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Yang Q, Hosseini E, Yao P, Pütz S, Gelléri M, Bonn M, Parekh SH, Liu X. Self-Blinking Thioflavin T for Super-resolution Imaging. J Phys Chem Lett 2024; 15:7591-7596. [PMID: 39028951 PMCID: PMC11299178 DOI: 10.1021/acs.jpclett.4c00195] [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: 01/19/2024] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Thioflavin T (ThT) is a typical dye used to visualize the aggregation and formation of fibrillar structures, e.g., amyloid fibrils and peptide nanofibrils. ThT has been considered to produce stable fluorescence when interacting with aggregated proteins. For single-molecule localization microscopy (SMLM)-based optical super-resolution imaging, a photoswitching/blinking fluorescence property is required. Here we demonstrate that, in contrast to previous reports, ThT exhibits intrinsic stochastic blinking properties, without the need for blinking imaging buffer, in stable binding conditions. The blinking properties (photon number, blinking time, and on-off duty cycle) of ThT at the single-molecule level (for ultralow concentrations) were investigated under different conditions. As a proof of concept, we performed SMLM imaging of ThT-labeled α-synuclein fibrils measured in air and PBS buffer.
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Affiliation(s)
- Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Elnaz Hosseini
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Peigen Yao
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sabine Pütz
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Márton Gelléri
- Institute
of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, University of
Texas at Austin, Austin, Texas 78712, United States
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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2
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Micocci S, Stefania R, Garello F, Fasoglio U, Hawala I, Tei L, Geninatti Crich S, Digilio G. Synthesis of fluorinated curcumin derivatives for detecting amyloid plaques by 19F-MRI. Org Biomol Chem 2024; 22:5948-5959. [PMID: 38979663 DOI: 10.1039/d4ob00730a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The most prominent pathophysiological hallmark of Alzheimer's disease is the aggregation of amyloid-β (Aβ) peptides into senile plaques. Curcumin and its derivatives exhibit a high affinity for binding to Aβ fibrils, effectively inhibiting their growth. This property holds promise for both therapeutic applications and diagnostic molecular imaging. In this study, curcumin was functionalized with perfluoro-tert-butyl groups to create candidate molecular probes specifically targeted to Aβ fibrils for use in 19F-magnetic resonance imaging. Two types of fluorinated derivatives were considered: mono-substituted (containing nine fluorine atoms per molecule) and disubstituted (containing eighteen fluorine atoms). The linker connecting the perfluoro moiety with the curcumin scaffold was evaluated for its impact on binding affinity and water solubility. All mono-substituted compounds and one disubstituted compound exhibited a binding affinity toward Aβ fibrils on the same order of magnitude as reference curcumin. The insertion of a charged carboxylate group into the linker enhanced the water solubility of the probes. Compound Curc-Glu-F9 (with one L-glutamyl moiety and a perfluoro-tert-butyl group), showed the best properties in terms of binding affinity towards Aβ fibrils, water solubility, and intensity of the 19F-NMR signal in the Aβ oligomer bound form.
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Affiliation(s)
- Sebastiano Micocci
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Torino, Italy
| | - Rachele Stefania
- Department of Science and Technological Innovation, University of Eastern Piedmont "Amedeo Avogadro", Viale Teresa Michel 11, 15120, Alessandria, Italy.
| | - Francesca Garello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Torino, Italy
| | - Umberto Fasoglio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Torino, Italy
| | - Ivan Hawala
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Torino, Italy
| | - Lorenzo Tei
- Department of Science and Technological Innovation, University of Eastern Piedmont "Amedeo Avogadro", Viale Teresa Michel 11, 15120, Alessandria, Italy.
| | - Simonetta Geninatti Crich
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Torino, Italy
| | - Giuseppe Digilio
- Department of Science and Technological Innovation, University of Eastern Piedmont "Amedeo Avogadro", Viale Teresa Michel 11, 15120, Alessandria, Italy.
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3
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Martins LDA, Ferreira PS, Leitão Dos Santos OA, Martins LO, Cabral Fernandes Barroso LG, Pereira HM, Waddington-Cruz M, Palhano FL, Foguel D. Structural and thermodynamic characterization of a highly amyloidogenic dimer of transthyretin involved in a severe cardiomyopathy. J Biol Chem 2024; 300:107495. [PMID: 38925327 PMCID: PMC11293521 DOI: 10.1016/j.jbc.2024.107495] [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: 12/22/2023] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Transthyretin (TTR) is an homotetrameric protein involved in the transport of thyroxine. More than 150 different mutations have been described in the TTR gene, several of them associated with familial amyloid cardiomyopathy. Recently, our group described a new variant of TTR in Brazil, namely A39D-TTR, which causes a severe cardiac condition. Position 39 is in the AB loop, a region of the protein that is located within the thyroxine-binding channels and is involved in tetramer formation. In the present study, we solved the structure and characterize the thermodynamic stability of this new variant of TTR using urea and high hydrostatic pressure. Interestingly, during the process of purification, A39D-TTR turned out to be a dimer and not a tetramer, a variation that might be explained by the close contact of the four aspartic acids at position 39, where they face each other inside the thyroxine channel. In the presence of subdenaturing concentrations of urea, bis-ANS binding and dynamic light scattering revealed A39D-TTR in the form of a molten-globule dimer. Co-expression of A39D and WT isoforms in the same bacterial cell did not produce heterodimers or heterotetramers, suggesting that somehow a negative charge at the AB loop precludes tetramer formation. A39D-TTR proved to be highly amyloidogenic, even at mildly acidic pH values where WT-TTR does not aggregate. Interestingly, despite being a dimer, aggregation of A39D-TTR was inhibited by diclofenac, which binds to the thyroxine channel in the tetramer, suggesting the existence of other pockets in A39D-TTR able to accommodate this molecule.
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Affiliation(s)
- Lucas do Amaral Martins
- Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Priscila S Ferreira
- Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Leticia Oliveira Martins
- Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Humberto M Pereira
- Instituto de Física de São Carlos, Universidade São Paulo, São Carlos, Brazil
| | - Márcia Waddington-Cruz
- Centro de Estudos de Paramiloidose Antônio Rodrigues de Mello, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Lucas Palhano
- Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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4
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Monti A, Scognamiglio PL, Ruvo M, Vitagliano L, Doti N. The Characterization of Multifaceted PREP1 Peptides Provides Insights into Correlations between Spectroscopic and Structural Properties of Amyloid-like Assemblies. Chemistry 2024; 30:e202400846. [PMID: 38682403 DOI: 10.1002/chem.202400846] [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: 02/29/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
The widespread ability of proteins and peptides to self-assemble by forming cross-β structure is one of the most significant discoveries in structural biology. Intriguingly, the cross-β association of proteins/peptides may generate intricate supramolecular architectures with uncommon spectroscopic properties. We have recently characterized self-assembled peptides extracted from the PREP1 protein that are endowed with interesting structural/spectroscopic properties. We here demonstrate that the green fluorescence emission of the peptide PREP1[117-132] (λem ~520 nm), can be induced by excitation with UV radiation. The associated unusually large Stokes shift (Δλ ~150 nm) represents, to the best of our knowledge, the first evidence of an internal resonance energy transfer in amyloid-like structures, where the blue emission of some assemblies becomes the excitation radiation for others. Moreover, the characterization of PREP1[117-132] variants provides insights into the sequence/structure and structure/spectroscopic properties relationships. Our data suggests that the green fluorescence is plausibly associated with antiparallel β-sheet states of the peptide whereas parallel β-sheet assemblies are only endowed with blue fluorescence. Notably, the different PREP1[117-132] variants also form assemblies characterized by distinct morphologies. Indeed, the parent peptide and single mutants form compact but structured aggregates whereas most of the double mutants exhibit elongated and highly extended fibers.
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Affiliation(s)
- Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via P. Castellino 111, 80131, Napoli, Italy
| | - Pasqualina Liana Scognamiglio
- Department of Sciences, University of Basilicata, Macchia Romana Campus 10, Viale dell'Ateneo Lucano, 85100, Potenza, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via P. Castellino 111, 80131, Napoli, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via P. Castellino 111, 80131, Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via P. Castellino 111, 80131, Napoli, Italy
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5
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Liang Y, Liu H, Jie Y, Liu M, He B, Wang J. Amyloid-like Aggregation of Wheat Gluten and Its Components during Cooking: Mechanisms and Structural Characterization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11080-11093. [PMID: 38690996 DOI: 10.1021/acs.jafc.3c09451] [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: 05/03/2024]
Abstract
Amyloid-like aggregation widely occurs during the processing and production of natural proteins, with evidence indicating its presence following the thermal processing of wheat gluten. However, significant gaps remain in understanding the underlying fibrillation mechanisms and structural polymorphisms. In this study, the amyloid-like aggregation behavior of wheat gluten and its components (glutenin and gliadin) during cooking was systematically analyzed through physicochemical assessment and structural characterization. The presence of amyloid-like fibrils (AFs) was confirmed using X-ray diffraction and Congo red staining, while Thioflavin T fluorescence revealed different patterns and rates of AFs growth among wheat gluten, glutenin, and gliadin. AFs in gliadin exhibited linear growth curves, while those in gluten and glutenin showed S-shaped curves, with the shortest lag phase and fastest growth rate (t1/2 = 2.11 min) observed in glutenin. Molecular weight analyses revealed AFs primarily in the 10-15 kDa range, shifting to higher weights over time. Glutenin-derived AFs had the smallest ζ-potential value (-19.5 mV) and the most significant size increase post cooking (approximately 400 nm). AFs in gluten involve interchain reorganization, hydrophobic interactions, and conformational transitions, leading to additional cross β-sheets. Atomic force microscopy depicted varying fibril structures during cooking, notably longer, taller, and stiffer AFs from glutenin.
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Affiliation(s)
- Ying Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hao Liu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangyi Jie
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Mei Liu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Baoshan He
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jinshui Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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6
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Yao JY, Li L, Xu JX, Liu YH, Shi J, Yu XQ, Kong QQ, Li K. Real-Time Monitoring of Tyrosine Hydroxylase Activity with a Ratiometric Fluorescent Probe. Anal Chem 2024; 96:7082-7090. [PMID: 38652135 DOI: 10.1021/acs.analchem.4c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Parkinson's disease (PD) represents the second most widespread neurodegenerative disease, and early monitoring and diagnosis are urgent at present. Tyrosine hydroxylase (TH) is a key enzyme for producing dopamine, the levels of which can serve as an indicator for assessing the severity and progression of PD. This renders the specific detection and visualization of TH a strategically vital way to meet the above demands. However, a fluorescent probe for TH monitoring is still missing. Herein, three rationally designed wash-free ratiometric fluorescent probes were proposed. Among them, TH-1 exhibited ideal photophysical properties and specific dual-channel bioimaging of TH activity in SH-SY5Y nerve cells. Moreover, the probe allowed for in vivo imaging of TH activity in zebrafish brain and living striatal slices of mice. Overall, the ratiometric fluorescent probe TH-1 could serve as a potential tool for real-time monitoring of PD in complex biosystems.
