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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 PMCID: PMC11246123 DOI: 10.4103/nrr.nrr-d-23-01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/19/2023] [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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Zhang J, Zhang Y, Wang J, Xia Y, Zhang J, Chen L. Recent advances in Alzheimer's disease: Mechanisms, clinical trials and new drug development strategies. Signal Transduct Target Ther 2024; 9:211. [PMID: 39174535 PMCID: PMC11344989 DOI: 10.1038/s41392-024-01911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/18/2024] [Accepted: 07/02/2024] [Indexed: 08/24/2024] Open
Abstract
Alzheimer's disease (AD) stands as the predominant form of dementia, presenting significant and escalating global challenges. Its etiology is intricate and diverse, stemming from a combination of factors such as aging, genetics, and environment. Our current understanding of AD pathologies involves various hypotheses, such as the cholinergic, amyloid, tau protein, inflammatory, oxidative stress, metal ion, glutamate excitotoxicity, microbiota-gut-brain axis, and abnormal autophagy. Nonetheless, unraveling the interplay among these pathological aspects and pinpointing the primary initiators of AD require further elucidation and validation. In the past decades, most clinical drugs have been discontinued due to limited effectiveness or adverse effects. Presently, available drugs primarily offer symptomatic relief and often accompanied by undesirable side effects. However, recent approvals of aducanumab (1) and lecanemab (2) by the Food and Drug Administration (FDA) present the potential in disrease-modifying effects. Nevertheless, the long-term efficacy and safety of these drugs need further validation. Consequently, the quest for safer and more effective AD drugs persists as a formidable and pressing task. This review discusses the current understanding of AD pathogenesis, advances in diagnostic biomarkers, the latest updates of clinical trials, and emerging technologies for AD drug development. We highlight recent progress in the discovery of selective inhibitors, dual-target inhibitors, allosteric modulators, covalent inhibitors, proteolysis-targeting chimeras (PROTACs), and protein-protein interaction (PPI) modulators. Our goal is to provide insights into the prospective development and clinical application of novel AD drugs.
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Affiliation(s)
- Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yinglu Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, TN, USA
| | - Yilin Xia
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxian Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lei Chen
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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3
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Tao B, Gong W, Xu C, Ma Z, Mei J, Chen M. The relationship between hypoxia and Alzheimer's disease: an updated review. Front Aging Neurosci 2024; 16:1402774. [PMID: 39086755 PMCID: PMC11288848 DOI: 10.3389/fnagi.2024.1402774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/04/2024] [Indexed: 08/02/2024] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases, and the most prevalent form of dementia. The main hallmarks for the diagnosis of AD are extracellular amyloid-beta (Aβ) plaque deposition and intracellular accumulation of highly hyperphosphorylated Tau protein as neurofibrillary tangles. The brain consumes more oxygen than any other organs, so it is more easily to be affected by hypoxia. Hypoxia has long been recognized as one of the possible causes of AD and other neurodegenerative diseases, but the exact mechanism has not been clarified. In this review, we will elucidate the connection between hypoxia-inducible factors-1α and AD, including its contribution to AD and its possible protective effects. Additionally, we will discuss the relationship between oxidative stress and AD as evidence show that oxidative stress acts on AD-related pathogenic factors such as mitochondrial dysfunction, Aβ deposition, inflammation, etc. Currently, there is no cure for AD. Given the close association between hypoxia, oxidative stress, and AD, along with current research on the protective effects of antioxidants against AD, we speculate that antioxidants could be a potential therapeutic approach for AD and worth further study.
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Affiliation(s)
- Borui Tao
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Wei Gong
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengyuan Xu
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhihui Ma
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Jinyu Mei
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ming Chen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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4
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Li S, Hou Z, Ye T, Song X, Hu X, Chen J. Saponin components in Polygala tenuifolia as potential candidate drugs for treating dementia. Front Pharmacol 2024; 15:1431894. [PMID: 39050746 PMCID: PMC11266144 DOI: 10.3389/fphar.2024.1431894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Objective This study aims to elucidate the intervention effects of saponin components from Polygala tenuifolia Willd (Polygalaceae) on dementia, providing experimental evidence and new insights for the research and application of saponins in the field of dementia. Materials and Methods This review is based on a search of the PubMed, NCBI, and Google Scholar databases from their inception to 13 May 2024, using terms such as "P. tenuifolia," "P. tenuifolia and saponins," "toxicity," "dementia," "Alzheimer's disease," "Parkinson's disease dementia," and "vascular dementia." The article summarizes the saponin components of P. tenuifolia, including tenuigenin, tenuifolin, polygalasaponins XXXII, and onjisaponin B, as well as the pathophysiological mechanisms of dementia. Importantly, it highlights the potential mechanisms by which the active components of P. tenuifolia prevent and treat diseases and relevant clinical studies. Results The saponin components of P. tenuifolia can reduce β-amyloid accumulation, exhibit antioxidant effects, regulate neurotransmitters, improve synaptic function, possess anti-inflammatory properties, inhibit neuronal apoptosis, and modulate autophagy. Therefore, P. tenuifolia may play a role in the prevention and treatment of dementia. Conclusion The saponin components of P. tenuifolia have shown certain therapeutic effects on dementia. They can prevent and treat dementia through various mechanisms.
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Affiliation(s)
- Songzhe Li
- College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhitao Hou
- College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ting Ye
- The Second Hospital Affiliated Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Xiaochen Song
- College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xinying Hu
- College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jing Chen
- College of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
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Pettersson M, Johnson DS, Humphrey JM, Am Ende CW, Butler TW, Dorff PH, Efremov IV, Evrard E, Green ME, Helal CJ, Kauffman GW, Mullins PB, Navaratnam T, O'Donnell CJ, O'Sullivan TJ, Patel NC, Stepan AF, Stiff CM, Subramanyam C, Trapa P, Tran TP, Vetelino BC, Yang E, Xie L, Pustilnik LR, Steyn SJ, Wood KM, Bales KR, Hajos-Korcsok E, Verhoest PR. Discovery of Clinical Candidate PF-06648671: A Potent γ-Secretase Modulator for the Treatment of Alzheimer's Disease. J Med Chem 2024; 67:10248-10262. [PMID: 38848667 DOI: 10.1021/acs.jmedchem.4c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Herein, we describe the design and synthesis of γ-secretase modulator (GSM) clinical candidate PF-06648671 (22) for the treatment of Alzheimer's disease. A key component of the design involved a 2,5-cis-tetrahydrofuran (THF) linker to impart conformational rigidity and lock the compound into a putative bioactive conformation. This effort was guided using a pharmacophore model since crystallographic information was not available for the membrane-bound γ-secretase protein complex at the time of this work. PF-06648671 achieved excellent alignment of whole cell in vitro potency (Aβ42 IC50 = 9.8 nM) and absorption, distribution, metabolism, and excretion (ADME) parameters. This resulted in favorable in vivo pharmacokinetic (PK) profile in preclinical species, and PF-06648671 achieved a human PK profile suitable for once-a-day dosing. Furthermore, PF-06648671 was found to have favorable brain availability in rodent, which translated into excellent central exposure in human and robust reduction of amyloid β (Aβ) 42 in cerebrospinal fluid (CSF).
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Affiliation(s)
- Martin Pettersson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Douglas S Johnson
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - John M Humphrey
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Todd W Butler
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Peter H Dorff
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Ivan V Efremov
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Edelweiss Evrard
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Michael E Green
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Christopher J Helal
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Gregory W Kauffman
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Patrick B Mullins
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Thayalan Navaratnam
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Theresa J O'Sullivan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Nandini C Patel
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Antonia F Stepan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Cory M Stiff
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | | | - Patrick Trapa
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Tuan P Tran
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Beth Cooper Vetelino
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Eddie Yang
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Longfei Xie
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Leslie R Pustilnik
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Stefanus J Steyn
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kathleen M Wood
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kelly R Bales
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Eva Hajos-Korcsok
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Patrick R Verhoest
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
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Guo X, Li H, Yan C, Lei J, Zhou R, Shi Y. Molecular mechanism of substrate recognition and cleavage by human γ-secretase. Science 2024; 384:1091-1095. [PMID: 38843321 DOI: 10.1126/science.adn5820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
Successive cleavages of amyloid precursor protein C-terminal fragment with 99 residues (APP-C99) by γ-secretase result in amyloid-β (Aβ) peptides of varying lengths. Most cleavages have a step size of three residues. To elucidate the underlying mechanism, we determined the atomic structures of human γ-secretase bound individually to APP-C99, Aβ49, Aβ46, and Aβ43. In all cases, the substrate displays the same structural features: a transmembrane α-helix, a three-residue linker, and a β-strand that forms a hybrid β-sheet with presenilin 1 (PS1). Proteolytic cleavage occurs just ahead of the substrate β-strand. Each cleavage is followed by unwinding and translocation of the substrate α-helix by one turn and the formation of a new β-strand. This mechanism is consistent with existing biochemical data and may explain the cleavages of other substrates by γ-secretase.
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Affiliation(s)
- Xuefei Guo
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haotian Li
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Zhou
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Westlake Laboratory of Life Science and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang, China
- Research Center for Industries of the Future; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang, China
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7
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Zhou X, Liu Z, Bai G, Dazhang B, Zhao P, Wang X, Jiang G. Bioinformatics analysis of the potential receptor and therapeutic drugs for Alzheimer's disease with comorbid Parkinson's disease. Front Aging Neurosci 2024; 16:1411320. [PMID: 38894850 PMCID: PMC11185263 DOI: 10.3389/fnagi.2024.1411320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Background Now, there are no sensitive biomarkers for improving Alzheimer's disease (AD) and comorbid Parkinson's disease (PD). The aim of the present study was to analyze differentially expressed genes (DEGs) in brain tissue from AD and PD patients via bioinformatics analysis, as well as to explore precise diagnostic and therapeutic targets for AD and comorbid PD. Methods GFE122063 and GSE7621 data sets from GEO in NCBI, were used to screen differentially expressed genes (DEGs) for AD and PD, and identify the intersected genes, respectively. Intersected genes were analyzed by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, STRING site and Cytoscape were used to construct a protein-protein interaction (PPI) network, CytoNCA algorithm to analyze and evaluate centrality, Mcode plug-in to analyze module, and Cytohubba to screen key genes. Combined GO-KEGG enrichment analysis with Cytoscape algorithm to screen the key gene in AD complicated with PD. Then, the DEGs for AD and PD were imported into the Association Map (CMap) online platform to screen out the top 10 small molecule drugs, and using molecular docking techniques to evaluate the interactions between small molecule drugs and key genes receptors. Results In total, 231 upregulated genes and 300 downregulated genes were identified. GO analysis revealed that the DEGs were highly enriched in signal transduction, and KEGG analysis revealed that the DEGs were associated with the MAPK and PI3K-Akt signaling pathways. Epidermal growth factor receptor (EGFR) was identified as a potential receptor gene in AD and comorbid PD. EGFR was upregulated in both AD and PD, and the proteins that interact with EGFR were enriched in the Ras/Raf/MAPK and PI3K/Akt signaling pathways. Semagacestat was identified as a drug with therapeutic potential for treating AD complicated with PD. There was a high binding affinity between semagacestat and EGFRNTD, with seven hydrogen bonds and one hydrophobic bond. Discussion Semagacestat may improve the health of patients with AD complicated with PD through the regulation of the Ras/Raf/MAPK and PI3K/Akt signaling pathways by EGFR, providing evidence supporting the structural modification of semagacestat to develop a more effective drug for treating AD complicated with PD.
