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Matsuo T, Yamamoto S, Matsuo K. Phospholipid-induced secondary structural changes of lysozyme polymorphic amyloid fibrils studied using vacuum-ultraviolet circular dichroism. Phys Chem Chem Phys 2024; 26:18943-18952. [PMID: 38952218 DOI: 10.1039/d4cp00965g] [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: 07/03/2024]
Abstract
The hallmark of amyloidosis, such as Alzheimer's disease and Parkinson's disease, is the deposition of amyloid fibrils in various internal organs. The onset of the disease is related to the strength of cytotoxicity caused by toxic amyloid species. Furthermore, amyloid fibrils show polymorphism, where some types of fibrils are cytotoxic while others are not. It is thus essential to understand the molecular mechanism of cytotoxicity, part of which is caused by the interaction between amyloid polymorphic fibrils and cell membranes. Here, using amyloid polymorphs of hen egg white lysozyme, which is associated with hereditary systemic amyloidosis, showing different levels of cytotoxicity and liposomes of DMPC and DMPG, changes in the secondary structure of the polymorphs and the structural state of phospholipid membranes caused by the interaction were investigated using vacuum-ultraviolet circular dichroism (VUVCD) and Laurdan fluorescence measurements, respectively. Analysis has shown that the more cytotoxic polymorph increases the antiparallel β-sheet content and causes more disorder in the membrane structure while the other less cytotoxic polymorph shows the opposite structural changes and causes less structural disorder in the membrane. These results suggest a close correlation between the structural properties of amyloid fibrils and the degree of structural disorder of phospholipid membranes, both of which are involved in the fundamental process leading to amyloid cytotoxicity.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Chiba, 263-8555, Japan.
| | - Seigi Yamamoto
- Laboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
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2
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Suresh K, Dahal E, Badano A. Synthetic β-sheets mimicking fibrillar and oligomeric structures for evaluation of spectral X-ray scattering technique for biomarker quantification. Cell Biosci 2024; 14:26. [PMID: 38374092 PMCID: PMC10877803 DOI: 10.1186/s13578-024-01208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Archetypical cross-β spines sharpen the boundary between functional and pathological proteins including β-amyloid, tau, α-synuclein and transthyretin are linked to many debilitating human neurodegenerative and non-neurodegenerative amyloidoses. An increased focus on development of pathogenic β-sheet specific fluid and imaging structural biomarkers and conformation-specific monoclonal antibodies in targeted therapies has been recently observed. Identification and quantification of pathogenic oligomers remain challenging for existing neuroimaging modalities. RESULTS We propose two artificial β-sheets which can mimic the nanoscopic structural characteristics of pathogenic oligomers and fibrils for evaluating the performance of a label free, X-ray based biomarker detection and quantification technique. Highly similar structure with elliptical cross-section and parallel cross-β motif is observed among recombinant α-synuclein fibril, Aβ-42 fibril and artificial β-sheet fibrils. We then use these β-sheet models to assess the performance of spectral small angle X-ray scattering (sSAXS) technique for detecting β-sheet structures. sSAXS showed quantitatively accurate detection of antiparallel, cross-β artificial oligomers from a tissue mimicking environment and significant distinction between different oligomer packing densities such as diffuse and dense packings. CONCLUSION The proposed synthetic β-sheet models mimicked the nanoscopic structural characteristics of β-sheets of fibrillar and oligomeric states of Aβ and α-synuclein based on the ATR-FTIR and SAXS data. The tunability of β-sheet proportions and shapes of structural motifs, and the low-cost of these β-sheet models can become useful test materials for evaluating β-sheet or amyloid specific biomarkers in a wide range of neurological diseases. By using the proposed synthetic β-sheet models, our study indicates that the sSAXS has potential to evaluate different stages of β-sheet-enriched structures including oligomers of pathogenic proteins.
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Affiliation(s)
- Karthika Suresh
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA.
| | - Eshan Dahal
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Aldo Badano
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA
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3
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Sun C, Slade L, Mbonu P, Ordner H, Mitchell C, Mitchell M, Liang FC. Membrane protein chaperone and sodium chloride modulate the kinetics and morphology of amyloid beta aggregation. FEBS J 2024; 291:158-176. [PMID: 37786925 DOI: 10.1111/febs.16967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Protein aggregation is a biological phenomenon caused by the accumulation of misfolded proteins. Amyloid beta (Aβ) peptides are derived from the cleavage of a larger membrane protein molecule and accumulate to form plaques extracellularly. According to the amyloid hypothesis, accumulation of Aβ aggregates in the brain is primarily responsible for the pathogenesis of Alzheimer's disease (AD). Therefore, the disassembly of Aβ aggregates may provide opportunities for alleviating or treating AD. Here, we show that the novel protein targeting machinery from chloroplast, chloroplast signal recognition particle 43 (cpSRP43), is an ATP-independent membrane protein chaperone that can both prevent and reverse Aβ aggregation effectively. Using of thioflavin T dye, we obtained the aggregation kinetics of Aβ aggregation and determined that the chaperone prevents Aβ aggregation in a concentration-dependent manner. Size exclusion chromatography and sedimentation assays showed that 10-fold excess of cpSRP43 can keep Aβ in the soluble monomeric form. Electron microscopy showed that the fibril structure was disrupted in the presence of this chaperone. Importantly, cpSRP43 utilizes the binding energy to actively remodel the preformed Aβ aggregates without assistance by a co-chaperone and ATP, emphasizing its unique function among protein chaperones. Moreover, when sodium chloride concentration is higher than 25 mm, the Aβ aggregation rate increases drastically to form tightly associated aggregates and generate more oligomers. Our results demonstrate that the presence of cpSRP43 and low NaCl levels inhibit or retard Aβ peptide aggregation, potentially opening new avenues to strategically develop an effective treatment for AD.
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Affiliation(s)
- Christopher Sun
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Leah Slade
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Prisca Mbonu
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Hunter Ordner
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Connor Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Matthew Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Fu-Cheng Liang
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
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4
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Izuo N, Watanabe N, Noda Y, Saito T, Saido TC, Yokote K, Hotta H, Shimizu T. Insulin resistance induces earlier initiation of cognitive dysfunction mediated by cholinergic deregulation in a mouse model of Alzheimer's disease. Aging Cell 2023; 22:e13994. [PMID: 37822109 PMCID: PMC10652326 DOI: 10.1111/acel.13994] [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: 06/06/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
Although insulin resistance increases the risk of Alzheimer's disease (AD), the mechanisms remain unclear, partly because no animal model exhibits the insulin-resistant phenotype without persistent hyperglycemia. Here we established an AD model with whole-body insulin resistance without persistent hyperglycemia (APP/IR-dKI mice) by crossbreeding constitutive knock-in mice with P1195L-mutated insulin receptor (IR-KI mice) and those with mutated amyloid precursor protein (AppNL-G-F mice: APP-KI mice). APP/IR-dKI mice exhibited cognitive impairment at an earlier age than APP-KI mice. Since cholinergic dysfunction is a major characteristic of AD, pharmacological interventions on the cholinergic system were performed to investigate the mechanism. Antagonism to a nicotinic acetylcholine receptor α7 (nAChRα7) suppressed cognitive function and cortical blood flow (CBF) response to cholinergic-regulated peripheral stimulation in APP-KI mice but not APP/IR-dKI mice. Cortical expression of Chrna7, encoding nAChRα7, was downregulated in APP/IR-dKI mice compared with APP-KI. Amyloid β burden did not differ between APP-KI and APP/IR-dKI mice. Therefore, insulin resistance, not persistent hyperglycemia, induces the earlier onset of cognitive dysfunction and CBF deregulation mediated by nAChRα7 downregulation. Our mouse model will help clarify the association between type 2 diabetes mellitus and AD.
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Affiliation(s)
- Naotaka Izuo
- Department of Endocrinology, Hematology and Gerontology, Graduate School of MedicineChiba UniversityChibaJapan
- Department of Pharmaceutical Therapy and Neuropharmacology, Graduate School of Medical and Pharmaceutical SciencesUniversity of ToyamaToyamaJapan
| | - Nobuhiro Watanabe
- Department of Autonomic NeuroscienceTokyo Metropolitan Institute for Geriatrics and GerontologyTokyoJapan
| | - Yoshihiro Noda
- Department of Animal FacilityTokyo Metropolitan Institute for Geriatrics and GerontologyTokyoJapan
| | - Takashi Saito
- Laboratory for Proteolytic NeuroscienceRIKEN Center for Brain ScienceWakoJapan
- Department of Neurocognitive ScienceInstitute of Brain Science, Nagoya City University Graduate School of Medical SciencesNagoyaJapan
| | - Takaomi C. Saido
- Laboratory for Proteolytic NeuroscienceRIKEN Center for Brain ScienceWakoJapan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Harumi Hotta
- Department of Autonomic NeuroscienceTokyo Metropolitan Institute for Geriatrics and GerontologyTokyoJapan
| | - Takahiko Shimizu
- Department of Endocrinology, Hematology and Gerontology, Graduate School of MedicineChiba UniversityChibaJapan
- Aging Stress Response Research Project TeamNational Center for Geriatrics and GerontologyObuJapan
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5
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Yang Y, Zhang W, Murzin AG, Schweighauser M, Huang M, Lövestam S, Peak-Chew SY, Saito T, Saido TC, Macdonald J, Lavenir I, Ghetti B, Graff C, Kumar A, Nordberg A, Goedert M, Scheres SHW. Cryo-EM structures of amyloid-β filaments with the Arctic mutation (E22G) from human and mouse brains. Acta Neuropathol 2023; 145:325-333. [PMID: 36611124 PMCID: PMC9925504 DOI: 10.1007/s00401-022-02533-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023]
Abstract
The Arctic mutation, encoding E693G in the amyloid precursor protein (APP) gene [E22G in amyloid-β (Aβ)], causes dominantly inherited Alzheimer's disease. Here, we report the high-resolution cryo-EM structures of Aβ filaments from the frontal cortex of a previously described case (AβPParc1) with the Arctic mutation. Most filaments consist of two pairs of non-identical protofilaments that comprise residues V12-V40 (human Arctic fold A) and E11-G37 (human Arctic fold B). They have a substructure (residues F20-G37) in common with the folds of type I and type II Aβ42. When compared to the structures of wild-type Aβ42 filaments, there are subtle conformational changes in the human Arctic folds, because of the lack of a side chain at G22, which may strengthen hydrogen bonding between mutant Aβ molecules and promote filament formation. A minority of Aβ42 filaments of type II was also present, as were tau paired helical filaments. In addition, we report the cryo-EM structures of Aβ filaments with the Arctic mutation from mouse knock-in line AppNL-G-F. Most filaments are made of two identical mutant protofilaments that extend from D1 to G37 (AppNL-G-F murine Arctic fold). In a minority of filaments, two dimeric folds pack against each other in an anti-parallel fashion. The AppNL-G-F murine Arctic fold differs from the human Arctic folds, but shares some substructure.