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Affiliation(s)
- Jia-Yi Yao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China
| | - Lu Li
- Orthopedic Department, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Ji-Xuan Xu
- Orthopedic Department, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China
| | - Jing Shi
- Orthopedic Department, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Department of Chemistry, Xihua University, Chengdu 610039, P. R. China
| | - Qing-Quan Kong
- Orthopedic Department, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China
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7
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Dong Q, Cui Z, Wu X, Li L, Lu F, Liu F. Natural flavonoid hesperetin blocks amyloid β-protein fibrillogenesis, depolymerizes preformed fibrils and alleviates cytotoxicity caused by amyloids. Food Funct 2024; 15:4233-4245. [PMID: 38517352 DOI: 10.1039/d3fo05566c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The aggregation of β-amyloid (Aβ) peptides to form amyloid plaques is one of the primary hallmarks for Alzheimer's disease (AD). Dietary flavonoid supplements containing hesperetin have an ability to decline the risk of developing AD, but the molecular mechanism is still unclear. In this work, hesperetin, a flavanone abundant in citrus fruits, has been proven to prevent the formation of Aβ aggregates and depolymerized preformed fibrils in a concentration-dependent fashion. Hesperetin inhibited the conformational conversion from the natural structure to a β-sheet-rich conformation. It was found that hesperetin significantly reduced the cytotoxicity and relieved oxidative stress eventuated by Aβ aggregates in a concentration-dependent manner. Additionally, the beneficial effects of hesperetin were confirmed in Caenorhabditis elegans, including the inhibition of the formation and deposition of Aβ aggregates and extension of their lifespan. Finally, the results of molecular dynamics simulations showed that hesperetin directly interacted with an Aβ42 pentamer mainly through strong non-polar and electrostatic interactions, which destroyed the structural stability of the preformed pentamer. To summarize, hesperetin exhibits great potential as a prospective dietary supplement for preventing and improving AD.
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Affiliation(s)
- Qinchen Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Zhan Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Xinming Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Li Li
- College of Sciences, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
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8
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Ansari NK, Rais A, Naeem A. Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A. Protein J 2024; 43:362-374. [PMID: 38431536 DOI: 10.1007/s10930-024-10187-z] [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] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation is related to numerous pathological conditions like Alzheimer's and Parkinson's disease. In our study, we have shown that an already existing FDA-approved drug; methotrexate (MTX) can be reprofiled on preformed α-chymotrypsinogen A (α-Cgn A) aggregates. The zymogen showed formation of aggregates upon interaction with mercuric ions, with increasing concentration of Hg2Cl2 (0-150 µM). The hike in ThT and ANS fluorescence concomitant with blue shift, bathochromic shift and the hyperchromic effect in the CR absorbance, RLS and turbidity measurements, substantiate the zymogen β-rich aggregate formation. The secondary structural alterations of α- Cgn A as analyzed by CD measurements, FTIR and Raman spectra showed the transformation of native β-barrel conformation to β-inter-molecular rich aggregates. The native α- Cgn A have about 30% α-helical content which was found to be about 3% in presence of mercuric ions suggesting the formation of aggregates. The amorphous aggregates were visualized by SEM. On incubation of Hg2Cl2 treated α- Cgn A with increasing concentration of the MTX resulted in reversing aggregates to the native-like structure. These results were supported by remarkable decrease in ThT and ANS fluorescence intensities and CR absorbance and also consistent with CD, FTIR, and Raman spectroscopy data. MTX was found to increase the α-helical content of the zymogen from 3 to 15% proposing that drug is efficient in disrupting the β-inter-molecular rich aggregates and reverting it to native like structure. The SEM images are in accordance with CD data showing the disintegration of aggregates. The most effective concentration of the drug was found to be 120 µM. Molecular docking analysis showed that MTX molecule was surrounded by the hydrophobic residues including Phe39, His40, Arg145, Tyr146, Thr151, Gly193, Ser195, and Gly216 and conventional hydrogen bonds, including Gln73 (bond length: 2.67Å), Gly142 (2.59Å), Thr144 (2.81Å), Asn150 (2.73Å), Asp153 (2.71Å), and Cys191 (2.53Å). This investigation will help to find the use of already existing drugs to cure protein misfolding-related abnormalities.
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Affiliation(s)
- Neha Kausar Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Amaan Rais
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India.
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9
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Duran-Meza E, Araya-Secchi R, Romero-Hasler P, Soto-Bustamante EA, Castro-Fernandez V, Castillo-Caceres C, Monasterio O, Diaz-Espinoza R. Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6094-6106. [PMID: 38470353 DOI: 10.1021/acs.langmuir.3c02983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Raul Araya-Secchi
- Computational Biophysics group, Facultad de Ingenieria, Tecnologia y Diseño, Universidad San Sebastian, Bellavista 7, Recoleta, Santiago 8420524, Chile
- Centro Basal Ciencia & Vida, Universidad San Sebastian, Santiago 8420524, Chile
| | - Patricio Romero-Hasler
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Eduardo Arturo Soto-Bustamante
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
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10
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Francisco T, Malafaia D, Melo L, Silva AMS, Albuquerque HMT. Recent Advances in Fluorescent Theranostics for Alzheimer's Disease: A Comprehensive Survey on Design, Synthesis, and Properties. ACS OMEGA 2024; 9:13556-13591. [PMID: 38559945 PMCID: PMC10975685 DOI: 10.1021/acsomega.3c10417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 04/04/2024]
Abstract
Alzheimer's disease (AD) is the most common form of neurodegenerative dementia that is rapidly becoming a major health problem, especially in developed countries because of their increasing life expectancy. Two main problems are often associated with the disease: (i) the absence of a widely accessible "gold-standard" for early diagnosis and (ii) lack of effective therapies with disease-modifying effects. The recent success of the monoclonal antibody lecanemab played an important role not only in clarifying a possible druggable pathway but also in spelling the revival of small molecule drug discovery. Unlike bulky biologics, small molecules are structurally less complex, generally cheaper, and compatible with at-home oral consumption, making it feasible for people to start their drug regimen early and stay on it longer. In this sense, small-molecule near-infrared fluorescent theranostics have been gaining more and more attention from the scientific community, as they have the potential to simultaneously provide diagnostic outputs and deliver therapeutic action, paving the way toward personalized medicine in AD patients. They also have the potential to shift the diagnostic "status-quo" from expensive and limited-access PET radiotracers toward inexpensive and handy imaging tools widely available for primary patient screening and preclinical animal studies. Herein, we review the most recent advances in the field of fluorescent theranostics for Alzheimer's disease, detailing their design strategies, synthetic approaches and imaging and therapeutic properties in vitro and in vivo. With this Review, we intend to provide a milestone in the acquired knowledge in the field of AD theranostics, encouraging the future development of properly designed theranostic compounds with improved chances to reach clinical applications.
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Affiliation(s)
- Telmo
N. Francisco
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus
de Santiago, 3810-193 Aveiro, Portugal
| | - Daniela Malafaia
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus
de Santiago, 3810-193 Aveiro, Portugal
| | - Lúcia Melo
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus
de Santiago, 3810-193 Aveiro, Portugal
| | - Artur M. S. Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus
de Santiago, 3810-193 Aveiro, Portugal
| | - Hélio M. T. Albuquerque
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus
de Santiago, 3810-193 Aveiro, Portugal
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11
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Carrillo D, Duran-Meza E, Castillo-Caceres C, Alarcon DE, Guzman H, Diaz-Espinoza R. Catalytic amyloids for nucleotide hydrolysis. Methods Enzymol 2024; 697:269-291. [PMID: 38816126 DOI: 10.1016/bs.mie.2024.01.017] [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: 06/01/2024]
Abstract
The design of small peptides that assemble into catalytically active intermolecular structures has proven to be a successful strategy towards developing minimalistic catalysts that exhibit some of the unique functional features of enzymes. Among these, catalytic amyloids have emerged as a fruitful source to unravel many different activities. These assemblies can potentially have broad applications that range from biotechnology to prebiotic chemistry. Although many peptides that assemble into catalytic amyloids have been developed in recent years, the elucidation of convergent mechanistic aspects of the catalysis and the structure/function relationship is still a challenge. Novel catalytic activities are necessary to better address these issues and expand the current repertoire of applicability. In this chapter, we described a methodology to produce catalytic amyloids that are specifically active towards the hydrolysis of phosphoanhydride bonds of nucleotides. The design of potentially active amyloid-prone peptide sequences is explored using as template the active site of enzymes with nucleotidyltransferase activity. The procedures include an approach for sequence design, in vitro aggregation assays, morphological characterization of the amyloid state and a comprehensive methodology to measure activity in vitro using nucleoside and deoxynucleosides triphosphates as model substrates. The proposed strategy can also be implemented to explore different types of activities for the design of future catalytic amyloids.
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Affiliation(s)
- Daniel Carrillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile; Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Diego Eduardo Alarcon
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Hardy Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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12
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Stepanchuk AA, Stys PK. Spectral Fluorescence Pathology of Protein Misfolding Disorders. ACS Chem Neurosci 2024; 15:898-908. [PMID: 38407017 DOI: 10.1021/acschemneuro.3c00798] [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: 02/27/2024] Open
Abstract
Protein misfolding has been extensively studied in the context of neurodegenerative disorders and systemic amyloidoses. Due to misfolding and aggregation of proteins being highly heterogeneous and generating a variety of structures, a growing body of evidence illustrates numerous ways how the aggregates contribute to progression of diseases such as Alzheimer's disease, Parkinson's disease, and prion disorders. Different misfolded species of the same protein, commonly referred to as strains, appear to play a significant role in shaping the disease clinical phenotype and clinical progression. The distinct toxicity profiles of various misfolded proteins underscore their importance. Current diagnostics struggle to differentiate among these strains early in the disease course. This review explores the potential of spectral fluorescence approaches to illuminate the complexities of protein misfolding pathology and discusses the applications of advanced spectral methods in the detection and characterization of protein misfolding disorders. By examining spectrally variable probes, current data analysis approaches, and important considerations for the use of these techniques, this review aims to provide an overview of the progress made in this field and highlights directions for future research.
