrant aggregation of proteins is a key molecular event in the development and progression of a wide range of neurodegenerative disorders. We have shown previously that squalamine and trodusquemine, two natural products in the aminosterol class, can modulate the aggregation of the amyloid-β peptide (Aβ) and of α-synuclein (αS), which are associated with Alzheimer's and Parkinson's diseases. In this work, we expand our previous analyses to two squalamine derivatives, des-squalamine and α-squalamine, obtaining further insights into the mechanism by which aminosterols modulate Aβ and αS aggregation. We then characterize the ability of these small molecules to alter the physicochemical properties of stabilized oligomeric species in vitro and to suppress the toxicity of these aggregates to varying degrees toward human neuroblastoma cells. We found that, despite the fact that these aminosterols exert opposing effects on Aβ and αS aggregation under the conditions that we tested, the modifications that they induced to the toxicity of oligomers were similar. Our results indicate that the suppression of toxicity is mediated by the displacement of toxic oligomeric species from cellular membranes by the aminosterols. This study, thus, provides evidence that aminosterols could be rationally optimized in drug discovery programs to target oligomer toxicity in Alzheimer's and Parkinson's diseases., Competing Interests: DB and MZ are inventors in a patent for the use of aminosterols in the treatment of Parkinson’s disease. DB and MZ are co-founders of Enterin Inc. and serve as the President and CSO, respectively, of the company. MV, TPJK, and JH are co-founders, and BM and MP are employees of Wren Therapeutics Ltd., which is independently pursuing inhibitors of protein misfolding and aggregation. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Limbocker, Staats, Chia, Ruggeri, Mannini, Xu, Perni, Cascella, Bigi, Sasser, Block, Wright, Kreiser, Custy, Meisl, Errico, Habchi, Flagmeier, Kartanas, Hollows, Nguyen, LeForte, Barbut, Kumita, Cecchi, Zasloff, Knowles, Dobson, Chiti and Vendruscolo.)
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- 2021
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15. Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease.
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Perni M, van der Goot A, Limbocker R, van Ham TJ, Aprile FA, Xu CK, Flagmeier P, Thijssen K, Sormanni P, Fusco G, Chen SW, Challa PK, Kirkegaard JB, Laine RF, Ma KY, Müller MBD, Sinnige T, Kumita JR, Cohen SIA, Seinstra R, Kaminski Schierle GS, Kaminski CF, Barbut D, De Simone A, Knowles TPJ, Zasloff M, Nollen EAA, Vendruscolo M, and Dobson CM
- Abstract
The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Patients carrying the A30P mutation typically exhibit a similar age of onset and symptoms as sporadic PD, while those carrying the A53T mutation generally have an earlier age of onset and an accelerated progression. We report two C. elegans models of PD (PD
A30P and PDA53T ), which express these mutational variants in the muscle cells, and probed their behavior relative to animals expressing the wild-type protein (PDWT ). PDA30P worms showed a reduced speed of movement and an increased paralysis rate, control worms, but no change in the frequency of body bends. By contrast, in PDA53T worms both speed and frequency of body bends were significantly decreased, and paralysis rate was increased. α-Synuclein was also observed to be less well localized into aggregates in PDA30P worms compared to PDA53T and PDWT worms, and amyloid-like features were evident later in the life of the animals, despite comparable levels of expression of α-synuclein. Furthermore, squalamine, a natural product currently in clinical trials for treating symptomatic aspects of PD, was found to reduce significantly the aggregation of α-synuclein and its associated toxicity in PDA53T and PDWT worms, but had less marked effects in PDA30P . In addition, using an antibody that targets the N-terminal region of α-synuclein, we observed a suppression of toxicity in PDA30P , PDA53T and PDWT worms. These results illustrate the use of these two C. elegans models in fundamental and applied PD research., Competing Interests: MZ and DB are inventors in a patent for the use of squalamine in the treatment of PD. CD, MV, SCo, and TK are co-founders, and MP is an employee of Wren Therapeutics, which is independently pursuing inhibitors of protein misfolding and aggregation. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Perni, van der Goot, Limbocker, van Ham, Aprile, Xu, Flagmeier, Thijssen, Sormanni, Fusco, Chen, Challa, Kirkegaard, Laine, Ma, Müller, Sinnige, Kumita, Cohen, Seinstra, Kaminski Schierle, Kaminski, Barbut, De Simone, Knowles, Zasloff, Nollen, Vendruscolo and Dobson.)- Published
- 2021
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16. Therapeutic Strategies to Reduce the Toxicity of Misfolded Protein Oligomers.
