1
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Tsukano C, Uchino A, Irie K. Synthesis and applications of symmetric amino acid derivatives. Org Biomol Chem 2024; 22:411-428. [PMID: 37877370 DOI: 10.1039/d3ob01379k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Symmetric α-amino acid derivatives can be used for the synthesis of intermolecularly linked peptides such as dimer-type peptides, and modified peptides in which two amino acids are intramolecularly linked. They are also synthetic intermediates for the total synthesis of natural products and functional molecules. These symmetric amino acid derivatives must be prepared based on organic synthesis. It is necessary to develop an optimal synthetic strategy for constructing the target symmetric amino acid derivative. In this review, we will introduce strategies for synthesizing symmetric amino acid derivatives. Additionally, selected applications of these amino acids in the life sciences will be described.
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Affiliation(s)
- Chihiro Tsukano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Ayumi Uchino
- 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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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2022:10.1002/mas.21814. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Chikugo A, Irie Y, Tsukano C, Uchino A, Maki T, Kume T, Kawase T, Hirose K, Kageyama Y, Tooyama I, Irie K. Optimization of the Linker Length in the Dimer Model of E22P-Aβ40 Tethered at Position 38. ACS Chem Neurosci 2022; 13:2913-2923. [PMID: 36095282 DOI: 10.1021/acschemneuro.2c00436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Since amyloid β (Aβ) oligomers are more cytotoxic than fibrils, various dimer models have been synthesized. We focused on the C-terminal region that could form a hydrophobic core in the aggregation process and identified a toxic conformer-restricted dimer model (E22P,G38DAP-Aβ40 dimer) with an l,l-2,6-diaminopimelic acid linker (n = 3) at position 38, which exhibited moderate cytotoxicity. We synthesized four additional linkers (n = 2, 4, 5, 7) to determine the most appropriate distance between the two Aβ40 monomers for a toxic dimer model. Each di-Fmoc-protected two-valent amino acid was synthesized from a corresponding dialdehyde or cycloalkene followed by ozonolysis, using a Horner-Wadsworth-Emmons reaction and asymmetric hydrogenation. Then, the corresponding Aβ40 dimer models with these linkers at position 38 were synthesized using the solid-phase Fmoc strategy. Their cytotoxicity toward SH-SY5Y cells suggested that the shorter the linker length, the stronger the cytotoxicity. Particularly, the E22P,G38DAA-Aβ40 dimer (n = 2) formed protofibrillar aggregates and exhibited the highest cytotoxicity, equivalent to E22P-Aβ42, the most cytotoxic analogue of Aβ42. Ion mobility-mass spectrometry (IM-MS) measurement indicated that all dimer models except the E22P,G38DAA-Aβ40 dimer existed as stable oligomers (12-24-mer). NativePAGE analysis supported the IM-MS data, but larger oligomers (30-150-mer) were also detected after a 24 h incubation. Moreover, E22P,G38DAA-Aβ40, E22P,G38DAP-Aβ40, and E22P,G38DAZ-Aβ40 (n = 5) dimers suppressed long-term potentiation (LTP). Overall, the ability to form fibrils with cross β-sheet structures was key to achieving cytotoxicity, and forming stable oligomers less than 150-mer did not correlate with cytotoxicity and LTP suppression.
