101
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Wong E, Frost GR, Li YM. γ-Secretase Modulatory Proteins: The Guiding Hand Behind the Running Scissors. Front Aging Neurosci 2020; 12:614690. [PMID: 33343338 PMCID: PMC7738330 DOI: 10.3389/fnagi.2020.614690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Described as the "proteasome of the membrane" or the "scissors in the membrane," γ-secretase has notoriously complicated biology, and even after decades of research, the full extent of its regulatory mechanism remains unclear. γ-Secretase is an intramembrane aspartyl protease complex composed of four obligatory subunits: Nicastrin (NCT), Presenilin (PS), Presenilin Enhancer-2 (Pen-2), and Anterior pharynx-defective-1 (Aph-1). γ-Secretase cleaves numerous type 1 transmembrane substrates, with no apparent homology, and plays major roles in broad biological pathways such as development, neurogenesis, and cancer. Notch and the amyloid precursor protein (APP) and are undoubtedly the best-studied γ-secretase substrates because of their role in cancer and Alzheimer's disease (AD) and therefore became the focus of increasing studies as an attractive therapeutic target. The regulation of γ-secretase is intricate and involves the function of multiple cellular entities. Recently, γ-secretase modulatory proteins (GSMPs), which are non-essential subunits and yet modulate γ-secretase activity and specificity, have emerged as an important component in guiding γ-secretase. GSMPs are responsive to cellular and environmental changes and therefore, provide another layer of regulation of γ-secretase. This type of enzymatic regulation allows for a rapid and fine-tuning of γ-secretase activity when appropriate signals appear enabling a temporal level of regulation. In this review article, we discuss the latest developments on GSMPs and implications on the development of effective therapeutics for γ-secretase-associated diseases such as AD and cancer.
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Affiliation(s)
- Eitan Wong
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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102
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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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103
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Perez-Fidalgo JA, Ortega B, Simon S, Samartzis EP, Boussios S. NOTCH signalling in ovarian cancer angiogenesis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1705. [PMID: 33490217 PMCID: PMC7812236 DOI: 10.21037/atm-20-4497] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Notch signalling pathway is involved in the new vessel formation process by regulating tip and stalk cells, which are key cells in the sprout formation. This process is essential in both normal ovary and cancer angiogenesis and is regulated by Notch-VEGF crosstalk. Furthermore, Notch has been linked in ovary with stem cell maintenance and epithelial mesenchymal transition processes. Dysregulation of the Notch pathway is frequent in ovarian cancer (OC) and it has been associated with impaired survival and advanced stages or lymph node involvement. Notch also plays a role in chemoresistance to platinum. In this context, this pathway has emerged as an attractive target for precision medicine in OC. Two main targets of this pathway concentrate the clinical development of compounds blocking Notch: gamma secretase and Delta-like ligand 4. Most of the clinical trials including OC patients have been developed in phase I or phase Ib. Despite being in an early phase, both of these compounds, navicixizumab or demcizumab, two monoclonal antibodies targeting Dll4, showed promising efficacy data in platinum-resistant OC patients in recent studies. This review will focus on the mechanisms of the Notch pathway with special interest in angiogenesis regulation and the implication of Notch as a potential therapeutic target in OC.
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Affiliation(s)
- Jose Alejandro Perez-Fidalgo
- Department of Medical Oncology, Hospital Clinico Universitario of Valencia, Biomedical Research Institute INCLIVA, CIBERONC, Valencia, Spain
| | - Belen Ortega
- Department of Medical Oncology, Hospital Clinico Universitario of Valencia, Biomedical Research Institute INCLIVA, CIBERONC, Valencia, Spain
| | - Soraya Simon
- Department of Medical Oncology, Hospital Clinico Universitario of Valencia, Biomedical Research Institute INCLIVA, CIBERONC, Valencia, Spain
| | | | - Stergios Boussios
- King's College London, School of Medicine, Guy's Campus, London, UK.,Medway NHS Foundation Trust, Gillingham, Kent, UK.,AELIA Organization, 9th Km Thessaloniki-Thermi, Thessaloniki, Greece
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104
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Alzheimer's disease: Recent treatment strategies. Eur J Pharmacol 2020; 887:173554. [DOI: 10.1016/j.ejphar.2020.173554] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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105
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Li B, Zhu C, Dong L, Qin J, Xiang W, Davidson AJ, Feng S, Wang Y, Shen X, Weng C, Wang C, Zhu T, Teng L, Wang J, Englert C, Chen J, Jiang H. ADAM10 mediates ectopic proximal tubule development and renal fibrosis through Notch signalling. J Pathol 2020; 252:274-289. [PMID: 32715474 PMCID: PMC7702158 DOI: 10.1002/path.5517] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Disturbed intrauterine development increases the risk of renal disease. Various studies have reported that Notch signalling plays a significant role in kidney development and kidney diseases. A disintegrin and metalloproteinase domain 10 (ADAM10), an upstream protease of the Notch pathway, is also reportedly involved in renal fibrosis. However, how ADAM10 interacts with the Notch pathway and causes renal fibrosis is not fully understood. In this study, using a prenatal chlorpyrifos (CPF) exposure mouse model, we investigated the role of the ADAM10/Notch axis in kidney development and fibrosis. We found that prenatal CPF‐exposure mice presented overexpression of Adam10, Notch1 and Notch2, and led to premature depletion of Six2+ nephron progenitors and ectopic formation of proximal tubules (PTs) in the embryonic kidney. These abnormal phenotypic changes persisted in mature kidneys due to the continuous activation of ADAM10/Notch and showed aggravated renal fibrosis in adults. Finally, both ADAM10 and NOTCH2 expression were positively correlated with the degree of renal interstitial fibrosis in IgA nephropathy patients, and increased ADAM10 expression was negatively correlated with decreased kidney function evaluated by serum creatinine, cystatin C, and estimated glomerular filtration rate. Regression analysis also indicated that ADAM10 expression was an independent risk factor for fibrosis in IgAN. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Bingjue Li
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Chaohong Zhu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Lihua Dong
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jing Qin
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou, PR China
| | - Wenyu Xiang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Alan J Davidson
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand
| | - Shi Feng
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Yucheng Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Xiujin Shen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Chunhua Weng
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Cuili Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Tingting Zhu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Lisha Teng
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Junwen Wang
- Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,College of Health Solutions, Arizona State University, Scottsdale, AZ, USA
| | - Christoph Englert
- Molecular Genetics Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.,Institute of Biochemistry and Biophysics, Friedrich-Schiller-University, Jena, Germany
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
| | - Hong Jiang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Key Laboratory of Nephropathy, Hangzhou, PR China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Hangzhou, PR China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health, Hangzhou, PR China.,Institute of Nephropathy, Zhejiang University, Hangzhou, PR China
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106
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Substrate recruitment by γ-secretase. Semin Cell Dev Biol 2020; 105:54-63. [DOI: 10.1016/j.semcdb.2020.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/27/2022]
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107
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Hitzenberger M, Götz A, Menig S, Brunschweiger B, Zacharias M, Scharnagl C. The dynamics of γ-secretase and its substrates. Semin Cell Dev Biol 2020; 105:86-101. [DOI: 10.1016/j.semcdb.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