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Kreiser RP, Wright AK, Block NR, Hollows JE, Nguyen LT, LeForte K, Mannini B, Vendruscolo M, and Limbocker R
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- Animals, Humans, Protein Aggregation, Pathological metabolism, Protein Aggregation, Pathological pathology, Proteostasis Deficiencies metabolism, Proteostasis Deficiencies pathology, Protein Aggregation, Pathological therapy, Protein Multimerization, Proteostasis Deficiencies therapy
- Abstract
The aberrant aggregation of proteins is implicated in the onset and pathogenesis of a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Mounting evidence indicates that misfolded protein oligomers produced as intermediates in the aggregation process are potent neurotoxic agents in these diseases. Because of the transient and heterogeneous nature of these elusive aggregates, however, it has proven challenging to develop therapeutics that can effectively target them. Here, we review approaches aimed at reducing oligomer toxicity, including (1) modulating the oligomer populations (e.g., by altering the kinetics of aggregation by inhibiting, enhancing, or redirecting the process), (2) modulating the oligomer properties (e.g., through the size-hydrophobicity-toxicity relationship), (3) modulating the oligomer interactions (e.g., by protecting cell membranes by displacing oligomers), and (4) reducing oligomer toxicity by potentiating the protein homeostasis system. We analyze examples of these complementary approaches, which may lead to the development of compounds capable of preventing or treating neurodegenerative disorders associated with protein aggregation.
- Published
- 2020
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17. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease.
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Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, and Vendruscolo M
- Subjects
- Amyloid beta-Peptides metabolism, Drug Discovery, Humans, Hydrophobic and Hydrophilic Interactions, Peptide Fragments metabolism, Alzheimer Disease drug therapy, Alzheimer Disease metabolism
- Abstract
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).)
- Published
- 2020
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18. A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease.
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Ikenoue T, Aprile FA, Sormanni P, Ruggeri FS, Perni M, Heller GT, Haas CP, Middel C, Limbocker R, Mannini B, Michaels TCT, Knowles TPJ, Dobson CM, and Vendruscolo M
- Subjects
- Amyloid metabolism, Animals, Disease Models, Animal, Peptide Fragments, Plaque, Amyloid metabolism, Alzheimer Disease metabolism, Amyloid beta-Peptides metabolism, Caenorhabditis elegans metabolism, Protein Aggregation, Pathological metabolism
- Abstract
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31-42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer's disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
- Published
- 2020
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19. Trodusquemine displaces protein misfolded oligomers from cell membranes and abrogates their cytotoxicity through a generic mechanism.
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Limbocker R, Mannini B, Ruggeri FS, Cascella R, Xu CK, Perni M, Chia S, Chen SW, Habchi J, Bigi A, Kreiser RP, Wright AK, Albright JA, Kartanas T, Kumita JR, Cremades N, Zasloff M, Cecchi C, Knowles TPJ, Chiti F, Vendruscolo M, and Dobson CM
- Subjects
- Amyloid beta-Peptides chemistry, Amyloid beta-Peptides toxicity, Biophysical Phenomena drug effects, Carboxyl and Carbamoyl Transferases chemistry, Carboxyl and Carbamoyl Transferases toxicity, Cell Death drug effects, Cell Line, Tumor, Cell Membrane drug effects, Escherichia coli Proteins chemistry, Escherichia coli Proteins toxicity, Humans, Spermine pharmacology, alpha-Synuclein chemistry, alpha-Synuclein toxicity, Cell Membrane metabolism, Cholestanes pharmacology, Protein Folding drug effects, Protein Multimerization drug effects, Spermine analogs & derivatives
- Abstract
The onset and progression of numerous protein misfolding diseases are associated with the presence of oligomers formed during the aberrant aggregation of several different proteins, including amyloid-β (Aβ) in Alzheimer's disease and α-synuclein (αS) in Parkinson's disease. These small, soluble aggregates are currently major targets for drug discovery. In this study, we show that trodusquemine, a naturally-occurring aminosterol, markedly reduces the cytotoxicity of αS, Aβ and HypF-N oligomers to human neuroblastoma cells by displacing the oligomers from cell membranes in the absence of any substantial morphological and structural changes to the oligomers. These results indicate that the reduced toxicity results from a mechanism that is common to oligomers from different proteins, shed light on the origin of the toxicity of the most deleterious species associated with protein aggregation and suggest that aminosterols have the therapeutically-relevant potential to protect cells from the oligomer-induced cytotoxicity associated with numerous protein misfolding diseases.
- Published
- 2020
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20. Rationally Designed Antibodies as Research Tools to Study the Structure-Toxicity Relationship of Amyloid-β Oligomers.
