1
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Chen G, Wang Y, Zheng Z, Jiang W, Leppert A, Zhong X, Belorusova A, Siegal G, Jegerschöld C, Koeck PJB, Abelein A, Hebert H, Knight SD, Johansson J. Molecular basis for different substrate-binding sites and chaperone functions of the BRICHOS domain. Protein Sci 2024; 33:e5063. [PMID: 38864729 PMCID: PMC11168071 DOI: 10.1002/pro.5063] [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: 02/06/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Proteins can misfold into fibrillar or amorphous aggregates and molecular chaperones act as crucial guardians against these undesirable processes. The BRICHOS chaperone domain, found in several otherwise unrelated proproteins that contain amyloidogenic regions, effectively inhibits amyloid formation and toxicity but can in some cases also prevent non-fibrillar, amorphous protein aggregation. Here, we elucidate the molecular basis behind the multifaceted chaperone activities of the BRICHOS domain from the Bri2 proprotein. High-confidence AlphaFold2 and RoseTTAFold predictions suggest that the intramolecular amyloidogenic region (Bri23) is part of the hydrophobic core of the proprotein, where it occupies the proposed amyloid binding site, explaining the markedly reduced ability of the proprotein to prevent an exogenous amyloidogenic peptide from aggregating. However, the BRICHOS-Bri23 complex maintains its ability to form large polydisperse oligomers that prevent amorphous protein aggregation. A cryo-EM-derived model of the Bri2 BRICHOS oligomer is compatible with surface-exposed hydrophobic motifs that get exposed and come together during oligomerization, explaining its effects against amorphous aggregation. These findings provide a molecular basis for the BRICHOS chaperone domain function, where distinct surfaces are employed against different forms of protein aggregation.
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Affiliation(s)
- Gefei Chen
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Yu Wang
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- College of Wildlife and Protected Area, Northeast Forestry UniversityHarbinChina
| | - Zihan Zheng
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of PharmacologyXi'an Jiaotong UniversityXi'anChina
| | - Wangshu Jiang
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Axel Leppert
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Present address:
Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetSolnaSweden
| | - Xueying Zhong
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | | | | | - Caroline Jegerschöld
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Philip J. B. Koeck
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Axel Abelein
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Hans Hebert
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Stefan D. Knight
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Jan Johansson
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
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2
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McManus RM, Latz E. NLRP3 inflammasome signalling in Alzheimer's disease. Neuropharmacology 2024; 252:109941. [PMID: 38565393 DOI: 10.1016/j.neuropharm.2024.109941] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Every year, 10 million people develop dementia, the most common of which is Alzheimer's disease (AD). To date, there is no way to prevent cognitive decline and therapies are limited. This review provides a neuroimmunological perspective on the progression of AD, and discusses the immune-targeted therapies that are in preclinical and clinical trials that may impact the development of this disease. Specifically, we look to the role of the NLRP3 inflammasome, its triggers in the brain and how its activation can contribute to the progression of dementia. We summarise the range of inhibitors targeting the NLRP3 inflammasome and its downstream pathways that are under investigation, and discuss future therapeutic perspectives for this devastating condition.
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Affiliation(s)
- Róisín M McManus
- German Center for Neurodegenerative Diseases (DZNE), Venusberg Campus 1/99, 53127, Bonn, Germany; Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany.
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany; Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491, Trondheim, Norway; Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, 01605, USA; Deutsches Rheuma-Forschungszentrum (DRFZ), Charitéplatz 1, 10117, Berlin, Germany
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3
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Leimu L, Holm P, Gąciarz A, Haavisto O, Prince S, Pesonen U, Huovinen T, Lamminmäki U. Epitope-specific antibody fragments block aggregation of AGelD187N, an aberrant peptide in gelsolin amyloidosis. J Biol Chem 2024:107507. [PMID: 38944121 DOI: 10.1016/j.jbc.2024.107507] [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: 04/26/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Aggregation of aberrant fragment of plasma gelsolin, AGelD187N, is a crucial event underlying the pathophysiology of Finnish gelsolin amyloidosis, an inherited form of systemic amyloidosis. The amyloidogenic gelsolin fragment AGelD187N does not play any physiological role in the body, unlike most aggregating proteins related to other protein misfolding diseases. However, no therapeutic agents that specifically and effectively target and neutralize AGelD187N exist. We employed phage display technology to identify novel single-chain variable fragments (scFvs) that bind to different epitopes in the monomeric AGelD187N that were further maturated by variable domain shuffling and converted to antigen-binding fragment (Fab) antibodies. The generated antibody fragments had nanomolar binding affinity for full-length AGelD187N, as evaluated by biolayer interferometry. Importantly, all four Fabs selected for functional studies efficiently inhibited the amyloid formation of full-length AGelD187N as examined by thioflavin fluorescence assay and transmission electron microscopy. Two Fabs, neither of which bound to the previously proposed fibril-forming region of AGelD187N, completely blocked the amyloid formation of AGelD187N. Moreover, no small soluble aggregates, which are considered pathogenic species in protein misfolding diseases, were formed after successful inhibition of amyloid formation by the most promising aggregation inhibitor, as investigated by size exclusion chromatography combined with multi-angle light scattering. We conclude that all regions of the full-length AGelD187N are important in modulating its assembly into fibrils and that the discovered epitope-specific anti-AGelD187N antibody fragments provide a promising starting point for a disease-modifying therapy for gelsolin amyloidosis, which is currently lacking.
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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.
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Department of Life Technologies, University of Turku, Turku, Finland; Organon R&D Finland, Turku, Finland
| | - Anna Gąciarz
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Mobidiag, A Hologic Company, Espoo, Finland
| | - Oskar Haavisto
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland.
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4
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Gialama D, Vadukul DM, Thrush RJ, Radford SE, Aprile FA. A Potent Sybody Selectively Inhibits α-Synuclein Amyloid Formation by Binding to the P1 Region. J Med Chem 2024; 67:9857-9868. [PMID: 38842931 PMCID: PMC11215725 DOI: 10.1021/acs.jmedchem.3c02408] [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: 12/21/2023] [Revised: 04/25/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
Increasing research efforts focus on exploiting antibodies to inhibit the amyloid formation of neurodegenerative proteins. Nevertheless, it is challenging to discover antibodies that inhibit this process in a specific manner. Using ribosome display, we screened for synthetic single-domain antibodies, i.e., sybodies, of the P1 region of α-synuclein (residues 36-42), a protein that forms amyloid in Parkinson's disease and multiple-system atrophy. Hits were assessed for direct binding to a P1 peptide and the inhibition of amyloid formation. We discovered a sybody, named αSP1, that inhibits amyloid formation of α-synuclein at substoichiometric concentrations in a specific manner, even within highly crowded heterogeneous mixtures. Fluorescence resonance energy transfer-based binding assays and seeding experiments with and without αSP1 further demonstrate the importance of the P1 region for both primary and secondary nucleation mechanisms of amyloid assembly.
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Affiliation(s)
- Dimitra Gialama
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Devkee M. Vadukul
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Rebecca J. Thrush
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Francesco A. Aprile
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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5
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Axell E, Hu J, Lindberg M, Dear AJ, Ortigosa-Pascual L, Andrzejewska EA, Šneiderienė G, Thacker D, Knowles TPJ, Sparr E, Linse S. The role of shear forces in primary and secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2322572121. [PMID: 38875148 PMCID: PMC11194593 DOI: 10.1073/pnas.2322572121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Shear forces affect self-assembly processes ranging from crystallization to fiber formation. Here, the effect of mild agitation on amyloid fibril formation was explored for four peptides and investigated in detail for A[Formula: see text]42, which is associated with Alzheimer's disease. To gain mechanistic insights into the effect of mild agitation, nonseeded and seeded aggregation reactions were set up at various peptide concentrations with and without an inhibitor. First, an effect on fibril fragmentation was excluded by comparing the monomer-concentration dependence of aggregation kinetics under idle and agitated conditions. Second, using a secondary nucleation inhibitor, Brichos, the agitation effect on primary nucleation was decoupled from secondary nucleation. Third, an effect on secondary nucleation was established in the absence of inhibitor. Fourth, an effect on elongation was excluded by comparing the seeding potency of fibrils formed under idle or agitated conditions. We find that both primary and secondary nucleation steps are accelerated by gentle agitation. The increased shear forces facilitate both the detachment of newly formed aggregates from catalytic surfaces and the rate at which molecules are transported in the bulk solution to encounter nucleation sites on the fibril and other surfaces. Ultrastructural evidence obtained with cryogenic transmission electron microscopy and free-flow electrophoresis in microfluidics devices imply that agitation speeds up the detachment of nucleated species from the fibril surface. Our findings shed light on the aggregation mechanism and the role of detachment for efficient secondary nucleation. The results inform on how to modulate the relative importance of different microscopic steps in drug discovery and investigations.
