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Dangi A, Qureshi T, Chinnathambi S, Kiran Marelli U. Macrocyclic peptides derived from AcPHF6* and AcPHF6 to selectively modulate the Tau aggregation. Bioorg Chem 2024; 151:107625. [PMID: 39013241 DOI: 10.1016/j.bioorg.2024.107625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Ten macrocyclic peptides, each comprising 14 amino acids, were designed and synthesized based on the Tau aggregation model hexapeptides AcPHF6* and AcPHF6. The design took into account the aggregation tendencies of each residue in AcPHF6* and AcPHF6, their aggregation models, while employing peptide-based structural design principles including N-methylation to promote turns and to block hydrogen bond propagation and elongation of the aggregation chain. NMR analysis supported that all these peptides adopted an antiparallel β-sheet conformation. Self-aggregation studies characterized the aggregation properties of these peptides, identifying two peptides with the highest (P3) and lowest (P8) aggregation tendencies. In cross-aggregation studies with the parent peptides AcPHF6* and AcPHF6, P3 and P8 were found to promote and reduce aggregation, respectively. Furthermore, P3 and P8 demonstrated an enhancement and diminution effect on the aggregation of K18wt, indicating their capacity to modulate aggregation even at the macromolecular level. Thus, the two simple peptides, P3 and P8 selectively exhibit pro- or anti-aggregation effects on PHF peptides and Tau. This study, has thus developed structurally well-defined non-complex peptides, derived from AcPHF6* and AcPHF6, to modulate Tau aggregation as desired, offering applications in Tau model studies and the development of Tau aggregation inhibitors or promoters.
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Affiliation(s)
- Abha Dangi
- Central NMR Facility, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India
| | - Tazeen Qureshi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India.
| | - Udaya Kiran Marelli
- Central NMR Facility, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India.
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2
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Chinnathambi S, Dubey T. Photo-Excited Dyes: Emerging Technique Against Tau Protein Aggregation. Methods Mol Biol 2024; 2754:105-116. [PMID: 38512663 DOI: 10.1007/978-1-0716-3629-9_6] [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] [Indexed: 03/23/2024]
Abstract
Tau aggregates are considered a pathological hallmark of Alzheimer's disease. The screening of molecules against Tau aggregation is a novel strategy for Alzheimer's disease. The photo-excited molecules have proven to be effective as a therapeutic agent in several diseases. In recent studies, the photo-excited dyes showed an inhibitory effect on Alzheimer's disease-related Tau protein aggregation and toxicity. The present chapter deals with the effect of rose bengal on the aggregation of Tau. The in vitro studies carried out with the help of electron microscopy, ThS fluorescence, and circular dichroism suggested that RB attenuated the Tau aggregation under in vitro conditions, whereas PE-RB disaggregated the mature Tau fibrils. Photo-excited rose bengal and the classical rose bengal induced a low degree of toxicity in cells. Thus, for the treatment of Alzheimer's disease, the rose bengal could be considered a potential molecule.
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Affiliation(s)
- Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Institute of National Importance, Bangalore, Karnataka, India.
| | - Tushar Dubey
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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3
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Desale SE, Chinnathambi S. α- Linolenic acid modulates phagocytosis and endosomal pathways of extracellular Tau in microglia. Cell Adh Migr 2021; 15:84-100. [PMID: 33724164 PMCID: PMC7971307 DOI: 10.1080/19336918.2021.1898727] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/19/2020] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Microglia, the resident immune cells, were found to be activated to inflammatory phenotype in Alzheimer's disease (AD). The extracellular burden of amyloid-β plaques and Tau seed fabricate the activation of microglia. The seeding effect of extracellular Tau species is an emerging aspect to study about Tauopathies in AD. Tau seeds enhance the propagation of disease along with its contribution to microglia-mediated inflammation. The excessive neuroinflammation cumulatively hampers phagocytic function of microglia reducing the clearance of extracellular protein aggregates. Omega-3 fatty acids, especially docosahexaenoic acid and eicosapentaenoic acid, are recognized to induce anti-inflammatory phenotype of microglia. In addition to increased cytokine production, omega-3 fatty acids enhance phagocytic receptors expression in microglia. In this study, we have observed the phagocytosis of extracellular Tau in the presence of α-linolenic acid (ALA). The increased phagocytosis of extracellular Tau monomer and aggregates have been observed upon ALA exposure to microglia cells. After internalization, the degradation status of Tau has been studied with early and late endosomal markers Rab5 and Rab7. Further, the lysosome-mediated degradation of internalized Tau was studied with LAMP-2A, a lysosome marker. The enhanced migratory ability in the presence of ALA could be beneficial for microglia to access the target and clear it. The increased migration of microglia was found to induce the microtubule-organizing center repolarization. The data indicate that the dietary fatty acids ALA could significantly enhance phagocytosis and intracellular degradation of internalized Tau. Our results suggest that microglia could be influenced to reduce extracellular Tau seed with dietary fatty acids.