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108
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Escamilla-Ayala A, Wouters R, Sannerud R, Annaert W. Contribution of the Presenilins in the cell biology, structure and function of γ-secretase. Semin Cell Dev Biol 2020; 105:12-26. [DOI: 10.1016/j.semcdb.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 01/25/2023]
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109
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Mekala S, Nelson G, Li YM. Recent developments of small molecule γ-secretase modulators for Alzheimer's disease. RSC Med Chem 2020; 11:1003-1022. [PMID: 33479693 DOI: 10.1039/d0md00196a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/29/2020] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of progressive neurodegenerative disorder, marked by memory loss and a decline in cognitive function. The major hallmarks of AD are the presence of intracellular neurofibrillary tau tangles (NFTs) composed of hyperphosphorylated tau proteins and extracellular plaques composed of amyloid beta peptides (Aβ). The amyloid (Aβ) cascade hypothesis proposes that the AD pathogenesis is initiated by the accumulation of Aβ peptides in the parenchyma of the brain. An aspartyl intramembranal protease called γ-secretase is responsible for the production of Aβ by the cleavage of the amyloid precursor protein (APP). Clinical studies of γ-secretase inhibitors (GSIs) for AD failed due to the lack of substrate specificity. Therefore, γ-secretase modulators (GSMs) have been developed as potential disease modifying agents to modulate the γ-secretase cleavage activity towards the production of toxic Aβ42 peptides. Following the first-generation 'nonsteroidal anti-inflammatory drug' (NSAID) based GSMs, second-generation GSMs (carboxylic acid based NSAID derivatives and non-NSAID derived heterocyclic analogues), as well as natural product-based GSMs, have been developed. In this review, we focus on the recent developments of small molecule-based GSMs that show potential improvements in terms of drug-like properties as well as their current status in human clinical trials and the future perspectives of GSM research.
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Affiliation(s)
- Shekar Mekala
- Chemical Biology Program , Memorial Sloan-Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , USA . ;
| | - Grady Nelson
- Chemical Biology Program , Memorial Sloan-Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , USA . ;
| | - Yue-Ming Li
- Chemical Biology Program , Memorial Sloan-Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , USA . ; .,Pharmacology Graduate Program , Weill Graduate School of Medical Sciences of Cornell University , New York , New York 10021 , USA
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110
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Steiner A, Schlepckow K, Brunner B, Steiner H, Haass C, Hagn F. γ-Secretase cleavage of the Alzheimer risk factor TREM2 is determined by its intrinsic structural dynamics. EMBO J 2020; 39:e104247. [PMID: 32830336 PMCID: PMC7560206 DOI: 10.15252/embj.2019104247] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Sequence variants of the microglial expressed TREM2 (triggering receptor expressed on myeloid cells 2) are a major risk factor for late onset Alzheimer's disease. TREM2 requires a stable interaction with DAP12 in the membrane to initiate signaling, which is terminated by TREM2 ectodomain shedding and subsequent intramembrane cleavage by γ‐secretase. To understand the structural basis for the specificity of the intramembrane cleavage event, we determined the solution structure of the TREM2 transmembrane helix (TMH). Caused by the presence of a charged amino acid in the membrane region, the TREM2‐TMH adopts a kinked structure with increased flexibility. Charge removal leads to TMH stabilization and reduced dynamics, similar to its structure in complex with DAP12. Strikingly, these dynamical features match with the site of the initial γ‐secretase cleavage event. These data suggest an unprecedented cleavage mechanism by γ‐secretase where flexible TMH regions act as key determinants of substrate cleavage specificity.
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Affiliation(s)
- Andrea Steiner
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kai Schlepckow
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Bettina Brunner
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Biomedical Center (BMC), Chair of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.,Biomedical Center (BMC), Chair of Metabolic Biochemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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111
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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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112
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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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113
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Zhao J, Liu X, Xia W, Zhang Y, Wang C. Targeting Amyloidogenic Processing of APP in Alzheimer's Disease. Front Mol Neurosci 2020; 13:137. [PMID: 32848600 PMCID: PMC7418514 DOI: 10.3389/fnmol.2020.00137] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of senile dementia, characterized by neurofibrillary tangle and amyloid plaque in brain pathology. Major efforts in AD drug were devoted to the interference with the production and accumulation of amyloid-β peptide (Aβ), which plays a causal role in the pathogenesis of AD. Aβ is generated from amyloid precursor protein (APP), by consecutive cleavage by β-secretase and γ-secretase. Therefore, β-secretase and γ-secretase inhibition have been the focus for AD drug discovery efforts for amyloid reduction. Here, we review β-secretase inhibitors and γ-secretase inhibitors/modulators, and their efficacies in clinical trials. In addition, we discussed the novel concept of specifically targeting the γ-secretase substrate APP. Targeting amyloidogenic processing of APP is still a fundamentally sound strategy to develop disease-modifying AD therapies and recent advance in γ-secretase/APP complex structure provides new opportunities in designing selective inhibitors/modulators for AD.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Weiming Xia
- Geriatric Research Education Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States
- Department of Pharmacology and Experimental Therapeutics, School of Medicine, Boston University, Boston, MA, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
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114
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Lysyk L, Brassard R, Touret N, Lemieux MJ. PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane. J Mol Biol 2020; 432:5052-5062. [DOI: 10.1016/j.jmb.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023]
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115
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Signal Peptide Peptidase-Type Proteases: Versatile Regulators with Functions Ranging from Limited Proteolysis to Protein Degradation. J Mol Biol 2020; 432:5063-5078. [DOI: 10.1016/j.jmb.2020.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/02/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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116
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Mentrup T, Cabrera-Cabrera F, Fluhrer R, Schröder B. Physiological functions of SPP/SPPL intramembrane proteases. Cell Mol Life Sci 2020; 77:2959-2979. [PMID: 32052089 PMCID: PMC7366577 DOI: 10.1007/s00018-020-03470-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/09/2020] [Accepted: 01/22/2020] [Indexed: 01/07/2023]
Abstract
Intramembrane proteolysis describes the cleavage of substrate proteins within their hydrophobic transmembrane segments. Several families of intramembrane proteases have been identified including the aspartyl proteases Signal peptide peptidase (SPP) and its homologues, the SPP-like (SPPL) proteases SPPL2a, SPPL2b, SPPL2c and SPPL3. As presenilin homologues, they employ a similar catalytic mechanism as the well-studied γ-secretase. However, SPP/SPPL proteases cleave transmembrane proteins with a type II topology. The characterisation of SPP/SPPL-deficient mouse models has highlighted a still growing spectrum of biological functions and also promoted the substrate discovery of these proteases. In this review, we will summarise the current hypotheses how phenotypes of these mouse models are linked to the molecular function of the enzymes. At the cellular level, SPP/SPPL-mediated cleavage events rather provide specific regulatory switches than unspecific bulk proteolysis. By this means, a plethora of different cell biological pathways is influenced including signal transduction, membrane trafficking and protein glycosylation.