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Affiliation(s)
- Yang Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Wenjuan Zhang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Medical Research Council Prion Unit and Institute of Prion Diseases, University College London, London, UK
| | - Alexey G Murzin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Melissa Huang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sofia Lövestam
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sew Y Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Takashi Saito
- RIKEN Brain Science Institute, Saitama, Japan
- Department of Neurocognitive Science, Nagoya City University, Nagoya, Japan
| | | | | | - Isabelle Lavenir
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Caroline Graff
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Theme Inflammation and Aging, Karolinska University Hospital, Stockholm, Sweden
| | - Amit Kumar
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Agneta Nordberg
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Theme Inflammation and Aging, Karolinska University Hospital, Stockholm, Sweden
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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6
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Daoutsali E, Pepers BA, Stamatakis S, van der Graaf LM, Terwindt GM, Parfitt DA, Buijsen RAM, van Roon-Mom WMC. Amyloid beta accumulations and enhanced neuronal differentiation in cerebral organoids of Dutch-type cerebral amyloid angiopathy patients. Front Aging Neurosci 2023; 14:1048584. [PMID: 36733499 PMCID: PMC9887998 DOI: 10.3389/fnagi.2022.1048584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction ADutch-type cerebral amyloid angiopathy (D-CAA) is a hereditary brain disorder caused by a point mutation in the amyloid precursor protein (APP) gene. The mutation is located within the amyloid beta (Aβ) domain of APP and leads to Aβ peptide accumulation in and around the cerebral vasculature. There lack of disease models to study the cellular and molecular pathological mechanisms of D-CAA together with the absence of a disease phenotype in vitro in overexpression cell models, as well as the limited availability of D-CAA animal models indicates the need for a D-CAA patient-derived model. Methods We generated cerebral organoids from four D-CAA patients and four controls, cultured them up to 110 days and performed immunofluorescent and targeted gene expression analyses at two time points (D52 and D110). Results D-CAA cerebral organoids exhibited Aβ accumulations, showed enhanced neuronal and astrocytic gene expression and TGFβ pathway de-regulation. Conclusions These results illustrate the potential of cerebral organoids as in vitro disease model of D-CAA that can be used to understand disease mechanisms of D-CAA and can serve as therapeutic intervention platform for various Aβ-related disorders.
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Affiliation(s)
- Elena Daoutsali
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands,*Correspondence: Willeke M. C. van Roon-Mom, ; Elena Daoutsali,
| | - Barry A. Pepers
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Stavros Stamatakis
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Gisela M. Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, Netherlands
| | - David A. Parfitt
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Ronald A. M. Buijsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Willeke M. C. van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands,*Correspondence: Willeke M. C. van Roon-Mom, ; Elena Daoutsali,
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7
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Murakami K, Sakaguchi Y, Taniwa K, Izuo N, Hanaki M, Kawase T, Hirose K, Shimizu T, Irie K. Lysine-targeting inhibition of amyloid β oligomerization by a green perilla-derived metastable chalcone in vitro and in vivo. RSC Chem Biol 2022; 3:1380-1396. [PMID: 36544574 PMCID: PMC9709778 DOI: 10.1039/d2cb00194b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/16/2022] [Indexed: 12/05/2022] Open
Abstract
Oligomers of amyloid β (Aβ) represent an early aggregative form that causes neurotoxicity in the pathogenesis of Alzheimer's disease (AD). Thus, preventing Aβ aggregation is important for preventing AD. Despite intensive studies on dietary compounds with anti-aggregation properties, some identified compounds are susceptible to autoxidation and/or hydration upon incubation in water, leaving unanswered issues regarding which active structures in metastable compounds are actually responsible for the inhibition of Aβ aggregation. In this study, we observed the site-specific inhibition of 42-mer Aβ (Aβ42) oligomerization by the green perilla-derived chalcone 2',3'-dihydroxy-4',6'-dimethoxychalcone (DDC), which was converted to its decomposed flavonoids (dDDC, 1-3) via nucleophilic aromatic substitution with water molecules. DDC suppressed Aβ42 fibrillization and slowed the transformation of the β-sheet structure, which is rich in Aβ42 aggregates. To validate the contribution of dDDC to the inhibitory effects of DDC on Aβ42 aggregation, we synthesized 1-3 and identified 3, a catechol-type flavonoid, as one of the active forms of DDC. 1H-15N SOFAST-HMQC NMR revealed that 1-3 as well as DDC could interact with residues between His13 and Leu17, which were near the intermolecular β-sheet (Gln15-Ala21). The nucleation in Aβ42 aggregates involves the rate-limiting formation of low-molecular-weight oligomers. The formation of a Schiff base with dDDC at Lys16 and Lys28 in the dimer through autoxidation of dDDC was associated with the suppression of Aβ42 nucleation. Of note, in two AD mouse models using immunoaffinity purification-mass spectrometry, adduct formation between dDDC and brain Aβ was observed in a similar manner as reported in vitro. The present findings unraveled the lysine-targeting inhibitory mechanism of metastable dietary ingredients regarding Aβ oligomerization.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto UniversityKyoto606-8502Japan
| | - Yoshiki Sakaguchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto UniversityKyoto606-8502Japan
| | - Kota Taniwa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto UniversityKyoto606-8502Japan
| | - Naotaka Izuo
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba UniversityChiba260-8670Japan
| | - Mizuho Hanaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto UniversityKyoto606-8502Japan
| | | | | | - Takahiko Shimizu
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba UniversityChiba260-8670Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto UniversityKyoto606-8502Japan
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8
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Sampei T, Wu Y, Shigemori H. Amyloid Polypeptide Disaggregation Activity of Passion Fruit Seed-Derived Polyphenol Compounds. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221092710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In an aging society, the prevalence of Alzheimer disease (AD) and type 2 diabetes (T2D) has increased. It is currently hypothesized that these diseases are caused by the aggregation of amyloid β (Aβ) in the brain and human islet amyloid polypeptide (hIAPP) in the islets of Langerhans, respectively. Therefore, the disaggregation of these existing amyloid aggregates is a promising approach to the prevention and treatment of both diseases. In our previous studies, we found a remarkable Aβ and hIAPP aggregation inhibitory activity of polyphenolic compounds containing catechol moieties. Compared to previous reports on their aggregation inhibitory activity, there are few on the disaggregation activity of polyphenolic compounds. Additionally, there are few findings on the disaggregation activity of polyphenolic compounds on hIAPP. In this study, we investigated the Aβ and hIAPP disaggregation activity of scirpusin B, a polyphenolic compound found in passion fruit seeds, and related compounds. Thioflavin T (Th-T) assays and transmission electron microscopy (TEM) were performed on these compounds to evaluate their Aβ42 and hIAPP disaggregation activities. The results showed that scirpusin B and its related compounds showed remarkable disaggregation activity. The structure–activity relationship of these compounds revealed that the presence of catechol moieties is important for this activity. This study also showed that polyphenols from passion fruit seeds have significant disaggregation activity against amyloid polypeptide aggregation.
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Affiliation(s)
- Tatsuya Sampei
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yingxue Wu
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideyuki Shigemori
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Ibaraki, Japan
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9
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Kim YM, Park S, Choi SY, Oh SB, Jung M, Pack CG, Hwang JJ, Tak E, Lee JY. Clusterin Binding Modulates the Aggregation and Neurotoxicity of Amyloid-β(1-42). Mol Neurobiol 2022; 59:6228-6244. [PMID: 35904715 DOI: 10.1007/s12035-022-02973-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder characterized by the accumulation of amyloid-β (Aβ) aggregates in the brain. Clusterin (CLU), also known as apolipoprotein J, is a potent risk factor associated with AD pathogenesis, in which Aβ aggregation is essentially involved. We observed close colocalization of CLU and Aβ(1-42) (Aβ42) in parenchymal amyloid plaques or vascular amyloid deposits in the brains of human amyloid precursor protein (hAPP)-transgenic Tg2576 mice. Therefore, to elucidate the binding interaction between CLU and Aβ42 and its impact on amyloid aggregation and toxicity, the two synthetic proteins were incubated together under physiological conditions, and their structural and morphological variations were investigated using biochemical, biophysical, and microscopic analyses. Synthetic CLU spontaneously bound to different possible variants of Aβ42 aggregates with very high affinity (Kd = 2.647 nM) in vitro to form solid CLU-Aβ42 complexes. This CLU binding prevented further aggregation of Aβ42 into larger oligomers or fibrils, enriching the population of smaller Aβ42 oligomers and protofibrils and monomers. CLU either alleviated or augmented Aβ42-induced cytotoxicity and apoptosis in the neuroblastoma-derived SH-SY5Y and N2a cells, depending on the incubation period and the molar ratio of CLU:Aβ42 involved in the reaction before addition to the cells. Thus, the effects of CLU on Aβ42-induced cytotoxicity were likely determined by the extent to which it bound and sequestered toxic Aβ42 oligomers or protofibrils. These findings suggest that CLU could influence amyloid neurotoxicity and pathogenesis by modulating Aβ aggregation.