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Affiliation(s)
- Anastasiia A Stepanchuk
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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13
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Ramesh H, Bhuyan AK. The food and pharmaceutical additive benzoic acid induces amyloid fibrillation of an intrinsically disordered protein. Biophys Chem 2024; 306:107172. [PMID: 38183957 DOI: 10.1016/j.bpc.2024.107172] [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: 10/14/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
Benzoic acid (BA) is a microbe-inhibiting flavoring agent used extensively as an additive in foods, pharmaceuticals, and hygiene and cosmetic products. The level of BA in foodstuffs prescribed by world bodies and governmental agencies is assumed to be safe so as to prevent adverse health effects. The safety level of BA is however controversial, and whether different conditions of its use would be generally regarded as safe (GRAS) has been rarely determined. In the quest of how food additives affect the structure and conformation of proteins, this study evaluates the interaction of BA with an intrinsically disordered protein (IDP) at pH 4.2 that matches the pH conditions applicable for the commercial use of benzoate preservatives, and examines its structural transformation by NMR, fluorescence, and high-resolution microscopy. The interaction with BA transforms the protein to a denatured aggregated mesophase that undergoes reconfiguration to yield rigid amyloid fibrils. Significantly, fibrils are observed even with 0.1 mM BA while the recommended level of its use as a preservative is in the 0.4-8 mM range. The discussion refrains from safety comments with no projection of the BA level that could be GRAS.
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Affiliation(s)
- Halavath Ramesh
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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14
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Chisholm TS, Hunter CA. A closer look at amyloid ligands, and what they tell us about protein aggregates. Chem Soc Rev 2024; 53:1354-1374. [PMID: 38116736 DOI: 10.1039/d3cs00518f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The accumulation of amyloid fibrils is characteristic of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease. Detecting these fibrils with fluorescent or radiolabelled ligands is one strategy for diagnosing and better understanding these diseases. A vast number of amyloid-binding ligands have been reported in the literature as a result. To obtain a better understanding of how amyloid ligands bind, we have compiled a database of 3457 experimental dissociation constants for 2076 unique amyloid-binding ligands. These ligands target Aβ, tau, or αSyn fibrils, as well as relevant biological samples including AD brain homogenates. From this database significant variation in the reported dissociation constants of ligands was found, possibly due to differences in the morphology of the fibrils being studied. Ligands were also found to bind to Aβ(1-40) and Aβ(1-42) fibrils with similar affinities, whereas a greater difference was found for binding to Aβ and tau or αSyn fibrils. Next, the binding of ligands to fibrils was shown to be largely limited by the hydrophobic effect. Some Aβ ligands do not fit into this hydrophobicity-limited model, suggesting that polar interactions can play an important role when binding to this target. Finally several binding site models were outlined for amyloid fibrils that describe what ligands target what binding sites. These models provide a foundation for interpreting and designing site-specific binding assays.
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Affiliation(s)
- Timothy S Chisholm
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
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15
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Morozova OV, Manuvera VA, Barinov NA, Subcheva EN, Laktyushkin VS, Ivanov DA, Lazarev VN, Klinov DV. Self-assembling amyloid-like nanostructures from SARS-CoV-2 S1, S2, RBD and N recombinant proteins. Arch Biochem Biophys 2024; 752:109843. [PMID: 38072298 DOI: 10.1016/j.abb.2023.109843] [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: 10/02/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
Self-assembling nanoparticles (saNP) and nanofibers were found in the recombinant coronavirus SARS-CoV-2 S1, S2, RBD and N proteins purified by affinity chromatography using Ni Sepharose. Scanning electron (SEM), atomic force (AFM) microscopy on mica or graphite surface and in liquid as well as dynamic light scattering (DLS) revealed nanostructures of various sizes. AFM in liquid cell without drying on the surface showed mean height of S1 saNP 80.03 nm, polydispersity index (PDI) 0.006; for S2 saNP mean height 93.32 nm, PDI = 0.008; for N saNP mean height 16.71 nm, PDI = 0.99; for RBD saNP mean height 16.25 nm, PDI = 0.55. Ratios between the height and radius of each saNP in the range 0.1-0.5 suggested solid protein NP but not vesicles with internal empty spaces. The solid but not empty structures of the protein saNP were also confirmed by STEM after treatment of saNP with the standard contrasting agent uranyl acetate. The saNP remained stable after multiple freeze-thaw cycles in water and hyperosmotic solutions for 2 years at -20 °C. Receptor-mediated penetration of the SARS-CoV-2 S1 and RBD saNP in the African green mokey kidney Vero cells with the specific receptors for β-coronavirus reproduction was more efficient compared to unspecific endocytosis into MDCK cells without the specific receptors. Amyloid-like structures were revealed in the SARS-CoV-2 S1, S2, RBD and N saNP by means of their interaction with Thioflavin T and Congo Red dyes. Taken together, spontaneous formation of the amyloid-like self-assembling nanostructures due to the internal affinity of the SARS-CoV-2 virion proteins might induce proteinopathy in patients, including conformational neurodegenerative diseases, change stability of vaccines and diagnostic systems.
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Affiliation(s)
- Olga V Morozova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435, Moscow, Russian Federation; Ivanovsky Institute of Virology of the National Research Center of Epidemiology and Microbiology of N.F. Gamaleya of the Russian Ministry of Health, 16 Gamaleya Street, 123098, Moscow, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700, Dolgoprudny, Moscow Region, Russian Federation; Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation.
| | - Valentin A Manuvera
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435, Moscow, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700, Dolgoprudny, Moscow Region, Russian Federation
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435, Moscow, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700, Dolgoprudny, Moscow Region, Russian Federation; Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation
| | - Elena N Subcheva
- Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation
| | - Victor S Laktyushkin
- Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation
| | - Dimitri A Ivanov
- Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse, 68057, France
| | - Vassili N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435, Moscow, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700, Dolgoprudny, Moscow Region, Russian Federation
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Street, 119435, Moscow, Russian Federation; Moscow Institute of Physics and Technology, 9 Institutsky Per., 141700, Dolgoprudny, Moscow Region, Russian Federation; Sirius University of Science and Technology, Olimpiyskiy ave. b.1, township Sirius, Krasnodar region, 354340, Russian Federation
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16
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Wasko J, Wolszczak M, Zajaczkowska Z, Dudek M, Kolesinska B. Human serum albumin as a potential drug delivery system for N-methylated hot spot insulin analogs inhibiting hormone aggregation. Bioorg Chem 2024; 143:107104. [PMID: 38194903 DOI: 10.1016/j.bioorg.2024.107104] [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: 09/13/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024]
Abstract
The purpose of this study was to investigate whether Human Serum Albumin (HSA) can bind N-methylated analogs of hot spots of native insulin. Three N-methylated derivatives of the A13-A19 fragment of native insulin were used: L(N-Me)YQLENY (1), LYQ(N-Me)LENY (2), and L(N-Me)YQ(N-Me)LENY (3). The studied N-methylated insulin fragments possess inhibiting potential against hormone aggregation. A variety of research techniques, including spectroscopic methods and microscopy assays, were used to study the interaction of HSA with the N-methylated insulin fragments. Based on spectroscopic measurements with Congo Red and Thioflavin T, all the analyzed N-methylated peptides were able to interact with the HSA surface. The CD spectrum registered for HSA in the presence of L(N-Me)YQLENY showed the smallest content of α-helix conformation, indicating the most compact HSA structure. Based on the results of MST, the dissociation constants (Kd) for complexes of HSA and peptides 1-3 were 19.2 nM (complex 1), 15.6 nM (complex 2), and 8.07 nM (complex 3). Microscopy assays, dynamic light scattering measurements as well as computer simulation of protein-ligand interaction also confirmed the possibility of docking the N-methylated inhibitors within HSA.
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Affiliation(s)
- Joanna Wasko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
| | - Marian Wolszczak
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, Poland.
| | - Zuzanna Zajaczkowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
| | - Mariusz Dudek
- Institute of Materials Science and Engineering, The Faculty of Mechanical Engineering, Lodz University of Technology, Stefanowskiego 1/15, Poland.
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
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17
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Wang Y, Rencus-Lazar S, Zhou H, Yin Y, Jiang X, Cai K, Gazit E, Ji W. Bioinspired Amino Acid Based Materials in Bionanotechnology: From Minimalistic Building Blocks and Assembly Mechanism to Applications. ACS NANO 2024; 18:1257-1288. [PMID: 38157317 DOI: 10.1021/acsnano.3c08183] [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: 01/03/2024]
Abstract
Inspired by natural hierarchical self-assembly of proteins and peptides, amino acids, as the basic building units, have been shown to self-assemble to form highly ordered structures through supramolecular interactions. The fabrication of functional biomaterials comprised of extremely simple biomolecules has gained increasing interest due to the advantages of biocompatibility, easy functionalization, and structural modularity. In particular, amino acid based assemblies have shown attractive physical characteristics for various bionanotechnology applications. Herein, we propose a review paper to summarize the design strategies as well as research advances of amino acid based supramolecular assemblies as smart functional materials. We first briefly introduce bioinspired reductionist design strategies and assembly mechanism for amino acid based molecular assembly materials through noncovalent interactions in condensed states, including self-assembly, metal ion mediated coordination assembly, and coassembly. In the following part, we provide an overview of the properties and functions of amino acid based materials toward applications in nanotechnology and biomedicine. Finally, we give an overview of the remaining challenges and future perspectives on the fabrication of amino acid based supramolecular biomaterials with desired properties. We believe that this review will promote the prosperous development of innovative bioinspired functional materials formed by minimalistic building blocks.