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Affiliation(s)
- Torben Mentrup
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Florencia Cabrera-Cabrera
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Faculty of Medicine, University of Augsburg, Universitätsstraße 2, 86135, Augsburg, Germany
- Biomedizinisches Centrum (BMC), Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 17, 81377, Munich, Germany
- DZNE-German Center for Neurodegenerative Diseases, Munich, Feodor-Lynen-Strasse 17, 81377, Munich, Germany
| | - Bernd Schröder
- Institute for Physiological Chemistry, Medizinisch-Theoretisches Zentrum MTZ, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany.
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117
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Mandal M, Buevich A, Caldwell JP, Hyde L, Huang X, Liu X, McKittrick B, Mazzola RD, Pissarnitski D, Palani A, Zhang L, Parker E, Xiao L, Rindgen D, Zhu Z. Generation of Leads for γ-Secretase Modulation. J Med Chem 2020; 63:8216-8230. [DOI: 10.1021/acs.jmedchem.0c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mihirbaran Mandal
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Alexei Buevich
- Department of NMR Structure Elucidation, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John P. Caldwell
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lynn Hyde
- Department of Neuroscience, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xianhai Huang
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xiaoxiang Liu
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian McKittrick
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Robert D. Mazzola
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Dmitri Pissarnitski
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Anandan Palani
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lili Zhang
- Department of Neuroscience, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Eric Parker
- Department of Neuroscience, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Li Xiao
- Department of Modeling and Informatics, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Diane Rindgen
- Department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Zhaoning Zhu
- Department of Medicinal Chemistry, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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118
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Escamilla-Ayala AA, Sannerud R, Mondin M, Poersch K, Vermeire W, Paparelli L, Berlage C, Koenig M, Chavez-Gutierrez L, Ulbrich MH, Munck S, Mizuno H, Annaert W. Super-resolution microscopy reveals majorly mono- and dimeric presenilin1/γ-secretase at the cell surface. eLife 2020; 9:56679. [PMID: 32631487 PMCID: PMC7340497 DOI: 10.7554/elife.56679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
γ-Secretase is a multi-subunit enzyme whose aberrant activity is associated with Alzheimer’s disease and cancer. While its structure is atomically resolved, γ-secretase localization in the membrane in situ relies mostly on biochemical data. Here, we combined fluorescent tagging of γ-secretase subunits with super-resolution microscopy in fibroblasts. Structured illumination microscopy revealed single γ-secretase complexes with a monodisperse distribution and in a 1:1 stoichiometry of PSEN1 and nicastrin subunits. In living cells, sptPALM revealed PSEN1/γ-secretase mainly with directed motility and frequenting ‘hotspots’ or high track-density areas that are sensitive to γ-secretase inhibitors. We visualized γ-secretase association with substrates like amyloid precursor protein and N-cadherin, but not with its sheddases ADAM10 or BACE1 at the cell surface, arguing against pre-formed megadalton complexes. Nonetheless, in living cells PSEN1/γ-secretase transiently visits ADAM10 hotspots. Our results highlight the power of super-resolution microscopy for the study of γ-secretase distribution and dynamics in the membrane.
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Affiliation(s)
- Abril Angélica Escamilla-Ayala
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Magali Mondin
- Bordeaux Imaging Center, UMS 3420, CNRS-University of Bordeaux, US4 INSERM, Bordeaux, France
| | - Karin Poersch
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wendy Vermeire
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Laura Paparelli
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB Bio Imaging Core, Leuven, Belgium
| | - Caroline Berlage
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Lucia Chavez-Gutierrez
- Department of Neurosciences, KU Leuven, Leuven, Belgium.,Laboratory of Proteolytic Mechanisms in Neurodegeneration, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Maximilian H Ulbrich
- Institute of Internal Medicine IV, Medical Center of the University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Sebastian Munck
- Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB Bio Imaging Core, Leuven, Belgium
| | - Hideaki Mizuno
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, KU Leuven, Heverlee, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
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119
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Substrate-based chemical probes for Alzheimer’s γ-secretase. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02565-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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120
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Güner G, Lichtenthaler SF. The substrate repertoire of γ-secretase/presenilin. Semin Cell Dev Biol 2020; 105:27-42. [PMID: 32616437 DOI: 10.1016/j.semcdb.2020.05.019] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 12/09/2022]
Abstract
The intramembrane protease γ-secretase is a hetero-tetrameric protein complex with presenilin as the catalytic subunit and cleaves its membrane protein substrates within their single transmembrane domains. γ-Secretase is well known for its role in Notch signalling and in Alzheimer's disease, where it catalyzes the formation of the pathogenic amyloid β (Aβ) peptide. However, in the 21 years since its discovery many more substrates and substrate candidates of γ-secretase were identified. Although the physiological relevance of the cleavage of many substrates remains to be studied in more detail, the substrates demonstrate a broad role for γ-secretase in embryonic development, adult tissue homeostasis, signal transduction and protein degradation. Consequently, chronic γ-secretase inhibition may cause significant side effects due to inhibition of cleavage of multiple substrates. This review provides a list of 149 γ-secretase substrates identified to date and highlights by which expeirmental approach substrate cleavage was validated. Additionally, the review lists the cleavage sites where they are known and discusses the functional implications of γ-secretase cleavage with a focus on substrates identified in the recent past, such as CHL1, TREM2 and TNFR1. A comparative analysis demonstrates that γ-secretase substrates mostly have a long extracellular domain and require ectodomain shedding before γ-secretase cleavage, but that γ-secretase is also able to cleave naturally short substrates, such as the B cell maturation antigen. Taken together, the list of substrates provides a resource that may help in the future development of drugs inhibiting or modulating γ-secretase activity in a substrate-specific manner.
