1
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Controlling amyloid formation of intrinsically disordered proteins and peptides: slowing down or speeding up? Essays Biochem 2022; 66:959-975. [PMID: 35975807 DOI: 10.1042/ebc20220046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022]
Abstract
The pathological assembly of intrinsically disordered proteins/peptides (IDPs) into amyloid fibrils is associated with a range of human pathologies, including neurodegeneration, metabolic diseases and systemic amyloidosis. These debilitating disorders affect hundreds of millions of people worldwide, and the number of people affected is increasing sharply. However, the discovery of therapeutic agents has been immensely challenging largely because of (i) the diverse number of aggregation pathways and the multi-conformational and transient nature of the related proteins or peptides and (ii) the under-development of experimental pipelines for the identification of disease-modifying molecules and their mode-of-action. Here, we describe current approaches used in the search for small-molecule modulators able to control or arrest amyloid formation commencing from IDPs and review recently reported accelerators and inhibitors of amyloid formation for this class of proteins. We compare their targets, mode-of-action and effects on amyloid-associated cytotoxicity. Recent successes in the control of IDP-associated amyloid formation using small molecules highlight exciting possibilities for future intervention in protein-misfolding diseases, despite the challenges of targeting these highly dynamic precursors of amyloid assembly.
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2
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Wang J, Liu J, Dong Q, An Y, Su J, Xie H, Sun B, Liu J. The Influence of Heparan Sulfate on Breast Amyloidosis and the Toxicity of the Pre-fibrils Formed by β-casein. Protein J 2022; 41:543-549. [PMID: 35962883 DOI: 10.1007/s10930-022-10071-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2022] [Indexed: 11/27/2022]
Abstract
Heparan sulfate (HS) as a mediator is usually involved in both inflammation and fibrosis. Besides, pre-fibrils are the intermediates of amyloid fibrils that usually cause cell death and tissue damage, like the amyloid-β in Alzheimer's disease, α-synuclein in Parkinson disease and islet amyloid polypeptide in type II diabetes mellitus. However, the related study was involved rarely in breast. Therefore, the combing technologies including hematoxylin-eosin staining and thioflavin S staining were used to investigate the influence of HS on breast amyloidosis. To further study the toxicity of the pre-fibrils formed by β-casein on the HC11 cells and the breast mammary gland, the combing technologies including pentamer formyl thiophene acetic acid fluorescence analysis, MTT assay, Annexin V/PI staining and hematoxylin-eosin staining were performed. The results demonstrated that HS, acted as an endogenous molecule, induced the inflammation and amyloid fibril formation at the same time, and there was a close relationship between inflammation and fibrosis of breast. In addition, the pre-fibrils formed by β-casein were toxic because they induced the death and apoptosis of HC11 cells, as well as the inflammation of mammary gland of rats. Therefore, the early examination and identify of the pre-fibrils in the breast were worth considering to prevent the disease development, and it was interesting to explore the HS mimetics to impair the breast amyloidosis and attenuate the inflammatory response in the future.
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Affiliation(s)
- Jia Wang
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jiayin Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Qinghai Dong
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Yang An
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jun Su
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Hongliu Xie
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Bo Sun
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jihua Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China.
