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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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Mishra T, Singh S, Singh TG. Therapeutic Implications and Regulations of Protein Post-translational Modifications in Parkinsons Disease. Cell Mol Neurobiol 2024; 44:53. [PMID: 38960968 PMCID: PMC11222187 DOI: 10.1007/s10571-024-01471-8] [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: 12/01/2022] [Accepted: 03/16/2024] [Indexed: 07/05/2024]
Abstract
Parkinsons disease (PD) is a neurodegenerative disorder characterized by dopaminergic neuron loss and alpha-synuclein aggregation. This comprehensive review examines the intricate role of post-translational modifications (PTMs) in PD pathogenesis, focusing on DNA methylation, histone modifications, phosphorylation, SUMOylation, and ubiquitination. Targeted PTM modulation, particularly in key proteins like Parkin, DJ1, and PINK1, emerges as a promising therapeutic strategy for mitigating dopaminergic degeneration in PD. Dysregulated PTMs significantly contribute to the accumulation of toxic protein aggregates and dopaminergic neuronal dysfunction observed in PD. Targeting PTMs, including epigenetic strategies, addressing aberrant phosphorylation events, and modulating SUMOylation processes, provides potential avenues for intervention. The ubiquitin-proteasome system, governed by enzymes like Parkin and Nedd4, offers potential targets for clearing misfolded proteins and developing disease-modifying interventions. Compounds like ginkgolic acid, SUMO E1 enzyme inhibitors, and natural compounds like Indole-3-carbinol illustrate the feasibility of modulating PTMs for therapeutic purposes in PD. This review underscores the therapeutic potential of PTM-targeted interventions in modulating PD-related pathways, emphasizing the need for further research in this promising area of Parkinsons disease therapeutics.
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Affiliation(s)
- Twinkle Mishra
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Shareen Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
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3
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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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4
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Meanwell NA. Sub-stoichiometric Modulation of Viral Targets-Potent Antiviral Agents That Exploit Target Vulnerability. ACS Med Chem Lett 2023; 14:1021-1030. [PMID: 37583823 PMCID: PMC10424314 DOI: 10.1021/acsmedchemlett.3c00279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 08/17/2023] Open
Abstract
The modulation of oligomeric viral targets at sub-stoichiometric ratios of drug to target has been advocated for its efficacy and potency, but there are only a limited number of documented examples. In this Viewpoint, we summarize the invention of the HIV-1 maturation inhibitor fipravirimat and discuss the emerging details around the mode of action of this class of drug that reflects inhibition of a protein composed of 1,300-1,600 monomers that interact in a cooperative fashion. Similarly, the HCV NS5A inhibitor daclatasvir has been shown to act in a highly sub-stoichiometric fashion, inhibiting viral replication at concentrations that are ∼23,500 lower than that of the protein target.
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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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Development of Small Molecules Targeting α-Synuclein Aggregation: A Promising Strategy to Treat Parkinson’s Disease. Pharmaceutics 2023; 15:pharmaceutics15030839. [PMID: 36986700 PMCID: PMC10059018 DOI: 10.3390/pharmaceutics15030839] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [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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7
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Dimitrova YN, Gutierrez JA, Huard K. It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes. RSC Med Chem 2023; 14:22-46. [PMID: 36760737 PMCID: PMC9890894 DOI: 10.1039/d2md00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.
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Affiliation(s)
| | | | - Kim Huard
- Genentech 1 DNA Way South San Francisco CA 94080 USA
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8
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Gao V, Briano JA, Komer LE, Burré J. Functional and Pathological Effects of α-Synuclein on Synaptic SNARE Complexes. J Mol Biol 2023; 435:167714. [PMID: 35787839 PMCID: PMC10472340 DOI: 10.1016/j.jmb.2022.167714] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023]
Abstract
α-Synuclein is an abundant protein at the neuronal synapse that has been implicated in Parkinson's disease for over 25 years and characterizes the hallmark pathology of a group of neurodegenerative diseases now known as the synucleinopathies. Physiologically, α-synuclein exists in an equilibrium between a synaptic vesicle membrane-bound α-helical multimer and a cytosolic largely unstructured monomer. Through its membrane-bound state, α-synuclein functions in neurotransmitter release by modulating several steps in the synaptic vesicle cycle, including synaptic vesicle clustering and docking, SNARE complex assembly, and homeostasis of synaptic vesicle pools. These functions have been ascribed to α-synuclein's interactions with the synaptic vesicle SNARE protein VAMP2/synaptobrevin-2, the synaptic vesicle-attached synapsins, and the synaptic vesicle membrane itself. How α-synuclein affects these processes, and whether disease is due to loss-of-function or gain-of-toxic-function of α-synuclein remains unclear. In this review, we provide an in-depth summary of the existing literature, discuss possible reasons for the discrepancies in the field, and propose a working model that reconciles the findings in the literature.
