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Miao Y, Wolfe MS. Emerging structures and dynamic mechanisms of γ-secretase for Alzheimer's disease. Neural Regen Res 2025; 20:174-180. [PMID: 38767485 DOI: 10.4103/nrr.nrr-d-23-01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/11/2024] [Indexed: 05/22/2024] Open
Abstract
γ-Secretase, called "the proteasome of the membrane," is a membrane-embedded protease complex that cleaves 150+ peptide substrates with central roles in biology and medicine, including amyloid precursor protein and the Notch family of cell-surface receptors. Mutations in γ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer's disease. γ-Secretase has thus served as a critical drug target for treating familial Alzheimer's disease and the more common late-onset Alzheimer's disease as well. However, critical gaps remain in understanding the mechanisms of processive proteolysis of substrates, the effects of familial Alzheimer's disease mutations, and allosteric modulation of substrate cleavage by γ-secretase. In this review, we focus on recent studies of structural dynamic mechanisms of γ-secretase. Different mechanisms, including the "Fit-Stay-Trim," "Sliding-Unwinding," and "Tilting-Unwinding," have been proposed for substrate proteolysis of amyloid precursor protein by γ-secretase based on all-atom molecular dynamics simulations. While an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-bound γ-secretase, molecular dynamics simulations on a resolved model of Notch1-bound γ-secretase that was reconstructed using the amyloid precursor protein-bound γ-secretase as a template successfully captured γ-secretase activation for proper cleavages of both wildtype and mutant Notch, being consistent with biochemical experimental findings. The approach could be potentially applied to decipher the processing mechanisms of various substrates by γ-secretase. In addition, controversy over the effects of familial Alzheimer's disease mutations, particularly the issue of whether they stabilize or destabilize γ-secretase-substrate complexes, is discussed. Finally, an outlook is provided for future studies of γ-secretase, including pathways of substrate binding and product release, effects of modulators on familial Alzheimer's disease mutations of the γ-secretase-substrate complexes. Comprehensive understanding of the functional mechanisms of γ-secretase will greatly facilitate the rational design of effective drug molecules for treating familial Alzheimer's disease and perhaps Alzheimer's disease in general.
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Affiliation(s)
- Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
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2
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A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase. Commun Biol 2022; 5:837. [PMID: 35982231 PMCID: PMC9388646 DOI: 10.1038/s42003-022-03818-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Human γ-secretase cleaves the transmembrane domains (TMDs) of amyloid precursor protein (APP) into pathologically relevant amyloid-β peptides (Aβs). The detailed mechanisms of the unique endoproteolytic cleavage by the presenilin 1 domain (PS1) of γ-secretase are still poorly understood. Herein, we provide thermodynamic insights into how the α-helical APP TMD is processed by γ-secretase and elucidate the specificity of Aβ48/Aβ49 cleavage using unbiased molecular dynamics and bias-exchange metadynamics simulations. The thermodynamic data show that the unwinding of APP TMD is driven by water hydration in the intracellular pocket of PS1, and the scissile bond T32-L33 or L33-V34 of the APP TMD can slide down and up to interact with D257/D385 to achieve endoproteolysis. In the wild-type system, the L33-V34 scissile bond is more easily hijacked by D257/D385 than T32-L33, resulting in higher Aβ49 cleavage, while the T32N mutation on the APP TMD decreases the energy barrier of the sliding of the scissile bonds and increases the hydrogen bond occupancy for Aβ48 cleavage. In summary, the thermodynamic analysis elucidates possible mechanisms of APP TMD processing by PS1, which might facilitate rational drug design targeting γ-secretase. Thermodynamic analysis from unbiased molecular dynamics and bias-exchange metadynamics simulations reveals possible mechanisms on how γ-secretase cleaves the transmembrane domains of amyloid precursor protein into amyloid-β peptides.
