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Qiu C, Wei R, Bian J, Lin X, Bai T, He J, Guo X, Chu Y. Novel 4-triazole phenyl amide (4-TPA) molecules: Potent promoters of α-synuclein fibril disassembly. Eur J Med Chem 2024; 273:116490. [PMID: 38772136 DOI: 10.1016/j.ejmech.2024.116490] [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: 03/20/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Parkinson's disease profoundly compromises patients' daily lives, and the disassembly of α-synuclein aggregates, a primary pathological factor, represents a promising therapeutic approach. In this study, we conducted a systematic screening and optimization process to identify the novel scaffold B37, a 4-triazolyl-phenylamine derivative, exhibiting a potent disassembly activity of 1.1 μM against α-synuclein preformed fibrils. Notably, B37 demonstrated significant neuroprotective effects, ameliorated autophagic dysfunction induced by preformed fibrils, mitigated oxidative stress, and restored the co-localization of preformed fibrils with lysosomes. Transmission electron microscopy corroborated its in vitro disassembly function. Pharmacokinetic profiling revealed favorable parameters with a receptible blood-brain barrier permeability. B37 emerges as a promising lead compound for further optimization, aiming to develop a highly effective agent targeting the disassembly of α-synuclein aggregates to treat neurodegenerative diseases like Parkinson's disease.
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Affiliation(s)
- Chenyang Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ruonan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiang Bian
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xin Lin
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Tengfei Bai
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jie He
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xiaomin Guo
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yong Chu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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2
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Hernández-García S, García-Cano B, Martínez-Rodríguez P, Henarejos-Escudero P, Gandía-Herrero F. Olive oil tyrosols reduce α-synuclein aggregation in vitro and in vivo after ingestion in a Caenorhabditis elegans Parkinson's model. Food Funct 2024. [PMID: 38817211 DOI: 10.1039/d4fo01663g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Parkinson's disease is the neurodegenerative motor disorder with the highest incidence worldwide. Among other factors, Parkinson's disease is caused by the accumulation of α-synuclein aggregates in a patient's brain. In this work, five molecules present in the diet are proposed as possible nutraceuticals to prevent and/or reduce the formation of α-synuclein oligomers that lead to Parkinson's disease. The olive oil polyphenols tyrosol, hydroxytyrosol (HT), hydroxytyrosol acetate (HTA) and dihydroxyphenyl acetic acid (DOPAC) besides vitamin C were tested using a cellular model of α-synuclein aggregation and a Caenorhabditis elegans Parkinson's disease animal model. Levodopa was included in the assays as the main drug prescribed to treat the disease as well as dopamine, its direct metabolite. HTA and DOPAC completely hindered α-synuclein aggregation in vitro, while dopamine reduced the aggregation by 28.7%. The Parallel Artificial Membrane Permeability Assay (PAMPA) showed that HTA had the highest permeability through brain lipids among the compounds tested. Furthermore, the C. elegans Parkinson's disease model made it possible to assess the chosen compounds in vivo. The more effective substances in vivo were DOPAC and HTA which reduced the αS aggregation inside the animals by 79.2% and 76.2%, respectively. Moreover, dopamine also reduced the aggregates by 67.4% in the in vivo experiment. Thus, the results reveal the potential of olive oil tyrosols as nutraceuticals against α-synuclein aggregation.
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Affiliation(s)
- Samanta Hernández-García
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria. Regional Campus of International Excellence "Campus Mare Nostrum". Universidad de Murcia, Murcia, Spain.
| | - Beatriz García-Cano
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria. Regional Campus of International Excellence "Campus Mare Nostrum". Universidad de Murcia, Murcia, Spain.
| | - Pedro Martínez-Rodríguez
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria. Regional Campus of International Excellence "Campus Mare Nostrum". Universidad de Murcia, Murcia, Spain.
| | - Paula Henarejos-Escudero
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria. Regional Campus of International Excellence "Campus Mare Nostrum". Universidad de Murcia, Murcia, Spain.
| | - Fernando Gandía-Herrero
- Departamento de Bioquímica y Biología Molecular A, Unidad Docente de Biología, Facultad de Veterinaria. Regional Campus of International Excellence "Campus Mare Nostrum". Universidad de Murcia, Murcia, Spain.
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3
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Todd TW, Islam NN, Cook CN, Caulfield TR, Petrucelli L. Cryo-EM structures of pathogenic fibrils and their impact on neurodegenerative disease research. Neuron 2024:S0896-6273(24)00359-3. [PMID: 38834068 DOI: 10.1016/j.neuron.2024.05.012] [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: 08/22/2023] [Revised: 03/13/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Naeyma N Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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4
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Wilson DL, Carreon A, Chinnam S, Sharifan H, Ahlawat J, Narayan M. Screening Carbon Nano Materials for Preventing Amyloid Protein Aggregation by Adopting a Facile Method. Cell Biochem Biophys 2024:10.1007/s12013-024-01293-x. [PMID: 38802601 DOI: 10.1007/s12013-024-01293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others are associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. The dissolution of mature fibrils and toxic amyloidogenic intermediates, including oligomers, continues to be the pinnacle in the treatment of neurodegenerative disorders. Yet, methods to effectively and quantitatively report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. Here we describe a simplified method that implements the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique implements an optimized but well-known, simple, inexpensive, and quantitative assessment previously used to assess the oligomerization of amyloid monomers and subsequent amyloid fibrils. This method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers, dimers, and trimers and/or retain amyloid proteins in their monomeric forms. Most importantly, our optimized method diminishes existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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Affiliation(s)
- Daisy L Wilson
- The Environmental Science & Engineering Program, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Ana Carreon
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA
| | - Sampath Chinnam
- Department of Chemistry, M.S. Ramaiah Institute of Technology (Autonoumous Institution, Affiliated to Visvesvaraya Technological University, Belgaum), Bengaluru, Karnataka, 560054, India
| | - Hamidreza Sharifan
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA
| | - Jyoti Ahlawat
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA.
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, the University of Texas at El Paso (UTEP), El Paso, TX, 79968, USA.
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5
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Fernández-Calvet A, Matilla-Cuenca L, Izco M, Navarro S, Serrano M, Ventura S, Blesa J, Herráiz M, Alkorta-Aranburu G, Galera S, Ruiz de Los Mozos I, Mansego ML, Toledo-Arana A, Alvarez-Erviti L, Valle J. Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration. Nat Commun 2024; 15:4150. [PMID: 38755164 PMCID: PMC11099085 DOI: 10.1038/s41467-024-48309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Age-related neurodegenerative diseases involving amyloid aggregation remain one of the biggest challenges of modern medicine. Alterations in the gastrointestinal microbiome play an active role in the aetiology of neurological disorders. Here, we dissect the amyloidogenic properties of biofilm-associated proteins (BAPs) of the gut microbiota and their implications for synucleinopathies. We demonstrate that BAPs are naturally assembled as amyloid-like fibrils in insoluble fractions isolated from the human gut microbiota. We show that BAP genes are part of the accessory genomes, revealing microbiome variability. Remarkably, the abundance of certain BAP genes in the gut microbiome is correlated with Parkinson's disease (PD) incidence. Using cultured dopaminergic neurons and Caenorhabditis elegans models, we report that BAP-derived amyloids induce α-synuclein aggregation. Our results show that the chaperone-mediated autophagy is compromised by BAP amyloids. Indeed, inoculation of BAP fibrils into the brains of wild-type mice promote key pathological features of PD. Therefore, our findings establish the use of BAP amyloids as potential targets and biomarkers of α-synucleinopathies.
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Affiliation(s)
- Ariadna Fernández-Calvet
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Leticia Matilla-Cuenca
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - María Izco
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Miriam Serrano
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Javier Blesa
- HM CINAC (Centro Integral de Neurociencias Abarca Campal), Hospital Universitario HM Puerta del Sur, HM Hospitales, Madrid, Spain
- Instituto de Investigación Sanitaria, HM Hospitales, Madrid, Spain
| | - Maite Herráiz
- Department of Gastroenterology, Clínica Universitaria and Medical School, University of Navarra, Navarra, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Gorka Alkorta-Aranburu
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
- CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Sergio Galera
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
| | | | - María Luisa Mansego
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Lydia Alvarez-Erviti
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain.
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6
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Vaidya B, Gupta P, Biswas S, Laha JK, Roy I, Sharma SS. Effect of Clemizole on Alpha-Synuclein-Preformed Fibrils-Induced Parkinson's Disease Pathology: A Pharmacological Investigation. Neuromolecular Med 2024; 26:19. [PMID: 38703217 DOI: 10.1007/s12017-024-08785-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder associated with mitochondrial dysfunctions and oxidative stress. However, to date, therapeutics targeting these pathological events have not managed to translate from bench to bedside for clinical use. One of the major reasons for the lack of translational success has been the use of classical model systems that do not replicate the disease pathology and progression with the same degree of robustness. Therefore, we employed a more physiologically relevant model involving alpha-synuclein-preformed fibrils (PFF) exposure to SH-SY5Y cells and Sprague Dawley rats. We further explored the possible involvement of transient receptor potential canonical 5 (TRPC5) channels in PD-like pathology induced by these alpha-synuclein-preformed fibrils with emphasis on amelioration of oxidative stress and mitochondrial health. We observed that alpha-synuclein PFF exposure produced neurobehavioural deficits that were positively ameliorated after treatment with the TRPC5 inhibitor clemizole. Furthermore, Clemizole also reduced p-alpha-synuclein and diminished oxidative stress levels which resulted in overall improvements in mitochondrial biogenesis and functions. Finally, the results of the pharmacological modulation were further validated using siRNA-mediated knockdown of TRPC5 channels, which also decreased p-alpha-synuclein expression. Together, the results of this study could be superimposed in the future for exploring the beneficial effects of TRPC5 channel modulation for other neurodegenerative disorders and synucleopathies.