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Affiliation(s)
- Virginia Gao
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Department of Neurology, New York Presbyterian/Weill Cornell Medicine, New York, NY, USA.
| | - Juan A Briano
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lauren E Komer
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA. https://www.twitter.com/lauren_komer
| | - Jacqueline Burré
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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9
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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: 0] [Impact Index Per Article: 0] [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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10
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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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11
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Hughes S, van Dop M, Kolsters N, van de Klashorst D, Pogosova A, Rijs AM. Using a Caenorhabditis elegans Parkinson's Disease Model to Assess Disease Progression and Therapy Efficiency. Pharmaceuticals (Basel) 2022; 15:512. [PMID: 35631338 PMCID: PMC9143865 DOI: 10.3390/ph15050512] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Despite Parkinson's Disease (PD) being the second most common neurodegenerative disease, treatment options are limited. Consequently, there is an urgent need to identify and screen new therapeutic compounds that slow or reverse the pathology of PD. Unfortunately, few new therapeutics are being produced, partly due to the low throughput and/or poor predictability of the currently used model organisms and in vivo screening methods. Our objective was to develop a simple and affordable platform for drug screening utilizing the nematode Caenorhabditis elegans. The effect of Levodopa, the "Gold standard" of PD treatment, was explored in nematodes expressing the disease-causing α-synuclein protein. We focused on two key hallmarks of PD: plaque formation and mobility. Exposure to Levodopa ameliorated the mobility defect in C. elegans, similar to people living with PD who take the drug. Further, long-term Levodopa exposure was not detrimental to lifespan. This C. elegans-based method was used to screen a selection of small-molecule drugs for an impact on α-synuclein aggregation and mobility, identifying several promising compounds worthy of further investigation, most notably Ambroxol. The simple methodology means it can be adopted in many labs to pre-screen candidate compounds for a positive impact on disease progression.
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Affiliation(s)
- Samantha Hughes
- HAN BioCentre, HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands; (M.v.D.); (N.K.); (D.v.d.K.); (A.P.)
- A-LIFE Amsterdam Institute for Life and Environment, Section Environmental Health and Toxicology, Vrije Univeristeit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Maritza van Dop
- HAN BioCentre, HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands; (M.v.D.); (N.K.); (D.v.d.K.); (A.P.)
| | - Nikki Kolsters
- HAN BioCentre, HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands; (M.v.D.); (N.K.); (D.v.d.K.); (A.P.)
| | - David van de Klashorst
- HAN BioCentre, HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands; (M.v.D.); (N.K.); (D.v.d.K.); (A.P.)
| | - Anastasia Pogosova
- HAN BioCentre, HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands; (M.v.D.); (N.K.); (D.v.d.K.); (A.P.)
| | - Anouk M. Rijs
- Division of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular and Life Sciences, Vrije Univeristeit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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12
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Peña-Díaz S, Pujols J, Vasili E, Pinheiro F, Santos J, Manglano-Artuñedo Z, Outeiro TF, Ventura S. The small aromatic compound SynuClean-D inhibits the aggregation and seeded polymerization of multiple α-synuclein strains. J Biol Chem 2022; 298:101902. [PMID: 35390347 PMCID: PMC9079179 DOI: 10.1016/j.jbc.2022.101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/25/2022] Open
Abstract
Parkinson’s disease is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra, as well as the accumulation of intraneuronal proteinaceous inclusions known as Lewy bodies and Lewy neurites. The major protein component of Lewy inclusions is the intrinsically disordered protein α-synuclein (α-Syn), which can adopt diverse amyloid structures. Different conformational strains of α-Syn have been proposed to be related to the onset of distinct synucleinopathies; however, how specific amyloid fibrils cause distinctive pathological traits is not clear. Here, we generated three different α-Syn amyloid conformations at different pH and salt concentrations and analyzed the activity of SynuClean-D (SC-D), a small aromatic molecule, on these strains. We show that incubation of α-Syn with SC-D reduced the formation of aggregates and the seeded polymerization of α-Syn in all cases. Moreover, we found that SC-D exhibited a general fibril disaggregation activity. Finally, we demonstrate that treatment with SC-D also reduced strain-specific intracellular accumulation of phosphorylated α-Syn inclusions. Taken together, we conclude that SC-D may be a promising hit compound to inhibit polymorphic α-Syn aggregation.
