1
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Kepp KP, Robakis NK, Høilund-Carlsen PF, Sensi SL, Vissel B. The amyloid cascade hypothesis: an updated critical review. Brain 2023; 146:3969-3990. [PMID: 37183523 DOI: 10.1093/brain/awad159] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023] Open
Abstract
Results from recent clinical trials of antibodies that target amyloid-β (Aβ) for Alzheimer's disease have created excitement and have been heralded as corroboration of the amyloid cascade hypothesis. However, while Aβ may contribute to disease, genetic, clinical, imaging and biochemical data suggest a more complex aetiology. Here we review the history and weaknesses of the amyloid cascade hypothesis in view of the new evidence obtained from clinical trials of anti-amyloid antibodies. These trials indicate that the treatments have either no or uncertain clinical effect on cognition. Despite the importance of amyloid in the definition of Alzheimer's disease, we argue that the data point to Aβ playing a minor aetiological role. We also discuss data suggesting that the concerted activity of many pathogenic factors contribute to Alzheimer's disease and propose that evolving multi-factor disease models will better underpin the search for more effective strategies to treat the disease.
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Affiliation(s)
- Kasper P Kepp
- Section of Biophysical and Biomedicinal chemistry, DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nikolaos K Robakis
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY 10029, USA
| | - Poul F Høilund-Carlsen
- Department of Nuclear Medicine, Odense University Hospital, 5000 Odense C, Denmark
- Department of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Stefano L Sensi
- Center for Advanced Studies and Technology-CAST, and Institute for Advanced Biotechnology (ITAB), University G. d'Annunzio of Chieti-Pescara, Chieti, 66013, Italy
- Department of Neuroscience, Imaging, and Clinical Sciences, University G. d'Annunzio of Chieti-Pescara, Chieti, 66013, Italy
| | - Bryce Vissel
- St Vincent's Hospital Centre for Applied Medical Research, St Vincent's Hospital, Sydney, 2010, Australia
- School of Clinical Medicine, UNSW Medicine and Health, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, Sydney, NSW 2052, Australia
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2
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Do HN, Devkota S, Bhattarai A, Wolfe MS, Miao Y. Effects of presenilin-1 familial Alzheimer's disease mutations on γ-secretase activation for cleavage of amyloid precursor protein. Commun Biol 2023; 6:174. [PMID: 36788318 PMCID: PMC9929099 DOI: 10.1038/s42003-023-04539-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer's disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the "Active" state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the "Active" state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.
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Affiliation(s)
- Hung N. Do
- grid.266515.30000 0001 2106 0692Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047 USA
| | - Sujan Devkota
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047 USA
| | - Apurba Bhattarai
- grid.266515.30000 0001 2106 0692Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047 USA
| | - Michael S. Wolfe
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047 USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA.
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3
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Kepp KP, Sensi SL, Johnsen KB, Barrio JR, Høilund-Carlsen PF, Neve RL, Alavi A, Herrup K, Perry G, Robakis NK, Vissel B, Espay AJ. The Anti-Amyloid Monoclonal Antibody Lecanemab: 16 Cautionary Notes. J Alzheimers Dis 2023; 94:497-507. [PMID: 37334596 DOI: 10.3233/jad-230099] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
After the CLARITY-AD clinical trial results of lecanemab were interpreted as positive, and supporting the amyloid hypothesis, the drug received accelerated Food and Drug Administration approval. However, we argue that benefits of lecanemab treatment are uncertain and may yield net harm for some patients, and that the data do not support the amyloid hypothesis. We note potential biases from inclusion, unblinding, dropouts, and other issues. Given substantial adverse effects and subgroup heterogeneity, we conclude that lecanemab's efficacy is not clinically meaningful, consistent with numerous analyses suggesting that amyloid-β and its derivatives are not the main causative agents of Alzheimer's disease dementia.
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Affiliation(s)
- Kasper P Kepp
- Department of Chemistry, Section of Biophysical and Biomedicinal Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stefano L Sensi
- Center for Advanced Studies and Technology - CAST, and Institute for Advanced Biotechnology (ITAB), University G. d'Annunzio of Chieti-Pescara, Italy
- Department of Neuroscience, Imaging, and Clinical Sciences, University G. d'Annunzio of Chieti-Pescara, Italy
| | - Kasper B Johnsen
- Department of Health Science and Technology, Neurobiology Research and Drug Delivery Group, Aalborg University, Aalborg, Denmark
| | - Jorge R Barrio
- Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Poul F Høilund-Carlsen
- Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Rachael L Neve
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Abass Alavi
- Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, PA USA
| | - Karl Herrup
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - George Perry
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Nikolaos K Robakis
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY, USA
| | - Bryce Vissel
- St Vincent's Hospital Centre for Applied Medical Research, St Vincent's Hospital, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Alberto J Espay
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
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4
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Rossi G, Salvi E, Mehmeti E, Ricci M, Villa C, Prioni S, Moda F, Di Fede G, Tiraboschi P, Redaelli V, Coppola C, Koch G, Canu E, Filippi M, Agosta F, Giaccone G, Caroppo P. Semantic and right temporal variant of FTD: Next generation sequencing genetic analysis on a single-center cohort. Front Aging Neurosci 2022; 14:1085406. [PMID: 36570531 PMCID: PMC9773257 DOI: 10.3389/fnagi.2022.1085406] [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: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Semantic and right temporal variant of frontotemporal dementia (svFTD and rtvFTD) are rare clinical phenotypes in which, in most cases, the underlying pathology is TDP-43 proteinopathy. They are usually sporadic disorders, but recent evidences suggest a higher frequency of genetic mutations for the right temporal versus the semantic variant. However, the genetic basis of these forms is not clear. In this study we performed a genetic screening of a single-center cohort of svFTD and rtvFTD patients, aiming at identifying the associated genetic variants. A panel of 73 dementia candidate genes has been analyzed by NGS target sequencing including both causal and risk/modifier genes in 23 patients (15 svFTD and 8 rtvFTD) and 73 healthy age-matched controls. We first performed a single variant analysis considering rare variants and then a gene-based aggregation analysis to evaluate the cumulative effects of multiple rare variants in a single gene. We found 12 variants in nearly 40% of patients (9/23), described as pathogenic or classified as VUS/likely pathogenic. The overall rate was higher in svFTD than in rtvFTD. Three mutations were located in MAPT gene and single mutations in the following genes: SQSTM1, VCP, PSEN1, TBK1, OPTN, CHCHD10, PRKN, DCTN1. Our study revealed the presence of variants in genes involved in pathways relevant for the pathology, especially autophagy and inflammation. We suggest that molecular analysis should be performed in all svFTD and rtvFTD patients, to better understand the genotype-phenotype correlation and the pathogenetic mechanisms that could drive the clinical phenotypes in FTD.