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Affiliation(s)
- Yuehui Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Haoran Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yuanyuan Yin
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, People's Republic of China
| | - Xuemei Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wei Ji
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People's Republic of China
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18
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Mahato J, Mukherjee R, Bose A, Mehra S, Gadhe L, Maji SK, Chowdhury A. Sensitized Emission Imaging Allows Nanoscale Surface Polarity Mapping of α-Synuclein Amyloid Fibrils. ACS Chem Neurosci 2024; 15:108-118. [PMID: 38099928 DOI: 10.1021/acschemneuro.3c00467] [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: 01/04/2024] Open
Abstract
When misfolded, α-Synuclein (α-Syn), a natively disordered protein, aggregates to form amyloid fibrils responsible for the neurodegeneration observed in Parkinson's disease. Structural studies revealed distinct molecular packing of α-Syn in different fibril polymorphs and variations of interprotofilament connections in the fibrillar architecture. Fibril polymorphs have been hypothesized to exhibit diverse surface polarities depending on the folding state of the protein during aggregation; however, the spatial variation of surface polarity in amyloid fibrils remains unexplored. To map the local polarity (or hydrophobicity) along α-Syn fibrils, we visualized the spectral characteristics of two dyes with distinct polarities-hydrophilic Thioflavin T (ThT) and hydrophobic Nile red (NR)─when both are bound to α-Syn fibrils. Dual-channel fluorescence imaging reveals uneven partitioning of ThT and NR along individual fibrils, implying that relatively more polar/hydrophobic patches are spread over a few hundred nanometers. Remarkably, spectrally resolved sensitized emission imaging of α-Syn fibrils provides unambiguous evidence of energy transfer from ThT to NR, implying that dyes of dissimilar polarity are in close proximity. Furthermore, spatially resolved fluorescence spectroscopy of the solvatochromic probe NR allowed us to quantitatively map the range and variation of the polarity parameter ET30 along individual fibrils. Our results suggest the existence of interlaced polar and nonpolar nanoscale domains throughout the fibrils; however, the relative populations of these patches vary considerably over larger length scales likely due to heterogeneous packing of α-Syn during fibrilization and dissimilar exposed polarities of polymorphic segments. The employed method may provide a foundation for imaging modalities of other similar structurally unresolved systems with diverse hydrophobic-hydrophilic topology.
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Affiliation(s)
- Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Rajat Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Abhik Bose
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
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19
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Hisamuddin M, Rizvi I, Malik A, Nabi F, Hassan MN, Ali SM, Khan JM, Khan TH, Khan RH. Characterization of pH-induced conformational changes in recombinant DENV NS2B-NS3pro. Int J Biol Macromol 2023; 253:126823. [PMID: 37703975 DOI: 10.1016/j.ijbiomac.2023.126823] [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: 06/15/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
The increasing frequency of Dengue is a cause of severe epidemics and therefore demands strategies for effective prevention, diagnosis, and treatment. DENV-protease is being investigated as a potential therapeutic target. However, due to the flat and highly charged active site of the DENV-protease, designing orthosteric medicines is very difficult. In this study, we have done a thorough analysis of pH-dependent conformational changes in recombinantly expressed DENV protease using various spectroscopic techniques. Our spectroscopic study of DENV protease (NS2B-NS3pro) at different pH conditions gives important insights into the dynamicity of structural conformation. At physiological pH, the DENV-protease exists in a random-coiled state. Lowering the pH promotes the formation of alpha-helical and beta-sheet structures i.e. gain of secondary structure as shown by Far-UV CD. The light scattering and Thioflavin T (ThT)-binding assay proved the aggregation-prone tendency of DENV-protease at pH 4.0. Further, the confocal microscopy image intensity showed the amorphous aggregate formation of DENV protease at pH 4.0. Thus, the DENV protease acquires different conformations with changes in pH conditions. Together, these results have the potential to facilitate the design of a conformation destabilizer-based therapeutic strategy for dengue fever.
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Affiliation(s)
- Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Irum Rizvi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Syed Moasfar Ali
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Tabish H Khan
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, MO, USA
| | - Rizwan H Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India.
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20
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Portugal Barron D, Guo Z. The supersaturation perspective on the amyloid hypothesis. Chem Sci 2023; 15:46-54. [PMID: 38131088 PMCID: PMC10731913 DOI: 10.1039/d3sc03981a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/27/2023] [Indexed: 12/23/2023] Open
Abstract
Development of therapeutic interventions for Alzheimer's over the past three decades has been guided by the amyloid hypothesis, which puts Aβ deposition as the initiating event of a pathogenic cascade leading to dementia. In the current form, the amyloid hypothesis lacks a comprehensive framework that considers the complex nature of Aβ aggregation. The explanation of how Aβ deposition leads to downstream pathology, and how reducing Aβ plaque load via anti-amyloid therapy can lead to improvement in cognition remains insufficient. In this perspective we integrate the concept of Aβ supersaturation into the amyloid hypothesis, laying out a framework for the mechanistic understanding and therapeutic intervention of Alzheimer's disease. We discuss the important distinction between in vitro and in vivo patterns of Aβ aggregation, the impact of different aggregation stages on therapeutic strategies, and how future investigations could integrate this concept in order to produce a more thorough understanding and better treatment for Alzheimer's and other amyloid-related disorders.
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Affiliation(s)
- Diana Portugal Barron
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
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21
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [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: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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22
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Li YQ, He L, Aryal M, Wicander J, Korza G, Setlow P. Thioflavin-T does not report on electrochemical potential and memory of dormant or germinating bacterial spores. mBio 2023; 14:e0222023. [PMID: 37830807 PMCID: PMC10653816 DOI: 10.1128/mbio.02220-23] [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: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Bacillus and Clostridium spores cause food spoilage and disease because of spores' dormancy and resistance to microbicides. However, when spores "come back to life" in germination, their resistance properties are lost. Thus, understanding the mechanisms of spore germination could facilitate the development of "germinate to eradicate" strategies. One germination feature is the memory of a pulsed germinant stimulus leading to greater germination following a second pulse. Recent observations of increases in spore binding of the potentiometric dye thioflavin-T early in their germination of spores led to the suggestion that increasing electrochemical potential is how spores "remember" germinant pulses. However, new work finds no increased thioflavin-T binding in the physiological germination of Coatless spores or of intact spores germinating with dodecylamine, even though spore memory is seen in both cases. Thus, using thioflavin-T uptake by germinating spores to assess the involvement of electrochemical potential in memory of germinant exposure, as suggested recently, is questionable.
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Affiliation(s)
- Yong-qing Li
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
- Department of Physics, East Carolina University, Greenville, North Carolina, USA
| | - Lin He
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
| | - Makunda Aryal
- Department of Physics, East Carolina University, Greenville, North Carolina, USA
| | - James Wicander
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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23
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Mukherjee P, Ganai S. Thioflavin-T: A Quantum Yield-Based Molecular Viscometer for Glycerol-Monohydroxy Alcohol Mixtures. ACS OMEGA 2023; 8:36604-36613. [PMID: 37810704 PMCID: PMC10552499 DOI: 10.1021/acsomega.3c06428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Molecular rotor dye thioflavin T (ThT) is almost nonfluorescent in low-viscosity solvents but highly fluorescent when bound to amyloid fibrils. This unique property arises from the rotation of the dimethylaniline moiety relative to the benzothiazole moiety in the excited state, which drives the dye from an emissive locally excited state to a twisted intramolecular charge-transfer state. This process is viscosity-controlled, and therefore, we can use the quantum yield of ThT to assess the viscosity of the environment. In this study, we have investigated the quantum yield of ThT (φThT) in various compositions of six alcoholic solvent mixtures of glycerol with methanol, ethanol, n-propanol, iso-propanol, n-butanol, and tert-butanol. We have proposed an empirical model using φThT as a function of the mole fraction of glycerol to estimate the interaction parameters between the components of the solvent mixtures. This analysis allowed us to predict the extent of nonideality of the solvent mixtures. The Förster-Hoffmann- and Loutfy-Arnold-type power law relationship was established between the quantum yield of ThT and bulk viscosity for solvent mixtures of methanol, ethanol, n-butanol, and tert-butanol with glycerol, and it was found to be similar in nature in all the four mixtures. Applying this knowledge, we proposed a methodology to quantify and predict the bulk viscosity coefficient values of several compositions of n-propanol-glycerol and iso-propanol-glycerol mixtures which have not been previously documented.
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Affiliation(s)
- Puspal Mukherjee
- Department of Chemistry, School of
Sciences, Netaji Subhas Open University, Kolkata, West Bengal. 700064, India
| | - Sintu Ganai
- Department of Chemistry, School of
Sciences, Netaji Subhas Open University, Kolkata, West Bengal. 700064, India
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24
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Warerkar OD, Mudliar NH, Ahuja T, Shahane SD, Singh PK. A highly sensitive hemicyanine-based near-infrared fluorescence sensor for detecting toxic amyloid aggregates in human serum. Int J Biol Macromol 2023; 247:125621. [PMID: 37392920 DOI: 10.1016/j.ijbiomac.2023.125621] [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: 03/08/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
The development of an accurate and sensitive sensor for detecting amyloid plaques, which are responsible for many protein disorders like Alzheimer's disease, is crucial for early diagnosis. Recently, there has been a notable increase in the development of fluorescence probes that exhibit emission in the red region (>600 nm), aiming to effectively tackle the challenges encountered when working with complex biological matrices. In the current investigation, a hemicyanine-based probe, called LDS730, has been used for the sensing of amyloid fibrils, which belong to the Near-Infrared Fluorescence (NIRF) family of dyes. NIRF probes provide higher precision in detection, prevent photo-damage, and minimize the autofluorescence of biological specimens. The LDS730 sensor emits in the near-infrared region and shows a 110-fold increase in fluorescence turn-on emission when bound to insulin fibrils, making it a highly sensitive sensor. The sensor has an emission maximum of ~710 nm in a fibril-bound state, which shows a significant red shift along with a Stokes' shift of ~50 nm. The LDS730 sensor also displays excellent performance in the complicated human serum matrix, with a limit of detection (LOD) of 103 nM. Molecular docking calculations suggest that the most likely binding location of LDS730 in the fibrillar structure is the inner channels of amyloid fibrils along its long axis, and the sensor engages in several types of hydrophobic interactions with neighboring amino acid residues of the fibrillar structure. Overall, this new amyloid sensor has great potential for the early detection of amyloid plaques and for improving diagnostic accuracy.
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Affiliation(s)
- Oshin D Warerkar
- SVKM's Shri C. B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Niyati H Mudliar
- SVKM's Shri C. B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Tanya Ahuja
- SVKM's Shri C. B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Sailee D Shahane
- SVKM's Shri C. B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Prabhat K Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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25
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Leimu L, Haavisto O, Nesati V, Holm P, Haapalinna A, Salbo R, Pesonen U. Development of an in vitro aggregation assay for long synthetic polypeptide, amyloidogenic gelsolin fragment AGelD187N 173-242. PLoS One 2023; 18:e0290179. [PMID: 37590229 PMCID: PMC10434866 DOI: 10.1371/journal.pone.0290179] [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: 04/11/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Aggregation of the gelsolin protein fragment is the hallmark of the hereditary systemic disease gelsolin amyloidosis. As with other protein misfolding diseases, there is an urgent need for efficient disease-modifying treatment for gelsolin amyloidosis. The formation of amyloids can be reproduced by incubating the disease-causing amyloidogenic 8 kDa polypeptide, 70-residue gelsolin protein fragment, AGelD187N 173-242, in vitro and monitoring the process by thioflavin T dye. However, for screening of potential aggregation inhibitors, the required protein amounts are large and the biotechnological production of amyloidogenic proteins has many challenges. Conversely, use of shorter synthetic regions of AGelD187N 173-242 does not mimic the in vivo aggregation kinetics of full-length fragment as they have different aggregation propensity. In this study, we present an in vitro aggregation assay for full-length AGelD187N 173-242 that has been produced by solid-phase chemical synthesis and after that monomerized carefully. Chemical synthesis allows us to produce high quantities of full-length fragment efficiently and at low cost. We demonstrate that the generated aggregates are fibrillar in nature and how the purity, terminal modification, initial aggregates and seeding affect the aggregation kinetics of a synthetic gelsolin fragment. We also present sufficient quality criteria for the initial monomerized synthetic polypeptide.