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Affiliation(s)
- Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Eftychia Vasili
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Jaime Santos
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Zoe Manglano-Artuñedo
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; Max Planck Institute for Experimental Medicine, Göttingen, Germany; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, Newcastle, United Kingdom; Scientific Employee With a Honorary Contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina. Universitat Autonoma de Barcelona, Bellaterra, Spain; Departament de Bioquimica i Biologia Molecular. Universitat Autonoma de Barcelona, Bellaterra, Spain; ICREA, Passeig Lluis Companys 23, Barcelona, Spain.
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13
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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: 4] [Impact Index Per Article: 2.0] [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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14
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In vitro characterization of urea derivatives to inhibit alpha-synuclein early-stage aggregation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Hideshima M, Kimura Y, Aguirre C, Kakuda K, Takeuchi T, Choong CJ, Doi J, Nabekura K, Yamaguchi K, Nakajima K, Baba K, Nagano S, Goto Y, Nagai Y, Mochizuki H, Ikenaka K. Two-step screening method to identify α-synuclein aggregation inhibitors for Parkinson's disease. Sci Rep 2022; 12:351. [PMID: 35013421 PMCID: PMC8748996 DOI: 10.1038/s41598-021-04131-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease is a neurodegenerative disease characterized by the formation of neuronal inclusions of α-synuclein in patient brains. As the disease progresses, toxic α-synuclein aggregates transmit throughout the nervous system. No effective disease-modifying therapy has been established, and preventing α-synuclein aggregation is thought to be one of the most promising approaches to ameliorate the disease. In this study, we performed a two-step screening using the thioflavin T assay and a cell-based assay to identify α-synuclein aggregation inhibitors. The first screening, thioflavin T assay, allowed the identification of 30 molecules, among a total of 1262 FDA-approved small compounds, which showed inhibitory effects on α-synuclein fibrilization. In the second screening, a cell-based aggregation assay, seven out of these 30 candidates were found to prevent α-synuclein aggregation without causing substantial toxicity. Of the seven final candidates, tannic acid was the most promising compound. The robustness of our screening method was validated by a primary neuronal cell model and a Caenorhabditis elegans model, which demonstrated the effect of tannic acid against α-synuclein aggregation. In conclusion, our two-step screening system is a powerful method for the identification of α-synuclein aggregation inhibitors, and tannic acid is a promising candidate as a disease-modifying drug for Parkinson's disease.
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Affiliation(s)
- Makoto Hideshima
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuyoshi Kimura
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - César Aguirre
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keita Kakuda
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshihide Takeuchi
- Department of Neurology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-sayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chi-Jing Choong
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Junko Doi
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kei Nabekura
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kousuke Baba
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Seiichi Nagano
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-sayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Kensuke Ikenaka
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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16
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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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17
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Shillcock JC, Hastings J, Riguet N, Lashuel HA. Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations. Comput Struct Biotechnol J 2021; 20:309-321. [PMID: 35070162 PMCID: PMC8753129 DOI: 10.1016/j.csbj.2021.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/23/2022] Open
Abstract
The pathological growth of amyloid fibrils in neurons underlies the progression of neurodegenerative diseases including Alzheimer's and Parkinson's disease. Fibrils form when soluble monomers oligomerise in the cytoplasm. Their subsequent growth occurs via nucleated polymerization mechanisms involving the free ends of the fibrils augmented by secondary nucleation of new oligomers at their surface. Amyloid fibrils possess a complex interactome with diffusing cytoplasmic proteins that regulates many aspects of their growth, seeding capacity, biochemical activity and transition to pathological inclusions in diseased brains. Changes to their surface are also expected to modify their interactome, pathogenicity and spreading in the brain. Many assays visualise fibril formation, growth and inclusion formation by decorating monomeric proteins with fluorescent tags such as GFP. Recent studies from our group suggest that tags with sizes comparable to the fibril radius may modify the fibril surface accessibility and thus their PTM pattern, interactome and ability to form inclusions. Using coarse-grained molecular simulations of a single alpha synuclein fibril tagged with GFP we find that thermal fluctuations of the tags create a non-monotonic, size-dependent sieve around the fibril that perturbs its interactome with diffusing species. Our results indicate that experiments using tagged and untagged monomers to study the growth and interactome of fibrils should be compared with caution, and the confounding effects of the tags are more complex than a reduction in surface accessibility. The prevalence of fluorescent tags in amyloid fibril growth experiments suggests this has implications beyond the specific alpha synuclein fibrils we model here.