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Affiliation(s)
- Emil Axell
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Jing Hu
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Max Lindberg
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Alexander J. Dear
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Lei Ortigosa-Pascual
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Ewa A. Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Dev Thacker
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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6
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Wei J, Meisl G, Dear A, Oosterhuis M, Melki R, Emanuelsson C, Linse S, Knowles TPJ. Kinetic models reveal the interplay of protein production and aggregation. Chem Sci 2024; 15:8430-8442. [PMID: 38846392 PMCID: PMC11151821 DOI: 10.1039/d4sc00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Protein aggregation is a key process in the development of many neurodegenerative disorders, including dementias such as Alzheimer's disease. Significant progress has been made in understanding the molecular mechanisms of aggregate formation in pure buffer systems, much of which was enabled by the development of integrated rate laws that allowed for mechanistic analysis of aggregation kinetics. However, in order to translate these findings into disease-relevant conclusions and to make predictions about the effect of potential alterations to the aggregation reactions by the addition of putative inhibitors, the current models need to be extended to account for the altered situation encountered in living systems. In particular, in vivo, the total protein concentrations typically do not remain constant and aggregation-prone monomers are constantly being produced but also degraded by cells. Here, we build a theoretical model that explicitly takes into account monomer production, derive integrated rate laws and discuss the resulting scaling laws and limiting behaviours. We demonstrate that our models are suited for the aggregation-prone Huntington's disease-associated peptide HttQ45 utilizing a system for continuous in situ monomer production and the aggregation of the tumour suppressor protein P53. The aggregation-prone HttQ45 monomer was produced through enzymatic cleavage of a larger construct in which a fused protein domain served as an internal inhibitor. For P53, only the unfolded monomers form aggregates, making the unfolding a rate-limiting step which constitutes a source of aggregation-prone monomers. The new model opens up possibilities for a quantitative description of aggregation in living systems, allowing for example the modelling of inhibitors of aggregation in a dynamic environment of continuous protein synthesis.
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Affiliation(s)
- Jiapeng Wei
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander Dear
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry and Structural Biology, Lund University SE22100 Lund Sweden
| | - Matthijs Oosterhuis
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS 18 Route du Panorama, Fontenay-Aux-Roses cedex 92265 France
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, University of Cambridge J J Thomson Avenue CB3 0HE UK
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7
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Han Y, Desai AA, Zupancic JM, Smith MD, Tessier PM, Ruotolo BT. Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies. Protein Sci 2024; 33:e5008. [PMID: 38723181 PMCID: PMC11081520 DOI: 10.1002/pro.5008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024]
Abstract
One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid β (Aβ) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aβ species during the dynamic Aβ aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aβ oligomers and three Aβ-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aβ monomers, while aducanumab preferentially binds Aβ monomers and dimers and A34 preferentially binds Aβ dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aβ binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aβ antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.
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Affiliation(s)
- Yilin Han
- Department of ChemistryUniversity of MichiganAnn ArborMichiganUSA
| | - Alec A. Desai
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Jennifer M. Zupancic
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Matthew D. Smith
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Peter M. Tessier
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
- Department of Pharmaceutical SciencesUniversity of MichiganAnn ArborMichiganUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
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8
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O'Mahoney C, Watt I, Fiedler S, Devenish S, Srikanth S, Justice E, Dover T, Dean D, Peng C. Microfluidic Diffusional Sizing (MDS) Measurements of Secretory Neutralizing Antibody Affinity Against SARS-CoV-2. Ann Biomed Eng 2024; 52:1653-1664. [PMID: 38459195 PMCID: PMC11082020 DOI: 10.1007/s10439-024-03478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
SARS-CoV-2 has rampantly spread around the globe and continues to cause unprecedented loss through ongoing waves of (re)infection. Increasing our understanding of the protection against infection with SARS-CoV-2 is critical to ending the pandemic. Serological assays have been widely used to assess immune responses, but secretory antibodies, the essential first line of defense, have been studied to only a limited extent. Of particular interest and importance are neutralizing antibodies, which block the binding of the spike protein of SARS-CoV-2 to the human receptor angiotensin-converting enzyme-2 (ACE2) and thus are essential for immune defense. Here, we employed Microfluidic Diffusional Sizing (MDS), an immobilization-free technology, to characterize neutralizing antibody affinity to SARS-CoV-2 spike receptor-binding domain (RBD) and spike trimer in saliva. Affinity measurement was obtained through a contrived sample and buffer using recombinant SARS-CoV-2 RBD and monoclonal antibody. Limited saliva samples demonstrated that MDS applies to saliva neutralizing antibody measurement. The ability to disrupt a complex of ACE2-Fc and spike trimer is shown. Using a quantitative assay on the patient sample, we determined the affinity and binding site concentration of the neutralizing antibodies.
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Affiliation(s)
- Cara O'Mahoney
- Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Ian Watt
- Fluidic Analytics, Cambridge, UK
| | | | | | - Sujata Srikanth
- Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, USA
| | - Erica Justice
- Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, USA
| | - Tristan Dover
- Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, USA
| | - Delphine Dean
- Department of Bioengineering, Clemson University, Clemson, SC, USA
- Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, USA
| | - Congyue Peng
- Department of Bioengineering, Clemson University, Clemson, SC, USA.
- Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, USA.
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9
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Golota NC, Michael B, Saliba EP, Linse S, Griffin RG. Structural characterization of E22G Aβ 1-42 fibrils via1H detected MAS NMR. Phys Chem Chem Phys 2024; 26:14664-14674. [PMID: 38715538 PMCID: PMC11110645 DOI: 10.1039/d4cp00553h] [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: 02/07/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aβ1-42, E22G-Aβ1-42. We found E22G-AβM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aβ1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aβ1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aβ, E22G-Aβ1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aβ1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aβ1-42 fibrils. These results suggest that E22G-Aβ1-42 fibrils have a structure similar to that of wild type Aβ1-42.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward P Saliba
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, SE 22100, Sweden
| | - Robert G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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10
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Horne RI, Andrzejewska EA, Alam P, Brotzakis ZF, Srivastava A, Aubert A, Nowinska M, Gregory RC, Staats R, Possenti A, Chia S, Sormanni P, Ghetti B, Caughey B, Knowles TPJ, Vendruscolo M. Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol 2024; 20:634-645. [PMID: 38632492 PMCID: PMC11062903 DOI: 10.1038/s41589-024-01580-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/12/2024] [Indexed: 04/19/2024]
Abstract
Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been particularly challenging. To address this problem, we describe here a machine learning approach to identify small molecule inhibitors of α-synuclein aggregation, a process implicated in Parkinson's disease and other synucleinopathies. Because the proliferation of α-synuclein aggregates takes place through autocatalytic secondary nucleation, we aim to identify compounds that bind the catalytic sites on the surface of the aggregates. To achieve this goal, we use structure-based machine learning in an iterative manner to first identify and then progressively optimize secondary nucleation inhibitors. Our results demonstrate that this approach leads to the facile identification of compounds two orders of magnitude more potent than previously reported ones.
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Affiliation(s)
- Robert I Horne
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Parvez Alam
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Z Faidon Brotzakis
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Alice Aubert
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena Nowinska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rebecca C Gregory
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrea Possenti
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byron Caughey
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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11
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Santos J, Pallarès I, Ventura S. A glimpse into the structural properties of α-synuclein oligomers. Biofactors 2024; 50:439-449. [PMID: 38063360 DOI: 10.1002/biof.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/03/2023] [Indexed: 06/15/2024]
Abstract
α-Synuclein (αS) aggregation is the main neurological hallmark of a group of debilitating neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease is the most prevalent. αS oligomers formed during the initial stages of aggregation are considered key pathogenic drivers of disease onset and progression, standing as privileged targets for therapeutic intervention and diagnosis. However, the structure of αS oligomers and the mechanistic basis of oligomer to fibril conversion are yet poorly understood, thereby precluding the rational formulation of strategies aimed at targeting oligomeric species. In this review, we delve into the recent advances in the structural and mechanistic characterization of αS oligomers. We also discuss how these advances are transforming our understanding of these elusive species and paving the way for oligomer-targeting therapeutics and diagnosis.
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Affiliation(s)
- Jaime Santos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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12
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Nilsson BL, Celebi Torabfam G, Dias CL. Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations. J Phys Chem B 2024; 128:3320-3328. [PMID: 38447080 DOI: 10.1021/acs.jpcb.3c07861] [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: 03/08/2024]
Abstract
Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.
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Affiliation(s)
- Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0216, United States
| | - Gizem Celebi Torabfam
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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13
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Lindberg M, Axell E, Sparr E, Linse S. A label-free high-throughput protein solubility assay and its application to Aβ40. Biophys Chem 2024; 307:107165. [PMID: 38309218 DOI: 10.1016/j.bpc.2023.107165] [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: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
A major hallmark of Alzheimer's disease is the accumulation of aggregated amyloid β peptide (Aβ) in the brain. Here we develop a solubility assay for proteins and measure the solubility of Aβ40. In brief, the method utilizes 96-well filter plates to separate monomeric Aβ from aggregated Aβ, and the small species are quantified with the amine reactive dye o-phthalaldehyde (OPA). This procedure ensures that solubility is measured for unlabeled species, and makes the assay high-throughput and inexpensive. We demonstrate that the filter plates successfully separate fibrils from monomer, with negligible monomer adsorption, and that OPA can quantify Aβ peptides in a concentration range from 40 nM to 20 μM. We also show that adding a methionine residue to the N-terminus of Aβ1-40 decreases the solubility by <3-fold. The method will facilitate further solubility studies, and contribute to the understanding of the thermodynamics of amyloid fibril formation.