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3
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Poggiolini I, Gupta V, Lawton M, Lee S, El-Turabi A, Querejeta-Coma A, Trenkwalder C, Sixel-Döring F, Foubert-Samier A, Pavy-Le Traon A, Plazzi G, Biscarini F, Montplaisir J, Gagnon JF, Postuma RB, Antelmi E, Meissner WG, Mollenhauer B, Ben-Shlomo Y, Hu MT, Parkkinen L. Diagnostic value of cerebrospinal fluid alpha-synuclein seed quantification in synucleinopathies. Brain 2022; 145:584-595. [PMID: 34894214 PMCID: PMC9014737 DOI: 10.1093/brain/awab431] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 11/12/2022] Open
Abstract
Several studies have confirmed the α-synuclein real-time quaking-induced conversion (RT-QuIC) assay to have high sensitivity and specificity for Parkinson's disease. However, whether the assay can be used as a robust, quantitative measure to monitor disease progression, stratify different synucleinopathies and predict disease conversion in patients with idiopathic REM sleep behaviour disorder remains undetermined. The aim of this study was to assess the diagnostic value of CSF α-synuclein RT-QuIC quantitative parameters in regard to disease progression, stratification and conversion in synucleinopathies. We performed α-synuclein RT-QuIC in the CSF samples from 74 Parkinson's disease, 24 multiple system atrophy and 45 idiopathic REM sleep behaviour disorder patients alongside 55 healthy controls, analysing quantitative assay parameters in relation to clinical data. α-Synuclein RT-QuIC showed 89% sensitivity and 96% specificity for Parkinson's disease. There was no correlation between RT-QuIC quantitative parameters and Parkinson's disease clinical scores (e.g. Unified Parkinson's Disease Rating Scale motor), but RT-QuIC positivity and some quantitative parameters (e.g. Vmax) differed across the different phenotype clusters. RT-QuIC parameters also added value alongside standard clinical data in diagnosing Parkinson's disease. The sensitivity in multiple system atrophy was 75%, and CSF samples showed longer T50 and lower Vmax compared to Parkinson's disease. All RT-QuIC parameters correlated with worse clinical progression of multiple system atrophy (e.g. change in Unified Multiple System Atrophy Rating Scale). The overall sensitivity in idiopathic REM sleep behaviour disorder was 64%. In three of the four longitudinally followed idiopathic REM sleep behaviour disorder cohorts, we found around 90% sensitivity, but in one sample (DeNoPa) diagnosing idiopathic REM sleep behaviour disorder earlier from the community cases, this was much lower at 39%. During follow-up, 14 of 45 (31%) idiopathic REM sleep behaviour disorder patients converted to synucleinopathy with 9/14 (64%) of convertors showing baseline RT-QuIC positivity. In summary, our results showed that α-synuclein RT-QuIC adds value in diagnosing Parkinson's disease and may provide a way to distinguish variations within Parkinson's disease phenotype. However, the quantitative parameters did not correlate with disease severity in Parkinson's disease. The assay distinguished multiple system atrophy patients from Parkinson's disease patients and in contrast to Parkinson's disease, the quantitative parameters correlated with disease progression of multiple system atrophy. Our results also provided further evidence for α-synuclein RT-QuIC having potential as an early biomarker detecting synucleinopathy in idiopathic REM sleep behaviour disorder patients prior to conversion. Further analysis of longitudinally followed idiopathic REM sleep behaviour disorder patients is needed to better understand the relationship between α-synuclein RT-QuIC signature and the progression from prodromal to different synucleinopathies.
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Grants
- Wellcome Trust
- J-0901 Parkinson's UK
- MR/T046287/1 Medical Research Council
- EPSRC
- UKRI-MRC
- EU Horizon 2020 and Michael J. Fox Foundation
- IPMDS
- Canadian Institutes of Health Research and honoraria to serve on advisory boards for EISAI and JAZZ Pharma outside the present field of research
- Canadian Institutes in Health Research, Canada Research Chair, and National Institute on Aging
- Fonds de la Recherche en Sante
- Canadian Institute of Health Research
- The Parkinson Society of Canada
- Weston-Garfield Foundation
- Michael J. Fox Foundation and the Webster Foundation
- Takeda, Roche, Teva Neurosciences, Novartis Canada, Biogen, Boehringer Ingelheim, Theranexus, GE HealthCare, Jazz Pharmaceuticals, AbbVie, Jannsen, Otsuko, Phytopharmics and Inception Sciences
- Deutsche Forschungsgemeinschaft (DFG), EU (Horizon2020), Parkinson Fonds Deutschland, Deutsche Parkinson Vereinigung, Parkinson’s Foundation