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Affiliation(s)
- Gökhan Güner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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121
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Bhattarai A, Devkota S, Bhattarai S, Wolfe MS, Miao Y. Mechanisms of γ-Secretase Activation and Substrate Processing. ACS CENTRAL SCIENCE 2020; 6:969-983. [PMID: 32607444 PMCID: PMC7318072 DOI: 10.1021/acscentsci.0c00296] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Indexed: 05/14/2023]
Abstract
Amyloid β-peptide, the principal component of characteristic cerebral plaques of Alzheimer's disease (AD), is produced through intramembrane proteolysis of the amyloid precursor protein (APP) by γ-secretase. Despite the importance in the pathogenesis of AD, the mechanisms of intramembrane proteolysis and substrate processing by γ-secretase remain poorly understood. Here, complementary all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method and biochemical experiments were combined to investigate substrate processing of wildtype and mutant APP by γ-secretase. The GaMD simulations captured spontaneous activation of γ-secretase, with hydrogen bonded catalytic aspartates and water poised for proteolysis of APP at the ε cleavage site. Furthermore, GaMD simulations revealed that familial AD mutations I45F and T48P enhanced the initial ε cleavage between residues Leu49-Val50, while M51F mutation shifted the ε cleavage site to the amide bond between Thr48-Leu49. Detailed analysis of the GaMD simulations allowed us to identify distinct low-energy conformational states of γ-secretase, different secondary structures of the wildtype and mutant APP substrate, and important active-site subpockets for catalytic function of the enzyme. The simulation findings were highly consistent with experimental analyses of APP proteolytic products using mass spectrometry and Western blotting. Taken together, the GaMD simulations and biochemical experiments have enabled us to elucidate the mechanisms of γ-secretase activation and substrate processing, which should facilitate rational computer-aided drug design targeting this functionally important enzyme.
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Affiliation(s)
- Apurba Bhattarai
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sujan Devkota
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sanjay Bhattarai
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Michael S. Wolfe
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
- (M.S.W.)
| | - Yinglong Miao
- Center
for Computational Biology and Department of Molecular Biosciences, and Department of
Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
- (Y.M.)
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122
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Barros M, Houlihan WJ, Paresi CJ, Brendel M, Rynearson KD, Lee CW, Prikhodko O, Cregger C, Chang G, Wagner SL, Gilchrist ML, Li YM. γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6569-6579. [PMID: 32432881 PMCID: PMC7887708 DOI: 10.1021/acs.langmuir.0c01178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (Ld) lipid domains, whereas APP and γ-secretase partition as single or higher complex in both phases but highly favor the ordered phase, especially after recruiting lipids from the ordered phase, indicating that the activity and specificity of γ-secretase against these two substrates are modulated by membrane lateral organization. Moreover, time-elapse measurements reveal that γ-secretase can recruit specific membrane components from the cholesterol-rich Lo phase and thus creates a favorable lipid environment for substrate recognition and therefore activity. This work offers insight into how γ-secretase and lipid modulate each other and control its activity and specificity.
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Affiliation(s)
- Marilia Barros
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - William J Houlihan
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
| | - Matthew Brendel
- Molecular Cytology Core, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Kevin D Rynearson
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Olga Prikhodko
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | - Cristina Cregger
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, California 92093, United States
- Research Biologist, VA San Diego Healthcare System, La Jolla, California 92161, United States
| | - M Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
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123
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Liu X, Zhao J, Zhang Y, Ubarretxena-Belandia I, Forth S, Lieberman RL, Wang C. Substrate-Enzyme Interactions in Intramembrane Proteolysis: γ-Secretase as the Prototype. Front Mol Neurosci 2020; 13:65. [PMID: 32508589 PMCID: PMC7248309 DOI: 10.3389/fnmol.2020.00065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/03/2020] [Indexed: 11/15/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) catalyze the hydrolysis of peptide bonds within the transmembrane regions of membrane protein substrates, releasing bioactive fragments that play roles in many physiological and pathological processes. Based on their catalytic mechanism and nucleophile, I-CLiPs are classified into metallo, serine, aspartyl, and glutamyl proteases. Presenilin is the most prominent among I-CLiPs, as the catalytic subunit of γ-secretase (GS) complex responsible for cleaving the amyloid precursor protein (APP) and Notch, as well as many other membrane substrates. Recent cryo-electron microscopy (cryo-EM) structures of GS provide new details on how presenilin recognizes and cleaves APP and Notch. First, presenilin transmembrane helix (TM) 2 and 6 are dynamic. Second, upon binding to GS, the substrate TM helix is unwound from the C-terminus, resulting in an intermolecular β-sheet between the substrate and presenilin. The transition of the substrate C-terminus from α-helix to β-sheet is proposed to expose the scissile peptide bond in an extended conformation, leaving it susceptible to protease cleavage. Despite the astounding new insights in recent years, many crucial questions remain unanswered regarding the inner workings of γ-secretase, however. Key unanswered questions include how the enzyme recognizes and recruits substrates, how substrates are translocated from an initial docking site to the active site, how active site aspartates recruit and coordinate catalytic water, and the nature of the mechanisms of processive trimming of the substrate and product release. Answering these questions will have important implications for drug discovery aimed at selectively reducing the amyloid load in Alzheimer's disease (AD) with minimal side effects.
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Affiliation(s)
- Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, United States
| | - Iban Ubarretxena-Belandia
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Scott Forth
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, United States
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124
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Bansal R, Reshef R. Revving the CAR - Combination strategies to enhance CAR T cell effectiveness. Blood Rev 2020; 45:100695. [PMID: 32402724 DOI: 10.1016/j.blre.2020.100695] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/22/2020] [Accepted: 04/11/2020] [Indexed: 12/14/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy is currently approved for treatment of refractory B-cell malignancies. Response rates in these diseases are impressive by historical standards, but most patients do not have a durable response and there remains room for improvement. To date, CAR T cell activity has been even more limited in solid malignancies. These limitations are thought to be due to several pathways of resistance to CAR T cells, including cell-intrinsic mechanisms and the immunosuppressive tumor microenvironment. In this review, we discuss current experimental strategies that combine small molecules and monoclonal antibodies with CAR T cells to overcome these resistance mechanisms. We describe the biological rationale, pre-clinical data and clinical trials in progress that test the efficacy and safety of these combinations.
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Affiliation(s)
- Rajat Bansal
- Division of Hematology/Oncology, Columbia University Irving Medical Center, 177 Ft. Washington Ave, Floor: 6GN-435, New York, NY 10032, USA.
| | - Ran Reshef
- Division of Hematology/Oncology, Columbia University Irving Medical Center, 630 W. 168(th) Street Mailbox 127, New York, NY 10032, USA.