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Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Oskar Haavisto
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Victor Nesati
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | | | - Rune Salbo
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
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26
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Nikiforova A, Sedov I. Molecular Design of Magnetic Resonance Imaging Agents Binding to Amyloid Deposits. Int J Mol Sci 2023; 24:11152. [PMID: 37446329 DOI: 10.3390/ijms241311152] [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: 06/12/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The ability to detect and monitor amyloid deposition in the brain using non-invasive imaging techniques provides valuable insights into the early diagnosis and progression of Alzheimer's disease and helps to evaluate the efficacy of potential treatments. Magnetic resonance imaging (MRI) is a widely available technique offering high-spatial-resolution imaging. It can be used to visualize amyloid deposits with the help of amyloid-binding diagnostic agents injected into the body. In recent years, a number of amyloid-targeted MRI probes have been developed, but none of them has entered clinical practice. We review the advances in the field and deduce the requirements for the molecular structure and properties of a diagnostic probe candidate. These requirements make up the base for the rational design of MRI-active small molecules targeting amyloid deposits. Particular attention is paid to the novel cryo-EM structures of the fibril aggregates and their complexes, with known binders offering the possibility to use computational structure-based design methods. With continued research and development, MRI probes may revolutionize the diagnosis and treatment of neurodegenerative diseases, ultimately improving the lives of millions of people worldwide.
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Affiliation(s)
- Alena Nikiforova
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
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27
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Fang Y, Wang Q, Xiang C, Liu G, Li J. A Novel Aggregation-Induced Emission Fluorescent Probe for Detection of β-Amyloid Based on Pyridinyltriphenylamine and Quinoline-Malononitrile. BIOSENSORS 2023; 13:610. [PMID: 37366974 DOI: 10.3390/bios13060610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
β-amyloid is an important pathological feature of Alzheimer's disease. Its abnormal production and aggregation in the patient's brain is an important basis for the early diagnosis and confirmation of Alzheimer's disease. In this study, a novel aggregation-induced emission fluorescent probe, PTPA-QM, was designed and synthesized based on pyridinyltriphenylamine and quinoline-malononitrile. These molecules exhibit a donor-donor-π-acceptor structure with a distorted intramolecular charge transfer feature. PTPA-QM displayed the advantages of good selectivity toward viscosity. The fluorescence intensity of PTPA-QM in 99% glycerol solution was 22-fold higher than that in pure DMSO. PTPA-QM has been confirmed to have excellent membrane permeability and low toxicity. More importantly, PTPA-QM exhibits a high affinity towards β-amyloid in brain sections of 5XFAD mice and classical inflammatory cognitive impairment mice. In conclusion, our work provides a promising tool for the detection of β-amyloid.
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Affiliation(s)
- Yan Fang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Qi Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Chenlong Xiang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Guijin Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Junjian Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
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28
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MacKeigan TP, Morgan ML, Stys PK. Quantitation of Tissue Amyloid via Fluorescence Spectroscopy Using Controlled Concentrations of Thioflavin-S. Molecules 2023; 28:molecules28114483. [PMID: 37298959 DOI: 10.3390/molecules28114483] [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: 05/04/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Amyloids are misfolded proteins that aggregate into fibrillar structures, the accumulation of which is associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's disease (AD). Early, sensitive detection of these misfolded aggregates is of great interest to the field, as amyloid deposition begins well before the presentation of clinical symptoms. Thioflavin-S (ThS) is a fluorescent probe commonly used to detect amyloid pathology. Protocols for ThS staining vary, but they often use high staining concentrations followed by differentiation, which causes varying levels of non-specific staining and potentially leaves more subtle amyloid deposition unidentified. In this study, we developed an optimized ThS staining protocol for the sensitive detection of β-amyloids in the widely used 5xFAD Alzheimer's mouse model. Controlled dye concentrations together with fluorescence spectroscopy and advanced analytical methods enabled not only the visualization of plaque pathology, but also the detection of subtle and widespread protein misfolding throughout the 5xFAD white matter and greater parenchyma. Together, these findings demonstrate the efficacy of a controlled ThS staining protocol and highlight the potential use of ThS for the detection of protein misfolding that precedes clinical manifestation of disease.
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Affiliation(s)
- Tatiana P MacKeigan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Megan L Morgan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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29
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Merz GE, Chalkley MJ, Tan SK, Tse E, Lee J, Prusiner SB, Paras NA, DeGrado WF, Southworth DR. Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments. Nat Commun 2023; 14:3048. [PMID: 37236970 PMCID: PMC10220082 DOI: 10.1038/s41467-023-38537-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Accumulation of filamentous aggregates of tau protein in the brain is a pathological hallmark of Alzheimer's disease (AD) and many other neurodegenerative tauopathies. The filaments adopt disease-specific cross-β amyloid conformations that self-propagate and are implicated in neuronal loss. Development of molecular diagnostics and therapeutics is of critical importance. However, mechanisms of small molecule binding to the amyloid core is poorly understood. We used cryo-electron microscopy to determine a 2.7 Å structure of AD patient-derived tau paired-helical filaments bound to the PET ligand GTP-1. The compound is bound stoichiometrically at a single site along an exposed cleft of each protofilament in a stacked arrangement matching the fibril symmetry. Multiscale modeling reveals pi-pi aromatic interactions that pair favorably with the small molecule-protein contacts, supporting high specificity and affinity for the AD tau conformation. This binding mode offers critical insight into designing compounds to target different amyloid folds found across neurodegenerative diseases.
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Affiliation(s)
- Gregory E Merz
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew J Chalkley
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Joanne Lee
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Nick A Paras
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - William F DeGrado
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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30
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Zhang A, Portugal Barron D, Chen EW, Guo Z. A protein aggregation platform that distinguishes oligomers from amyloid fibrils. Analyst 2023; 148:2283-2294. [PMID: 37129054 PMCID: PMC10266934 DOI: 10.1039/d3an00487b] [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] [Indexed: 05/03/2023]
Abstract
Deposition of aggregated proteins is a pathological feature in many neurodegenerative disorders such as Alzheimer's and Parkinson's. In addition to insoluble amyloid fibrils, protein aggregation leads to the formation of soluble oligomers, which are more toxic and pathogenic than fibrils. However, it is challenging to screen for inhibitors targeting oligomers due to the overlapping processes of oligomerization and fibrillization. Here we report a protein aggregation platform that uses intact and split TEM-1 β-lactamase proteins as reporters of protein aggregation. The intact β-lactamase fused with an amyloid protein can report the overall protein aggregation, which leads to loss of lactamase activity. On the other hand, reconstitution of active β-lactamase from the split lactamase construct requires the formation of amyloid oligomers, making the split lactamase system sensitive to oligomerization. Using Aβ, a protein that forms amyloid plaques in Alzheimer's disease, we show that the growth curves of bacterial cells expressing either intact or split lactamase-Aβ fusion proteins can report changes in the Aβ aggregation. The cell lysate lactamase activity assays show that the oligomer fraction accounts for 20% of total activity for the split lactamase-Aβ construct, but only 3% of total activity for the intact lactamase-Aβ construct, confirming the sensitivity of the split lactamase to oligomerization. The combination of the intact and split lactamase constructs allows the distinction of aggregation modulators targeting oligomerization from those targeting overall aggregation. These low-cost bacterial cell-based and biochemical assays are suitable for high-throughput screening of aggregation inhibitors targeting oligomers of various amyloid proteins.
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Affiliation(s)
- Amy Zhang
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Diana Portugal Barron
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Erica W Chen
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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31
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Tanaka M, Takarada T, Nadanaka S, Kojima R, Hosoi K, Machiba Y, Kitagawa H, Yamada T. Influences of amino-terminal modifications on amyloid fibril formation of human serum amyloid A. Arch Biochem Biophys 2023; 742:109615. [PMID: 37105512 DOI: 10.1016/j.abb.2023.109615] [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: 02/26/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023]
Abstract
Human serum amyloid A (SAA) is a precursor protein involved in AA amyloidosis. The N-terminal region of the SAA molecule is crucial for amyloid fibril formation, and therefore modifications in this region are considered to influence the pathogenesis of AA amyloidosis. In the present study, using the N-terminal peptide corresponding to the putative first helix region of the SAA molecule, we investigated the influences of N-terminal modifications on amyloid fibril formation. Spectroscopic analyses revealed that carbamoylation of the N-terminal amino group delayed the onset of amyloid fibril formation. From transmission electron microscopic observations, the N-terminal carbamoylated aggregate showed remarkably different morphologies from the unmodified control. In contrast, acetylation of the N-terminal amino group or truncation of N-terminal amino acid(s) considerably diminished amyloidogenic properties. Furthermore, we also tested the cell toxicity of each peptide aggregate on cultured cells by two cytotoxic assays. Irrespective of carbamoylation or acetylation, MTT assay revealed that SAA peptides reduced the reductive activity of MTT on cells, whereas no apparent increase in LDH release was observed during an LDH assay. In contrast, N-terminal truncation did not affect either MTT reduction or LDH release. These results suggest that N-terminal modification of SAA molecules can act as a switch to regulate susceptibility to AA amyloidosis.
