1
|
Xie S, Liang Y, Song Y, Li T, Jia J. Repurposing Anidulafungin for Alzheimer's Disease via Fragment-Based Drug Discovery. ACS Chem Neurosci 2024. [PMID: 39096284 DOI: 10.1021/acschemneuro.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024] Open
Abstract
The misfolding and aggregation of beta-amyloid (Aβ) peptides have been implicated as key pathogenic events in the early stages of Alzheimer's disease (AD). Inhibiting Aβ aggregation represents a potential disease-modifying therapeutic approach to AD treatment. Previous studies have identified various molecules that inhibit Aβ aggregation, some of which share common chemical substructures (fragments) that may be key to their inhibitory activity. Employing fragment-based drug discovery (FBDD) methods may facilitate the identification of these fragments, which can subsequently be used to screen new inhibitors and provide leads for further drug development. In this study, we used an in silico FBDD approach to identify 17 fragment clusters that are significantly enriched among Aβ aggregation inhibitors. These fragments were then used to screen anti-infective agents, a promising drug class for repurposing against amyloid aggregation. This screening process identified 16 anti-infective drugs, 5 of which were chosen for further investigation. Among the 5 candidates, anidulafungin, an antifungal compound, showed high efficacy in inhibiting Aβ aggregation in vitro. Kinetic analysis revealed that anidulafungin selectively blocks the primary nucleation step of Aβ aggregation, substantially delaying Aβ fibril formation. Cell viability assays demonstrated that anidulafungin can reduce the toxicity of oligomeric Aβ on BV2 microglia cells. Molecular docking simulations predicted that anidulafungin interacted with various Aβ species, including monomers, oligomers, and fibrils, potentially explaining its activity against Aβ aggregation and toxicity. This study suggests that anidulafungin is a potential drug to be repurposed for AD, and FBDD is a promising approach for discovering drugs to combat Aβ aggregation.
Collapse
Affiliation(s)
- Siqi Xie
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Yumei Liang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Yang Song
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Tingting Li
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
| | - Jianping Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, P. R. China
- Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing 100053, P. R. China
- Clinical Center for Neurodegenerative Disease and Memory Impairment, Capital Medical University, Beijing 100053, P. R. China
- Center of Alzheimer's Disease, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing 100053, P. R. China
- Key Laboratory of Neurodegenerative Diseases, Ministry of Education, Beijing 100053, P. R. China
| |
Collapse
|
2
|
Niu Z, Gui X, Feng S, Reif B. Aggregation Mechanisms and Molecular Structures of Amyloid-β in Alzheimer's Disease. Chemistry 2024:e202400277. [PMID: 38888453 DOI: 10.1002/chem.202400277] [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: 01/22/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/20/2024]
Abstract
Amyloid plaques are a major pathological hallmark involved in Alzheimer's disease and consist of deposits of the amyloid-β peptide (Aβ). The aggregation process of Aβ is highly complex, which leads to polymorphous aggregates with different structures. In addition to aberrant aggregation, Aβ oligomers can undergo liquid-liquid phase separation (LLPS) and form dynamic condensates. It has been hypothesized that these amyloid liquid droplets affect and modulate amyloid fibril formation. In this review, we briefly introduce the relationship between stress granules and amyloid protein aggregation that is associated with neurodegenerative diseases. Then we highlight the regulatory role of LLPS in Aβ aggregation and discuss the potential relationship between Aβ phase transition and aggregation. Furthermore, we summarize the current structures of Aβ oligomers and amyloid fibrils, which have been determined using nuclear magnetic resonance (NMR) and cryo-electron microscopy (cryo-EM). The structural variations of Aβ aggregates provide an explanation for the different levels of toxicity, shed light on the aggregation mechanism and may pave the way towards structure-based drug design for both clinical diagnosis and treatment.
Collapse
Affiliation(s)
- Zheng Niu
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Xinrui Gui
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shuang Feng
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Bernd Reif
- Bavarian NMR Center (B NMRZ), Department of Bioscience, TUM School of Natural Sciences, Technische Universität München (TUM), Garching, 85747, Germany
- Institute of Structural Biology (STB), Helmholtz-Zentrum, München (HMGU), Neuherberg, 85764, Germany
| |
Collapse
|
3
|
Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF. De novo design of peptides that bind specific conformers of α-synuclein. Chem Sci 2024; 15:8414-8421. [PMID: 38846390 PMCID: PMC11151861 DOI: 10.1039/d3sc06245g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/14/2024] [Indexed: 06/09/2024] Open
Abstract
Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloids in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of α-synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of α-synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by α-synuclein, tau, or Aβ40. This designed peptide also markedly slowed the formation of α-synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.
Collapse
Affiliation(s)
- Hailey M Wallace
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
| | - Sophia Tan
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Henry S Pan
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Rose Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Junyi Xu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
- Department of Neurology, University of California San Francisco CA 94143 USA
| | - Nicholas F Polizzi
- Dana Farber Cancer Institute, Harvard Medical School Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA 02215 USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
| |
Collapse
|
4
|
Neha, Anwar S, Pinky, Hassan MI, Parvez S. Ropinirole reverses the effects of neuroinflammation, and cellular demise by downregulating the MARK4-NFκβ signaling system in Alzheimer's disease. Int J Biol Macromol 2024; 271:132425. [PMID: 38759860 DOI: 10.1016/j.ijbiomac.2024.132425] [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: 12/21/2023] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Ropinirole (ROP) is a dopamine agonist that can cross the blood-brain barrier (BBB), which is crucial for drugs targeting neurological conditions like Alzheimer's disease (AD). The rationale for the current research is to investigate the potential of ROP as an inhibitor of Microtubule affinity regulating kinase 4 (MARK4)-NFκβ in neurodegenerative diseases, specifically AD. The interaction between ROP and MARK4-NFκβ holds significant promise in the realm of drug discovery and therapeutic interventions for diseases like AD. Molecular docking and biophysical characterization demonstrate how ROP effectively hinders MARK4 activity, offering detailed insights into their molecular interactions. The present research also investigates the biological aspect of MARK4 shows promise in treating AD, with neuroinflammation playing a crucial role in the disease's progression. Aβ42 and ROP were co-administered directly into the cells for the establishment of the AD model. We confirmed that ROP can inhibit the path of MARK4 activity, as evidenced by biophysical characterization, and can enhance the cell viability, lowers the expression of MARK4, decrease the rate of oxidative stress, and attenuate the expression of NFκβ, leading to reduced neuronal apoptosis in an in vitro-induced Aβ model. Overall, this research provides valuable mechanistic insights into the neuroprotective potential of ROP and its ability to target the MARK4-NFκβ pathway.
Collapse
Affiliation(s)
- Neha
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| | - Saleha Anwar
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| | - Pinky
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| |
Collapse
|
5
|
Gillman C, Bu G, Danelius E, Hattne J, Nannenga BL, Gonen T. Eliminating the missing cone challenge through innovative approaches. J Struct Biol X 2024; 9:100102. [PMID: 38962493 PMCID: PMC11220036 DOI: 10.1016/j.yjsbx.2024.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.
Collapse
Affiliation(s)
- Cody Gillman
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guanhong Bu
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Emma Danelius
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
- Department of Physiology, University of California, Los Angeles, CA, USA
| |
Collapse
|
6
|
Nam Y, Prajapati R, Kim S, Shin SJ, Cheong DY, Park YH, Park HH, Lim D, Yoon Y, Lee G, Jung HA, Park I, Kim DH, Choi JS, Moon M. Dual regulatory effects of neferine on amyloid-β and tau aggregation studied by in silico, in vitro, and lab-on-a-chip technology. Biomed Pharmacother 2024; 172:116226. [PMID: 38301421 DOI: 10.1016/j.biopha.2024.116226] [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: 11/15/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by the presence of two critical pathogenic factors: amyloid-β (Aβ) and tau. Aβ and tau become neurotoxic aggregates via self-assembly, and these aggregates contribute to the pathogenesis of AD. Therefore, there has been growing interest in therapeutic strategies that simultaneously target Aβ and tau aggregates. Although neferine has attracted attention as a suitable candidate agent for alleviating AD pathology, there has been no study investigating whether neferine affects the modulation of Aβ or tau aggregation/dissociation. Herein, we investigated the dual regulatory effects of neferine on Aβ and tau aggregation/dissociation. We predicted the binding characteristics of neferine to Aβ and tau using molecular docking simulations. Next, thioflavin T and atomic force microscope analyses were used to evaluate the effects of neferine on the aggregation or dissociation of Aβ42 and tau K18. We verified the effect of neferine on Aβ fibril degradation using a microfluidic device. In addition, molecular dynamics simulation was used to predict a conformational change in the Aβ42-neferine complex. Moreover, we examined the neuroprotective effect of neferine against neurotoxicity induced by Aβ and tau and their fibrils in HT22 cells. Finally, we foresaw the pharmacokinetic properties of neferine. These results demonstrated that neferine, which has attracted attention as a potential treatment for AD, can directly affect Aβ and tau pathology.
Collapse
Affiliation(s)
- Yunkwon Nam
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Ritu Prajapati
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Sujin Kim
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Soo Jung Shin
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Yong Ho Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Hyun Ha Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Danyou Lim
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Yoojeong Yoon
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Insu Park
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea.
| | - Dong-Hyun Kim
- Departments of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea.
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Minho Moon
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea.
| |
Collapse
|
7
|
Gillman C, Bu G, Danelius E, Hattne J, Nannenga B, Gonen T. Eliminating the Missing Cone Challenge through Innovative Approaches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575283. [PMID: 38293160 PMCID: PMC10827066 DOI: 10.1101/2024.01.11.575283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If, as is typically the case, the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the grid cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that this method could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop crystallization approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the COVID-19 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting preferred orientations, unlocking new possibilities for structure determination by MicroED.