- Author
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Limbocker R, Mannini B, Cataldi R, Chhangur S, Wright AK, Kreiser RP, Albright JA, Chia S, Habchi J, Sormanni P, Kumita JR, Ruggeri FS, Dobson CM, Chiti F, Aprile FA, and Vendruscolo M
- Subjects
- Alzheimer Disease metabolism, Amyloid beta-Peptides metabolism, Amyloid beta-Protein Precursor metabolism, Antibody Formation immunology, Brain metabolism, Drug Design, Humans, Neurons metabolism, Peptide Fragments metabolism, Plaque, Amyloid metabolism, Protein Aggregates physiology, Protein Engineering methods, Structure-Activity Relationship, Amyloid beta-Peptides immunology, Antibodies immunology, Antibodies metabolism
- Abstract
Alzheimer's disease is associated with the aggregation of the amyloid-β peptide (Aβ), resulting in the deposition of amyloid plaques in brain tissue. Recent scrutiny of the mechanisms by which Aβ aggregates induce neuronal dysfunction has highlighted the importance of the Aβ oligomers of this protein fragment. Because of the transient and heterogeneous nature of these oligomers, however, it has been challenging to investigate the detailed mechanisms by which these species exert cytotoxicity. To address this problem, we demonstrate here the use of rationally designed single-domain antibodies (DesAbs) to characterize the structure-toxicity relationship of Aβ oligomers. For this purpose, we use Zn
2+ -stabilized oligomers of the 40-residue form of Aβ (Aβ40 ) as models of brain Aβ oligomers and two single-domain antibodies (DesAb18-24 and DesAb34-40 ), designed to bind to epitopes at residues 18-24 and 34-40 of Aβ40 , respectively. We found that the DesAbs induce a change in structure of the Zn2+ -stabilized Aβ40 oligomers, generating a simultaneous increase in their size and solvent-exposed hydrophobicity. We then observed that these increments in both the size and hydrophobicity of the oligomers neutralize each other in terms of their effects on cytotoxicity, as predicted by a recently proposed general structure-toxicity relationship, and observed experimentally. These results illustrate the use of the DesAbs as research tools to investigate the biophysical and cytotoxicity properties of Aβ oligomers.- Published
- 2020
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21. Rational design of a conformation-specific antibody for the quantification of Aβ oligomers.
- Author
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Aprile FA, Sormanni P, Podpolny M, Chhangur S, Needham LM, Ruggeri FS, Perni M, Limbocker R, Heller GT, Sneideris T, Scheidt T, Mannini B, Habchi J, Lee SF, Salinas PC, Knowles TPJ, Dobson CM, and Vendruscolo M
- Subjects
- Alzheimer Disease diagnosis, Alzheimer Disease metabolism, Amyloid beta-Peptides chemistry, Animals, Antibodies chemistry, Antibodies metabolism, Antibody Specificity, Caenorhabditis elegans, Disease Models, Animal, Epitopes, Hippocampus metabolism, Mice, Protein Binding, Protein Conformation, Single-Domain Antibodies, Amyloid beta-Peptides metabolism, Antibodies immunology, Protein Aggregates
- Abstract
Protein misfolding and aggregation is the hallmark of numerous human disorders, including Alzheimer's disease. This process involves the formation of transient and heterogeneous soluble oligomers, some of which are highly cytotoxic. A major challenge for the development of effective diagnostic and therapeutic tools is thus the detection and quantification of these elusive oligomers. Here, to address this problem, we develop a two-step rational design method for the discovery of oligomer-specific antibodies. The first step consists of an "antigen scanning" phase in which an initial panel of antibodies is designed to bind different epitopes covering the entire sequence of a target protein. This procedure enables the determination through in vitro assays of the regions exposed in the oligomers but not in the fibrillar deposits. The second step involves an "epitope mining" phase, in which a second panel of antibodies is designed to specifically target the regions identified during the scanning step. We illustrate this method in the case of the amyloid β (Aβ) peptide, whose oligomers are associated with Alzheimer's disease. Our results show that this approach enables the accurate detection and quantification of Aβ oligomers in vitro, and in Caenorhabditis elegans and mouse hippocampal tissues., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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22. Trodusquemine enhances Aβ 42 aggregation but suppresses its toxicity by displacing oligomers from cell membranes.