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Affiliation(s)
- Xuerong Zhou
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
| | - Zhifan Liu
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
| | - Guiqin Bai
- Department of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, China
| | - Bai Dazhang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
| | - Peilin Zhao
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
| | - Xiaoming Wang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
| | - Guohui Jiang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, China
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Odorčić I, Hamed MB, Lismont S, Chávez-Gutiérrez L, Efremov RG. Apo and Aβ46-bound γ-secretase structures provide insights into amyloid-β processing by the APH-1B isoform. Nat Commun 2024; 15:4479. [PMID: 38802343 PMCID: PMC11130327 DOI: 10.1038/s41467-024-48776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Deposition of amyloid-β (Aβ) peptides in the brain is a hallmark of Alzheimer's disease. Aβs are generated through sequential proteolysis of the amyloid precursor protein by the γ-secretase complexes (GSECs). Aβ peptide length, modulated by the Presenilin (PSEN) and APH-1 subunits of GSEC, is critical for Alzheimer's pathogenesis. Despite high relevance, mechanistic understanding of the proteolysis of Aβ, and its modulation by APH-1, remain incomplete. Here, we report cryo-EM structures of human GSEC (PSEN1/APH-1B) reconstituted into lipid nanodiscs in apo form and in complex with the intermediate Aβ46 substrate without cross-linking. We find that three non-conserved and structurally divergent APH-1 regions establish contacts with PSEN1, and that substrate-binding induces concerted rearrangements in one of the identified PSEN1/APH-1 interfaces, providing structural basis for APH-1 allosteric-like effects. In addition, the GSEC-Aβ46 structure reveals an interaction between Aβ46 and loop 1PSEN1, and identifies three other H-bonding interactions that, according to functional validation, are required for substrate recognition and efficient sequential catalysis.
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Affiliation(s)
- Ivica Odorčić
- Center for Structural Biology, VIB, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Mohamed Belal Hamed
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Sam Lismont
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium.
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Rouslan G Efremov
- Center for Structural Biology, VIB, Brussels, Belgium.
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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Sillapachaiyaporn C, Wongwan C, Mongkolpobsin K, Nilkhet S, Isidoro C, Chuchawankul S, Tencomnao T. Ergosterol promotes neurite outgrowth, inhibits amyloid-beta synthesis, and extends longevity: In vitro neuroblastoma and in vivo Caenorhabditis elegans evidence. Life Sci 2024; 345:122606. [PMID: 38574884 DOI: 10.1016/j.lfs.2024.122606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/16/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
AIMS Alzheimer's disease (AD), the most common neurodegenerative disorder associated with aging, is characterized by amyloid-β (Aβ) plaques in the hippocampus. Ergosterol, a mushroom sterol, exhibits neuroprotective activities; however, the underlying mechanisms of ergosterol in promoting neurite outgrowth and preventing Aβ-associated aging have never been investigated. We aim to determine the beneficial activities of ergosterol in neuronal cells and Caenorhabditis elegans (C. elegans). MATERIALS AND METHODS The neuritogenesis and molecular mechanisms of ergosterol were investigated in wild-type and Aβ precursor protein (APP)-overexpressing Neuro2a cells. The anti-amyloidosis properties of ergosterol were determined by evaluating in vitro Aβ production and the potential inhibition of Aβ-producing enzymes. Additionally, AD-associated transgenic C. elegans was utilized to investigate the in vivo attenuating effects of ergosterol. KEY FINDINGS Ergosterol promoted neurite outgrowth in Neuro2a cells through the upregulation of the transmembrane protein Teneurin-4 (Ten-4) mRNA and protein expressions, phosphorylation of the extracellular signal-regulated kinases (ERKs), activity of cAMP response element (CRE), and growth-associated protein-43 (GAP-43). Furthermore, ergosterol enhanced neurite outgrowth in transgenic Neuro2A cells overexpressing either the wild-type APP (Neuro2a-APPwt) or the Swedish mutant APP (Neuro2a-APPswe) through the Ten-4/ERK/CREB/GAP-43 signaling pathway. Interestingly, ergosterol inhibited Aβ synthesis in Neuro2a-APPwt cells. In silico analysis indicated that ergosterol can interact with the catalytic sites of β- and γ-secretases. In Aβ-overexpressing C. elegans, ergosterol decreased Aβ accumulation, increased chemotaxis behavior, and prolonged lifespan. SIGNIFICANCE Ergosterol is a potential candidate compound that might benefit AD patients by promoting neurite outgrowth, inhibiting Aβ synthesis, and enhancing longevity.
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Affiliation(s)
- Chanin Sillapachaiyaporn
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chamaiphorn Wongwan
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kuljira Mongkolpobsin
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Immunomodulation of Natural Products Research Unit, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunita Nilkhet
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Immunomodulation of Natural Products Research Unit, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ciro Isidoro
- Department of Health Sciences, University of Eastern Piedmont 'Amedeo Avogadro', Novara 28100, Italy
| | - Siriporn Chuchawankul
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Immunomodulation of Natural Products Research Unit, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tewin Tencomnao
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok 10330, Thailand.
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10
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Guzmán-Ocampo DC, Aguayo-Ortiz R, Dominguez L. Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction. J Chem Inf Model 2024; 64:3855-3864. [PMID: 38623052 DOI: 10.1021/acs.jcim.3c01993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Allosteric modulation plays a critical role in enzyme functionality and requires a deep understanding of the interactions between the active and allosteric sites. γ-Secretase (GS) is a key therapeutic target in the treatment of Alzheimer's disease (AD), through its role in the synthesis of amyloid β peptides that accumulate in AD patients. This study explores the structure and dynamic effects of GS modulation by E2012 binding, employing well-tempered metadynamics and conventional molecular dynamics simulations across three binding scenarios: (1) GS enzyme with and without L458 inhibitor, (2) the GS-substrate complex together with the modulator E2012 in two different binding modes, and (3) E2012 interacting with a C99 substrate fragment. Our findings reveal that the presence of L458 induces conformational changes that contribute to stabilization of the GS enzyme dynamics, previously reported as a key factor that allowed the resolution of the cryo-EM structure and the enhanced binding of E2012. Furthermore, we identified the most favorable binding site for E2012 within the GS-substrate complex, uncovering significant modulatory effects and a complex network of interactions that influence the position of the substrate for catalysis. In addition, we explore a potential substrate-modulator binding before the formation of the enzyme-substrate complex. The insights gained from our study emphasize the importance of these interactions in the development of potential therapeutic interventions that target the functionality of the GS enzyme in AD.
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Affiliation(s)
- 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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11
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Wang M, Liu K. Molecular dynamics simulations to explore the binding mode between the amyloid-β protein precursor (APP) and adaptor protein Mint2. Sci Rep 2024; 14:7975. [PMID: 38575686 PMCID: PMC10995209 DOI: 10.1038/s41598-024-58584-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Alzheimer's disease (AD) presents a significant challenge in neurodegenerative disease management, with limited therapeutic options available for its prevention and treatment. At the heart of AD pathogenesis is the amyloid-β (Aβ) protein precursor (APP), with the interaction between APP and the adaptor protein Mint2 being crucial. Despite previous explorations into the APP-Mint2 interaction, the dynamic regulatory mechanisms by which Mint2 modulates APP binding remain poorly understood. This study undertakes molecular dynamics simulations across four distinct systems-free Mint2, Mint2 bound to APP, a mutant form of Mint2, and the mutant form bound to APP-over an extensive 400 ns timeframe. Our findings reveal that the mutant Mint2 experiences significant secondary structural transformations, notably the formation of an α-helix in residues S55-K65 upon APP binding, within the 400 ns simulation period. Additionally, we observed a reduction in the active pocket size of the mutant Mint2 compared to its wild-type counterpart, enhancing its APP binding affinity. These insights hold promise for guiding the development of novel inhibitors targeting the Mints family, potentially paving the way for new therapeutic strategies in AD prevention and treatment.
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Affiliation(s)
- Min Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, China.
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun, 130022, China.
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
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12
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Alhawarri MB, Al-Thiabat MG, Dubey A, Tufail A, Fouad D, Alrimawi BH, Dayoob M. ADME profiling, molecular docking, DFT, and MEP analysis reveal cissamaline, cissamanine, and cissamdine from Cissampelos capensis L.f. as potential anti-Alzheimer's agents. RSC Adv 2024; 14:9878-9891. [PMID: 38528929 PMCID: PMC10961956 DOI: 10.1039/d4ra01070a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/17/2024] [Indexed: 03/27/2024] Open
Abstract
The current pharmacotherapies for Alzheimer's disease (AD) demonstrate limited efficacy and are associated with various side effects, highlighting the need for novel therapeutic agents. Natural products, particularly from medicinal plants, have emerged as a significant source of potential neuroprotective compounds. In this context, Cissampelos capensis L.f., renowned for its medicinal properties, has recently yielded three new proaporphine alkaloids; cissamaline, cissamanine, and cissamdine. Despite their promising bioactive profiles, the biological targets of these alkaloids in the context of AD have remained unexplored. This study undertakes a comprehensive in silico examination of the binding affinity and molecular interactions of these alkaloids with human protein targets implicated in AD. The drug likeness and ADME analyses indicate favorable pharmacokinetic profiles for these compounds, suggesting their potential efficacy in targeting the central nervous system. Molecular docking studies indicate that cissamaline, cissamanine, and cissamdine interact with key AD-associated proteins. These interactions are comparable to, or in some aspects slightly less potent than, those observed with established AD drugs, highlighting their potential as novel therapeutic agents for Alzheimer's disease. Crucially, Density Functional Theory (DFT) calculations offer deep insights into the electronic and energetic characteristics of these alkaloids. These calculations reveal distinct electronic properties, with differences in total energy, binding energy, HOMO-LUMO gaps, dipole moments, and electrophilicity indices. Such variations suggest unique reactivity profiles and molecular stability, pertinent to their pharmacological potential. Moreover, Molecular Electrostatic Potential (MEP) analyses provide visual representations of the electrostatic characteristics of these alkaloids. The analyses highlight areas prone to electrophilic and nucleophilic attacks, indicating their potential for specific biochemical interactions. This combination of DFT and MEP results elucidates the intricate electronic, energetic, and electrostatic properties of these compounds, underpinning their promise as AD therapeutic agents. The in silico findings of this study shed light on the promising potential of cissamaline, cissamanine, and cissamdine as agents for AD treatment. However, further in vitro and in vivo studies are necessary to validate these theoretical predictions and to understand the precise mechanisms through which these alkaloids may exert their therapeutic effects.