Collapse
|
8
|
Paul PS, Patel T, Cho JY, Yarahmady A, Khalili A, Semenchenko V, Wille H, Kulka M, Mok SA, Kar S. Native PLGA nanoparticles attenuate Aβ-seed induced tau aggregation under in vitro conditions: potential implication in Alzheimer's disease pathology. Sci Rep 2024; 14:144. [PMID: 38167993 PMCID: PMC10762165 DOI: 10.1038/s41598-023-50465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Evidence suggests that beta-amyloid (Aβ)-induced phosphorylation/aggregation of tau protein plays a critical role in the degeneration of neurons and development of Alzheimer's disease (AD), the most common cause of dementia affecting the elderly population. Many studies have pursued a variety of small molecules, including nanoparticles conjugated with drugs to interfere with Aβ and/or tau aggregation/toxicity as an effective strategy for AD treatment. We reported earlier that FDA approved PLGA nanoparticles without any drug can attenuate Aβ aggregation/toxicity in cellular/animal models of AD. In this study, we evaluated the effects of native PLGA on Aβ seed-induced aggregation of tau protein using a variety of biophysical, structural and spectroscopic approaches. Our results show that Aβ1-42 seeds enhanced aggregation of tau protein in the presence and absence of heparin and the effect was attenuated by native PLGA nanoparticles. Interestingly, PLGA inhibited aggregation of both 4R and 3R tau isoforms involved in the formation of neurofibrillary tangles in AD brains. Furthermore, Aβ seed-induced tau aggregation in the presence of arachidonic acid was suppressed by native PLGA. Collectively, our results suggest that native PLGA nanoparticles can inhibit the Aβ seed-induced aggregation of different tau protein isoforms highlighting their therapeutic implication in the treatment of AD.
Collapse
Affiliation(s)
- Pallabi Sil Paul
- Departments of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada
| | - Tark Patel
- Departments of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada
| | - Jae-Young Cho
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, T6G 2M9, Canada
| | - Allan Yarahmady
- Departments of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada
| | - Aria Khalili
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, T6G 2M9, Canada
| | - Valentyna Semenchenko
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, T6G 2M9, Canada
| | - Holger Wille
- Departments of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada
| | - Marianna Kulka
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, T6G 2M9, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Sue-Ann Mok
- Departments of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada
| | - Satyabrata Kar
- Departments of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T6G 2M8, Canada.
- Centre for Prions and Protein Folding Diseases, Departments of Medicine (Neurology) and Psychiatry, University of Alberta, Edmonton, AB, T6G 2M8, Canada.
| |
Collapse
|
9
|
Patow G, Stefanovski L, Ritter P, Deco G, Kobeleva X. Whole-brain modeling of the differential influences of amyloid-beta and tau in Alzheimer's disease. Alzheimers Res Ther 2023; 15:210. [PMID: 38053164 PMCID: PMC10696890 DOI: 10.1186/s13195-023-01349-9] [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: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Alzheimer's disease is a neurodegenerative condition associated with the accumulation of two misfolded proteins, amyloid-beta (A[Formula: see text]) and tau. We study their effect on neuronal activity, with the aim of assessing their individual and combined impact. METHODS We use a whole-brain dynamic model to find the optimal parameters that best describe the effects of A[Formula: see text] and tau on the excitation-inhibition balance of the local nodes. RESULTS We found a clear dominance of A[Formula: see text] over tau in the early disease stages (MCI), while tau dominates over A[Formula: see text] in the latest stages (AD). We identify crucial roles for A[Formula: see text] and tau in complex neuronal dynamics and demonstrate the viability of using regional distributions to define models of large-scale brain function in AD. CONCLUSIONS Our study provides further insight into the dynamics and complex interplay between these two proteins, opening the path for further investigations on biomarkers and candidate therapeutic targets in-silico.
Collapse
Affiliation(s)
- Gustavo Patow
- ViRVIG, Universitat de Girona, Girona, Spain.
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Center for Brain and Cognition, Computational Neuroscience Group, Barcelona, Spain.
| | - Leon Stefanovski
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology with Experimental Neurology, Brain Simulation Section, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, 10117, Germany
| | - Petra Ritter
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology with Experimental Neurology, Brain Simulation Section, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, 10117, Germany
- Bernstein Center for Computational Neuroscience, Berlin, Germany
- Einstein Center for Neuroscience Berlin, Berlin, Germany
- Einstein Center Digital Future Berlin, Berlin, Germany
| | - Gustavo Deco
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Center for Brain and Cognition, Computational Neuroscience Group, Barcelona, Spain
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xenia Kobeleva
- Computational Neurology Research Group, Ruhr University Bochum, Bochum, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Clinic for Neurology, University Hospital Bonn, Bonn, Germany
| |
Collapse
|
10
|
Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF. De novo Design of Peptides that Bind Specific Conformers of α-Synuclein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567090. [PMID: 38014268 PMCID: PMC10680688 DOI: 10.1101/2023.11.14.567090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloid in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of α-synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB database with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of α-synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by α-synuclein, tau, or Aβ40. This designed peptide also markedly slowed the formation of α-synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.
Collapse
|
11
|
Wu X, Zhu L, Wang G, Zhang Q, Qian Z. Dose-dependent binding behavior of anthraquinone derivative purpurin interacting with tau-derived peptide protofibril. Phys Chem Chem Phys 2023; 25:26787-26796. [PMID: 37781899 DOI: 10.1039/d3cp03883a] [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: 10/03/2023]
Abstract
Alzheimer's disease is hallmarked by microtubule-associated protein tau tangles and amyloid-β plaques. The β-structure propensity of tau inclusions is closely related to the hexapeptide motif VQIVYK (termed PHF6), and disruption of this motif prevents tau aggregation. Small-molecule inhibitors are considered a promising therapeutic strategy, but the molecular mechanisms underlying the correlation between dose and inhibitory effects are still unclear. In this work, we investigated the dose-induced influence of purpurin, an anthraquinone derivative, on the structural stability of the PHF6 fibrillar nucleus by performing microsecond all-atom molecular dynamics simulations in explicit water. The stability of PHF6 protofibrils of different sizes was first examined, and it was found that the structural stability of fibrillar oligomers increases with oligomer size, and that the octamer is the minimal stable nucleus for fibril formation. When purpurin molecules were added to the protofibril octamer at a low purpurin/peptide ratio, they bound to the octamer with different coupling states, and the different states may transition to each of the other states through an uncoupling state or directly through a short-time transition. With increasing purpurin/peptide ratio, purpurins tend to self-aggregate rather than bind to the protein surface. Interestingly, the contacts between individual purpurins and the octamer as a function of the purpurin number show a power-law behavior, which may serve as a useful indicator to reflect the binding efficiency of ligands to proteins in drug screening. The interaction analysis reveals that purpurin prefers to bind to the hydrophilic and aromatic Tyr and has the lowest probability with the hydrophobic Val located in the middle of PHF6. Aromatic stacking plays a key role in the octamer-purpurin interaction, in which the three aromatic rings of purpurin have different contributions. In addition, purpurin shows a remarkable disruptive effect on the protofibril octamer when the molar ratio of purpurin to peptide is 1 : 2; above this ratio, the binding mode and disruption effect of purpurin do not change significantly. Our work provides a detailed picture of the dynamics and interactions of purpurin binding to the PHF6 protofibril and expands the understanding of the dose-induced inhibitory mechanism.
Collapse
Affiliation(s)
- Xiaoxiao Wu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Lili Zhu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
- Shang Xing School, 6 Shangli Road, Shenzhen 518100, Guangdong, China
| | - Gang Wang
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, People's Republic of China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, and School of Exercise and Health, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| |
Collapse
|
12
|
Faridi N, Sanjari-Pour M, Wang P, Bathaie SZ. The Effect of Ultrasonication on the Fibrillar/ Oligomeric Structures of Aβ 1-42 at Different Concentrations. Protein J 2023; 42:575-585. [PMID: 37634212 PMCID: PMC10480282 DOI: 10.1007/s10930-023-10138-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2023] [Indexed: 08/29/2023]
Abstract
The number of disease states linked the aberrant regular protein conformations to oligomers and amyloid fibrils. Amyloid beta 1-42 (Aβ1-42) peptide is very hydrophobic and quickly forms the β-rich structure and fibrillar protein aggregates in some solutions and buffer conditions. Ultrasonication pulses can disrupt amyloid fibrils to smaller fragments and produce Aβ1-42 peptides of different sizes and oligomers. Herein, we investigated the effects of buffer and ultrasonication on Aβ1-42 structure at low and high concentrations. After ultrasonication, the Western blot results showed that Aβ1-42 fibrils were disaggregated into different sizes. The transmission electron microscopy results indicated Aβ1-42 at low concentration (25 µM) in Ham's/F12 phenol red-free culture medium formed short-size fragments and oligomers. In comparison, Aβ1-42 at higher concentration (100 µM) formed fibrils that break down into smaller fragments after ultrasonication. However, after regrowth, it formed mature fibrils again. Cell viability assay indicated that Aβ1-42 oligomers formed at a low concentration (25 µM) were more toxic to PC12 cells than other forms. In conclusion, by applying ultrasonication pulses and controlling peptide concentration and buffer condition, we can rich Aβ1-42 aggregates with a particular size and molecular structure.
Collapse
Affiliation(s)
- Nassim Faridi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran
| | - Maryam Sanjari-Pour
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
| | - Ping Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - S Zahra Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran.
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran.