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125
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Nie P, Vartak A, Li YM. γ-Secretase inhibitors and modulators: Mechanistic insights into the function and regulation of γ-Secretase. Semin Cell Dev Biol 2020; 105:43-53. [PMID: 32249070 DOI: 10.1016/j.semcdb.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Over two decades, γ-secretase has been the target for extensive therapeutic development due to its pivotal role in pathogenesis of Alzheimer's disease and cancer. However, it has proven to be a challenging task owing to its large set of substrates and our limited understanding of the enzyme's structural and mechanistic features. The scientific community is taking bigger strides towards solving this puzzle with recent advancement in techniques like cryogenic electron microscopy (cryo-EM) and photo-affinity labelling (PAL). This review highlights the significance of the PAL technique with multiple examples of photo-probes developed from γ-secretase inhibitors and modulators. The binding of these probes into active and/or allosteric sites of the enzyme has provided crucial information on the γ-secretase complex and improved our mechanistic understanding of this protease. Combining the knowledge of function and regulation of γ-secretase will be a decisive factor in developing novel γ-secretase modulators and biological therapeutics.
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Affiliation(s)
- Pengju Nie
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Abhishek Vartak
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
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126
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Trambauer J, Fukumori A, Steiner H. Pathogenic Aβ generation in familial Alzheimer’s disease: novel mechanistic insights and therapeutic implications. Curr Opin Neurobiol 2020; 61:73-81. [DOI: 10.1016/j.conb.2020.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/16/2020] [Accepted: 01/23/2020] [Indexed: 01/06/2023]
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127
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Yang ZJ, Yu ZY, Cai YM, Du RR, Cai L. Engineering of an enhanced synthetic Notch receptor by reducing ligand-independent activation. Commun Biol 2020; 3:116. [PMID: 32170210 PMCID: PMC7069970 DOI: 10.1038/s42003-020-0848-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/20/2020] [Indexed: 11/17/2022] Open
Abstract
Notch signaling is highly conserved in most animals and plays critical roles during neurogenesis as well as embryonic development. Synthetic Notch-based systems, modeled from Notch receptors, have been developed to sense and respond to a specific extracellular signal. Recent advancement of synNotch has shown promise for future use in cellular engineering to treat cancers. However, synNotch from Morsut et al. (2016) has a high level of ligand-independent activation, which limits its application. Here we show that adding an intracellular hydrophobic sequence (QHGQLWF, named as RAM7) present in native Notch, significantly reduced ligand-independent activation. Our enhanced synthetic Notch receptor (esNotch) demonstrates up to a 14.6-fold reduction in ligand-independent activation, without affecting its antigen-induced activation efficiency. Our work improves a previously reported transmembrane receptor and provides a powerful tool to develop better transmembrane signaling transduction modules for further advancement of eukaryotic synthetic biology.
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Affiliation(s)
- Zi-Jie Yang
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zi-Yan Yu
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi-Ming Cai
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, 77225, USA
| | - Rong-Rong Du
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Liang Cai
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
- The Center for Faculty Development of Fudan University, Shanghai, China.
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128
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Cai T, Tomita T. Structure-activity relationship of presenilin in γ-secretase-mediated intramembrane cleavage. Semin Cell Dev Biol 2020; 105:102-109. [PMID: 32171519 DOI: 10.1016/j.semcdb.2020.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
Abstract
Genetic research on familial cases of Alzheimer disease have identified presenilin (PS) as an important membrane protein in the pathomechanism of this disease. PS is the catalytic subunit of γ-secretase, which is responsible for the generation of amyloid-β peptide deposited in the brains of Alzheimer disease patients. γ-Secretase is an atypical protease composed of four membrane proteins (i.e., presenilin, nicastrin, anterior pharynx defective-1 (Aph-1), and presenilin enhancer-2 (Pen-2)) and mediates intramembrane proteolysis. Numerous investigations have been conducted toward understanding the structural features of γ-secretase components as well as the cleavage mechanism of γ-secretase. In this review, we summarize our current understanding of the structure and activity relationship of the γ-secretase complex.
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Affiliation(s)
- Tetsuo Cai
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
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129
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Epigenetic Regulation of Notch Signaling During Drosophila Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1218:59-75. [PMID: 32060871 DOI: 10.1007/978-3-030-34436-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Notch signaling exerts multiple important functions in various developmental processes, including cell differentiation and cell proliferation, while mis-regulation of this pathway results in a variety of complex diseases, such as cancer and developmental defects. The simplicity of the Notch pathway in Drosophila melanogaster, in combination with the availability of powerful genetics, makes this an attractive model for studying the fundamental mechanisms of how Notch signaling is regulated and how it functions in various cellular contexts. Recently, increasing evidence for epigenetic control of Notch signaling reveals the intimate link between epigenetic regulators and Notch signaling pathway. In this chapter, we summarize the research advances of Notch and CAF-1 in Drosophila development and the epigenetic regulation mechanisms of Notch signaling activity by CAF-1 as well as other epigenetic modification machineries, which enables Notch to orchestrate different biological inputs and outputs in specific cellular contexts.
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130
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Human-Induced Pluripotent Stem Cells and Herbal Small-Molecule Drugs for Treatment of Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21041327. [PMID: 32079110 PMCID: PMC7072986 DOI: 10.3390/ijms21041327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/28/2022] Open
Abstract
Alzheimer’s disease (AD) is characterized by extracellular amyloid plaques composed of the β-amyloid peptides and intracellular neurofibrillary tangles and associates with progressive declines in memory and cognition. Several genes play important roles and regulate enzymes that produce a pathological accumulation of β-amyloid in the brain, such as gamma secretase (γ-secretase). Induced pluripotent stem cells from patients with Alzheimer’s disease with different underlying genetic mechanisms may help model different phenotypes of Alzheimer’s disease and facilitate personalized drug screening platforms for the identification of small molecules. We also discuss recent developments by γ-secretase inhibitors and modulators in the treatment of AD. In addition, small-molecule drugs isolated from Chinese herbal medicines have been shown effective in treating Alzheimer’s disease. We propose a mechanism of small-molecule drugs in treating Alzheimer’s disease. Combining therapy with different small-molecule drugs may increase the chance of symptomatic treatment. A customized strategy tailored to individuals and in combination with therapy may be a more suitable treatment option for Alzheimer’s disease in the future.