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Affiliation(s)
- Yun-Mi Kim
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.,Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - SuJi Park
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Su Yeon Choi
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.,Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Shin Bi Oh
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - MinKyo Jung
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Chan-Gi Pack
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jung Jin Hwang
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Eunyoung Tak
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Joo-Yong Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea. .,Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.
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10
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Thu TTM, Li MS. Protein aggregation rate depends on mechanical stability of fibrillar structure . J Chem Phys 2022; 157:055101. [DOI: 10.1063/5.0088689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formation of the fibrillar structure of amyloid proteins/peptides is believed to be associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, etc. Since the rate of aggregation can influence neurotoxicity, finding the key factors that control this rate is of paramount importance. It was recently found evidence that the rate of protein aggregation is related to the mechanical stability of the fibrillar structure, such that the higher the mechanical stability, the faster the fibril is formed. However, this conclusion was supported by a limited dataset. In this work, we expand the previous study to a larger dataset, including the wild type of Aβ42 peptide and its 20 mutants, the aggregation rate of which was measured experimentally. By using all-atom steered molecular dynamics (SMD) simulations we can access the mechanical stability of the fibril structure, which is characterized by the rupture force, pulling work and unbinding free energy barrier. Our result confirms that mechanical stability is indeed related to the aggregation rate. Since estimation of the aggregation rate using all-atom simulations is almost forbidden by the current computational capabilities, our result is useful for predicting it based on information obtained from fast SMD simulations for fibrils.
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Affiliation(s)
| | - Mai Suan Li
- Theoretical Physics, Institute of Physics, Polish Academy of Sciences, Poland
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11
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Howitz WJ, Guaglianone G, McKnelly KJ, Haduong K, Ashby SN, Laayouni M, Nowick JS. Macrocyclic Peptides Derived from Familial Alzheimer's Disease Mutants Show Charge-Dependent Oligomeric Assembly and Toxicity. ACS Chem Neurosci 2022; 13:714-720. [PMID: 35191689 PMCID: PMC9042422 DOI: 10.1021/acschemneuro.1c00833] [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: 11/30/2022] Open
Abstract
This work probes the role of charge in the oligomeric assembly, toxicity, and membrane destabilization of a series of peptides derived from Aβ and the E22Q and E22K familial mutants. In the mutant Aβ peptides, an acidic residue (E) is replaced with either a neutral or basic residue (Q or K), thus altering the net charge of the peptide. Acetylation at peripheral positions permits modulation of charge of the peptides and allows investigation of the role of charge in their oligomeric assembly, cytotoxicity, and membrane disruption. Peptides with the same net charge generally behave similarly even if the amino acid residue at position 22 differs. As the net charge of the peptide decreases, so does the extent of assembly, cytotoxicity, and membrane destabilization, which were determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, lactate dehydrogenase (LDH)-release assays with SH-SY5Y cells, and dye leakage assays using liposomes. These findings suggest that the charge of the amino acid side chain, rather than its size or hydrophobicity, accounts for the differences in the oligomeric assembly and toxicity of the E22 familial mutants of Aβ.
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Affiliation(s)
- William J Howitz
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Gretchen Guaglianone
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kate J McKnelly
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Katelyn Haduong
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Shareen N Ashby
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mohamed Laayouni
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
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12
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Saranya V, Shankar R, Gatasheh MK, Zehra S. Impact of Au 144 metal clusters on the structural and inhibitory mechanism of Aβ 42 peptide: A theoretical approach. ENVIRONMENTAL RESEARCH 2022; 204:111920. [PMID: 34464618 DOI: 10.1016/j.envres.2021.111920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
One of the main causes for Alzheimer disease is the abnormal self-assembly of the amyloid-beta (Aβ) peptide, which in turn forms a toxic β-rich aggregation. A recent study suggests that gold nanoparticles (AuNPs) can inhibit the Aβ aggregation. Nevertheless, the effects of AuNPs on Aβ peptide system are still ambiguous and needs exploration that is more detailed. Molecular dynamics simulations have been carried out to investigate the aggregation mechanism of Aβ42 peptide for 500 ns. During simulation, C-terminus regions of Met 35-Ala42 residues exhibits β-sheet conformations. Meanwhile, the Au144MC coordination induces substantial α-helical character, both α-helix and 310-helix structure at 0-500ns, in the region of Asp1-Arg5 and Val36-Ile41 residues. The Au144MC strongly coordinates with Asp1, Ala2, Glu3, Phe4, Asp7, Tyr10 and Gln15 residues that plays the significant effects to loss the β-sheet geometry in the N-terminal region and it converted into random α-helix, turn and bend conformation. On comparing the RMSF of the Aβ42 peptide and Aβ42-Au144MC complex shows that the coordination of Au144MC results in greater rigidity of the Aβ42 peptide backbone regions with exemptions for the Asp1, Ala2, Glu3, Leu34, Ile41 and Ala42 residues due to the strong binding between the metal cluster and the CHC (Leu17-Ala21) region. The structural stability of the Aβ42 peptide and Aβ42-Au144MC complex is enhanced by the several intermolecular and intramolecular interactions and it was visibly revealed in the H-bond. From the above results, it is very evident that the Au144MC can be used as inhibitor agent for the oligomerization of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, India
| | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, 641046, India.
| | - Mansour K Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O.Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sadaf Zehra
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON, PO Box N9B 3P4, Canada
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13
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Matsushima Y, Irie Y, Kageyama Y, Bellier JP, Tooyama I, Maki T, Kume T, Yanagita RC, Irie K. Structure optimization of the toxic conformation model of amyloid β42 by intramolecular disulfide bond formation. Chembiochem 2022; 23:e202200029. [PMID: 35165998 DOI: 10.1002/cbic.202200029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2022] [Indexed: 11/07/2022]
Abstract
Amyloid β (Aβ) oligomers play a critical role in the pathology of Alzheimer's disease. Recently, we reported that a conformation-restricted Aβ42 with an intramolecular disulfide bond through cysteine residues at positions 17/28 formed stable oligomers with potent cytotoxicity. To further optimize this compound as a toxic conformer model, we synthesized three analogs with a combination of cysteine and homocysteine at positions 17/28. The analogs with Cys-Cys, Cys-homoCys, or homoCys-Cys, but not the homoCys-homoCys analog, exhibited potent cytotoxicity against SH-SY5Y and THP-1 cells even at 10 nM. In contrast, the cytotoxicity of conformation-restricted analogs at positions 16/29 or 18/27 was significantly weaker than that of wild-type Aβ42. Furthermore, a thioflavin-T assay, non-denaturing gel electrophoresis, and morphological study suggested that the majority of these conformation-restricted analogs existed in an oligomeric state in cell culture medium, indicating that the toxic conformation of Aβ42, rather than the oligomeric state, is essential to induce cytotoxicity.
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Affiliation(s)
- Yuka Matsushima
- Kyoto University Graduate School of Agriculture Faculty of Agriculture: Kyoto Daigaku Nogaku Kenkyuka Nogakubu, Division of Food Science and Biotechnology, JAPAN
| | - Yumi Irie
- Kyoto University Graduate School of Agriculture Faculty of Agriculture: Kyoto Daigaku Nogaku Kenkyuka Nogakubu, Division of Food Science and Biotechnology, JAPAN
| | - Yusuke Kageyama
- Shiga University of Medical Science: Shiga Ika Daigaku, Molecular Neuroscience Research Center, JAPAN
| | - Jean-Pierre Bellier
- Shiga University of Medical Science: Shiga Ika Daigaku, Molecular Neuroscience Research Center, JAPAN
| | - Ikuo Tooyama
- Shiga University of Medical Science: Shiga Ika Daigaku, Molecular Neuroscience Research Center, JAPAN
| | - Takahito Maki
- University of Toyama: Toyama Daigaku, Department of Applied Pharmacology, JAPAN
| | - Toshiaki Kume
- University of Toyama: Toyama Daigaku, Department of Applied Pharmacology, JAPAN
| | - Ryo C Yanagita
- Kagawa University Faculty of Agriculture Graduate School of Agriculture: Kagawa Daigaku Nogakubu Daigakuin Nogaku Kenkyuka, Department of Applied Biological Sciences, JAPAN
| | - Kazuhiro Irie
- Kyoto University Graduate School of Agriculture Faculty of Agriculture: Kyoto Daigaku Nogaku Kenkyuka Nogakubu, Division of Food Science and Biotechnology, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502, Kyoto, JAPAN
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14
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Shigemori H, Kobori A, Hosaka K. Inhibition of Amyloid β Aggregation by p-Terphenyl Derivatives Isolated from Boletopsis leucomelas. HETEROCYCLES 2022. [DOI: 10.3987/com-22-14628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Murakami K, Izuo N, Bitan G. Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases. J Biol Chem 2022; 298:101478. [PMID: 34896392 PMCID: PMC8728582 DOI: 10.1016/j.jbc.2021.101478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are oligonucleotides selected from large pools of random sequences based on their affinity for bioactive molecules and are used in similar ways to antibodies. Aptamers provide several advantages over antibodies, including their small size, facile, large-scale chemical synthesis, high stability, and low immunogenicity. Amyloidogenic proteins, whose aggregation is relevant to neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion diseases, are among the most challenging targets for aptamer development due to their conformational instability and heterogeneity, the same characteristics that make drug development against amyloidogenic proteins difficult. Recently, chemical tethering of aptagens (equivalent to antigens) and advances in high-throughput sequencing-based analysis have been used to overcome some of these challenges. In addition, internalization technologies using fusion to cellular receptors and extracellular vesicles have facilitated central nervous system (CNS) aptamer delivery. In view of the development of these techniques and resources, here we review antiamyloid aptamers, highlighting preclinical application to CNS therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Naotaka Izuo
- Laboratory of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA.