- UCLA-DOE Institute, University of California, Los Angeles, CA, USA.
| |
Collapse
|
13
|
Shrimali PC, Chen S, Das A, Dreher R, Howard MK, Ryan JJ, Buck J, Kim D, Sprunger ML, Rudra JS, Jackrel ME. Amyloidogenic propensity of self-assembling peptides and their adjuvant potential for use as DNA vaccines. Acta Biomater 2023; 169:464-476. [PMID: 37586449 DOI: 10.1016/j.actbio.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
De novo designed peptides that self-assemble into cross-β rich fibrillar biomaterials have been pursued as an innovative platform for the development of adjuvant- and inflammation-free vaccines. However, they share structural and morphological properties similar to amyloid species implicated in neurodegenerative diseases, which has been a long-standing concern for their successful translation. Here, we comprehensively characterize the amyloidogenic character of the amphipathic self-assembling cross-β peptide KFE8, compared to pathological amyloid and amyloid-like proteins α-synuclein (α-syn) and TDP-43. Further, we developed plasmid-based DNA vaccines with the KFE8 backbone serving as a scaffold for delivery of a GFP model antigen. We find that expression of tandem repeats of KFE8 is non-toxic and efficiently cleared by autophagy. We also demonstrate that preformed KFE8 fibrils do not cross-seed amyloid formation of α-syn in mammalian cells compared to α-syn preformed fibrils. In mice, vaccination with plasmids encoding the KFE32-GFP fusion protein elicited robust immune responses, inducing production of significantly higher levels of anti-GFP antibodies compared to soluble GFP. Antigen-specific CD8+T cells were also detected in the spleens of vaccinated mice and cytokine profiles from antigen recall assays indicate a balanced Th1/Th2 response. These findings illustrate that cross-β-rich peptide nanofibers have distinct physicochemical properties from those of pathological amyloidogenic proteins, and are an attractive platform for the development of DNA vaccines with self-adjuvanting properties and improved safety profiles. STATEMENT OF SIGNIFICANCE: Biomaterials comprised of self-assembling peptides hold great promise for the development of new vaccines that do not require use of adjuvants. However, these materials have safety concerns, as they self-assemble into cross-β rich fibrils that are structurally similar to amyloid species implicated in disease. Here, we comprehensively study the properties of these biomaterials. We demonstrate that they have distinct properties from pathological proteins. They are non-toxic and do not trigger amyloidogenesis. Vaccination of these materials in mice elicited a robust immune response. Most excitingly, our work suggests that this platform could be used to develop DNA-based vaccines, which have few storage requirements. Further, due to their genetic encoding, longer sequences can be generated and the vaccines will be amenable to modification.
Collapse
Affiliation(s)
- Paresh C Shrimali
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Sheng Chen
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Anirban Das
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA; Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Rachel Dreher
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Matthew K Howard
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Jeremy J Ryan
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Jeremy Buck
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Darren Kim
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Jai S Rudra
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
| |
Collapse
|
14
|
Holden MR, Krzesinski BJ, Weismiller HA, Shady JR, Margittai M. MAP2 caps tau fibrils and inhibits aggregation. J Biol Chem 2023; 299:104891. [PMID: 37286038 PMCID: PMC10404690 DOI: 10.1016/j.jbc.2023.104891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/13/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
Fibrils of the microtubule-associated protein tau are intimately linked to the pathology of Alzheimer's disease (AD) and related neurodegenerative disorders. A current paradigm for pathology spreading in the human brain is that short tau fibrils transfer between neurons and then recruit naive tau monomers onto their tips, perpetuating the fibrillar conformation with high fidelity and speed. Although it is known that the propagation could be modulated in a cell-specific manner and thereby contribute to phenotypic diversity, there is still limited understanding of how select molecules are involved in this process. MAP2 is a neuronal protein that shares significant sequence homology with the repeat-bearing amyloid core region of tau. There is discrepancy about MAP2's involvement in pathology and its relationship with tau fibrillization. Here, we employed the entire repeat regions of 3R and 4R MAP2, to investigate their modulatory role in tau fibrillization. We find that both proteins block the spontaneous and seeded aggregation of 4R tau, with 4R MAP2 being slightly more potent. The inhibition of tau seeding is observed in vitro, in HEK293 cells, and in AD brain extracts, underscoring its broader scope. MAP2 monomers specifically bind to the end of tau fibrils, preventing recruitment of further tau and MAP2 monomers onto the fibril tip. The findings uncover a new function for MAP2 as a tau fibril cap that could play a significant role in modulating tau propagation in disease and may hold promise as a potential intrinsic protein inhibitor.
Collapse
Affiliation(s)
- Michael R Holden
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Brad J Krzesinski
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Hilary A Weismiller
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Justin R Shady
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA.
| |
Collapse
|
15
|
Indig RY, Landau M. Designed inhibitors to reduce amyloid virulence and cytotoxicity and combat neurodegenerative and infectious diseases. Curr Opin Chem Biol 2023; 75:102318. [PMID: 37196450 DOI: 10.1016/j.cbpa.2023.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
The review highlights the role of amyloids in various diseases and the challenges associated with targeting human amyloids in therapeutic development. However, due to the better understanding of microbial amyloids' role as virulence factors, there is a growing interest in repurposing and designing anti-amyloid compounds for antivirulence therapy. The identification of amyloid inhibitors has not only significant clinical implications but also provides valuable insights into the structure and function of amyloids. The review showcases small molecules and peptides that specifically target amyloids in both humans and microbes, reducing cytotoxicity and biofilm formation, respectively. The review emphasizes the importance of further research on amyloid structures, mechanisms, and interactions across all life forms to yield new drug targets and improve the design of selective treatments. Overall, the review highlights the potential for amyloid inhibitors in therapeutic development for both human diseases and microbial infections.
Collapse
Affiliation(s)
- Rinat Yona Indig
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; Centre for Structural Systems Biology (CSSB) and Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
| |
Collapse
|
16
|
Hosseini AN, van der Spoel D. Simulations of Amyloid-Forming Peptides in the Crystal State. Protein J 2023:10.1007/s10930-023-10119-3. [PMID: 37145206 DOI: 10.1007/s10930-023-10119-3] [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] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
There still is little treatment available for amyloid diseases, despite their significant impact on individuals and the social and economic implications for society. One reason for this is that the physical nature of amyloid formation is not understood sufficiently well. Therefore, fundamental research at the molecular level remains necessary to support the development of therapeutics. A few structures of short peptides from amyloid-forming proteins have been determined. These can in principle be used as scaffolds for designing aggregation inhibitors. Attempts to this end have often used the tools of computational chemistry, in particular molecular simulation. However, few simulation studies of these peptides in the crystal state have been presented so far. Hence, to validate the capability of common force fields (AMBER19SB, CHARMM36m, and OPLS-AA/M) to yield insight into the dynamics and structural stability of amyloid peptide aggregates, we have performed molecular dynamics simulations of twelve different peptide crystals at two different temperatures. From the simulations, we evaluate the hydrogen bonding patterns, the isotropic B-factors, the change in energy, the Ramachandran plots, and the unit cell parameters and compare the results with the crystal structures. Most crystals are stable in the simulations but for all force fields there is at least one that deviates from the experimental crystal, suggesting more work is needed on these models.
Collapse
Affiliation(s)
- A Najla Hosseini
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden.
| |
Collapse
|
17
|
Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun 2023; 14:2379. [PMID: 37185252 PMCID: PMC10127185 DOI: 10.1038/s41467-023-37865-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP's propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.
Collapse
Affiliation(s)
- Einav Tayeb-Fligelman
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Jeannette T Bowler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Christen E Tai
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Michael R Sawaya
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Yi Xiao Jiang
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Sarah L Griner
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Xinyi Cheng
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Liisa Lutter
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Paul M Seidler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, CA, 90089-9121, USA
| | - Jiahui Lu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gregory M Rosenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Ke Hou
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Romany Abskharon
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Hope Pan
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - David R Boyer
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Yan Li
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Daniel H Anderson
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Kevin A Murray
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Genesis Falcon
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Lorena Saelices
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - David S Eisenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
| |
Collapse
|
18
|
Song Z, Gatch A, Sun Y, Ding F. Differential Binding and Conformational Dynamics of Tau Microtubule-Binding Repeats with a Preformed Amyloid-β Fibril Seed. ACS Chem Neurosci 2023; 14:1321-1330. [PMID: 36975100 PMCID: PMC10119806 DOI: 10.1021/acschemneuro.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Both senile plaques formed by amyloid-β (Aβ) and neurofibrillary tangles (NFTs) comprised of tau are pathological hallmarks of Alzheimer's disease (AD). The accumulation of NFTs better correlates with the loss of cognitive function than senile plaques, but NFTs are rarely observed without the presence of senile plaques. Hence, cross-seeding of tau by preformed Aβ amyloid fibril seeds has been proposed to drive the aggregation of tau and exacerbate AD progression, but the molecular mechanism remains unknown. Here, we first identified cross-interaction hotspots between Aβ and tau using atomistic discrete molecular dynamics simulations (DMD) and confirmed the critical role of the four microtubule-binding repeats of tau (R1-R4) in the cross-interaction with Aβ. We further investigated the binding structure and dynamics of each tau repeat with a preformed Aβ fibril seed. Specifically, R1 and R3 preferred to bind the Aβ fibril lateral surface instead of the elongation end. In contrast, R2 and R4 had higher binding propensities to the fibril elongation end than the lateral surface, enhancing β-sheet content by forming hydrogen bonds with the exposed hydrogen bond donors and acceptors. Together, our results suggest that the four repeats play distinct roles in driving the binding of tau to different surfaces of an Aβ fibril seed. Binding of tau to the lateral surface of Aβ fibril can increase the local concentration, while the binding to the elongation surface promotes β-sheet formation, both of which reduce the free energy barrier for tau aggregation nucleation and subsequent fibrillization.
Collapse
Affiliation(s)
- Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Adam Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| |
Collapse
|
19
|
Aillaud I, Funke SA. Tau Aggregation Inhibiting Peptides as Potential Therapeutics for Alzheimer Disease. Cell Mol Neurobiol 2023; 43:951-961. [PMID: 35596819 PMCID: PMC10006036 DOI: 10.1007/s10571-022-01230-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer disease (AD) is the most common progressive neurodegenerative disorder. AD causes enormous personal and economic burden to society as currently only limited palliative therapeutic options are available. The pathological hallmarks of the disease are extracellular plaques, composed of fibrillar amyloid-β (Aβ), and neurofibrillary tangles inside neurons, composed of Tau protein. Until recently, the search for AD therapeutics was focussed more on the Aβ peptide and its pathology, but the results were unsatisfying. As an alternative, Tau might be a promising therapeutic target as its pathology is closely correlated to clinical symptoms. In addition, pathological Tau aggregation occurs in a large group of diseases, called Tauopathies, and in most of them Aβ aggregation does not play a role in disease pathogenesis. The formation of Tau aggregates is triggered by two hexapeptide motifs within Tau; PHF6* and PHF6. Both fragments are interesting targets for the development of Tau aggregation inhibitors (TAI). Peptides represent a unique class of pharmaceutical compounds and are reasonable alternatives to chemical substances or antibodies. They are attributed with high biological activity, valuable specificity and low toxicity, and often are developed as drug candidates to interrupt protein-protein interactions. The preparation of peptides is simple, controllable and the peptides can be easily modified. However, their application may also have disadvantages. Currently, a few peptide compounds acting as TAI are described in the literature, most of them developed by structure-based design or phage display. Here, we review the current state of research in this promising field of AD therapy development.