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131
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Bhattarai S, Devkota S, Meneely KM, Xing M, Douglas JT, Wolfe MS. Design of Substrate Transmembrane Mimetics as Structural Probes for γ-Secretase. J Am Chem Soc 2020; 142:3351-3355. [PMID: 31999444 DOI: 10.1021/jacs.9b13405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
γ-Secretase is a membrane-embedded aspartyl protease complex central in biology and medicine. How this enzyme recognizes transmembrane substrates and catalyzes hydrolysis in the lipid bilayer is unclear. Inhibitors that mimic the entire substrate transmembrane domain and engage the active site should provide important tools for structural biology, yielding insight into substrate gating and trapping the protease in the active state. Here, we report transmembrane peptidomimetic inhibitors of the γ-secretase complex that contain an N-terminal helical peptide region that engages a substrate docking exosite and a C-terminal transition-state analog moiety targeted to the active site. Both regions are required for stoichiometric inhibition of γ-secretase. Moreover, enzyme inhibition kinetics and photoaffinity probe displacement experiments demonstrate that both the docking exosite and the active site are engaged by the bipartite inhibitors. The solution conformations of these potent transmembrane-mimetic inhibitors are similar to those of bound natural substrates, suggesting these probes are preorganized for high-affinity binding and should allow visualization of the active γ-secretase complex, poised for intramembrane proteolysis, by cryo-electron microscopy.
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132
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Tian Y, Meng L, Zhang Z. What is strain in neurodegenerative diseases? Cell Mol Life Sci 2020; 77:665-676. [PMID: 31531680 PMCID: PMC11105091 DOI: 10.1007/s00018-019-03298-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/11/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
Neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, are characterized by the aggregation of misfolded proteins, including Aβ, tau and α-synuclein. It is well recognized that these misfolded proteins are able to self-propagate and spread throughout the nervous system and cause neuronal injury in a way that resembles prion disease. These disease-specific misfolded proteins demonstrate unique features, including the seeding barrier, the conformational memory effect, strain selection and strain evolution, based on the presence of various strains. However, the accurate definition of the term strain remains to be clarified. Here, a clear interpretation is proposed by a retrospective of its history in prion research and the recent progress in neurodegeneration research. Furthermore, the causes contributing to the genesis of various strains are also summarized. Deeper insight into strains helps us to understand the phenomena we observe in this field and it also enlightens us on the elusive mechanisms and management of neurodegeneration.
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Affiliation(s)
- Ye Tian
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lanxia Meng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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133
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Wolfe MS. Unraveling the complexity of γ-secretase. Semin Cell Dev Biol 2020; 105:3-11. [PMID: 31980377 PMCID: PMC7371508 DOI: 10.1016/j.semcdb.2020.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/26/2019] [Accepted: 01/15/2020] [Indexed: 01/07/2023]
Abstract
γ-Secretase was initially defined as a proteolytic activity that cleaves within the transmembrane of the amyloid precursor protein (APP) to produce the amyloid β-peptide of Alzheimer's disease. The discovery of mutations in APP and the presenilins associated with familial Alzheimer's disease and their effects on APP processing dovetailed with pharmacological studies on γ-secretase, leading to the revelation that presenilins are unprecedented membrane-embedded aspartyl proteases. Other members of what became known as the γ-secretase complex were subsequently identified. In parallel with these advances, connections between presenilins and Notch receptors essential to metazoan development became evident, resulting in the concurrent realization that γ-secretase also carries out intramembrane proteolysis of Notch as part of its signaling mechanism. Substantial progress has been made toward elucidating how γ-secretase carries out complex processing of transmembrane domains, how it goes awry in familial Alzheimer's disease, the scope of its substrates, and the atomic details of its structure. Critical questions remain for future study, toward further unraveling the complexity of this unique membrane-embedded proteolytic machine and its roles in biology and disease.
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Affiliation(s)
- Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA.
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134
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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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135
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Barniol-Xicota M, Verhelst SHL. Isolation of intramembrane proteases in membrane-like environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183193. [PMID: 31945321 DOI: 10.1016/j.bbamem.2020.183193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Intramembrane proteases (IMPs) are proteolytic enzymes embedded in the lipid bilayer, where they cleave transmembrane substrates. The importance of IMPs relies on their role in a wide variety of cellular processes and diseases. In order to study the activity and function of IMPs, their purified form is often desired. The production of pure and active IMPs has proven to be a challenging task. This process unavoidably requires the use of solubilizing agents that will, to some extent, alter the native environment of these proteases. In this review we present the current solubilization and reconstitution techniques that have been applied to IMPs. In addition, we describe how these techniques had an influence on the activity and structural studies of IMPs, focusing on rhomboid proteases and γ-secretase.
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Affiliation(s)
- Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium.
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49, Box 802, B-3000, Belgium; Leibniz Institute for Analytical Sciences, ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
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136
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Yamamoto S. Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila. Dev Growth Differ 2020; 62:15-34. [PMID: 31943162 DOI: 10.1111/dgd.12640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022]
Abstract
Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.,Department of Neuroscience, BCM, Houston, TX, USA.,Program in Developmental Biology, BCM, Houston, TX, USA.,Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
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137
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Popugaeva E, Bezprozvanny I, Chernyuk D. Reversal of Calcium Dysregulation as Potential Approach for Treating Alzheimer's Disease. Curr Alzheimer Res 2020; 17:344-354. [PMID: 32469698 PMCID: PMC8210816 DOI: 10.2174/1567205017666200528162046] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/25/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
Despite decades of research and effort, there is still no effective disease-modifying treatment for Alzheimer's Disease (AD). Most of the recent AD clinical trials were targeting amyloid pathway, but all these trials failed. Although amyloid pathology is a hallmark and defining feature of AD, targeting the amyloid pathway has been very challenging due to low efficacy and serious side effects. Alternative approaches or mechanisms for our understanding of the major cause of memory loss in AD need to be considered as potential therapeutic targets. Increasing studies suggest that Ca2+ dysregulation in AD plays an important role in AD pathology and is associated with other AD abnormalities, such as excessive inflammation, increased ROS, impaired autophagy, neurodegeneration, synapse, and cognitive dysfunction. Ca2+ dysregulation in cytosolic space, Endoplasmic Reticulum (ER) and mitochondria have been reported in the context of various AD models. Drugs or strategies, to correct the Ca2+ dysregulation in AD, have been demonstrated to be promising as an approach for the treatment of AD in preclinical models. This review will discuss the mechanisms of Ca2+ dysregulation in AD and associated pathology and discuss potential approaches or strategies to develop novel drugs for the treatment of AD by targeting Ca2+ dysregulation.