- MRC, Wellcome Trust, NIHR and Parkinson’s UK
- Parkinson’s UK, NIHR Oxford Biomedical Research Centre, Cure Parkinson’s Trust, Lab10X, NIHR, Michael J Fox Foundation, H2020 European Union, GE Healthcare and PSP Association
- Parkinson’s UK, Weston Brain Institute and Michael J Fox Foundation
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Affiliation(s)
- Ilaria Poggiolini
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
| | - Vandana Gupta
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
| | - Michael Lawton
- School of Social and Community Medicine, Bristol Medical School, University of Bristol, UK
| | - Seoyun Lee
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
| | - Aadil El-Turabi
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK
| | - Agustin Querejeta-Coma
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
| | - Claudia Trenkwalder
- Department of Neurosurgery, University Medical Center Goettingen, Göttingen, Germany
- Paracelsus Elena Klinik, Centre for Movement Disorders, Kassel, Germany
| | - Friederike Sixel-Döring
- Paracelsus Elena Klinik, Centre for Movement Disorders, Kassel, Germany
- Department of Neurology, Philipps-University Marburg, Germany
| | - Alexandra Foubert-Samier
- French Reference Centre for MSA, University Hospital Bordeaux, Bordeaux, France
- Institute des Maladies Neurodégénératives, CHU Bordeaux and Univ. Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, France
| | - Anne Pavy-Le Traon
- French Reference Centre for MSA, University Hospital of Toulouse, Toulouse, France
| | - Giuseppe Plazzi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
- IRCCS—Institute of the Neurological Sciences of Bologna, Bologna, Italy
| | - Francesco Biscarini
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Jacques Montplaisir
- Center for Advanced Research in Sleep Medicine, CIUSSS-NÎM-Hôpital du Sacré-Cœur de Montréal, Montreal, Quebec, Canada
- Department of Psychiatry, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-François Gagnon
- Center for Advanced Research in Sleep Medicine, CIUSSS-NÎM-Hôpital du Sacré-Cœur de Montréal, Montreal, Quebec, Canada
- Department of Psychology, Université du Québec à Montréal, Montreal, Quebec, Canada
| | - Ronald B Postuma
- Center for Advanced Research in Sleep Medicine, CIUSSS-NÎM-Hôpital du Sacré-Cœur de Montréal, Montreal, Quebec, Canada
- Department of Neurology, McGill University, Montreal General Hospital, Montreal, Quebec, Canada
| | - Elena Antelmi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Wassilios G Meissner
- Institute des Maladies Neurodégénératives, CHU Bordeaux and Univ. Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, France
- Department of Medicine, University of Otago, Christchurch, and New Zealand Brain Research Institute, Christchurch, New Zealand
| | - Brit Mollenhauer
- Department of Neurosurgery, University Medical Center Goettingen, Göttingen, Germany
- Paracelsus Elena Klinik, Centre for Movement Disorders, Kassel, Germany
| | - Yoav Ben-Shlomo
- School of Social and Community Medicine, Bristol Medical School, University of Bristol, UK
| | - Michele T Hu
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, UK
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Ramesh M, Acharya A, Murugan NA, Ila H, Govindaraju T. Thiophene-Based Dual Modulators of Aβ and Tau Aggregation. Chembiochem 2021; 22:3348-3357. [PMID: 34546619 DOI: 10.1002/cbic.202100383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Indexed: 01/29/2023]
Abstract
Alzheimer's disease is characterized by the accumulation of amyloid beta (Aβ) and Tau aggregates in the brain, which induces various pathological events resulting in neurodegeneration. There have been continuous efforts to develop modulators of the Aβ and Tau aggregation process to halt or modify disease progression. A few small-molecule-based inhibitors that target both Aβ and Tau pathology have been reported. Here, we report the screening of a targeted library of small molecules to modulate Aβ and Tau aggregation together with their in vitro, in silico and cellular studies. In vitro ThT fluorescence assay, dot blot assay, gel electrophoresis and transmission electron microscopy (TEM) results have shown that thiophene-based lead molecules effectively modulate Aβ aggregation and inhibit Tau aggregation. In silico studies performed by employing molecular docking, molecular dynamics and binding-free energy calculations have helped in understanding the mechanism of interaction of the lead thiophene compounds with Aβ and Tau fibril targets. In cellulo studies revealed that the lead candidate is biocompatible and effectively ameliorates neuronal cells from Aβ and Tau-mediated amyloid toxicity.