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Affiliation(s)
- Maram B Alhawarri
- Department of Pharmacy, Faculty of Pharmacy, Jadara University P.O.Box 733 Irbid 21110 Jordan
| | - Mohammad G Al-Thiabat
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Gelugor 11800 Penang Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences Chennai-600077 Tamil Nadu India
- Computational Chemistry and Drug Discovery Division Quanta Calculus Greater Noida-201310 Uttar Pradesh India
| | - Aisha Tufail
- Computational Chemistry and Drug Discovery Division Quanta Calculus Greater Noida-201310 Uttar Pradesh India
| | - Dania Fouad
- Faculty of Dentistry, Ibn Sina University for Medical and Pharmaceutical Sciences Baghdad Iraq
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13
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De Strooper B, Karran E. New precision medicine avenues to the prevention of Alzheimer's disease from insights into the structure and function of γ-secretases. EMBO J 2024; 43:887-903. [PMID: 38396302 PMCID: PMC10943082 DOI: 10.1038/s44318-024-00057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/20/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Two phase-III clinical trials with anti-amyloid peptide antibodies have met their primary goal, i.e. slowing of Alzheimer's disease (AD) progression. However, antibody therapy may not be the optimal therapeutic modality for AD prevention, as we will discuss in the context of the earlier small molecules described as "γ-secretase modulators" (GSM). We review here the structure, function, and pathobiology of γ-secretases, with a focus on how mutations in presenilin genes result in early-onset AD. Significant progress has been made in generating compounds that act in a manner opposite to pathogenic presenilin mutations: they stabilize the proteinase-substrate complex, thereby increasing the processivity of substrate cleavage and altering the size spectrum of Aβ peptides produced. We propose the term "γ-secretase allosteric stabilizers" (GSAS) to distinguish these compounds from the rather heterogenous class of GSM. The GSAS represent, in theory, a precision medicine approach to the prevention of amyloid deposition, as they specifically target a discrete aspect in a complex cell biological signalling mechanism that initiates the pathological processes leading to Alzheimer's disease.
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Affiliation(s)
- Bart De Strooper
- Dementia Research Institute, Institute of Neurology, University College London, at the Francis Crick Institute, London, NW1 AT, UK.
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, and Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium.
| | - Eric Karran
- Cambridge Research Center, AbbVie, Inc., Cambridge, MA, USA
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14
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Jakowiecki J, Orzeł U, Miszta P, Młynarczyk K, Filipek S. Conformational Changes and Unfolding of β-Amyloid Substrates in the Active Site of γ-Secretase. Int J Mol Sci 2024; 25:2564. [PMID: 38473811 DOI: 10.3390/ijms25052564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Alzheimer's disease (AD) is the leading cause of dementia and is characterized by a presence of amyloid plaques, composed mostly of the amyloid-β (Aβ) peptides, in the brains of AD patients. The peptides are generated from the amyloid precursor protein (APP), which undergoes a sequence of cleavages, referred as trimming, performed by γ-secretase. Here, we investigated conformational changes in a series of β-amyloid substrates (from less and more amyloidogenic pathways) in the active site of presenilin-1, the catalytic subunit of γ-secretase. The substrates are trimmed every three residues, finally leading to Aβ40 and Aβ42, which are the major components of amyloid plaques. To study conformational changes, we employed all-atom molecular dynamics simulations, while for unfolding, we used steered molecular dynamics simulations in an implicit membrane-water environment to accelerate changes. We have found substantial differences in the flexibility of extended C-terminal parts between more and less amyloidogenic pathway substrates. We also propose that the positively charged residues of presenilin-1 may facilitate the stretching and unfolding of substrates. The calculated forces and work/energy of pulling were exceptionally high for Aβ40, indicating why trimming of this substrate is so infrequent.
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Affiliation(s)
- Jakub Jakowiecki
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - Urszula Orzeł
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - Przemysław Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - Krzysztof Młynarczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
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15
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Teng Z. Novel Development and Prospects in Pathogenesis, Diagnosis, and Therapy of Alzheimer's Disease. J Alzheimers Dis Rep 2024; 8:345-354. [PMID: 38405339 PMCID: PMC10894614 DOI: 10.3233/adr-230130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/29/2023] [Indexed: 02/27/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease with cognitive decline and behavioral dysfunction. AD will become a global public health concern due to its increasing prevalence brought on by the severity of global aging. It is critical to understand the pathogenic mechanisms of AD and investigate or pursue a viable therapy strategy in clinic. Amyloid-β (Aβ) accumulation and abnormally hyperphosphorylated tau protein are the main regulating variables in the pathological phase of AD. And neuroinflammation brought on by activated microglia was found to be one risk factor contributing to changes in Aβ and tau pathology. It is important to investigate the unique biomarkers of early diagnosis and advanced stage, which may help to elucidate the specific pathological process of AD and provide potential novel therapeutic targets or preventative measures.
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Affiliation(s)
- Zenghui Teng
- Medical Faculty, Institute of Neuro- and Sensory Physiology, Heinrich-Heine-University Düsseldorf, Germany
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16
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Feng M, Santhanam RK, Xing H, Zhou M, Jia H. Inhibition of γ-secretase/Notch pathway as a potential therapy for reversing cancer drug resistance. Biochem Pharmacol 2024; 220:115991. [PMID: 38135129 DOI: 10.1016/j.bcp.2023.115991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
The mechanism of tumor drug resistance is complex and may involve stem cell maintenance, epithelial-mesenchymal transition, the activation of survival signaling pathways, transporter protein expression, and tumor microenvironment remodeling, all of which are linked to γ-secretase/Notch signaling. Increasing evidence has shown that the activation of the γ-secretase/Notch pathway is a key driver of cancer progression and drug resistance development and that γ-secretase inhibitors (GSIs) may be the most promising agents for reversing chemotherapy resistance of tumors by targeting the γ-secretase/Notch pathway. Here, we systematically summarize the roles in supporting γ-secretase/Notch activation-associated transformation of cancer cells into cancer stem cells, promotion of the EMT process, PI3K/Akt, MEK/ERK and NF-κB activation, enhancement of ABC transporter protein expression, and TME alteration in mediating tumor drug resistance. Subsequently, we analyze the mechanism of GSIs targeting the γ-secretase/Notch pathway to reverse tumor drug resistance and propose the outstanding advantages of GSIs in treating breast cancer drug resistance over other tumors. Finally, we emphasize that the development of GSIs for reversing tumor drug resistance is promising.
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Affiliation(s)
- Mei Feng
- Science and Experimental Research Center of Shenyang Medical College, Shenyang 110034, China; Shenyang Key Laboratory of Vascular Biology, Shenyang 110034, China
| | - Ramesh Kumar Santhanam
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Huan Xing
- Science and Experimental Research Center of Shenyang Medical College, Shenyang 110034, China
| | - Mingsheng Zhou
- Science and Experimental Research Center of Shenyang Medical College, Shenyang 110034, China; Shenyang Key Laboratory of Vascular Biology, Shenyang 110034, China.
| | - Hui Jia
- School of Traditional Chinese Medicine, Shenyang Medical College, Shenyang 110034, China.
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17
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Cai J, Qiao Y, Chen L, Lu Y, Zheng D. Regulation of the Notch signaling pathway by natural products for cancer therapy. J Nutr Biochem 2024; 123:109483. [PMID: 37848105 DOI: 10.1016/j.jnutbio.2023.109483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023]
Abstract
The Notch signaling pathway is an evolutionarily conserved pathway that modulates normal biological processes involved in cellular differentiation, apoptosis, and stem cell self-renewal in a context-dependent fashion. Attributed to its pleiotropic physiological roles, both overexpression and silencing of the pathway are associated with the emergence, progression, and poorer prognosis in various types of cancer. To decrease disease incidence and promote survival, targeting Notch may have chemopreventive and anti-cancer effects. Natural products with profound historical origins have distinguished themselves from other therapies due to their easy access, high biological compatibility, low toxicity, and reliable effects at specific physiological sites in vivo. This review describes the Notch signaling pathway, particularly its normal activation process, and some main illnesses related to Notch signaling pathway dysregulation. Emphasis is placed on the effects and mechanisms of natural products targeting the Notch signaling pathway in diverse cancer types, including curcumin, ellagic acid (EA), resveratrol, genistein, epigallocatechin-3-gallate (EGCG), quercetin, and xanthohumol and so on. Existing evidence indicates that natural products are feasible solution to fight against cancer by targeting Notch signaling, either alone or in combination with current therapeutic agents.
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Affiliation(s)
- Jiayi Cai
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Yajie Qiao
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Lingbin Chen
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Youguang Lu
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350004, China; Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou 350001, China
| | - Dali Zheng
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350004, China.
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18
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Chen SY, Koch M, Chávez-Gutiérrez L, Zacharias M. How Modulator Binding at the Amyloidβ-γ-Secretase Interface Enhances Substrate Binding and Attenuates Membrane Distortion. J Med Chem 2023; 66:16772-16782. [PMID: 38059872 DOI: 10.1021/acs.jmedchem.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Inhibition of γ-secretase, an intramembrane protease, to reduce secretion of Amyloid-β (Aβ) peptides has been considered for treating Alzheimer's disease. However, γ-secretase inhibitors suffer from severe side effects. As an alternative, γ-secretase modulators (GSM) reduce the generation of toxic peptides by enhancing the cleavage processivity without diminishing the enzyme activity. Starting from a known γ-secretase structure without substrate but in complex with an E2012 GSM, we generated a structural model that included a bound Aβ43 peptide and studied interactions among enzyme, substrate, GSM, and lipids. Our result suggests that E2012 binding at the enzyme-substrate-membrane interface attenuates the membrane distortion by shielding the substrate-membrane interaction. The model predicts that the E2012 modulation is charge-dependent and explains the preserved hydrogen acceptor and the aromatic ring observed in many imidazole-based GSM. Predicted effects of γ-secretase mutations on E2012 modulation were confirmed experimentally. We anticipate that the study will facilitate the future development of effective GSMs.