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Affiliation(s)
- Giacomina Rossi
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy,*Correspondence: Giacomina Rossi,
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elkadia Mehmeti
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Martina Ricci
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cristina Villa
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Prioni
- Clinical Neuropsychology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Fabio Moda
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Di Fede
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pietro Tiraboschi
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Veronica Redaelli
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cinzia Coppola
- Department of Advanced Medical and Surgical Sciences, University of Campania “L. Vanvitelli”, Naples, Italy
| | - Giacomo Koch
- Non Invasive Brain Stimulation Unit/Department of Behavioral and Clinical Neurology, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Elisa Canu
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Filippi
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy,Neurology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy,Vita-Salute San Raffaele University, Milan, Italy,Unit of Neurorehabilitation, IRCCS San Raffaele Scientific Institute, Milan, Italy,Neurophysiology Service, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Agosta
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy,Neurology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy,Vita-Salute San Raffaele University, Milan, Italy
| | - Giorgio Giaccone
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Paola Caroppo
- Neurology V and Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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5
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Willumsen N, Arber C, Lovejoy C, Toombs J, Alatza A, Weston PSJ, Chávez-Gutiérrez L, Hardy J, Zetterberg H, Fox NC, Ryan NS, Lashley T, Wray S. The PSEN1 E280G mutation leads to increased amyloid-β43 production in induced pluripotent stem cell neurons and deposition in brain tissue. Brain Commun 2022; 5:fcac321. [PMID: 36687397 PMCID: PMC9847549 DOI: 10.1093/braincomms/fcac321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/06/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in the presenilin 1 gene, PSEN1, which cause familial Alzheimer's disease alter the processing of amyloid precursor protein, leading to the generation of various amyloid-β peptide species. These species differ in their potential for aggregation. Mutation-specific amyloid-β peptide profiles may thereby influence pathogenicity and clinical heterogeneity. There is particular interest in comparing mutations with typical and atypical clinical presentations, such as E280G. We generated PSEN1 E280G mutation induced pluripotent stem cells from two patients and differentiated them into cortical neurons, along with previously reported PSEN1 M146I, PSEN1 R278I and two control lines. We assessed both the amyloid-β peptide profiles and presenilin 1 protein maturity. We also compared amyloid-β peptide profiles in human post-mortem brain tissue from cases with matched mutations. Amyloid-β ratios significantly differed compared with controls and between different patients, implicating mutation-specific alterations in amyloid-β ratios. Amyloid-β42:40 was increased in the M146I and both E280G lines compared with controls. Amyloid-β42:40 was not increased in the R278I line compared with controls. The amyloid-β43:40 ratio was increased in R278I and both E280G lines compared with controls, but not in M146I cells. Distinct amyloid-β peptide patterns were also observed in human brain tissue from individuals with these mutations, showing some similar patterns to cell line observations. Reduced presenilin 1 maturation was observed in neurons with the PSEN1 R278I and E280G mutations, but not the M146I mutation. These results suggest that mutation location can differentially alter the presenilin 1 protein and affect its autoendoproteolysis and processivity, contributing to the pathological phenotype. Investigating differences in underlying molecular mechanisms of familial Alzheimer's disease may inform our understanding of clinical heterogeneity.
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Affiliation(s)
- Nanet Willumsen
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Charles Arber
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Christopher Lovejoy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Jamie Toombs
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- UK Dementia Research Institute, University College London, London WC1E 6AU, UK
| | - Argyro Alatza
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Philip S J Weston
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
| | - Lucia Chávez-Gutiérrez
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Department of Neurology, KU Leuven, 3000 Leuven, Belgium
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- UK Dementia Research Institute, University College London, London WC1E 6AU, UK
| | - Henrik Zetterberg
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- UK Dementia Research Institute, University College London, London WC1E 6AU, UK
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Nick C Fox
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
- UK Dementia Research Institute, University College London, London WC1E 6AU, UK
| | - Natalie S Ryan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
- UK Dementia Research Institute, University College London, London WC1E 6AU, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
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6
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Feilen LP, Chen SY, Fukumori A, Feederle R, Zacharias M, Steiner H. Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis. eLife 2022; 11:76090. [PMID: 35579427 PMCID: PMC9282858 DOI: 10.7554/elife.76090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here, we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer’s disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme’s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis. Cutting proteins into pieces is a crucial process in the cell, allowing several important processes to take place, including cell differentiation (which allows cells to develop into specific types), cell death, protein quality control, or even where in the cell a protein will end up. However, the specialized proteins that carry out this task, known as proteases, can also be involved in the development of disease. For example, in the brain, a protease called γ-secretase cuts up the amyloid-β protein precursor, producing toxic forms of amyloid-β peptides that are widely believed to cause Alzheimer’s disease. Proteases like γ-secretase carry out their role in the membrane, the layer of fats (also known as lipids) that forms the outer boundary of the cell. The environment in this area of the cell can influence the activity of proteases, but it is poorly understood how this happens. One way to address this question would be to compare the activity of γ-secretase in the lipid environment of the membrane to its activity when it is entirely surrounded by different molecules, such as detergent molecules. Unfortunately, γ-secretase is not active when it is removed from its lipid environment by a detergent, making it difficult to perform this comparison. To overcome this issue, Feilen et al. chose to study PSH, a protease similar to γ-secretase that produces the same amyloid-β peptides but remains active in detergent. When Feilen et al. mixed PSH with lipid molecules like those found in the membrane and amyloid-β precursor protein, PSH produced amyloid-β peptides including those that are thought to cause Alzheimer’s. However, when a detergent was substituted for the lipid molecules this led to longer amyloid-β peptides than usual, indicating that PSH was not able to cut proteins as effectively. The change in environment appeared to reduce PSH’s ability to progressively trim small segments from the peptides. Computer modelling of the protease’s structure in lipids versus detergent supported the experimental findings: the model predicted that the areas of PSH important for recognizing and cutting other proteins would be more stable in the membrane compared to the detergent. These results indicate that the cell membrane plays a vital role in the stability of the active regions of proteases that are cleaving in this environment. In the future, this could help to better understand how changes to the lipid molecules in the membrane may contribute to the activity of γ-secretase and its role in Alzheimer’s disease.
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Affiliation(s)
- Lukas P Feilen
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Shu-Yu Chen
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Akio Fukumori
- Department of Pharmacotherapeutics II, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Regina Feederle
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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7
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Abstract
Copper ions bind to biomolecules (e.g., peptides and proteins) playing an essential role in many biological and physiological pathways in the human body. The resulting complexes may contribute to the initiation of neurodegenerative diseases, cancer, and bacterial and viral diseases, or act as therapeutics. Some compounds can chemically damage biological macromolecules and initiate the development of pathogenic states. Conversely, a number of these compounds may have antibacterial, antiviral, and even anticancer properties. One of the most significant current discussions in Cu biochemistry relates to the mechanisms of the positive and negative actions of Cu ions based on the generation of reactive oxygen species, including radicals that can interact with DNA molecules. This review aims to analyze various peptide–copper complexes and the mechanism of their action.