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Affiliation(s)
- Smita Eknath Desale
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical LaboratoryPune, India
- Academy of Scientific and Innovative Research (Acsir), Ghaziabad, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical LaboratoryPune, India
- Academy of Scientific and Innovative Research (Acsir), Ghaziabad, India
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4
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Lyu C, Da Vela S, Al-Hilaly Y, Marshall KE, Thorogate R, Svergun D, Serpell LC, Pastore A, Hanger DP. The Disease Associated Tau35 Fragment has an Increased Propensity to Aggregate Compared to Full-Length Tau. Front Mol Biosci 2021; 8:779240. [PMID: 34778381 PMCID: PMC8581542 DOI: 10.3389/fmolb.2021.779240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Tau35 is a truncated form of tau found in human brain in a subset of tauopathies. Tau35 expression in mice recapitulates key features of human disease, including progressive increase in tau phosphorylation, along with cognitive and motor dysfunction. The appearance of aggregated tau suggests that Tau35 may have structural properties distinct from those of other tau species that could account for its pathological role in disease. To address this hypothesis, we performed a structural characterization of monomeric and aggregated Tau35 and compared the results to those of two longer isoforms, 2N3R and 2N4R tau. We used small angle X-ray scattering to show that Tau35, 2N3R and 2N4R tau all behave as disordered monomeric species but Tau35 exhibits higher rigidity. In the presence of the poly-anion heparin, Tau35 increases thioflavin T fluorescence significantly faster and to a greater extent than full-length tau, demonstrating a higher propensity to aggregate. By using atomic force microscopy, circular dichroism, transmission electron microscopy and X-ray fiber diffraction, we provide evidence that Tau35 aggregation is mechanistically and morphologically similar to previously reported tau fibrils but they are more densely packed. These data increase our understanding of the aggregation inducing properties of clinically relevant tau fragments and their potentially damaging role in the pathogenesis of human tauopathies.
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Affiliation(s)
- Chen Lyu
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Youssra Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Karen E. Marshall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Thorogate
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Diane P. Hanger
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
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5
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Sonawane SK, Chinnathambi S. Epigallocatechin-3-gallate modulates Tau Post-translational modifications and cytoskeletal network. Oncotarget 2021; 12:1083-1099. [PMID: 34084282 PMCID: PMC8169072 DOI: 10.18632/oncotarget.27963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Alzheimer's disease is a type of dementia denoted by progressive neuronal death due to the accumulation of proteinaceous aggregates of Tau. Post-translational modifications like hyperphosphorylation, truncation, glycation, etc. play a pivotal role in Tau pathogenesis. Glycation of Tau aids in paired helical filament formation and abates its microtubule-binding function. The chemical modulators of Tau PTMs, such as kinase inhibitors and antibody-based therapeutics, have been developed, but natural compounds, as modulators of Tau PTMs are not much explored. MATERIALS AND METHODS We applied biophysical and biochemical techniques like fluorescence kinetics, oligomerization analysis and transmission electron microscopy to investigate the impact of EGCG on Tau glycation in vitro. The effect of glycation on cytoskeleton instability and its EGCG-mediated rescue were studied by immunofluorescence microscopy in neuroblastoma cells. RESULTS EGCG inhibited methyl glyoxal (MG)-induced Tau glycation in vitro. EGCG potently inhibited MG-induced advanced glycation endproducts formation in neuroblastoma cells as well modulated the localization of AT100 phosphorylated Tau in the cells. In addition to preventing the glycation, EGCG enhanced actin-rich neuritic extensions and rescued actin and tubulin cytoskeleton severely disrupted by MG. EGCG maintained the integrity of the Microtubule Organizing Center (MTOC) stabilized microtubules by Microtubule-associated protein RP/EB family member 1 (EB1). CONCLUSIONS We report EGCG, a green tea polyphenol, as a modulator of in vitro methylglyoxal-induced Tau glycation and its impact on reducing advanced glycation end products in neuroblastoma cells. We unravel unprecedented function of EGCG in remodeling neuronal cytoskeletal integrity.