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Affiliation(s)
- Bhupesh Vaidya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education, S.A.S. Nagar, Mohali, Punjab, 160062, India
| | - Pankaj Gupta
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Soumojit Biswas
- Department of Biotechnology, National Institute of Pharmaceutical Education, S.A.S. Nagar, Mohali, Punjab, 160062, India
| | - Joydev K Laha
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education, S.A.S. Nagar, Mohali, Punjab, 160062, India
| | - Shyam Sunder Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education, S.A.S. Nagar, Mohali, Punjab, 160062, India.
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7
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Martínez-Camarena Á, Bellia F, Paz Clares M, Vecchio G, Nicolas J, García-España E. Polymeric Nanozyme with SOD Activity Capable of Inhibiting Self- and Metal-Induced α-Synuclein Aggregation. Chemistry 2024:e202401331. [PMID: 38687026 DOI: 10.1002/chem.202401331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/02/2024]
Abstract
Despite decades of research, Parkinson's disease is still an idiopathic pathology for which no cure has yet been found. This is partly explained by the multifactorial character of most neurodegenerative syndromes, whose generation involves multiple pathogenic factors. In Parkinson's disease, two of the most important ones are the aggregation of α-synuclein and oxidative stress. In this work, we address both issues by synthesizing a multifunctional nanozyme based on grafting a pyridinophane ligand that can strongly coordinate CuII, onto biodegradable PEGylated polyester nanoparticles. The resulting nanozyme exhibits remarkable superoxide dismutase activity together with the ability to inhibit the self-induced aggregation of α-synuclein into amyloid-type fibrils. Furthermore, the combination of the chelator and the polymer produces a cooperative effect whereby the resulting nanozyme can also halve CuII-induced α-synuclein aggregation.
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Affiliation(s)
- Álvaro Martínez-Camarena
- ICMol, Departament de Química Inorgànica, Universitat de València, C/Catedrático José Beltrán 2, Paterna, 46980, Spain
- Institut Galien Paris-Saclay, CNRS, Université Paris-Saclay, Orsay, 91400, France
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, Catania, 95125, Italy
- MatMoPol Research Group, Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avda. Complutense s/n, Madrid, 28040, Spain
| | - Francesco Bellia
- Istituto di Cristallografia, CNR, P. Gaifami 18, Catania, 95126, Italy
| | - M Paz Clares
- ICMol, Departament de Química Inorgànica, Universitat de València, C/Catedrático José Beltrán 2, Paterna, 46980, Spain
| | - Graziella Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, Catania, 95125, Italy
| | - Julien Nicolas
- Institut Galien Paris-Saclay, CNRS, Université Paris-Saclay, Orsay, 91400, France
| | - Enrique García-España
- ICMol, Departament de Química Inorgànica, Universitat de València, C/Catedrático José Beltrán 2, Paterna, 46980, Spain
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8
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Stillman NH, Joseph JA, Ahmed J, Baysah CZ, Dohoney RA, Ball TD, Thomas AG, Fitch TC, Donnelly CM, Kumar S. Protein mimetic 2D FAST rescues alpha synuclein aggregation mediated early and post disease Parkinson's phenotypes. Nat Commun 2024; 15:3658. [PMID: 38688913 PMCID: PMC11061149 DOI: 10.1038/s41467-024-47980-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Abberent protein-protein interactions potentiate many diseases and one example is the toxic, self-assembly of α-Synuclein in the dopaminergic neurons of patients with Parkinson's disease; therefore, a potential therapeutic strategy is the small molecule modulation of α-Synuclein aggregation. In this work, we develop an Oligopyridylamide based 2-dimensional Fragment-Assisted Structure-based Technique to identify antagonists of α-Synuclein aggregation. The technique utilizes a fragment-based screening of an extensive array of non-proteinogenic side chains in Oligopyridylamides, leading to the identification of NS132 as an antagonist of the multiple facets of α-Synuclein aggregation. We further identify a more cell permeable analog (NS163) without sacrificing activity. Oligopyridylamides rescue α-Synuclein aggregation mediated Parkinson's disease phenotypes in dopaminergic neurons in early and post disease Caenorhabditis elegans models. We forsee tremendous potential in our technique to identify lead therapeutics for Parkinson's disease and other diseases as it is expandable to other oligoamide scaffolds and a larger array of side chains.
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Affiliation(s)
- Nicholas H Stillman
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Johnson A Joseph
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Jemil Ahmed
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA
| | - Charles Zuwu Baysah
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Ryan A Dohoney
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tyler D Ball
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Alexandra G Thomas
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tessa C Fitch
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Courtney M Donnelly
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Sunil Kumar
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA.
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA.
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA.
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9
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Wilson DL, Carreon A, Chinnam S, Sharifan H, Ahlawat J, Narayan M. Screening Carbon Nano Materials for preventing amyloid protein aggregation by adopting a facile method. RESEARCH SQUARE 2024:rs.3.rs-4164618. [PMID: 38585783 PMCID: PMC10996794 DOI: 10.21203/rs.3.rs-4164618/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others is associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. The dissolution of mature fibrils and toxic amyloidogenic intermediates including oligomers continues to be the pinnacle in the treatment of neurodegenerative disorders. Yet, methods to effectively, and quantitatively, report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. Here we describe a simplified method that implements the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique implements an optimized but well-known, simple, inexpensive and quantitative assessment previously used to assess the oligomerization of amyloid monomers and subsequent amyloid fibrils. This method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers, dimers, and trimers and/or retain amyloid proteins in their monomeric forms. Most importantly, our optimized method diminishes existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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Affiliation(s)
| | | | - Sampath Chinnam
- M.S. Ramaiah Institute of Technology (Autonoumous Institution, Affiliated to Visvesvaraya Technological University
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10
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Zheng Z, Chen M, Feng S, Zhao H, Qu T, Zhao X, Ruan Q, Li L, Guo J. VDR and deubiquitination control neuronal oxidative stress and microglial inflammation in Parkinson's disease. Cell Death Discov 2024; 10:150. [PMID: 38514643 PMCID: PMC10957901 DOI: 10.1038/s41420-024-01912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
Close correlation between vitamin D (VitD) deficiency and Parkinson's Disease (PD) risk, VitD as an adjuvant treatment promising to improve PD progression. However, VitD excessive intake could induce hypercalcemia and renal damage. Therefore, upregulation of vitD receptor (VDR) is considered a compensatory strategy to overcome VitD insufficiency and alleviate PD symptoms. In this study, we discovered that VDR played antioxidative roles in dopaminergic neurons by decreasing reactive oxygen species (ROS) and maintaining mitochondrial membrane potential. Further, we newly identified VDR downstream events in C. elegans, including glutathione S-transferase (gst) and forkhead box transcription factor class O (daf-16) mediated oxidative stress resistance. VDR upregulation also mitigated microglial activation through inhibition of NLRP3/caspase-1-mediated inflammation and membrane permeabilization. These findings highlight the multifaceted protective effects of VDR in both neurons and microglia against the development of PD. Importantly, we discovered a novel deubiquitinase DUB3, whose N-terminal catalytic domain interacted with the C-terminal ligand-binding domain of VDR to reduce VDR ubiquitination. Identification of DUB3 as an essential player in the deubiquitinating mechanism of VDR provides valuable insights into VDR regulation and its potential as a therapeutic target for PD.
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Affiliation(s)
- Zihui Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
| | - Miao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
| | - Shengliang Feng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
| | - Huanhuan Zhao
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
| | - Tiange Qu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
| | - Xudong Zhao
- Department of General Practice, Affiliated Hospital of Xuzhou Medical University, 99 Huaihai West Road, Xuzhou, 221002, Jiangsu, P. R. China
| | - Qinli Ruan
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China.
| | - Lei Li
- Department of General Practice, Affiliated Hospital of Xuzhou Medical University, 99 Huaihai West Road, Xuzhou, 221002, Jiangsu, P. R. China.
| | - Jun Guo
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, P. R. China
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11
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Oláh J, Norris V, Lehotzky A, Ovádi J. Perspective Strategies for Interventions in Parkinsonism: Remedying the Neglected Role of TPPP. Cells 2024; 13:338. [PMID: 38391951 PMCID: PMC10886726 DOI: 10.3390/cells13040338] [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: 12/26/2023] [Revised: 01/31/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Neurological disorders such as Parkinsonism cause serious socio-economic problems as there are, at present, only therapies that treat their symptoms. The well-established hallmark alpha-synuclein (SYN) is enriched in the inclusion bodies characteristic of Parkinsonism. We discovered a prominent partner of SYN, termed Tubulin Polymerization Promoting Protein (TPPP), which has important physiological and pathological activities such as the regulation of the microtubule network and the promotion of SYN aggregation. The role of TPPP in Parkinsonism is often neglected in research, which we here attempt to remedy. In the normal brain, SYN and TPPP are expressed endogenously in neurons and oligodendrocytes, respectively, whilst, at an early stage of Parkinsonism, soluble hetero-associations of these proteins are found in both cell types. The cell-to-cell transmission of these proteins, which is central to disease progression, provides a unique situation for specific drug targeting. Different strategies for intervention and for the discovery of biomarkers include (i) interface targeting of the SYN-TPPP hetero-complex; (ii) proteolytic degradation of SYN and/or TPPP using the PROTAC technology; and (iii) depletion of the proteins by miRNA technology. We also discuss the potential roles of SYN and TPPP in the phenotype stabilization of neurons and oligodendrocytes.