Collapse
Affiliation(s)
- Isabelle Aillaud
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany
| | - Susanne Aileen Funke
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany.
| |
Collapse
|
20
|
Torok J, Anand C, Verma P, Raj A. Connectome-based biophysics models of Alzheimer's disease diagnosis and prognosis. Transl Res 2023; 254:13-23. [PMID: 36031051 PMCID: PMC11019890 DOI: 10.1016/j.trsl.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022]
Abstract
With the increasing prevalence of Alzheimer's disease (AD) among aging populations and the limited therapeutic options available to slow or reverse its progression, the need has never been greater for improved diagnostic tools for identifying patients in the preclinical and prodomal phases of AD. Biophysics models of the connectome-based spread of amyloid-beta (Aβ) and microtubule-associated protein tau (τ) have enjoyed recent success as tools for predicting the time course of AD-related pathological changes. However, given the complex etiology of AD, which involves not only connectome-based spread of protein pathology but also the interactions of many molecular and cellular players over multiple spatiotemporal scales, more robust, complete biophysics models are needed to better understand AD pathophysiology and ultimately provide accurate patient-specific diagnoses and prognoses. Here we discuss several areas of active research in AD whose insights can be used to enhance the mathematical modeling of AD pathology as well as recent attempts at developing improved connectome-based biophysics models. These efforts toward a comprehensive yet parsimonious mathematical description of AD hold great promise for improving both the diagnosis of patients at risk for AD and our mechanistic understanding of how AD progresses.
Collapse
Affiliation(s)
- Justin Torok
- Department of Radiology, University of California, San Francisco, San Francisco, California.
| | - Chaitali Anand
- Department of Radiology, University of California, San Francisco, San Francisco, California
| | - Parul Verma
- Department of Radiology, University of California, San Francisco, San Francisco, California
| | - Ashish Raj
- Department of Radiology, University of California, San Francisco, San Francisco, California; Department of Bioengineering, University of California, Berkeley and University of California, San Francisco, Berkeley, California; Department of Radiology, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
21
|
Sakalauskas A, Ziaunys M, Snieckute R, Janoniene A, Veiveris D, Zvirblis M, Dudutiene V, Smirnovas V. The Major Components of Cerebrospinal Fluid Dictate the Characteristics of Inhibitors against Amyloid-Beta Aggregation. Int J Mol Sci 2023; 24:ijms24065991. [PMID: 36983069 PMCID: PMC10059578 DOI: 10.3390/ijms24065991] [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: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
The main pathological hallmark of Alzheimer's disease (AD) is the aggregation of amyloid-β into amyloid fibrils, leading to a neurodegeneration cascade. The current medications are far from sufficient to prevent the onset of the disease, hence requiring more research to find new alternative drugs for curing AD. In vitro inhibition experiments are one of the primary tools in testing whether a molecule may be potent to impede the aggregation of amyloid-beta peptide (Aβ42). However, kinetic experiments in vitro do not match the mechanism found when aggregating Aβ42 in cerebrospinal fluid. The different aggregation mechanisms and the composition of the reaction mixtures may also impact the characteristics of the inhibitor molecules. For this reason, altering the reaction mixture to resemble components found in cerebrospinal fluid (CSF) is critical to partially compensate for the mismatch between the inhibition experiments in vivo and in vitro. In this study, we used an artificial cerebrospinal fluid that contained the major components found in CSF and performed Aβ42 aggregation inhibition studies using oxidized epigallocatechin-3-gallate (EGCG) and fluorinated benzenesulfonamide VR16-09. This led to a discovery of a complete turnaround of their inhibitory characteristics, rendering EGCG ineffective while significantly improving the efficacy of VR16-09. HSA was the main contributor in the mixture that significantly increased the anti-amyloid characteristics of VR16-09.
Collapse
Affiliation(s)
- Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Ruta Snieckute
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Agne Janoniene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Dominykas Veiveris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Mantas Zvirblis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Virginija Dudutiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| |
Collapse
|
22
|
Tonelli M, Catto M, Sabaté R, Francesconi V, Laurini E, Pricl S, Pisani L, Miniero DV, Liuzzi GM, Gatta E, Relini A, Gavín R, Del Rio JA, Sparatore F, Carotti A. Thioxanthenone-based derivatives as multitarget therapeutic leads for Alzheimer's disease. Eur J Med Chem 2023; 250:115169. [PMID: 36753881 DOI: 10.1016/j.ejmech.2023.115169] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
A set of twenty-five thioxanthene-9-one and xanthene-9-one derivatives, that were previously shown to inhibit cholinesterases (ChEs) and amyloid β (Aβ40) aggregation, were evaluated for the inhibition of tau protein aggregation. All compounds exhibited a good activity, and eight of them (5-8, 10, 14, 15 and 20) shared comparable low micromolar inhibitory potency versus Aβ40 aggregation and human acetylcholinesterase (AChE), while inhibiting human butyrylcholinesterase (BChE) even at submicromolar concentration. Compound 20 showed outstanding biological data, inhibiting tau protein and Aβ40 aggregation with IC50 = 1.8 and 1.3 μM, respectively. Moreover, at 0.1-10 μM it also exhibited neuroprotective activity against tau toxicity induced by okadoic acid in human neuroblastoma SH-SY5Y cells, that was comparable to that of estradiol and PD38. In preliminary toxicity studies, these interesting results for compound 20 are somewhat conflicting with a narrow safety window. However, compound 10, although endowed with a little lower potency for tau and Aβ aggregation inhibition additionally demonstrated good inhibition of ChEs and rather low cytotoxicity. Compound 4 is also worth of note for its high potency as hBChE inhibitor (IC50 = 7 nM) and for the three order of magnitude selectivity versus hAChE. Molecular modelling studies were performed to explain the different behavior of compounds 4 and 20 towards hBChE. The observed balance of the inhibitory potencies versus the relevant targets indicates the thioxanthene-9-one derivatives as potential MTDLs for AD therapy, provided that the safety window will be improved by further structural variations, currently under investigation.
Collapse
Affiliation(s)
- Michele Tonelli
- Department of Pharmacy, University of Genoa, 16132, Genoa, Italy.
| | - Marco Catto
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, 70125, Bari, Italy.
| | - Raimon Sabaté
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028, Barcelona, Spain.
| | | | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, 34127, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Leonardo Pisani
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, 70125, Bari, Italy
| | - Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125, Bari, Italy
| | - Grazia Maria Liuzzi
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125, Bari, Italy
| | - Elena Gatta
- Department of Physics, University of Genoa, 16146, Genoa, Italy
| | - Annalisa Relini
- Department of Physics, University of Genoa, 16146, Genoa, Italy
| | - Rosalina Gavín
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028, Barcelona, Spain
| | - Jose Antonio Del Rio
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028, Barcelona, Spain
| | - Fabio Sparatore
- Department of Pharmacy, University of Genoa, 16132, Genoa, Italy
| | - Angelo Carotti
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, 70125, Bari, Italy
| |
Collapse
|
23
|
Meftah S, Gan J. Alzheimer’s disease as a synaptopathy: Evidence for dysfunction of synapses during disease progression. Front Synaptic Neurosci 2023; 15:1129036. [PMID: 36970154 PMCID: PMC10033629 DOI: 10.3389/fnsyn.2023.1129036] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
The synapse has consistently been considered a vulnerable and critical target within Alzheimer’s disease, and synapse loss is, to date, one of the main biological correlates of cognitive decline within Alzheimer’s disease. This occurs prior to neuronal loss with ample evidence that synaptic dysfunction precedes this, in support of the idea that synaptic failure is a crucial stage within disease pathogenesis. The two main pathological hallmarks of Alzheimer’s disease, abnormal aggregates of amyloid or tau proteins, have had demonstrable effects on synaptic physiology in animal and cellular models of Alzheimer’s disease. There is also growing evidence that these two proteins may have a synergistic effect on neurophysiological dysfunction. Here, we review some of the main findings of synaptic alterations in Alzheimer’s disease, and what we know from Alzheimer’s disease animal and cellular models. First, we briefly summarize some of the human evidence to suggest that synapses are altered, including how this relates to network activity. Subsequently, animal and cellular models of Alzheimer’s disease are considered, highlighting mouse models of amyloid and tau pathology and the role these proteins may play in synaptic dysfunction, either in isolation or examining how the two pathologies may interact in dysfunction. This specifically focuses on neurophysiological function and dysfunction observed within these animal models, typically measured using electrophysiology or calcium imaging. Following synaptic dysfunction and loss, it would be impossible to imagine that this would not alter oscillatory activity within the brain. Therefore, this review also discusses how this may underpin some of the aberrant oscillatory patterns seen in animal models of Alzheimer’s disease and human patients. Finally, an overview of some key directions and considerations in the field of synaptic dysfunction in Alzheimer’s disease is covered. This includes current therapeutics that are targeted specifically at synaptic dysfunction, but also methods that modulate activity to rescue aberrant oscillatory patterns. Other important future avenues of note in this field include the role of non-neuronal cell types such as astrocytes and microglia, and mechanisms of dysfunction independent of amyloid and tau in Alzheimer’s disease. The synapse will certainly continue to be an important target within Alzheimer’s disease for the foreseeable future.