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Affiliation(s)
- Max Lindberg
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emil Axell
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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14
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Das V, Miller JH, Alladi CG, Annadurai N, De Sanctis JB, Hrubá L, Hajdúch M. Antineoplastics for treating Alzheimer's disease and dementia: Evidence from preclinical and observational studies. Med Res Rev 2024. [PMID: 38530106 DOI: 10.1002/med.22033] [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: 03/02/2023] [Revised: 02/15/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
As the world population ages, there will be an increasing need for effective therapies for aging-associated neurodegenerative disorders, which remain untreatable. Dementia due to Alzheimer's disease (AD) is one of the leading neurological diseases in the aging population. Current therapeutic approaches to treat this disorder are solely symptomatic, making the need for new molecular entities acting on the causes of the disease extremely urgent. One of the potential solutions is to use compounds that are already in the market. The structures have known pharmacokinetics, pharmacodynamics, toxicity profiles, and patient data available in several countries. Several drugs have been used successfully to treat diseases different from their original purposes, such as autoimmunity and peripheral inflammation. Herein, we divulge the repurposing of drugs in the area of neurodegenerative diseases, focusing on the therapeutic potential of antineoplastics to treat dementia due to AD and dementia. We briefly touch upon the shared pathological mechanism between AD and cancer and drug repurposing strategies, with a focus on artificial intelligence. Next, we bring out the current status of research on the development of drugs, provide supporting evidence from retrospective, clinical, and preclinical studies on antineoplastic use, and bring in new areas, such as repurposing drugs for the prion-like spreading of pathologies in treating AD.
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Affiliation(s)
- Viswanath Das
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Olomouc, Czech Republic
| | - John H Miller
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Charanraj Goud Alladi
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Narendran Annadurai
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Juan Bautista De Sanctis
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Olomouc, Czech Republic
| | - Lenka Hrubá
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Olomouc, Czech Republic
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15
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Sahtoe DD, Andrzejewska EA, Han HL, Rennella E, Schneider MM, Meisl G, Ahlrichs M, Decarreau J, Nguyen H, Kang A, Levine P, Lamb M, Li X, Bera AK, Kay LE, Knowles TPJ, Baker D. Design of amyloidogenic peptide traps. Nat Chem Biol 2024:10.1038/s41589-024-01578-5. [PMID: 38503834 DOI: 10.1038/s41589-024-01578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein-peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1-42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.
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Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
- Hubrecht Institute, Utrecht, the Netherlands.
| | - Ewa A Andrzejewska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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16
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Halipi V, Sasanian N, Feng J, Hu J, Lubart Q, Bernson D, van Leeuwen D, Ahmadpour D, Sparr E, Esbjörner EK. Extracellular Vesicles Slow Down Aβ(1-42) Aggregation by Interfering with the Amyloid Fibril Elongation Step. ACS Chem Neurosci 2024; 15:944-954. [PMID: 38408014 PMCID: PMC10921407 DOI: 10.1021/acschemneuro.3c00655] [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: 10/12/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Formation of amyloid-β (Aβ) fibrils is a central pathogenic feature of Alzheimer's disease. Cell-secreted extracellular vesicles (EVs) have been suggested as disease modulators, although their exact roles and relations to Aβ pathology remain unclear. We combined kinetics assays and biophysical analyses to explore how small (<220 nm) EVs from neuronal and non-neuronal human cell lines affected the aggregation of the disease-associated Aβ variant Aβ(1-42) into amyloid fibrils. Using thioflavin-T monitored kinetics and seeding assays, we found that EVs reduced Aβ(1-42) aggregation by inhibiting fibril elongation. Morphological analyses revealed this to result in the formation of short fibril fragments with increased thicknesses and less apparent twists. We suggest that EVs may have protective roles by reducing Aβ(1-42) amyloid loads, but also note that the formation of small amyloid fragments could be problematic from a neurotoxicity perspective. EVs may therefore have double-edged roles in the regulation of Aβ pathology in Alzheimer's disease.
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Affiliation(s)
- Vesa Halipi
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Nima Sasanian
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Julia Feng
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Jing Hu
- Division
of Physical Chemistry, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Quentin Lubart
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - David Bernson
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Daniel van Leeuwen
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Doryaneh Ahmadpour
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
| | - Emma Sparr
- Division
of Physical Chemistry, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Elin K. Esbjörner
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden
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17
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Qiao Y, Gu J, Yu M, Chi Y, Ma Y. Comparative Efficacy and Safety of Monoclonal Antibodies for Cognitive Decline in Patients with Alzheimer's Disease: A Systematic Review and Network Meta-Analysis. CNS Drugs 2024; 38:169-192. [PMID: 38429615 DOI: 10.1007/s40263-024-01067-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Recent clinical trials of anti-Aβ monoclonal antibodies (mAbs) in the treatment of early Alzheimer's disease (AD) have produced encouraging cognitive and clinical results. The purpose of this network meta-analysis (NMA) was to compare and rank mAb drugs according to their efficacy and safety. METHODS PubMed, Embase, Web of Science, and the Cochrane Library were searched for randomized controlled trials testing various mAbs for the treatment of cognitive decline in patients with AD, up to March 31, 2023. R software (version 4.2.3) along with JAGS and STATA software (version 15.0) were used for statistical analysis. Odds ratio (OR) for binary variables, mean difference (MD) for continuous variables, and their 95% confidence intervals (CI) were utilized to estimate treatment effects and rank probabilities for each mAb in terms of safety and efficacy outcomes. We calculated the surface under the cumulative ranking area (SUCRA) to evaluate each mAb, with higher SUCRA values indicating better efficacy or lower likelihood of adverse events. RESULTS Thirty-three randomized controlled trials with a total of 21,087 patients were included in the current NMA, involving eight different mAbs. SUCRA values showed that aducanumab (87.01% and 99.37%, respectively) was the most likely to achieve the best therapeutic effect based on the changes of Mini-Mental State Examination (MMSE) and Clinical Dementia Rating scale Sum of Boxes (CDR-SB) scores. Donanemab (88.50% and 99.00%, respectively) performed better than other therapies for Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog) and Positron Emission Tomography-Standardized Uptake Value ratio (PET-SUVr). Lecanemab (87.24%) may be the most promising way to slow down the decrease of Alzheimer's Disease Cooperative Study-Activities of Daily Living (ADCS-ADL) score. In the analysis of the incidence of adverse events (subjects with any treatment-emergent adverse event), gantenerumab (89.12%) had the least potential for adverse events, while lecanemab (0.79%) may cause more adverse events. Solanezumab (95.75% and 80.38%, respectively) had the lowest incidence of amyloid-related imaging abnormalities characterized by edema and effusion (ARIA-E) and by cerebral microhemorrhages (ARIA-H) of the included immunotherapies. While SUCRA values provided a comprehensive measure of treatment efficacy, the inherent statistical uncertainty required careful analysis in clinical application. CONCLUSION Despite immunotherapies significantly increasing the risks of adverse events and ARIA, the data suggest that mAbs can effectively improve the cognitive function of patients with mild and moderate AD. According to the NMA, aducanumab was the most likely to achieve significant improvements in different cognitive and clinical assessments (statistically improved MMSE and CDR-SB), followed by donanemab (statistically improved ADAS-Cog, and PET-SUVr) and lecanemab (statistically improved ADCS-ADL).
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Affiliation(s)
- Yue Qiao
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, China
| | - Jian Gu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, China
| | - Miao Yu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, China
| | - Yuewei Chi
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, China
| | - Ying Ma
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, China.