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Affiliation(s)
- Elena Popugaeva
- Department of Medical Physics, Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
| | - Ilya Bezprozvanny
- Department of Physiology, UT Southwestern Medical Center, Dallas, USA
| | - Daria Chernyuk
- Department of Medical Physics, Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
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138
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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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139
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Benjin X, Ling L. Developments, applications, and prospects of cryo-electron microscopy. Protein Sci 2019; 29:872-882. [PMID: 31854478 PMCID: PMC7096719 DOI: 10.1002/pro.3805] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022]
Abstract
Cryo‐electron microscopy (cryo‐EM) is a structural biological method that is used to determine the 3D structures of biomacromolecules. After years of development, cryo‐EM has made great achievements, which has led to a revolution in structural biology. In this article, the principle, characteristics, history, current situation, workflow, and common problems of cryo‐EM are systematically reviewed. In addition, the new development direction of cryo‐EM—cryo‐electron tomography (cryo‐ET), is discussed in detail. Also, cryo‐EM is prospected from the following aspects: the structural analysis of small proteins, the improvement of resolution and efficiency, and the relationship between cryo‐EM and drug development. This review is dedicated to giving readers a comprehensive understanding of the development and application of cryo‐EM, and to bringing them new insights.
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Affiliation(s)
- Xu Benjin
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
| | - Liu Ling
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
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140
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Katoh M, Katoh M. Precision medicine for human cancers with Notch signaling dysregulation (Review). Int J Mol Med 2019; 45:279-297. [PMID: 31894255 PMCID: PMC6984804 DOI: 10.3892/ijmm.2019.4418] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
NOTCH1, NOTCH2, NOTCH3 and NOTCH4 are transmembrane receptors that transduce juxtacrine signals of the delta-like canonical Notch ligand (DLL)1, DLL3, DLL4, jagged canonical Notch ligand (JAG)1 and JAG2. Canonical Notch signaling activates the transcription of BMI1 proto-oncogene polycomb ring finger, cyclin D1, CD44, cyclin dependent kinase inhibitor 1A, hes family bHLH transcription factor 1, hes related family bHLH transcription factor with YRPW motif 1, MYC, NOTCH3, RE1 silencing transcription factor and transcription factor 7 in a cellular context-dependent manner, while non-canonical Notch signaling activates NF-κB and Rac family small GTPase 1. Notch signaling is aberrantly activated in breast cancer, non-small-cell lung cancer and hematological malignancies, such as T-cell acute lymphoblastic leukemia and diffuse large B-cell lymphoma. However, Notch signaling is inactivated in small-cell lung cancer and squamous cell carcinomas. Loss-of-function NOTCH1 mutations are early events during esophageal tumorigenesis, whereas gain-of-function NOTCH1 mutations are late events during T-cell leukemogenesis and B-cell lymphomagenesis. Notch signaling cascades crosstalk with fibroblast growth factor and WNT signaling cascades in the tumor microenvironment to maintain cancer stem cells and remodel the tumor microenvironment. The Notch signaling network exerts oncogenic and tumor-suppressive effects in a cancer stage- or (sub)type-dependent manner. Small-molecule γ-secretase inhibitors (AL101, MRK-560, nirogacestat and others) and antibody-based biologics targeting Notch ligands or receptors [ABT-165, AMG 119, rovalpituzumab tesirine (Rova-T) and others] have been developed as investigational drugs. The DLL3-targeting antibody-drug conjugate (ADC) Rova-T, and DLL3-targeting chimeric antigen receptor-modified T cells (CAR-Ts), AMG 119, are promising anti-cancer therapeutics, as are other ADCs or CAR-Ts targeting tumor necrosis factor receptor superfamily member 17, CD19, CD22, CD30, CD79B, CD205, Claudin 18.2, fibroblast growth factor receptor (FGFR)2, FGFR3, receptor-type tyrosine-protein kinase FLT3, HER2, hepatocyte growth factor receptor, NECTIN4, inactive tyrosine-protein kinase 7, inactive tyrosine-protein kinase transmembrane receptor ROR1 and tumor-associated calcium signal transducer 2. ADCs and CAR-Ts could alter the therapeutic framework for refractory cancers, especially diffuse-type gastric cancer, ovarian cancer and pancreatic cancer with peritoneal dissemination. Phase III clinical trials of Rova-T for patients with small-cell lung cancer and a phase III clinical trial of nirogacestat for patients with desmoid tumors are ongoing. Integration of human intelligence, cognitive computing and explainable artificial intelligence is necessary to construct a Notch-related knowledge-base and optimize Notch-targeted therapy for patients with cancer.
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Affiliation(s)
- Masuko Katoh
- M & M PrecMed, Tokyo 113‑0033, National Cancer Center, Tokyo 104‑0045, Japan
| | - Masaru Katoh
- Department of Omics Network, National Cancer Center, Tokyo 104‑0045, Japan
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141
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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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142
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Beard HA, Barniol-Xicota M, Yang J, Verhelst SHL. Discovery of Cellular Roles of Intramembrane Proteases. ACS Chem Biol 2019; 14:2372-2388. [PMID: 31287658 DOI: 10.1021/acschembio.9b00404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intramembrane proteases (IMPs) are localized within lipid bilayers of membranes-either the cell membrane or membranes of various organelles. Cleavage of substrates often results in release from the membrane, leading to a downstream biological effect. This mechanism allows different signaling events to happen through intramembrane proteolysis. Over the years, various mechanistically distinct families of IMPs have been discovered, but the research progress has generally been slower than for soluble proteases due to the challenges associated with membrane proteins. In this review we summarize how each mechanistic family of IMPs was discovered, which chemical tools are available for the study of IMPs, and which techniques have been developed for the discovery of IMP substrates. Finally, we discuss the various roles in cellular physiology of some of these IMPs.
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Affiliation(s)
- Hester A. Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Jian Yang
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Steven H. L. Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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143
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Zhou R, Yang G, Shi Y. Macromolecular complex in recognition and proteolysis of amyloid precursor protein in Alzheimer's disease. Curr Opin Struct Biol 2019; 61:1-8. [PMID: 31629221 DOI: 10.1016/j.sbi.2019.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 09/07/2019] [Indexed: 12/31/2022]
Abstract
Proteolysis of amyloid precursor protein (APP), first extracellularly by β-secretase and then within the membrane by γ-secretase, produces β-amyloid peptides (Aβ). Aβ accumulates in the brain to form amyloid plaques, a hallmark of Alzheimer's disease (AD). Mutations in APP and presenilin (the catalytic subunit of γ-secretase) result in early onset of AD. Cryogenic electron microscopy (cryo-EM) structures of substrate-free and substrate-bound γ-secretase, determined at atomic resolutions, reveal the physical basis of distinct substrate specificity. These advances, together with the discovery and characterization of multiple proteins that interact with APP or presenilin, have given rise to an optimistic scenario for future mechanistic understanding of AD.
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Affiliation(s)
- Rui Zhou
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Guanghui Yang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.