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3
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Feilen LP, Chen SY, Fukumori A, Feederle R, Zacharias M, Steiner H. Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis. eLife 2022; 11:76090. [PMID: 35579427 PMCID: PMC9282858 DOI: 10.7554/elife.76090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here, we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer’s disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme’s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis. Cutting proteins into pieces is a crucial process in the cell, allowing several important processes to take place, including cell differentiation (which allows cells to develop into specific types), cell death, protein quality control, or even where in the cell a protein will end up. However, the specialized proteins that carry out this task, known as proteases, can also be involved in the development of disease. For example, in the brain, a protease called γ-secretase cuts up the amyloid-β protein precursor, producing toxic forms of amyloid-β peptides that are widely believed to cause Alzheimer’s disease. Proteases like γ-secretase carry out their role in the membrane, the layer of fats (also known as lipids) that forms the outer boundary of the cell. The environment in this area of the cell can influence the activity of proteases, but it is poorly understood how this happens. One way to address this question would be to compare the activity of γ-secretase in the lipid environment of the membrane to its activity when it is entirely surrounded by different molecules, such as detergent molecules. Unfortunately, γ-secretase is not active when it is removed from its lipid environment by a detergent, making it difficult to perform this comparison. To overcome this issue, Feilen et al. chose to study PSH, a protease similar to γ-secretase that produces the same amyloid-β peptides but remains active in detergent. When Feilen et al. mixed PSH with lipid molecules like those found in the membrane and amyloid-β precursor protein, PSH produced amyloid-β peptides including those that are thought to cause Alzheimer’s. However, when a detergent was substituted for the lipid molecules this led to longer amyloid-β peptides than usual, indicating that PSH was not able to cut proteins as effectively. The change in environment appeared to reduce PSH’s ability to progressively trim small segments from the peptides. Computer modelling of the protease’s structure in lipids versus detergent supported the experimental findings: the model predicted that the areas of PSH important for recognizing and cutting other proteins would be more stable in the membrane compared to the detergent. These results indicate that the cell membrane plays a vital role in the stability of the active regions of proteases that are cleaving in this environment. In the future, this could help to better understand how changes to the lipid molecules in the membrane may contribute to the activity of γ-secretase and its role in Alzheimer’s disease.
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Affiliation(s)
- Lukas P Feilen
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Shu-Yu Chen
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Akio Fukumori
- Department of Pharmacotherapeutics II, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Regina Feederle
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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4
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Wolfe MS, Miao Y. Structure and mechanism of the γ-secretase intramembrane protease complex. Curr Opin Struct Biol 2022; 74:102373. [PMID: 35461161 DOI: 10.1016/j.sbi.2022.102373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/08/2022] [Indexed: 12/25/2022]
Abstract
γ-Secretase is a membrane protein complex that proteolyzes within the transmembrane domain of >100 substrates, including those derived from the amyloid precursor protein and the Notch family of cell surface receptors. The nine-transmembrane presenilin is the catalytic component of this aspartyl protease complex that carries out hydrolysis in the lipid bilayer. Advances in cryoelectron microscopy have led to the elucidation of the structure of the γ-secretase complex at atomic resolution. Recently, structures of the enzyme have been determined with bound APP- or Notch-derived substrates, providing insight into the nature of substrate recognition and processing. Molecular dynamics simulations of substrate-bound enzymes suggest dynamic mechanisms of intramembrane proteolysis. Structures of the enzyme bound to small-molecule inhibitors and modulators have also been solved, setting the stage for rational structure-based drug discovery targeting γ-secretase.
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Affiliation(s)
- Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, 66045, USA.
| | - Yinglong Miao
- Center for Computational Biology, Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA. https://twitter.com/yinglongmiao
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5
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Bhattarai A, Devkota S, Do HN, Wang J, Bhattarai S, Wolfe MS, Miao Y. Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase. J Am Chem Soc 2022; 144:6215-6226. [PMID: 35377629 PMCID: PMC9798850 DOI: 10.1021/jacs.1c10533] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer's disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and Western blotting were used to quantify the efficiency of tripeptide trimming of wild-type (WT) and familial AD (FAD) mutant Aβ49. In comparison to WT Aβ49, the efficiency of tripeptide trimming was similar for the I45F, A42T, and V46F Aβ49 FAD mutants but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate the tripeptide trimming of Aβ49 by γ-secretase. The starting structure was the active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured the activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai, A., ACS Cent. Sci. 2020, 6, 969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming of Aβ49 by γ-secretase.