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18
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Tolar M, Hey JA, Power A, Abushakra S. The Single Toxin Origin of Alzheimer's Disease and Other Neurodegenerative Disorders Enables Targeted Approach to Treatment and Prevention. Int J Mol Sci 2024; 25:2727. [PMID: 38473975 PMCID: PMC10932387 DOI: 10.3390/ijms25052727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
New data suggest that the aggregation of misfolded native proteins initiates and drives the pathogenic cascade that leads to Alzheimer's disease (AD) and other age-related neurodegenerative disorders. We propose a unifying single toxin theory of brain neurodegeneration that identifies new targets and approaches to the development of disease-modifying treatments. An extensive body of genetic evidence suggests soluble aggregates of beta-amyloid (Aβ) as the primary neurotoxin in the pathogenesis of AD. New insights from fluid biomarkers, imaging, and clinical studies provide further evidence for the decisive impact of toxic Aβ species in the initiation and progression of AD. Understanding the distinct roles of soluble and insoluble amyloid aggregates on AD pathogenesis has been the key missing piece of the Alzheimer's puzzle. Data from clinical trials with anti-amyloid agents and recent advances in the diagnosis of AD demonstrate that the driving insult in biologically defined AD is the neurotoxicity of soluble Aβ aggregates, called oligomers and protofibrils, rather than the relatively inert insoluble mature fibrils and amyloid plaques. Amyloid oligomers appear to be the primary factor causing the synaptic impairment, neuronal stress, spreading of tau pathology, and eventual cell death that lead to the clinical syndrome of AD dementia. All other biochemical effects and neurodegenerative changes in the brain that are observed in AD are a response to or a downstream effect of this initial toxic insult by oligomers. Other neurodegenerative disorders follow a similar pattern of pathogenesis, in which normal brain proteins with important biological functions become trapped in the aging brain due to impaired clearance and then misfold and aggregate into neurotoxic species that exhibit prion-like behavior. These aggregates then spread through the brain and cause disease-specific neurodegeneration. Targeting the inhibition of this initial step in neurodegeneration by blocking the misfolding and aggregation of healthy proteins has the potential to slow or arrest disease progression, and if treatment is administered early in the course of AD and other neurodegenerative disorders, it may delay or prevent the onset of clinical symptoms.
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19
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Schlotheuber LJ, Lüchtefeld I, Eyer K. Antibodies, repertoires and microdevices in antibody discovery and characterization. LAB ON A CHIP 2024; 24:1207-1225. [PMID: 38165819 PMCID: PMC10898418 DOI: 10.1039/d3lc00887h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024]
Abstract
Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.
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Affiliation(s)
- Luca Johannes Schlotheuber
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ines Lüchtefeld
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
- ETH Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
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20
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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21
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Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. Self-replication of A β42 aggregates occurs on small and isolated fibril sites. Proc Natl Acad Sci U S A 2024; 121:e2220075121. [PMID: 38335256 PMCID: PMC10873593 DOI: 10.1073/pnas.2220075121] [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: 11/24/2022] [Accepted: 11/17/2023] [Indexed: 02/12/2024] Open
Abstract
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
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Affiliation(s)
- Samo Curk
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund22100, Sweden
| | - Thomas C. T. Michaels
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich8093, Switzerland
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
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22
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Kumar R, Le Marchand T, Adam L, Bobrovs R, Chen G, Fridmanis J, Kronqvist N, Biverstål H, Jaudzems K, Johansson J, Pintacuda G, Abelein A. Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain. Nat Commun 2024; 15:965. [PMID: 38302480 PMCID: PMC10834949 DOI: 10.1038/s41467-024-45192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Protein misfolding can generate toxic intermediates, which underlies several devastating diseases, such as Alzheimer's disease (AD). The surface of AD-associated amyloid-β peptide (Aβ) fibrils has been suggested to act as a catalyzer for self-replication and generation of potentially toxic species. Specifically tailored molecular chaperones, such as the BRICHOS protein domain, were shown to bind to amyloid fibrils and break this autocatalytic cycle. Here, we identify a site on the Aβ42 fibril surface, consisting of three C-terminal β-strands and particularly the solvent-exposed β-strand stretching from residues 26-28, which is efficiently sensed by a designed variant of Bri2 BRICHOS. Remarkably, while only a low amount of BRICHOS binds to Aβ42 fibrils, fibril-catalyzed nucleation processes are effectively prevented, suggesting that the identified site acts as a catalytic aggregation hotspot, which can specifically be blocked by BRICHOS. Hence, these findings provide an understanding how toxic nucleation events can be targeted by molecular chaperones.
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Affiliation(s)
- Rakesh Kumar
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Tanguy Le Marchand
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Laurène Adam
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Raitis Bobrovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Jēkabs Fridmanis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Guido Pintacuda
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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23
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Guo X, Yan L, Zhang D, Zhao Y. Passive immunotherapy for Alzheimer's disease. Ageing Res Rev 2024; 94:102192. [PMID: 38219962 DOI: 10.1016/j.arr.2024.102192] [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: 09/21/2023] [Revised: 12/03/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease characterized by cognitive impairment with few therapeutic options. Despite many failures in developing AD treatment during the past 20 years, significant advances have been achieved in passive immunotherapy of AD very recently. Here, we review characteristics, clinical trial data, and mechanisms of action for monoclonal antibodies (mAbs) targeting key players in AD pathogenesis, including amyloid-β (Aβ), tau and neuroinflammation modulators. We emphasized the efficacy of lecanemab and donanemab on cognition and amyloid clearance in AD patients in phase III clinical trials and discussed factors that may contribute to the efficacy and side effects of anti-Aβ mAbs. In addition, we provided important information on mAbs targeting tau or inflammatory regulators in clinical trials, and indicated that mAbs against the mid-region of tau or pathogenic tau have therapeutic potential for AD. In conclusion, passive immunotherapy targeting key players in AD pathogenesis offers a promising strategy for effective AD treatment.
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Affiliation(s)
- Xiaoyi Guo
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Li Yan
- School of Traditional Chinese Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Denghong Zhang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Yingjun Zhao
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China.
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24
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Otzen DE. Antibodies and α-synuclein: What to target against Parkinson's Disease? BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140943. [PMID: 37783321 DOI: 10.1016/j.bbapap.2023.140943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 10/04/2023]
Abstract
Parkinson's Disease (PD) is strongly linked to the aggregation of the protein α-synuclein (α-syn), an intrinsically disordered protein. However, strategies to combat PD by targeting the aggregation of α-syn are challenged by the multiple types of aggregates formed both in vivo and in vitro, the potential influence of chemical modifications and the as yet unresolved question of which aggregate types (oligomeric or fibrillar) are most cytotoxic. Here I briefly review the social history of α-syn, the many efforts to raise antibodies against α-syn and the disappointing results of clinical trials based on such antibodies. Ultimately a thorough understanding of the molecular and mechanistic properties of mAbs towards aggregated species of α-syn is an essential prerequisite for any clinical trial, but this is missing in most cases. I highlight new microfluidic techniques which may address this need and call for a more concerted effort to standardize antibody studies as the basis to allow us to link molecular insights to clinical efficacy.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK - 8000, Aarhus, Denmark.
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25
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Kumar V, Kaushik V, Kumar S, Levkovich SA, Gupta P, Laor Bar-Yosef D, Gazit E, Segal D. The von Hippel-Lindau protein forms fibrillar amyloid assemblies that are mitigated by the anti-amyloid molecule Purpurin. Biochem Biophys Res Commun 2024; 690:149250. [PMID: 38039781 DOI: 10.1016/j.bbrc.2023.149250] [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: 10/03/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
The von Hippel-Lindau protein (pVHL) is a tumor suppressor involved in oxygen regulation via dynamic nucleocytoplasmic shuttling. It plays a crucial role in cell survival by degrading hypoxia-inducible factors (HIFs). Mutations in the VHL gene cause angiogenic tumors, characterized as VHL syndrome. However, aggressive tumors involving wild-type pVHL have also been described but the underlying mechanism remains to be revealed. We have previously shown that pVHL possesses several short amyloid-forming motifs, making it aggregation-prone. In this study, using a series of biophysical assays, we demonstrated that a pVHL-derived fragment (pVHL104-140) that harbors the nuclear export motif and HIF binding site, forms amyloid-like fibrillar structures in vitro by following secondary-nucleation-based kinetics. The peptide also formed amyloids at acidic pH that mimics the tumor microenvironment. We, subsequently, validated the amyloid formation by pVHL in vitro. Using the Curli-dependent amyloid generator (C-DAG) expression system, we confirmed the amyloidogenesis of pVHL in bacterial cells. The pVHL amyloids are an attractive target for therapeutics of the VHL syndrome. Accordingly, we demonstrated in vitro that Purpurin is a potent inhibitor of pVHL fibrillation. The amyloidogenic behavior of wild-type pVHL and its inhibition provide novel insights into the molecular underpinning of the VHL syndrome and its possible treatment.
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Affiliation(s)
- Vijay Kumar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Vibha Kaushik
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Sourav Kumar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shon A Levkovich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Priya Gupta
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Dana Laor Bar-Yosef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Daniel Segal
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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26
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Hu J, Linse S, Sparr E. Ganglioside Micelles Affect Amyloid β Aggregation by Coassembly. ACS Chem Neurosci 2023; 14:4335-4343. [PMID: 38050745 PMCID: PMC10739608 DOI: 10.1021/acschemneuro.3c00524] [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: 08/09/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
Amyloid β peptide (Aβ) is the crucial protein component of extracellular plaques in Alzheimer's disease. The plaques also contain gangliosides lipids, which are abundant in membranes of neuronal cells and in cell-derived vesicles and exosomes. When present at concentrations above its critical micelle concentration (cmc), gangliosides can occur as mixed micelles. Here, we study the coassembly of the ganglioside GM1 and the Aβ peptides Aβ40 and 42 by means of microfluidic diffusional sizing, confocal microscopy, and cryogenic transmission electron microscopy. We also study the effects of lipid-peptide interactions on the amyloid aggregation process by fluorescence spectroscopy. Our results reveal coassembly of GM1 lipids with both Aβ monomers and Aβ fibrils. The results of the nonseeded kinetics experiments show that Aβ40 aggregation is delayed with increasing GM1 concentration, while that of Aβ42 is accelerated. In seeded aggregation reactions, the addition of GM1 leads to a retardation of the aggregation process of both peptides. Thus, while the effect on nucleation differs between the two peptides, GM1 may inhibit the elongation of both types of fibrils. These results shed light on glycolipid-peptide interactions that may play an important role in Alzheimer's pathology.