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8
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Tang Y, Zhang D, Gong X, Zheng J. A mechanistic survey of Alzheimer's disease. Biophys Chem 2021; 281:106735. [PMID: 34894476 DOI: 10.1016/j.bpc.2021.106735] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, OH, United States of America
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America.
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9
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He XY, Xu Y, Xia QJ, Zhao XM, Li S, He XQ, Wang RR, Wang TH. Combined Scutellarin and C 18H 17NO 6 Imperils the Survival of Glioma: Partly Associated With the Repression of PSEN1/PI3K-AKT Signaling Axis. Front Oncol 2021; 11:663262. [PMID: 34568005 PMCID: PMC8460401 DOI: 10.3389/fonc.2021.663262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Glioma, the most common intracranial tumor, harbors great harm. Since the treatment for it has reached the bottleneck stage, the development of new drugs becomes a trend. Therefore, we focus on the effect of scutellarin (SCU) and its combination with C18H17NO6 (abbreviated as combination) on glioma and its possible mechanism in this study. Firstly, SCU and C18H17NO6 both suppressed the proliferation of U251 and LN229 cells in a dose-dependent manner, and C18H17NO6 augmented the inhibition effect of SCU on U251 and LN229 cells in vitro. Moreover, there was an interactive effect between them. Secondly, SCU and C18H17NO6 decreased U251 cells in G2 phase and LN229 cells in G2 and S phases but increased U251 cells in S phase, respectively. Meanwhile, the combination could further reduce U251 cells in G2 phase and LN229 cells in G2 and S phases. Thirdly, SCU and C18H17NO6 both induced the apoptosis of U251 and LN229. The combination further increased the apoptosis rate of both cells compared with the two drugs alone. Furthermore, SCU and C18H17NO6 both inhibited the lateral and vertical migration of both cells, which was further repressed by the combination. More importantly, the effect of SCU and the combination was better than positive control-temozolomide, and the toxicity was low. Additionally, SCU and C18H17NO6 could suppress the growth of glioma in vivo, and the effect of the combination was better. Finally, SCU and the combination upregulated the presenilin 1 (PSEN1) level but inactivated the phosphatidylinositol 3−kinase (PI3K)-protein kinase B (AKT) signaling in vitro and in vivo. Accordingly, we concluded that scutellarin and its combination with C18H17NO6 suppressed the proliferation/growth and migration and induced the apoptosis of glioma, in which the mechanism might be associated with the repression of PSEN1/PI3K-AKT signaling axis.
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Affiliation(s)
- Xiu-Ying He
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Xu
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qing-Jie Xia
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Ming Zhao
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Li
- Institute of Neuroscience, Laboratory Zoology Department, Kunming Medical University, Kunming, China
| | - Xiao-Qiong He
- School of Public Health, Kunming Medical University, Kunming, China
| | - Ru-Rong Wang
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ting-Hua Wang
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,Institute of Neuroscience, Laboratory Zoology Department, Kunming Medical University, Kunming, China
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10
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Mehra R, Kepp KP. Computational prediction and molecular mechanism of γ-secretase modulators. Eur J Pharm Sci 2021; 157:105626. [DOI: 10.1016/j.ejps.2020.105626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022]
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11
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A computer-simulated mechanism of familial Alzheimer’s disease: Mutations enhance thermal dynamics and favor looser substrate-binding to γ-secretase. J Struct Biol 2020; 212:107648. [DOI: 10.1016/j.jsb.2020.107648] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/22/2020] [Accepted: 10/09/2020] [Indexed: 11/22/2022]
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12
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Wang H, Sun R, Shi Y, Xia M, Zhao J, Yang M, Ma L, Sun Y, Li G, Zhang H, Qin W, Zhang J. Probable Novel PSEN1 Gln222Leu Mutation in a Chinese Family with Early-Onset Alzheimer's Disease. Curr Alzheimer Res 2020; 16:764-769. [PMID: 31385772 DOI: 10.2174/1567205016666190806161342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/20/2019] [Accepted: 08/05/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND The rate of occurrence of Alzheimer's disease is increasing around the world. However, there is still no significant breakthrough in the study of its etiology and pathogenesis. OBJECTIVE To screen Alzheimer's disease pathogenic genes, which may be conducive to the elucidation of the pathogenic mechanisms of Alzheimer's disease And predict the pathogenicity by various computer software. METHODS Clinical and neuroimaging examination, Whole Exome Sequencing, and Sanger sequencing were performed in the proband. Mutation sites were verified in 158 subjects. RESULTS We reported a proband carrying a probably novel pathogenic mutation, which clinically manifests as progressive memory loss, visual-spatial disorders, apraxia, psychobehavioral disorders, and temperamental and personality changes. Whole Exome Sequencing detected a novel missense mutation at codon 222 (Q222L), which is a heterozygous A to T point mutation at position 665 (c.665A>T) in exon 5 of the presenilin 1 leading to a glutamine-to-leucine substitution. The mutation was also identified by Sanger sequencing in one family member; nevertheless, it was not detected in the other 7 unaffected family members, 50 sporadic Alzheimer's disease patients and 100 control subjects. CONCLUSION A novel mutation in exon 5 of the presenilin 1 gene (Gln222Leu) in a Chinese family with early-onset Alzheimer's disease has been reported, besides, it was predicted that the missense mutation was probably a novel pathogenic mutation that was reported for the first time in a Chinese family with early-onset Alzheimer's disease.
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Affiliation(s)
- Huayuan Wang
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruihua Sun
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Shi
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingrong Xia
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jing Zhao
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Miaomiao Yang
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Limin Ma
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yajing Sun
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Gai Li
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haohan Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Weiwei Qin
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiewen Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
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13
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Dehury B, Kepp KP. Membrane dynamics of γ-secretase with the anterior pharynx-defective 1B subunit. J Cell Biochem 2020; 122:69-85. [PMID: 32830360 DOI: 10.1002/jcb.29832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023]
Abstract
The four-subunit protease complex γ-secretase cleaves many single-pass transmembrane (TM) substrates, including Notch and β-amyloid precursor protein to generate amyloid-β (Aβ), central to Alzheimer's disease. Two of the subunits anterior pharynx-defective 1 (APH-1) and presenilin (PS) exist in two homologous forms APH1-A and APH1-B, and PS1 and PS2. The consequences of these variations are poorly understood and could affect Aβ production and γ-secretase medicine. Here, we developed the first complete structural model of the APH-1B subunit using the published cryo-electron microscopy (cryo-EM) structures of APH1-A (Protein Data Bank: 5FN2, 5A63, and 6IYC). We then performed all-atom molecular dynamics simulations at 303 K in a realistic bilayer system to understand both APH-1B alone and in γ-secretase without and with substrate C83-bound. We show that APH-1B adopts a 7TM topology with a water channel topology similar to APH-1A. We demonstrate direct transport of water through this channel, mainly via Glu84, Arg87, His170, and His196. The apo and holo states closely resemble the experimental cryo-EM structures with APH-1A, however with subtle differences: The substrate-bound APH-1B γ-secretase was quite stable, but some TM helices of PS1 and APH-1B rearranged in the membrane consistent with the disorder seen in the cryo-EM data. This produces different accessibility of water molecules for the catalytic aspartates of PS1, critical for Aβ production. In particular, we find that the typical distance between the catalytic aspartates of PS1 and the C83 cleavage sites are shorter in APH-1B, that is, it represents a more closed state, due to interactions with the C-terminal fragment of PS1. Our structural-dynamic model of APH-1B alone and in γ-secretase suggests generally similar topology but some notable differences in water accessibility which may be relevant to the protein's existence in two forms and their specific function and location.