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Affiliation(s)
- Masafumi Tanaka
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan.
| | - Toru Takarada
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Satomi Nadanaka
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Risa Kojima
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Kimiko Hosoi
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Yuki Machiba
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Hiroshi Kitagawa
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Toshiyuki Yamada
- Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke, 329-0498, Japan
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32
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Lantz L, Shirani H, Ghetti B, Vidal R, Klingstedt T, Nilsson KPR. Thiophene-Based Ligands for Histological Multiplex Spectral Detection of Distinct Protein Aggregates in Alzheimer's Disease. Chemistry 2023; 29:e202203568. [PMID: 36645413 PMCID: PMC10101888 DOI: 10.1002/chem.202203568] [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: 11/16/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/17/2023]
Abstract
The aggregation and accumulation of proteins in the brain is the defining feature of many devastating neurodegenerative diseases. The development of fluorescent ligands that bind to these accumulations, or deposits, is essential for the characterization of these neuropathological lesions. We report the synthesis of donor-acceptor-donor (D-A-D) thiophene-based ligands with different emission properties. The D-A-D ligands displayed selectivity towards distinct disease-associated protein deposits in histological sections from postmortem brain tissue of individuals affected by Alzheimer's disease (AD). The ability of the ligands to selectively identify AD-associated pathological alterations, such as deposits composed of aggregates of the amyloid-β (Aβ) peptide or tau, was reduced when the chemical composition of the ligands was altered. When combining the D-A-D ligands with conventional thiophene-based ligands, superior spectral separation of distinct protein aggregates in AD tissue sections was obtained. Our findings provide the structural and functional basis for the development of new fluorescent ligands that can distinguish between aggregated proteinaceous species, as well as offer novel strategies for developing multiplex fluorescence detection of protein aggregates in tissue sections.
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Affiliation(s)
- Linda Lantz
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Hamid Shirani
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, 46202, Indiana, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, 46202, Indiana, USA
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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33
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Dervişoğlu R, Antonschmidt L, Nimerovsky E, Sant V, Kim M, Ryazanov S, Leonov A, Carlos Fuentes-Monteverde J, Wegstroth M, Giller K, Mathies G, Giese A, Becker S, Griesinger C, Andreas LB. Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR. Methods 2023; 214:18-27. [PMID: 37037308 DOI: 10.1016/j.ymeth.2023.04.002] [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: 11/30/2022] [Revised: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Small molecules that bind to oligomeric protein species such as membrane proteins and fibrils are of clinical interest for development of therapeutics and diagnostics. Definition of the binding site at atomic resolution via NMR is often challenging due to low binding stoichiometry of the small molecule. For fibrils and aggregation intermediates grown in the presence of lipids, we report atomic-resolution contacts to the small molecule at sub nm distance via solid-state NMR using dynamic nuclear polarization (DNP) and orthogonally labelled samples of the protein and the small molecule. We apply this approach to α-synuclein (αS) aggregates in complex with the small molecule anle138b, which is a clinical drug candidate for disease modifying therapy. The small central pyrazole moiety of anle138b is detected in close proximity to the protein backbone and differences in the contacts between fibrils and early intermediates are observed. For intermediate species, the 100 K condition for DNP helps to preserve the aggregation state, while for both fibrils and oligomers, the DNP enhancement is essential to obtain sufficient sensitivity.
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Affiliation(s)
- Rıza Dervişoğlu
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Leif Antonschmidt
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Evgeny Nimerovsky
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Myeongkyu Kim
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sergey Ryazanov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Andrei Leonov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | | | - Melanie Wegstroth
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Stefan Becker
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Kumari K, Sharma GS, Gupta A, Singh KS, Singh LR. Functionally active cross-linked protein oligomers formed by homocysteine thiolactone. Sci Rep 2023; 13:5620. [PMID: 37024663 PMCID: PMC10079695 DOI: 10.1038/s41598-023-32694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Deposition of high-order protein oligomers is a common hallmark of a large number of human diseases and therefore, has been of immense medical interest. From the past several decades, efforts are being made to characterize protein oligomers and explore how they are linked with the disease pathologies. In general, oligomers are non-functional, rather cytotoxic in nature while the functional (non-cytotoxic) oligomers are quite rare. In the present study, we identified new protein oligomers of Ribonuclease-A and Lysozyme that contain functionally active fractions. These functional oligomers are disulfide cross-linked, native-like, and obtained as a result of the covalent modification of the proteins by the toxic metabolite, homocysteine thiolactone accumulated under hyperhomocysteinemia (a condition responsible for cardiovascular complications including atherosclerosis). These results have been obtained from the extensive analysis of the nature of oligomers, functional status, and structural integrity of the proteins using orthogonal techniques. The study implicates the existence of such oligomers as protein sinks that may sequester toxic homocysteines in humans.
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Affiliation(s)
- Kritika Kumari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, 110075, India
| | - Akshita Gupta
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
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Poboinev VV, Khrustalev VV, Akunevich AA, Shalygo NV, Stojarov AN, Khrustaleva TA, Kordyukova LV. Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1. Protein J 2023:10.1007/s10930-023-10101-z. [PMID: 36952102 PMCID: PMC10034248 DOI: 10.1007/s10930-023-10101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
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36
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Zhang Y, Dee DR. Morphology, Formation Kinetics and Core Composition of Pea and Soy 7S and 11S Globulin Amyloid Fibrils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4755-4765. [PMID: 36890640 DOI: 10.1021/acs.jafc.2c08704] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Legume seed storage proteins can be induced to form amyloid fibrils upon heating at low pH, which could improve their functionality for use in food and materials. However, the amyloidogenic regions of legume proteins are largely unknown. Here, we used LC-MS/MS to determine the amyloid core regions of fibrils formed by enriched pea and soy 7S and 11S globulins at pH 2, 80 °C, and characterized their hydrolysis, assembly kinetics, and morphology. A lag phase was absent from the fibrillation kinetics of pea and soy 7S globulins, while 11S globulins and crude extracts displayed a similar lag time. Pea and soy protein fibrils differed in morphology, with most pea fibrils being straight and soy fibrils being worm-like. Pea and soy globulins were abundant in amyloid-forming peptides, with over 100 unique fibril-core peptides from pea 7S and around 50 unique fibril-core peptides identified from pea 11S, soy 7S, and soy 11S globulins. Amyloidogenic regions derive predominantly from the homologous core region of 7S globulins and the basic subunit of 11S globulins. Overall, pea and soy 7S and 11S globulins are rich in amyloidogenic regions. This study will help understand their fibrillation mechanism and engineer protein fibrils with specific structures and functionality.
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Affiliation(s)
- Yuran Zhang
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Derek R Dee
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, 2205 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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Saric M, Scheibel T. Two-in-One Spider Silk Protein with Combined Mechanical Features in All-Aqueous Spun Fibers. Biomacromolecules 2023; 24:1744-1750. [PMID: 36913547 DOI: 10.1021/acs.biomac.2c01500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Major ampullate (MA) spider silk reveals outstanding mechanical properties in terms of a unique combination of high tensile strength and extensibility, unmatched by most other known native or synthetic fiber materials. MA silk contains at least two spider silk proteins (spidroins), and here, a novel two-in-one (TIO) spidroin was engineered, resembling amino acid sequences of such two of the European garden spider. The combination of mechanical and chemical features of both underlying proteins facilitated the hierarchical self-assembly into β-sheet-rich superstructures. Due to the presence of native terminal dimerization domains, highly concentrated aqueous spinning dopes could be prepared from recombinant TIO spidroins. Subsequently, fibers were spun in a biomimetic, aqueous wet-spinning process, yielding mechanical properties at least twice as high as fibers spun from individual spidroins or blends. The presented processing route holds great potential for future applications using ecological green high-performance fibers.
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Affiliation(s)
- Merisa Saric
- Lehrstuhl Biomaterialien, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, 95447 Bayreuth, Germany
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, 95447 Bayreuth, Germany.,Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.,Bayreuther Materialzentrum (BayMat), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.,Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.,Bayrisches Polymerinstitut (BPI), Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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Puneeth Kumar DRGKR, Reja RM, Senapati DK, Singh M, Nalawade SA, George G, Kaul G, Akhir A, Chopra S, Raghothama S, Gopi HN. A cationic amphiphilic peptide chaperone rescues Aβ 42 aggregation and cytotoxicity. RSC Med Chem 2023; 14:332-340. [PMID: 36846376 PMCID: PMC9945854 DOI: 10.1039/d2md00414c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Directing Aβ42 to adopt a conformation that is free from aggregation and cell toxicity is an attractive and viable strategy to design therapeutics for Alzheimer's disease. Over the years, extensive efforts have been made to disrupt the aggregation of Aβ42 using various types of inhibitors but with limited success. Herein, we report the inhibition of aggregation of Aβ42 and disintegration of matured fibrils of Aβ42 into smaller assemblies by a 15-mer cationic amphiphilic peptide. The biophysical analysis comprising thioflavin T (ThT) mediated amyloid aggregation kinetic analysis, dynamic light scattering, ELISA, AFM, and TEM suggested that the peptide effectively disrupts Aβ42 aggregation. The circular dichroism (CD) and 2D-NMR HSQC analysis reveal that upon interaction, the peptide induces a conformational change in Aβ42 that is free from aggregation. Further, the cell assay experiments revealed that this peptide is non-toxic to cells and also rescues the cells from the toxicity of Aβ42. Peptides with a shorter length displayed either weak or no inhibitory effect on Aβ42 aggregation and cytotoxicity. These results suggest that the 15-residue cationic amphiphilic peptide reported here may serve as a potential therapeutic candidate for Alzheimer's disease.
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Affiliation(s)
- DRGKoppalu R. Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | - Rahi M. Reja
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | | | - Manjeet Singh
- Department of Chemistry, Indian Institute of Science Education and Research Dr. Homi Bhabha Road, Pashan Pune-411008 India
| | - Sachin A. Nalawade
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | - Gijo George
- NMR Research Centre, Indian Institute of ScienceBangalore-560012India
| | - Grace Kaul
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia,AcSIR: Academy of Scientific and Innovative Research (AcSIR)Ghaziabad 201002India
| | - Abdul Akhir
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia
| | - Sidharth Chopra
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia,AcSIR: Academy of Scientific and Innovative Research (AcSIR)Ghaziabad 201002India
| | | | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
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The role of surface activity on the amyloid fibrillation pathway of bovine serum albumin upon interaction with glyphosate. Int J Biol Macromol 2023; 226:1166-1177. [PMID: 36427623 DOI: 10.1016/j.ijbiomac.2022.11.230] [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: 09/25/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
As an active ingredient in its derivative products, glyphosate has emerged as the most widespread herbicide in recent decades. Bovine serum albumin (BSA) as a carrier protein may be adversely affected by structural changes due to binding affinity with glyphosate, which may lead to dysfunctionality or metabolic disorders. This study aimed to investigate the interaction of glyphosate with BSA and its thermal fibrillation pathway employing techniques such as dynamic surface tension, fluorescence quenching, ThT binding, circular dichroism spectroscopy, and reactive oxygen species (ROS) measurement, as well as molecular dynamics (MD) studies. The adsorption dynamic analysis suggested hydrophobic moiety at higher concentrations of glyphosate upon interaction with BSA. MD results suggested a slight fluctuation due to glyphosate interaction with protein molecules. The carboxy group presented in glyphosate made a hydrogen bond with the hydroxyl group of TYR147. The fluorescence quenching and diffusion studies approved BSA's increased unfolding and hydrophobicity resulting from glyphosate interaction, which would induce fibrillation/aggregation, according to our fibrillation kinetics data. The surface activity of glyphosate at higher concentrations and its approved involvement in structural changes of BSA through hydrogen bonding may raise concerns about its potential side effect on farm animals and the food cycle.