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Affiliation(s)
- Jing Hu
- Division
of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Sara Linse
- Division
of Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Emma Sparr
- Division
of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
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27
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Kumar S, Wulf J, Basore K, Pozzi N. Structural analyses of β 2-glycoprotein I: is there a circular conformation? J Thromb Haemost 2023; 21:3511-3521. [PMID: 37536570 PMCID: PMC10834832 DOI: 10.1016/j.jtha.2023.07.016] [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: 05/22/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Antiphospholipid antibodies targeting β2-glycoprotein I (β2GPI) cause thrombosis and pregnancy morbidity in antiphospholipid syndrome (APS) patients. How these antibodies recognize β2GPI remains controversial. OBJECTIVES This study aimed to elucidate the structure of β2GPI and evaluate how pathogenic anti-domain I (DI) antibodies recognize it in human plasma. METHODS β2GPI was made recombinant and purified from human plasma using different protocols. Structural and functional analyses were conducted using orthogonal techniques, namely, electron microscopy, size-exclusion chromatography, single-molecule Förster resonance energy transfer, and microfluidic diffusional sizing. RESULTS Electron microscopy and size-exclusion chromatography showed that the structure of β2GPI produced recombinantly and purified from plasma is elongated, even when subjected to conditions previously reported to favor circularization. Single-molecule Förster resonance energy transfer analyses of β2GPI labeled at positions 88 in DII and 278 in DV showed that these residues are located >90 Å apart, consistent with an elongated form. They also documented that the distance between these 2 residues did not change when the protein was reconstituted in human plasma. Microfluidic diffusional sizing documented that β2GPI binds with moderate affinity to a prototypical anti-DI antibody targeting the epitope G40-R43 despite being elongated. CONCLUSION Circulating β2GPI is elongated and, therefore, fully capable of binding to anti-DI antibodies. Binding of β2GPI to negatively charged phospholipids drives autoantibody recognition by increasing the local concentration of the antigen and not by dramatically changing its conformation. These findings clarify the structural properties of β2GPI, which have important implications for understanding APS pathogenesis and the development of APS diagnostics and therapeutics.
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Affiliation(s)
- Suresh Kumar
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - John Wulf
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St Louis, Missouri, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St Louis, Missouri, USA
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA.
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28
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Sandler S, Horne RI, Rocchetti S, Novak R, Hsu NS, Castellana Cruz M, Faidon Brotzakis Z, Gregory RC, Chia S, Bernardes GJL, Keyser UF, Vendruscolo M. Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores. J Am Chem Soc 2023; 145:25776-25788. [PMID: 37972287 PMCID: PMC10690769 DOI: 10.1021/jacs.3c09335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Misfolded protein oligomers are of central importance in both the diagnosis and treatment of Alzheimer's and Parkinson's diseases. However, accurate high-throughput methods to detect and quantify oligomer populations are still needed. We present here a single-molecule approach for the detection and quantification of oligomeric species. The approach is based on the use of solid-state nanopores and multiplexed DNA barcoding to identify and characterize oligomers from multiple samples. We study α-synuclein oligomers in the presence of several small-molecule inhibitors of α-synuclein aggregation as an illustration of the potential applicability of this method to the development of diagnostic and therapeutic methods for Parkinson's disease.
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Affiliation(s)
- Sarah
E. Sandler
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Robert I. Horne
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sara Rocchetti
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Robert Novak
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Nai-Shu Hsu
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Marta Castellana Cruz
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rebecca C. Gregory
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Bioprocessing
Technology Institute, Agency for Science, Technology and Research
(A*STAR), Singapore 138668
| | - Gonçalo J. L. Bernardes
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ulrich F. Keyser
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
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29
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Yu TG, Lee J, Yoon J, Choi JM, Kim DG, Heo WD, Song JJ, Kim HS. Engineering of a Fluorescent Protein for a Sensing of an Intrinsically Disordered Protein through Transition in the Chromophore State. JACS AU 2023; 3:3055-3065. [PMID: 38034956 PMCID: PMC10685427 DOI: 10.1021/jacsau.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
Intrinsically disordered proteins (IDPs) not only play important roles in biological processes but are also linked with the pathogenesis of various human diseases. Specific and reliable sensing of IDPs is crucial for exploring their roles but remains elusive due to structural plasticity. Here, we present the development of a new type of fluorescent protein for the ratiometric sensing and tracking of an IDP. A β-strand of green fluorescent protein (GFP) was truncated, and the resulting GFP was further engineered to undergo the transition in the absorption maximum upon binding of a target motif within amyloid-β (Aβ) as a model IDP through rational design and directed evolution. Spectroscopic and structural analyses of the engineered truncated GFP demonstrated that a shift in the absorption maximum is driven by the change in the chromophore state from an anionic (460 nm) state into a neutral (390 nm) state as the Aβ binds, allowing a ratiometric detection of Aβ. The utility of the developed GFP was shown by the efficient and specific detection of an Aβ and the tracking of its conformational change and localization in astrocytes.
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Affiliation(s)
- Tae-Geun Yu
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jinsu Lee
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jungmin Yoon
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jung Min Choi
- School
of Food Biotechnology and Nutrition, Kyungsung
University, Busan 48434, Korea
| | - Dong-Gun Kim
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Won Do Heo
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ji-Joon Song
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hak-Sung Kim
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
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30
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Abstract
The formation of amyloid fibrils is a complex phenomenon that remains poorly understood at the atomic scale. Herein, we perform extended unbiased all-atom simulations in explicit solvent of a short amphipathic peptide to shed light on the three mechanisms accounting for fibril formation, namely, nucleation via primary and secondary mechanisms, and fibril growth. We find that primary nucleation takes place via the formation of an intermediate state made of two laminated β-sheets oriented perpendicular to each other. The amyloid fibril spine subsequently emerges from the rotation of these β-sheets to account for peptides that are parallel to each other and perpendicular to the main axis of the fibril. Growth of this spine, in turn, takes place via a dock-and-lock mechanism. We find that peptides dock onto the fibril tip either from bulk solution or after diffusing on the fibril surface. The latter docking pathway contributes significantly to populate the fibril tip with peptides. We also find that side chain interactions drive the motion of peptides in the lock phase during growth, enabling them to adopt the structure imposed by the fibril tip with atomic fidelity. Conversely, the docked peptide becomes trapped in a local free energy minimum when docked-conformations are sampled randomly. Our simulations also highlight the role played by nonpolar fibril surface patches in catalyzing and orienting the formation of small cross-β structures. More broadly, our simulations provide important new insights into the pathways and interactions accounting for primary and secondary nucleation as well as the growth of amyloid fibrils.
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Affiliation(s)
- Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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31
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Kandi S, Cline EN, Rivera BM, Viola KL, Zhu J, Condello C, LeDuc RD, Klein WL, Kelleher NL, Patrie SM. Amyloid β Proteoforms Elucidated by Quantitative LC/MS in the 5xFAD Mouse Model of Alzheimer's Disease. J Proteome Res 2023; 22:3475-3488. [PMID: 37847596 PMCID: PMC10840081 DOI: 10.1021/acs.jproteome.3c00353] [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] [Indexed: 10/19/2023]
Abstract
Numerous Aβ proteoforms, identified in the human brain, possess differential neurotoxic and aggregation propensities. These proteoforms contribute in unknown ways to the conformations and resultant pathogenicity of oligomers, protofibrils, and fibrils in Alzheimer's disease (AD) manifestation owing to the lack of molecular-level specificity to the exact chemical composition of underlying protein products with widespread interrogating techniques, like immunoassays. We evaluated Aβ proteoform flux using quantitative top-down mass spectrometry (TDMS) in a well-studied 5xFAD mouse model of age-dependent Aβ-amyloidosis. Though the brain-derived Aβ proteoform landscape is largely occupied by Aβ1-42, 25 different forms of Aβ with differential solubility were identified. These proteoforms fall into three natural groups defined by hierarchical clustering of expression levels in the context of mouse age and proteoform solubility, with each group sharing physiochemical properties associated with either N/C-terminal truncations or both. Overall, the TDMS workflow outlined may hold tremendous potential for investigating proteoform-level relationships between insoluble fibrils and soluble Aβ, including low-molecular-weight oligomers hypothesized to serve as the key drivers of neurotoxicity. Similarly, the workflow may also help to validate the utility of AD-relevant animal models to recapitulate amyloidosis mechanisms or possibly explain disconnects observed in therapeutic efficacy in animal models vs humans.