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Affiliation(s)
- Julian C. Shillcock
- Blue Brain Project, Ecole polytechnique fédérale de Lausanne, CH-1202 Geneva, Switzerland
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Janna Hastings
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nathan Riguet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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18
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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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19
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Sharma R, Srivastava T, Pandey AR, Mishra T, Gupta B, Reddy SS, Singh SP, Narender T, Tripathi A, Chandramouli B, Sashidhara KV, Priya S, Kumar N. Identification of Natural Products as Potential Pharmacological Chaperones for Protein Misfolding Diseases. ChemMedChem 2021; 16:2146-2156. [PMID: 33760394 DOI: 10.1002/cmdc.202100147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/12/2023]
Abstract
Defective protein folding and accumulation of misfolded proteins is associated with neurodegenerative, cardiovascular, secretory, and metabolic disorders. Efforts are being made to identify small-molecule modulators or structural-correctors for conformationally destabilized proteins implicated in various protein aggregation diseases. Using a metastable-reporter-based primary screen, we evaluated pharmacological chaperone activity of a diverse class of natural products. We found that a flavonoid glycoside (C-10, chrysoeriol-7-O-β-D-glucopyranoside) stabilizes metastable proteins, prevents its aggregation, and remodels the oligomers into protease-sensitive species. Data was corroborated with additional secondary screen with disease-specific pathogenic protein. In vitro and cell-based experiments showed that C-10 inhibits α-synuclein aggregation which is implicated in synucleinopathies-related neurodegeneration. C-10 interferes in its structural transition into β-sheeted fibrils and mitigates α-synuclein aggregation-associated cytotoxic effects. Computational modeling suggests that C-10 binds to unique sites in α-synuclein which may interfere in its aggregation amplification. These findings open an avenue for comprehensive SAR development for flavonoid glycosides as pharmacological chaperones for metastable and aggregation-prone proteins implicated in protein conformational diseases.
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Affiliation(s)
- Richa Sharma
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tulika Srivastava
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Alka Raj Pandey
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Tripti Mishra
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Bhagyashri Gupta
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | | | - Suriya P Singh
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tadigoppula Narender
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Aradhya Tripathi
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | | | - Koneni V Sashidhara
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Smriti Priya
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
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20
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Abramov D, Guiberson NGL, Burré J. STXBP1 encephalopathies: Clinical spectrum, disease mechanisms, and therapeutic strategies. J Neurochem 2021; 157:165-178. [PMID: 32643187 PMCID: PMC7812771 DOI: 10.1111/jnc.15120] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
Abstract
Mutations in Munc18-1/STXBP1 (syntaxin-binding protein 1) are linked to various severe early epileptic encephalopathies and neurodevelopmental disorders. Heterozygous mutations in the STXBP1 gene include missense, nonsense, frameshift, and splice site mutations, as well as intragenic deletions and duplications and whole-gene deletions. No genotype-phenotype correlation has been identified so far, and patients are treated by anti-epileptic drugs because of the lack of a specific disease-modifying therapy. The molecular disease mechanisms underlying STXBP1-linked disorders are yet to be fully understood, but both haploinsufficiency and dominant-negative mechanisms have been proposed. This review focuses on the current understanding of the phenotypic spectrum of STXBP1-linked disorders, as well as discusses disease mechanisms in the context of the numerous pathways in which STXBP1 functions in the brain. We additionally evaluate the available animal models to study these disorders and highlight potential therapeutic approaches for treating these devastating diseases.