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16
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Tanaka T, Betkekar VV, Ohmori K, Suzuki K, Shigemori H. Evaluation of Amyloid Polypeptide Aggregation Inhibition and Disaggregation Activity of A-Type Procyanidins. Pharmaceuticals (Basel) 2021; 14:ph14111118. [PMID: 34832900 PMCID: PMC8623168 DOI: 10.3390/ph14111118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 01/21/2023] Open
Abstract
The number of people worldwide suffering from Alzheimer’s disease (AD) and type 2 diabetes (T2D) is on the rise. Amyloid polypeptides are thought to be associated with the onset of both diseases. Amyloid-β (Aβ) that aggregates in the brain and human islet amyloid polypeptide (hIAPP) that aggregates in the pancreas are considered cytotoxic and the cause of the development of AD and T2D, respectively. Thus, inhibiting amyloid polypeptide aggregation and disaggregation existing amyloid aggregates are promising approaches in the therapy and prevention against both diseases. Therefore, in this research, we evaluated the Aβ/hIAPP anti-aggregation and disaggregation activities of A-type procyanidins 1–7 and their substructures 8 and 9, by conducting structure–activity relationship studies and identified the active site. The thioflavin-T (Th-T) assay, which quantifies the degree of aggregation of amyloid polypeptides based on fluorescence intensity, and transmission electron microscopy (TEM), employed to directly observe amyloid polypeptides, were used to evaluate the activity. The results showed that catechol-containing compounds 1–6 exhibited Aβ/hIAPP anti-aggregation and disaggregation activities, while compound 7, without catechol, showed no activity. This suggests that the presence of catechol is important for both activities. Daily intake of foods containing A-type procyanidins may be effective in the prevention and treatment of both diseases.
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Affiliation(s)
- Taisei Tanaka
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan;
| | - Vipul V. Betkekar
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan; (V.V.B.); (K.O.); (K.S.)
| | - Ken Ohmori
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan; (V.V.B.); (K.O.); (K.S.)
| | - Keisuke Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan; (V.V.B.); (K.O.); (K.S.)
| | - Hideyuki Shigemori
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
- Correspondence: ; Tel.: +81-29-853-4603
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17
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Boopathi S, Poma AB, Garduño-Juárez R. An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure. Int J Mol Sci 2021; 22:10798. [PMID: 34639140 PMCID: PMC8509255 DOI: 10.3390/ijms221910798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023] Open
Abstract
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to fibril formation is crucial to develop therapeutic strategies for Alzheimer's disease (AD). Although experimental techniques rely on the measure of time- and space-average properties, they face severe difficulties in the investigation of Aβ peptide aggregation due to their intrinsically disorder character. Computer simulation is a tool that allows tracing the molecular motion of molecules; hence it complements Aβ experiments, as it allows to explore the binding mechanism between metal ions and Aβ oligomers close to the cellular membrane at the atomic resolution. In this context, integrated studies of experiments and computer simulations can assist in mapping the complete pathways of aggregation and toxicity of Aβ peptides. Aβ oligomers are disordered proteins, and due to a rapid exploration of their intrinsic conformational space in real-time, they are challenging therapeutic targets. Therefore, no good drug candidate could have been identified for clinical use. Our previous investigations identified two small molecules, M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine) and Gabapentin, capable of Aβ binding and inhibiting molecular aggregation, synaptotoxicity, intracellular calcium signaling, cellular toxicity and memory losses induced by Aβ. Thus, we recommend these molecules as novel candidates to assist anti-AD drug discovery in the near future. This review discusses the most recent research investigations about the Aβ dynamics in water, close contact with cell membranes, and several therapeutic strategies to remove plaque formation.
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Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research Polish Academy of Science, Pawińskiego 5B, 02-106 Warsaw, Poland
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
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18
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Fei X, Zhang Y, Mei Y, Yue X, Jiang W, Ai L, Yu Y, Luo H, Li H, Luo W, Yang X, Lyv J, He R, Song W, Tong Z. Degradation of FA reduces Aβ neurotoxicity and Alzheimer-related phenotypes. Mol Psychiatry 2021; 26:5578-5591. [PMID: 33328587 DOI: 10.1038/s41380-020-00929-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 02/05/2023]
Abstract
Dysregulation of formaldehyde (FA) has been implicated in the development of Alzheimer's Disease (AD). Elevated FA levels in Alzheimer's patients and animal models are associated with impaired cognitive functions. However, the exact role of FA in AD remains unknown. We now identified that oxidative demethylation at serine8/26 of amyloid-beta protein (Aβ) induced FA generation and FA cross-linked with the lysine28 residue in the β-turn of Aβ monomer to form Aβ dimers, and then accelerated Aβ oligomerization and fibrillogenesis in vitro. However, Aβ42 mutation in serine8/26, lysine28 abolished Aβ self-aggregation. Furthermore, Aβ inhibited the activity of formaldehyde dehydrogenase (FDH), the enzyme for FA degradation, resulting in FA accumulation. In turn, excess of FA stimulated Aβ aggregation both in vitro and in vivo by increasing the formation of Aβ oligomers and fibrils. We found that degradation of FA by formaldehyde scavenger-NaHSO3 or coenzyme Q10 reduced Aβ aggregation and ameliorated the neurotoxicity, and improved the cognitive performance in APP/PS1 mice. Our study provides evidence that endogenous FA is essential for Aβ self-aggregation and scavenging FA could be an effective strategy for treating AD.
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Affiliation(s)
- Xuechao Fei
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
| | - Yun Zhang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Yufei Mei
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangpei Yue
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
| | - Wenjing Jiang
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
- Center for Cognitive Disorders, Beijing Geriatric Hospital, 100095, Beijing, China
| | - Li Ai
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
| | - Yan Yu
- Chinese institute of Rehabilitation Science, China Rehabilitation Research Center, Beijing Key Laboratory of Neural Injury and Rehabilitation, 100068, Beijing, China
| | - Hongjun Luo
- Central Laboratory, Shantou University Medical College, Guangdong, 515041, China
| | - Hui Li
- Central Laboratory, Shantou University Medical College, Guangdong, 515041, China
| | - Wenhong Luo
- Central Laboratory, Shantou University Medical College, Guangdong, 515041, China
| | - Xu Yang
- Section of Environmental Biomedicine, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jihui Lyv
- Center for Cognitive Disorders, Beijing Geriatric Hospital, 100095, Beijing, China
| | - Rongqiao He
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China
- State Key Lab of Brain and Cognitive Science and Key Lab of Mental Health, IBP, UCAS, Beijing, China
| | - Weihong Song
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China.
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
| | - Zhiqian Tong
- Alzheimer's disease Center, Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, 100069, Beijing, China.
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19
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Murakami K, Horii S, Hanaki M, Irie K. Searching for Natural Products That Delay Nucleation Phase and Promote Elongation Phase of Amyloid β42 toward Alzheimer's Disease Therapeutics. ACS Chem Neurosci 2021; 12:3467-3476. [PMID: 34463471 DOI: 10.1021/acschemneuro.1c00489] [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: 11/28/2022] Open
Abstract
Aggregation of amyloid β42 (Aβ42) is one of the hallmarks of Alzheimer's disease (AD). The mechanism of Aβ42 aggregation mainly consists of two phases, nucleation and elongation (including plateau region as a saturation phase). During the nucleation phase, the monomer gradually forms toxic oligomers. During the elongation phase, each nucleus acts as a template and associates with monomers to initiate less toxic fibrillization. We previously proposed a method of classifying compounds into nine groups based on their ability to modulate the nucleation and/or elongation phases. An orcein derivative (O4), which is a phenoxazine dye isolated from the lichen Roccella tinctoria and containing a 2,5-cyclohexadienone moiety, was reported to convert oligomers into relatively inert fibrils, resulting in the reduction of the neurotoxicity of Aβ42. Focusing on O4 in the pursuit of anti-AD drugs, we herein screened 480 natural products including NPDepo (RIKEN) for the compounds that delayed the nucleation phase and promoted the elongation phase. The signal intensities for Aβ42 treated with each of the 15 compounds that met these criteria were lowered in dot blotting using antioligomer antibody, and the fibril formation of Aβ42 in the presence of these compounds was observed in transmission electron microscopy. Among the 15 compounds, 12 compounds (80%) reduced the toxicity of Aβ42 against mouse neuroblastoma Neuro-2a cells. Some of these anticytotoxic compounds contain 2-pyrone and 4-pyrone that interacted with Aβ42, maybe by shifting the equilibrium of Aβ from toxic oligomer into inert fibrils.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shiori Horii
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Mizuho Hanaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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20
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Soto-Ospina A, Araque Marín P, Bedoya G, Sepulveda-Falla D, Villegas Lanau A. Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site. Front Mol Biosci 2021; 8:649990. [PMID: 34150846 PMCID: PMC8206637 DOI: 10.3389/fmolb.2021.649990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer's disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.