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Affiliation(s)
- Soumya Kandi
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Erika N Cline
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Brianna M Rivera
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
| | - Kirsten L Viola
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiuhe Zhu
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
| | - Richard D LeDuc
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William L Klein
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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32
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Österlund N, Frankel R, Carlsson A, Thacker D, Karlsson M, Matus V, Gräslund A, Emanuelsson C, Linse S. The C-terminal domain of the antiamyloid chaperone DNAJB6 binds to amyloid-β peptide fibrils and inhibits secondary nucleation. J Biol Chem 2023; 299:105317. [PMID: 37797698 PMCID: PMC10641233 DOI: 10.1016/j.jbc.2023.105317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
The DNAJB6 chaperone inhibits fibril formation of aggregation-prone client peptides through interaction with aggregated and oligomeric forms of the amyloid peptides. Here, we studied the role of its C-terminal domain (CTD) using constructs comprising either the entire CTD or the first two or all four of the CTD β-strands grafted onto a scaffold protein. Each construct was expressed as WT and as a variant with alanines replacing five highly conserved and functionally important serine and threonine residues in the first β-strand. We investigated the stability, oligomerization, antiamyloid activity, and affinity for amyloid-β (Aβ42) species using optical spectroscopy, native mass spectrometry, chemical crosslinking, and surface plasmon resonance technology. While DNAJB6 forms large and polydisperse oligomers, CTD was found to form only monomers, dimers, and tetramers of low affinity. Kinetic analyses showed a shift in inhibition mechanism. Whereas full-length DNAJB6 activity is dependent on the serine and threonine residues and efficiently inhibits primary and secondary nucleation, all CTD constructs inhibit secondary nucleation only, independently of the serine and threonine residues, although their dimerization and thermal stabilities are reduced by alanine substitution. While the full-length DNAJB6 inhibition of primary nucleation is related to its propensity to form coaggregates with Aβ, the CTD constructs instead bind to Aβ42 fibrils, which affects the nucleation events at the fibril surface. The retardation of secondary nucleation by DNAJB6 can thus be ascribed to the first two β-strands of its CTD, whereas the inhibition of primary nucleation is dependent on the entire protein or regions outside the CTD.
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Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Rebecca Frankel
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Carlsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Dev Thacker
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Maja Karlsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Vanessa Matus
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Cecilia Emanuelsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden.
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33
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Abelein A. Metal Binding of Alzheimer's Amyloid-β and Its Effect on Peptide Self-Assembly. Acc Chem Res 2023; 56:2653-2663. [PMID: 37733746 PMCID: PMC10552549 DOI: 10.1021/acs.accounts.3c00370] [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: 07/04/2023] [Indexed: 09/23/2023]
Abstract
Metal ions have been identified as key factors modulating the aggregation of amyloid-β peptide (Aβ) implicated in Alzheimer's disease (AD). The presence of elevated levels of metal ions in the amyloid plaques in AD patients supports the notion that the dysfunction of metal homeostasis is connected to the development of AD pathology. Here, recent findings from high- and low-resolution biophysical techniques are put into perspective, providing detailed insights into the molecular structures and dynamics of metal-bound Aβ complexes and the effect of metal ions on the Aβ aggregation process. In particular, the development of theoretical kinetic models deducing different microscopic nucleation events from the macroscopic aggregation behavior has enabled deciphering of the effect of metal ions on specific nucleation processes. In addition to these macroscopic measurements of bulk aggregation to quantify microscopic rates, recent NMR studies have revealed details about the structures and dynamics of metal-Aβ complexes, thereby linking structural events to bulk aggregation. Interestingly, transition-metal ions, such as copper, zinc, and silver ions, form a compact complex with the N-terminal part of monomeric Aβ, respectively, where the metal-bound "folded" state is in dynamic equilibrium with an "unfolded" state. The rates and thermodynamic features of these exchange dynamics have been determined by using NMR relaxation dispersion experiments. Additionally, the application of specifically tailored paramagnetic NMR experiments on the Cu(II)-Aβ complex has been fruitful in obtaining structural constraints within the blind sphere of conventional NMR experiments. This enables the determination of molecular structures of the "folded" Cu(II)-coordinated N-terminal region of Aβ. Furthermore, the discussed transition-metal ions modulate Aβ self-assembly in a concentration-dependent manner, where low metal ion concentrations inhibit Aβ fibril formation, while at high metal ion concentrations other processes occur, resulting in amorphous aggregate formation. Remarkably, the metal-Aβ interaction predominately reduces one specific nucleation step, the fibril-end elongation, whereas primary and surface-catalyzed secondary nucleation mechanisms are less affected. Specific inhibition of fibril-end elongation theoretically predicts an enhanced generation of Aβ oligomers, which is an interesting contribution to understanding metal-Aβ-associated neurotoxic effects. Taken together, the metal binding process creates a metal-bound Aβ complex, which is seemingly inert to aggregation. This process hence efficiently reduces the aggregation-prone peptide pool, which on the macroscopic level is reflected as slower aggregation kinetics. Thus, the specific binding of metals to the Aβ monomer can be linked to the macroscopic inhibitory effect on Aβ bulk aggregation, providing a molecular understanding of the Aβ aggregation mechanism in the presence of metal ions, where the metal ion can be seen as a minimalist agent against Aβ self-assembly. These insights can help to target Aβ aggregation in vivo, where metal ions are key factors modulating the Aβ self-assembly and Aβ-associated neurotoxicity.
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Affiliation(s)
- Axel Abelein
- Department of Biosciences
and Nutrition, Karolinska Institutet, 141 52 Huddinge, Sweden
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34
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Jucker M, Walker LC. Alzheimer's disease: From immunotherapy to immunoprevention. Cell 2023; 186:4260-4270. [PMID: 37729908 PMCID: PMC10578497 DOI: 10.1016/j.cell.2023.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023]
Abstract
Recent Aβ-immunotherapy trials have yielded the first clear evidence that removing aggregated Aβ from the brains of symptomatic patients can slow the progression of Alzheimer's disease. The clinical benefit achieved in these trials has been modest, however, highlighting the need for both a deeper understanding of disease mechanisms and the importance of intervening early in the pathogenic cascade. An immunoprevention strategy for Alzheimer's disease is required that will integrate the findings from clinical trials with mechanistic insights from preclinical disease models to select promising antibodies, optimize the timing of intervention, identify early biomarkers, and mitigate potential side effects.
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Affiliation(s)
- Mathias Jucker
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.
| | - Lary C Walker
- Department of Neurology and Emory National Primate Research Center, Emory University, Atlanta, GA 30322, USA.
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35
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Horne R, Metrick MA, Man W, Rinauro DJ, Brotzakis ZF, Chia S, Meisl G, Vendruscolo M. Secondary Processes Dominate the Quiescent, Spontaneous Aggregation of α-Synuclein at Physiological pH with Sodium Salts. ACS Chem Neurosci 2023; 14:3125-3131. [PMID: 37578897 PMCID: PMC10485892 DOI: 10.1021/acschemneuro.3c00282] [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: 04/29/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023] Open
Abstract
The accurate recapitulation in an in vitro assay of the aggregation process of α-synuclein in Parkinson's disease has been a significant challenge. As α-synuclein does not aggregate spontaneously in most currently used in vitro assays, primary nucleation is triggered by the presence of surfaces such as lipid membranes or interfaces created by shaking, to achieve aggregation on accessible time scales. In addition, secondary nucleation is typically only observed by lowering the pH below 5.8. Here we investigated assay conditions that enables spontaneous primary nucleation and secondary nucleation at pH 7.4. Using 400 mM sodium phosphate, we observed quiescent spontaneous aggregation of α-synuclein and established that this aggregation is dominated by secondary processes. Furthermore, the presence of potassium ions enhanced the reproducibility of quiescent α-synuclein aggregation. This work provides a framework for the study of spontaneous α-synuclein aggregation at physiological pH.
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Affiliation(s)
- Robert
I. Horne
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael A. Metrick
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- College
of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Wing Man
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Dillon J. Rinauro
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Bioprocessing
Technology Institute, Agency of Science, Technology and Research (A*STAR), 138668, Singapore
| | - Georg Meisl
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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36
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Staats R, Brotzakis ZF, Chia S, Horne RI, Vendruscolo M. Optimization of a small molecule inhibitor of secondary nucleation in α-synuclein aggregation. Front Mol Biosci 2023; 10:1155753. [PMID: 37701726 PMCID: PMC10493395 DOI: 10.3389/fmolb.2023.1155753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023] Open
Abstract
Parkinson's disease is characterised by the deposition in the brain of amyloid aggregates of α-synuclein. The surfaces of these amyloid aggregates can catalyse the formation of new aggregates, giving rise to a positive feedback mechanism responsible for the rapid proliferation of α-synuclein deposits. We report a procedure to enhance the potency of a small molecule to inhibit the aggregate proliferation process using a combination of in silico and in vitro methods. The optimized small molecule shows potency already at a compound:protein stoichiometry of 1:20. These results illustrate a strategy to accelerate the optimisation of small molecules against α-synuclein aggregation by targeting secondary nucleation.