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Affiliation(s)
- Judit Oláh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.L.); (J.O.)
| | - Vic Norris
- Laboratory of Bacterial Communication and Anti-Infection Strategies, EA 4312, University of Rouen, 76821 Mont Saint Aignan, France;
| | - Attila Lehotzky
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.L.); (J.O.)
| | - Judit Ovádi
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.L.); (J.O.)
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12
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da Silva LPD, da Cruz Guedes E, Fernandes ICO, Pedroza LAL, da Silva Pereira GJ, Gubert P. Exploring Caenorhabditis elegans as Parkinson's Disease Model: Neurotoxins and Genetic Implications. Neurotox Res 2024; 42:11. [PMID: 38319410 DOI: 10.1007/s12640-024-00686-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world, the first being Alzheimer's disease. Patients with PD have a loss of dopaminergic neurons in the substantia nigra of the basal ganglia, which controls voluntary movements, causing a motor impairment as a result of dopaminergic signaling impairment. Studies have shown that mutations in several genes, such as SNCA, PARK2, PINK1, DJ-1, ATP13A2, and LRRK2, and the exposure to neurotoxic agents can potentially increase the chances of PD development. The nematode Caenorhabditis elegans (C. elegans) plays an important role in studying the risk factors, such as genetic factors, aging, exposure to chemicals, disease progression, and drug treatments for PD. C. elegans has a conserved neurotransmission system during evolution; it produces dopamine, through the eight dopaminergic neurons; it can be used to study the effect of neurotoxins and also has strains that express human α-synuclein. Furthermore, the human PD-related genes, LRK-1, PINK-1, PDR-1, DJR-1.1, and CATP-6, are present and functional in this model. Therefore, this review focuses on highlighting and discussing the use of C. elegans an in vivo model in PD-related studies. Here, we identified that nematodes exposed to the neurotoxins, such as 6-OHDA, MPTP, paraquat, and rotenone, had a progressive loss of dopaminergic neurons, dopamine deficits, and decreased survival rate. Several studies have reported that expression of human LRRK2 (G2019S) caused neurodegeneration and pink-1, pdr-1, and djr-1.1 deletion caused several effects PD-related in C. elegans, including mitochondrial dysfunctions. Of note, the deletion of catp-6 in nematodes caused behavioral dysfunction, mitochondrial damage, and reduced survival. In addition, nematodes expressing α-synuclein had neurodegeneration and dopamine-dependent deficits. Therefore, C. elegans can be considered an accurate animal model of PD that can be used to elucidate to assess the underlying mechanisms implicated in PD to find novel therapeutic targets.
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Affiliation(s)
- Larissa Pereira Dantas da Silva
- Keizo Asami Institute, iLIKA, Universidade Federal de Pernambuco, Moraes Rego Avenue, 1235, Recife, Pernambuco, 50670-901, Brazil
| | - Erika da Cruz Guedes
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Isabel Cristina Oliveira Fernandes
- Keizo Asami Institute, iLIKA, Universidade Federal de Pernambuco, Moraes Rego Avenue, 1235, Recife, Pernambuco, 50670-901, Brazil
- Postgraduate Program in Biological Science, Universidade Federal de Pernambuco, Pernambuco, Recife, Brazil
| | - Lucas Aleixo Leal Pedroza
- Keizo Asami Institute, iLIKA, Universidade Federal de Pernambuco, Moraes Rego Avenue, 1235, Recife, Pernambuco, 50670-901, Brazil
| | | | - Priscila Gubert
- Keizo Asami Institute, iLIKA, Universidade Federal de Pernambuco, Moraes Rego Avenue, 1235, Recife, Pernambuco, 50670-901, Brazil.
- Postgraduate Program in Biological Science, Universidade Federal de Pernambuco, Pernambuco, Recife, Brazil.
- Postgraduate Program in Pure and Applied Chemistry, Universidade Federal do Oeste da Bahia, Bahia, Brazil.
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13
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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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14
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Gilboa T, Swank Z, Thakur R, Gould RA, Ooi KH, Norman M, Flynn EA, Deveney BT, Chen A, Borberg E, Kuzkina A, Ndayisaba A, Khurana V, Weitz DA, Walt DR. Toward the quantification of α-synuclein aggregates with digital seed amplification assays. Proc Natl Acad Sci U S A 2024; 121:e2312031121. [PMID: 38194461 PMCID: PMC10801878 DOI: 10.1073/pnas.2312031121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024] Open
Abstract
The quantification and characterization of aggregated α-synuclein in clinical samples offer immense potential toward diagnosing, treating, and better understanding neurodegenerative synucleinopathies. Here, we developed digital seed amplification assays to detect single α-synuclein aggregates by partitioning the reaction into microcompartments. Using pre-formed α-synuclein fibrils as reaction seeds, we measured aggregate concentrations as low as 4 pg/mL. To improve our sensitivity, we captured aggregates on antibody-coated magnetic beads before running the amplification reaction. By first characterizing the pre-formed fibrils with transmission electron microscopy and size exclusion chromatography, we determined the specific aggregates targeted by each assay platform. Using brain tissue and cerebrospinal fluid samples collected from patients with Parkinson's Disease and multiple system atrophy, we demonstrated that the assay can detect endogenous pathological α-synuclein aggregates. Furthermore, as another application for these assays, we studied the inhibition of α-synuclein aggregation in the presence of small-molecule inhibitors and used a custom image analysis pipeline to quantify changes in aggregate growth and filament morphology.
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Affiliation(s)
- Tal Gilboa
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Zoe Swank
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Rohan Thakur
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
- Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Russell A. Gould
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Kean Hean Ooi
- Department of Medical Sciences, Harvard Medical School, Boston, MA02115
| | - Maia Norman
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
- Physician Scientist Training Program, Massachusetts General Hospital/McLean Residency in Adult Psychiatry, Boston, MA02114
| | - Elizabeth A. Flynn
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Brendan T. Deveney
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
| | - Anqi Chen
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
| | - Ella Borberg
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
| | - Anastasia Kuzkina
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
| | - Alain Ndayisaba
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
| | - Vikram Khurana
- Harvard Medical School, Boston, MA02115
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA02115
- Harvard Stem Cell Institute, Cambridge, MA02138
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - David A. Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- John A. Paulson School of Engineering & Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Harvard Medical School, Boston, MA02115
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15
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Wu Y, Chen Y, Yu X, Zhang M, Li Z. Towards Understanding Neurodegenerative Diseases: Insights from Caenorhabditis elegans. Int J Mol Sci 2023; 25:443. [PMID: 38203614 PMCID: PMC10778690 DOI: 10.3390/ijms25010443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The elevated occurrence of debilitating neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD) and Machado-Joseph disease (MJD), demands urgent disease-modifying therapeutics. Owing to the evolutionarily conserved molecular signalling pathways with mammalian species and facile genetic manipulation, the nematode Caenorhabditis elegans (C. elegans) emerges as a powerful and manipulative model system for mechanistic insights into neurodegenerative diseases. Herein, we review several representative C. elegans models established for five common neurodegenerative diseases, which closely simulate disease phenotypes specifically in the gain-of-function aspect. We exemplify applications of high-throughput genetic and drug screenings to illustrate the potential of C. elegans to probe novel therapeutic targets. This review highlights the utility of C. elegans as a comprehensive and versatile platform for the dissection of neurodegenerative diseases at the molecular level.
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Affiliation(s)
| | | | | | | | - Zhaoyu Li
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.W.); (Y.C.); (X.Y.); (M.Z.)