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Affiliation(s)
- Alejandro Soto-Ospina
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- School of Life Sciences, Research and Innovation in Chemistry Formulations Group, EIA University, Envigado, Colombia
| | - Gabriel Bedoya
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrés Villegas Lanau
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
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21
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Illes-Toth E, Meisl G, Rempel DL, Knowles TPJ, Gross ML. Pulsed Hydrogen-Deuterium Exchange Reveals Altered Structures and Mechanisms in the Aggregation of Familial Alzheimer's Disease Mutants. ACS Chem Neurosci 2021; 12:1972-1982. [PMID: 33988976 DOI: 10.1021/acschemneuro.1c00072] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mutations of the Amyloid Precursor Protein, from which the amyloid β peptide Aβ42 is cleaved, are associated with familial Alzheimer's disease. The disease-relevant familial mutations include the Arctic (E22G), Iowa (D23N), Italian (E22K), Dutch (E22Q), Japanese (D7N), English (D6R), and Flemish (A21G) variants. A detailed mechanistic understanding of the aggregation behavior of the mutant peptides at the residue level is, however, still lacking. We report here a study of the aggregation kinetics of these mutants in vitro by pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to obtain a temporally and sequence resolved picture of their self-assembly. For all variants, HDX occurs to give a bimodal distribution representing two soluble classes of aggregates, one protected and one solvent-exposed. There is no evidence of other classes of structural intermediates within the detection limits of the HDX approach. The fractional changes in the bimodal exchange profiles for several regions of Aβ42 reveal that the central and C-terminal peptides gain protection upon fibril formation, whereas the N-terminal regions remain largely solvent-accessible. For these mutants, all peptide fragments follow the same kinetics, acquiring solvent protection at the same time, further supporting that there are no significant populations of intermediate species under our experimental conditions. The results demonstrate the potential of pulsed HDX-MS for resolving the region-specific aggregation behavior of Aβ42 isoforms in solution where X-ray crystallography and solid-state NMR (ssNMR) are challenged.
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Affiliation(s)
- Eva Illes-Toth
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
| | - Georg Meisl
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Don L. Rempel
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
| | - Tuomas P. J. Knowles
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michael L. Gross
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
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22
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An evaluation of the self-assembly enhancing properties of cell-derived hexameric amyloid-β. Sci Rep 2021; 11:11570. [PMID: 34078941 PMCID: PMC8172837 DOI: 10.1038/s41598-021-90680-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
A key hallmark of Alzheimer’s disease is the extracellular deposition of amyloid plaques composed primarily of the amyloidogenic amyloid-β (Aβ) peptide. The Aβ peptide is a product of sequential cleavage of the Amyloid Precursor Protein, the first step of which gives rise to a C-terminal Fragment (C99). Cleavage of C99 by γ-secretase activity releases Aβ of several lengths and the Aβ42 isoform in particular has been identified as being neurotoxic. The misfolding of Aβ leads to subsequent amyloid fibril formation by nucleated polymerisation. This requires an initial and critical nucleus for self-assembly. Here, we identify and characterise the composition and self-assembly properties of cell-derived hexameric Aβ42 and show its assembly enhancing properties which are dependent on the Aβ monomer availability. Identification of nucleating assemblies that contribute to self-assembly in this way may serve as therapeutic targets to prevent the formation of toxic oligomers.
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23
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Hofmann J, Ginex T, Espargaró A, Scheiner M, Gunesch S, Aragó M, Stigloher C, Sabaté R, Luque FJ, Decker M. Azobioisosteres of Curcumin with Pronounced Activity against Amyloid Aggregation, Intracellular Oxidative Stress, and Neuroinflammation. Chemistry 2021; 27:6015-6027. [PMID: 33666306 PMCID: PMC8048673 DOI: 10.1002/chem.202005263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/14/2021] [Indexed: 01/01/2023]
Abstract
Many (poly-)phenolic natural products, for example, curcumin and taxifolin, have been studied for their activity against specific hallmarks of neurodegeneration, such as amyloid-β 42 (Aβ42) aggregation and neuroinflammation. Due to their drawbacks, arising from poor pharmacokinetics, rapid metabolism, and even instability in aqueous medium, the biological activity of azobenzene compounds carrying a pharmacophoric catechol group, which have been designed as bioisoteres of curcumin has been examined. Molecular simulations reveal the ability of these compounds to form a hydrophobic cluster with Aβ42, which adopts different folds, affecting the propensity to populate fibril-like conformations. Furthermore, the curcumin bioisosteres exceeded the parent compound in activity against Aβ42 aggregation inhibition, glutamate-induced intracellular oxidative stress in HT22 cells, and neuroinflammation in microglial BV-2 cells. The most active compound prevented apoptosis of HT22 cells at a concentration of 2.5 μm (83 % cell survival), whereas curcumin only showed very low protection at 10 μm (21 % cell survival).
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Affiliation(s)
- Julian Hofmann
- Pharmaceutical and Medicinal ChemistryInstitute of, Pharmacy and Food ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Tiziana Ginex
- Department of Nutrition Food Science and GastronomyFaculty of Pharmacy, Institute of Theoretical and Computational, Chemistry and Institute of Biomedicine, Campus TorriberaUniversity of BarcelonaSanta Coloma de Gramenet08921Spain
| | - Alba Espargaró
- Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy Institute of Nanoscience and Nanotechnology, (IN2UB)University of Barcelona08028BarcelonaSpain
| | - Matthias Scheiner
- Pharmaceutical and Medicinal ChemistryInstitute of, Pharmacy and Food ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Sandra Gunesch
- Pharmaceutical and Medicinal ChemistryInstitute of, Pharmacy and Food ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Marc Aragó
- Department of Nutrition Food Science and GastronomyFaculty of Pharmacy, Institute of Theoretical and Computational, Chemistry and Institute of Biomedicine, Campus TorriberaUniversity of BarcelonaSanta Coloma de Gramenet08921Spain
| | - Christian Stigloher
- Imaging Core FacilityBiocenter/Theodor-Boveri-InstituteUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Raimon Sabaté
- Pharmacy and Pharmaceutical Technology and Physical-ChemistrySchool of Pharmacy Institute of Nanoscience and Nanotechnology, (IN2UB)University of Barcelona08028BarcelonaSpain
| | - F. Javier Luque
- Department of Nutrition Food Science and GastronomyFaculty of Pharmacy, Institute of Theoretical and Computational, Chemistry and Institute of Biomedicine, Campus TorriberaUniversity of BarcelonaSanta Coloma de Gramenet08921Spain
| | - Michael Decker
- Pharmaceutical and Medicinal ChemistryInstitute of, Pharmacy and Food ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
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24
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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25
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Fu Z, Van Nostrand WE, Smith SO. Anti-Parallel β-Hairpin Structure in Soluble Aβ Oligomers of Aβ40-Dutch and Aβ40-Iowa. Int J Mol Sci 2021; 22:ijms22031225. [PMID: 33513738 PMCID: PMC7865275 DOI: 10.3390/ijms22031225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022] Open
Abstract
The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the dominant component of cored parenchymal plaques associated with AD, while Aβ40 is the predominant component of vascular amyloid associated with CAA. There are familial CAA mutations at positions Glu22 and Asp23 that lead to aggressive Aβ aggregation, drive vascular amyloid deposition and result in degradation of vascular membranes. In this study, we compared the transition of the monomeric Aβ40-WT peptide into soluble oligomers and fibrils with the corresponding transitions of the Aβ40-Dutch (E22Q), Aβ40-Iowa (D23N) and Aβ40-Dutch, Iowa (E22Q, D23N) mutants. FTIR measurements show that in a fashion similar to Aβ40-WT, the familial CAA mutants form transient intermediates with anti-parallel β-structure. This structure appears before the formation of cross-β-sheet fibrils as determined by thioflavin T fluorescence and circular dichroism spectroscopy and occurs when AFM images reveal the presence of soluble oligomers and protofibrils. Although the anti-parallel β-hairpin is a common intermediate on the pathway to Aβ fibrils for the four peptides studied, the rate of conversion to cross-β-sheet fibril structure differs for each.