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Affiliation(s)
- Shweta Kishor Sonawane
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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6
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Gorantla N, Sunny LP, Rajasekhar K, Nagaraju PG, CG PP, Govindaraju T, Chinnathambi S. Amyloid-β-Derived Peptidomimetics Inhibits Tau Aggregation. ACS OMEGA 2021; 6:11131-11138. [PMID: 34056268 PMCID: PMC8153954 DOI: 10.1021/acsomega.9b03497] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/18/2020] [Indexed: 05/08/2023]
Abstract
The aggregation of tau protein is one of the hallmarks for Alzheimer's disease, resulting in neurodegeneration. The peptidomimetics strategy to prevent tau aggregation is more specific over other small molecules. In the present study, we analyzed the effect of amyloid-β-derived peptidomimetics for inhibiting heparin-induced tau aggregation in vitro. These peptides and their derivatives were known to prevent aggregation of amyloid-β. KLVFF is a hydrophobic sequence of the pentapeptide that prevented tau aggregation as observed by thioflavin S fluorescence, transmission electron microscopy, and circular dichroism spectroscopy. P4 and P5 also prevented assembly of tau into aggregates and formed short fibrils. The β-sheet breaker LPFFD was however ineffective in preventing tau aggregation. The peptides further demonstrated reversal of tau-induced cytotoxicity in a dose-dependent manner. Our results suggested that these peptides can also be used to inhibit tau aggregation and also, toxicity induced by tau could be considered as potential molecules that have an effect on tau as well as amyloid-β.
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Affiliation(s)
- Nalini
V. Gorantla
- Neurobiology
Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy
of Scientific and Innovative Research (AcSIR), 411008 Pune, India
| | - Lisni P. Sunny
- Neurobiology
Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy
of Scientific and Innovative Research (AcSIR), 411008 Pune, India
| | - Kolla Rajasekhar
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Pramod G. Nagaraju
- Department
of Molecular Nutrition, CSIR-CFTRI, 570020 Mysore, India
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Poornima Priyadarshini CG
- Department
of Molecular Nutrition, CSIR-CFTRI, 570020 Mysore, India
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Subashchandrabose Chinnathambi
- Neurobiology
Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy
of Scientific and Innovative Research (AcSIR), 411008 Pune, India
- . Phone: +91-20-25902232. Fax: +91-20-25902648
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7
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Balmik AA, Sonawane SK, Chinnathambi S. The extracellular HDAC6 ZnF UBP domain modulates the actin network and post-translational modifications of Tau. Cell Commun Signal 2021; 19:49. [PMID: 33933071 PMCID: PMC8088071 DOI: 10.1186/s12964-021-00736-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microtubule-associated protein Tau undergoes aggregation in Alzheimer`s disease (AD) and a group of other related diseases collectively known as Tauopathies. In AD, Tau forms aggregates, which are deposited intracellularly as neurofibrillary tangles. Histone deacetylase-6 (HDAC6) plays an important role in aggresome formation, where it recruits polyubiquitinated aggregates to the motor protein dynein. METHODS Here, we have studied the effects of HDAC6 ZnF UBP on Tau phosphorylation, ApoE localization, GSK-3β regulation and cytoskeletal organization in neuronal cells by immunocytochemical analysis. This analysis reveals that the cell exposure to the UBP-type zinc finger domain of HDAC6 (HDAC6 ZnF UBP) can modulate Tau phosphorylation and actin cytoskeleton organization. RESULTS HDAC6 ZnF UBP treatment to cells did not affect their viability and resulted in enhanced neurite extension and formation of structures similar to podosomes, lamellipodia and podonuts suggesting the role of this domain in actin re-organization. Also, HDAC6 ZnF UBP treatment caused increase in nuclear localization of ApoE and tubulin localization in microtubule organizing centre (MTOC). Therefore, our studies suggest the regulatory role of this domain in different aspects of neurodegenerative diseases. Upon HDAC6 ZnF UBP treatment, inactive phosphorylated form of GSK-3β increases without any change in total GSK-3β level. CONCLUSIONS HDAC6 ZnF UBP was found to be involved in cytoskeletal re-organization by modulating actin dynamics and tubulin localization. Overall, our study suggests that ZnF domain of HDAC6 performs various regulatory functions apart from its classical function in aggresome formation in protein misfolding diseases. Video abstract.