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Affiliation(s)
- Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sujan Devkota
- Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Hung Nguyen Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Sanjay Bhattarai
- Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Michael S. Wolfe
- Corresponding Authors Michael S. Wolfe – Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States; ; Yinglong Miao – Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States;
| | - Yinglong Miao
- Corresponding Authors Michael S. Wolfe – Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States; ; Yinglong Miao – Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States;
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6
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Small molecules targeting γ-secretase and their potential biological applications. Eur J Med Chem 2022; 232:114169. [DOI: 10.1016/j.ejmech.2022.114169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/30/2022] [Accepted: 01/30/2022] [Indexed: 12/14/2022]
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7
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Santiago Á, Guzmán-Ocampo DC, Aguayo-Ortiz R, Dominguez L. Characterizing the Chemical Space of γ-Secretase Inhibitors and Modulators. ACS Chem Neurosci 2021; 12:2765-2775. [PMID: 34291906 DOI: 10.1021/acschemneuro.1c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
γ-Secretase (GS) is one of the most attractive molecular targets for the treatment of Alzheimer's disease (AD). Its key role in the final step of amyloid-β peptides generation and its relationship in the cascade of events for disease development have caught the attention of many pharmaceutical groups. Over the past years, different inhibitors and modulators have been evaluated as promising therapeutics against AD. However, despite the great chemical diversity of the reported compounds, a global classification and visual representation of the chemical space for GS inhibitors and modulators remain unavailable. In the present work, we carried out a two-dimensional (2D) chemical space analysis from different classes and subclasses of GS inhibitors and modulators based on their structural similarity. Along with the novel structural information available for GS complexes, our analysis opens the possibility to identify compounds with high molecular similarity, critical to finding new chemical structures through the optimization of existing compounds and relating them with a potential binding site.
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Affiliation(s)
- Ángel Santiago
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Dulce C. Guzmán-Ocampo
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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8
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Cruz-Vicente P, Passarinha LA, Silvestre S, Gallardo E. Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches. Molecules 2021; 26:2193. [PMID: 33920326 PMCID: PMC8069930 DOI: 10.3390/molecules26082193] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative diseases (ND), including Alzheimer's (AD) and Parkinson's Disease (PD), are becoming increasingly more common and are recognized as a social problem in modern societies. These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide. Currently, there is no existing cure for AD nor PD and the clinically used drugs aim only at symptomatic relief, and are not capable of stopping neurodegeneration. Over the last years, several drug candidates reached clinical trials phases, but they were suspended, mainly because of the unsatisfactory pharmacological benefits. Recently, the number of compounds developed using in silico approaches has been increasing at a promising rate, mainly evaluating the affinity for several macromolecular targets and applying filters to exclude compounds with potentially unfavorable pharmacokinetics. Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico approaches to design novel drug candidates for AD and PD treatment will be presented. In addition, future perspectives for the treatment of these ND will also be briefly discussed.
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Affiliation(s)
- Pedro Cruz-Vicente
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Luís A. Passarinha
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
| | - Samuel Silvestre
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Eugenia Gallardo
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
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9
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Yang G, Zhou R, Guo X, Yan C, Lei J, Shi Y. Structural basis of γ-secretase inhibition and modulation by small molecule drugs. Cell 2020; 184:521-533.e14. [PMID: 33373587 DOI: 10.1016/j.cell.2020.11.049] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 01/01/2023]
Abstract
Development of γ-secretase inhibitors (GSIs) and modulators (GSMs) represents an attractive therapeutic opportunity for Alzheimer's disease (AD) and cancers. However, how these GSIs and GSMs target γ-secretase has remained largely unknown. Here, we report the cryoelectron microscopy (cryo-EM) structures of human γ-secretase bound individually to two GSI clinical candidates, Semagacestat and Avagacestat, a transition state analog GSI L685,458, and a classic GSM E2012, at overall resolutions of 2.6-3.1 Å. Remarkably, each of the GSIs occupies the same general location on presenilin 1 (PS1) that accommodates the β strand from amyloid precursor protein or Notch, interfering with substrate recruitment. L685,458 directly coordinates the two catalytic aspartate residues of PS1. E2012 binds to an allosteric site of γ-secretase on the extracellular side, potentially explaining its modulating activity. Structural analysis reveals a set of shared themes and variations for inhibitor and modulator recognition that will guide development of the next-generation substrate-selective inhibitors.