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Affiliation(s)
- Debra Abramov
- Appel Institute for Alzheimer's Disease Research, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Noah Guy Lewis Guiberson
- Appel Institute for Alzheimer's Disease Research, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Jacqueline Burré
- Appel Institute for Alzheimer's Disease Research, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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21
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Maqbool M, Gadhavi J, Singh A, Hivare P, Gupta S, Hoda N. Unravelling the potency of triazole analogues for inhibiting α-synuclein fibrillogenesis and in vitro disaggregation. Org Biomol Chem 2021; 19:1589-1603. [PMID: 33527970 DOI: 10.1039/d0ob02226h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A series of triazole-based compounds was synthesized using a click chemistry approach and evaluated for the inhibition of α-synuclein (α-syn) fibrillogenesis and its disaggregation. Compounds Tr3, Tr7, Tr12, Tr15, and Tr16 exhibited good effect in inhibiting α-syn fibrillogenesis confirmed by Thioflavin-T assay and fluorescence microscopy and α-syn disaggregation confirmed by fluorescence microscopy. Molecular docking was used to understand the plausible mechanism of the test compounds for inhibiting the α-syn fibrillogenesis and to verify the in vitro results. Compounds Tr3, Tr7, Tr12, Tr15 and Tr16 showed good binding interactions with the essential amino acid residues of α-syn. The compounds which were found to be good inhibitors or disaggregators had no toxic effects on the SH-SY5Y cell line. These compounds have the potential to be developed as therapeutic interventions against synucleinopathies including Parkinson's disease and Lewy body dementia.
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Affiliation(s)
- Mudasir Maqbool
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
| | - Joshna Gadhavi
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Anju Singh
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
| | - Pravin Hivare
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Sharad Gupta
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
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22
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Peña-Díaz S, Pujols J, Pinheiro F, Santos J, Pallarés I, Navarro S, Conde-Gimenez M, García J, Salvatella X, Dalfó E, Sancho J, Ventura S. Inhibition of α-Synuclein Aggregation and Mature Fibril Disassembling With a Minimalistic Compound, ZPDm. Front Bioeng Biotechnol 2020; 8:588947. [PMID: 33178678 PMCID: PMC7597392 DOI: 10.3389/fbioe.2020.588947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Synucleinopathies are a group of disorders characterized by the accumulation of α-Synuclein amyloid inclusions in the brain. Preventing α-Synuclein aggregation is challenging because of the disordered nature of the protein and the stochastic nature of fibrillogenesis, but, at the same time, it is a promising approach for therapeutic intervention in these pathologies. A high-throughput screening initiative allowed us to discover ZPDm, the smallest active molecule in a library of more than 14.000 compounds. Although the ZPDm structure is highly related to that of the previously described ZPD-2 aggregation inhibitor, we show here that their mechanisms of action are entirely different. ZPDm inhibits the aggregation of wild-type, A30P, and H50Q α-Synuclein variants in vitro and interferes with α-Synuclein seeded aggregation in protein misfolding cyclic amplification assays. However, ZPDm distinctive feature is its strong potency to dismantle preformed α-Synuclein amyloid fibrils. Studies in a Caenorhabditis elegans model of Parkinson's Disease, prove that these in vitro properties are translated into a significant reduction in the accumulation of α-Synuclein inclusions in ZPDm treated animals. Together with previous data, the present work illustrates how different chemical groups on top of a common molecular scaffold can result in divergent but complementary anti-amyloid activities.
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Affiliation(s)
- Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaime Santos
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarés
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Conde-Gimenez
- Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, and Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Esther Dalfó
- Medicine, M2, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, and Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
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23
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Torpey JH, Meade RM, Mistry R, Mason JM, Madine J. Insights Into Peptide Inhibition of Alpha-Synuclein Aggregation. Front Neurosci 2020; 14:561462. [PMID: 33177976 PMCID: PMC7594713 DOI: 10.3389/fnins.2020.561462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
α-Synuclein (aSyn) aggregation is an attractive target for therapeutic development for a range of neurodegenerative conditions, collectively termed synucleinopathies. Here, we probe the mechanism of action of a peptide 4554W, (KDGIVNGVKA), previously identified through intracellular library screening, to prevent aSyn aggregation and associated toxicity. We utilize NMR to probe association and identify that 4554W associates with a "partially aggregated" form of aSyn, with enhanced association occurring over time. We also report the ability of 4554W to undergo modification through deamidation of the central asparagine residue, occurring on the same timescale as aSyn aggregation in vitro, with peptide modification enhancing its association with aSyn. Additionally, we report that 4554W can act to reduce fibril formation of five Parkinson's disease associated aSyn mutants. Inhibitory peptide binding to partially aggregated forms of aSyn, as identified here, is particularly attractive from a therapeutic perspective, as it would eliminate the need to administer the therapy at pre-aggregation stages, which are difficult to diagnose. Taken together the data suggest that 4554W could be a suitable candidate for future therapeutic development against wild-type, and most mutant aSyn aggregation.