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Affiliation(s)
- Abhishek Ankur Balmik
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shweta Kishor Sonawane
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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8
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Dubey T, Chinnathambi S. Photodynamic sensitizers modulate cytoskeleton structural dynamics in neuronal cells. Cytoskeleton (Hoboken) 2021; 78:232-248. [DOI: 10.1002/cm.21655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 01/10/2023]
Affiliation(s)
- Tushar Dubey
- Neurobiology Group, Division of Biochemical Sciences CSIR‐National Chemical Laboratory Pune India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences CSIR‐National Chemical Laboratory Pune India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
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9
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Sonawane SK, Uversky VN, Chinnathambi S. Baicalein inhibits heparin-induced Tau aggregation by initializing non-toxic Tau oligomer formation. Cell Commun Signal 2021; 19:16. [PMID: 33579328 PMCID: PMC7879681 DOI: 10.1186/s12964-021-00704-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/02/2021] [Indexed: 12/14/2022] Open
Abstract
Background Amyloid aggregate deposition is the key feature of Alzheimer’s disease. The proteinaceous aggregates found in the afflicted brain are the intra-neuronal neurofibrillary tangles formed by the microtubule-associated protein Tau and extracellular deposits, senile plaques, of amyloid beta (Aβ) peptide proteolytically derived from the amyloid precursor protein. Accumulation of these aggregates has manifestations in the later stages of the disease, such as memory loss and cognitive inabilities originating from the neuronal dysfunction, neurodegeneration, and brain atrophy. Treatment of this disease at the late stages is difficult, and many clinical trials have failed. Hence, the goal is to find means capable of preventing the aggregation of these intrinsically disordered proteins by inhibiting the early stages of their pathological transformations. Polyphenols are known to be neuroprotective agents with the noticeable potential against many neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, and Prion diseases. Methods We analyzed the capability of Baicalein to inhibit aggregation of human Tau protein by a multifactorial analysis that included several biophysical and biochemical techniques. Results The potency of Baicalein, a polyphenol from the Scutellaria baicalensis Georgi, against in vitro Tau aggregation and PHF dissolution has been screened and validated. ThS fluorescence assay revealed the potent inhibitory activity of Baicalein, whereas ANS revealed its mechanism of Tau inhibition viz. by oligomer capture and dissociation. In addition, Baicalein dissolved the preformed mature fibrils of Tau thereby possessing a dual target action. Tau oligomers formed by Baicalein were non-toxic to neuronal cells, highlighting its role as a potent molecule to be screened against AD. Conclusion In conclusion, Baicalein inhibits aggregation of hTau40 by enhancing the formation of SDS-stable oligomers and preventing fibril formation. Baicalein-induced oligomers do not affect the viability of the neuroblastoma cells. Therefore, Baicalein can be considered as a lead molecule against Tau pathology in AD. Video Abstract
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Affiliation(s)
- Shweta Kishor Sonawane
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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10
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Balmik AA, Chidambaram H, Dangi A, Marelli UK, Chinnathambi S. HDAC6 ZnF UBP as the Modifier of Tau Structure and Function. Biochemistry 2020; 59:4546-4562. [PMID: 33237772 DOI: 10.1021/acs.biochem.0c00585] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Histone deacetylase 6 is a class II histone deacetylase primarily present in the cytoplasm and involved in the regulation of various cellular functions. It consists of two catalytic deacetylase domains and a unique zinc finger ubiquitin binding protein domain, which sets it apart from other HDACs. HDAC6 is known to regulate cellular activities by modifying the function of microtubules, HSP90, and cortactin through deacetylation. Apart from the catalytic activity of HDAC6, it interacts with other proteins through either the SE14 domain or the ZnF UBP domain to modulate their functions. Here, we have studied the role of the HDAC6 ZnF UBP domain as a modifier of Tau aggregation by its direct interaction with the polyproline region/repeat region of Tau. Interaction of HDAC6 ZnF UBP with Tau was found to reduce the propensity of Tau to self-aggregate and to disaggregate preformed aggregates in a concentration-dependent manner and also bring about the conformational changes in Tau protein. The interaction of HDAC6 ZnF UBP with Tau results in its degradation, suggesting either proteolytic activity of HDAC6 ZnF UBP or its role in enhancing autoproteolysis of Tau.