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Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
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14
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Dehury B, Tang N, Mehra R, Blundell TL, Kepp KP. Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature. RSC Adv 2020; 10:31215-31232. [PMID: 35520661 PMCID: PMC9056423 DOI: 10.1039/d0ra04683c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/15/2020] [Indexed: 12/29/2022] Open
Abstract
γ-Secretase cleaves the C99 fragment of the amyloid precursor protein, leading to formation of aggregated β-amyloid peptide central to Alzheimer's disease, and Notch, essential for cell regulation. Recent cryogenic electron microscopy (cryo-EM) structures indicate major changes upon substrate binding, a β-sheet recognition motif, and a possible helix unwinding to expose peptide bonds towards nucleophilic attack. Here we report side-by-side comparison of the 303 K dynamics of the two proteins in realistic membranes using molecular dynamics simulations. Our ensembles agree with the cryo-EM data (full-protein Cα-RMSD = 1.62–2.19 Å) but reveal distinct presenilin helix conformation states and thermal β-strand to coil transitions of C83 and Notch100. We identify distinct 303 K hydrogen bond dynamics and water accessibility of the catalytic sites. The RKRR motif (1758–1761) contributes significantly to Notch binding and serves as a “membrane anchor” that prevents Notch displacement. Water that transiently hydrogen bonds to G1753 and V1754 probably represents the catalytic nucleophile. At 303 K, Notch and C83 binding induce different conformation states, with Notch mostly present in a closed state with shorter Asp–Asp distance. This may explain the different outcome of Notch and C99 cleavage, as the latter is more imprecise with many products. Our identified conformation states may aid efforts to develop conformation-selective drugs that target C99 and Notch cleavage differently, e.g. Notch-sparing γ-secretase modulators. Distinct membrane dynamics and conformations of C83- and Notch-bound γ-secretase may aid the development of Notch-sparing treatments of Alzheimer's disease.![]()
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409.,Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Rukmankesh Mehra
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
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15
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Jiang B, Bi M, Li J, Liu Q, Xiao NA, Fang J, Shi MY, Yu ZW, Ma QL, Tong SJ, Zheng KM. A Pathogenic Variant p.Phe177Val in PSEN1 Causes Early-Onset Alzheimer's Disease in a Chinese Family. Front Genet 2020; 11:713. [PMID: 32754199 PMCID: PMC7366492 DOI: 10.3389/fgene.2020.00713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/11/2020] [Indexed: 11/25/2022] Open
Abstract
Familial Alzheimer’s disease (FAD) present as a positive family history of cognitive decline, with early onset and an autosomal dominant inheritance pattern. FAD is mainly caused by the mutations in the genes encoding for amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). In the present study, we identified a variant (c.529T > G, p.Phe177Val) in PSEN1 across three generations in a Chinese family with FAD using whole-exome sequencing. The mean age of onset was 39 years (range: 37 to 40 years) in this family. In cell transfection studies, the mutant PSEN1 protein carrying p.Phe177Val increased both the production of Aβ42 and the ratio of Aβ42 over Aβ40, as compared to wild-type PSEN1. Our results confirm the pathogenicity of PSEN1 p.Phe177Val variant in FAD and broaden the clinical phenotype spectrum of FAD patients with PSEN1 p.Phe177Val variant.
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Affiliation(s)
- Bin Jiang
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Min Bi
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Jun Li
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Qi Liu
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Nai-An Xiao
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Jie Fang
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Man-Yi Shi
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Zi-Wen Yu
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Qi-Lin Ma
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Sui-Jun Tong
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
| | - Kun-Mu Zheng
- Department of Neurology, First Affiliated Hospital, Xiamen University, Xiamen, China
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16
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Chatterjee S, Salimi A, Lee JY. Insights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:5963-5976. [DOI: 10.1080/07391102.2020.1794967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
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17
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Mehra R, Kepp KP. Identification of Structural Calcium Binding Sites in Membrane-Bound Presenilin 1 and 2. J Phys Chem B 2020; 124:4697-4711. [PMID: 32420742 DOI: 10.1021/acs.jpcb.0c01712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Variants of presenilin (PS1 and PS2) are the main genetic risk factors of familial Alzheimer's disease and thus central to the disease etiology. Although mostly studied as catalytic units of γ-secretase controlling Aβ production, presenilins also affect calcium levels, which are disturbed in Alzheimer's disease. We investigated the interaction of calcium with both PS1 and PS2 using all-atom molecular dynamics (MD) simulations in realistic membrane models, with the specific aim to identify any Ca2+ sites. We did not observe any complete Ca2+ leak event, but we identified four persistent Ca2+ sites in membrane-bound PS1 and PS2: One in HL2 near the C-terminal of TM6, one in HL2 toward the N-terminal of TM7, a site at the catalytic aspartate on TM7, and a site at the PALP motif on TM9. The sites feature negatively charged glutamates and aspartates typical of calcium binding. Structural homology to diaspartate calcium transport proteins and mutation studies of calcium efflux support our identified calcium sites. Calcium consistently dampens HL2 motions in all comparisons (PS1, protonated PS1, PS2, protonated PS2). Due to their location in HL2 and the active site, we propose that the calcium sites control autoproteolytic maturation of presenilin by a pH-dependent conformational restriction of the HL2 recognition loop, which also regulates calcium transport proteins such as inositol 1,4,5-triphosphate receptor and ryanodine receptor. Our structural dynamics could provide a possible molecular basis for the need of both calcium and presenilin for lysosome proteolytic function, perhaps relevant also to other protein misfolding diseases.