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Limbocker R, Chia S, Ruggeri FS, Perni M, Cascella R, Heller GT, Meisl G, Mannini B, Habchi J, Michaels TCT, Challa PK, Ahn M, Casford ST, Fernando N, Xu CK, Kloss ND, Cohen SIA, Kumita JR, Cecchi C, Zasloff M, Linse S, Knowles TPJ, Chiti F, Vendruscolo M, and Dobson CM
- Subjects
- Amyloid beta-Peptides drug effects, Animals, Caenorhabditis elegans, Cell Line, Tumor, Cholestanes pharmacology, Drug Evaluation, Preclinical, Peptide Fragments drug effects, Spermine pharmacology, Spermine therapeutic use, Alzheimer Disease drug therapy, Amyloid beta-Peptides metabolism, Cholestanes therapeutic use, Peptide Fragments metabolism, Spermine analogs & derivatives
- Abstract
Transient oligomeric species formed during the aggregation process of the 42-residue form of the amyloid-β peptide (Aβ
42 ) are key pathogenic agents in Alzheimer's disease (AD). To investigate the relationship between Aβ42 aggregation and its cytotoxicity and the influence of a potential drug on both phenomena, we have studied the effects of trodusquemine. This aminosterol enhances the rate of aggregation by promoting monomer-dependent secondary nucleation, but significantly reduces the toxicity of the resulting oligomers to neuroblastoma cells by inhibiting their binding to the cellular membranes. When administered to a C. elegans model of AD, we again observe an increase in aggregate formation alongside the suppression of Aβ42 -induced toxicity. In addition to oligomer displacement, the reduced toxicity could also point towards an increased rate of conversion of oligomers to less toxic fibrils. The ability of a small molecule to reduce the toxicity of oligomeric species represents a potential therapeutic strategy against AD.- Published
- 2019
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23. Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine.
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Perni M, Flagmeier P, Limbocker R, Cascella R, Aprile FA, Galvagnion C, Heller GT, Meisl G, Chen SW, Kumita JR, Challa PK, Kirkegaard JB, Cohen SIA, Mannini B, Barbut D, Nollen EAA, Cecchi C, Cremades N, Knowles TPJ, Chiti F, Zasloff M, Vendruscolo M, and Dobson CM
- Subjects
- Animals, Caenorhabditis elegans physiology, Cell Line, Cholestanes therapeutic use, Disease Models, Animal, Humans, Neurons drug effects, Neurons metabolism, Parkinson Disease metabolism, Protein Aggregation, Pathological metabolism, Spermine pharmacology, Spermine therapeutic use, Cholestanes pharmacology, Parkinson Disease drug therapy, Protein Aggregates drug effects, Protein Aggregation, Pathological prevention & control, Spermine analogs & derivatives, alpha-Synuclein metabolism
- Abstract
The aggregation of α-synuclein, an intrinsically disordered protein that is highly abundant in neurons, is closely associated with the onset and progression of Parkinson's disease. We have shown previously that the aminosterol squalamine can inhibit the lipid induced initiation process in the aggregation of α-synuclein, and we report here that the related compound trodusquemine is capable of inhibiting not only this process but also the fibril-dependent secondary pathways in the aggregation reaction. We further demonstrate that trodusquemine can effectively suppress the toxicity of α-synuclein oligomers in neuronal cells, and that its administration, even after the initial growth phase, leads to a dramatic reduction in the number of α-synuclein inclusions in a Caenorhabditis elegans model of Parkinson's disease, eliminates the related muscle paralysis, and increases lifespan. On the basis of these findings, we show that trodusquemine is able to inhibit multiple events in the aggregation process of α-synuclein and hence to provide important information about the link between such events and neurodegeneration, as it is initiated and progresses. Particularly in the light of the previously reported ability of trodusquemine to cross the blood-brain barrier and to promote tissue regeneration, the present results suggest that this compound has the potential to be an important therapeutic candidate for Parkinson's disease and related disorders.
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- 2018
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24. Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery.