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Affiliation(s)
- Madhu Ramesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Anand Acharya
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - N Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044, Stockholm, Sweden
| | - Hiriyakkanavar Ila
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
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5
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Sandin L, Sjödin S, Brorsson AC, Kågedal K, Civitelli L. The Luminescent Conjugated Oligothiophene h-FTAA Attenuates the Toxicity of Different Aβ Species. Biochemistry 2021; 60:2773-2780. [PMID: 34469142 PMCID: PMC8459454 DOI: 10.1021/acs.biochem.1c00265] [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: 11/28/2022]
Abstract
The prevailing opinion is that prefibrillar β-amyloid (Aβ) species, rather than end-stage amyloid fibrils, cause neuronal dysfunction in Alzheimer's disease, although the mechanisms behind Aβ neurotoxicity remain to be elucidated. Luminescent conjugated oligothiophenes (LCOs) exhibit spectral properties upon binding to amyloid proteins and have previously been reported to change the toxicity of Aβ1-42 and prion protein. In a previous study, we showed that an LCO, pentamer formyl thiophene acetic acid (p-FTAA), changed the toxicity of Aβ1-42. Here we investigated whether an LCO, heptamer formyl thiophene acetic acid (h-FTAA), could change the toxicity of Aβ1-42 by comparing its behavior with that of p-FTAA. Moreover, we investigated the effects on toxicity when Aβ with the Arctic mutation (AβArc) was aggregated with both LCOs. Cell viability assays on SH-SY5Y neuroblastoma cells demonstrated that h-FTAA has a stronger impact on Aβ1-42 toxicity than does p-FTAA. Interestingly, h-FTAA, but not p-FTAA, rescued the AβArc-mediated toxicity. Aggregation kinetics and binding assay experiments with Aβ1-42 and AβArc when aggregated with both LCOs showed that h-FTAA and p-FTAA either interact with different species or affect the aggregation in different ways. In conclusion, h-FTAA protects against Aβ1-42 and AβArc toxicity, thus showing h-FTAA to be a useful tool for improving our understanding of the process of Aβ aggregation linked to cytotoxicity.
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Affiliation(s)
- Linnea Sandin
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping 581 83, Sweden
| | - Simon Sjödin
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping 581 83, Sweden
| | - Ann-Christin Brorsson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden
| | - Katarina Kågedal
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping 581 83, Sweden
| | - Livia Civitelli
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping 581 83, Sweden
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6
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Kelley M, Sant’Anna R, Fernandes L, Palhano FL. Pentameric Thiophene as a Probe to Monitor EGCG's Remodeling Activity of Mature Amyloid Fibrils: Overcoming Signal Artifacts of Thioflavin T. ACS OMEGA 2021; 6:8700-8705. [PMID: 33817533 PMCID: PMC8015118 DOI: 10.1021/acsomega.1c00680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Thioflavin T fluorescence is a gold standard probe for the detection of amyloid fibrils. Herein, we showed that mature amyloid fibrils incubated with polyphenol epigallocatechin gallate (EGCG) present a fast reduction of the thioflavin T fluorescence, which is not related to remodeling activity. We propose the use of the pentameric thiophene fluorescence for monitoring the polyphenol remodeling activity.
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7
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Ikenoue T, Aprile FA, Sormanni P, Vendruscolo M. Rationally Designed Bicyclic Peptides Prevent the Conversion of Aβ42 Assemblies Into Fibrillar Structures. Front Neurosci 2021; 15:623097. [PMID: 33716651 PMCID: PMC7947257 DOI: 10.3389/fnins.2021.623097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/27/2022] Open
Abstract
There is great interest in drug discovery programs targeted at the aggregation of the 42-residue form of the amyloid β peptide (Aβ42), since this molecular process is closely associated with Alzheimer’s disease. The use of bicyclic peptides may offer novel opportunities for the effective modification of Aβ42 aggregation and the inhibition of its cytotoxicity, as these compounds combine the molecular recognition ability of antibodies with a relatively small size of about 2 kD. Here, to pursue this approach, we rationally designed a panel of six bicyclic peptides targeting various epitopes along the sequence of Aβ42 to scan its most amyloidogenic region (residues 13–42). Our kinetic analysis and structural studies revealed that at sub-stoichiometric concentrations the designed bicyclic peptides induce a delay in the condensation of Aβ42 and the subsequent transition to a fibrillar state, while at higher concentrations they inhibit such transition. We thus suggest that designed bicyclic peptides can be employed to inhibit amyloid formation by redirecting the aggregation process toward amorphous assemblies.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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8
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Kreiser RP, Wright AK, Block NR, Hollows JE, Nguyen LT, LeForte K, Mannini B, Vendruscolo M, Limbocker R. Therapeutic Strategies to Reduce the Toxicity of Misfolded Protein Oligomers. Int J Mol Sci 2020; 21:ijms21228651. [PMID: 33212787 PMCID: PMC7696907 DOI: 10.3390/ijms21228651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The aberrant aggregation of proteins is implicated in the onset and pathogenesis of a wide range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. Mounting evidence indicates that misfolded protein oligomers produced as intermediates in the aggregation process are potent neurotoxic agents in these diseases. Because of the transient and heterogeneous nature of these elusive aggregates, however, it has proven challenging to develop therapeutics that can effectively target them. Here, we review approaches aimed at reducing oligomer toxicity, including (1) modulating the oligomer populations (e.g., by altering the kinetics of aggregation by inhibiting, enhancing, or redirecting the process), (2) modulating the oligomer properties (e.g., through the size–hydrophobicity–toxicity relationship), (3) modulating the oligomer interactions (e.g., by protecting cell membranes by displacing oligomers), and (4) reducing oligomer toxicity by potentiating the protein homeostasis system. We analyze examples of these complementary approaches, which may lead to the development of compounds capable of preventing or treating neurodegenerative disorders associated with protein aggregation.