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Affiliation(s)
| | | | | | | | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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37
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Johansson B, Oasa S, Muntsant Soria A, Tiiman A, Söderberg L, Amandius E, Möller C, Lannfelt L, Terenius L, Giménez-Llort L, Vukojević V. The interwoven fibril-like structure of amyloid-beta plaques in mouse brain tissue visualized using super-resolution STED microscopy. Cell Biosci 2023; 13:142. [PMID: 37542303 PMCID: PMC10403925 DOI: 10.1186/s13578-023-01086-4] [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: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Standard neuropathologic analysis of Alzheimer's brain relies on traditional fluorescence microscopy, which suffers from limited spatial resolution due to light diffraction. As a result, it fails to reveal intricate details of amyloid plaques. While electron microscopy (EM) offers higher resolution, its extensive sample preparation, involving fixation, dehydration, embedding, and sectioning, can introduce artifacts and distortions in the complex brain tissue. Moreover, EM lacks molecular specificity and has limited field of view and imaging depth. RESULTS In our study, we employed super-resolution Stimulated Emission Depletion (STED) microscopy in conjunction with the anti-human APP recombinant antibody 1C3 fluorescently labelled with DyLightTM633 (1C3-DyLight633). This combination allowed us to visualize amyloidogenic aggregates in vitro and in brain sections from a 17-month-old 3×Tg-AD mouse with sub-diffraction limited spatial resolution. Remarkably, we achieved a spatial resolution of 29 nm in vitro and 62 nm in brain tissue sections, surpassing the capabilities of conventional confocal microscopy by 5-10 times. Consequently, we could discern individual fibrils within plaques, an achievement previously only possible with EM. CONCLUSIONS The utilization of STED microscopy represents a groundbreaking advancement in the field, enabling researchers to delve into the characterization of local mechanisms that underlie Amyloid (Aβ) deposition into plaques and their subsequent clearance. This unprecedented level of detail is especially crucial for comprehending the etiology of Alzheimer's disease and developing the next generation of anti-amyloid treatments. By facilitating the evaluation of drug candidates and non-pharmacological interventions aiming to reduce amyloid burden, STED microscopy emerges as an indispensable tool for driving scientific progress in Alzheimer's research.
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Affiliation(s)
- Björn Johansson
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
- Theme Aging, Karolinska University Hospital, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Sho Oasa
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Aida Muntsant Soria
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Ann Tiiman
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | | | | | | | | | - Lars Terenius
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Lydia Giménez-Llort
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Vladana Vukojević
- Department of Clinical Neuroscience, Karolinska Institutet, SE-17176, Stockholm, Sweden.
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38
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Gupta A, Lu C, Wang F, Chou T, Shan S. An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis. Protein Sci 2023; 32:e4728. [PMID: 37433015 PMCID: PMC10367600 DOI: 10.1002/pro.4728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/18/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023]
Abstract
Numerous age-linked diseases are rooted in protein misfolding; this has motivated the development of small molecules and therapeutic antibodies that target the aggregation of disease-linked proteins. Here we explore another approach: molecular chaperones with engineerable protein scaffolds such as the ankyrin repeat domain (ARD). We tested the ability of cpSRP43, a small, robust, ATP- and cofactor-independent plant chaperone built from an ARD, to antagonize disease-linked protein aggregation. cpSRP43 delays the aggregation of multiple proteins including the amyloid beta peptide (Aβ) associated with Alzheimer's disease and α-synuclein associated with Parkinson's disease. Kinetic modeling and biochemical analyses show that cpSRP43 targets early oligomers during Aβ aggregation, preventing their transition to a self-propagating nucleus on the fibril surface. Accordingly, cpSRP43 rescued neuronal cells from the toxicity of extracellular Aβ42 aggregates. The substrate-binding domain of cpSRP43, composed primarily of the ARD, is necessary and sufficient to prevent Aβ42 aggregation and protect cells against Aβ42 toxicity. This work provides an example in which an ARD chaperone non-native to mammalian cells harbors anti-amyloidal activity, which may be exploited for bioengineering.
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Affiliation(s)
- Arpit Gupta
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Chuqi Lu
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Feng Wang
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Tsui‐Fen Chou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shu‐ou Shan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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39
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202215785. [PMID: 38515735 PMCID: PMC10952214 DOI: 10.1002/ange.202215785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 03/08/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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40
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. Angew Chem Int Ed Engl 2023; 62:e202215785. [PMID: 36876912 PMCID: PMC10953358 DOI: 10.1002/anie.202215785] [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: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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41
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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42
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Abelein A, Johansson J. Amyloid inhibition by molecular chaperones in vitro can be translated to Alzheimer's pathology in vivo. RSC Med Chem 2023; 14:848-857. [PMID: 37252101 PMCID: PMC10211315 DOI: 10.1039/d3md00040k] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 09/23/2023] Open
Abstract
Molecular chaperones are important components in the cellular quality-control machinery and increasing evidence points to potential new roles for them as suppressors of amyloid formation in neurodegenerative diseases, such as Alzheimer's disease. Approaches to treat Alzheimer's disease have not yet resulted in an effective treatment, suggesting that alternative strategies may be useful. Here, we discuss new treatment approaches based on molecular chaperones that inhibit amyloid-β (Aβ) aggregation by different microscopic mechanisms of action. Molecular chaperones that specifically target secondary nucleation reactions during Aβ aggregation in vitro - a process closely associated with Aβ oligomer generation - have shown promising results in animal treatment studies. The inhibition of Aβ oligomer generation in vitro seemingly correlates with the effects of treatment, giving indirect clues about the molecular mechanisms present in vivo. Interestingly, recent immunotherapy advances, which have demonstrated significant improvements in clinical phase III trials, have used antibodies that selectively act against Aβ oligomer formation, supporting the notion that specific inhibition of Aβ neurotoxicity is more rewarding than reducing overall amyloid fibril formation. Hence, specific modulation of chaperone activity represents a promising new strategy for treatment of neurodegenerative disorders.
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Affiliation(s)
- Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet 141 83 Huddinge Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet 141 83 Huddinge Sweden
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43
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Schneider MM, Scheidt T, Priddey AJ, Xu CK, Hu M, Meisl G, Devenish SRA, Dobson CM, Kosmoliaptsis V, Knowles TPJ. Microfluidic antibody affinity profiling of alloantibody-HLA interactions in human serum. Biosens Bioelectron 2023; 228:115196. [PMID: 36921387 DOI: 10.1016/j.bios.2023.115196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
Antibody profiling is a fundamental component of understanding the humoral response in a wide range of disease areas. Most currently used approaches operate by capturing antibodies onto functionalised surfaces. Such measurements of surface binding are governed by an overall antibody titre, while the two fundamental molecular parameters, antibody affinity and antibody concentration, are challenging to determine individually from such approaches. Here, by applying microfluidic diffusional sizing (MDS), we show how we can overcome this challenge and demonstrate reliable quantification of alloantibody binding affinity and concentration of alloantibodies binding to Human Leukocyte Antigens (HLA), an extensively used clinical biomarker in organ transplantation, both in buffer and in crude human serum. Capitalising on the ability to vary both serum and HLA concentrations during MDS, we show that both affinity and concentration of HLA-specific antibodies can be determined directly in serum when neither of these parameters is known. Finally, we provide proof of principle in clinical transplant patient sera that our assay enables differentiation of alloantibody reactivity against HLA proteins of highly similar structure, providing information not attainable through currently available techniques. These results outline a path towards detection and in-depth profiling of humoral immunity and may enable further insights into the clinical relevance of antibody reactivity in clinical transplantation and beyond.
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Affiliation(s)
- Matthias M Schneider
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tom Scheidt
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ashley J Priddey
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Mengsha Hu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge, CB1 8DH, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK; NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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44
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Qiu W, Liu H, Liu Y, Lu X, Wang L, Hu Y, Feng F, Li Q, Sun H. Regulation of beta-amyloid for the treatment of Alzheimer's disease: Research progress of therapeutic strategies and bioactive compounds. Med Res Rev 2023. [PMID: 36945751 DOI: 10.1002/med.21947] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/09/2023] [Accepted: 02/26/2023] [Indexed: 03/23/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease that is difficult to treat. Extracellular amyloid is the principal pathological criterion for the diagnosis of AD. Amyloid β (Aβ) interacts with various receptor molecules on the plasma membrane and mediates a series of signaling pathways that play a vital role in the occurrence and development of AD. Research on receptors that interact with Aβ is currently ongoing. Overall, there are no effective medications to treat AD. In this review, we first discuss the importance of Aβ in the pathogenesis of AD, then summarize the latest progress of Aβ-related targets and compounds. Finally, we put forward the challenges and opportunities in the development of effective AD therapies.
