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Pitasi G, Fornt-Suñé M, Bucolo F, Gitto R, Ventura S, De Luca L. Exploitation of the nitro- and/or 4-Trifluoromethyl-decorated phenyl fragment to develop small inhibitors of Alpha-Syn fibril aggregation. Bioorg Med Chem Lett 2024; 111:129905. [PMID: 39067714 DOI: 10.1016/j.bmcl.2024.129905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Here, we report new 2-nitro and/or 4-trifluoromethylphenyl-based small molecules developed as inhibitors of alpha-Syn fibril formation. The set of eighteen compounds was inspired by well-known alpha-Syn aggregation modulators retrieved from literature. The preliminary biochemical data suggested that the two molecules out of eighteen compounds exerted activity comparable to that of reference compound SynuClean-D (SC-D, 5-nitro-6-(3-nitrophenyl)-2-oxo-4-(trifluoromethyl)-1H-pyridine-3-carbonitrile), according to Thioflavin T kinetics. Pharmacophore modelling deciphered the main structural requirements for alpha-Syn aggregation modulators. Moreover, docking and molecular dynamics simulations depicted the binding mode with the targeted alpha-Syn fibrils. The structural data of these new potential α-Syn binders might furnish additional information for understanding the mechanism of action of the ligands that specifically target the NAC domain as theranostic agents for α-synucleopathies.
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Affiliation(s)
- Giovanna Pitasi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale F. Stagno D'Alcontres 31, I-98166 Messina, Italy
| | - Marc Fornt-Suñé
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Federica Bucolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale F. Stagno D'Alcontres 31, I-98166 Messina, Italy
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale F. Stagno D'Alcontres 31, I-98166 Messina, Italy
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale F. Stagno D'Alcontres 31, I-98166 Messina, Italy.
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2
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Galkin M, Priss A, Kyriukha Y, Shvadchak V. Navigating α-Synuclein Aggregation Inhibition: Methods, Mechanisms, and Molecular Targets. CHEM REC 2024; 24:e202300282. [PMID: 37919046 DOI: 10.1002/tcr.202300282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/08/2023] [Indexed: 11/04/2023]
Abstract
Parkinson's disease is a yet incurable, age-related neurodegenerative disorder characterized by the aggregation of small neuronal protein α-synuclein into amyloid fibrils. Inhibition of this process is a prospective strategy for developing a disease-modifying treatment. We overview here small molecule, peptide, and protein inhibitors of α-synuclein fibrillization reported to date. Special attention was paid to the specificity of inhibitors and critical analysis of their action mechanisms. Namely, the importance of oxidation of polyphenols and cross-linking of α-synuclein into inhibitory dimers was highlighted. We also compared strategies of targeting monomeric, oligomeric, and fibrillar α-synuclein species, thoroughly discussed the strong and weak sides of different approaches to testing the inhibitors.
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Affiliation(s)
- Maksym Galkin
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anastasiia Priss
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yevhenii Kyriukha
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States
| | - Volodymyr Shvadchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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3
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Tu W, Zheng C, Zheng Y, Feng Z, Lin H, Jiang Y, Chen W, Chen Y, Lee Y, Su J, Zheng W. The investigation of interaction and chaperon-like activity of α-synuclein as a protein in pathophysiology of Parkinson's disease upon direct interaction with tectorigenin. Int J Biol Macromol 2023; 249:125702. [PMID: 37414324 DOI: 10.1016/j.ijbiomac.2023.125702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Analyzing the therapeutic potential of a therapeutic biomolecule requires an understanding of how it may interact with proteins and modify their corresponding functions. α-Synuclein is a protein which is widely involved in the pathogenesis of Parkinson's disease (PD) and shows chaperon-like activity. We have selected tectorigenin, a most common methoxyisoflavone extracted from plants, among therapeutic bioactive molecules that are documented to have different therapeutic effects. Herein, we aimed to explore how tectorigenin interacts with α-synuclein in vitro by mimicking the physiological environment. Spectroscopic as well as theoretical studies including molecular docking simulation, were used to examine the effects of tectorigenin on the conformation and dynamics of α-synuclein. It was shown that tectorigenin is able to quench the protein emission spectra relied on a mixed static-dynamic quenching mechanism. Furthermore, it was displayed that tectorigenin binding to α-synuclein leads to microenvironmental changes in the tertiary structure of protein, however the protein's secondary structure was almost unchanged. It was also deduced that tectorigenin results in thermal stability of α-synuclein structure, evidenced by less perturbation of α-synuclein secondary structure following elevation of temperature in the presence of tectorigenin relative to that of free form. Molecular docking simulation demonstrated that non-covalent reactions, mainly hydrogen bonds, had a key role in the interaction and stabilization of α-synuclein in the presence of tectorigenin. Moreover, chaperon-like activity of α-synuclein was improved in the presence of tectorigenin against two model proteins, βL-crystallin and catalase. The findings showed that tectorigenin can lead to stabilization of α-synuclein, which may be used as a therapeutic agent in prevention of neurodegenerative diseases.