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Affiliation(s)
- Shu-Yu Chen
- Center for Functional Protein Assemblies, Garching 85748, Germany
| | - Matthias Koch
- VIB/KU Leuven, VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
| | | | - Martin Zacharias
- Center for Functional Protein Assemblies, Garching 85748, Germany
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19
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Li Z, Yin B, Zhang S, Lan Z, Zhang L. Targeting protein kinases for the treatment of Alzheimer's disease: Recent progress and future perspectives. Eur J Med Chem 2023; 261:115817. [PMID: 37722288 DOI: 10.1016/j.ejmech.2023.115817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Alzheimer's disease (AD) is a serious neurodegenerative disease characterized by memory impairment, mental retardation, impaired motor balance, loss of self-care and even death. Among the complex and diverse pathological changes in AD, protein kinases are deeply involved in abnormal phosphorylation of Tau proteins to form intracellular neuronal fiber tangles, neuronal loss, extracellular β-amyloid (Aβ) deposits to form amyloid plaques, and synaptic disturbances. As a disease of the elderly, the growing geriatric population is directly driving the market demand for AD therapeutics, and protein kinases are potential targets for the future fight against AD. This perspective provides an in-depth look at the role of the major protein kinases (GSK-3β, CDK5, p38 MAPK, ERK1/2, and JNK3) in the pathogenesis of AD. At the same time, the development of different protein kinase inhibitors and the current state of clinical advancement are also outlined.
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Affiliation(s)
- Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Bo Yin
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Shuangqian Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhigang Lan
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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20
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Pathak Y, Camps I, Mishra A, Tripathi V. Targeting notch signaling pathway in breast cancer stem cells through drug repurposing approach. Mol Divers 2023; 27:2431-2440. [PMID: 36376717 DOI: 10.1007/s11030-022-10561-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Breast cancer is recognized globally as one of the leading causes of malignant morbidity. It is a heterogeneous disease that accounts for 30 percent of all women diagnosed with cancer. To bring an anti-cancer drug from the bench to the bedside is an expensive and time-consuming process. The drug repurposing approach targets new enemies (new diseases) with old weapons (known drugs). The present study identified an FDA-approved drug targeting the γ-secretase complex involved in the Notch signaling pathway in breast cancer stem cells (BCSCs). A literature survey and in-silico study identified Venetoclax as a γ-secretase inhibitor (GSI) from 1615 FDA-approved drug compounds. In-silico docking potential of Venetoclax was better than the standard γ-secretase inhibitor RO4929097. Also, the molecular dynamics simulations of 200 ns confirmed the stability of the Venetoclax-γ-secretase complex. These findings suggest that the use of Venetoclax represents a potential γ-secretase inhibitor in breast cancer stem cells. Eventually, the in vitro and clinical evaluation will be needed to confirm the potential chemopreventive and treatment effects of Venetoclax against breast cancer and breast cancer stem cells. Venetoclax appeared as the most promising drug of the 1615 FDA-approved drugs. Our in-silico findings suggest that Venetoclax may act as a γ-secretase inhibitor against the Notch signaling pathway in breast cancer stem cells.
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Affiliation(s)
- Yamini Pathak
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Ihosvany Camps
- Laboratório de Modelagem Computacional - LaModel, Instituto de Ciências Exatas - ICEx, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Minas Gerais, Brazil
- High Performance & Quantum Computing Labs, Waterloo, Canada
| | - Amaresh Mishra
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India
| | - Vishwas Tripathi
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201310, India.
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21
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Koch M, Enzlein T, Chen S, Petit D, Lismont S, Zacharias M, Hopf C, Chávez‐Gutiérrez L. APP substrate ectodomain defines amyloid-β peptide length by restraining γ-secretase processivity and facilitating product release. EMBO J 2023; 42:e114372. [PMID: 37853914 PMCID: PMC10690472 DOI: 10.15252/embj.2023114372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
Sequential proteolysis of the amyloid precursor protein (APP) by γ-secretases generates amyloid-β (Aβ) peptides and defines the proportion of short-to-long Aβ peptides, which is tightly connected to Alzheimer's disease (AD) pathogenesis. Here, we study the mechanism that controls substrate processing by γ-secretases and Aβ peptide length. We found that polar interactions established by the APPC99 ectodomain (ECD), involving but not limited to its juxtamembrane region, restrain both the extent and degree of γ-secretases processive cleavage by destabilizing enzyme-substrate interactions. We show that increasing hydrophobicity, via mutation or ligand binding, at APPC99 -ECD attenuates substrate-driven product release and rescues the effects of Alzheimer's disease-associated pathogenic γ-secretase and APP variants on Aβ length. In addition, our study reveals that APPC99 -ECD facilitates the paradoxical production of longer Aβs caused by some γ-secretase inhibitors, which act as high-affinity competitors of the substrate. These findings assign a pivotal role to the substrate ECD in the sequential proteolysis by γ-secretases and suggest it as a sweet spot for the potential design of APP-targeting compounds selectively promoting its processing by these enzymes.
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Affiliation(s)
- Matthias Koch
- VIB/KU Leuven, VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
| | - Thomas Enzlein
- VIB/KU Leuven, VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)Mannheim University of Applied SciencesMannheimGermany
| | - Shu‐Yu Chen
- Physics Department and Center of Functional Protein AssembliesTechnical University of MunichGarchingGermany
| | - Dieter Petit
- VIB/KU Leuven, VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
| | - Sam Lismont
- VIB/KU Leuven, VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
| | - Martin Zacharias
- Physics Department and Center of Functional Protein AssembliesTechnical University of MunichGarchingGermany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)Mannheim University of Applied SciencesMannheimGermany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
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22
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Suárez-González E, Sandoval-Ramírez J, Flores-Hernández J, Carrasco-Carballo A. Ginkgo biloba: Antioxidant Activity and In Silico Central Nervous System Potential. Curr Issues Mol Biol 2023; 45:9674-9691. [PMID: 38132450 PMCID: PMC10742658 DOI: 10.3390/cimb45120604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 12/23/2023] Open
Abstract
Ginkgo biloba (GB) extracts have been used in clinical studies as an alternative therapy for Alzheimer's disease (AD), but the exact bioaction mechanism has not yet been elucidated. In this work, an in silico study on GB metabolites was carried out using SwissTargetPrediction to determine the proteins associated with AD. The resulting proteins, AChE, MAO-A, MAO-B, β-secretase and γ-secretase, were studied by molecular docking, resulting in the finding that kaempferol, quercetin, and luteolin have multitarget potential against AD. These compounds also exhibit antioxidant activity towards reactive oxygen species (ROS), so antioxidant tests were performed on the extracts using the DPPH and ABTS techniques. The ethanol and ethyl acetate GB extracts showed an important inhibition percentage, higher than 80%, at a dose of 0.01 mg/mL. The effect of GB extracts on AD resulted in multitarget action through two pathways: firstly, inhibiting enzymes responsible for degrading neurotransmitters and forming amyloid plaques; secondly, decreasing ROS in the central nervous system (CNS), reducing its deterioration, and promoting the formation of amyloid plaques. The results of this work demonstrate the great potential of GB as a medicinal plant.
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Affiliation(s)
- Eduardo Suárez-González
- Laboratorio de Elucidación y Síntesis en Química Orgánica, ICUAP-BUAP, Puebla 72570, Mexico;
- Laboratorio de Neuromodulación, Instituto de Fisiología, BUAP, Puebla 72570, Mexico
| | - Jesús Sandoval-Ramírez
- Laboratorio de Síntesis y Modificación de Productos Naturales, FCQ-BUAP, Puebla 72570, Mexico;
| | | | - Alan Carrasco-Carballo
- Laboratorio de Elucidación y Síntesis en Química Orgánica, ICUAP-BUAP, Puebla 72570, Mexico;
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23
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Medina E, Perez DH, Antfolk D, Luca VC. New tricks for an old pathway: emerging Notch-based biotechnologies and therapeutics. Trends Pharmacol Sci 2023; 44:934-948. [PMID: 37891017 PMCID: PMC10841456 DOI: 10.1016/j.tips.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023]
Abstract
The Notch pathway regulates a diverse array of cell fate decisions, making it an enticing target in cancer therapy and regenerative medicine. During the early stages of Notch drug development, off-target toxicity precluded the approval of Notch inhibitors for the treatment of cancer. However, recent advances in our understanding of Notch structure and signaling have led to the development of several innovative Notch-based biotechnologies. In addition to new classes of inhibitors, pharmacological Notch activators have been shown to enhance osteogenesis and various aspects of T cell function. Furthermore, the mechanosensitive negative regulatory region (NRR) of the Notch receptor has been converted into synthetic Notch (synNotch) receptors with fully customizable signaling circuits. We review emergent Notch-based compounds, biologics, and cell therapies while highlighting the challenges and opportunities they face on the path to clinical development.
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Affiliation(s)
- Elliot Medina
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL, USA
| | - David H Perez
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA
| | - Daniel Antfolk
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Vincent C Luca
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA.
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24
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Höppner S, Schröder B, Fluhrer R. Structure and function of SPP/SPPL proteases: insights from biochemical evidence and predictive modeling. FEBS J 2023; 290:5456-5474. [PMID: 37786993 DOI: 10.1111/febs.16968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/13/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
More than 20 years ago, signal peptide peptidase (SPP) and its homologues, the signal peptide peptidase-like (SPPL) proteases have been identified based on their sequence similarity to presenilins, a related family of intramembrane aspartyl proteases. Other than those for the presenilins, no high-resolution structures for the SPP/SPPL proteases are available. Despite this limitation, over the years bioinformatical and biochemical data have accumulated, which altogether have provided a picture of the overall structure and topology of these proteases, their localization in the cell, the process of substrate recognition, their cleavage mechanism, and their function. Recently, the artificial intelligence-based structure prediction tool AlphaFold has added high-confidence models of the expected fold of SPP/SPPL proteases. In this review, we summarize known structural aspects of the SPP/SPPL family as well as their substrates. Of particular interest are the emerging substrate recognition and catalytic mechanisms that might lead to the prediction and identification of more potential substrates and deeper insight into physiological and pathophysiological roles of proteolysis.