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Affiliation(s)
- Rukmankesh Mehra
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
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18
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Polychronidou E, Avramouli A, Vlamos P. Alzheimer's Disease: The Role of Mutations in Protein Folding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1195:227-236. [PMID: 32468481 DOI: 10.1007/978-3-030-32633-3_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Misfolded proteins result when a protein follows the wrong folding pathway. Accumulation of misfolded proteins can cause disorders, known as amyloid diseases. Unfortunately, some of them are very common. The most prevalent one is Alzheimer's disease. Alzheimer's disease is a neurodegenerative disorder and the commonest form of dementia. The current study aims to assess the impact of somatic mutations in PSEN1 gene. The said mutations are the most common cause of familial Alzheimer's disease. As protein functionality can be affected by mutations, the study of possible alterations in the tertiary structure of proteins may reveal new insights related to the relationship between mutations and protein functions. To examine the effect of mutations, the primary structures and their related mutations were retrieved from public databases. Each structure (mutated and unmutated) was predicted based on effective structure prediction methodologies. A benchmarking of the structural predictive tools was accomplished. Comparative analyses of mutated and unmutated proteins were performed based on classic bioinformatics methods (TM-Score, RMSD, etc.) as well as on established shape-based descriptors retrieved from object recognition methodologies. Unsupervised methodologies were applied to the structures, in order to identify groups of mutation with similar mutational impact. Our results provide an essential knowledge toward protein's functionality in structure-based drug design.
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19
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Chávez-Gutiérrez L, Szaruga M. Mechanisms of neurodegeneration - Insights from familial Alzheimer's disease. Semin Cell Dev Biol 2020; 105:75-85. [PMID: 32418657 DOI: 10.1016/j.semcdb.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
The rising prevalence of Alzheimer's disease (AD), together with the lack of effective treatments, portray it as one of the major health challenges of our times. Untangling AD implies advancing the knowledge of the biology that gets disrupted during the disease while deciphering the molecular and cellular mechanisms leading to AD-related neurodegeneration. In fact, a solid mechanistic understanding of the disease processes stands as an essential prerequisite for the development of safe and effective treatments. Genetics has provided invaluable clues to the genesis of the disease by revealing deterministic genes - Presenilins (PSENs) and the Amyloid Precursor Protein (APP) - that, when affected, lead in an autosomal dominant manner to early-onset, familial AD (FAD). PSEN is the catalytic subunit of the membrane-embedded γ-secretase complexes, which act as proteolytic switches regulating key cell signalling cascades. Importantly, these intramembrane proteases are responsible for the production of Amyloid β (Aβ) peptides from APP. The convergence of pathogenic mutations on one functional pathway, the amyloidogenic cleavage of APP, strongly supports the significance of this process in AD pathogenesis. Here, we review and discuss the state-of-the-art knowledge of the molecular mechanisms underlying FAD, their implications for the sporadic form of the disease and for the development of safe AD therapeutics.
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Affiliation(s)
- Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium.
| | - Maria Szaruga
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
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20
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Mehra R, Dehury B, Kepp KP. Cryo-temperature effects on membrane protein structure and dynamics. Phys Chem Chem Phys 2020; 22:5427-5438. [DOI: 10.1039/c9cp06723j] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cryo-electron structures revolutionize biology, yet cooling effects are unclear. Using a simulation protocol of hot, cold, and rapidly cooled γ-secretase we identify cryo-contraction and modes relevant to Aβ production and cryo-analysis in general.
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Affiliation(s)
- Rukmankesh Mehra
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
| | - Budheswar Dehury
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
| | - Kasper P. Kepp
- DTU Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
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21
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Tang N, Sandahl TD, Ott P, Kepp KP. Computing the Pathogenicity of Wilson's Disease ATP7B Mutations: Implications for Disease Prevalence. J Chem Inf Model 2019; 59:5230-5243. [PMID: 31751128 DOI: 10.1021/acs.jcim.9b00852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson's disease. Controversially, clinical prevalence seems much smaller than the prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed, although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations. Our results show that the quality of the methods varies widely. We show the importance of optimizing the threshold of the methods used to distinguish pathogenic from nonpathogenic mutations against data of clinically confirmed pathogenic and nonpathogenic mutations. We find that most methods use thresholds that predict too many ATP7B mutations to be pathogenic. Thus, our findings explain the current controversy on Wilson's disease prevalence because meta-analysis and text search methods include many computational estimates that lead to higher disease prevalence than clinically observed. As proteins and diseases differ widely, a one-size-fits-all threshold cannot distinguish pathogenic and nonpathogenic mutations efficiently, as shown here. We also show that amino acid changes with small evolutionary substitution probability, mainly due to amino acid volume, are more associated with the disease, implying a pathological effect on the conformational state of the protein, which could affect copper transport or adenosine triphosphate recognition and hydrolysis. These findings may be a first step toward a more quantitative genotype-phenotype relationship of Wilson's disease.
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Affiliation(s)
- Ning Tang
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
| | - Thomas D Sandahl
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Peter Ott
- Department of Hepatology and Gastroenterology , Aarhus University Hospital , 8200 Aarhus , Denmark
| | - Kasper P Kepp
- DTU Chemistry , Technical University of Denmark , Kemitorvet 206 , 2800 Kongens Lyngby , Denmark
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22
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Computational analysis of Alzheimer-causing mutations in amyloid precursor protein and presenilin 1. Arch Biochem Biophys 2019; 678:108168. [DOI: 10.1016/j.abb.2019.108168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/25/2019] [Accepted: 11/02/2019] [Indexed: 12/13/2022]
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23
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Dehury B, Tang N, Kepp KP. Insights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:3196-3210. [PMID: 31405326 DOI: 10.1080/07391102.2019.1655481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Presenilins 1 and 2 (PS1 or PS2) are main genetic risk factors of familial Alzheimer's disease (AD) that produce the β-amyloid (Aβ) peptides and also have important stand-alone functions related to, e.g. calcium signaling. Most work so far has focused on PS1, but humans carry both PS1 and PS2, and mutations in both cause AD. Here, we develop a computational model of PS2 in the membrane to address the question how pathogenic PS2 mutations affect the membrane-embedded protein. The models are based on cryo-electron microscopy structures of PS1 translated to PS2, augmented with missing residues and a complete all-atom membrane-water system, and equilibrated using three independent 500-ns simulations of molecular dynamics with a structure-balanced force field. We show that the nine-transmembrane channel structure is substantially controlled by major dynamics in the hydrophilic loop bridging TM6 and TM7, which functions as a 'plug' in the PS2 membrane channel. TM2, TM6, TM7 and TM9 flexibility controls the size of this channel. We find that most pathogenic PS2 mutations significantly reduce stability relative to random mutations, using a statistical ANOVA test with all possible mutations in the affected sites as a control. The associated loss of compactness may also impair calcium affinity. Remarkably, similar properties of the open state are known to impair the binding of substrates to γ-secretase, and we thus argue that the two mechanisms could be functionally related.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ning Tang
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
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Dehury B, Tang N, Blundell TL, Kepp KP. Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1. RSC Adv 2019; 9:20901-20916. [PMID: 35515530 PMCID: PMC9065803 DOI: 10.1039/c9ra02623a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Severe early-onset familial Alzheimer's disease (FAD) is caused by more than 200 different mutations in the genes coding for presenilin, the catalytic subunit of the 4-subunit protease complex γ-secretase, which cleaves the C99 fragment of the amyloid precursor protein (APP) to produce Aβ peptides. γ-Secretase exists with either of two homologues, PS1 and PS2. All cryo-electron microscopic structures and computational work has so far focused on γ-secretase with PS1, yet PS2 mutations also cause FAD. A central question is thus whether there are structural and dynamic differences between PS1 and PS2. To address this question, we use the cryo-electron microscopic data for PS1 to develop the first structural and dynamic model of PS2-γ-secretase in the catalytically relevant mature membrane-bound state at ambient temperature, equilibrated by three independent 500 ns molecular dynamics simulations. We find that the characteristic nicastrin extra-cellular domain breathing mode and major movements in the cytosolic loop between TM6 and TM7 occur in both PS2- and PS1-γ-secretase. The overall structures and conformational states are similar, suggesting similar catalytic activities. However, at the sequence level, charge-controlled membrane-anchoring is extracellular for PS1 and intracellular for PS2, which suggests different subcellular locations. The tilt angles of the TM2, TM6, TM7 and TM9 helices differ in the two forms of γ-secretase, suggesting that the two proteins have somewhat different substrate processing and channel sizes. Our MD simulations consistently indicated that PS2 retains several water molecules near the catalytic site at the bilayer, as required for catalysis. The possible reasons for the differences of PS1 and PS2 are discussed in relation to their location and function.