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Affiliation(s)
- Wenzhan Tu
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Cheng Zheng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yuyin Zheng
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Zhenhua Feng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Haiyan Lin
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yiwei Jiang
- Alberta Institute, Wenzhou Medical University, Wenzhou 325000, China
| | - WangChao Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yuhan Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Lee
- Second affiliation of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jianzhong Su
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.
| | - Wu Zheng
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
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4
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Elnageeb ME, Elfaki I, Adam KM, Ahmed EM, Elkhalifa EM, Abuagla HA, Ahmed AAEM, Ali EW, Eltieb EI, Edris AM. In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies. Diseases 2023; 11:115. [PMID: 37754311 PMCID: PMC10529770 DOI: 10.3390/diseases11030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023] Open
Abstract
Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson's disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case-control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches.
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Affiliation(s)
- Mohamed E. Elnageeb
- Department of Basic Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi Arabia
| | - Khalid M. Adam
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elsadig Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
- Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan
| | - Elkhalifa M. Elkhalifa
- Department of Anatomy, Faculty of Medicine and Health Sciences, Nile Valley University, Atbara 46611, Sudan
| | - Hytham A. Abuagla
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Abubakr Ali Elamin Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elshazali Widaa Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elmoiz Idris Eltieb
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Ali M. Edris
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
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5
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Siwecka N, Saramowicz K, Galita G, Rozpędek-Kamińska W, Majsterek I. Inhibition of Protein Aggregation and Endoplasmic Reticulum Stress as a Targeted Therapy for α-Synucleinopathy. Pharmaceutics 2023; 15:2051. [PMID: 37631265 PMCID: PMC10459316 DOI: 10.3390/pharmaceutics15082051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
α-synuclein (α-syn) is an intrinsically disordered protein abundant in the central nervous system. Physiologically, the protein regulates vesicle trafficking and neurotransmitter release in the presynaptic terminals. Pathologies related to misfolding and aggregation of α-syn are referred to as α-synucleinopathies, and they constitute a frequent cause of neurodegeneration. The most common α-synucleinopathy, Parkinson's disease (PD), is caused by abnormal accumulation of α-syn in the dopaminergic neurons of the midbrain. This results in protein overload, activation of endoplasmic reticulum (ER) stress, and, ultimately, neural cell apoptosis and neurodegeneration. To date, the available treatment options for PD are only symptomatic and rely on dopamine replacement therapy or palliative surgery. As the prevalence of PD has skyrocketed in recent years, there is a pending issue for development of new disease-modifying strategies. These include anti-aggregative agents that target α-syn directly (gene therapy, small molecules and immunization), indirectly (modulators of ER stress, oxidative stress and clearance pathways) or combine both actions (natural compounds). Herein, we provide an overview on the characteristic features of the structure and pathogenic mechanisms of α-syn that could be targeted with novel molecular-based therapies.
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Affiliation(s)
| | | | | | | | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (N.S.); (K.S.); (G.G.); (W.R.-K.)
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6
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Rosado-Ramos R, Poças GM, Marques D, Foito A, M Sevillano D, Lopes-da-Silva M, Gonçalves LG, Menezes R, Ottens M, Stewart D, Ibáñez de Opakua A, Zweckstetter M, Seabra MC, Mendes CS, Outeiro TF, Domingos PM, Santos CN. Genipin prevents alpha-synuclein aggregation and toxicity by affecting endocytosis, metabolism and lipid storage. Nat Commun 2023; 14:1918. [PMID: 37024503 PMCID: PMC10079842 DOI: 10.1038/s41467-023-37561-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Parkinson's Disease (PD) is a common neurodegenerative disorder affecting millions of people worldwide for which there are only symptomatic therapies. Small molecules able to target key pathological processes in PD have emerged as interesting options for modifying disease progression. We have previously shown that a (poly)phenol-enriched fraction (PEF) of Corema album L. leaf extract modulates central events in PD pathogenesis, namely α-synuclein (αSyn) toxicity, aggregation and clearance. PEF was now subjected to a bio-guided fractionation with the aim of identifying the critical bioactive compound. We identified genipin, an iridoid, which relieves αSyn toxicity and aggregation. Furthermore, genipin promotes metabolic alterations and modulates lipid storage and endocytosis. Importantly, genipin was able to prevent the motor deficits caused by the overexpression of αSyn in a Drosophila melanogaster model of PD. These findings widens the possibility for the exploitation of genipin for PD therapeutics.