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Affiliation(s)
- Ziao Fu
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
| | - William E. Van Nostrand
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA;
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Steven O. Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
- Correspondence: ; Tel.: +1-631-632-1210
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26
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Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. J Chem Inf Model 2021; 61:298-310. [PMID: 33440932 DOI: 10.1021/acs.jcim.0c01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydration thermodynamics of amyloid-β (Aβ) and its pathogenic familial Alzheimer's disease (FAD) mutants such as A2V, Taiwan (D7H), Tottori (D7N), and English (H6R) and the protective A2T mutant is investigated by a combination of all-atom, explicit water molecular dynamics (MD) simulations and the three-dimensional reference interaction site model (3D-RISM) theory. The change in the hydration free energy on mutation is decomposed into the energetic and entropic components, which comprise electrostatic and nonelectrostatic contributions. An increase in the hydration free energy is observed for A2V, D7H, D7N, and H6R mutations that increase the aggregation propensity of Aβ and lead to an early onset of Alzheimer's disease, while a reverse trend is noted for the protective A2T mutation. An antiphase correlation is found between the change in the hydration energy and the internal energy of Aβ upon mutation. A residue-wise decomposition analysis shows that the change in the hydration free energy of Aβ on mutation is primarily due to the hydration/dehydration of the side-chain atoms of the negatively charged residues. The decrease in the hydration of the negatively charged residues on mutation may decrease the solubility of the mutant, which increases the observed aggregation propensity of the FAD mutants. Results obtained from the theory show an excellent match with the experimentally reported data.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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27
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Masuda Y. Bioactive 3D structures of naturally occurring peptides and their application in drug design. Biosci Biotechnol Biochem 2021; 85:24-32. [PMID: 33577656 DOI: 10.1093/bbb/zbaa008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 11/14/2022]
Abstract
Naturally occurring peptides form unique 3D structures, which are critical for their bioactivities. To gain useful insights into drug design, the relationship between the 3D structure and bioactivity of the peptides has been studied. Solid-state nuclear magnetic resonance (NMR) analysis of the 42-residue amyloid β-protein (Aβ42) suggested the presence of toxic conformers with a turn structure at positions 22 and 23 in the aggregates. Antibodies specific to this turn structure could be utilized for immunotherapy and early diagnosis of Alzheimer's disease. Solution NMR analysis of apratoxin A, a cyclic depsipeptide with potent cytotoxicity, proposed an accurate structural model with an important bend structure, which led to the development of highly active mimetics. X-ray crystal analysis of PF1171F, a cyclic hexapeptide with insecticidal activity, indicated the formation of 4 intramolecular hydrogen bonds, which play an important role in cell membrane permeability of PF1171F.
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Affiliation(s)
- Yuichi Masuda
- Graduate School of Bioresources, Mie University, Tsu, Japan
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28
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Effects of clovamide and its related compounds on the aggregations of amyloid polypeptides. J Nat Med 2021; 75:299-307. [PMID: 33389592 DOI: 10.1007/s11418-020-01467-w] [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] [Received: 08/20/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease (AD) and type 2 diabetes (T2D) are common diseases in the elderly, and the increasing number of patients with these diseases has become a serious health problem worldwide. The aggregation and development of plaque of amyloid polypeptides (amyloid β; Aβ and human islet amyloid polypeptide; hIAPP, amylin) are found in the brains of patients with AD and the pancreas of patients with T2D and are considered to be, in part, the causes of both diseases, respectively. Therefore, preventing amyloid aggregation may be a promising therapeutic strategy for preventing AD and T2D. In addition, the disaggregation of the already aggregated amyloid polypeptides is expected to contribute to the prevention and treatment of both diseases as amyloid polypeptide aggregations begin several decades before the onset of disease. Therefore, in this study, we investigated the hIAPP aggregation inhibitory activity and Aβ42/hIAPP disaggregation activity of clovamide which had shown inhibitory activity against Aβ42 aggregation in our previous studies. In addition, active sites were identified (structure-activity relationship analysis) using clovamide-related compounds in which hydroxyl groups of these compounds were either eliminated or methylated. Our results showed that the compounds with one or two catechol moieties showed strong hIAPP aggregation inhibitory activity and Aβ42/hIAPP disaggregation activity; and the non-catechol type compounds showed little or no activity. This suggests that the catechol moiety is important in amyloid polypeptide aggregation inhibition and disaggregation. Thus, clovamide and its related compounds may be promising therapeutic strategies for inhibiting amyloid polypeptide-related pathology in AD and T2D.
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29
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Söldner CA, Sticht H, Horn AH. Molecular Simulations and Alzheimer׳s Disease. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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30
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Murakami K, Yamaguchi T, Izuo N, Kume T, Hara H, Irie K. Synthetic and Biophysical Studies on the Toxic Conformer in Amyloid β with the E22Δ Mutation in Alzheimer Pathology. ACS Chem Neurosci 2020; 11:3017-3024. [PMID: 32790274 DOI: 10.1021/acschemneuro.0c00331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The toxic conformer of the 40- or 42-mer-amyloid β-proteins (Aβ) (Aβ40, Aβ42) with a turn at positions 22 and 23 plays a role in oligomer formation, leading to neurotoxicity as part of the pathogenesis of Alzheimer's disease (AD). A deletion mutant at Glu22 (E22Δ) of Aβ, known as an Osaka mutation, accelerates oligomerization. Although E22Δ-Aβ has not been found to be toxic to cultured neuronal cells and is instead synaptotoxic in long-term potentiation, there is no information on the toxic conformer of E22Δ-Aβ in AD. The site-directed spin labeling study of E22Δ-Aβ40 by continuous wave-electron spin resonance (CW-ESR) spectroscopy in part showed the spatial proximity between positions 10 and 35, which are characteristic of the toxic conformation of Aβ, indicating the existence of a toxic conformer of Aβ with the E22Δ mutation. To obtain structural insight, E22Δ-Aβ42 substitutes with proline (F20P, A21P, D23P, and V24P), in which proline is known as a turn inducer but is a β-sheet breaker, were synthesized. An enzyme immunoassay using the 24B3 antibody recognizing toxic conformer of Aβ was carried out. 24B3 reacted with these substitutes of E22Δ-Aβ42 as well as E22Δ-Aβ42 in a similar manner to WT-Aβ42. Notably, only A21P-E22Δ-Aβ42 exhibited strong neurotoxicity in rat primary neurons after 8 days of incubation, with potent high-order oligomerization compared with E22Δ-Aβ42. These results suggest that E22Δ-Aβ42 could enhance neurotoxicity by generating a toxic oligomer conformation with a turn near position 21.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Tomomi Yamaguchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Naotaka Izuo
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Toshiaki Kume
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hideyuki Hara
- BioSpin Division, Bruker Japan K. K., Yokohama 221-0022, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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31
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Amirkulova DB, Chakraborty M, White AD. Experimentally Consistent Simulation of Aβ 21-30 Peptides with a Minimal NMR Bias. J Phys Chem B 2020; 124:8266-8277. [PMID: 32845146 DOI: 10.1021/acs.jpcb.0c07129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolded amyloid peptides are neurotoxic molecules associated with Alzheimer's disease. The Aβ21-30 peptide fragment is a decapeptide fragment of the complete Aβ42 peptide which is a hypothesized cause of Alzheimer's disease via amyloid fibrillogenesis. Aβ21-30 is investigated here with a combination of NMR (nuclear magnetic resonance) spectroscopy experiments and molecular dynamics simulations with experiment directed simulation (EDS). EDS is a maximum entropy biasing method that augments a molecular dynamics simulation with experimental data (NMR chemical shifts) to improve agreement with experiments and thus accuracy. EDS molecular dynamics shows that the Aβ21-30 monomer has a β turn stabilized by the following interactions: S26-K28, D23-S26, and D23-K28. NMR, total correlation spectroscopy, and rotating frame Overhauser effect spectroscopy experiments provide independent agreement. Subsequent two- and four-monomer EDS simulations show aggregation. Diffusion coefficients calculated from molecular simulation also agreed with experimentally measured values only after using EDS, providing independent assessment of accuracy. This work demonstrates how accuracy can be improved by directly using experimental data in molecular dynamics of complex processes like self-assembly.