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Affiliation(s)
- Abhishek Ankur Balmik
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Hariharakrishnan Chidambaram
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Abha Dangi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.,Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Udaya Kiran Marelli
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.,Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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11
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Sonawane SK, Chidambaram H, Boral D, Gorantla NV, Balmik AA, Dangi A, Ramasamy S, Marelli UK, Chinnathambi S. EGCG impedes human Tau aggregation and interacts with Tau. Sci Rep 2020; 10:12579. [PMID: 32724104 PMCID: PMC7387440 DOI: 10.1038/s41598-020-69429-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
Tau aggregation and accumulation is a key event in the pathogenesis of Alzheimer’s disease. Inhibition of Tau aggregation is therefore a potential therapeutic strategy to ameliorate the disease. Phytochemicals are being highlighted as potential aggregation inhibitors. Epigallocatechin-3-gallate (EGCG) is an active phytochemical of green tea that has shown its potency against various diseases including aggregation inhibition of repeat Tau. The potency of EGCG in altering the PHF assembly of full-length human Tau has not been fully explored. By various biophysical and biochemical analyses like ThS fluorescence assay, MALDI-TOF analysis and Isothermal Titration Calorimetry, we demonstrate dual effect of EGCG on aggregation inhibition and disassembly of full-length Tau and their binding affinity. The IC50 for Tau aggregation by EGCG was found to be 64.2 μM.
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Affiliation(s)
- Shweta Kishor Sonawane
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Hariharakrishnan Chidambaram
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Debjyoti Boral
- Structural Biology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Nalini Vijay Gorantla
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Abhishek Ankur Balmik
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Abha Dangi
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Sureshkumar Ramasamy
- Structural Biology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Udaya Kiran Marelli
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India.
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12
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Dubey T, Gorantla NV, Chandrashekara KT, Chinnathambi S. Photodynamic exposure of Rose-Bengal inhibits Tau aggregation and modulates cytoskeletal network in neuronal cells. Sci Rep 2020; 10:12380. [PMID: 32704015 PMCID: PMC7378248 DOI: 10.1038/s41598-020-69403-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023] Open
Abstract
The intracellular Tau aggregates are known to be associated with Alzheimer’s disease. The inhibition of Tau aggregation is an important strategy for screening of therapeutic molecules in Alzheimer's disease. Several classes of dyes possess a unique property of photo-excitation, which is applied as a therapeutic measure against numerous neurological dysfunctions. Rose Bengal is a Xanthene dye, which has been widely used as a photosensitizer in photodynamic therapy. The aim of this work was to study the protective role of Rose Bengal against Tau aggregation and cytoskeleton modulations. The aggregation inhibition and disaggregation potency of Rose Bengal and photo-excited Rose Bengal were observed by in-vitro fluorescence, circular dichroism, and electron microscopy. Rose Bengal and photo-excited Rose Bengal induce minimal cytotoxicity in neuronal cells. In our studies, we observed that Rose Bengal and photo-excited Rose Bengal modulate the cytoskeleton network of actin and tubulin. The immunofluorescence studies showed the increased filopodia structures after photo-excited Rose Bengal treatment. Furthermore, Rose Bengal treatment increases the connections between the cells. Rose Bengal and photo-excited Rose Bengal treatment-induced actin-rich podosome-like structures associated with cell membranes. The in-vivo studies on UAS E-14 Tau mutant Drosophila suggested that exposure to Rose Bengal and photo-excited Rose Bengal efficiency rescues the behavioural and memory deficit in flies. Thus, the overall results suggest that Rose Bengal could have a therapeutic potency against Tau aggregation.