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Affiliation(s)
- Rita Rosado-Ramos
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Gonçalo M Poças
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Daniela Marques
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Alexandre Foito
- Environmental and Biochemical Sciences, The James Hutton Institute, DD2 5DA, Dundee, Scotland
| | - David M Sevillano
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Mafalda Lopes-da-Silva
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Luís G Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Regina Menezes
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
- CBIOS - Universidade Lusófona's Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal
| | - Marcel Ottens
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Derek Stewart
- Environmental and Biochemical Sciences, The James Hutton Institute, DD2 5DA, Dundee, Scotland
| | | | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Miguel C Seabra
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - César S Mendes
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Tiago Fleming Outeiro
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE2 4HH, UK
- Scientific employee with an honorary contract at German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075, Göttingen, Germany
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Cláudia N Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.
- iNOVA4Health, NOVA Medical School Faculdade de Ciências Médicas, NMS FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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7
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Peña-Díaz S, García-Pardo J, Ventura S. Development of Small Molecules Targeting α-Synuclein Aggregation: A Promising Strategy to Treat Parkinson's Disease. Pharmaceutics 2023; 15:839. [PMID: 36986700 PMCID: PMC10059018 DOI: 10.3390/pharmaceutics15030839] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Parkinson's disease, the second most common neurodegenerative disorder worldwide, is characterized by the accumulation of protein deposits in the dopaminergic neurons. These deposits are primarily composed of aggregated forms of α-Synuclein (α-Syn). Despite the extensive research on this disease, only symptomatic treatments are currently available. However, in recent years, several compounds, mainly of an aromatic character, targeting α-Syn self-assembly and amyloid formation have been identified. These compounds, discovered by different approaches, are chemically diverse and exhibit a plethora of mechanisms of action. This work aims to provide a historical overview of the physiopathology and molecular aspects associated with Parkinson's disease and the current trends in small compound development to target α-Syn aggregation. Although these molecules are still under development, they constitute an important step toward discovering effective anti-aggregational therapies for Parkinson's disease.
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Affiliation(s)
- Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Javier García-Pardo
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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8
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De Luca L, Vittorio S, Peña-Díaz S, Pitasi G, Fornt-Suñé M, Bucolo F, Ventura S, Gitto R. Ligand-Based Discovery of a Small Molecule as Inhibitor of α-Synuclein Amyloid Formation. Int J Mol Sci 2022; 23:ijms232314844. [PMID: 36499173 PMCID: PMC9738895 DOI: 10.3390/ijms232314844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/12/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
α-Synuclein (α-Syn) aggregates are implicated in Parkinson's disease (PD), so inhibitors of α-Syn aggregation have been intensively explored. It has been demonstrated that small molecules might be able to reduce α-Syn aggregation in fibrils, thus exerting neuroprotective effects in models of PD. To expand our knowledge about the structural requirements for blocking the recognition process into the oligomeric assembly of α-Syn aggregates, we performed a ligand-based virtual screening procedure using two well-known α-Syn aggregation inhibitors, SynuClean-D and ZPD-2, as query compounds. A collection of thirty-four compounds bearing distinct chemical functionalities and mutual chemical features were studied in a Th-T fluorescence test, thus identifying 5-(2,6-dinitro-4-(trifluoromethyl)benzyl)-1-methyl-1H-tetrazole (named MeSC-04) as a potent α-Syn amyloid formation inhibitor that demonstrated similar behavior when compared to SynuClean-D in the thioflavin-T-monitored kinetic assays, with both molecules reducing the number and size of amyloid fibrils, as evidenced by electron microscopy. Molecular modeling studies suggested the binding mode of MeSC-04 through the identification of putative druggable pockets on α-syn fibrils and a subsequent consensus docking methodology. Overall, this work could furnish new insights in the development of α-Syn amyloid inhibitors from synthetic sources.