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16
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Pintado-Grima C, Bárcenas O, Iglesias V, Santos J, Manglano-Artuñedo Z, Pallarès I, Burdukiewicz M, Ventura S. aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation. Database (Oxford) 2023; 2023:baad084. [PMID: 38011719 PMCID: PMC10681447 DOI: 10.1093/database/baad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder, yet effective treatments able to stop or delay disease progression remain elusive. The aggregation of a presynaptic protein, α-synuclein (aSyn), is the primary neurological hallmark of PD and, thus, a promising target for therapeutic intervention. However, the lack of consensus on the molecular properties required to specifically bind the toxic species formed during aSyn aggregation has hindered the development of therapeutic molecules. Recently, we defined and experimentally validated a peptide architecture that demonstrated high affinity and selectivity in binding to aSyn toxic oligomers and fibrils, effectively preventing aSyn pathogenic aggregation. Human peptides with such properties may have neuroprotective activities and hold a huge therapeutic interest. Driven by this idea, here, we developed a discriminative algorithm for the screening of human endogenous neuropeptides, antimicrobial peptides and diet-derived bioactive peptides with the potential to inhibit aSyn aggregation. We identified over 100 unique biogenic peptide candidates and ensembled a comprehensive database (aSynPEP-DB) that collects their physicochemical features, source datasets and additional therapeutic-relevant information, including their sites of expression and associated pathways. Besides, we provide access to the discriminative algorithm to extend its application to the screening of artificial peptides or new peptide datasets. aSynPEP-DB is a unique repository of peptides with the potential to modulate aSyn aggregation, serving as a platform for the identification of previously unexplored therapeutic agents. Database URL: https://asynpepdb.ppmclab.com/.
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Affiliation(s)
- Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
| | - Zoe Manglano-Artuñedo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, Białystok 15-369, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
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17
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Khatooni Z, Akhtari K, Wilson HL. Conformational dynamics of α-synuclein and study of its intramolecular forces in the presence of selected compounds. Sci Rep 2023; 13:19020. [PMID: 37923923 PMCID: PMC10624887 DOI: 10.1038/s41598-023-46181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023] Open
Abstract
Protein misfolding and aggregation play crucial roles in amyloidogenic diseases through the self-assembly of intrinsically disordered proteins (IDPs) in type II diabetes (T2D), Alzheimer's disease (AD) and Parkinson's disease (PD). PD is the most common neurodegenerative disorder after AD, and is associated with the loss of dopaminergic signaling, which causes motor and nonmotor signs and symptoms. Lewy bodies and Lewy neurites are common pathological hallmarks of PD that are mainly composed of aggregates of disordered α-synuclein (α-Syn). There have been many efforts to develop chemical compounds to prevent aggregation or facilitate disruption of the aggregates. Furthermore, the roles and interactions of many compounds have yet to be revealed at the atomistic level, especially their impacts on the dynamics and chain-chain interactions of the oligomers, which are of interest in this study. The conformational diversity and detailed interactions among homo-oligomer chains of α-Syn are not fully discovered; identifying these might help uncover a practical approach to developing a potent therapy. In this study, we used an in-silico investigation to address the conformational diversity of α-Syn oligomer. The roles of several point mutations in protein aggregation in PD are known; we take this further by evaluating the interaction energies and contributions of all residues in stability and residue-chain interactions. In this study, we docked chemical derivatives of three compounds with high drug-likeness properties to evaluate the roles of our ligands in the conformational dynamicity of the oligomers, with emphasis on intramolecular forces. Free energy evaluation of the modeled inter and intramolecular interactions through MD simulation shows effective interaction and binding between α-Syn and our compounds. However, we find that they do not significantly disrupt the chain-chain interactions, compared to unliganded simulation.
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Affiliation(s)
- Zahed Khatooni
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada.
| | - Keivan Akhtari
- Department of Physics, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Heather L Wilson
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
- School of Public Health, Vaccinology & Immunotherapeutics Program, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
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18
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Jahan I, Ahmad A, Deep S. Effect of flavonoids on the destabilization of α-synuclein fibrils and their conversion to amorphous aggregate: A molecular dynamics simulation and experimental study. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140951. [PMID: 37574034 DOI: 10.1016/j.bbapap.2023.140951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The second most prevalent neurodegenerative disease, Parkinson's disease (PD), is caused by the accumulation and deposition of fibrillar aggregates of the α-Syn into the Lewy bodies. To create a potent pharmacological candidate to destabilize the preformed α-Syn fibril, it is important to understand the precise molecular mechanism underlying the destabilization of the α-Syn fibril. Through molecular dynamics simulations and experiments, we have examined the molecular mechanisms causing the destabilization and suppression of a newly discovered α-Syn fibril with a Greek-key-like shape and an aggregation prone state (APS) of α-Syn in the presence and absence of various Flvs. According to MD simulation and experimental evidence, morin, quercetin, and myricetin are the Flvs, most capable of destabilizing the fibrils and converting them into amorphous aggregates. Compared to galangin and kaempferol, they have more hydroxyl groups and form more hydrogen bonds with fibrils.The processes by which morin and myricetin prevent new fibril production from APS and destabilize the fibrils are different. According to linear interaction energy analysis, van der Waals interaction predominates with morin, and electrostatic interaction dominates with myricetin. Our MD simulation and experimental findings provide mechanistic insights into how Flvs destabilize α-Syn fibrils and change their morphology, opening the door to developing structure-based drugs for treating Parkinson's disease.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Aziz Ahmad
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Delhi 110016, India.
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19
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Hu J, Guan X, Zhao M, Xie P, Guo J, Tan J. Genome-wide CRISPR-Cas9 Knockout Screening Reveals a TSPAN3-mediated Endo-lysosome Pathway Regulating the Degradation of α-Synuclein Oligomers. Mol Neurobiol 2023; 60:6731-6747. [PMID: 37477766 DOI: 10.1007/s12035-023-03495-5] [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: 03/25/2023] [Accepted: 07/09/2023] [Indexed: 07/22/2023]
Abstract
Misfolding and aggregation of α-Synuclein (α-Syn), which are hallmark pathological features of neurodegenerative diseases such as Parkinson's disease (PD) and dementia with Lewy Bodies, continue to be significant areas of research. Among the diverse forms of α-Syn - monomer, oligomer, and fibril, the oligomer is considered the most toxic. However, the mechanisms governing α-Syn oligomerization are not yet fully understood. In this study, we utilized genome-wide CRISPR/Cas9 loss-of-function screening in human HEK293 cells to identify negative regulators of α-Syn oligomerization. We found that tetraspanin 3 (TSPAN3), a presumptive four-pass transmembrane protein, but not its homolog TSPAN7, significantly modulates α-Syn oligomer levels. TSPAN3 was observed to interact with α-Syn oligomers, regulate the amount of α-Syn oligomers on the cell membrane, and promote their degradation via the clathrin-AP2 mediated endo-lysosome pathway. Our findings highlight TSPAN3 as a potential regulator of α-Syn oligomers, presenting a promising target for future PD prevention and treatment strategies.
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Affiliation(s)
- JunJian Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, 410078, Hunan, China
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, China
| | - Xinjie Guan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, 410078, Hunan, China
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Miao Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, 410078, Hunan, China
| | - Pengqing Xie
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, 410078, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jieqiong Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, 410078, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China.
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20
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Garcia-Pardo J, Ventura S. Chemical targeting of amyloids. Nat Chem Biol 2023; 19:1176-1177. [PMID: 37495777 DOI: 10.1038/s41589-023-01394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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21
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Wang G, Zhu L, Wu X, Qian Z. Influence of Protonation on the Norepinephrine Inhibiting α-Synuclein 71-82 Oligomerization. J Phys Chem B 2023; 127:7848-7857. [PMID: 37683121 DOI: 10.1021/acs.jpcb.3c03270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
The pathogenesis of Parkinson's disease (PD) is closely linked to the massive presence of Lewy vesicles and Lewy axons in the cytoplasm of neurons, mainly consisting of α-synuclein (αS). Norepinephrine (NE), whose secretion can be increased by exercise, has been demonstrated to prevent the fibrillation of αS and to break down the mature αS fibrils. In this work, we focus on the influence of protonation on the inhibitory ability of NE by using amyloid core fragment αS71-82 as a template. All-atom replica-exchange molecular dynamics simulations (accumulating to 33.6 μs) in explicit water were performed to explore the inhibitory effect of protonated and nonprotonated NE on αS oligomerization. Our results show that NE/NE+ can lead to a significant decrease in β-sheet content with increasing temperature, while isolated αS maintains relatively higher β-sheet conformations until 363 K, implying that both NE and NE+ can lower the critical temperature required for αS fibril decomposition. NE and NE+ also lead to the formation of less compact αS oligomers by preventing the backbone hydrogen bonds and the side-chain packing. The protonation would affect the binding affinity, interaction modes, and binding intensity of NE with αS. Interesting, NE and NE+ have a distinct binding free energy in the electrostatic and solvation terms, which mostly counter each other and produce a weak binding intensity with αS. Our work contributes to a better understanding of the inhibitory mechanism of NE and NE+ on αS oligomerization relevant to PD pathogenesis, which may provide clues for the design of antiamyloid medicine.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
| | - Lili Zhu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
- Shang Xing School, 6 Shangli Road, Shenzhen 518100, Guangdong, China
| | - Xiaoxiao Wu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
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22
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Peng Y, Ye JR, Wang SS, He WB, Feng ZP, Sun HS, Chu SF, Zhang Z, Chen NH. A small molecule 20C from Gastrodia elata inhibits α-synuclein aggregation and prevents progression of Parkinson's disease. Cell Death Dis 2023; 14:594. [PMID: 37673867 PMCID: PMC10482970 DOI: 10.1038/s41419-023-06116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Parkinson's disease (PD) is pathologically manifested by the aggregation of α-synuclein, which has been envisioned as a promising disease-modifying target for PD. Here, we identified 20C, a bibenzyl compound derived from Gastrodia elata, able to inhibit the aggregation of A53T variants of α-synuclein directly in vitro. Computational analysis revealed that 20C binds to cavities in mature α-synuclein fibrils, and it indeed displays a strong interaction with α-synuclein and reduced their β-sheet structure by microscale thermophoresis and circular dichroism, respectively. Moreover, incubating neural cells with 20C reduced the amounts of α-synuclein inclusions significantly. The treatment of A53T α-Syn transgenic mice with 20C significantly reduces the toxic α-synuclein levels, improves behavioral performance, rescues dopaminergic neuron, and enhances functional connections between SNc and PD associated brain areas. The transcriptome analysis of SNc demonstrated that 20C improves mitochondrial dynamics, which protects mitochondrial morphology and function against α-synuclein induced degeneration. Overall, 20C appears to be a promising candidate for the treatment of PD.