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Affiliation(s)
- Ryan P. Kreiser
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Aidan K. Wright
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Natalie R. Block
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Jared E. Hollows
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Lam T. Nguyen
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Kathleen LeForte
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK;
- Correspondence: (M.V.); (R.L.)
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
- Correspondence: (M.V.); (R.L.)
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9
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Oliveira AC, Costa T, Justino LLG, Fausto R, Morfin JF, Tóth É, Geraldes CFGC, Burrows HD. Photophysical studies on lanthanide(III) chelates conjugated to Pittsburgh compound B as luminescent probes targeted to Aβ amyloid aggregates. Photochem Photobiol Sci 2020; 19:1522-1537. [PMID: 32966544 DOI: 10.1039/d0pp00214c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The photophysical properties of Eu3+ and Tb3+ complexes of DOTAGA and DO3A-monoamide conjugates of the Pittsburgh compound B (PiB) chromophore, prepared using linkers of different lengths and flexibilities, and which form stable negatively charged (LnL1), and uncharged (LnL2) complexes, respectively, were studied as potential probes for optical detection of amyloid aggregates. The phenylbenzothiazole (PiB) moiety absorbs light at wavelengths longer than 330 nm with a high molar absorption coefficient in both probes, and acts as an antenna in these systems. The presence of the luminescent Ln3+ ion quenches the excited states of PiB through an energy transfer process from the triplet state of PiB to the metal centre, and structured emission is seen from Eu3+ and Tb3+. The luminescence study indicates the presence of a 5D4 → T1 back transfer process in the Tb3+ complexes. It also provides insights on structural properties of the Eu3+ complexes, such as the high symmetry environment of the Eu3+ ion in a single macrocyclic conformation and the presence of one water molecule in its inner coordination sphere. The overall quantum yield of luminescence of EuL1 is higher than for EuL2. However, their low values reflect the low overall sensitization efficiency of the energy transfer process, which is a consequence of the large distances between the metal center and the antenna, especially in the EuL2 complex. DFT calculations confirmed that the most stable conformation of the Eu3+ complexes involves a combination of a square antiprismatic (SAP) geometry of the chelate and an extended conformation of the linker. The large calculated average distances between the metal center and the antenna point to the predominance of the Förster energy transfer mechanism, especially for EuL2. This study provides insights into the behavior of amyloid-targeted Ln3+ complexes as optical probes, and contributes towards their rational design.
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Affiliation(s)
- Alexandre C Oliveira
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Telma Costa
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Licinia L G Justino
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Rui Fausto
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Jean-François Morfin
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Éva Tóth
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Carlos F G C Geraldes
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal. and University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-393 Coimbra, Portugal. and CIBIT/ICNAS - Instituto de Ciências Nucleares Aplicadas à Saúde, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Hugh D Burrows
- University of Coimbra, Coimbra Chemistry Centre (CQC), Department of Chemistry, 3004-535 Coimbra, Portugal.