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Affiliation(s)
- Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy
| | - Serena Vittorio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy
| | - Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Giovanna Pitasi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy
| | - Marc Fornt-Suñé
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Federica Bucolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
- ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy
- Correspondence:
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9
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Bhoite SS, Han Y, Ruotolo BT, Chapman MR. Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids. J Biol Chem 2022; 298:102088. [PMID: 35654142 PMCID: PMC9253359 DOI: 10.1016/j.jbc.2022.102088] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 01/31/2023] Open
Abstract
The gut microbiome has been shown to have key implications in the pathogenesis of Parkinson's disease (PD). The Escherichia coli functional amyloid CsgA is known to accelerate α-synuclein aggregation in vitro and induce PD symptoms in mice. However, the mechanism governing CsgA-mediated acceleration of α-synuclein aggregation is unclear. Here, we show that CsgA can form stable homodimeric species that correlate with faster α-synuclein amyloid aggregation. Furthermore, we identify and characterize new CsgA homologs encoded by bacteria present in the human microbiome. These CsgA homologs display diverse aggregation kinetics, and they differ in their ability to modulate α-synuclein aggregation. Remarkably, we demonstrate that slowing down CsgA aggregation leads to an increased acceleration of α-synuclein aggregation, suggesting that the intrinsic amyloidogenicity of gut bacterial CsgA homologs affects their ability to accelerate α-synuclein aggregation. Finally, we identify a complex between CsgA and α-synuclein that functions as a platform to accelerate α-synuclein aggregation. Taken together, our work reveals complex interplay between bacterial amyloids and α-synuclein that better informs our understanding of PD causation.
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Affiliation(s)
- Sujeet S Bhoite
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
| | - Matthew R Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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10
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Gitto R, Vittorio S, Bucolo F, Peña-Díaz S, Siracusa R, Cuzzocrea S, Ventura S, Di Paola R, De Luca L. Discovery of Neuroprotective Agents Based on a 5-(4-Pyridinyl)-1,2,4-triazole Scaffold. ACS Chem Neurosci 2022; 13:581-586. [PMID: 35179861 PMCID: PMC9937533 DOI: 10.1021/acschemneuro.1c00849] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) is characterized by the death of dopaminergic neurons. The common histopathological hallmark in PD patients is the formation of intracellular proteinaceous accumulations. The main constituent of these inclusions is alpha-synuclein (α-syn), an intrinsically disordered protein that in pathological conditions creates amyloid aggregates that lead to neurotoxicity and neurodegeneration. The main goal of our study was to optimize our previously identified α-syn aggregation inhibitors of 5-(4-pyridinyl)-1,2,4-triazole chemotype in terms of in vivo efficacy. Our efforts resulted in the identification of ethyl 2-((4-amino-5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl)thio)acetate (15), which displayed the ability to prevent 1-methyl-4-phenyl-1,2,3,6-tetrahydropiridine-induced bradykinesia as well as to affect the levels of PD markers after the administration of the same neurotoxin. In addition to the in vivo evaluation, for the 5-(4-pyridinyl)-1,2,4-triazole-based compounds, we measured the prevention of the fibrillization process using light scattering and a ThT binding assay; these compounds have been shown to slightly reduce the α-syn aggregation.