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Affiliation(s)
- Ye Peng
- School of Pharmacy, Minzu University of China, Beijing, 100081, China
| | - Jun-Rui Ye
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medical & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Sha-Sha Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Wen-Bin He
- Shanxi University of Chinese Medicine, National International Joint Research Center for Molecular Chinese Medicine, Taiyuan, 030024, China
| | - Zhong-Ping Feng
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hong-Shuo Sun
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Shi-Feng Chu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medical & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zhao Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medical & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Nai-Hong Chen
- School of Pharmacy, Minzu University of China, Beijing, 100081, China.
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medical & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
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23
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Staats R, Brotzakis ZF, Chia S, Horne RI, Vendruscolo M. Optimization of a small molecule inhibitor of secondary nucleation in α-synuclein aggregation. Front Mol Biosci 2023; 10:1155753. [PMID: 37701726 PMCID: PMC10493395 DOI: 10.3389/fmolb.2023.1155753] [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: 01/31/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023] Open
Abstract
Parkinson's disease is characterised by the deposition in the brain of amyloid aggregates of α-synuclein. The surfaces of these amyloid aggregates can catalyse the formation of new aggregates, giving rise to a positive feedback mechanism responsible for the rapid proliferation of α-synuclein deposits. We report a procedure to enhance the potency of a small molecule to inhibit the aggregate proliferation process using a combination of in silico and in vitro methods. The optimized small molecule shows potency already at a compound:protein stoichiometry of 1:20. These results illustrate a strategy to accelerate the optimisation of small molecules against α-synuclein aggregation by targeting secondary nucleation.
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Affiliation(s)
| | | | | | | | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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24
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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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25
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Srivastava T, Tyagi D, Fatima S, Sathyan MTV, Raj R, Sharma A, Chaturvedi M, Sinha M, Shishodia SK, Kumar D, Sharma SK, Shankar J, Satish A, Priya S. A natural small molecule-mediated inhibition of alpha-synuclein aggregation leads to neuroprotection in Caenorhabditis elegans. J Neurochem 2023. [PMID: 37429595 DOI: 10.1111/jnc.15907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/16/2023] [Accepted: 06/04/2023] [Indexed: 07/12/2023]
Abstract
Small molecules are being explored intensively for their applications as therapeutic molecules in the management of metabolic and neurological disorders. The natural small molecules can inhibit protein aggregation and underlying cellular pathogenesis of neurodegenerative diseases involving multi-factorial mechanisms of action. Certain natural small molecular inhibitors of pathogenic protein aggregation are highly efficient and have shown promising therapeutic potential. In the present study, Shikonin (SHK), a natural plant-based naphthoquinone has been investigated for its aggregation inhibition activity against α-synuclein (α-syn) and the neuroprotective potential in Caenorhabditis elegans (C. elegans). SHK significantly inhibited aggregation of α-syn at sub-stochiometric concentrations, delayed the linear lag phase and growth kinetics of seeded and unseeded α-syn aggregation. The binding of SHK to the C-terminus of α-syn maintained α-helical and disordered secondary structures with reduced beta-sheet content and complexity of aggregates. Further, in C. elegans transgenic PD models, SHK significantly reduced α-syn aggregation, improved locomotor activity and prevented dopaminergic (DA) neuronal degeneration, indicating the neuroprotective role of SHK. The present study highlights the potential of natural small molecules in the prevention of protein aggregation that may further be explored for their therapeutic efficacy in the management of protein aggregation and neurodegenerative diseases.
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Affiliation(s)
- Tulika Srivastava
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Divya Tyagi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Ecotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
| | - Siraj Fatima
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Malur Thirumalesh Vishnu Sathyan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Ecotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
| | - Ritu Raj
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research (CBMR), Lucknow, India
| | - Aniket Sharma
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
- Department of Animal Science, College of Agriculture and Natural Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Meetali Sinha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) Vishvigyan Bhawan, Lucknow, India
| | - Sonia Kumari Shishodia
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
- University Institute of Biotechnology (UIBT), Chandigarh University, Mohali, India
| | - Dinesh Kumar
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research (CBMR), Lucknow, India
| | - Sandeep K Sharma
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
| | - Jata Shankar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Aruna Satish
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Ecotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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26
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Tong Y, Zhu W, Chen J, Wen T, Xu F, Pang J. Discovery of Small-Molecule Degraders for Alpha-Synuclein Aggregates. J Med Chem 2023. [PMID: 37267712 DOI: 10.1021/acs.jmedchem.3c00274] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Alpha-synuclein (αSyn) species, especially the oligomers and fibers, are associated with multiple neurodegenerative diseases and cannot be directly targeted under the conventional pharmacological paradigm. Proteolysis-targeting chimera technology confers degradation of various "undruggable" targets; however, hardly any small-molecule degrader for αSyn aggregates has been reported yet. Herein, by using the probe molecule sery308 as a warhead, a series of small-molecule degraders for αSyn aggregates were designed and synthesized. Their degradation effects on αSyn aggregates were evaluated on a modified pre-formed fibril-seeding cell model. Compound 2b exhibited the highest degradation efficiency (DC50 = 7.51 ± 0.53 μM) with high selectivity. Mechanistic exploration revealed that both proteasomal and lysosomal pathways were involved in this kind of degradation. Moreover, the therapeutic effects of 2b were tested on SH-SY5Y (human neuroblastoma cell line) cells and Caenorhabditis elegans. Our results provided a new class of small-molecule candidates against synucleinopathies and broadened the substrate spectrum of PROTAC-based degraders.
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Affiliation(s)
- Yichen Tong
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Wentao Zhu
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Jian Chen
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Tianzhi Wen
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization & Innovative Drug Development of Chinese Ministry of Education (MOE) & Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
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27
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Indig RY, Landau M. Designed inhibitors to reduce amyloid virulence and cytotoxicity and combat neurodegenerative and infectious diseases. Curr Opin Chem Biol 2023; 75:102318. [PMID: 37196450 DOI: 10.1016/j.cbpa.2023.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
The review highlights the role of amyloids in various diseases and the challenges associated with targeting human amyloids in therapeutic development. However, due to the better understanding of microbial amyloids' role as virulence factors, there is a growing interest in repurposing and designing anti-amyloid compounds for antivirulence therapy. The identification of amyloid inhibitors has not only significant clinical implications but also provides valuable insights into the structure and function of amyloids. The review showcases small molecules and peptides that specifically target amyloids in both humans and microbes, reducing cytotoxicity and biofilm formation, respectively. The review emphasizes the importance of further research on amyloid structures, mechanisms, and interactions across all life forms to yield new drug targets and improve the design of selective treatments. Overall, the review highlights the potential for amyloid inhibitors in therapeutic development for both human diseases and microbial infections.
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Affiliation(s)
- Rinat Yona Indig
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; Centre for Structural Systems Biology (CSSB) and Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
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28
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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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29
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Mankoo OK, Kaur A, Goyal D, Goyal B. Unravelling the destabilization potential of ellagic acid on α-synuclein fibrils using molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:8128-8143. [PMID: 36877087 DOI: 10.1039/d2cp06006j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The aberrant deposition of α-synuclein (α-Syn) protein into the intracellular neuronal aggregates termed Lewy bodies and Lewy neurites characterizes the devastating neurodegenerative condition known as Parkinson's disease (PD). The disruption of pre-existing disease-relevant α-Syn fibrils is recognized as a viable therapeutic approach for PD. Ellagic acid (EA), a natural polyphenolic compound, is experimentally proven as a potential candidate that prevents or reverses the α-Syn fibrillization process. However, the detailed inhibitory mechanism of EA against the destabilization of α-Syn fibril remains largely unclear. In this work, the influence of EA on α-Syn fibril and its putative binding mechanism were explored using molecular dynamics (MD) simulations. EA interacted primarily with the non-amyloid-β component (NAC) of α-Syn fibril, disrupting its β-sheet content and thereby increasing the coil content. The E46-K80 salt bridge, critical for the stability of Greek-key-like α-Syn fibril, was disrupted in the presence of EA. The binding free energy analysis using the MM-PBSA method demonstrates the favourable binding of EA to α-Syn fibril (ΔGbinding = -34.62 ± 11.33 kcal mol-1). Interestingly, the binding affinity between chains H and J of the α-Syn fibril was significantly reduced on the incorporation of EA, which highlights the disruptive ability of EA towards α-Syn fibril. The MD simulations provide mechanistic insights into the α-Syn fibril disruption by EA, which gives a valuable direction for the development of potential inhibitors of α-Syn fibrillization and its associated cytotoxicity.