Collapse
Affiliation(s)
- Soraya Meftah
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jian Gan
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Jian Gan,
| |
Collapse
|
24
|
Ge WY, Deng X, Shi WP, Lin WJ, Chen LL, Liang H, Wang XT, Zhang TD, Zhao FZ, Guo WH, Yin DC. Amyloid Protein Cross-Seeding Provides a New Perspective on Multiple Diseases In Vivo. Biomacromolecules 2023; 24:1-18. [PMID: 36507729 DOI: 10.1021/acs.biomac.2c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Amyloid protein cross-seeding is a peculiar phenomenon of cross-spreading among different diseases. Unlike traditional infectious ones, diseases caused by amyloid protein cross-seeding are spread by misfolded proteins instead of pathogens. As a consequence of the interactions among misfolded heterologous proteins or polypeptides, amyloid protein cross-seeding is considered to be the crucial cause of overlapping pathological transmission between various protein misfolding disorders (PMDs) in multiple tissues and cells. Here, we briefly review the phenomenon of cross-seeding among amyloid proteins. As an interesting example worth mentioning, the potential links between the novel coronavirus pneumonia (COVID-19) and some neurodegenerative diseases might be related to the amyloid protein cross-seeding, thus may cause an undesirable trend in the incidence of PMDs around the world. We then summarize the theoretical models as well as the experimental techniques for studying amyloid protein cross-seeding. Finally, we conclude with an outlook on the challenges and opportunities for basic research in this field. Cross-seeding of amyloid opens up a new perspective in our understanding of the process of amyloidogenesis, which is crucial for the development of new treatments for diseases. It is therefore valuable but still challenging to explore the cross-seeding system of amyloid protein as well as to reveal the structural basis and the intricate processes.
Collapse
Affiliation(s)
- Wan-Yi Ge
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xudong Deng
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Pu Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Juan Lin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Liang-Liang Chen
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huan Liang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xue-Ting Wang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tuo-Di Zhang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Feng-Zhu Zhao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Non-commissioned Officer School, Army Medical University, Shijiazhuang 050081, China
| | - Wei-Hong Guo
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| |
Collapse
|
25
|
Condello C, Merz GE, Aoyagi A, DeGrado WF, Prusiner SB. Aβ and Tau Prions Causing Alzheimer's Disease. Methods Mol Biol 2023; 2561:293-337. [PMID: 36399277 DOI: 10.1007/978-1-0716-2655-9_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Studies show that patients with Alzheimer's disease (AD) have both Aβ and tau prions, and thus, AD is a double-prion disease. AD patients with the greatest longevity exhibited low levels of both Aβ and tau prions; tau prions were nearly absent in the brains of almost half of the patients who lived beyond 80 years of age. Using cellular bioassays for prions in postmortem samples, we found that both Aβ and tau proteins misfold into prions leading to AD, which is either a sporadic or familial dementing disorder. Although AD is transmissible experimentally, there is no evidence that AD is either communicable or contagious. Since the progression of AD correlates poorly with insoluble Aβ in the central nervous system (CNS), it was difficult to distinguish between inert amyloids and Aβ prions. To measure the progression of AD, we devised rapid bioassays to measure the abundance of isoform-specific Aβ prions in the brains of transgenic (Tg) mice and in postmortem human CNS samples from AD victims and people who died of other neurodegenerative diseases (NDs). We found significant correlations between the longevity of individuals with AD, sex, and genetic background, despite the fact that all postmortem brain tissue had essentially the same confirmed neuropathology.Although brains from all AD patients had measurable levels of Aβ prions at death, the oldest individuals had lower Aβ prion levels than the younger ones. Additionally, the long-lived individuals had low tau prion levels that correlated with the extent of phosphorylated tau (p-tau). Unexpectedly, a longevity-dependent decrease in tau prions was found in spite of increasing amounts of total insoluble tau. When corrected for the abundance of insoluble tau, the tau prion levels decreased exponentially with respect to the age at death with a half-time of approximately one decade, and this correlated with the abundance of phosphorylated tau.Even though our findings with tau prions were not unexpected, they were counterintuitive; thus, tau phosphorylation and tau prion activity decreased exponentially with longevity in patients with AD ranging from ages 37 to 99 years. Our findings demonstrated an inverse correlation between longevity in AD patients and the abundance of neurotoxic tau prions. Moreover, our discovery may have profound implications for the selection of phenotypically distinct patient populations and the development of diagnostics and effective therapeutics for AD.
Collapse
Affiliation(s)
- Carlo Condello
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Gregory E Merz
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Atsushi Aoyagi
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - William F DeGrado
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
26
|
The co-effect of copper and lipid vesicles on Aβ aggregation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184082. [PMID: 36374760 DOI: 10.1016/j.bbamem.2022.184082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
Both metal ions and lipid membranes have a wide distribution in amyloid plaques and play significant roles in AD pathogenesis. Although influences of different metal ions or lipid vesicles on the aggregation of Aβ peptides have been extensively studied, their combined effects are less understood. In this study, we reported a unique effect of copper ion on Aβ aggregation in the presence of lipid vesicles, different from other divalent metal ions. Cu2+ in a super stoichiometric amount leads to the rapid formation of β-sheet rich structure, containing abundant low molecular weight (LMW) oligomers. We demonstrated that oligomerization of Aβ40 induced by Cu2+ binding was an essential prerequisite for the rapid conformation transition. Overall, the finding provided a new view on the complex triple system of Aβ, copper ion and lipid vesicles, which might help understanding of Aβ pathologies.
Collapse
|
27
|
Kabir ER, Chowdhury NM, Yasmin H, Kabir MT, Akter R, Perveen A, Ashraf GM, Akter S, Rahman MH, Sweilam SH. Unveiling the Potential of Polyphenols as Anti-Amyloid Molecules in Alzheimer's Disease. Curr Neuropharmacol 2023; 21:787-807. [PMID: 36221865 PMCID: PMC10227919 DOI: 10.2174/1570159x20666221010113812] [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: 02/23/2022] [Revised: 08/03/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease that mostly affects the elderly population. Mechanisms underlying AD pathogenesis are yet to be fully revealed, but there are several hypotheses regarding AD. Even though free radicals and inflammation are likely to be linked with AD pathogenesis, still amyloid-beta (Aβ) cascade is the dominant hypothesis. According to the Aβ hypothesis, a progressive buildup of extracellular and intracellular Aβ aggregates has a significant contribution to the AD-linked neurodegeneration process. Since Aβ plays an important role in the etiology of AD, therefore Aβ-linked pathways are mainly targeted in order to develop potential AD therapies. Accumulation of Aβ plaques in the brains of AD individuals is an important hallmark of AD. These plaques are mainly composed of Aβ (a peptide of 39-42 amino acids) aggregates produced via the proteolytic cleavage of the amyloid precursor protein. Numerous studies have demonstrated that various polyphenols (PPHs), including cyanidins, anthocyanins, curcumin, catechins and their gallate esters were found to markedly suppress Aβ aggregation and prevent the formation of Aβ oligomers and toxicity, which is further suggesting that these PPHs might be regarded as effective therapeutic agents for the AD treatment. This review summarizes the roles of Aβ in AD pathogenesis, the Aβ aggregation pathway, types of PPHs, and distribution of PPHs in dietary sources. Furthermore, we have predominantly focused on the potential of food-derived PPHs as putative anti-amyloid drugs.
Collapse
Affiliation(s)
- Eva Rahman Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | | | - Hasina Yasmin
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Md. Tanvir Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Rokeya Akter
- Department of Pharmacy, Jagannath University, Dhaka, Bangladesh
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, Virginia 22030, USA
| | | | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Cairo-Suez Road, Badr City 11829, Egypt
| |
Collapse
|
28
|
Lysophospholipids: A Potential Drug Candidates for Neurodegenerative Disorders. Biomedicines 2022; 10:biomedicines10123126. [PMID: 36551882 PMCID: PMC9775253 DOI: 10.3390/biomedicines10123126] [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: 10/22/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases (NDs) commonly present misfolded and aggregated proteins. Considerable research has been performed to unearth the molecular processes underpinning this pathological aggregation and develop therapeutic strategies targeting NDs. Fibrillary deposits of α-synuclein (α-Syn), a highly conserved and thermostable protein, are a critical feature in the development of NDs such as Alzheimer's disease (AD), Lewy body disease (LBD), Parkinson's disease (PD), and multiple system atrophy (MSA). Inhibition of α-Syn aggregation can thus serve as a potential approach for therapeutic intervention. Recently, the degradation of target proteins by small molecules has emerged as a new therapeutic modality, gaining the hotspot in pharmaceutical research. Additionally, interest is growing in the use of food-derived bioactive compounds as intervention agents against NDs via functional foods and dietary supplements. According to reports, dietary bioactive phospholipids may have cognition-enhancing and neuroprotective effects, owing to their abilities to influence cognition and mental health in vivo and in vitro. However, the mechanisms by which lipids may prevent the pathological aggregation of α-Syn warrant further clarification. Here, we review evidence for the potential mechanisms underlying this effect, with a particular focus on how porcine liver decomposition product (PLDP)-derived lysophospholipids (LPLs) may inhibit α-Syn aggregation.
Collapse
|
29
|
Ramesh M, Govindaraju T. Multipronged diagnostic and therapeutic strategies for Alzheimer's disease. Chem Sci 2022; 13:13657-13689. [PMID: 36544728 PMCID: PMC9710308 DOI: 10.1039/d2sc03932j] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/13/2022] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and a major contributor to dementia cases worldwide. AD is clinically characterized by learning, memory, and cognitive deficits. The accumulation of extracellular amyloid β (Aβ) plaques and neurofibrillary tangles (NFTs) of tau are the pathological hallmarks of AD and are explored as targets for clinical diagnosis and therapy. AD pathology is poorly understood and there are no fully approved diagnosis and treatments. Notwithstanding the gap, decades of research in understanding disease mechanisms have revealed the multifactorial nature of AD. As a result, multipronged and holistic approaches are pertinent to targeting multiple biomarkers and targets for developing effective diagnosis and therapeutics. In this perspective, recent developments in Aβ and tau targeted diagnostic and therapeutic tools are discussed. Novel indirect, combination, and circulating biomarkers as potential diagnostic targets are highlighted. We underline the importance of multiplexing and multimodal detection of multiple biomarkers to generate biomarker fingerprints as a reliable diagnostic strategy. The classical therapeutics targeting Aβ and tau aggregation pathways are described with bottlenecks in the strategy. Drug discovery efforts targeting multifaceted toxicity involving protein aggregation, metal toxicity, oxidative stress, mitochondrial damage, and neuroinflammation are highlighted. Recent efforts focused on multipronged strategies to rationally design multifunctional modulators targeting multiple pathological factors are presented as future drug development strategies to discover potential therapeutics for AD.