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Affiliation(s)
- Weimin Qiu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hui Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yijun Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xin Lu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Lei Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yanyu Hu
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
- Department of Natural Medicinal Chemistry, Jiangsu Food and Pharmaceuticals Science College, Institute of Food and Pharmaceuticals Research, Jiangsu, Huaian, China
| | - Qi Li
- Department of Pharmacology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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45
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Emmenegger M, Worth R, Fiedler S, Devenish SRA, Knowles TPJ, Aguzzi A. Protocol to determine antibody affinity and concentration in complex solutions using microfluidic antibody affinity profiling. STAR Protoc 2023; 4:102095. [PMID: 36853663 PMCID: PMC9925161 DOI: 10.1016/j.xpro.2023.102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/24/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
Conventional methods of measuring affinity are limited by artificial immobilization, large sample volumes, and homogeneous solutions. This protocol describes microfluidic antibody affinity profiling on complex human samples in solution to obtain a fingerprint reflecting both affinity and active concentration of the target protein. To illustrate the protocol, we analyze the antibody response in SARS-CoV-2 omicron-naïve samples against different SARS-CoV-2 variants of concern. However, the protocol and the technology are amenable to a broad spectrum of biomedical questions. For complete details on the use and execution of this protocol, please refer to Emmenegger et al. (2022),1 Schneider et al. (2022),2 and Fiedler et al. (2022).3.
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Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
| | - Roland Worth
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sebastian Fiedler
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
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46
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Somin S, Kulasiri D, Samarasinghe S. Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling. Transl Neurodegener 2023; 12:11. [PMID: 36907887 PMCID: PMC10009979 DOI: 10.1186/s40035-023-00344-2] [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: 11/07/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
Treatment for Alzheimer's disease (AD) can be more effective in the early stages. Although we do not completely understand the aetiology of the early stages of AD, potential pathological factors (amyloid beta [Aβ] and tau) and other co-factors have been identified as causes of AD, which may indicate some of the mechanism at work in the early stages of AD. Today, one of the primary techniques used to help delay or prevent AD in the early stages involves alleviating the unwanted effects of oxidative stress on Aβ clearance. 4-Hydroxynonenal (HNE), a product of lipid peroxidation caused by oxidative stress, plays a key role in the adduction of the degrading proteases. This HNE employs a mechanism which decreases catalytic activity. This process ultimately impairs Aβ clearance. The degradation of HNE-modified proteins helps to alleviate the unwanted effects of oxidative stress. Having a clear understanding of the mechanisms associated with the degradation of the HNE-modified proteins is essential for the development of strategies and for alleviating the unwanted effects of oxidative stress. The strategies which could be employed to decrease the effects of oxidative stress include enhancing antioxidant activity, as well as the use of nanozymes and/or specific inhibitors. One area which shows promise in reducing oxidative stress is protein design. However, more research is needed to improve the effectiveness and accuracy of this technique. This paper discusses the interplay of potential pathological factors and AD. In particular, it focuses on the effect of oxidative stress on the expression of the Aβ-degrading proteases through adduction of the degrading proteases caused by HNE. The paper also elucidates other strategies that can be used to alleviate the unwanted effects of oxidative stress on Aβ clearance. To improve the effectiveness and accuracy of protein design, we explain the application of quantum mechanical/molecular mechanical approach.
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Affiliation(s)
- Sarawoot Somin
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand.,Department of Wine, Food and Molecular Biosciences, Lincoln University, Christchurch, 7647, New Zealand
| | - Don Kulasiri
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand. .,Department of Wine, Food and Molecular Biosciences, Lincoln University, Christchurch, 7647, New Zealand.
| | - Sandhya Samarasinghe
- Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Christchurch, 7647, New Zealand
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47
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Wojtunik-Kulesza K, Rudkowska M, Orzeł-Sajdłowska A. Aducanumab-Hope or Disappointment for Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24054367. [PMID: 36901797 PMCID: PMC10002282 DOI: 10.3390/ijms24054367] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
In June 2021, the world was informed about a new drug for Alzheimer's disease approved by the FDA. Aducanumab (BIIB037, ADU), being a monoclonal antibody IgG1, is the newest AD treatment. The activity of the drug is targeted towards amyloid β, which is considered one of the main causes of Alzheimer's disease. Clinical trials have revealed time- and dose-dependent activity towards Aβ reduction, as well as cognition improvement. Biogen, the company responsible for conducting research and introducing the drug to the market, presents the drug as a solution to cognitive impairment, but its limitations, costs, and side effects are controversial. The framework of the paper focuses on the mechanism of aducanumab's action along with the positive and negative sides of the therapy. The review presents the basis of the amyloid hypothesis that is the cornerstone of therapy, as well as the latest information about aducanumab, its mechanism of action, and the possibility of the use of the drug.
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Affiliation(s)
- Karolina Wojtunik-Kulesza
- Department of Inorganic Chemistry, Medical University of Lublin, 20-059 Lublin, Poland
- Correspondence:
| | - Monika Rudkowska
- Independent Laboratory of Behavioral Studies, Medical University of Lublin, Jaczewskiego 4, 20-090 Lublin, Poland
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48
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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49
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Manchanda S, Galan-Acosta L, Abelein A, Tambaro S, Chen G, Nilsson P, Johansson J. Intravenous treatment with a molecular chaperone designed against β-amyloid toxicity improves Alzheimer's disease pathology in mouse models. Mol Ther 2023; 31:487-502. [PMID: 35982621 PMCID: PMC9931549 DOI: 10.1016/j.ymthe.2022.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/12/2022] [Accepted: 08/12/2022] [Indexed: 02/07/2023] Open
Abstract
Attempts to treat Alzheimer's disease with immunotherapy against the β-amyloid (Aβ) peptide or with enzyme inhibitors to reduce Aβ production have not yet resulted in effective treatment, suggesting that alternative strategies may be useful. Here we explore the possibility of targeting the toxicity associated with Aβ aggregation by using the recombinant human (rh) Bri2 BRICHOS chaperone domain, mutated to act selectively against Aβ42 oligomer generation and neurotoxicity in vitro. We find that treatment of Aβ precursor protein (App) knockin mice with repeated intravenous injections of rh Bri2 BRICHOS R221E, from an age close to the start of development of Alzheimer's disease-like pathology, improves recognition and working memory, as assessed using novel object recognition and Y maze tests, and reduces Aβ plaque deposition and activation of astrocytes and microglia. When treatment was started about 4 months after Alzheimer's disease-like pathology was already established, memory improvement was not detected, but Aβ plaque deposition and gliosis were reduced, and substantially reduced astrocyte accumulation in the vicinity of Aβ plaques was observed. The degrees of treatment effects observed in the App knockin mouse models apparently correlate with the amounts of Bri2 BRICHOS detected in brain sections after the end of the treatment period.
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Affiliation(s)
- Shaffi Manchanda
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Lorena Galan-Acosta
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Simone Tambaro
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Per Nilsson
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Stockholm, Sweden.
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50
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Geerts H, Walker M, Rose R, Bergeler S, van der Graaf PH, Schuck E, Koyama A, Yasuda S, Hussein Z, Reyderman L, Swanson C, Cabal A. A combined physiologically-based pharmacokinetic and quantitative systems pharmacology model for modeling amyloid aggregation in Alzheimer's disease. CPT Pharmacometrics Syst Pharmacol 2023; 12:444-461. [PMID: 36632701 PMCID: PMC10088087 DOI: 10.1002/psp4.12912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Antibody-mediated removal of aggregated β-amyloid (Aβ) is the current, most clinically advanced potential disease-modifying treatment approach for Alzheimer's disease. We describe a quantitative systems pharmacology (QSP) approach of the dynamics of Aβ monomers, oligomers, protofibrils, and plaque using a detailed microscopic model of Aβ40 and Aβ42 aggregation and clearance of aggregated Aβ by activated microglia cells, which is enhanced by the interaction of antibody-bound Aβ. The model allows for the prediction of Aβ positron emission tomography (PET) imaging load as measured by a standardized uptake value ratio. A physiology-based pharmacokinetic model is seamlessly integrated to describe target exposure of monoclonal antibodies and simulate dynamics of cerebrospinal fluid (CSF) and plasma biomarkers, including CSF Aβ42 and plasma Aβ42 /Aβ40 ratio biomarkers. Apolipoprotein E genotype is implemented as a difference in microglia clearance. By incorporating antibody-bound, plaque-mediated macrophage activation in the perivascular compartment, the model also predicts the incidence of amyloid-related imaging abnormalities with edema (ARIA-E). The QSP platform is calibrated with pharmacological and clinical information on aducanumab, bapineuzumab, crenezumab, gantenerumab, lecanemab, and solanezumab, predicting adequately the change in PET imaging measured amyloid load and the changes in the plasma Aβ42 /Aβ40 ratio while slightly overestimating the change in CSF Aβ42 . ARIA-E is well predicted for all antibodies except bapineuzumab. This QSP model could support the clinical trial design of different amyloid-modulating interventions, define optimal titration and maintenance schedules, and provide a first step to understand the variability of biomarker response in clinical practice.
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