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Affiliation(s)
- Sabine Höppner
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
| | - Bernd Schröder
- Institute for Physiological Chemistry, Technische Universität Dresden, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
- Center for Interdisciplinary Health Research, University of Augsburg, Germany
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25
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Zhang N, Nao J, Dong X. Neuroprotective Mechanisms of Salidroside in Alzheimer's Disease: A Systematic Review and Meta-analysis of Preclinical Studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17597-17614. [PMID: 37934032 DOI: 10.1021/acs.jafc.3c06672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease of the central nervous system that occurs in old age and pre-aging, characterized by progressive cognitive dysfunction and behavioral impairment. Salidroside (Sal) is a phenylpropanoid mainly isolated from Rhodiola species with various pharmacological effects. However, the exact anti-AD mechanism of Sal has not been clearly elucidated. This meta-analysis aims to investigate the possible mechanisms by which Sal exerts its anti-AD effects by evaluating behavioral indicators and biochemical characteristics. A total of 20 studies were included, and the results showed that the Sal treatment significantly improved behavior abnormalities in AD animal models. With regard to neurobiochemical indicators, Sal treatment could effectively increase the antioxidant enzyme superoxide dismutase, decrease the oxidative stress indicator malondialdehyde, and decrease the inflammatory indicators interleukin 1β, interleukin 6, and tumor necrosis factor α. Sal treatment was effective in reducing neuropathological indicators, such as amyloid-β levels and the number of apoptotic cells. When the relevant literature on the treatment of rodent AD models is combined with Sal, the therapeutic potential of Sal through multiple mechanisms was confirmed. However, further confirmation by higher quality studies, larger sample sizes, and more comprehensive outcome evaluations in clinical trials is needed in the future.
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Affiliation(s)
- Nan Zhang
- Department of Neurology, Seventh Clinical College of China Medical University, 24 Central Street, Xinfu District, Fushun, Liaoning 113000, People's Republic of China
| | - Jianfei Nao
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning 110000, People's Republic of China
| | - Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning 110000, People's Republic of China
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26
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Hou P, Zielonka M, Serneels L, Martinez-Muriana A, Fattorelli N, Wolfs L, Poovathingal S, T'Syen D, Balusu S, Theys T, Fiers M, Mancuso R, Howden AJM, De Strooper B. The γ-secretase substrate proteome and its role in cell signaling regulation. Mol Cell 2023; 83:4106-4122.e10. [PMID: 37977120 DOI: 10.1016/j.molcel.2023.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/22/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
γ-Secretases mediate the regulated intramembrane proteolysis (RIP) of more than 150 integral membrane proteins. We developed an unbiased γ-secretase substrate identification (G-SECSI) method to study to what extent these proteins are processed in parallel. We demonstrate here parallel processing of at least 85 membrane proteins in human microglia in steady-state cell culture conditions. Pharmacological inhibition of γ-secretase caused substantial changes of human microglial transcriptomes, including the expression of genes related to the disease-associated microglia (DAM) response described in Alzheimer disease (AD). While the overall effects of γ-secretase deficiency on transcriptomic cell states remained limited in control conditions, exposure of mouse microglia to AD-inducing amyloid plaques strongly blocked their capacity to mount this putatively protective DAM cell state. We conclude that γ-secretase serves as a critical signaling hub integrating the effects of multiple extracellular stimuli into the overall transcriptome of the cell.
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Affiliation(s)
- Pengfei Hou
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Magdalena Zielonka
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Lutgarde Serneels
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Anna Martinez-Muriana
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Nicola Fattorelli
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Leen Wolfs
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Suresh Poovathingal
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium; Single Cell & Microfluidics Expertise Unit, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium
| | - Dries T'Syen
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Sriram Balusu
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Tom Theys
- Department of Neurosciences, Research Group Experimental Neurosurgery and Neuroanatomy, KU Leuven, Leuven 3000, Belgium
| | - Mark Fiers
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium; Center for Human Genetics, KU Leuven, Leuven 3000, Belgium; Dementia Research Institute, Institute of Neurology, University College London, London WC1E 6BT, UK
| | - Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp 2610, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | - Andrew J M Howden
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Bart De Strooper
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium; Center for Human Genetics, KU Leuven, Leuven 3000, Belgium; Dementia Research Institute, Institute of Neurology, University College London, London WC1E 6BT, UK.
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27
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Li J, Wu X, Tan X, Wang S, Qu R, Wu X, Chen Z, Wang Z, Chen G. The efficacy and safety of anti-Aβ agents for delaying cognitive decline in Alzheimer's disease: a meta-analysis. Front Aging Neurosci 2023; 15:1257973. [PMID: 38020763 PMCID: PMC10661413 DOI: 10.3389/fnagi.2023.1257973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Background This meta-analysis evaluates the efficacy and safety of amyloid-β (Aβ) targeted therapies for delaying cognitive deterioration in Alzheimer's disease (AD). Methods PubMed, EMBASE, the Cochrane Library, and ClinicalTrials.gov were systematically searched to identify relevant studies published before January 18, 2023. Results We pooled 33,689 participants from 42 studies. The meta-analysis showed no difference between anti-Aβ drugs and placebo in the Alzheimer's Disease Assessment Scale-Cognitive Subscale (ADAS-Cog), and anti-Aβ drugs were associated with a high risk of adverse events [ADAS-Cog: MDs = -0.08 (-0.32 to 0.15), p = 0.4785; AEs: RR = 1.07 (1.02 to 1.11), p = 0.0014]. Monoclonal antibodies outperformed the placebo in delaying cognitive deterioration as measured by ADAS-Cog, Clinical Dementia Rating-Sum of Boxes (CDR-SB), Mini-Mental State Examination (MMSE) and Alzheimer's Disease Cooperative Study-Activities of Daily Living (ADCS-ADL), without increasing the risk of adverse events [ADAS-Cog: MDs = -0.55 (-0.89 to 0.21), p = 0.001; CDR-SB: MDs = -0.19 (-0.29 to -0.10), p < 0.0001; MMSE: MDs = 0.19 (0.00 to 0.39), p = 0.05; ADCS-ADL: MDs = 1.26 (0.84 to 1.68), p < 0.00001]. Intravenous immunoglobulin and γ-secretase modulators (GSM) increased cognitive decline in CDR-SB [MDs = 0.45 (0.17 to 0.74), p = 0.002], but had acceptable safety profiles in AD patients. γ-secretase inhibitors (GSI) increased cognitive decline in ADAS-Cog, and also in MMSE and ADCS-ADL. BACE-1 inhibitors aggravated cognitive deterioration in the outcome of the Neuropsychiatric Inventory (NPI). GSI and BACE-1 inhibitors caused safety concerns. No evidence indicates active Aβ immunotherapy, MPAC, or tramiprosate have effects on cognitive function and tramiprosate is associated with serious adverse events. Conclusion Current evidence does not show that anti-Aβ drugs have an effect on cognitive performance in AD patients. However, monoclonal antibodies can delay cognitive decline in AD. Development of other types of anti-Aβ drugs should be cautious. Systematic Review Registration PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023391596.
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Affiliation(s)
- Jiaxuan Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Tan
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu Province, China
| | - Shixin Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Ruisi Qu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xiaofeng Wu
- Department of Ultrasound, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Zhouqing Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
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28
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Essayan-Perez S, Südhof TC. Neuronal γ-secretase regulates lipid metabolism, linking cholesterol to synaptic dysfunction in Alzheimer's disease. Neuron 2023; 111:3176-3194.e7. [PMID: 37543038 PMCID: PMC10592349 DOI: 10.1016/j.neuron.2023.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
Presenilin mutations that alter γ-secretase activity cause familial Alzheimer's disease (AD), whereas ApoE4, an apolipoprotein for cholesterol transport, predisposes to sporadic AD. Both sporadic and familial AD feature synaptic dysfunction. Whether γ-secretase is involved in cholesterol metabolism and whether such involvement impacts synaptic function remains unknown. Here, we show that in human neurons, chronic pharmacological or genetic suppression of γ-secretase increases synapse numbers but decreases synaptic transmission by lowering the presynaptic release probability without altering dendritic or axonal arborizations. In search of a mechanism underlying these synaptic impairments, we discovered that chronic γ-secretase suppression robustly decreases cholesterol levels in neurons but not in glia, which in turn stimulates neuron-specific cholesterol-synthesis gene expression. Suppression of cholesterol levels by HMG-CoA reductase inhibitors (statins) impaired synaptic function similar to γ-secretase inhibition. Thus, γ-secretase enables synaptic function by maintaining cholesterol levels, whereas the chronic suppression of γ-secretase impairs synapses by lowering cholesterol levels.
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Affiliation(s)
- Sofia Essayan-Perez
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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29
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Nordvall G, Lundkvist J, Sandin J. Gamma-secretase modulators: a promising route for the treatment of Alzheimer's disease. Front Mol Neurosci 2023; 16:1279740. [PMID: 37908487 PMCID: PMC10613654 DOI: 10.3389/fnmol.2023.1279740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 11/02/2023] Open
Abstract
Recent clinical data with three therapeutic anti-Aβ antibodies have demonstrated that removal of Aβ-amyloid plaques in early Alzheimer's disease (AD) can attenuate disease progression. This ground-breaking progress in AD medicine has validated both the amyloid cascade hypothesis and Aβ-amyloid as therapeutic targets. These results also strongly support therapeutic approaches that aim to reduce the production of amyloidogenic Aβ to prevent the formation of Aβ-pathology. One such strategy, so-called gamma-secretase modulators (GSM), has been thoroughly explored in preclinical settings but has yet to be fully tested in clinical trials. Recent scientific progress has shed new light on the role of Aβ in Alzheimer's disease and suggests that GSMs exhibit specific pharmacological features that hold great promise for the prevention and treatment of Alzheimer's disease. In this short review, we discuss the data that support why it is important to continue to progress in this class of compounds.