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40
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Meena P, Kishore N. Potential of tetradecyltrimethylammonium bromide in preventing fibrillation/aggregation of lysozyme: biophysical studies. J Biomol Struct Dyn 2022; 40:13378-13391. [PMID: 34662249 DOI: 10.1080/07391102.2021.1987989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A key step in the prevention of neurodegenerative disorders is to inhibit protein aggregation or fibrillation process. Functionality recognition is an essential strategy in developing effective therapeutics in addressing the treatment of amyloidosis. Here, we have focused on an approach based on structure-property energetics correlation associated with tetradecyltrimethylammonium bromide (TTAB), a cationic surfactant that acts as an inhibitor targeting different stages of hen egg-white lysozyme fibrillation. Characterization of amyloid fibrils and the inhibitory capability of 16 mM TTAB surfactant on fibrillation were investigated with the calorimetric, spectroscopic and microscopic techniques. ThT binding fluorescence studies inferred that micellar TTAB exerts its maximum inhibitory effect against amyloid fibrillation than monomer TTAB. The TEM measurements also confirmed complete absence of amyloid fibrils at micellar TTAB. At the same time, the transformation of β-sheet to α-helix under the action of TTAB was confirmed by the Far-UV CD spectroscopy. Although there have been some reports suggesting that cationic surfactants can induce aggregation in proteins, this work suggests that polar interactions between head groups of TTAB and amyloid fibrils are the predominant factors that cause retardation in fibrillation by interrupting/disturbing the intermolecular hydrogen bond of β-sheets. The present finding has explored the knowledge-based details in developing efficient potent inhibitors and provides a platform to treat diseases associated with protein misfolding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pooja Meena
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
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Alvarez AB, Caruso B, Petersen SB, Rodríguez PEA, Fidelio GD. Melittin-solid phospholipid mixed films trigger amyloid-like nano-fibril arrangements at air-water interface. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184048. [PMID: 36115495 DOI: 10.1016/j.bbamem.2022.184048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
We used the Langmuir monolayers technique to study the surface properties of melittin toxin mixed with either liquid-condensed DSPC or liquid-expanded POPC phospholipids. Pure melittin peptide forms stable insoluble monolayers at the air-water interface without interacting with Thioflavin T (Th-T), a sensitive probe to detect protein amyloid formation. When melittin peptide is mixed with DSPC lipid at 50 % of peptide area proportion at the surface, we observed the formation of fibril-like structures detected by Brewster angle microscopy (BAM), but they were not observable with POPC. The nano-structures in the melittin-DSPC mixtures became Th-T positive labeling when the arrangement was observed with fluorescence microscopy. In this condition, Th-T undergoes an unexpected shift in the typical emission wavelength of this amyloid marker when a 2D fluorescence analysis is conducted. Even when reflectivity analysis of BAM imaging evidenced that these structures would correspond to the DSPC lipid component of the mixture, the interpretation of ATR-FTIR and Th-T data suggested that both components were involved in a new lipid-peptide rearrangement. These nano-fibril arrangements were also evidenced by scanning electron and atomic force microscopy when the films were transferred to a mica support. The fibril formation was not detected when melittin was mixed with the liquid-expanded POPC lipid. We postulated that DSPC lipids can dynamically trigger the process of amyloid-like nano-arrangement formation at the interface. This process is favored by the relative peptide content, the quality of the interfacial environment, and the physical state of the lipid at the surface.
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Affiliation(s)
- Alain Bolaño Alvarez
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Argentina
| | - Benjamín Caruso
- Cátedra de Química Biológica, Departamento de Química, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Argentina; Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), CONICET, Universidad Nacional de Córdoba. Córdoba, Argentina
| | | | | | - Gerardo D Fidelio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Argentina.
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42
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:ijms232113428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9600503916
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Majid N, Siddiqi MK, Alam A, Malik S, Ali W, Khan RH. Cholic acid inhibits amyloid fibrillation: Interplay of protonation and deprotonation. Int J Biol Macromol 2022; 221:900-912. [PMID: 36096254 DOI: 10.1016/j.ijbiomac.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 11/29/2022]
Abstract
Amyloidopathies are the consequence of misfolding with subsequent aggregation affecting people worldwide. Irrespective of speedy advancement in the field of therapeutics no agent for treating amyloidopathies has been discovered and thus targeting amyloid fibrillation process via repositioning of small molecules can be fruitful. According to previous reports potential amyloid inhibitors possess unique features like, hydrophobicity, aromaticity, charge etc. Herein, we have explored the effect of Cholic acid (CA) on amyloid fibrillation irrespective of the charge (determined by Zetasizer) using four proteins Human Serum Albumin, Bovine Serum Albumin, Human Insulin and Beta-lactoglobulin (HSA, BSA, HI and BLG) employing biophysical, imaging and computational techniques. ThT results revealed that CA in both protonated and deprotonated form is potent to curb HSA, BSA, BLG aggregation ~50% and HI aggregation ~96% in a dose dependent manner (in accord with CD, ANS and Congo red assay). Interestingly, CA treated samples displayed reduced cytotoxicity (Hemolytic assay) with altered morphology (TEM) and mechanism behind inhibition may be the interaction of CA with proteins via hydrophobic interactions and hydrogen bonding (supported by molecular docking results). This study proved CA (irrespective of the pH) a potential inhibitor of amyloidosis thus can be helpful in generalizing and repurposing the related drugs/compounds for their anti-aggregation behavior as an implication towards treating amyloidopathies.
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Affiliation(s)
- Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | | | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Sadia Malik
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Wareesha Ali
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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44
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Tomas-Grau R, González-Lizárraga F, Ploper D, Avila CL, Socías SB, Besnault P, Tourville A, Mella RM, Villacé P, Salado C, Rose C, Seon-Méniel B, Brunel JM, Ferrié L, Raisman-Vozari R, Michel PP, Figadère B, Chehín R. Neuroprotective Effects of a Novel Demeclocycline Derivative Lacking Antibiotic Activity: From a Hit to a Promising Lead Compound. Cells 2022; 11:cells11172759. [PMID: 36078167 PMCID: PMC9454755 DOI: 10.3390/cells11172759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 12/09/2022] Open
Abstract
The antibiotic tetracycline demeclocycline (DMC) was recently reported to rescue α-synuclein (α-Syn) fibril-induced pathology. However, the antimicrobial activity of DMC precludes its potential use in long-term neuroprotective treatments. Here, we synthesized a doubly reduced DMC (DDMC) derivative with residual antibiotic activity and improved neuroprotective effects. The molecule was obtained by removal the dimethylamino substituent at position 4 and the reduction of the hydroxyl group at position 12a on ring A of DMC. The modifications strongly diminished its antibiotic activity against Gram-positive and Gram-negative bacteria. Moreover, this compound preserved the low toxicity of DMC in dopaminergic cell lines while improving its ability to interfere with α-Syn amyloid-like aggregation, showing the highest effectiveness of all tetracyclines tested. Likewise, DDMC demonstrated the ability to reduce seeding induced by the exogenous addition of α-Syn preformed fibrils (α-SynPFF) in biophysical assays and in a SH-SY5Y-α-Syn-tRFP cell model. In addition, DDMC rendered α-SynPFF less inflammogenic. Our results suggest that DDMC may be a promising drug candidate for hit-to-lead development and preclinical studies in Parkinson's disease and other synucleinopathies.
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Affiliation(s)
- Rodrigo Tomas-Grau
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Florencia González-Lizárraga
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Diego Ploper
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - César L. Avila
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Sergio B. Socías
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
| | - Pierre Besnault
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Aurore Tourville
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Rosa M. Mella
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Patricia Villacé
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Clarisa Salado
- Innoprot SL, Parque Tecnológico de Bizkaia, Edificio 502, 48160 Derio, Spain
| | - Clémence Rose
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
| | | | - Jean-Michel Brunel
- UMR_MD1 “Membranes et Cibles Thérapeutiques”, U1261 INSERM, Aix-Marseille Université, 13385 Marseille, France
| | - Laurent Ferrié
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
| | - Rita Raisman-Vozari
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Patrick P. Michel
- Paris Brain Institute-ICM, Inserm, CNRS, Sorbonne Université APHP, Hôpital de la Pitié la Pitié-Salpêtrière, 75013 Paris, France
| | - Bruno Figadère
- BioCIS, Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France
- Correspondence: (B.F.); (R.C.)
| | - Rosana Chehín
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Pasaje Dorrego 1080, San Miguel de Tucumán 4000, Argentina
- Correspondence: (B.F.); (R.C.)
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Tran CH, Saha R, Blanco C, Bagchi D, Chen IA. Modulation of α-Synuclein Aggregation In Vitro by a DNA Aptamer. Biochemistry 2022; 61:1757-1765. [PMID: 35994742 PMCID: PMC9454088 DOI: 10.1021/acs.biochem.2c00207] [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] [Indexed: 11/30/2022]
Abstract
Protein aggregation is an important problem for human health and biotechnology, with consequences in areas ranging from neurodegenerative diseases to protein production yields. Methods to modulate protein aggregation are therefore essential. One suggested method to modulate protein aggregation is the use of nucleic acid aptamers, that is, single-stranded nucleic acids that have been selected to specifically bind to a target. Previous studies in some systems have demonstrated that aptamers may inhibit protein aggregation, including for α-synuclein, a protein implicated in synucleinopathies. However, the mechanisms by which aptamers might affect or modulate aggregation have not been fully determined. In this study, we investigated the effect of an aptamer that binds α-synuclein oligomer, T-SO508, on α-synuclein aggregation in vitro using thioflavin T to monitor aggregation kinetics, and we performed atomic force microscopy, transmission electron microscopy, and analytical ultracentrifugation to characterize intermediate structures. The results indicated that T-SO508, but not control DNA sequences, extends the lag phase of aggregation and stabilizes formation of a small non-fibrillar aggregate complex. Attempts to use the aptamer-induced complexes to seed fibril formation did not in fact accelerate aggregation, indicating that these structures are off-pathway for aggregation. This study highlights a potential mechanism by which aptamers may modulate the aggregation properties of proteins.