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Affiliation(s)
- Tushar Dubey
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Nalini Vijay Gorantla
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | | | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
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13
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Sonawane SK, Chinnathambi S. P301 L, an FTDP-17 Mutant, Exhibits Enhanced Glycation in vitro. J Alzheimers Dis 2020; 75:61-71. [PMID: 32250308 DOI: 10.3233/jad-191348] [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: 11/15/2022]
Abstract
BACKGROUND Frontotemporal dementia and parkinsonism-linked to chromosome-17 are a group of diseases with tau mutations leading to primary tauopathies which include progressive supranuclear palsy, corticobasal syndrome, and frontotemporal lobar degeneration. Alzheimer's disease is a non-primary tauopathy, which displays tau neuropathology of excess tangle formation and accumulation. FTDP-17 mutations are responsible for early onset of AD, which can be attributed to compromised physiological functions due to the mutations. Tau is a microtubule-binding protein that secures the integrity of polymerized microtubules in neuronal cells. It malfunctions owing to various insults and stress conditions-like mutations and post-translational modifications. OBJECTIVE In this study, we modified the wild type and tau mutants by methyl glyoxal and thus studied whether glycation can enhance the aggregation of predisposed mutant tau. METHODS Tau glycation was studied by fluorescence assays, SDS-PAGE analysis, conformational evaluation, and transmission electron microscopy. RESULTS Our study suggests that FTDP-17 mutant P301 L leads to enhanced glycation-induced aggregation as well as advanced glycation end products formation. Glycation forms amorphous aggregates of tau and its mutants without altering its native conformation. CONCLUSION The metabolic anomalies and genetic predisposition have found to accelerate tau-mediated neurodegeneration and prove detrimental for the early-onset of Alzheimer's disease.
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Affiliation(s)
- Shweta Kishor Sonawane
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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14
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Basic Limonoid modulates Chaperone-mediated Proteostasis and dissolve Tau fibrils. Sci Rep 2020; 10:4023. [PMID: 32132570 PMCID: PMC7055235 DOI: 10.1038/s41598-020-60773-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/17/2020] [Indexed: 02/07/2023] Open
Abstract
The Alzheimer's disease pathology is associated with accumulation of intracellular neurofibrillary tangles and extracellular senile plaques. The formation of initial nucleus triggers conformational changes in Tau and leads to its deposition. Hence, there is a need to eliminate these toxic proteins for proper functioning of neuronal cells. In this aspect, we screened the effect of basic limonoids such as gedunin, epoxyazadiradione, azadirone and azadiradione on inhibiting Tau aggregation as well as disintegration of induced Tau aggregates. It was observed that these basic limonoids effectively prevented aggregates formation by Tau and also exhibited the property of destabilizing matured Tau aggregates. The molecular docking analysis suggests that the basic limonoids interact with hexapeptide regions of aggregated Tau. Although these limonoids caused the conformational changes in Tau to β-sheet structure, the cytological studies indicate that basic limonoids rescued cell death. The dual role of limonoids in Tau aggregation inhibition and disintegration of matured aggregates suggests them to be potent molecules in overcoming Tau pathology. Further, their origin from a medicinally important plant neem, which known to possess remarkable biological activities was also found to play protective role in HEK293T cells. Basic limonoids were non-toxic to HEK293T cells and also aided in activation of HSF1 by inducing its accumulation in nucleus. Western blotting and immunofluorescence studies showed that HSF1 in downstream increased the transcription of Hsp70 thus, aggravating cytosolic Hsp70 levels that can channel clearance of aberrant Tau. All these results mark basic limonoids as potential therapeutic natural products.