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Affiliation(s)
- Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh 160011, India.
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala 147004, Punjab, India.
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30
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Ahlawat J, Wilson DL, Carreon A, Narayan M. Resolving the soluble-to-toxic transformation of amyloidogenic proteins: A method to assess intervention by small-molecules. RESEARCH SQUARE 2023:rs.3.rs-2631727. [PMID: 36945382 PMCID: PMC10029074 DOI: 10.21203/rs.3.rs-2631727/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The soluble-to-toxic transformation of intrinsically disordered amyloidogenic proteins such as amyloid beta (Aβ), α-synuclein, mutant Huntingtin Protein (mHTT) and islet amyloid polypeptide (IAPP) among others is associated with disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and Type 2 Diabetes (T2D), respectively. Conversely, the dissolution of mature fibrils and toxic amyloidogenic intermediates including oligomers remains the holy grail in the treatment of neurodegenerative disorders. Yet, methods to effectively, and quantitatively, report on the interconversion between amyloid monomers, oligomers and mature fibrils fall short. For the first time, we describe the use of gel electrophoresis to address the transformation between soluble monomeric amyloid proteins and mature amyloid fibrils. The technique permits rapid, inexpensive and quantitative assessment of the fraction of amyloid monomers that form intermediates and mature fibrils. In addition, the method facilitates the screening of small molecules that disintegrate oligomers and fibrils into monomers or retain amyloid proteins in their monomeric forms. Importantly, our methodological advance diminishes major existing barriers associated with existing (alternative) techniques to evaluate fibril formation and intervention.
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31
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Lü MH, Wang ZP, Xing LZ, Zhang W, Han F, Huang GL, Liu W, Zhang YX, Xu J, Cui J. Hybrids of polyphenolic/quinone acids, the potential preventive and therapeutic drugs for PD: Disaggregate α-Syn fibrils, inhibit inclusions, and repair damaged neurons in mice. Eur J Med Chem 2023; 249:115122. [PMID: 36680987 DOI: 10.1016/j.ejmech.2023.115122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Neurotoxic α-Syn fibers, the main components of Lewy bodies, play a key role in the development of PD characterized by a progressive loss of dopaminergic neurons. Here, we designed and synthesized the hybrids of polyphenolic/quinone acids. The candidate compounds showed high α-Syn aggregation inhibitory activities in vitro with IC50 down to 1.6 μM. The inhibition went through the aggregation process by stabilizing the conformation of α-Syn proteostasis and preventing β-sheets aggregation, especially in the lag phase. Furthermore, the candidate drugs could disintegrate the preformed varisized aggregates into pony-size aggregates and functional monomers and continually inhibit the re-aggregation. The activities of anti-aggregation and aggregates depolymerization result in the reduction of inclusions in neuron cells. The candidate drugs also show high anti-oxidation and low cytotoxicity. They finally repair the damaged neurons in 6-OHDA-lesioned C57 mice and significantly improve PD-like symptoms of the PD model mice. The hybrids are promising molecules for PD prevention and therapy.© 2022 Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- Ming-Huan Lü
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China; Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, China
| | - Zhen-Ping Wang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Li-Zi Xing
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Wei Zhang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Feng Han
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Guo-Long Huang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Wei Liu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China
| | - Yun-Xiao Zhang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Daxue Road 75, Zhengzhou, 450052, China.
| | - Ji Xu
- School of Basic Medical Science, Neuroscience Research Institute, Academy of Medical Sciences, Zhengzhou University, Kexue Road 100, Zhengzhou, 45000, China.
| | - Jinquan Cui
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, China.
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Caenorhabditis elegans as a Model System to Study Human Neurodegenerative Disorders. Biomolecules 2023; 13:biom13030478. [PMID: 36979413 PMCID: PMC10046667 DOI: 10.3390/biom13030478] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/18/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
In recent years, advances in science and technology have improved our quality of life, enabling us to tackle diseases and increase human life expectancy. However, longevity is accompanied by an accretion in the frequency of age-related neurodegenerative diseases, creating a growing burden, with pervasive social impact for human societies. The cost of managing such chronic disorders and the lack of effective treatments highlight the need to decipher their molecular and genetic underpinnings, in order to discover new therapeutic targets. In this effort, the nematode Caenorhabditis elegans serves as a powerful tool to recapitulate several disease-related phenotypes and provides a highly malleable genetic model that allows the implementation of multidisciplinary approaches, in addition to large-scale genetic and pharmacological screens. Its anatomical transparency allows the use of co-expressed fluorescent proteins to track the progress of neurodegeneration. Moreover, the functional conservation of neuronal processes, along with the high homology between nematode and human genomes, render C. elegans extremely suitable for the study of human neurodegenerative disorders. This review describes nematode models used to study neurodegeneration and underscores their contribution in the effort to dissect the molecular basis of human diseases and identify novel gene targets with therapeutic potential.
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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: 0] [Impact Index Per Article: 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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Yang Z, Yao Y, Zhou Y, Li X, Tang Y, Wei G. EGCG attenuates α-synuclein protofibril-membrane interactions and disrupts the protofibril. Int J Biol Macromol 2023; 230:123194. [PMID: 36623616 DOI: 10.1016/j.ijbiomac.2023.123194] [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: 10/01/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
The fibrillary aggregates of α-synuclein (α-syn) are closely associated with the etiology of Parkinson's disease (PD). Mounting evidence shows that the interaction of α-syn with biological membranes is a culprit for its aggregation and cytotoxicity. While some small molecules can effectively inhibit α-syn fibrillization in solution, their potential roles in the presence of membrane are rarely studied. Among them, green tea extract epigallocatechin gallate (EGCG) is currently under active investigation. Herein, we investigated the effects of EGCG on α-syn protofibril (an intermediate of α-syn fibril formation) in the presence of a model membrane and on the interactions between α-syn protofibril and the membrane, as well as the underlying mechanisms, by performing microsecond all-atom molecular dynamics simulations. The results show that EGCG has destabilization effects on α-syn protofibril, albeit to a lesser extent than that in solution. Intriguingly, we find that EGCG forms overwhelming H-bonding and cation-π interactions with membrane and thus attenuates protofibril-membrane interactions. Moreover, the decreased protofibril-membrane interactions impede the membrane damage by α-syn protofibril and enable the membrane integrity. These findings provide atomistic understanding towards the attenuation of α-syn protofibril-induced cytotoxicity by EGCG in cellular environment, which is helpful for the development of EGCG-based therapeutic strategies against PD.
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Affiliation(s)
- Zhongyuan Yang
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, Shanghai 200438, People's Republic of China
| | - Yifei Yao
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, Shanghai 200438, People's Republic of China
| | - Yun Zhou
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, Shanghai 200438, People's Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Yiming Tang
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, Shanghai 200438, People's Republic of China.
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, Shanghai 200438, People's Republic of China.
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Anti-Parkinson Effects of Holothuria leucospilota-Derived Palmitic Acid in Caenorhabditis elegans Model of Parkinson’s Disease. Mar Drugs 2023; 21:md21030141. [PMID: 36976190 PMCID: PMC10051922 DOI: 10.3390/md21030141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease which is still incurable. Sea cucumber-derived compounds have been reported to be promising candidate drugs for treating age-related neurological disorders. The present study evaluated the beneficial effects of the Holothuria leucospilota (H. leucospilota)-derived compound 3 isolated from ethyl acetate fraction (HLEA-P3) using Caenorhabditis elegans PD models. HLEA-P3 (1 to 50 µg/mL) restored the viability of dopaminergic neurons. Surprisingly, 5 and 25 µg/mL HLEA-P3 improved dopamine-dependent behaviors, reduced oxidative stress and prolonged lifespan of PD worms induced by neurotoxin 6-hydroxydopamine (6-OHDA). Additionally, HLEA-P3 (5 to 50 µg/mL) decreased α-synuclein aggregation. Particularly, 5 and 25 µg/mL HLEA-P3 improved locomotion, reduced lipid accumulation and extended lifespan of transgenic C. elegans strain NL5901. Gene expression analysis revealed that treatment with 5 and 25 µg/mL HLEA-P3 could upregulate the genes encoding antioxidant enzymes (gst-4, gst-10 and gcs-1) and autophagic mediators (bec-1 and atg-7) and downregulate the fatty acid desaturase gene (fat-5). These findings explained the molecular mechanism of HLEA-P3-mediated protection against PD-like pathologies. The chemical characterization elucidated that HLEA-P3 is palmitic acid. Taken together, these findings revealed the anti-Parkinson effects of H. leucospilota-derived palmitic acid in 6-OHDA induced- and α-synuclein-based models of PD which might be useful in nutritional therapy for treating PD.