Collapse
Affiliation(s)
- Madhu Ramesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru Karnataka 560064 India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru Karnataka 560064 India
| |
Collapse
|
30
|
Regmi S, Liu DD, Shen M, Kevadiya BD, Ganguly A, Primavera R, Chetty S, Yarani R, Thakor AS. Mesenchymal stromal cells for the treatment of Alzheimer’s disease: Strategies and limitations. Front Mol Neurosci 2022; 15:1011225. [PMID: 36277497 PMCID: PMC9584646 DOI: 10.3389/fnmol.2022.1011225] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
Alzheimer’s disease (AD) is a major cause of age-related dementia and is characterized by progressive brain damage that gradually destroys memory and the ability to learn, which ultimately leads to the decline of a patient’s ability to perform daily activities. Although some of the pharmacological treatments of AD are available for symptomatic relief, they are not able to limit the progression of AD and have several side effects. Mesenchymal stem/stromal cells (MSCs) could be a potential therapeutic option for treating AD due to their immunomodulatory, anti-inflammatory, regenerative, antioxidant, anti-apoptotic, and neuroprotective effects. MSCs not only secret neuroprotective and anti-inflammatory factors to promote the survival of neurons, but they also transfer functional mitochondria and miRNAs to boost their bioenergetic profile as well as improve microglial clearance of accumulated protein aggregates. This review focuses on different clinical and preclinical studies using MSC as a therapy for treating AD, their outcomes, limitations and the strategies to potentiate their clinical translation.
Collapse
|
31
|
Velander P, Wu L, Hildreth SB, Vogelaar NJ, Mukhopadhyay B, Helm RF, Zhang S, Xu B. Catechol-containing compounds are a broad class of protein aggregation inhibitors: Redox state is a key determinant of the inhibitory activities. Pharmacol Res 2022; 184:106409. [PMID: 35995346 PMCID: PMC10074477 DOI: 10.1016/j.phrs.2022.106409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 12/30/2022]
Abstract
A range of neurodegenerative and related aging diseases, such as Alzheimer's disease and type 2 diabetes, are linked to toxic protein aggregation. Yet the mechanisms of protein aggregation inhibition by small molecule inhibitors remain poorly understood, in part because most protein targets of aggregation assembly are partially unfolded or intrinsically disordered, which hinders detailed structural characterization of protein-inhibitor complexes and structural-based inhibitor design. Herein we employed a parallel small molecule library-screening approach to identify inhibitors against three prototype amyloidogenic proteins in neurodegeneration and related proteinopathies: amylin, Aβ and tau. One remarkable class of inhibitors identified from these screens against different amyloidogenic proteins was catechol-containing compounds and redox-related quinones/anthraquinones. Secondary assays validated most of the identified inhibitors. In vivo efficacy evaluation of a selected catechol-containing compound, rosmarinic acid, demonstrated its strong mitigating effects of amylin amyloid deposition and related diabetic pathology in transgenic HIP rats. Further systematic investigation of selected class of inhibitors under aerobic and anaerobic conditions revealed that the redox state of the broad class of catechol-containing compounds is a key determinant of the amyloid inhibitor activities. The molecular insights we gained not only explain why a large number of catechol-containing polyphenolic natural compounds, often enriched in healthy diet, have anti-neurodegeneration and anti-aging activities, but also could guide the rational design of therapeutic or nutraceutical strategies to target a broad range of neurodegenerative and related aging diseases.
Collapse
Affiliation(s)
- Paul Velander
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Ling Wu
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; BRITE Research Institute and Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA; Affiliated Faculty, Duke/UNC Alzheimer's Disease Research Center, Durham, NC 27710, USA
| | - Sherry B Hildreth
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Nancy J Vogelaar
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; Center for Drug Discovery, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Shijun Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bin Xu
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; Center for Drug Discovery, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; School of Neuroscience, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; BRITE Research Institute and Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA; Affiliated Faculty, Duke/UNC Alzheimer's Disease Research Center, Durham, NC 27710, USA.
| |
Collapse
|
32
|
Murakami K, Ono K. Interactions of amyloid coaggregates with biomolecules and its relevance to neurodegeneration. FASEB J 2022; 36:e22493. [PMID: 35971743 DOI: 10.1096/fj.202200235r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloidogenic proteins is a pathological hallmark of various neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In these diseases, oligomeric intermediates or toxic aggregates of amyloids cause neuronal damage and degeneration. Despite the substantial effort made over recent decades to implement therapeutic interventions, these neurodegenerative diseases are not yet understood at the molecular level. In many cases, multiple disease-causing amyloids overlap in a sole pathological feature or a sole disease-causing amyloid represents multiple pathological features. Various amyloid pathologies can coexist in the same brain with or without clinical presentation and may even occur in individuals without disease. From sparse data, speculation has arisen regarding the coaggregation of amyloids with disparate amyloid species and other biomolecules, which are the same characteristics that make diagnostics and drug development challenging. However, advances in research related to biomolecular condensates and structural analysis have been used to overcome some of these challenges. Considering the development of these resources and techniques, herein we review the cross-seeding of amyloidosis, for example, involving the amyloids amyloid β, tau, α-synuclein, and human islet amyloid polypeptide, and their cross-inhibition by transthyretin and BRICHOS. The interplay of nucleic acid-binding proteins, such as prions, TAR DNA-binding protein 43, fused in sarcoma/translated in liposarcoma, and fragile X mental retardation polyglycine, with nucleic acids in the pathology of neurodegeneration are also described, and we thereby highlight the potential clinical applications in central nervous system therapy.
Collapse
Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenjiro Ono
- Department of Neurology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
33
|
Abstract
Neurodegenerative diseases are characterized by the pathologic accumulation of aggregated proteins. Known as amyloid, these fibrillar aggregates include proteins such as tau and amyloid-β (Aβ) in Alzheimer's disease (AD) and alpha-synuclein (αSyn) in Parkinson's disease (PD). The development and spread of amyloid fibrils within the brain correlates with disease onset and progression, and inhibiting amyloid formation is a possible route toward therapeutic development. Recent advances have enabled the determination of amyloid fibril structures to atomic-level resolution, improving the possibility of structure-based inhibitor design. In this work, we use these amyloid structures to design inhibitors that bind to the ends of fibrils, "capping" them so as to prevent further growth. Using de novo protein design, we develop a library of miniprotein inhibitors of 35 to 48 residues that target the amyloid structures of tau, Aβ, and αSyn. Biophysical characterization of top in silico designed inhibitors shows they form stable folds, have no sequence similarity to naturally occurring proteins, and specifically prevent the aggregation of their targeted amyloid-prone proteins in vitro. The inhibitors also prevent the seeded aggregation and toxicity of fibrils in cells. In vivo evaluation reveals their ability to reduce aggregation and rescue motor deficits in Caenorhabditis elegans models of PD and AD.
Collapse
|
34
|
Abstract
![]()
Electron crystallography
has a storied history which rivals that
of its more established X-ray-enabled counterpart. Recent advances
in data collection and analysis have sparked a renaissance in the
field, opening a new chapter for this venerable technique. Burgeoning
interest in electron crystallography has spawned innovative methods
described by various interchangeable labels (3D ED, MicroED, cRED,
etc.). This Review covers concepts and findings relevant to the practicing
crystallographer, with an emphasis on experiments aimed at using electron
diffraction to elucidate the atomic structure of three-dimensional
molecular crystals.
Collapse
Affiliation(s)
- Ambarneil Saha
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Shervin S Nia
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - José A Rodríguez
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
35
|
Aβ and Tau Interact with Metal Ions, Lipid Membranes and Peptide-Based Amyloid Inhibitors: Are These Common Features Relevant in Alzheimer’s Disease? Molecules 2022; 27:molecules27165066. [PMID: 36014310 PMCID: PMC9414153 DOI: 10.3390/molecules27165066] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 12/13/2022] Open
Abstract
In the last two decades, the amyloid hypothesis, i.e., the abnormal accumulation of toxic Aβ assemblies in the brain, has been considered the mainstream concept sustaining research in Alzheimer’s Disease (AD). However, the course of cognitive decline and AD development better correlates with tau accumulation rather than amyloid peptide deposition. Moreover, all clinical trials of amyloid-targeting drug candidates have been unsuccessful, implicitly suggesting that the amyloid hypothesis needs significant amendments. Accumulating evidence supports the existence of a series of potentially dangerous relationships between Aβ oligomeric species and tau protein in AD. However, the molecular determinants underlying pathogenic Aβ/tau cross interactions are not fully understood. Here, we discuss the common features of Aβ and tau molecules, with special emphasis on: (i) the critical role played by metal dyshomeostasis in promoting both Aβ and tau aggregation and oxidative stress, in AD; (ii) the effects of lipid membranes on Aβ and tau (co)-aggregation at the membrane interface; (iii) the potential of small peptide-based inhibitors of Aβ and tau misfolding as therapeutic tools in AD. Although the molecular mechanism underlying the direct Aβ/tau interaction remains largely unknown, the arguments discussed in this review may help reinforcing the current view of a synergistic Aβ/tau molecular crosstalk in AD and stimulate further research to mechanism elucidation and next-generation AD therapeutics.
Collapse
|
36
|
Nag N, Tripathi T. Tau-FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer's disease. Brief Funct Genomics 2022; 22:161-167. [PMID: 35923096 DOI: 10.1093/bfgp/elac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/14/2022] Open
Abstract
An emerging pathophysiology associated with the neurodegenerative Alzheimer's disease (AD) is the impairment of nucleocytoplasmic transport (NCT). The impairment can originate from damage to the nuclear pore complex (NPC) or other factors involved in NCT. The phenylalanine-glycine nucleoporins (FG-Nups) form a crucial component of the NPC, which is central to NCT. Recent discoveries have highlighted that the neuropathological protein tau is involved in direct interactions with the FG-Nups and impairment of the NCT process. Targeting such interactions may lead to the identification of novel interaction inhibitors and offer new therapeutic alternatives for the treatment of AD. This review highlights recent findings associated with impaired NCT in AD and the interaction between tau and the FG-Nups.