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Affiliation(s)
- Claire H Tran
- Program in Biomolecular Sciences and Engineering, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Ranajay Saha
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Celia Blanco
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Damayanti Bagchi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Irene A Chen
- Program in Biomolecular Sciences and Engineering, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
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Mallesh R, Khan J, Pradhan K, Roy R, Jana NR, Jaisankar P, Ghosh S. Design and Development of Benzothiazole-Based Fluorescent Probes for Selective Detection of Aβ Aggregates in Alzheimer's Disease. ACS Chem Neurosci 2022; 13:2503-2516. [PMID: 35926183 DOI: 10.1021/acschemneuro.2c00361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The formation and accumulation of amyloid beta (Aβ) peptide are considered the crucial events that are responsible for the progression of Alzheimer's disease (AD). Herein, we have designed and synthesized a series of fluorescent probes by using electron acceptor-donor end groups interacting with a π-conjugating system for the detection of Aβ aggregates. The chemical structure of these probes denoted as RMs, having a conjugated π-system (C═C), showed a maximum emission in PBS (>600 nm), which is the best range for a fluorescent imaging probe. Among all these probes, RM-28 showed an excellent fluorescence property with an emission maximum of >598 nm upon binding to Aβ aggregates. RM-28 also showed high sensitivity (7.5-fold) and high affinities toward Aβ aggregates (Kd = 175.69 ± 4.8 nM; Ka = 0.5 × 107 M-1). It can cross the blood-brain barrier of mice efficiently. The affinity of RM-28 toward Aβ aggregates was observed in 3xTg-AD brain sections of the hippocampus and cortex region using a fluorescent imaging technique, as well as an in vitro fluorescence-based binding assay with Aβ aggregates. Moreover, RM-28 is highly specific to Aβ aggregates and does not bind with intracellular proteins like bovine serum albumin (BSA) and α-synuclein (α-Syn) aggregates. The results indicate that the probe RM-28 emerges as an efficient and veritable highly specific fluorescent probe for the detection of Aβ aggregates in both in vitro and in vivo model systems.
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Affiliation(s)
- Rathnam Mallesh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India.,National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
| | - Juhee Khan
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Krishnangsu Pradhan
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Nihar Ranjan Jana
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Parasuraman Jaisankar
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Surajit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India.,National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
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47
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Khan AN, Nabi F, Ajmal MR, Ali SM, Almutairi FM, Alalawy AI, Khan RH. Moxifloxacin Disrupts and Attenuates Aβ42 Fibril and Oligomer Formation: Plausibly Repositioning an Antibiotic as Therapeutic against Alzheimer's Disease. ACS Chem Neurosci 2022; 13:2529-2539. [PMID: 35930676 DOI: 10.1021/acschemneuro.2c00371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The aggregation of Aβ42 is established as a key factor in the development of Alzheimer's disease (AD). Consequently, molecules that inhibit aggregation of peptide may lead to therapies to prevent or control AD. Several studies suggest that oligomeric intermediates present during aggregation may be more cytotoxic than fibrils themselves. In this work, we examine the inhibitory activity of an antibiotic MXF on aggregation (fibrils and oligomers) and disaggregation of Aβ42 using various biophysical and microscopic studies. Computational analysis was done to offer mechanistic insight. The amyloid formation of Aβ42 is suppressed by MXF, as demonstrated by the decrease in both the corresponding ThT fluorescence intensity and other biophysical techniques. The lag phase of amyloid formation doubled from 4.53 to 9.66 h in the presence of MXF. The addition of MXF at the completion of the fibrillation reaction, as monitored by ThT, led to a rapid, concentration dependent, exponential decrease in fluorescence signal that was consistent with loss of fibrils. We used TEM to directly demonstrate that MXF caused fibrils to disassemble. Our docking results show that MXF binds to both monomeric and fibrillar forms of Aβ42 with significant affinities. We also observed breaking of fibrils in the presence of MXF through molecular dynamics simulation. These findings suggest that antibiotic MXF could be a promising lead compound with dual role as fibril/oligomer inhibitor and disaggregase for further development as potential repurposed therapeutic against AD.
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Affiliation(s)
- Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Mohammad Rehan Ajmal
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Syed Moasfar Ali
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Fahad M Almutairi
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Adel I Alalawy
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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Malik S, Zaidi N, Siddiqi MK, Majid N, Masroor A, Salam S, Khan RH. Mechanistic insight into inhibition of amyloid fibrillation of human serum albumin by Vildagliptin. Colloids Surf B Biointerfaces 2022; 216:112563. [PMID: 35588684 DOI: 10.1016/j.colsurfb.2022.112563] [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: 03/10/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Protein aggregation leads to several human pathologies such as Alzheimer's disease (AD), type 2 diabetes (T2D), Parkinson's disease (PD), etc. Due to the overlap in the mechanisms of type 2 diabetes and brain disorders, common effective pharmacological interventions to treat both T2D and AD is under extensive research. Therefore, major aim of research is to repurpose already established treatment of diabetes to cure AD as well. This study evaluates mechanistic insight into anti-amyloidogenic potential of anti-diabetic drug Vildagliptin (VLD) on human serum albumin fibrillation (HSA) by using biophysical, calorimetric, imaging techniques along with hemolytic assay. Dynamic light scattering (DLS) and Rayleigh light scattering (RLS) results showed presence of few small-sized aggregates in the presence of VLD which are formed by deaccelerating the amyloidogenesis as shown by thioflavin T (ThT) fluorescence and Congo red (CR) binding assay. Further, Isothermal titration calorimetry (ITC), steady state fluorescence quenching, molecular docking results revealed that VLD form complex with amyloid facilitating state of HSA and consequently mask the hydrophobic residues involved in amyloidogenesis as evident from decrease in ANS fluorescence. Differential scanning calorimetry (DSC) results confirm that VLD stabilizes the amyloid facilitating state of HSA. In addition, SEM images demonstrated that VLD alleviates the hemolytic effect induced by fibrils of HSA. This study reports VLD as a potential inhibitor of amyloid fibrillation and provides promising results to repurpose VLD as a drug candidate for the cure of Alzheimer's diseases along with diabetes.
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Affiliation(s)
- Sadia Malik
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | | | - Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Aiman Masroor
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Samreen Salam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan H Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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49
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Grether NB, Napravnik F, Imhof T, Linke RP, Bräsen JH, Schmitz J, Dohrn M, Schneider C, Svačina MKR, Stetefeld J, Koch M, Lehmann HC. Amyloidogenicity assessment of transthyretin gene variants. Ann Clin Transl Neurol 2022; 9:1252-1263. [PMID: 35903975 PMCID: PMC9380149 DOI: 10.1002/acn3.51626] [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: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Hereditary transthyretin‐mediated amyloidosis is a treatable condition caused by amyloidogenic variants in the transthyretin‐gene resulting in severe peripheral neuropathy or cardiomyopathy. Only about a third of over 130 known variants are clearly pathogenic, most are classified as variants of uncertain significance. A clear delineation of these into pathogenic or non‐pathogenic is highly desirable but hampered by low frequency and penetrance. We thus sought to characterize their amylogenic potential by an unbiased in vitro approach. Methods Thioflavin T and turbidity assays were used to compare the potential of mammalian cell expressed wt‐transthyretin and 12 variant proteins (either variants of uncertain significance, benign, pathogenic) to aggregate and produce amyloid fibrils in vitro. As proof of principle, the assays were applied to transthyretin‐Ala65Val, a variant that was newly detected in a family with peripheral neuropathy and amyloid deposits in biopsies. In silico analysis was performed to compare the position of the benign and pathogenic variants. Results Transthyretin‐Ala65Val showed a significantly higher amyloidogenic potential than wt‐transthyretin, in both turbidity‐ and Thioflavin T‐assays, comparable to known pathogenic variants. The other eight tested variants did not show an increased amyloidogenic potential. In silico structural analysis further confirmed differences between pathogenic and benign variants in position and interactions. Interpretation We propose a biochemical approach to assess amyloidogenic potential of transthyretin variants. As exemplified by transthyretin‐Ala65Val, data of three assays together with histopathology clearly demonstrates its amyloidogenicity.
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Affiliation(s)
- Nicolai B Grether
- Department of Neurology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Felix Napravnik
- Department of Neurology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, Cologne, Germany
| | | | - Jan H Bräsen
- Nephropathology Unit, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Jessica Schmitz
- Nephropathology Unit, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Maike Dohrn
- Department of Neurology, Medical Faculty of the RWTH Aachen University Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Christian Schneider
- Department of Neurology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Martin K R Svačina
- Department of Neurology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Helmar C Lehmann
- Department of Neurology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
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50
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Gupta T, Mondal AK, Pani I, Chattopadhyay K, Pal SK. Elucidating liquid crystal-aqueous interface for the study of cholesterol-mediated action of a β-barrel pore forming toxin. SOFT MATTER 2022; 18:5293-5301. [PMID: 35790122 DOI: 10.1039/d2sm00447j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pore-forming toxins (PFTs) produced by pathogenic bacteria serve as prominent virulence factors with potent cell-killing activity. Most of the β-barrel PFTs form transmembrane oligomeric pores in the membrane lipid bilayer in the presence of cholesterol. The pore-formation mechanisms of the PFTs highlight well-orchestrated regulated events in the membrane environment, which involve dramatic changes in the protein structure and organization. Also, concerted crosstalk between protein and membrane lipid components appears to play crucial roles in the process. Membrane-damaging lesions formed by the pore assembly of the PFTs would also be expected to impose drastic alterations in the membrane organization, details of which remain obscure in most of the cases. Prior reports have established that aqueous interfaces of liquid crystals (LCs) offer promise as responsive interfaces for biomolecular events (at physiologically relevant concentrations), which can be visualized as optical signals. Inspired by this, herein, we sought to understand the lipid membrane interactions of a β-barrel PFT i.e., Vibrio cholerae cytolysin (VCC), using LC-aqueous interfaces. Our results show the formation of dendritic patterns upon the addition of VCC to the lipid embedded with cholesterol over the LC film. In contrast, we did not observe any LC reorientation upon the addition of VCC to the lipid-laden LC-aqueous interface in the absence of cholesterol. An array of techniques such as polarizing optical microscopy (POM), atomic force microscopy (AFM), and fluorescence measurements were utilized to decipher the LC response to the lipid interactions of VCC occurring at these interfaces. Altogether, the results obtained from our study provide a novel platform to explore the mechanistic aspects of the protein-membrane interactions, in the process of membrane pore-formation by the membrane-damaging PFTs.
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Affiliation(s)
- Tarang Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
| | - Anish Kumar Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
| | - Ipsita Pani
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
| | - Santanu Kumar Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector-81, SAS Nagar, Mohali 140306, India.
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