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Perni M, Challa PK, Kirkegaard JB, Limbocker R, Koopman M, Hardenberg MC, Sormanni P, Müller T, Saar KL, Roode LWY, Habchi J, Vecchi G, Fernando N, Casford S, Nollen EAA, Vendruscolo M, Dobson CM, and Knowles TPJ
- Subjects
- Animals, Behavior, Animal, Data Interpretation, Statistical, Disease Models, Animal, Drug Evaluation, Preclinical instrumentation, Drug Evaluation, Preclinical methods, Machine Learning, Neurodegenerative Diseases physiopathology, Pattern Recognition, Automated methods, Phenotype, Reproducibility of Results, Software, Caenorhabditis elegans physiology, Optical Imaging instrumentation, Optical Imaging methods
- Abstract
Background: The nematode worm C. elegans is a model organism widely used for studies of genetics and of human disease. The health and fitness of the worms can be quantified in different ways, such as by measuring their bending frequency, speed or lifespan. Manual assays, however, are time consuming and limited in their scope providing a strong motivation for automation., New Method: We describe the development and application of an advanced machine vision system for characterising the behaviour of C. elegans, the Wide Field-of-View Nematode Tracking Platform (WF-NTP), which enables massively parallel data acquisition and automated multi-parameter behavioural profiling of thousands of worms simultaneously., Results: We screened more than a million worms from several established models of neurodegenerative disorders and characterised the effects of potential therapeutic molecules for Alzheimer's and Parkinson's diseases. By using very large numbers of animals we show that the sensitivity and reproducibility of behavioural assays is very greatly increased. The results reveal the ability of this platform to detect even subtle phenotypes., Comparison With Existing Methods: The WF-NTP method has substantially greater capacity compared to current automated platforms that typically either focus on characterising single worms at high resolution or tracking the properties of populations of less than 50 animals., Conclusions: The WF-NTP extends significantly the power of existing automated platforms by combining enhanced optical imaging techniques with an advanced software platform. We anticipate that this approach will further extend the scope and utility of C. elegans as a model organism., (Copyright © 2018. Published by Elsevier B.V.)
- Published
- 2018
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25. A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity.
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Perni M, Galvagnion C, Maltsev A, Meisl G, Müller MB, Challa PK, Kirkegaard JB, Flagmeier P, Cohen SI, Cascella R, Chen SW, Limbocker R, Sormanni P, Heller GT, Aprile FA, Cremades N, Cecchi C, Chiti F, Nollen EA, Knowles TP, Vendruscolo M, Bax A, Zasloff M, and Dobson CM
- Subjects
- Algorithms, Amino Acid Sequence, Animals, Animals, Genetically Modified, Biological Products chemistry, Biological Products pharmacology, Caenorhabditis elegans genetics, Caenorhabditis elegans metabolism, Cell Line, Tumor, Cholestanols chemistry, Cholestanols pharmacology, Humans, Membrane Lipids chemistry, Membrane Lipids metabolism, Molecular Structure, Neuroblastoma metabolism, Neuroblastoma pathology, Paresis genetics, Paresis metabolism, Paresis prevention & control, Parkinson Disease metabolism, Protein Binding drug effects, Protein Multimerization drug effects, alpha-Synuclein genetics, alpha-Synuclein metabolism, Protein Aggregates drug effects, Protein Aggregation, Pathological prevention & control, alpha-Synuclein chemistry
- Abstract
The self-assembly of α-synuclein is closely associated with Parkinson's disease and related syndromes. We show that squalamine, a natural product with known anticancer and antiviral activity, dramatically affects α-synuclein aggregation in vitro and in vivo. We elucidate the mechanism of action of squalamine by investigating its interaction with lipid vesicles, which are known to stimulate nucleation, and find that this compound displaces α-synuclein from the surfaces of such vesicles, thereby blocking the first steps in its aggregation process. We also show that squalamine almost completely suppresses the toxicity of α-synuclein oligomers in human neuroblastoma cells by inhibiting their interactions with lipid membranes. We further examine the effects of squalamine in a Caenorhabditis elegans strain overexpressing α-synuclein, observing a dramatic reduction of α-synuclein aggregation and an almost complete elimination of muscle paralysis. These findings suggest that squalamine could be a means of therapeutic intervention in Parkinson's disease and related conditions., Competing Interests: M.Z. is the inventor on a patent application that has been filed related to the compound described in this paper. The other authors declare no conflict of interest.
- Published
- 2017
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26. Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer's disease.
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Habchi J, Chia S, Limbocker R, Mannini B, Ahn M, Perni M, Hansson O, Arosio P, Kumita JR, Challa PK, Cohen SI, Linse S, Dobson CM, Knowles TP, and Vendruscolo M
- Subjects
- Alzheimer Disease, Amyloid beta-Peptides metabolism, Animals, Caenorhabditis elegans, Cerebrospinal Fluid chemistry, Humans, Peptide Fragments metabolism, Small Molecule Libraries, Amyloid beta-Peptides chemistry, Drug Discovery, Peptide Fragments chemistry
- Abstract
The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer's disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery., Competing Interests: Part of the work described in this paper has been the subject of a patent application filed by Cambridge Enterprise, a wholly owned subsidiary of the University of Cambridge (now licensed to Wren Therapeutics Ltd., where M.V. is Chief Scientific Officer; S.I.A.C., C.M.D., and M.V. are members of the Board of Directors; and S.I.A.C., S.L., C.M.D., and T.P.J.K. are consultants).
- Published
- 2017
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