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Affiliation(s)
- James H Torpey
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard M Meade
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ravina Mistry
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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24
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Vittorio S, Adornato I, Gitto R, Peña-Díaz S, Ventura S, De Luca L. Rational design of small molecules able to inhibit α-synuclein amyloid aggregation for the treatment of Parkinson's disease. J Enzyme Inhib Med Chem 2020; 35:1727-1735. [PMID: 32924648 PMCID: PMC7534360 DOI: 10.1080/14756366.2020.1816999] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Parkinson’s disease is one of the most common neurodegenerative disorders in elderly age. One of the mechanisms involved in the neurodegeneration appears related to the aggregation of the presynaptic protein alpha synuclein (α-syn) into toxic oligomers and fibrils. To date, no highly effective treatment is currently available; therefore, there is an increasing interest in the search of new therapeutic tools. The modulation of α-syn aggregation represents an emergent and promising disease-modifying strategy for reducing or blocking the neurodegenerative process. Herein, by combining in silico and in vitro screenings we initially identified 3-(cinnamylsulfanyl)-5-(4-pyridinyl)-1,2,4-triazol-4-amine (3) as α-syn aggregation inhibitor that was then considered a promising hit for the further design of a new series of small molecules. Therefore, we rationally designed new hit-derivatives that were synthesised and evaluated by biological assays. Lastly, the binding mode of the newer inhibitors was predicted by docking studies.
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Affiliation(s)
- Serena Vittorio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale Palatucci, Messina, Italy
| | - Ilenia Adornato
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale Palatucci, Messina, Italy
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale Palatucci, Messina, Italy
| | - Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, Spain.,Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, Spain.,Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, Spain.,ICREA, Passeig Lluis Companys 23, Barcelona, Spain
| | - Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina Viale Palatucci, Messina, Italy
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25
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The Aggregation Conditions Define Whether EGCG is an Inhibitor or Enhancer of α-Synuclein Amyloid Fibril Formation. Int J Mol Sci 2020; 21:ijms21061995. [PMID: 32183378 PMCID: PMC7139648 DOI: 10.3390/ijms21061995] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
The amyloid fibril formation by α-synuclein is a hallmark of various neurodegenerative disorders, most notably Parkinson’s disease. Epigallocatechin gallate (EGCG) has been reported to be an efficient inhibitor of amyloid formation by numerous proteins, among them α-synuclein. Here, we show that this applies only to a small region of the relevant parameter space, in particular to solution conditions where EGCG readily oxidizes, and we find that the oxidation product is a much more potent inhibitor compared to the unmodified EGCG. In addition to its inhibitory effects, EGCG and its oxidation products can under some conditions even accelerate α-synuclein amyloid fibril formation through facilitating its heterogeneous primary nucleation. Furthermore, we show through quantitative seeding experiments that, contrary to previous reports, EGCG is not able to re-model α-synuclein amyloid fibrils into seeding-incompetent structures. Taken together, our results paint a complex picture of EGCG as a compound that can under some conditions inhibit the amyloid fibril formation of α-synuclein, but the inhibitory action is not robust against various physiologically relevant changes in experimental conditions. Our results are important for the development of strategies to identify and characterize promising amyloid inhibitors.
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26
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Pena-Diaz S, Pujols J, Ventura S. Small molecules to prevent the neurodegeneration caused by α-synuclein aggregation. Neural Regen Res 2020; 15:2260-2261. [PMID: 32594046 PMCID: PMC7749473 DOI: 10.4103/1673-5374.284993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Samuel Pena-Diaz
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jordi Pujols
- 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, Bellaterra; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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