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Affiliation(s)
- Gunnar Nordvall
- AlzeCure Pharma AB, Huddinge, Sweden
- Department of Neurobiology, Care Sciences, and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lundkvist
- AlzeCure Pharma AB, Huddinge, Sweden
- Department of Neurobiology, Care Sciences, and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
- Sinfonia Biotherapeutics AB, Huddinge, Sweden
| | - Johan Sandin
- AlzeCure Pharma AB, Huddinge, Sweden
- Department of Neurobiology, Care Sciences, and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
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30
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Singh AK, Prajapati KS, Kumar S. Hesperidin potentially interacts with the catalytic site of gamma-secretase and modifies notch sensitive genes and cancer stemness marker expression in colon cancer cells and colonosphere. J Biomol Struct Dyn 2023; 41:8432-8444. [PMID: 36239003 DOI: 10.1080/07391102.2022.2134213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 10/17/2022]
Abstract
Gamma secretase (GS) produces Notch Intracellular Domain (NICD) by trans-membrane cleavage of notch receptor. The NICD enters the nucleus and activates the notch signaling pathway (NSP) by activating notch-responsive gene transcription. Hyperactivation of NSP is related to cancer aggressiveness, therapy resistance, and poor therapy outcome, and decreased overall disease-free survival in patients. Till date, none of the GS inhibitors (GSI) has been clinically approved due to their toxicity in patients. Thus in the present study, we explored the GS catalytic site binding potential of hesperidin (natural flavone glycoside) and its effect on notch responsive gene expression in HCT-116 cells. Molecular docking, MM-GBSA binding energy calculations, and molecular dynamics (MD) simulation experiments were performed to study the GS catalytic site binding potential of hesperidin. The compound showed better GS catalytic site binding potential at the active site compared to experimentally validated GSI, N-N-(3, 5-Difluorophenacetyl)-L-alanyl-S-phenylglycine t-butyl ester (DAPT) in molecular docking and MM-GBSA experiments. MD simulation results showed that hesperidin forms stable and energetically favorable complex with gamma secretase in comparison to standard inhibitor (DAPT)-GS complex. Further, in vitro experiments showed that hesperidin inhibited cell growth and sphere formation potential in HCT-116 cells. Further, hesperidin treatment altered notch responsive genes (Hes1, Hey1, and E-cad) and cancer stemness/self-renewal markers expression at transcription levels. In conclusion, hesperidin produces toxicity in HCT-116 cells and decreases colonosphere formation by inhibiting transcription of notch signaling pathway target genes and stemness markers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
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31
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Zhang J, Liu L, Wei X, Zhao C, Li S, Li J, Le TD. Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers. PLoS Comput Biol 2023; 19:e1011308. [PMID: 37812646 PMCID: PMC10586676 DOI: 10.1371/journal.pcbi.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
Non-coding RNAs (ncRNAs) act as important modulators of gene expression and they have been confirmed to play critical roles in the physiology and development of malignant tumors. Understanding the synergism of multiple ncRNAs in competing endogenous RNA (ceRNA) regulation can provide important insights into the mechanisms of malignant tumors caused by ncRNA regulation. In this work, we present a framework, SCOM, for identifying ncRNA synergistic competition. We systematically construct the landscape of ncRNA synergistic competition across 31 malignant tumors, and reveal that malignant tumors tend to share hub ncRNAs rather than the ncRNA interactions involved in the synergistic competition. In addition, the synergistic competition ncRNAs (i.e. ncRNAs involved in the synergistic competition) are likely to be involved in drug resistance, contribute to distinguishing molecular subtypes of malignant tumors, and participate in immune regulation. Furthermore, SCOM can help to infer ncRNA synergistic competition across malignant tumors and uncover potential diagnostic and prognostic biomarkers of malignant tumors. Altogether, the SCOM framework (https://github.com/zhangjunpeng411/SCOM/) and the resulting web-based database SCOMdb (https://comblab.cn/SCOMdb/) serve as a useful resource for exploring ncRNA regulation and to accelerate the identification of carcinogenic biomarkers.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Sijing Li
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
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32
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Czerwonka A, Kałafut J, Nees M. Modulation of Notch Signaling by Small-Molecular Compounds and Its Potential in Anticancer Studies. Cancers (Basel) 2023; 15:4563. [PMID: 37760535 PMCID: PMC10526229 DOI: 10.3390/cancers15184563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Notch signaling is responsible for conveying messages between cells through direct contact, playing a pivotal role in tissue development and homeostasis. The modulation of Notch-related processes, such as cell growth, differentiation, viability, and cell fate, offer opportunities to better understand and prevent disease progression, including cancer. Currently, research efforts are mainly focused on attempts to inhibit Notch signaling in tumors with strong oncogenic, gain-of-function (GoF) or hyperactivation of Notch signaling. The goal is to reduce the growth and proliferation of cancer cells, interfere with neo-angiogenesis, increase chemosensitivity, potentially target cancer stem cells, tumor dormancy, and invasion, and induce apoptosis. Attempts to pharmacologically enhance or restore disturbed Notch signaling for anticancer therapies are less frequent. However, in some cancer types, such as squamous cell carcinomas, preferentially, loss-of-function (LoF) mutations have been confirmed, and restoring but not blocking Notch functions may be beneficial for therapy. The modulation of Notch signaling can be performed at several key levels related to NOTCH receptor expression, translation, posttranslational (proteolytic) processing, glycosylation, transport, and activation. This further includes blocking the interaction with Notch-related nuclear DNA transcription. Examples of small-molecular chemical compounds, that modulate individual elements of Notch signaling at the mentioned levels, have been described in the recent literature.
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Affiliation(s)
- Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland; (J.K.); (M.N.)
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33
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Efraimidis E, Krokidis MG, Exarchos TP, Lazar T, Vlamos P. In Silico Structural Analysis Exploring Conformational Folding of Protein Variants in Alzheimer's Disease. Int J Mol Sci 2023; 24:13543. [PMID: 37686347 PMCID: PMC10487466 DOI: 10.3390/ijms241713543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Accurate protein structure prediction using computational methods remains a challenge in molecular biology. Recent advances in AI-powered algorithms provide a transformative effect in solving this problem. Even though AlphaFold's performance has improved since its release, there are still limitations that apply to its efficacy. In this study, a selection of proteins related to the pathology of Alzheimer's disease was modeled, with Presenilin-1 (PSN1) and its mutated variants in the foreground. Their structural predictions were evaluated using the ColabFold implementation of AlphaFold, which utilizes MMseqs2 for the creation of multiple sequence alignments (MSAs). A higher number of recycles than the one used in the AlphaFold DB was selected, and no templates were used. In addition, prediction by RoseTTAFold was also applied to address how structures from the two deep learning frameworks match reality. The resulting conformations were compared with the corresponding experimental structures, providing potential insights into the predictive ability of this approach in this particular group of proteins. Furthermore, a comprehensive examination was performed on features such as predicted regions of disorder and the potential effect of mutations on PSN1. Our findings consist of highly accurate superpositions with little or no deviation from experimentally determined domain-level models.
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Affiliation(s)
- Evangelos Efraimidis
- Bioinformatics and Neuroinformatics MSc Program, Hellenic Open University, 26335 Patras, Greece;
| | - Marios G. Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece; (M.G.K.); (T.P.E.)
| | - Themis P. Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece; (M.G.K.); (T.P.E.)
| | - Tamas Lazar
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B1050 Brussels, Belgium;
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, B1050 Brussels, Belgium
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece; (M.G.K.); (T.P.E.)
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Trasviña-Arenas CH, Ayala Medina LA, Vique-Sánchez JL. γ-Secretase Inhibitors Selected by Molecular Docking, to Develop a New Drug Against Alzheimer's Disease. Rep Biochem Mol Biol 2023; 12:340-349. [PMID: 38317814 PMCID: PMC10838598 DOI: 10.61186/rbmb.12.2.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/15/2023] [Indexed: 02/07/2024]
Abstract
Background Alzheimer´s disease (AD) is one of the most common forms of dementia, is characterized by memory loss and cognitive impairment that affects more than 30 million people worldwide. The pathogenesis of Alzheimer's disease is primary driven by brain accumulation of the amyloid β peptide generated from the amyloid-β precursor protein (APP) via cleavages by β- and γ-secretase. In this study, we propose an approach by molecular docking to select compounds as γ-secretase inhibitors for decreasing the APP generation. Methods We selected potential γ-secretase inhibitors by molecular docking in the potential site between Asp257, Lue268, Asp385, Ile387, Phe388, and Leu432 amino acids in presenilin-1 (PS-1), using a chemical library of over 500,000 compounds. Results Eight compounds (AZ1 - AZ8) were selected by molecular docking to develop γ-secretase inhibitors for decreasing the APP generation. Conclusions AZ1 - AZ8 compounds could be interacting in the potential site between Asp257, Lue268, Asp385, Ile387, Phe388, and Leu432 amino acids in PS-1. These compounds could specifically interact in the binding pocket in PS-1 to prevent/decrease the APP generation, to develop a new drug against Alzheimer's disease.
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Affiliation(s)
- Carlos Humberto Trasviña-Arenas
- Research Center on Aging, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), Calzada de los Tenorios No. 235, 14330, Mexico City, Mexico.
| | | | - José Luis Vique-Sánchez
- School of Medicine Campus Mexicali, Autonomous University of Baja California, Mexicali, 21000, BC, México.
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Chi M, Jie Y, Li Y, Wang D, Li M, Li D, E M, Li Y, Liu N, Gu A, Rong G. Novel structured ADAM17 small-molecule inhibitor represses ADAM17/Notch pathway activation and the NSCLC cells' resistance to anti-tumour drugs. Front Pharmacol 2023; 14:1189245. [PMID: 37456760 PMCID: PMC10338884 DOI: 10.3389/fphar.2023.1189245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Background and aims: The outcomes of current treatment for non-small cell lung cancer (NSCLC) are unsatisfactory and development of new and more efficacious therapeutic strategies are required. The Notch pathway, which is necessary for cell survival to avert apoptosis, induces the resistance of cancer cells to antitumour drugs. Notch pathway activation is controlled by the cleavage of Notch proteins/receptors mediated by A disintegrin and metalloproteinase 17 (ADAM17); therefore, ADAM17 is a reliable intervention target for anti-tumour therapy to overcome the drug resistance of cancer cells. This work aims to develop and elucidate the activation of Compound 2b, a novel-structured small-molecule inhibitor of ADAM17, which was designed and developed and its therapeutic efficacy in NSCLC was assessed via multi-assays. Methods and results: A lead compound for a potential inhibitor of ADAM17 was explored via pharmacophore modelling, molecular docking, and biochemical screening. It was augmented by substituting two important chemical groups [R1 and R2 of the quinoxaline-2,3-diamine (its chemical skeleton)]; subsequently, serial homologs of the lead compound were used to obtain anoptimized compound (2b) with high inhibitory activity compared with leading compound against ADAM17 to inhibit the cleavage of Notch proteins and the accumulation of the Notch intracellular domain in the nuclei of NSCLC cells. The inhibitory activity of compound 2b was demonstrated by quantitative polymerase chain reaction and Western blotting. The specificity of compound 2b on ADAM17 was confirmed via point-mutation. Compound 2b enhanced the activation of antitumor drugs on NSCLC cells, in cell lines and nude mice models, by targeting the ADAM17/Notch pathway. Conclusion: Compound 2b may be a promising strategy for NSCLC treatment.