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Affiliation(s)
- Dilnoza B Amirkulova
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Maghesree Chakraborty
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Andrew D White
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
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32
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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33
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Aggarwal L, Biswas P. Interaction Volume Is a Measure of the Aggregation Propensity of Amyloid-β. J Phys Chem Lett 2020; 11:3993-4000. [PMID: 32352786 DOI: 10.1021/acs.jpclett.0c00922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study highlights the significance of the partial molar volume of amino acids in predicting the aggregation propensity of an intrinsically disordered protein, amyloid-β (Aβ), and its mutants in aqueous solution. The change in the interaction volume of the protein or mutant is quantitatively correlated with its calculated experimental aggregation propensity. This method also reveals how the interaction volume may be tuned by changing the charge and hydrophobicity of Aβ. While a positive change in the interaction volume and a higher aggregation propensity are observed for mutants with a decrease in the overall charge and/or an increase in hydrophobicity, a reverse trend is observed for the mutants with a decrease in the hydrophobicity and/or an increase in its charge. Hence, the interaction volume may be considered as a key parameter for monitoring protein aggregation that bridges the gap between the experimental aggregation kinetics and solvation thermodynamics.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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34
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Murakami K, Kato H, Hanaki M, Monobe Y, Akagi KI, Kawase T, Hirose K, Irie K. Synthetic and biochemical studies on the effect of persulfidation on disulfide dimer models of amyloid β42 at position 35 in Alzheimer's etiology. RSC Adv 2020; 10:19506-19512. [PMID: 35515472 PMCID: PMC9054097 DOI: 10.1039/d0ra03429k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/08/2020] [Indexed: 11/21/2022] Open
Abstract
Protein persulfidation plays a role in redox signaling as an anti-oxidant. Dimers of amyloid β42 (Aβ42), which induces oxidative stress-associated neurotoxicity as a causative agent of Alzheimer's disease (AD), are minimum units of oligomers in AD pathology. Met35 can be susceptible to persulfidation through its substitution to homoCys residue under the condition of oxidative stress. In order to verify whether persulfidation has an effect in AD, herein we report a chemical approach by synthesizing disulfide dimers of Aβ42 and their evaluation of biochemical properties. A homoCys-disulfide dimer model at position 35 of Aβ42 formed a partial β-sheet structure, but its neurotoxicity was much weaker than that of the corresponding monomer. In contrast, the congener with an alkyl linker generated β-sheet-rich 8–16-mer oligomers with potent neurotoxicity. The length of protofibrils generated from the homoCys-disulfide dimer model was shorter than that of its congener with an alkyl linker. Therefore, the current data do not support the involvement of Aβ42 persulfidation in Alzheimer's disease. Our data do not support the Aβ42 persulfidation hypothesis in Alzheimer's etiology because the neurotoxicity of the homoCys-disulfide-Aβ42 dimer was very weak.![]()
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University Kyoto 606-8502 Japan
| | - Haruka Kato
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University Kyoto 606-8502 Japan
| | - Mizuho Hanaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University Kyoto 606-8502 Japan
| | - Yoko Monobe
- National Institute of Biomedical Innovation, Health and Nutrition Osaka 567-0085 Japan
| | - Ken-Ichi Akagi
- National Institute of Biomedical Innovation, Health and Nutrition Osaka 567-0085 Japan
| | | | | | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University Kyoto 606-8502 Japan
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35
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Murakami K, Obata Y, Sekikawa A, Ueda H, Izuo N, Awano T, Takabe K, Shimizu T, Irie K. An RNA aptamer with potent affinity for a toxic dimer of amyloid β42 has potential utility for histochemical studies of Alzheimer's disease. J Biol Chem 2020; 295:4870-4880. [PMID: 32127399 DOI: 10.1074/jbc.ra119.010955] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/29/2020] [Indexed: 01/16/2023] Open
Abstract
Oligomers of β-amyloid 42 (Aβ42), rather than fibrils, drive the pathogenesis of Alzheimer's disease (AD). In particular, toxic oligomeric species called protofibrils (PFs) have attracted significant attention. Herein, we report RNA aptamers with higher affinity toward PFs derived from a toxic Aβ42 dimer than toward fibrils produced from WT Aβ42 or from a toxic, conformationally constrained Aβ42 variant, E22P-Aβ42. We obtained these RNA aptamers by using the preincubated dimer model of E22P-Aβ42, which dimerized via a linker located at Val-40, as the target of in vitro selection. This dimer formed PFs during incubation. Several physicochemical characteristics of an identified aptamer, E22P-AbD43, suggested that preferential affinity of this aptamer toward PFs is due to its higher affinity for the toxic dimer unit (KD = 20 ± 6.0 nm) of Aβ42 than for less-toxic Aβ40 aggregates. Comparison of CD data from the full-length and random regions of E22P-AbD43 suggested that the preferential binding of E22P-AbD43 toward the dimer might be related to the formation of a G-quadruplex structure. E22P-AbD43 significantly inhibited the nucleation phase of the dimer and its associated neurotoxicity in SH-SY5Y human neuroblastoma cells. Of note, E22P-AbD43 also significantly protected against the neurotoxicity of WT Aβ42 and E22P-Aβ42. Furthermore, in an AD mouse model, E22P-AbD43 preferentially recognized diffuse aggregates, which likely originated from PFs or higher-order oligomers with curvilinear structures, compared with senile plaques formed from fibrils. We conclude that the E22P-AbD43 aptamer is a promising research and diagnostic tool for further studies of AD etiology.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yayoi Obata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Asa Sekikawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Haruka Ueda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Naotaka Izuo
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Tatsuya Awano
- Division of Forest and Biomaterials Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Keiji Takabe
- Division of Forest and Biomaterials Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiko Shimizu
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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36
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Irie K. New diagnostic method for Alzheimer’s disease based on the toxic conformation theory of amyloid β. Biosci Biotechnol Biochem 2020; 84:1-16. [DOI: 10.1080/09168451.2019.1667222] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Abstract
Recent investigations suggest that soluble oligomeric amyloid β (Aβ) species may be involved in early onset of Alzheimer’s disease (AD). Using systematic proline replacement, solid-state NMR, and ESR, we identified a toxic turn at position 22 and 23 of Aβ42, the most potent neurotoxic Aβ species. Through radicalization, the toxic turn can induce formation of the C-terminal hydrophobic core to obtain putative Aβ42 dimers and trimers. Synthesized dimer and trimer models showed that the C-terminal hydrophobic core plays a critical role in the formation of high molecular weight oligomers with neurotoxicity. Accordingly, an anti-toxic turn antibody (24B3) that selectively recognizes a toxic dimer model of E22P-Aβ42 was developed. Sandwich enzyme-linked immunosorbent assay with 24B3 and 82E1 detected a significantly higher ratio of Aβ42 with a toxic turn to total Aβ42 in cerebrospinal fluid of AD patients compared with controls, suggesting that 24B3 could be useful for early onset of AD diagnosis.
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Affiliation(s)
- Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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37
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Molecular dynamics simulations of copper binding to amyloid-β Glu22 mutants. Heliyon 2019; 6:e03071. [PMID: 31909253 PMCID: PMC6940626 DOI: 10.1016/j.heliyon.2019.e03071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 11/25/2019] [Accepted: 12/13/2019] [Indexed: 11/21/2022] Open
Abstract
We report microsecond timescale ligand field molecular dynamics simulations of the copper complexes of three known mutants of the amyloid-β peptide, E22G, E22Q and E22K, alongside the naturally occurring sequence. We find that all three mutants lead to formation of less compact structures than the wild-type: E22Q is the most similar to the native peptide, while E22G and especially E22K are markedly different in size, shape and stability. Turn and coil structures dominate all structures studied but subtle differences in helical and β-sheet distribution are noted, especially in the C-terminal region. The origin of these changes is traced to disruption of key salt bridges: in particular, the Asp23-Lys28 bridge that is prevalent in the wild-type is absent in E22G and E22K, while Lys22 in the latter mutant forms a strong association with Asp23. We surmise that the drastically different pattern of salt bridges in the mutants lead to adoption of a different structural ensemble of the peptide backbone, and speculate that this might affect the ability of the mutant peptides to aggregate in the same manner as known for the wild-type.
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38
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Xi W, Vanderford EK, Liao Q, Hansmann UHE. Stability of Aβ-fibril fragments in the presence of fatty acids. Protein Sci 2019; 28:1973-1981. [PMID: 31461191 DOI: 10.1002/pro.3719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 11/07/2022]
Abstract
We consider the effect of lauric acid on the stability of various fibril-like assemblies of Aβ peptides. For this purpose, we have performed molecular dynamics simulations of these assemblies either in complex with lauric acid or without presence of the ligand. While we do not observe a stabilizing effect on Aβ40 -fibrils, we find that addition of lauric acid strengthens the stability of fibrils built from the triple-stranded S-shaped Aβ42 -peptides considered to be more toxic. Or results may help to understand how the specifics of the brain-environment modulate amyloid formation and propagation.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Elliott K Vanderford
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Qinxin Liao
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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39
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Thu TTM, Co NT, Tu LA, Li MS. Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state. J Chem Phys 2019; 150:225101. [PMID: 31202253 DOI: 10.1063/1.5096379] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the key factors that govern the rate of protein aggregation is of immense interest since protein aggregation is associated with a number of neurodegenerative diseases. Previous experimental and theoretical studies have revealed that the hydrophobicity, charge, and population of the fibril-prone monomeric state control the fibril formation rate. Because the fibril structures consist of cross beta sheets, it is widely believed that those sequences that have a high beta content (β) in the monomeric state should have high aggregation rates as the monomer can serve as a template for fibril growth. However, this important fact has never been explicitly proven, motivating us to carry out this study. Using replica exchange molecular dynamics simulation with implicit water, we have computed β of 19 mutations of amyloid beta peptide of 42 residues (Aβ42) for which the aggregation rate κ has been measured experimentally. We have found that κ depends on β in such a way that the higher the propensity to aggregation, the higher the beta content in the monomeric state. Thus, we have solved a long-standing problem of the dependence of fibril formation time of the β-structure on a quantitative level.
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Affiliation(s)
- Tran Thi Minh Thu
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Ly Anh Tu
- Department of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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40
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Abstract
Amyloid precursor A4 (770 amino acids (aa)) dimerizes and aggregates, as do its C-terminal (99 aa) and amyloid Aβ (40,42 aa Aβ40,Aβ42) fragments. The titled question has been discussed extensively, and here it is addressed further using thermodynamic scaling theory to analyze mutational trends in structural factors and kinetics. Special attention is given to Family Alzheimer's disease mutations in C99 outside Aβ42 centered on Aβ46. The scaling analysis is connected to extensive C99 docking simulations which included membranes ( Sun et al. J. Chem. Inf. Model. 2017 , 57 , 1375 - 1387 ), thereby confirming their C99 results and extending them to A4.
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Affiliation(s)
- James C. Phillips
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, United States
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41
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Izuo N, Murakami K, Fujihara Y, Maeda M, Saito T, Saido TC, Irie K, Shimizu T. An App knock-in mouse inducing the formation of a toxic conformer of Aβ as a model for evaluating only oligomer-induced cognitive decline in Alzheimer's disease. Biochem Biophys Res Commun 2019; 515:462-467. [PMID: 31164199 DOI: 10.1016/j.bbrc.2019.05.131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/19/2019] [Indexed: 12/27/2022]
Abstract
Irie and colleagues identified a "toxic conformer", which possesses a turn structure at positions 22-23, among various conformations of Aβ and have been reporting its potent oligomeric capacity and neurotoxicity. This toxic conformer was detected in the brains of AD patients and AD model mice (Tg2576 line), and passive immunization targeting this conformer ameliorated the cognitive dysfunction in an AD model. In this study, we developed a novel AD mouse model (AppNL-P-F/NL-P-F) with Swedish mutation (NL), Iberian mutation (F), and mutation (P) overproducing E22P-Aβ, a mimic of the toxic conformer, utilizing the knock-in technique that well recapitulates the Aβ pathology of AD patients in mice and avoids the artificial phenotype observed in transgenic-type model mice. We confirmed that AppNL-P-F/NL-P-F mice produce Aβ by ELISA and accumulate senile plaques by immunohistochemistry at eight months of age. In WB, we observed a potential trimer band and high molecular-weight oligomer bands without a monomeric band in the TBS-soluble fraction of AppNL-P-F/NL-P-F mice at six months of age. In the novel object recognition test, cognitive impairment was observed at six months of age in these mice. These findings suggest that the toxic conformer of Aβ induces cognitive dysfunction mediated by its oligomer formation in this mouse brain. AppNL-P-F/NL-P-F mice may be a useful model for evaluating Aβ oligomer-induced cognitive impairment in AD and will aid in exploring therapeutic targets for AD pathology.