Collapse
Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Regional Director's Office, Indira Gandhi National Open University (IGNOU), Regional Centre Kohima, Kenuozou, Kohima 797001, India
| |
Collapse
|
37
|
Cuadros R, Pérez M, Ruiz-Gabarre D, Hernández F, García-Escudero V, Avila J. Specific Peptide from the Novel W-Tau Isoform Inhibits Tau and Amyloid β Peptide Aggregation In Vitro. ACS Chem Neurosci 2022; 13:1974-1978. [PMID: 35695727 PMCID: PMC9264359 DOI: 10.1021/acschemneuro.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
W-Tau, a new tau human-specific splicing isoform generated by intron retention, has been recently described. This isoform contains an 18-residue unique sequence corresponding to the translation of the retained region of intron 12. In this work, we have described that such 18-amino-acid peptide from the retained intron 12 can inhibit tau and β amyloid peptides aggregation under in vitro conditions. This inhibitory function is also present in smaller fragments of the 18-residue peptide.
Collapse
Affiliation(s)
- Raquel Cuadros
- Centro de Biología Molecular "Severo Ochoa" (CBMSO) CSIC/UAM, C/Nicolás Cabrera, 1, 28049 Madrid, Spain.,Networking Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Mar Pérez
- Departamento de Anatomía Histología y Neurociencia, Facultad de Medicina UAM, 28029 Madrid, Spain
| | - Daniel Ruiz-Gabarre
- Centro de Biología Molecular "Severo Ochoa" (CBMSO) CSIC/UAM, C/Nicolás Cabrera, 1, 28049 Madrid, Spain.,Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Félix Hernández
- Centro de Biología Molecular "Severo Ochoa" (CBMSO) CSIC/UAM, C/Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Vega García-Escudero
- Networking Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain.,Departamento de Anatomía Histología y Neurociencia, Facultad de Medicina UAM, 28029 Madrid, Spain.,Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Jesús Avila
- Centro de Biología Molecular "Severo Ochoa" (CBMSO) CSIC/UAM, C/Nicolás Cabrera, 1, 28049 Madrid, Spain.,Networking Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| |
Collapse
|
38
|
Hu J, Zhao Y, Li Y. Rationally designed amyloid inhibitors based on amyloid-related structural studies. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
39
|
Hernández F, Ferrer I, Pérez M, Zabala JC, Del Rio JA, Avila J. Tau aggregation. Neuroscience 2022; 518:64-69. [PMID: 35525497 DOI: 10.1016/j.neuroscience.2022.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
Abstract
Here we revisit tau protein aggregation at primary, secondary, tertiary and quaternary structures. In addition, the presence of non-aggregated tau protein, which has been recently discovered, is also commented on.
Collapse
Affiliation(s)
- Félix Hernández
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid, Spain
| | - Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Bellvitge, University Hospital-IDIBELL, Hospitalet de Llobregat, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Mar Pérez
- Departamento de Anatomía Histología y Neurociencia, Facultad de Medicina UAM, Madrid, Spain
| | - Juan Carlos Zabala
- Department of Molecular Biology, Facultad de Medicina, Universidad de Cantabria, Santander 39005 Spain
| | - Jose Antonio Del Rio
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
| | - Jesús Avila
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid, Spain; Networking Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain.
| |
Collapse
|
40
|
Louros N, Ramakers M, Michiels E, Konstantoulea K, Morelli C, Garcia T, Moonen N, D'Haeyer S, Goossens V, Thal DR, Audenaert D, Rousseau F, Schymkowitz J. Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers. Nat Commun 2022; 13:1351. [PMID: 35292653 PMCID: PMC8924238 DOI: 10.1038/s41467-022-28955-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using tau as a model system we demonstrate that proteins with local sequence homology to tau amyloid nucleating regions can modify fibril nucleation, morphology, assembly and spreading of aggregates in cultured cells. Depending on the type of mutation such interactions inhibit or promote aggregation in a manner that can be predicted from structure. We find that these heterotypic amyloid interactions can result in the subcellular mis-localisation of these proteins. Moreover, equilibrium studies indicate that the critical concentration of aggregation is altered by heterotypic interactions. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and we discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression. In this work, Louros et al. uncover a rule book for interactions of amyloids with other proteins. This grammar was shown to promote cellular spreading of tau aggregates in cells, but can also be harvested to develop structure-based aggregation blockers.
Collapse
Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Chiara Morelli
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Nele Moonen
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sam D'Haeyer
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Vera Goossens
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Dietmar Rudolf Thal
- KU Leuven, Leuven Brain Institute, 3000, Leuven, Belgium.,Laboratory for Neuropathology, KU Leuven, and Department of Pathology, UZ Leuven, 3000, Leuven, Belgium
| | - Dominique Audenaert
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
41
|
Amyloid Cross-Seeding: Mechanism, Implication, and Inhibition. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061776. [PMID: 35335141 PMCID: PMC8955620 DOI: 10.3390/molecules27061776] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023]
Abstract
Most neurodegenerative diseases such as Alzheimer’s disease, type 2 diabetes, Parkinson’s disease, etc. are caused by inclusions and plaques containing misfolded protein aggregates. These protein aggregates are essentially formed by the interactions of either the same (homologous) or different (heterologous) sequences. Several experimental pieces of evidence have revealed the presence of cross-seeding in amyloid proteins, which results in a multicomponent assembly; however, the molecular and structural details remain less explored. Here, we discuss the amyloid proteins and the cross-seeding phenomena in detail. Data suggest that targeting the common epitope of the interacting amyloid proteins may be a better therapeutic option than targeting only one species. We also examine the dual inhibitors that target the amyloid proteins participating in the cross-seeding events. The future scopes and major challenges in understanding the mechanism and developing therapeutics are also considered. Detailed knowledge of the amyloid cross-seeding will stimulate further research in the practical aspects and better designing anti-amyloid therapeutics.
Collapse
|
42
|
Nag N, Tripathi T. Cross-Seeding with Homologous Sequences Alters Amyloid Aggregation Kinetics and Fibril Structure. ACS Chem Neurosci 2022; 13:537-539. [PMID: 35152697 DOI: 10.1021/acschemneuro.2c00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Protein aggregation through homotypic interactions is a hallmark of neurodegenerative diseases. Recently, heterotypic amyloid interactions through cross-seeding were found to modify protein aggregation and are reported in the brain of Alzheimer's disease patients. However, whether amyloid-β (Aβ) assembly can be modulated by heterotypic interactions between Aβ aggregation-prone regions (APRs) and short homologous segments in unrelated human proteins needs to be elucidated. A recent study revealed that the aggregation kinetics and fibril morphology of Aβ is altered by heterotypic interactions between its APRs and homologous segments of unrelated proteins. The data provide novel insights into the structure, origins, and aggregation principles of the amyloid assembly process.
Collapse
Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| |
Collapse
|
43
|
Ruiz-Gabarre D, Carnero-Espejo A, Ávila J, García-Escudero V. What's in a Gene? The Outstanding Diversity of MAPT. Cells 2022; 11:840. [PMID: 35269461 PMCID: PMC8909800 DOI: 10.3390/cells11050840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
Tau protein is a microtubule-associated protein encoded by the MAPT gene that carries out a myriad of physiological functions and has been linked to certain pathologies collectively termed tauopathies, including Alzheimer's disease, frontotemporal dementia, Huntington's disease, progressive supranuclear palsy, etc. Alternative splicing is a physiological process by which cells generate several transcripts from one single gene and may in turn give rise to different proteins from the same gene. MAPT transcripts have been proven to be subjected to alternative splicing, generating six main isoforms in the central nervous system. Research throughout the years has demonstrated that the splicing landscape of the MAPT gene is far more complex than that, including at least exon skipping events, the use of 3' and 5' alternative splice sites and, as has been recently discovered, also intron retention. In addition, MAPT alternative splicing has been showed to be regulated spatially and developmentally, further evidencing the complexity of the gene's splicing regulation. It is unclear what would drive the need for the existence of so many isoforms encoded by the same gene, but a wide range of functions have been ascribed to these Tau isoforms, both in physiology and pathology. In this review we offer a comprehensive up-to-date exploration of the mechanisms leading to the outstanding diversity of isoforms expressed from the MAPT gene and the functions in which such isoforms are involved, including their potential role in the onset and development of tauopathies such as Alzheimer's disease.
Collapse
Affiliation(s)
- Daniel Ruiz-Gabarre
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Almudena Carnero-Espejo
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Jesús Ávila
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Vega García-Escudero
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| |
Collapse
|
44
|
Interactions of intrinsically disordered proteins with the unconventional chaperone human serum albumin: From mechanisms of amyloid inhibition to therapeutic opportunities. Biophys Chem 2022; 282:106743. [PMID: 35093643 DOI: 10.1016/j.bpc.2021.106743] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/29/2022]
Abstract
Human Serum Albumin (HSA), the most abundant protein in plasma, serves a diverse repertoire of biological functions including regulation of oncotic pressure and redox potential, transport of serum solutes, but also chaperoning of misfolded proteins. Here we review how HSA interacts with a wide spectrum of client proteins including intrinsically disordered proteins (IDPs) such as Aβ, the islet amyloid peptide (IAPP), alpha synuclein and stressed globular proteins such as insulin. The comparative analysis of the HSA chaperone - client interactions reveals that the amyloid-inhibitory function of HSA arises from at least four emerging mechanisms. Two mechanisms (the monomer stabilizer model and the monomer competitor model) involve the direct binding of HSA to either IDP monomers or oligomers, while other mechanisms (metal chelation and membrane protection) rely on the indirect modulation by HSA of other factors that drive IDP aggregation. While HSA is not the only extracellular chaperone, given its abundance, HSA is likely to account for a significant fraction of the chaperoning effects in plasma, thus opening new therapeutic opportunities in the context of the peripheral sink hypothesis.