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10
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Ikenoue T, Aprile FA, Sormanni P, Ruggeri FS, Perni M, Heller GT, Haas CP, Middel C, Limbocker R, Mannini B, Michaels TCT, Knowles TPJ, Dobson CM, Vendruscolo M. A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease. Sci Rep 2020; 10:15280. [PMID: 32943652 PMCID: PMC7498612 DOI: 10.1038/s41598-020-69626-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31–42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer’s disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco S Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christian P Haas
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christoph Middel
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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11
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Uddin A, Roy B, Jose GP, Hossain SS, Hazra P. Sensing and modulation of amyloid fibrils by photo-switchable organic dots. NANOSCALE 2020; 12:16805-16818. [PMID: 32761038 DOI: 10.1039/d0nr04312e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Abnormal aggregation of amyloidogenic proteins (like Aβ 42, amylin, α-synuclein, insulin) and the deposition of these aggregates is believed to be associated with several diseases known as amyloidosis. The pathway of aggregation involves three distinct phases: the oligomeric, elongation and plateau phases. Among them, the oligomeric phase of Aβ 42 and α-synuclein involves the generation of transient oligomeric species suspected to cause several neurological disorders, including Alzheimer's and Parkinson's diseases. Over the past few years, scientists have devoted much more effort to devising new fluorescent molecular probes to estimate the mechanisms of formation, and have gained vital information about possible therapeutic routes for amyloidosis. However, such fluorescent probes face serious limitations because of self-quenching at high concentrations of the probe; therefore, they are inappropriate for quantitative analysis and bio-imaging experiments. Hence, smart biocompatible fluorescent probes are indispensable, as they not only overcome the drawbacks of conventional fluorescent probes, but also have the potential ability to fight amyloidosis through modulation of the pathways involved. In this work, for the first time we introduce a series of promising photo-switchable aggregation-induced emission (AIE) dots (DPAPMI, CPMI) and aggregation caused quenching (ACQ) dots (DMAPMI) which can detect amyloid fibrils in terms of switching and enhancing their fluorescence emission. Interestingly, the organic dots enhance the aggregation rate of insulin by speeding up the microscopic processes, specifically secondary nucleation (with rate constant k2) and the elongation process (with rate constant k+). Moreover, the comparison of kinetics studies with ThT suggests that our organic dots can sense pre-fibrillar aggregates of insulin during the aggregation process, which may be beneficial for the early detection of amyloid fibrils. In summary, our study indicates that these organic dots can be used for the imaging and early stage detection of amyloid fibril formation and the modulation of amyloid formation pathways.
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Affiliation(s)
- Aslam Uddin
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhaba Road, Pashan, Pune, Maharashtra, India.
| | - Bibhisan Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhaba Road, Pashan, Pune, Maharashtra, India.
| | - Gregor P Jose
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhaba Road, Pashan, Pune, Maharashtra, India
| | - Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhaba Road, Pashan, Pune, Maharashtra, India. and Centre for Energy Science, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhaba Road, Pashan, Pune, Maharashtra, India
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12
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Parlak O, Richter-Dahlfors A. Bacterial Sensing and Biofilm Monitoring for Infection Diagnostics. Macromol Biosci 2020; 20:e2000129. [PMID: 32588553 DOI: 10.1002/mabi.202000129] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Recent insights into the rapidly emerging field of bacterial sensing and biofilm monitoring for infection diagnostics are discussed as well as recent key developments and emerging technologies in the field. Electrochemical sensing of bacteria and bacterial biofilm via synthetic, natural, and engineered recognition, as well as direct redox-sensing approaches via algorithm-based optical sensing, and tailor-made optotracing technology are discussed. These technologies are highlighted to answer the very critical question: "how can fast and accurate bacterial sensing and biofilm monitoring be achieved? Following on from that: "how can these different sensing concepts be translated for use in infection diagnostics? A central obstacle to this transformation is the absence of direct and fast analysis methods that provide high-throughput results and bio-interfaces that can control and regulate the means of communication between biological and electronic systems. Here, the overall progress made to date in building such translational efforts at the level of an individual bacterial cell to a bacterial community is discussed.