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Cambridge CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
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Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production. Biochem J 2019; 476:1173-1189. [PMID: 30910800 DOI: 10.1042/bcj20190023] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/11/2022]
Abstract
The membrane protease γ-secretase cleaves the C99 fragment of the amyloid precursor protein, thus producing the Aβ peptides central to Alzheimer's disease. Cryo-electron microscopy has provided the topology but misses the membrane and loop parts that contribute to substrate binding. We report here an essentially complete atomic model of C99 within wild-type γ-secretase that respects all the experimental constraints and additionally describes loop, helix, and C99 substrate dynamics in a realistic all-atom membrane. Our model represents the matured auto-cleaved state required for catalysis. From two independent 500-ns molecular dynamic simulations, we identify two conformation states of C99 in equilibrium, a compact and a loose state. Our simulations provide a basis for C99 processing and Aβ formation and explain the production of longer and shorter Aβ, as the compact state retains C99 for longer and thus probably trims to shorter Aβ peptides. We expect pathogenic presenilin mutations to stabilize the loose over the compact state. The simulations detail the role of the Lys53-Lys54-Lys55 anchor for C99 binding, a loss of helicity of bound C99, and positioning of Thr48 and Leu49 leading to alternative trimming pathways on opposite sides of the C99 helix in three amino acid steps. The C99 binding topology resembles that of C83-bound γ-secretase without membrane but lacks a presenilin 1-C99 β-sheet, which could be induced by C83's stronger binding. The loose state should be selectively disfavored by γ-secretase modulators to increase C99 trimming and reduce the formation of longer Aβ, a strategy that is currently much explored but has lacked a structural basis.
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Castro MA, Hadziselimovic A, Sanders CR. The vexing complexity of the amyloidogenic pathway. Protein Sci 2019; 28:1177-1193. [PMID: 30897251 DOI: 10.1002/pro.3606] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Abstract
The role of the amyloidogenic pathway in the etiology of Alzheimer's disease (AD), particularly the common sporadic late onset forms of the disease, is controversial. To some degree, this is a consequence of the failure of drug and therapeutic antibody trials based either on targeting the proteases in this pathway or its amyloid end products. Here, we explore the formidable complexity of the biochemistry and cell biology associated with this pathway. For example, we review evidence that the immediate precursor of amyloid-β, the C99 domain of the amyloid precursor protein (APP), may itself be toxic. We also review important new results that appear to finally establish a direct genetic link between mutations in APP and the sporadic forms of AD. Based on the complexity of amyloidogenesis, it seems possible that a major contributor to the failure of related drug trials is that we have an incomplete understanding of this pathway and how it is linked to Alzheimer's pathogenesis. If so, this highlights a need for further characterization of this pathway, not its abandonment.
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Affiliation(s)
- Manuel A Castro
- Departments of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37240
| | - Arina Hadziselimovic
- Departments of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37240
| | - Charles R Sanders
- Departments of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37240
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Lee S, Mankhong S, Kang JH. Extracellular Vesicle as a Source of Alzheimer's Biomarkers: Opportunities and Challenges. Int J Mol Sci 2019; 20:ijms20071728. [PMID: 30965555 PMCID: PMC6479979 DOI: 10.3390/ijms20071728] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease characterized by memory decline and cognitive dysfunction. Although the primary causes of AD are not clear, it is widely accepted that the accumulation of amyloid beta (Aβ) and consecutive hyper-phosphorylation of tau, synaptic loss, oxidative stress and neuronal death might play a vital role in AD pathogenesis. Recently, it has been widely suggested that extracellular vesicles (EVs), which are released from virtually all cell types, are a mediator in regulating AD pathogenesis. Clinical evidence for the diagnostic performance of EV-associated biomarkers, particularly exosome biomarkers in the blood, is also emerging. In this review, we briefly introduce the biological function of EVs in the central nervous system and discuss the roles of EVs in AD pathogenesis. In particular, the roles of EVs associated with autophagy and lysosomal degradation systems in AD proteinopathy and in disease propagation are discussed. Next, we summarize candidates for biochemical AD biomarkers in EVs, including proteins and miRNAs. The accumulating data brings hope that the application of EVs will be helpful for early diagnostics and the identification of new therapeutic targets for AD. However, at the same time, there are several challenges in developing valid EV biomarkers. We highlight considerations for the development of AD biomarkers from circulating EVs, which includes the standardization of pre-analytical sources of variability, yield and purity of isolated EVs and quantification of EV biomarkers. The development of valid EV AD biomarkers may be facilitated by collaboration between investigators and the industry.
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Affiliation(s)
- Seongju Lee
- Department of Anatomy, College of Medicine, Inha University, Incheon 22212, Korea.
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea.
| | - Sakulrat Mankhong
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea.
- Department of Pharmacology, College of Medicine, Inha University, Incheon 22212, Korea.
| | - Ju-Hee Kang
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea.
- Department of Pharmacology, College of Medicine, Inha University, Incheon 22212, Korea.