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Affiliation(s)
- Guanghui Yang
- Beijing Advanced Innovation Center for Structural Biology and Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Rui Zhou
- Beijing Advanced Innovation Center for Structural Biology and Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuefei Guo
- Beijing Advanced Innovation Center for Structural Biology and Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology and Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology and Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.
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10
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Chen SY, Zacharias M. How Mutations Perturb γ-Secretase Active Site Studied by Free Energy Simulations. ACS Chem Neurosci 2020; 11:3321-3332. [PMID: 32960571 DOI: 10.1021/acschemneuro.0c00440] [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] [Indexed: 11/29/2022] Open
Abstract
γ-Secretase is involved in processing of the amyloid precursor protein (APP) and generation of short Aβ peptides that may play a key role in neurodegenerative diseases such as Alzheimer's disease (AD). Several mutations in γ-secretase influence its activity, resulting in early AD onset (Familial AD or FAD mutations). The molecular details of how mutations, not located close to the active site, can affect enzyme activity is not understood. In molecular dynamics simulations of γ-secretase in the absence of substrate (apo), we identified two active site conformational states characterized by a direct contact between catalytic Asp residues (closed state) and an open water-bridged state. In the presence of substrate, only conformations compatible with the open active site geometry are accessible. Systematic free energy simulations on wild type and FAD mutations indicate a free energy difference between closed and open states that is significantly modulated by FAD mutations and correlates with the corresponding experimental activity. For mutations with reduced activity, an increased penalty for open-state transitions was found. Only for two mutations located at the active site a direct perturbation of the open-state geometry was observed that could directly explain the drop of enzyme activity. The simulations suggest that modulation of the closed/open equilibrium and perturbation of the open (active) catalytic geometry are possible mechanisms of how FAD mutations affect γ-secretase activity. The results also offer an explanation for the experimental finding that FAD mutations, although not located at the interface to the substrate, mainly destabilize the enzyme-substrate complex.
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Affiliation(s)
- Shu-Yu Chen
- Physik-Department T38,Techniche Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38,Techniche Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
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11
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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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12
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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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13
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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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14
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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: 20] [Impact Index Per Article: 5.0] [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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15
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Funamoto S, Tagami S, Okochi M, Morishima-Kawashima M. Successive cleavage of β-amyloid precursor protein by γ-secretase. Semin Cell Dev Biol 2020; 105:64-74. [PMID: 32354467 DOI: 10.1016/j.semcdb.2020.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022]
Abstract
γ-Secretase is a multimeric aspartyl protease that cleaves the membrane-spanning region of the β-carboxyl terminal fragment (βCTF) generated from β-amyloid precursor protein. γ-Secretase defines the generated molecular species of amyloid β-protein (Aβ), a critical molecule in the pathogenesis of Alzheimer's disease (AD). Many therapeutic trials for AD have targeted γ-secretase. However, in contrast to the great efforts in drug discovery, the enzymatic features and cleavage mechanism of γ-secretase are poorly understood. Here we review our protein-chemical analyses of the cleavage products generated from βCTF by γ-secretase, which revealed that Aβ was produced by γ-secretase through successive cleavages of βCTF, mainly at three-residue intervals. Two representative product lines were identified. ε-Cleavages occur first at Leu49-Val50 and Thr48-Leu49 of βCTF (in accordance with Aβ numbering). Longer generated Aβs, Aβ49 and Aβ48, are precursors to the majority of Aβ40 and Aβ42, concomitantly releasing the tripeptides, ITL, VIV, and IAT; and VIT and TVI, respectively. A portion of Aβ42 is processed further to Aβ38, releasing a tetrapeptide, VVIA. The presence of additional multiple minor pathways may reflect labile cleavage activities derived from the conformational flexibility of γ-secretase through molecular interactions. Because these peptide byproducts are not secreted and remain within the cells, they may serve as an indicator that reflects γ-secretase activity more directly than secreted Aβ.
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Affiliation(s)
- Satoru Funamoto
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Shinji Tagami
- Neuropsychiatry, Department of Integrated Medicine, Division of Internal Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masayasu Okochi
- Neuropsychiatry, Department of Integrated Medicine, Division of Internal Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Maho Morishima-Kawashima
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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16
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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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17
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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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