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Affiliation(s)
- Onur Parlak
- AIMES-Center for the Advancement of Integrated Medical and Engineering Science, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, SE-171 77, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Agneta Richter-Dahlfors
- AIMES-Center for the Advancement of Integrated Medical and Engineering Science, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, SE-171 77, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, SE-171 77, Sweden.,Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
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13
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Jokar S, Khazaei S, Behnammanesh H, Shamloo A, Erfani M, Beiki D, Bavi O. Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer's disease therapy. Biophys Rev 2019; 11:10.1007/s12551-019-00606-2. [PMID: 31713720 DOI: 10.1007/s12551-019-00606-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported that amyloid hypothesis-based treatments can be developed as a new approach to overcome the limitations and challenges associated with conventional AD therapeutics. In this review, we will provide a comprehensive view of the challenges in AD therapy and pathophysiology. We also discuss currently known compounds that can inhibit amyloid-β (Aβ) aggregation and their potential role in advancing current AD treatments. We have specifically focused on Aβ aggregation inhibitors including metal chelators, nanostructures, organic molecules, peptides (or peptide mimics), and antibodies. To date, these molecules have been the subject of numerous in vitro and in vivo assays as well as molecular dynamics simulations to explore their mechanism of action and the fundamental structural groups involved in Aβ aggregation. Ultimately, the aim of these studies (and current review) is to achieve a rational design for effective therapeutic agents for AD treatment and diagnostics.
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Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Saeedeh Khazaei
- Department of Pharmaceutical Biomaterials , Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Hossein Behnammanesh
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, P.O. Box: 11365-11155, Tehran, Iran
| | - Mostafa Erfani
- Radiation Application Research School, Nuclear Science and Technology Research Institute (NSTRI), P.O. Box: 14155-1339, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, P.O. Box: 71555-313, Shiraz, Iran.
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14
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Abstract
Intrinsically disordered proteins play vital roles in biology, and their dysfunction contributes to many major disease states. These proteins remain challenging targets for rational ligand discovery or drug design because they are highly dynamic and fluctuate through a diverse set of conformations, frustrating structure-based approaches. To meet this challenge, we have developed protocols to efficiently identify active small molecule ligands of disordered proteins. Our approach utilizes enhanced sampling molecular dynamics and conformational analysis approaches optimized for disordered targets, coupled with computational docking and machine learning-based screens of compound libraries. By applying this protocol to an amyloid-forming segment of microtubule-associated protein tau, we successfully identified novel, chemically diverse tau ligands, including an inhibitor that delays the aggregation reaction in vitro without affecting the amount of aggregate formed at the steady state. Our results indicate that we have expanded the toolkit of protein aggregation inhibitors into new areas of chemical space and demonstrate the feasibility of our ligand discovery strategy.
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Affiliation(s)
- David W Baggett
- Department of Medicinal Chemistry , University of Washington , 1959 Northeast Pacific Street , Box 357610, Seattle , Washington 98195 , United States
| | - Abhinav Nath
- Department of Medicinal Chemistry , University of Washington , 1959 Northeast Pacific Street , Box 357610, Seattle , Washington 98195 , United States
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15
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Sonzini S, Stanyon HF, Scherman OA. Decreasing amyloid toxicity through an increased rate of aggregation. Phys Chem Chem Phys 2017; 19:1458-1465. [PMID: 27982149 PMCID: PMC5310522 DOI: 10.1039/c6cp06765d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/24/2016] [Indexed: 01/11/2023]
Abstract
Amyloid β is one of the peptides involved in the onset of Alzheimer's disease, yet the structure of the toxic species and its underlying mechanism remain elusive on account of the dynamic nature of the Aβ oligomerisation process. While it has been reported that incubation of Amyloid β (1-42) sequences (Aβ42) lead to formation of aggregates that vary in morphology and toxicity, we demonstrate that addition of a discrete macrocyclic host molecule, cucurbit[8]uril (CB[8]), substantially reduces toxicity in the neuronal cell line SH-SY5Y. The macrocycle preferentially targets Phe residues in Aβ42 complexing them in a 2 : 1 fashion in neighboring peptide strands. A small but significant structural 'switch' occurs, which induces an increased aggregation rate, suggesting a different cell-uptake mechanism for Aβ42 in the presence of CB[8]. Dramatically increasing the rate of Aβ42 aggregation with CB[8] bypasses the toxic, oligomeric state offering an alternative approach to counter Alzheimer's disease.
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Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Helen F Stanyon
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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16
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Barbarella G, Zangoli M, Di Maria F. Synthesis and Applications of Thiophene Derivatives as Organic Materials. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Aronsson C, Selegård R, Aili D. Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix–Loop–Helix Peptide Superstructures for Controlled Encapsulation and Release. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christopher Aronsson
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Robert Selegård
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Daniel Aili
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
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