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28
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Insights into the Potential Role of Mercury in Alzheimer's Disease. J Mol Neurosci 2019; 67:511-533. [PMID: 30877448 DOI: 10.1007/s12031-019-01274-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
Mercury (Hg), which is a non-essential element, is considered a highly toxic pollutant for biological systems even when present at trace levels. Elevated Hg exposure with the growing release of atmospheric pollutant Hg and rising accumulations of mono-methylmercury (highly neurotoxic) in seafood products have increased its toxic potential for humans. This review aims to highlight the potential relationship between Hg exposure and Alzheimer's disease (AD), based on the existing literature in the field. Recent reports have hypothesized that Hg exposure could increase the potential risk of developing AD. Also, AD is known as a complex neurological disorder with increased amounts of both extracellular neuritic plaques and intracellular neurofibrillary tangles, which may also be related to lifestyle and genetic variables. Research reports on AD and relationships between Hg and AD indicate that neurotransmitters such as serotonin, acetylcholine, dopamine, norepinephrine, and glutamate are dysregulated in patients with AD. Many researchers have suggested that AD patients should be evaluated for Hg exposure and toxicity. Some authors suggest further exploration of the Hg concentrations in AD patients. Dysfunctional signaling pathways in AD and Hg exposure appear to be interlinked with some driving factors such as arachidonic acid, homocysteine, dehydroepiandrosterone (DHEA) sulfate, hydrogen peroxide, glucosamine glycans, glutathione, acetyl-L carnitine, melatonin, and HDL. This evidence suggests the need for a better understanding of the relationship between AD and Hg exposure, and potential mechanisms underlying the effects of Hg exposure on regional brain functions. Also, further studies evaluating brain functions are needed to explore the long-term effects of subclinical and untreated Hg toxicity on the brain function of AD patients.
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Tang N, Dehury B, Kepp KP. Computing the Pathogenicity of Alzheimer’s Disease Presenilin 1 Mutations. J Chem Inf Model 2019; 59:858-870. [DOI: 10.1021/acs.jcim.8b00896] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ning Tang
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kasper P. Kepp
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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30
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Tang N, Kepp KP. Aβ42/Aβ40 Ratios of Presenilin 1 Mutations Correlate with Clinical Onset of Alzheimer’s Disease. J Alzheimers Dis 2018; 66:939-945. [DOI: 10.3233/jad-180829] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ning Tang
- Technical University of Denmark, DTU Chemistry, Kgs. Lyngby, Denmark
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Kgs. Lyngby, Denmark
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31
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Aguayo-Ortiz R, Straub JE, Dominguez L. Influence of membrane lipid composition on the structure and activity of γ-secretase. Phys Chem Chem Phys 2018; 20:27294-27304. [PMID: 30357233 DOI: 10.1039/c8cp04138e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
γ-Secretase (GS) is a multi-subunit membrane-embedded aspartyl protease that cleaves more than 80 integral membrane proteins, including the amyloid precursor protein (APP) to produce the amyloid-β (Aβ) peptide. Oligomerization and aggregation of the 42-amino acid length Aβ isoform in the brain has been associated with the development and progression of Alzheimer's disease (AD). Based on recent experimental structural studies and using multiscale computational modeling approaches, the conformational states and protein-membrane interactions of the GS complex embedded in six homogeneous and six heterogeneous lipid bilayers were characterized. In order to identify potential lipid and cholesterol binding sites, GS regions with high lipid/cholesterol occupancy values were analyzed using atomistic and coarse-grained simulations. Long lipid residence times were observed to be correlated with a large number of hydrogen bonds between the charged headgroups and key GS amino acids. This observation provides a plausible explanation for the inhibition of GS by charged lipids observed in previous experimental studies. Computed lateral pressure profiles suggest that higher transmembrane pressures favor active state conformations of the catalytic subunit. A probable mechanism for the regulation of the local stress response in cholesterol-rich multicomponent lipid bilayers is identified. Finally, it is demonstrated that interactions between the nicastrin extracellular domain and lipid headgroups leads to a compact structural conformation of the GS complex. Overall, this study provides valuable insight into the effect of bilayer lipid composition on the GS structural ensemble and its function.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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32
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Popugaeva E, Pchitskaya E, Bezprozvanny I. Dysregulation of Intracellular Calcium Signaling in Alzheimer's Disease. Antioxid Redox Signal 2018; 29:1176-1188. [PMID: 29890840 PMCID: PMC6157344 DOI: 10.1089/ars.2018.7506] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SIGNIFICANCE Calcium (Ca2+) hypothesis of Alzheimer's disease (AD) gains popularity. It points to new signaling pathways that may underlie AD pathogenesis. Based on calcium hypothesis, novel targets for the development of potential AD therapies are identified. Recent Advances: Recently, the key role of neuronal store-operated calcium entry (nSOCE) in the development of AD has been described. Correct regulation of nSOCE is necessary for the stability of postsynaptic contacts to preserve the memory formation. Molecular identity of hippocampal nSOCE is defined. Perspective nSOCE-activating molecule, prototype of future anti-AD drugs, is described. CRITICAL ISSUES Endoplasmic reticulum Ca2+ overload happens in many but not in all AD models. The nSOCE targeting therapy described in this review may not be universally applicable. FUTURE DIRECTIONS There is a need to determine whether AD is a syndrome with one critical signaling pathway that initiates pathology, or it is a disorder with many different signaling pathways that are disrupted simultaneously or one after each other. It is necessary to validate applicability of nSOCE-activating therapy for the development of anti-AD medication. There is an experimental correlation between downregulated nSOCE and disrupted postsynaptic contacts in AD mouse models. Signaling mechanisms downstream of nSOCE which are responsible for the regulation of stability of postsynaptic contacts have to be discovered. That will bring new targets for the development of AD-preventing therapies. Antioxid. Redox Signal. 29, 1176-1188.
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Affiliation(s)
- Elena Popugaeva
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation
| | - Ekaterina Pchitskaya
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation
| | - Ilya Bezprozvanny
- 1 Laboratory of Molecular Neurodegeneration, Department of Medical Physics, Peter the Great St.Petersburg Polytechnic University , St.Petersburg, Russian Federation.,2 Department of Physiology, UT Southwestern Medical Center at Dallas , Dallas, Texas
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33
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Aguayo-Ortiz R, Dominguez L. Simulating the γ-secretase enzyme: Recent advances and future directions. Biochimie 2018; 147:130-135. [DOI: 10.1016/j.biochi.2018.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/27/2018] [Indexed: 11/17/2022]
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34
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Uddin MS, Stachowiak A, Mamun AA, Tzvetkov NT, Takeda S, Atanasov AG, Bergantin LB, Abdel-Daim MM, Stankiewicz AM. Autophagy and Alzheimer's Disease: From Molecular Mechanisms to Therapeutic Implications. Front Aging Neurosci 2018; 10:04. [PMID: 29441009 PMCID: PMC5797541 DOI: 10.3389/fnagi.2018.00004] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/08/2018] [Indexed: 01/07/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of progressive dementia in the elderly. It is characterized by a progressive and irreversible loss of cognitive abilities and formation of senile plaques, composed mainly of amyloid β (Aβ), and neurofibrillary tangles (NFTs), composed of tau protein, in the hippocampus and cortex of afflicted humans. In brains of AD patients the metabolism of Aβ is dysregulated, which leads to the accumulation and aggregation of Aβ. Metabolism of Aβ and tau proteins is crucially influenced by autophagy. Autophagy is a lysosome-dependent, homeostatic process, in which organelles and proteins are degraded and recycled into energy. Thus, dysfunction of autophagy is suggested to lead to the accretion of noxious proteins in the AD brain. In the present review, we describe the process of autophagy and its importance in AD. Additionally, we discuss mechanisms and genes linking autophagy and AD, i.e., the mTOR pathway, neuroinflammation, endocannabinoid system, ATG7, BCL2, BECN1, CDK5, CLU, CTSD, FOXO1, GFAP, ITPR1, MAPT, PSEN1, SNCA, UBQLN1, and UCHL1. We also present pharmacological agents acting via modulation of autophagy that may show promise in AD therapy. This review updates our knowledge on autophagy mechanisms proposing novel therapeutic targets for the treatment of AD.