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Affiliation(s)
- Meng Chi
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yamin Jie
- Department of Radiation Oncology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Ying Li
- Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Duo Wang
- Department of Neurology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Man Li
- Department of Endoscopy, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Dan Li
- Department of Radiation Oncology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Mingyan E
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Heilongjiang, China
| | - Yongwu Li
- Department of Nuclear Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Na Liu
- Department of Nuclear Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Anxin Gu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Heilongjiang, China
| | - Guanghua Rong
- Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
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Yang T, Qu X, Zhao J, Wang X, Wang Q, Dai J, Zhu C, Li J, Jiang L. Macrophage PTEN controls STING-induced inflammation and necroptosis through NICD/NRF2 signaling in APAP-induced liver injury. Cell Commun Signal 2023; 21:160. [PMID: 37370115 DOI: 10.1186/s12964-023-01175-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) signaling has been known to play a critical role in maintaining cellular and tissue homeostasis, which also has an essential role in the inflammatory response. However, it remains unidentified whether and how the macrophage PTEN may govern the innate immune signaling stimulator of interferon genes (STING) mediated inflammation and hepatocyte necroptosis in APAP-induced liver injury (AILI). METHODS Myeloid-specific PTEN knockout (PTENM-KO) and floxed PTEN (PTENFL/FL) mice were treated with APAP (400 mg/kg) or PBS. In a parallel in vitro study, bone marrow-derived macrophages (BMMs) were isolated from these conditional knockout mice and transfected with CRISPR/Cas9-mediated Notch1 knockout (KO) or CRISPR/Cas9-mediated STING activation vector followed by LPS (100 ng/ml) stimulation. RESULTS Here, we report that myeloid-specific PTEN knockout (PTENM-KO) mice were resistant to oxidative stress-induced hepatocellular injury with reduced macrophage/neutrophil accumulation and proinflammatory mediators in AILI. PTENM-KO increased the interaction of nuclear Notch intracellular domain (NICD) and nuclear factor (erythroid-derived 2)-like 2 (NRF2) in the macrophage nucleus, reducing reactive oxygen species (ROS) generation. Mechanistically, it is worth noting that macrophage NICD and NRF2 co-localize within the nucleus under inflammatory conditions. Additionally, Notch1 promotes the interaction of immunoglobulin kappa J region (RBPjκ) with NRF2. Disruption of the Notch1 signal in PTEN deletion macrophages, reduced RBPjκ and NRF2 binding, and activated STING signaling. Moreover, PTENM-KO macrophages with STING activated led to ROS generation and TNF-α release, resulting in hepatocyte necroptosis upon co-culture with primary hepatocytes. CONCLUSIONS Our findings demonstrate that the macrophage PTEN-NICD/NRF2-STING axis is critical to regulating oxidative stress-induced liver inflammation and necroptosis in AILI and implies the therapeutic potential for managing sterile liver inflammation. Video Abstract.
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Affiliation(s)
- Tao Yang
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Jiangsu University, The Zhenjiang Clinical Medical College of Nanjing Medical University, Zhenjiang, China
| | - Xiaoye Qu
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiaying Zhao
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Xiao Wang
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Qian Wang
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Jingjing Dai
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Chuanlong Zhu
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China.
| | - Longfeng Jiang
- Department of Infectious Diseases, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China.
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Chen SY, Feilen LP, Chávez-Gutiérrez L, Steiner H, Zacharias M. Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site. Commun Biol 2023; 6:670. [PMID: 37355752 PMCID: PMC10290658 DOI: 10.1038/s42003-023-05039-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
γ-Secretase is an aspartyl intramembrane protease that cleaves the amyloid precursor protein (APP) involved in Alzheimer's disease pathology and other transmembrane proteins. Substrate-bound structures reveal a stable hybrid β-sheet immediately following the substrate scissile bond consisting of β1 and β2 from the enzyme and β3 from the substrate. Molecular dynamics simulations and enhanced sampling simulations demonstrate that the hybrid β-sheet stability is strongly correlated with the formation of a stable cleavage-compatible active geometry and it also controls water access to the active site. The hybrid β-sheet is only stable for substrates with 3 or more C-terminal residues beyond the scissile bond. The simulation model allowed us to predict the effect of Pro and Phe mutations that weaken the formation of the hybrid β-sheet which were confirmed by experimental testing. Our study provides a direct explanation why γ-secretase preferentially cleaves APP in steps of 3 residues and how the hybrid β-sheet facilitates γ-secretase proteolysis.
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Affiliation(s)
- Shu-Yu Chen
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Lukas P Feilen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany.
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Hou X, Zhang X, Zou H, Guan M, Fu C, Wang W, Zhang ZR, Geng Y, Chen Y. Differential and substrate-specific inhibition of γ-secretase by the C-terminal region of ApoE2, ApoE3, and ApoE4. Neuron 2023; 111:1898-1913.e5. [PMID: 37040764 DOI: 10.1016/j.neuron.2023.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/16/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
Aberrant low γ-secretase activity is associated with most of the presenilin mutations that underlie familial Alzheimer's disease (fAD). However, the role of γ-secretase in the more prevalent sporadic AD (sAD) remains unaddressed. Here, we report that human apolipoprotein E (ApoE), the most important genetic risk factor of sAD, interacts with γ-secretase and inhibits it with substrate specificity in cell-autonomous manners through its conserved C-terminal region (CT). This ApoE CT-mediated inhibitory activity is differentially compromised in different ApoE isoforms, resulting in an ApoE2 > ApoE3 > ApoE4 potency rank order inversely correlating to their associated AD risk. Interestingly, in an AD mouse model, neuronal ApoE CT migrates to amyloid plaques in the subiculum from other regions and alleviates the plaque burden. Together, our data reveal a hidden role of ApoE as a γ-secretase inhibitor with substrate specificity and suggest that this precision γ-inhibition by ApoE may protect against the risk of sAD.
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Affiliation(s)
- Xianglong Hou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuexin Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingfeng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoying Fu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Wenyuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Yang Geng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China.
| | - Yelin Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China.
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Niu Y, Lin P. Advances of computer-aided drug design (CADD) in the development of anti-Azheimer's-disease drugs. Drug Discov Today 2023:103665. [PMID: 37302540 DOI: 10.1016/j.drudis.2023.103665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Alzheimer's disease (AD) is a degenerative disease of the nervous system that progressively destroys memory and thinking skills. Currently there is no treatment to prevent or cure AD; targeting the direct cause of neuronal degeneration would constitute a rational strategy and hopefully offer better options for the treatment of AD. This paper first summarizes the physiological and pathological pathogenesis of AD and then discusses the representative drug candidates for targeted therapy of AD and their binding mode with their targets. Finally, the applications of computer-aided drug design in discovering anti-AD drugs are reviewed. Teaser.
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Affiliation(s)
- Yuzhen Niu
- Weifang University of Science and Technology, Weifang, 262700, China
| | - Ping Lin
- Weifang University of Science and Technology, Weifang, 262700, China; Institute of modern physics, Chinese Academy of Science, Lanzhou 730000, China.
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40
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Epremyan KK, Mamaev DV, Zvyagilskaya RA. Alzheimer's Disease: Significant Benefit from the Yeast-Based Models. Int J Mol Sci 2023; 24:9791. [PMID: 37372938 DOI: 10.3390/ijms24129791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Alzheimer's disease (AD) is an age-related, multifaceted neurological disorder associated with accumulation of aggregated proteins (amyloid Aβ and hyperphosphorylated tau), loss of synapses and neurons, and alterations in microglia. AD was recognized by the World Health Organization as a global public health priority. The pursuit of a better understanding of AD forced researchers to pay attention to well-defined single-celled yeasts. Yeasts, despite obvious limitations in application to neuroscience, show high preservation of basic biological processes with all eukaryotic organisms and offer great advantages over other disease models due to the simplicity, high growth rates on low-cost substrates, relatively simple genetic manipulations, the large knowledge base and data collections, and availability of an unprecedented amount of genomic and proteomic toolboxes and high-throughput screening techniques, inaccessible to higher organisms. Research reviewed above clearly indicates that yeast models, together with other, more simple eukaryotic models including animal models, C. elegans and Drosophila, significantly contributed to understanding Aβ and tau biology. These models allowed high throughput screening of factors and drugs that interfere with Aβ oligomerization, aggregation and toxicity, and tau hyperphosphorylation. In the future, yeast models will remain relevant, with a focus on creating novel high throughput systems to facilitate the identification of the earliest AD biomarkers among different cellular networks in order to achieve the main goal-to develop new promising therapeutic strategies to treat or prevent the disease.
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Affiliation(s)
- Khoren K Epremyan
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Dmitry V Mamaev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Renata A Zvyagilskaya
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
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Contreras W, Bazan JF, Mentrup T. The transmembrane domain of Frey1 harbors a transplantable inhibitory motif for intramembrane proteases. Cell Mol Life Sci 2023; 80:170. [PMID: 37261541 DOI: 10.1007/s00018-023-04823-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Although aspartic intramembrane-cleaving proteases (I-CLIPs) are crucial switches of multiple signaling pathways and involved in several devastating diseases, little is known about their physiological regulation. We have recently identified Frey regulator of sperm-oocyte fusion 1 (Frey1) as an inhibitory protein of Signal Peptide Peptidase-like 2c (SPPL2c), a member of this protease family. Employing structure modeling along with cell-based inhibition and interaction studies, we identify a short motif within the Frey1 transmembrane domain essential for inhibition of SPPL2c. Intriguingly, this motif can be transplanted to the SPPL2c substrate PLN, thereby transforming it into an inhibitor of this enzyme. It can be adopted for the generation of Notch1-based γ-Secretase inhibitors demonstrating its versatile use among aspartic I-CLIPs. In summary, we describe a mechanism of aspartic I-CLIP inhibition which allows the targeted generation of specific inhibitors of these enzymes and might enable the identification of endogenous negative regulators of these enzymes.
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Affiliation(s)
- Whendy Contreras
- Institute of Physiological Chemistry, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Torben Mentrup
- Institute of Physiological Chemistry, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany.
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Serneels L, Narlawar R, Benito LP, Municoy M, Guallar V, T'Syen D, Dewilde M, Bischoff F, Fraiponts E, Tresadern G, Roevens PWM, Gijsen HJM, De Strooper B. Selective inhibitors of the PSEN1-gamma-secretase complex. J Biol Chem 2023:104794. [PMID: 37164155 DOI: 10.1016/j.jbc.2023.104794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Clinical development of γ-secretases, a family of intramembrane cleaving proteases, as therapeutic targets for a variety of disorders including cancer and Alzheimer's disease, was aborted because of serious mechanism based side effects in phase III trials of unselective inhibitors. Selective inhibition of specific γ-secretase complexes, containing either PSEN1 or PSEN2 as catalytic subunit and APH1A or APH1B as supporting subunits, do provide a feasible therapeutic window in preclinical models of these disorders. We explore here the pharmacophoric features required for PSEN1 versus PSEN2 selective inhibition. We synthesized a series of brain penetrant 2-azabicyclo[2,2,2]octane sulfonamides and identified a compound with low nanomolar potency and high selectivity (>250-fold) towards the PSEN1-APH1B sub-complex versus PSEN2 sub-complexes. We used modelling and site directed mutagenesis to identify critical amino acids along the entry part of this inhibitor into the catalytic site of PSEN1. Specific targeting one of the different γ-secretase complexes might provide safer drugs in the future.