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Galzitskaya OV, Grishin SY, Glyakina AV, Dovidchenko NV, Konstantinova AV, Kravchenko SV, Surin AK. The Strategies of Development of New Non-Toxic Inhibitors of Amyloid Formation. Int J Mol Sci 2023; 24:ijms24043781. [PMID: 36835194 PMCID: PMC9964835 DOI: 10.3390/ijms24043781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
In recent years, due to the aging of the population and the development of diagnostic medicine, the number of identified diseases associated with the accumulation of amyloid proteins has increased. Some of these proteins are known to cause a number of degenerative diseases in humans, such as amyloid-beta (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease (PD), and insulin and its analogues in insulin-derived amyloidosis. In this regard, it is important to develop strategies for the search and development of effective inhibitors of amyloid formation. Many studies have been carried out aimed at elucidating the mechanisms of amyloid aggregation of proteins and peptides. This review focuses on three amyloidogenic peptides and proteins-Aβ, α-synuclein, and insulin-for which we will consider amyloid fibril formation mechanisms and analyze existing and prospective strategies for the development of effective and non-toxic inhibitors of amyloid formation. The development of non-toxic inhibitors of amyloid will allow them to be used more effectively for the treatment of diseases associated with amyloid.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikita V. Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Anastasiia V. Konstantinova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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37
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Murray KA, Hu CJ, Pan H, Lu J, Abskharon R, Bowler JT, Rosenberg GM, Williams CK, Elezi G, Balbirnie M, Faull KF, Vinters HV, Seidler PM, Eisenberg DS. Small molecules disaggregate alpha-synuclein and prevent seeding from patient brain-derived fibrils. Proc Natl Acad Sci U S A 2023; 120:e2217835120. [PMID: 36757890 PMCID: PMC9963379 DOI: 10.1073/pnas.2217835120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/31/2022] [Indexed: 02/10/2023] Open
Abstract
The amyloid aggregation of alpha-synuclein within the brain is associated with the pathogenesis of Parkinson's disease (PD) and other related synucleinopathies, including multiple system atrophy (MSA). Alpha-synuclein aggregates are a major therapeutic target for treatment of these diseases. We identify two small molecules capable of disassembling preformed alpha-synuclein fibrils. The compounds, termed CNS-11 and CNS-11g, disaggregate recombinant alpha-synuclein fibrils in vitro, prevent the intracellular seeded aggregation of alpha-synuclein fibrils, and mitigate alpha-synuclein fibril cytotoxicity in neuronal cells. Furthermore, we demonstrate that both compounds disassemble fibrils extracted from MSA patient brains and prevent their intracellular seeding. They also reduce in vivo alpha-synuclein aggregates in C. elegans. Both compounds also penetrate brain tissue in mice. A molecular dynamics-based computational model suggests the compounds may exert their disaggregating effects on the N terminus of the fibril core. These compounds appear to be promising therapeutic leads for targeting alpha-synuclein for the treatment of synucleinopathies.
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Affiliation(s)
- Kevin A. Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Carolyn J. Hu
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Hope Pan
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Jeannette T. Bowler
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Gregory M. Rosenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Christopher K. Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Gazmend Elezi
- Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Melinda Balbirnie
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
| | - Kym F. Faull
- Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Harry V. Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Paul M. Seidler
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA90089
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
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38
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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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Lee D, Jung HG, Park D, Bang J, Hong JH, Lee SW, Roh S, Jang JW, Kim Y, Hwang KS, Lee YS, Park JY, Jung ID, Lee JH, Lee G, Yoon DS. Biomimetically Engineered Amyloid-Shelled Gold Nanocomplexes for Discovering α-Synuclein Oligomer-Degrading Drugs. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2538-2551. [PMID: 36548054 DOI: 10.1021/acsami.2c14650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The assembly of α-synuclein (αS) oligomers is recognized as the main pathological driver of synucleinopathies. While the elimination of toxic αS oligomers shows promise for the treatment of Parkinson's disease (PD), the discovery of αS oligomer degradation drugs has been hindered by the lack of proper drug screening tools. Here, we report a drug screening platform for monitoring the efficacy of αS-oligomer-degrading drugs using amyloid-shelled gold nanocomplexes (ASGNs). We fabricate ASGNs in the presence of dopamine, mimicking the in vivo generation process of pathological αS oligomers. To test our platform, the first of its kind for PD drugs, we use αS-degrading proteases and various small molecular substances that have shown efficacy in PD treatment. We demonstrate that the ASGN-based in vitro platform has strong potential to discover effective αS-oligomer-targeting drugs, and thus it may reduce the attrition problem in drug discovery for PD treatment.
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Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul02841, South Korea
| | - Dongsung Park
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul02447, South Korea
| | - Junho Bang
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul02841, South Korea
| | - Ji Hye Hong
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
| | - Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University, Sejong30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong30019, South Korea
| | - Jae Won Jang
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul02841, South Korea
| | - Yonghwan Kim
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul02841, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul02447, South Korea
| | - Young-Sun Lee
- ASTRION, 47, Gaeunsa-gil, Seongbuk-gu, Seoul02842, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul02841, Republic of Korea
| | - Jae-Yong Park
- ASTRION, 47, Gaeunsa-gil, Seongbuk-gu, Seoul02842, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul02841, Republic of Korea
| | - In Duk Jung
- ASTRION, 47, Gaeunsa-gil, Seongbuk-gu, Seoul02842, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul01897, South Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong30019, South Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul02841, South Korea
- ASTRION, 47, Gaeunsa-gil, Seongbuk-gu, Seoul02842, Republic of Korea
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40
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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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Ramirez E, Min S, Ganegamage SK, Shimanaka K, Sosa MG, Dettmer U, Rochet JC, Fortin JS. Discovery of 4-aminoindole carboxamide derivatives to curtail alpha-synuclein and tau isoform 2N4R oligomer formation. RESULTS IN CHEMISTRY 2023; 5:100938. [PMID: 37346091 PMCID: PMC10284320 DOI: 10.1016/j.rechem.2023.100938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Alzheimer's disease (AD) is a multifactorial, chronic neurodegenerative disease characterized by the presence of extracellular β-amyloid (Aβ) plaques, intraneuronal neurofibrillary tangles (NFTs), activated microglial cells, and an inflammatory state (involving reactive oxygen species production) in the brain. NFTs are comprised of misfolded and hyperphosphorylated forms of the microtubule-binding protein tau. Interestingly, the trimeric form of the 2N4R splice isoform of tau has been found to be more toxic than the trimeric 1N4R isoform in neuron precursor cells. Few drug discovery programs have focused on specific tau isoforms. The present drug discovery project is centered on the anti-aggregation effect of a series of seventeen 4- or 5-aminoindole carboxamides on the 2N4R isoform of tau. The selection of the best compounds was performed using α-synuclein (α-syn). The anti-oligomer and -fibril activities of newly synthesized aminoindole carboxamide derivatives were evaluated with biophysical methods, such as thioflavin T fluorescence assays, photo-induced cross-linking of unmodified proteins, and transmission electron microscopy. To evaluate the reduction of inclusions and cytoprotective effects, M17D neuroblastoma cells expressing inclusion-forming α-syn were treated with the best amide representatives. The 4-aminoindole carboxamide derivatives exhibited a better anti-fibrillar activity compared to their 5-aminoindole counterparts. The amide derivatives 2, 8, and 17 exerted anti-oligomer and anti-fibril activities on α-syn and the 2N4R isoform of tau. At a concentration of 40 μM, compound 8 reduced inclusion formation in M17D neuroblastoma cells expressing inclusion-prone αSynuclein3K::YFP. Our results demonstrate the potential of 4-aminoindole carboxamide derivatives with regard to inhibiting the oligomer formation of α-syn and tau (2N4R isoform) for further optimization prior to pre-clinical studies.
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Affiliation(s)
- Eduardo Ramirez
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University
| | - Sehong Min
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University
| | | | - Kazuma Shimanaka
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Magaly Guzman Sosa
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, United States
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University
| | - Jessica S Fortin
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University
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42
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In Silico Study of the Interactions of Anle138b Isomer, an Inhibitor of Amyloid Aggregation, with Partner Proteins. Int J Mol Sci 2022; 23:ijms232416096. [PMID: 36555748 PMCID: PMC9786835 DOI: 10.3390/ijms232416096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Herein, we aimed to highlight current "gaps" in the understanding of the potential interactions between the Anle138b isomer ligand, a promising agent for clinical research, and the intrinsically disordered alpha-synuclein protein. The presence of extensive unstructured areas in alpha-synuclein determines its existence in the cell of partner proteins, including the cyclophilin A chaperone, which prevents the aggregation of alpha-synuclein molecules that are destructive to cell life. Using flexible and cascaded molecular docking techniques, we aimed to expand our understanding of the molecular architecture of the protein complex between alpha-synuclein, cyclophilin A and the Anle138b isomer ligand. We demonstrated the possibility of intricate complex formation under cellular conditions and revealed that the main interactions that stabilize the complex are hydrophobic and involve hydrogen.