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Affiliation(s)
- Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
| | - Anna Stachowiak
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Magdalenka, Poland
| | | | - Nikolay T Tzvetkov
- Department of Molecular Biology and Biochemical Pharmacology, Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Shinya Takeda
- Department of Clinical Psychology, Tottori University Graduate School of Medical Sciences, Tottori, Japan
| | - Atanas G Atanasov
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Magdalenka, Poland.,Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Leandro B Bergantin
- Department of Pharmacology, Federal University of São Paulo, São Paulo, Brazil
| | - Mohamed M Abdel-Daim
- Department of Pharmacology, Suez Canal University, Ismailia, Egypt.,Department of Ophthalmology and Micro-technology, Yokohama City University, Yokohama, Japan
| | - Adrian M Stankiewicz
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Magdalenka, Poland
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35
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Yang G, Yu K, Kubicek J, Labahn J. Expression, purification, and preliminary characterization of human presenilin-2. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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37
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Yang G, Yu K, Kaitatzi CS, Singh A, Labahn J. Influence of solubilization and AD-mutations on stability and structure of human presenilins. Sci Rep 2017; 7:17970. [PMID: 29269939 PMCID: PMC5740079 DOI: 10.1038/s41598-017-18313-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
Presenilin (PS1 or PS2) functions as the catalytic subunit of γ-secretase, which produces the toxic amyloid beta peptides in Alzheimer’s disease (AD). The dependence of folding and structural stability of PSs on the lipophilic environment and mutation were investigated by far UV CD spectroscopy. The secondary structure content and stability of PS2 depended on the lipophilic environment. PS2 undergoes a temperature-dependent structural transition from α-helical to β-structure at 331 K. The restructured protein formed structures which tested positive in spectroscopic amyloid fibrils assays. The AD mutant PS1L266F, PS1L424V and PS1ΔE9 displayed reduced stability which supports a proposed ‘loss of function’ mechanism of AD based on protein instability. The exon 9 coded sequence in the inhibitory loop of the zymogen was found to be required for the modulation of the thermal stability of PS1 by the lipophilic environment.
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Affiliation(s)
- Ge Yang
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Kun Yu
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Christina-Symina Kaitatzi
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Physics Department, University of Patras, University Campus, 26504, Rio Achaia, Greece
| | - Abhilasha Singh
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB), CSSB-FZJ, Notkestr. 85, 22607, Hamburg, Germany. .,Institute of Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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38
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Somavarapu AK, Kepp KP. Membrane Dynamics of γ-Secretase Provides a Molecular Basis for β-Amyloid Binding and Processing. ACS Chem Neurosci 2017; 8:2424-2436. [PMID: 28841371 DOI: 10.1021/acschemneuro.7b00208] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
γ-Secretase produces β-amyloid (Aβ) within its presenilin (PS1) subunit, mutations in which cause Alzheimer's disease, and current therapies thus seek to modulate its activity. While the general structure is known from recent electron microscopy studies, direct loop and membrane interactions and explicit dynamics relevant to substrate processing remain unknown. We report a modeled structure utilizing the optimal multitemplate information available, including loops and missing side chains, account of maturation cleavage, and explicit all-atom molecular dynamics in the membrane. We observe three distinct conformations of γ-secretase (open, semiopen, and closed) that remarkably differ by tilting of helices 2 and 3 of PS1, directly controlling active site availability. The large hydrophilic loop of PS1 where maturation occurs reveals a new helix segment that parallels the likely helix character of other substrates. The semiopen conformation consistently shows the best fit of Aβ peptides, that is, longer residence before release and by inference more trimming. In contrast, the closed, hydrophobic conformation is largely inactive and the open conformation is active but provides fewer optimal interactions and induces shorter residence time and by inference releases Aβ peptides of longer lengths. Our simulations thus provide a molecular basis for substrate processing and changes in the Aβ42/Aβ40 ratio. Accordingly, selective binding to protect the semiopen "innocent" conformation provides a molecular recipe for effective γ-secretase modulators; we provide the full atomic structures for these states that may play a key role in developing selective γ-secretase modulators for treatment of Alzheimer's disease.
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Affiliation(s)
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark
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40
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Kepp KP. Ten Challenges of the Amyloid Hypothesis of Alzheimer’s Disease. J Alzheimers Dis 2016; 55:447-457. [DOI: 10.3233/jad-160550] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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41
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Kepp KP. Alzheimer's disease due to loss of function: A new synthesis of the available data. Prog Neurobiol 2016; 143:36-60. [PMID: 27327400 DOI: 10.1016/j.pneurobio.2016.06.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 12/11/2022]
Abstract
Alzheimer's Disease (AD) is a highly complex disease involving a broad range of clinical, cellular, and biochemical manifestations that are currently not understood in combination. This has led to many views of AD, e.g. the amyloid, tau, presenilin, oxidative stress, and metal hypotheses. The amyloid hypothesis has dominated the field with its assumption that buildup of pathogenic β-amyloid (Aβ) peptide causes disease. This paradigm has been criticized, yet most data suggest that Aβ plays a key role in the disease. Here, a new loss-of-function hypothesis is synthesized that accounts for the anomalies of the amyloid hypothesis, e.g. the curious pathogenicity of the Aβ42/Aβ40 ratio, the loss of Aβ caused by presenilin mutation, the mixed phenotypes of APP mutations, the poor clinical-biochemical correlations for genetic variant carriers, and the failure of Aβ reducing drugs. The amyloid-loss view accounts for recent findings on the structure and chemical features of Aβ variants and their coupling to human patient data. The lost normal function of APP/Aβ is argued to be metal transport across neuronal membranes, a view with no apparent anomalies and substantially more explanatory power than the gain-of-function amyloid hypothesis. In the loss-of-function scenario, the central event of Aβ aggregation is interpreted as a loss of soluble, functional monomer Aβ rather than toxic overload of oligomers. Accordingly, new research models and treatment strategies should focus on remediation of the functional amyloid balance, rather than strict containment of Aβ, which, for reasons rationalized in this review, has failed clinically.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kongens Lyngby, Denmark.
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