Collapse
|
45
|
Roda AR, Serra-Mir G, Montoliu-Gaya L, Tiessler L, Villegas S. Amyloid-beta peptide and tau protein crosstalk in Alzheimer's disease. Neural Regen Res 2022; 17:1666-1674. [PMID: 35017413 PMCID: PMC8820696 DOI: 10.4103/1673-5374.332127] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease is a neurodegenerative disease that accounts for most of the 50-million dementia cases worldwide in 2018. A large amount of evidence supports the amyloid cascade hypothesis, which states that amyloid-beta accumulation triggers tau hyperphosphorylation and aggregation in form of neurofibrillary tangles, and these aggregates lead to inflammation, synaptic impairment, neuronal loss, and thus to cognitive decline and behavioral abnormalities. The poor correlation found between cognitive decline and amyloid plaques, have led the scientific community to question whether amyloid-beta accumulation is actually triggering neurodegeneration in Alzheimer’s disease. The occurrence of tau neurofibrillary tangles better correlates to neuronal loss and clinical symptoms and, although amyloid-beta may initiate the cascade of events, tau impairment is likely the effector molecule of neurodegeneration. Recently, it has been shown that amyloid-beta and tau cooperatively work to impair transcription of genes involved in synaptic function and, more importantly, that downregulation of tau partially reverses transcriptional perturbations. Despite mounting evidence points to an interplay between amyloid-beta and tau, some factors could independently affect both pathologies. Thus, the dual pathway hypothesis, which states that there are common upstream triggers causing both amyloid-beta and tau abnormalities has been proposed. Among others, the immune system seems to be strongly involved in amyloid-beta and tau pathologies. Other factors, as the apolipoprotein E ε4 isoform has been suggested to act as a link between amyloid-beta and tau hyperphosphorylation. Interestingly, amyloid-beta-immunotherapy reduces not only amyloid-beta but also tau levels in animal models and in clinical trials. Likewise, it has been shown that tau-immunotherapy also reduces amyloid-beta levels. Thus, even though amyloid-beta immunotherapy is more advanced than tau-immunotherapy, combined amyloid-beta and tau-directed therapies at early stages of the disease have recently been proposed as a strategy to stop the progression of Alzheimer’s disease.
Collapse
Affiliation(s)
- Alejandro R Roda
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Gabriel Serra-Mir
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laia Montoliu-Gaya
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Lidia Tiessler
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sandra Villegas
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| |
Collapse
|
46
|
Tatar M. The role of Aβ in Alzheimer's Disease as an Evolutionary Outcome of Optimized Innate Immune Defense. J Prev Alzheimers Dis 2022; 9:580-588. [PMID: 36281662 PMCID: PMC10535726 DOI: 10.14283/jpad.2022.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Alzheimer's Disease is a progressive manifestation of aging associated with accumulated Amyloid β. It remains frustratingly unclear why this protein accumulates and how it contributes to Alzheimer's Disease pathology. In one recent hypothesis, Amyloid β is suggested to function as an antimicrobial peptide in innate immune defense within the brain, where Amyloid β gains toxicity when it becomes abundant. This essay proposes an evolutionary explanation for why Amyloid β expression is regulated at an optimum based on its function as a defense and how this leads to disease. Among its potential physiological functions, Amyloid β confers benefits to reduce direct pathogen damage while this simultaneously entails cellular cost of defense. Optimal Amyloid β expression occurs when the gain in fitness from an incremental increase is balanced by the marginal cost of this increase. It proposes that natural selection acting upon the young favored systems to maintain Amyloid β at an optimal level through mechanisms that induce the defense and repress its expression. With age, the force of natural selection declines and permits mechanisms of negative feedback repression to degenerate. Consequently, Amyloid β is expressed beyond its optimum. Age also elevates cumulative pathogen exposure, reduces pathogen barriers and reactivates latent pathogens. The net effect is elevated, chronic induction of Amyloid β in the brain. The model recommends attention to innate immune negative regulation in the brain to discover ways to restore these functions toward a youthful state in the elderly.
Collapse
Affiliation(s)
- M Tatar
- Marc Tatar, Department of Ecology, Evolution and Organismal Biology, Box GW, Walter Hall Brown University, Providence RI 02912, USA, Office: +1 401-863-3455, Fax: +1 401-863-2166,
| |
Collapse
|
47
|
Heterotypic amyloid interactions: Clues to polymorphic bias and selective cellular vulnerability? Curr Opin Struct Biol 2021; 72:176-186. [PMID: 34942566 DOI: 10.1016/j.sbi.2021.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/18/2022]
Abstract
The number of atomic-resolution structures of disease-associated amyloids has greatly increased in recent years. These structures have confirmed not only the polymorphic nature of amyloids but also the association of specific polymorphs to particular proteinopathies. These observations are strengthening the view that amyloid polymorphism is a marker for specific pathological subtypes (e.g. in tauopathies or synucleinopathies). The nature of this association and how it relates to the selective cellular vulnerability of amyloid nucleation, propagation and toxicity are still unclear. Here, we provide an overview of the mechanistic insights provided by recent patient-derived amyloid structures. We discuss the framework organisation of amyloid polymorphism and how heterotypic amyloid interactions with the physiological environment could modify the solubility and assembly of amyloidogenic proteins. We conclude by hypothesising how such interactions could contribute to selective cellular vulnerability.
Collapse
|
48
|
Falkenstein M, Reiner-Link D, Zivkovic A, Gering I, Willbold D, Stark H. Histamine H 3 receptor antagonists with peptidomimetic (keto)piperazine structures to inhibit Aβ oligomerisation. Bioorg Med Chem 2021; 50:116462. [PMID: 34695709 DOI: 10.1016/j.bmc.2021.116462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Alzheimeŕs disease (AD) is the most prominent neurodegenerative disorder with high medical need. Protein-protein-interactions (PPI) interactions have a critical role in AD where β-amyloid structures (Aβ) build toxic oligomers. Design of disease modifying multi target directed ligand (MTDL) has been performed, which disable PPI on the one hand and on the other hand, act as procognitive antagonists at the histamine H3 receptor (H3R). The synthetized compounds are structurally based on peptidomimetic amino acid-like structures mainly as keto, diketo-, or acyl variations of a piperazine moiety connected to an H3R pharmacophore. Most of them showed low nanomolar affinities at H3R and some with promising affinity to Aβ-monomers. The structure-activity relationships (SAR) described offer new possibilities for MTDL with an optimized profile combining symptomatic and potential causal therapeutic approaches in AD.
Collapse
Affiliation(s)
- Markus Falkenstein
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - David Reiner-Link
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Aleksandra Zivkovic
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Ian Gering
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Physical Biology, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany.
| |
Collapse
|
49
|
Ramesh M, Acharya A, Murugan NA, Ila H, Govindaraju T. Thiophene-Based Dual Modulators of Aβ and Tau Aggregation. Chembiochem 2021; 22:3348-3357. [PMID: 34546619 DOI: 10.1002/cbic.202100383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Indexed: 01/29/2023]
Abstract
Alzheimer's disease is characterized by the accumulation of amyloid beta (Aβ) and Tau aggregates in the brain, which induces various pathological events resulting in neurodegeneration. There have been continuous efforts to develop modulators of the Aβ and Tau aggregation process to halt or modify disease progression. A few small-molecule-based inhibitors that target both Aβ and Tau pathology have been reported. Here, we report the screening of a targeted library of small molecules to modulate Aβ and Tau aggregation together with their in vitro, in silico and cellular studies. In vitro ThT fluorescence assay, dot blot assay, gel electrophoresis and transmission electron microscopy (TEM) results have shown that thiophene-based lead molecules effectively modulate Aβ aggregation and inhibit Tau aggregation. In silico studies performed by employing molecular docking, molecular dynamics and binding-free energy calculations have helped in understanding the mechanism of interaction of the lead thiophene compounds with Aβ and Tau fibril targets. In cellulo studies revealed that the lead candidate is biocompatible and effectively ameliorates neuronal cells from Aβ and Tau-mediated amyloid toxicity.
Collapse
Affiliation(s)
- Madhu Ramesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Anand Acharya
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - N Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044, Stockholm, Sweden
| | - Hiriyakkanavar Ila
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, Karnataka, India
| |
Collapse
|
50
|
Quint WH, Matečko-Burmann I, Schilcher I, Löffler T, Schöll M, Burmann BM, Vogels T. Bispecific Tau Antibodies with Additional Binding to C1q or Alpha-Synuclein. J Alzheimers Dis 2021; 80:813-829. [PMID: 33579845 DOI: 10.3233/jad-201334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) and other tauopathies are neurodegenerative disorders characterized by cellular accumulation of aggregated tau protein. Tau pathology within these disorders is accompanied by chronic neuroinflammation, such as activation of the classical complement pathway by complement initiation factor C1q. Additionally, about half of the AD cases present with inclusions composed of aggregated alpha-synuclein called Lewy bodies. Lewy bodies in disorders such as Parkinson's disease and Lewy body dementia also frequently occur together with tau pathology. OBJECTIVE Immunotherapy is currently the most promising treatment strategy for tauopathies. However, the presence of multiple pathological processes within tauopathies makes it desirable to simultaneously target more than one disease pathway. METHODS Herein, we have developed three bispecific antibodies based on published antibody binding region sequences. One bispecific antibody binds to tau plus alpha-synuclein and two bispecific antibodies bind to tau plus C1q. RESULTS Affinity of the bispecific antibodies to their targets compared to their monospecific counterparts ranged from nearly identical to one order of magnitude lower. All bispecific antibodies retained binding to aggregated protein in patient-derived brain sections. The bispecific antibodies also retained their ability to inhibit aggregation of recombinant tau, regardless of whether the tau binding sites were in IgG or scFv format. Mono- and bispecific antibodies inhibited cellular seeding induced by AD-derived pathological tau with similar efficacy. Finally, both Tau-C1q bispecific antibodies completely inhibited the classical complement pathway. CONCLUSION Bispecific antibodies that bind to multiple pathological targets may therefore present a promising approach to treat tauopathies and other neurodegenerative disorders.
Collapse
Affiliation(s)
| | - Irena Matečko-Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
| | | | - Tina Löffler
- QPS Austria GmbH, Neuropharmacology, Grambach, Austria
| | - Michael Schöll
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden.,Department of Neurodegenerative Disease, UCL Queen Square, Institute of Neurology, University College London, London, UK
| | - Björn Marcus Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Vogels
- Maptimmune BV, The Hague, The Netherlands.,Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden.,Department of Neurodegenerative Disease, UCL Queen Square, Institute of Neurology, University College London, London, UK
| |
Collapse
|