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Affiliation(s)
- Lutgarde Serneels
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Leuven, Belgium
| | - Rajeshwar Narlawar
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Leuven, Belgium; Discovery Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Laura Perez Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Marti Municoy
- Nostrum Biodiscovery, Jordi Girona 29, Nexus II D128, 08034, Barcelona, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Dries T'Syen
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Leuven, Belgium
| | - Maarten Dewilde
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Leuven, Belgium
| | - François Bischoff
- Discovery Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Erwin Fraiponts
- Charles River Laboratories, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Peter W M Roevens
- Campus Strategy & Partnerships, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Harrie J M Gijsen
- Discovery Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Bart De Strooper
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Leuven, Belgium; Dementia Research Institute, University College London, London, UK.
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Zhu KF, Yuan C, Du YM, Sun KL, Zhang XK, Vogel H, Jia XD, Gao YZ, Zhang QF, Wang DP, Zhang HW. Applications and prospects of cryo-EM in drug discovery. Mil Med Res 2023; 10:10. [PMID: 36872349 PMCID: PMC9986049 DOI: 10.1186/s40779-023-00446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy (cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence (AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of medium-resolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.
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Affiliation(s)
- Kong-Fu Zhu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Chuang Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
| | - Yong-Ming Du
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Kai-Lei Sun
- Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Hong Kong, 999077 China
| | - Xiao-Kang Zhang
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055 Guangdong China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
| | - Xu-Dong Jia
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Yuan-Zhu Gao
- Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Qin-Fen Zhang
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Da-Ping Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518000 Guangdong China
| | - Hua-Wei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
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Wang M, Liu K, Ma Y, Han W. Probing the Mechanisms of Inhibitors Binding to Presenilin Homologue Using Molecular Dynamics Simulations. Molecules 2023; 28:molecules28052076. [PMID: 36903320 PMCID: PMC10004098 DOI: 10.3390/molecules28052076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
γ-secretase is an intramembrane proteolytic enzyme that is mainly involved in the cleavage and hydrolysis of the amyloid precursor (APP). The catalytic subunit presenilin 1 (PS1) is the catalytic subunit of γ-secretase. Since it was found that PS1 is responsible for Aβ-producing proteolytic activity, which is involved in Alzheimer's disease, it is believed that reducing the activity of PS1 and preventing or delaying the production of Aβ could help treat Alzheimer's disease. Consequently, in recent years, researchers have begun investigating the potential clinical efficacy of PS1 inhibitors. Currently, most PS1 inhibitors are only used as a tool to study the structure and function of PS1, and a few inhibitors with a high selectivity have been tested in clinics. Less-selective PS1 inhibitors were found to not only inhibit Aβ production but also inhibit Notch cleavage, which led to serious adverse events. The archaeal presenilin homologue (PSH) is a surrogate protease of presenilin that is useful for agent screening. In this study, we performed 200 ns molecular dynamics simulations (MD) of four systems to explore the conformational changes of different ligands binding to PSH. Our results indicated that the PSH-L679 system formed 3-10 helices in TM4, loosening up TM4 and allowing substrates to enter the catalytic pocket, thereby making it less inhibitory. Additionally, we found that III-31-C can bring TM4 and TM6 closer, resulting in the contraction of the PSH active pocket. Altogether, these results provide the basis for the potential design of newer PS1 inhibitors.
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Affiliation(s)
| | | | | | - Weiwei Han
- Correspondence: ; Tel.: +86-(431)-85155218
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Specific Mutations near the Amyloid Precursor Protein Cleavage Site Increase γ-Secretase Sensitivity and Modulate Amyloid-β Production. Int J Mol Sci 2023; 24:ijms24043970. [PMID: 36835396 PMCID: PMC9959964 DOI: 10.3390/ijms24043970] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Amyloid-β peptides (Aβs) are produced via cleavage of the transmembrane region of the amyloid precursor protein (APP) by γ-secretase and are responsible for Alzheimer's disease. Familial Alzheimer's disease (FAD) is associated with APP mutations that disrupt the cleavage reaction and increase the production of neurotoxic Aβs, i.e., Aβ42 and Aβ43. Study of the mutations that activate and restore the cleavage of FAD mutants is necessary to understand the mechanism of Aβ production. In this study, using a yeast reconstruction system, we revealed that one of the APP FAD mutations, T714I, severely reduced the cleavage, and identified secondary APP mutations that restored the cleavage of APP T714I. Some mutants were able to modulate Aβ production by changing the proportions of Aβ species when introduced into mammalian cells. Secondary mutations include proline and aspartate residues; proline mutations are thought to act through helical structural destabilization, while aspartate mutations are thought to promote interactions in the substrate binding pocket. Our results elucidate the APP cleavage mechanism and could facilitate drug discovery.
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Do HN, Devkota S, Bhattarai A, Wolfe MS, Miao Y. Effects of presenilin-1 familial Alzheimer's disease mutations on γ-secretase activation for cleavage of amyloid precursor protein. Commun Biol 2023; 6:174. [PMID: 36788318 PMCID: PMC9929099 DOI: 10.1038/s42003-023-04539-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer's disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the "Active" state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the "Active" state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.
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Affiliation(s)
- Hung N. Do
- grid.266515.30000 0001 2106 0692Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047 USA
| | - Sujan Devkota
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047 USA
| | - Apurba Bhattarai
- grid.266515.30000 0001 2106 0692Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047 USA
| | - Michael S. Wolfe
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047 USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA.
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Conti Filho CE, Loss LB, Marcolongo-Pereira C, Rossoni Junior JV, Barcelos RM, Chiarelli-Neto O, da Silva BS, Passamani Ambrosio R, Castro FCDAQ, Teixeira SF, Mezzomo NJ. Advances in Alzheimer's disease's pharmacological treatment. Front Pharmacol 2023; 14:1101452. [PMID: 36817126 PMCID: PMC9933512 DOI: 10.3389/fphar.2023.1101452] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia in the elderly. Several hypotheses emerged from AD pathophysiological mechanisms. However, no neuronal protective or regenerative drug is available nowadays. Researchers still work in drug development and are finding new molecular targets to treat AD. Therefore, this study aimed to summarize main advances in AD pharmacological therapy. Clinical trials registered in the National Library of Medicine database were selected and analyzed accordingly to molecular targets, therapeutic effects, and safety profile. The most common outcome was the lack of efficacy. Only seven trials concluded that tested drugs were safe and induced any kind of therapeutic improvement. Three works showed therapeutic effects followed by toxicity. In addition to aducanumab recent FDA approval, antibodies against amyloid-β (Aβ) showed no noteworthy results. 5-HT6 antagonists, tau inhibitors and nicotinic agonists' data were discouraging. However, anti-Aβ vaccine, BACE inhibitor and anti-neuroinflammation drugs showed promising results.
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The Binding of Different Substrate Molecules at the Docking Site and the Active Site of γ-Secretase Can Trigger Toxic Events in Sporadic and Familial Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24031835. [PMID: 36768156 PMCID: PMC9915333 DOI: 10.3390/ijms24031835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Pathogenic changes in γ-secretase activity, along with its response to different drugs, can be affected by changes in the saturation of γ-secretase with its substrate. We analyze the saturation of γ-secretase with its substrate using multiscale molecular dynamics studies. We found that an increase in the saturation of γ-secretase with its substrate could result in the parallel binding of different substrate molecules at the docking site and the active site. The C-terminal domain of the substrate bound at the docking site can interact with the most dynamic presenilin sites at the cytosolic end of the active site tunnel. Such interactions can inhibit the ongoing catalytic activity and increase the production of the longer, more hydrophobic, and more toxic Aβ proteins. Similar disruptions in dynamic presenilin structures can be observed with different drugs and disease-causing mutations. Both, C99-βCTF-APP substrate and its different Aβ products, can support the toxic aggregation. The aggregation depends on the substrate N-terminal domain. Thus, the C99-βCTF-APP substrate and β-secretase path can be more toxic than the C83-αCTF-APP substrate and α-secretase path. Nicastrin can control the toxic aggregation in the closed conformation. The binding of the C99-βCTF-APP substrate to γ-secretase can be controlled by substrate channeling between the nicastrin and β-secretase. We conclude that the presented two-substrate mechanism could explain the pathogenic changes in γ-secretase activity and Aβ metabolism in different sporadic and familial cases of Alzheimer's disease. Future drug-development efforts should target different cellular mechanisms that regulate the optimal balance between γ-secretase activity and amyloid metabolism.
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Singh AK, Choudhary P, Singh S, Kumar S. In silico identification of potential γ-secretase inhibitor of marine-algal origin: an anticancer intervention. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2159053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
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Fei Z, Pan B, Pei R, Chen Z, Du X, Cao H, Li C. Efficacy and safety of blood derivatives therapy in Alzheimer's disease: a systematic review and meta-analysis. Syst Rev 2022; 11:256. [PMID: 36443888 PMCID: PMC9706869 DOI: 10.1186/s13643-022-02115-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 11/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Blood derivatives therapy is a conventional clinical treatment, while the treatment for Alzheimer's disease (AD) is relatively novel. To provide clinical references for treating AD, this meta-analysis was performed to evaluate the efficacy and safety of blood derivatives therapy on the patients with AD. METHODS A systematic articles search was performed for eligible studies published up to December 6, 2021 through the PubMed, Embase, Cochrane library, ClinicalTrials.gov , Chinese National Knowledge Infrastructure database, and Wanfang databases. The included articles were screened by using rigorous inclusion and exclusion criteria. Study selection and data-extraction were performed by two authors independently. Random effects model or fixed effects model was used. Quality of studies and risk of bias were evaluated according to the Cochrane risk of bias tool. All analyses were conducted using Review Manager 5.4. The study was designed and conducted according to the Preferring Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline. RESULTS A total of three plasma administrations (two plasma exchange and one young plasma infusion) and five intravenous immunoglobulin (IVIG) randomized controlled trials with a sample size of 1148 subjects diagnosed with AD were included. There was no significant difference in cognitive improvement and all-cause discontinuation between intervention and placebo groups (RR 1.10, 95% CI 0.79-1.54). And Intervention groups showed not a statistically significant improvement in cognition of included subjects measured by the ADAS-Cog (MD 0.36, 95% CI 0.87-1.59), ADCS-ADL (MD -1.34, 95% CI - 5.01-2.32) and NPI (MD 2.20, 95% CI 0.07-4.32) score compared to the control groups. IVIG is well tolerated for AD patients even under the maximum dose (0.4 g/kg), but it is inferior to placebo in Neuropsychiatric Inventory scale in AD patients (MD 2.19, 95% CI 0.02-4.37). CONCLUSIONS The benefits of blood derivatives therapy for AD are limited. It is necessary to perform well-designed randomized controlled trials with large sample sizes focusing on the appropriate blood derivatives for the specific AD sub-populations in the future. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42021233886.
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Affiliation(s)
- Zhangcheng Fei
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China
| | - Bo Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China
| | - Renjun Pei
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China
| | - Zhongsheng Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China
| | - Xi Du
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China
| | - Haijun Cao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China.
| | - Changqing Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, China.
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