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Affiliation(s)
- Rosaria Gitto
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Serena Vittorio
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Federica Bucolo
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Samuel Peña-Díaz
- Institut
de Biotecnologia i Biomedicina, Universitat
Autonoma de Barcelona, 08193 Bellaterra, Spain,Departament
de Bioquimica i Biologia Molecular, Universitat
Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Rosalba Siracusa
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Salvatore Cuzzocrea
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Salvador Ventura
- Institut
de Biotecnologia i Biomedicina, Universitat
Autonoma de Barcelona, 08193 Bellaterra, Spain,Departament
de Bioquimica i Biologia Molecular, Universitat
Autonoma de Barcelona, 08193 Bellaterra, Spain,ICREA, Passeig Lluis
Companys 23, 08010 Barcelona, Spain
| | - Rosanna Di Paola
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy
| | - Laura De Luca
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98125 Messina, Italy,
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11
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Abstract
Parkinson’s disease, the second most prevalent neurodegenerative disorder worldwide, is characterized by a progressive loss of dopaminergic neurons in substantia nigra pars compacta, causing motor symptoms. This disorder’s main hallmark is the formation of intraneuronal protein inclusions, named Lewy bodies and neurites. The major component of these arrangements is α-synuclein, an intrinsically disordered and soluble protein that, in pathological conditions, can form toxic and cell-to-cell transmissible amyloid structures. Preventing α-synuclein aggregation has attracted significant effort in the search for a disease-modifying therapy for Parkinson’s disease. Small molecules like SynuClean-D, epigallocatechin gallate, trodusquemine, or anle138b exemplify this therapeutic potential. Here, we describe a subset of compounds containing a single aromatic ring, like dopamine, ZPDm, gallic acid, or entacapone, which act as molecular chaperones against α-synuclein aggregation. The simplicity of their structures contrasts with the complexity of the aggregation process, yet the block efficiently α-synuclein assembly into amyloid fibrils, in many cases, redirecting the reaction towards the formation of non-toxic off-pathway oligomers. Moreover, some of these compounds can disentangle mature α-synuclein amyloid fibrils. Their simple structures allow structure-activity relationship analysis to elucidate the role of different functional groups in the inhibition of α-synuclein aggregation and fibril dismantling, making them informative lead scaffolds for the rational development of efficient drugs.
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Affiliation(s)
- Samuel Pena-DIaz
- Institut de Biotecnologia i Biomedicina; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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12
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Mahía A, Peña-Díaz S, Navarro S, José Galano-Frutos J, Pallarés I, Pujols J, Díaz-de-Villegas MD, Gálvez JA, Ventura S, Sancho J. Design, synthesis and structure-activity evaluation of novel 2-pyridone-based inhibitors of α-synuclein aggregation with potentially improved BBB permeability. Bioorg Chem 2021; 117:105472. [PMID: 34775206 DOI: 10.1016/j.bioorg.2021.105472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/20/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023]
Abstract
The treatment of Parkinson's disease (PD), the second most common neurodegenerative human disorder, continues to be symptomatic. Development of drugs able to stop or at least slowdown PD progression would benefit several million people worldwide. SynuClean-D is a low molecular weight 2-pyridone-based promising drug candidate that inhibits the aggregation of α-synuclein in human cultured cells and prevents degeneration of dopaminergic neurons in a Caenorhabditis elegans model of PD. Improving SynuClean-D pharmacokinetic/pharmacodynamic properties, performing structure/activity studies and testing its efficacy in mammalian models of PD requires the use of gr-amounts of the compound. However, not enough compound is on sale, and no synthetic route has been reported until now, which hampers the molecule progress towards clinical trials. To circumvent those problems, we describe here an efficient and economical route that enables the synthesis of SynuClean-D with good yields as well as the synthesis of SynuClean-D derivatives. Structure-activity comparison of the new compounds with SynuClean-D reveals the functional groups of the molecule that can be disposed of without activity loss and those that are crucial to interfere with α-synuclein aggregation. Several of the derivatives obtained retain the parent's compound excellent in vitro anti-aggregative activity, without compromising its low toxicity. Computational predictions and preliminary testing indicate that the blood brain barrier (BBB) permeability of SynuClean-D is low. Importantly, several of the newly designed and obtained active derivatives are predicted to display good BBB permeability. The synthetic route developed here will facilitate their synthesis for BBB permeability determination and for efficacy testing in mammalian models of PD.
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Affiliation(s)
- Alejandro Mahía
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Samuel Peña-Díaz
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Susanna Navarro
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Juan José Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain
| | - Irantzu Pallarés
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi Pujols
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - María D Díaz-de-Villegas
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-University of Zaragoza, 50009 Zaragoza, Spain
| | - José A Gálvez
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-University of Zaragoza, 50009 Zaragoza, Spain.
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; ICREA, 08010 Barcelona, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain.
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13
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Candelise N, Scaricamazza S, Salvatori I, Ferri A, Valle C, Manganelli V, Garofalo T, Sorice M, Misasi R. Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications. Int J Mol Sci 2021; 22:ijms22116016. [PMID: 34199513 PMCID: PMC8199687 DOI: 10.3390/ijms22116016] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.
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Affiliation(s)
- Niccolò Candelise
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-338-891-2668
| | - Silvia Scaricamazza
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
| | - Illari Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Alberto Ferri
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Tina Garofalo
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Maurizio Sorice
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Roberta Misasi
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
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