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15
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Das R, Balmik AA, Chinnathambi S. Phagocytosis of full-length Tau oligomers by Actin-remodeling of activated microglia. J Neuroinflammation 2020; 17:10. [PMID: 31915009 PMCID: PMC6950897 DOI: 10.1186/s12974-019-1694-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Alzheimer's disease is associated with the accumulation of intracellular Tau tangles within neurons and extracellular amyloid-β plaques in the brain parenchyma, which altogether results in synaptic loss and neurodegeneration. Extracellular concentrations of oligomers and aggregated proteins initiate microglial activation and convert their state of synaptic surveillance into a destructive inflammatory state. Although Tau oligomers have fleeting nature, they were shown to mediate neurotoxicity and microglial pro-inflammation. Due to the instability of oligomers, in vitro experiments become challenging, and hence, the stability of the full-length Tau oligomers is a major concern. METHODS In this study, we have prepared and stabilized hTau40WT oligomers, which were purified by size-exclusion chromatography. The formation of the oligomers was confirmed by western blot, thioflavin-S, 8-anilinonaphthaalene-1-sulfonic acid fluorescence, and circular dichroism spectroscopy, which determine the intermolecular cross-β sheet structure and hydrophobicity. The efficiency of N9 microglial cells to phagocytose hTau40WT oligomer and subsequent microglial activation was studied by immunofluorescence microscopy with apotome. The one-way ANOVA was performed for the statistical analysis of fluorometric assay and microscopic analysis. RESULTS Full-length Tau oligomers were detected in heterogeneous globular structures ranging from 5 to 50 nm as observed by high-resolution transmission electron microscopy, which was further characterized by oligomer-specific A11 antibody. Immunocytochemistry studies for oligomer treatment were evidenced with A11+ Iba1high microglia, suggesting that the phagocytosis of extracellular Tau oligomers leads to microglial activation. Also, the microglia were observed with remodeled filopodia-like actin structures upon the exposure of oligomers and aggregated Tau. CONCLUSION The peri-membrane polymerization of actin filament and co-localization of Iba1 relate to the microglial movements for phagocytosis. Here, these findings suggest that microglia modified actin cytoskeleton for phagocytosis and rapid clearance of Tau oligomers in Alzheimer's disease condition.
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Affiliation(s)
- Rashmi Das
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Abhishek Ankur Balmik
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Pune, 411008, India.
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16
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Gorantla N, Landge VG, Nagaraju PG, Priyadarshini CG P, Balaraman E, Chinnathambi S. Molecular Cobalt(II) Complexes for Tau Polymerization in Alzheimer's Disease. ACS OMEGA 2019; 4:16702-16714. [PMID: 31646215 PMCID: PMC6796896 DOI: 10.1021/acsomega.9b00692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/01/2019] [Indexed: 05/15/2023]
Abstract
Tau is an axonal protein known to form abnormal aggregates and is the biomarker of Alzheimer's disease. Metal-based therapeutics for inhibition of Tau aggregation is limited and rarely reported in contemporary science. Here, we report the first example of rationally designed molecular cobalt(II)-complexes for effective inhibition of Tau and disaggregation of preformed Tau fibrils. The mechanistic studies reveal that prevention of Tau aggregation by cobalt-based metal complexes (CBMCs) is concentration-dependent and Tau seldom exhibits conformational changes. Interestingly, CBMCs play dual role in causing disassembly of preformed aggregates as well as inhibition of complete Tau aggregation. Furthermore, CBMCs were nontoxic and maintained the tubulin network intact. CBMCs also prevented okadaic acid-induced toxicity in SH-SY5Y cells thus, preventing hyperphosphorylation of Tau. We believe that this unprecedented finding by the newly developed molecular complexes has a potential toward metal-based therapeutics for Alzheimer's disease.