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Affiliation(s)
- Naotaka Izuo
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan; Vascular Neurodegeneration Laboratory, The Florey Institute of Neuroscience and Mental Health, Melbourne University, VIC, Australia
| | - Kazuma Murakami
- Division of Food Science & Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshitaka Fujihara
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Masahiro Maeda
- Immuno-Biological Laboratories Co, Ltd, Fujioka-shi, Gumma, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
| | - Kazuhiro Irie
- Division of Food Science & Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahiko Shimizu
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan; Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Japan.
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42
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Salimi A, Li H, Shi H, Lee JY. Intrinsic origin of amyloid aggregation: Behavior of histidine (εεε) and (δδδ) tautomer homodimers of Aβ (1–40). Biochim Biophys Acta Gen Subj 2019; 1863:795-801. [DOI: 10.1016/j.bbagen.2019.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 02/08/2023]
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43
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Mudedla SK, Murugan NA, Ågren H. Effect of Familial Mutations on the Interconversion of α-Helix to β-Sheet Structures in an Amyloid-Forming Peptide: Insight from Umbrella Sampling Simulations. ACS Chem Neurosci 2019; 10:1347-1354. [PMID: 30586502 DOI: 10.1021/acschemneuro.8b00425] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Understanding the initial events of aggregation of amyloid β monomers to form β-sheet rich fibrils is useful for the development of therapeutics for Alzheimer's disease. In this context, the changes in energetics involved in the aggregation of helical amyloid β monomers into β-sheet rich dimers have been investigated using umbrella sampling simulations and density functional theory calculations. The results from umbrella sampling simulations for the free energy profile for the interconversion closely agree with the results of density functional theory calculations. The results reveal that helical peptides converted to β-sheet structures through coil-like conformations as intermediates that are mostly stabilized by intramolecular hydrogen bonds. The stabilization of intermediate structures could be a possible way to inhibit fibril formation. Mutations substantially decrease the height of the energy barrier for interconversion from α-helix to β-sheet structure when compared to that of the wild type, something that is attributed to an increase in the number of intramolecular hydrogen bonds between backbone atoms in the coil structures that correspond to a maximum value on the free energy surface. The reduction of the energy barrier leads to an enhancement of the rate of aggregation of amyloid β monomers upon introduction of various familial mutations, which is consistent with previous experimental reports.
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Affiliation(s)
- Sathish Kumar Mudedla
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
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44
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Lin Y, Im H, Diem LT, Ham S. Characterizing the structural and thermodynamic properties of Aβ42 and Aβ40. Biochem Biophys Res Commun 2019; 510:442-448. [PMID: 30722990 DOI: 10.1016/j.bbrc.2019.01.124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 01/20/2023]
Abstract
The self-assembly of amyloid-beta (Aβ) proteins in aqueous extracellular environments is implicated in Alzheimer's disease. Among several alloforms of Aβ proteins differing in sequence length, the 42- and 40-residue forms (Aβ42 and Aβ40) are the most abundant ones in the human body. Although the only difference is the additional I41A42 residues in the C-terminus, Aβ42 exhibits more aggregation tendency and stronger neurotoxicity than Aβ40. Here, we investigate the molecular factors that confer more aggregation potential to Aβ42 than to Aβ40 based on molecular dynamics simulations combined with solvation thermodynamic analyses. It is observed that the most salient structural feature of Aβ42 relative to Aβ40 is the more enhanced β-sheet forming tendency, in particular in the C-terminal region. While such a structural characteristic of Aβ42 will certainly serve to facilitate the formation of aggregate species rich in β-sheet structure, we also detect its interesting thermodynamic consequence. Indeed, we find from the decomposition analysis that the C-terminal region substantially increases the solvation free energy (i.e., overall "hydrophobicity") of Aβ42, which is caused by the dehydration of the backbone moieties showing the enhanced tendency of forming the β-structure. Together with the two additional hydrophobic residues (I41A42), this leads to the higher solvation free energy of Aβ42, implying the larger water-mediated attraction toward the self-assembly. Thus, our computational results provide structural and thermodynamic grounds on why Aβ42 has more aggregation propensity than Aβ40 in aqueous environments.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Haeri Im
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Le Thi Diem
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul, 04310, South Korea.
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45
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Irie Y, Hanaki M, Murakami K, Imamoto T, Furuta T, Kawabata T, Kawase T, Hirose K, Monobe Y, Akagi KI, Yanagita RC, Irie K. Synthesis and biochemical characterization of quasi-stable trimer models of full-length amyloid β40 with a toxic conformation. Chem Commun (Camb) 2019; 55:182-185. [DOI: 10.1039/c8cc08618d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The only trimer model to exhibit weak but significant neurotoxicity against SH-SY5Y cells was the one which was linked at position 38.
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Affiliation(s)
- Yumi Irie
- Division of Food Science and Biotechnology
- Graduate School of Agriculture
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Mizuho Hanaki
- Division of Food Science and Biotechnology
- Graduate School of Agriculture
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Kazuma Murakami
- Division of Food Science and Biotechnology
- Graduate School of Agriculture
- Kyoto University
- Kyoto 606-8502
- Japan
| | | | - Takumi Furuta
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Takeo Kawabata
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | | | | | - Yoko Monobe
- National Institute of Biomedical Innovation
- Health and Nutrition
- Osaka 567-0085
- Japan
| | - Ken-ichi Akagi
- National Institute of Biomedical Innovation
- Health and Nutrition
- Osaka 567-0085
- Japan
| | - Ryo C. Yanagita
- Department of Applied Biological Science
- Faculty of Agriculture
- Kagawa University
- Kagawa 761-0795
- Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology
- Graduate School of Agriculture
- Kyoto University
- Kyoto 606-8502
- Japan
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46
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Li X, Lei J, Qi R, Xie L, Wei G. Mechanistic insight into E22Q-mutation-induced antiparallel-to-parallel β-sheet transition of Aβ16−22fibrils: an all-atom simulation study. Phys Chem Chem Phys 2019; 21:15686-15694. [DOI: 10.1039/c9cp02561h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
E22Q mutation of Aβ16−22fibrils facilitates parallel β-sheet formation by enhancing Q22–Q22 hydrogen-bonding interaction and A21–A21, F20–F20, F19–F19 and V18–V18 hydrophobic interaction.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Luogang Xie
- College of Physics and Electronic Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 453002
- People's Republic of China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
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47
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Xi W, Hansmann UHE. Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant Aβ 40 fibrils. J Chem Phys 2018; 148:045103. [PMID: 29390821 DOI: 10.1063/1.5016166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Using a variant of Hamilton-replica-exchange, we study for wild type and Iowa mutant Aβ40 the conversion between fibrils with antiparallel β-sheets and such with parallel β-sheets. We show that wild type and mutant form distinct salt bridges that in turn stabilize different fibril organizations. The conversion between the two fibril forms leads to the release of small aggregates that in the Iowa mutant may shift the equilibrium from fibrils to more toxic oligomers.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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48
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Basu S, Biswas P. Salt-bridge dynamics in intrinsically disordered proteins: A trade-off between electrostatic interactions and structural flexibility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:624-641. [DOI: 10.1016/j.bbapap.2018.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/13/2018] [Accepted: 03/07/2018] [Indexed: 12/29/2022]
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49
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Tsunoda T, Takase M, Shigemori H. Structure-activity relationship of clovamide and its related compounds for the inhibition of amyloid β aggregation. Bioorg Med Chem 2018; 26:3202-3209. [PMID: 29706525 DOI: 10.1016/j.bmc.2018.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD), a neurodegenerative disorder, is characterized by aggregation of amyloid β-protein (Aβ). Aβ aggregates through β-sheet formation and induces cytotoxicity against neuronal cells. Inhibition of Aβ aggregation by naturally occurring compounds is thus a promising strategy for the treatment of AD. We have already reported that caffeoylquinic acids and phenylethanoid glycosides, which possess two or more catechol moieties, strongly inhibited Aβ aggregation. Clovamide (1) containing two catechol moieties, isolated from cacao beans (Theobroma cacao L.), is believed to exhibit preventive effects on Aβ aggregation. To investigate the structure-activity relationship of clovamide (1) for the inhibition of Aβ aggregation, we synthesized 1 and related compounds 2-11 through reaction between l-DOPA, d-DOPA, l-tyrosine, or l-phenylalanine and caffeic acid, p-coumaric acid, or cinnamic acid, and compounds 12 and 13 were derived from 1. Among tested compounds 1-13, those containing one or two catechol moieties exhibited potent anti-aggregation activity, whereas the non-catechol-type related compounds showed little or no activity. This suggests that at least one catechol moiety is essential for inhibition of Aβ42 aggregation, and this activity increases depending on the number of catechol moieties. Consequently, clovamide (1) and its related compounds may be a promising therapeutic option for inhibiting Aβ-mediated pathology in AD.
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Affiliation(s)
- Tatsuhiko Tsunoda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Mio Takase
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideyuki Shigemori
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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50
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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