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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Sanguanphun T, Sornkaew N, Malaiwong N, Chalorak P, Jattujan P, Niamnont N, Sobhon P, Meemon K. Neuroprotective effects of a medium chain fatty acid, decanoic acid, isolated from H. leucospilota against Parkinsonism in C. elegans PD model. Front Pharmacol 2022; 13:1004568. [PMID: 36582526 PMCID: PMC9792845 DOI: 10.3389/fphar.2022.1004568] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Sea cucumbers are marine organism that have long been used for food and traditional medicine in Asian countries. Recently, we have shown that ethyl acetate fraction (HLEA) of the crude extract of the black sea cucumber, Holothuria leucospilota, could alleviate Parkinsonism in Caenorhabditis elegans PD models. In this study, we found that the effective neuroprotective activity is attributed to HLEA-P1 compound chemically isolated and identified in H. leucospilota ethyl acetate. We reported here that HLEA-P1 could attenuate DAergic neurodegeneration, improve DAergic-dependent behaviors, reduce oxidative stress in 6-OHDA-induced C. elegans. In addition, HLEA-P1 reduced α-synuclein aggregation, improved behavior deficit and recovered lipid deposition in transgenic C. elegans overexpressing α-synuclein. We also found that HLEA-P1 activates nuclear localization of DAF-16 transcription factor of insulin/IGF-1 signaling (IIS) pathway. Treatment with 25 μg/ml of HLEA-P1 upregulated transcriptional activity of DAF-16 target genes including anti-oxidant genes (such as sod-3) and small heat shock proteins (such as hsp16.1, hsp16.2, and hsp12.6) in 6-OHDA-induced worms. In α-synuclein-overexpressed C. elegans strain, treatment with 5 μg/ml of HLEA-P1 significantly activated mRNA expression of sod-3 and hsp16.2. Chemical analysis demonstrated that HLEA-P1 compound is decanoic acid/capric acid. Taken together, our findings revealed that decanoic acid isolated from H. leucospilota exerts anti-Parkinson effect in C. elegans PD models by partly modulating IIS/DAF-16 pathway.
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Affiliation(s)
- Tanatcha Sanguanphun
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nilubon Sornkaew
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Nawaphat Malaiwong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pawanrat Chalorak
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Radiological Technology and Medical Physics, Chulalongkorn University, Bangkok, Thailand
| | - Prapaporn Jattujan
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nakorn Niamnont
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand,Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, Thailand,*Correspondence: Krai Meemon,
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Bopardikar M, Koti Ainavarapu SR, Hosur RV. Pyrogallol, Corilagin and Chebulagic acid target the "fuzzy coat" of alpha-synuclein to inhibit the fibrillization of the protein. RSC Adv 2022; 12:35770-35777. [PMID: 36545068 PMCID: PMC9749937 DOI: 10.1039/d2ra04358k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/13/2022] [Indexed: 12/15/2022] Open
Abstract
The accumulation of the intrinsically disordered protein alpha-synuclein (αSyn) in the form of insoluble fibrillar aggregates in the central nervous system is linked to a variety of neurodegenerative disorders such as Parkinson's disease, Lewy body dementia, and multiple system atrophy. Here we show that Pyrogallol, Corilagin and Chebulagic acid, compounds containing a different number of catechol rings, are independently capable of delaying and reducing the extent of αSyn fibrillization. The efficiency of inhibition was found to correlate with the number of catechol rings. Further, our NMR studies reveal that these compounds interact with the N-terminal region of αSyn which is unstructured even in the fibrillar form of the protein and is known as the "fuzzy coat" of fibrils. Thus, Corilagin and Chebulagic acid target the fuzzy coat of αSyn and not the amyloid core which is a common target for the inhibition of protein fibrillization. Our results indicate that the N-terminus also plays a key role in the fibrillization of αSyn.
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Affiliation(s)
- Mandar Bopardikar
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina CampusSantacruzMumbai 400098India
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Shin JY, Lee B, Ham S, Kim JH, Kim H, Kim H, Jo MG, Kim HJ, Park SW, Kweon HS, Kim YJ, Yun SP, Lee Y. Pharmacological inhibition of AIMP2 aggregation attenuates α-synuclein aggregation and toxicity in Parkinson’s disease. Biomed Pharmacother 2022; 156:113908. [DOI: 10.1016/j.biopha.2022.113908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/02/2022] Open
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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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Rafiei Y, Salmani B, Mirzaei-Behbahani B, Taleb M, Meratan AA, Ramezani M, Nikfarjam N, Becker S, Rezaei-Ghaleh N. Polyphenols-Based Nanosheets of Propolis Modulate Cytotoxic Amyloid Fibril Assembly of α-Synuclein. ACS Chem Neurosci 2022; 13:3168-3179. [PMID: 36314062 DOI: 10.1021/acschemneuro.2c00465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Natural compounds with anti-aggregation capacity are increasingly recognized as viable candidates against neurodegenerative diseases. Recently, the polyphenolic fraction of propolis (PFP), a complex bee product, has been shown to inhibit amyloid aggregation of a model protein especially in the nanosheet form. Here, we examine the aggregation-modulating effects of the PFP nanosheets on α-synuclein (α-syn), an intrinsically disordered protein involved in the pathogenesis of Parkinson's disease. Based on a range of biophysical data including intrinsic and extrinsic fluorescence, circular dichroism (CD) data, and nuclear magnetic resonance spectroscopy, we propose a model for the interaction of α-syn with PFP nanosheets, where the positively charged N-terminal and the middle non-amyloid component regions of α-syn act as the main binding sites with the negatively charged PFP nanosheets. The Thioflavin T (ThT) fluorescence, Congo red absorbance, and CD data reveal a prominent dose-dependent inhibitory effect of PFP nanosheets on α-syn amyloid aggregation, and the microscopy images and MTT assay data suggest that the PFP nanosheets redirect α-syn aggregation toward nontoxic off-pathway oligomers. When preformed α-syn amyloid fibrils are present, fluorescence images show co-localization of PFP nanosheets and ThT, further confirming the binding of PFP nanosheets with α-syn amyloid fibrils. Taken together, our results demonstrate the binding and anti-aggregation activity of PFP nanosheets in a disease-related protein system and propose them as potential nature-based tools for probing and targeting pathological protein aggregates in neurodegenerative diseases.
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Affiliation(s)
- Yasin Rafiei
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Bahram Salmani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Behnaz Mirzaei-Behbahani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Mahshid Taleb
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Mohammad Ramezani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Nasser Nikfarjam
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, Göttingen D-37077, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, Göttingen D-37077, Germany.,Institute of Physical Biology, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, Düsseldorf D-40225, Germany.,Institute of Biological Information Processing (IBI-7): Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, Jülich D-52428, Germany
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Uddin A, Malla JA, Kumar H, Kumari M, Sinha S, Sharma VK, Kumar Y, Talukdar P, Lahiri M, Maiti TK, Hazra P. Development of a Systematic Strategy toward Promotion of α-Synuclein Aggregation Using 2-Hydroxyisophthalamide-Based Systems. Biochemistry 2022; 61:2267-2279. [PMID: 36219819 DOI: 10.1021/acs.biochem.2c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Establishing a potent scheme against α-synuclein aggregation involved in Parkinson's disease has been evaluated as a promising route to identify compounds that either inhibit or promote the aggregation process of α-synuclein. In the last two decades, this perspective has guided a dramatic increase in the efforts, focused on developing potent drugs either for retardation or promotion of the self-assembly process of α-synuclein. To address this issue, using a chemical kinetics platform, we developed a strategy that enabled a progressively detailed analysis of the molecular events leading to protein aggregation at the microscopic level in the presence of a recently synthesized 2-hydroxyisophthalamide class of small organic molecules based on their binding affinity. Furthermore, qualitatively, we have developed a strategy of disintegration of α-synuclein fibrils in the presence of these organic molecules. Finally, we have shown that these organic molecules effectively suppress the toxicity of α-synuclein oligomers in neuron cells.
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Affiliation(s)
- Aslam Uddin
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Javid Ahmad Malla
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Harish Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Manisha Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad121001, India
| | - Suman Sinha
- Institute of Pharmaceutical Research, GLA University, Mathura281406, India
| | - Virender Kumar Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Yashwant Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Mayurika Lahiri
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad121001, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
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50
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Ma L, Li X, Liu C, Yan W, Ma J, Petersen RB, Peng A, Huang K. Modelling Parkinson's Disease in C. elegans: Strengths and Limitations. Curr Pharm Des 2022; 28:3033-3048. [PMID: 36111767 DOI: 10.2174/1381612828666220915103502] [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: 03/29/2022] [Accepted: 08/08/2022] [Indexed: 01/28/2023]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease that affects the motor system and progressively worsens with age. Current treatment options for PD mainly target symptoms, due to our limited understanding of the etiology and pathophysiology of PD. A variety of preclinical models have been developed to study different aspects of the disease. The models have been used to elucidate the pathogenesis and for testing new treatments. These models include cell models, non-mammalian models, rodent models, and non-human primate models. Over the past few decades, Caenorhabditis elegans (C. elegans) has been widely adopted as a model system due to its small size, transparent body, short generation time and life cycle, fully sequenced genome, the tractability of genetic manipulation and suitability for large scale screening for disease modifiers. Here, we review studies using C. elegans as a model for PD and highlight the strengths and limitations of the C. elegans model. Various C. elegans PD models, including neurotoxin-induced models and genetic models, are described in detail. Moreover, met.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China.,Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengyu Liu
- Department of Transfusion Medicine, Wuhan Hospital of Traditional Chinese and Western Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanyao Yan
- Department of Pharmacy, Wuhan Fourth Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinlu Ma
- Human Resources Department, Wuhan Mental Health Center, Wuhan, China.,Human Resources Department, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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