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144
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Arber C, Villegas-Llerena C, Toombs J, Pocock JM, Ryan NS, Fox NC, Zetterberg H, Hardy J, Wray S. Amyloid precursor protein processing in human neurons with an allelic series of the PSEN1 intron 4 deletion mutation and total presenilin-1 knockout. Brain Commun 2019; 1:fcz024. [PMID: 32395715 PMCID: PMC7212081 DOI: 10.1093/braincomms/fcz024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mutations in presenilin-1 (PSEN1), encoding the catalytic subunit of the amyloid precursor protein-processing enzyme γ-secretase, cause familial Alzheimer’s disease. However, the mechanism of disease is yet to be fully understood and it remains contentious whether mutations exert their effects predominantly through gain or loss of function. To address this question, we generated an isogenic allelic series for the PSEN1 mutation intron 4 deletion; represented by control, heterozygous and homozygous mutant induced pluripotent stem cells in addition to a presenilin-1 knockout line. Induced pluripotent stem cell-derived cortical neurons reveal reduced, yet detectable amyloid-beta levels in the presenilin-1 knockout line, and a mutant gene dosage-dependent defect in amyloid precursor protein processing in PSEN1 intron 4 deletion lines, consistent with reduced processivity of γ-secretase. The different effects of presenilin-1 knockout and the PSEN1 intron 4 deletion mutation on amyloid precursor protein-C99 fragment accumulation, nicastrin maturation and amyloid-beta peptide generation support distinct consequences of familial Alzheimer’s disease-associated mutations and knockout of presenilin-1 on the function of γ-secretase.
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Affiliation(s)
- Charles Arber
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Claudio Villegas-Llerena
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK.,Department of Neuroinflammation, 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 at UCL, London, UK
| | - Jennifer M Pocock
- Department of Neuroinflammation, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Natalie S Ryan
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Nick C Fox
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK.,UK Dementia Research Institute at UCL, London, UK.,Department of Neurodegenerative Disease, Dementia Research Centre, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Henrik Zetterberg
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK.,UK Dementia Research Institute at UCL, London, UK.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Mo¨ lndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
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145
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Shi C, Öster C, Bohg C, Li L, Lange S, Chevelkov V, Lange A. Structure and Dynamics of the Rhomboid Protease GlpG in Liposomes Studied by Solid-State NMR. J Am Chem Soc 2019; 141:17314-17321. [DOI: 10.1021/jacs.9b08952] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, People’s Republic of China
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Claudia Bohg
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Longmei Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, People’s Republic of China
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany
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146
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Long JM, Holtzman DM. Alzheimer Disease: An Update on Pathobiology and Treatment Strategies. Cell 2019; 179:312-339. [PMID: 31564456 PMCID: PMC6778042 DOI: 10.1016/j.cell.2019.09.001] [Citation(s) in RCA: 1462] [Impact Index Per Article: 292.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
Alzheimer disease (AD) is a heterogeneous disease with a complex pathobiology. The presence of extracellular β-amyloid deposition as neuritic plaques and intracellular accumulation of hyperphosphorylated tau as neurofibrillary tangles remains the primary neuropathologic criteria for AD diagnosis. However, a number of recent fundamental discoveries highlight important pathological roles for other critical cellular and molecular processes. Despite this, no disease-modifying treatment currently exists, and numerous phase 3 clinical trials have failed to demonstrate benefits. Here, we review recent advances in our understanding of AD pathobiology and discuss current treatment strategies, highlighting recent clinical trials and opportunities for developing future disease-modifying therapies.
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Affiliation(s)
- Justin M Long
- Department of Neurology, Hope Center for Neurological Disorders, Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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147
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Malhotra S, Träger S, Dal Peraro M, Topf M. Modelling structures in cryo-EM maps. Curr Opin Struct Biol 2019; 58:105-114. [PMID: 31394387 DOI: 10.1016/j.sbi.2019.05.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 12/20/2022]
Abstract
Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to use for atomic model building, fitting, refinement and validation in the 3D map resulting from these experiments depends primarily on the resolution of the map and the prior information on the corresponding model. Here, we survey some of such methods and approaches and highlight their uses in specific recent examples.
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Affiliation(s)
- Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
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148
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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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149
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Genetic intolerance analysis as a tool for protein science. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183058. [PMID: 31494120 DOI: 10.1016/j.bbamem.2019.183058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 01/04/2023]
Abstract
Recent advances in whole genome and exome sequencing have dramatically increased the database of human gene variations. There are now enough sequenced human exomes and genomes to begin to identify gene variations that are notable because they are NOT observed in sequenced human genomes, apparently because they are subject to "purifying selection", exemplifying genetic intolerance. Such "dysprocreative" gene variations are embryonic lethal or prevent reproduction through any one of a number of possible mechanisms. Here we review an emerging quantitative approach, "Missense Tolerance Ratio" (MTR) analysis, that is used to assess protein-encoding gene (cDNA) sequence intolerance to missense mutations based on analysis of the >100 K and growing number of currently available human genome and exome sequences. This approach is already useful for analyzing intolerance to mutations in cDNA segments with a resolution on the order of 90 bases. Moreover, as the number of sequenced genomes/exomes increases by orders of magnitude it may eventually be possible to assess mutational tolerance in a statistically robust manner at or near single site resolution. Here we focus on how cDNA intolerance analysis complements other bioinformatic methods to illuminate structure-folding-function relationships for the encoded proteins. A set of disease-linked membrane proteins is employed to provide examples.
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150
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Hitzenberger M, Zacharias M. Uncovering the Binding Mode of γ -Secretase Inhibitors. ACS Chem Neurosci 2019; 10:3398-3403. [PMID: 31244051 DOI: 10.1021/acschemneuro.9b00272] [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] [Indexed: 01/07/2023] Open
Abstract
Knowledge of how transition state inhibitors bind to γ-secretase is of major importance for the design of new Alzheimer's disease therapies. On the basis of the known structure of γ-secretase in complex with a fragment of the amyloid precursor protein, we generated a structural model of γ-secretase in complex with the effective L-685,458 transition state inhibitor. The predicted binding mode is in excellent agreement with experimental data, mimicking all enzyme-substrate interactions at the active site and forming the relevant transition state geometry with the active site aspartate residues. The model also indicates the possible location and nature of the amino acid residues forming the proposed binding pockets S1', S2', and S3' near the active site that are occupied by chemical groups of the inhibitor. In addition, we found that the stability of the complex is very likely sensitive to the pH value. Comparative simulations on the binding of L-685,458 and the epimer L682,679 allowed us to explain the strongly reduced affinity of the epimer for γ-secretase. The structural model could form a valuable basis for the design of new or modified γ-secretase inhibitors.
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Affiliation(s)
- Manuel Hitzenberger
- Physics Department T38, Technical University of Munich, James-Frank-Strasse 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Frank-Strasse 1, 85748 Garching, Germany
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