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Affiliation(s)
- Nalini
Vijay Gorantla
- Neurobiology
Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy
of Scientific and Innovative
Research (AcSIR), 411008 Pune, India
| | - Vinod G. Landge
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Tirupati, 517507 Tirupati, India
| | - Pramod Gudigenahally Nagaraju
- Academy
of Scientific and Innovative
Research (AcSIR), 411008 Pune, India
- Department
of Molecular Nutrition, CSIR-CFTRI, 570020 Mysore, India
| | - Poornima Priyadarshini CG
- Academy
of Scientific and Innovative
Research (AcSIR), 411008 Pune, India
- Department
of Molecular Nutrition, CSIR-CFTRI, 570020 Mysore, India
| | - Ekambaram Balaraman
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Tirupati, 517507 Tirupati, India
| | - Subashchandrabose Chinnathambi
- Neurobiology
Group, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy
of Scientific and Innovative
Research (AcSIR), 411008 Pune, India
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17
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Sonawane SK, Ahmad A, Chinnathambi S. Protein-Capped Metal Nanoparticles Inhibit Tau Aggregation in Alzheimer's Disease. ACS OMEGA 2019; 4:12833-12840. [PMID: 31460408 PMCID: PMC6682074 DOI: 10.1021/acsomega.9b01411] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/24/2019] [Indexed: 05/24/2023]
Abstract
The Alzheimer's disease (AD) therapeutic research is yielding a large number of potent molecules. The nanoparticle-based therapeutics against the protein aggregation in AD is also taking a lead especially with amyloid-β as a primary target. In this work, we have screened for the first time protein-capped (PC) metal nanoparticles for their potency in inhibiting Tau aggregation in vitro. We present a novel function of PC-Fe3O4 and PC-CdS nanoparticles as potent Tau aggregation inhibitors by fluorescence spectrometry, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and electron microscopy. We demonstrate that the biologically synthesized PC-metal nanoparticles, especially iron oxide do not affect the viability of neuroblastoma cells. Moreover, PC-CdS nanoparticles show dual properties of inhibition and disaggregation of Tau. Thus, the nanoparticles can take a lead as potent Tau aggregation inhibitors and can be modified for specific drug delivery due to their very small size. The current work presents unprecedented strategy to design anti-Tau aggregation drugs, which provides interesting insights to understand the role of biological nanostructures in Alzheimer's disease.
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Affiliation(s)
- Shweta Kishor Sonawane
- Neurobiology Group,
Division of Biochemical Sciences, CSIR-National
Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy of Scientific
and Innovative Research (AcSIR), 411008 Pune, India
| | - Absar Ahmad
- Neurobiology Group,
Division of Biochemical Sciences, CSIR-National
Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group,
Division of Biochemical Sciences, CSIR-National
Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
- Academy of Scientific
and Innovative Research (AcSIR), 411008 Pune, India
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18
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Dan A, Chen HF. Secondary structures transition of tau protein with intrinsically disordered proteins specific force field. Chem Biol Drug Des 2018; 93:242-253. [PMID: 30259679 DOI: 10.1111/cbdd.13407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 02/06/2023]
Abstract
Microtubule-associated Tau protein plays a key role in assembling microtubule and modulating the functional organization of the neuron and developing axonal morphology, growth, and polarity. The pathological Tau can aggregate into cross-beta amyloid as one of the hallmarks for Alzheimer's disease (AD). Therefore, one of the top priorities in AD research is to figure out the structural model of Tau aggregation and to screen the inhibitors. The latest generation intrinsically disordered protein specific force field ff14IDPSFF significantly improved the distributions of heterogeneous conformations for intrinsically disordered proteins (IDPs). Here, the molecular dynamics (MD) simulations with three force fields of ff14SB, ff14IDPs, and ff14IDPSFF were employed to investigate the secondary structures transition of Tau (267-312) fragment. The results indicate that ff14IDPSFF can generate more heterogeneous conformers, and the predicted secondary structural distribution is closer to that of the experimental observation. In addition, predicted secondary chemical shifts from ff14IDPSFF are the most approach to those of experiment. Secondary structures transition kinetics for Tau(267-312) with ff14IDPSFF shows that the secondary structures were gradually transformed from α-helix to β-strand and the β-strand located at the regions of the residues 274-280 and residues 305-311. Besides, the driving force for the secondary structures transition of Tau(267-312) is mainly hydrophobic interactions which located at hexa-peptides 275 VQIINK280 and 306 VQIVYK311 . Secondary structure transition of Tau protein can give insight into the aggregation mechanism for AD.
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Affiliation(s)
- Aohuan Dan
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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19
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Bruce HA, Du D, Matak-Vinkovic D, Bandyra KJ, Broadhurst RW, Martin E, Sobott F, Shkumatov AV, Luisi BF. Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes. Nucleic Acids Res 2018; 46:387-402. [PMID: 29136196 PMCID: PMC5758883 DOI: 10.1093/nar/gkx1083] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/16/2017] [Accepted: 10/22/2017] [Indexed: 12/20/2022] Open
Abstract
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We have structurally characterized a subassembly of the degradosome-comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.
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Affiliation(s)
- Heather A Bruce
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Katarzyna J Bandyra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - R William Broadhurst
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Esther Martin
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Alexander V Shkumatov
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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