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Affiliation(s)
- Ayaka Chikugo
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Yumi Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Chihiro Tsukano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Ayumi Uchino
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Takahito Maki
- Department of Applied Pharmacology, Graduate School of Medical and Pharmaceutical Sciences, University of Toyama, Toyama930-0194, Japan
| | - Toshiaki Kume
- Department of Applied Pharmacology, Graduate School of Medical and Pharmaceutical Sciences, University of Toyama, Toyama930-0194, Japan
| | | | | | - Yusuke Kageyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga520-2192, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga520-2192, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
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4
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Uchino A, Irie Y, Tsukano C, Kawase T, Hirose K, Kageyama Y, Tooyama I, Yanagita RC, Irie K. Synthesis and Characterization of Propeller- and Parallel-Type Full-Length Amyloid β40 Trimer Models. ACS Chem Neurosci 2022; 13:2517-2528. [PMID: 35930616 DOI: 10.1021/acschemneuro.2c00363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Oligomers of the amyloid β (Aβ) protein play a critical role in the pathogenesis of Alzheimer's disease. However, their heterogeneity and lability deter the identification of their tertiary structures and mechanisms of action. Aβ trimers and Aβ dimers may represent the smallest aggregation unit with cytotoxicity. Although propeller-type trimer models of E22P-Aβ40 tethered by an aromatic linker have recently been synthesized, they unexpectedly exhibited little cytotoxicity. To increase the flexibility of trimeric propeller-type models, we designed and synthesized trimer models with an alkyl linker, tert-butyltris-l-alanine (tButA), at position 36 or 38. In addition, we synthesized two parallel-type trimer models tethered at position 38 using alkyl linkers of different lengths, α,α-di-l-norvalyl-l-glycine (di-nV-Gly) and α,α-di-l-homonorleucyl-l-glycine (di-hnL-Gly), based on the previously reported toxic dimer model. The propeller-type E22P,V36tButA-Aβ40 trimer (4), which was designed to mimic the C-terminal anti-parallel β-sheet structures proposed by the structural analysis of 150 kDa oligomers of Aβ42, and the parallel-type E22P,G38di-nV-Gly-Aβ40 trimer (6) showed significant cytotoxicity against SH-SY5Y cells and aggregative ability to form protofibrillar species. In contrast, the E22P,G38tButA-Aβ40 trimer (5) and E22P,G38di-hnL-Gly-Aβ40 trimer (7) exhibited weak cytotoxicity, though they formed quasi-stable oligomers observed by ion mobility-mass spectrometry and native polyacrylamide gel electrophoresis. These results suggest that 4 and 6 could have some phase of the structure of toxic Aβ oligomers with a C-terminal hydrophobic core and that the conformation and/or aggregation process rather than the formation of stable oligomers contribute to the induction of cytotoxicity.
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Affiliation(s)
- Ayumi Uchino
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yumi Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Chihiro Tsukano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | | | | | - Yusuke Kageyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga 520-2192, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga 520-2192, 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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5
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Mei J, Yang H, Ahmad S, Ma X, Xu W, Gao W, Li Y, Wang C, Ai H. Toxicity Mechanism of Aβ42 Oligomer in the Binding between the GABA BR1a sushi1 Domain and Amyloid Precursor Protein 9mer: A Mechanism like Substitution Reaction. ACS Chem Neurosci 2022; 13:2048-2059. [PMID: 35737468 DOI: 10.1021/acschemneuro.2c00311] [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: 11/30/2022] Open
Abstract
Amyloid-β peptide (Aβ), characterized by its abnormal folding into neurotoxic aggregates, impairs synaptic plasticity and causes synaptic loss associated with Alzheimer's disease (AD). The neurotoxicity of Aβ oligomers via the binding to various cell-surface receptors was frequently observed experimentally; however, the toxic mechanism still remains unknown. In this paper, we study the intervention of Aβ oligomers to the receptor-peptide binding in the GABABR1a sushi1-APP 9mer complex, a key node in increasing short-term synaptic facilitation in the mouse hippocampus and decreasing neuronal activity by inhibiting neurotransmitter release by molecular dynamics simulations. The residue types of Aβ42 oligomers involved in the intervention and core contact areas of the receptor were first identified, by which an unprecedented toxicity mechanism of Aβ42 oligomers is proposed. These involved residues of Aβ42 oligomers are positively charged residues Asp and Glu, and the core area of GABABR1a sushi1 domain is the Coil one, sharing the rich negatively charged residues R19/R21/R25/R45 with the pocket, in which APP 9mer is locked. The presence of an Aβ42 oligomer rather than of a monomer stretches these key residues in the core area and consequently "unlocks and releases" the APP 9mer from its initial pocket, unsteadying the sushi1 domain and taking into toxic effect. It looks like a chemical "substitution" reaction, Aβ42 oligomer + GABABR1a sushi1-APP 9mer complex → Aβ42 oligomer-GABABR1a sushi1 complex + APP 9mer. Further analysis reveals that the toxicity of Aβ42 oligomer to GABABR1a sushi1 domain stability depends on the residue number of the contact area and the size of Aβ42 oligomer, in which semi-extended trimeric Aβ42 oligomer is identified as the most toxic one. This work provides a novel insight into the mechanism of Aβ oligomeric toxicity to neuroreceptors and sets an important precedent for dealing with Aβ oligomeric toxicity to other receptors at the molecular level.
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Affiliation(s)
- Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Sajjad Ahmad
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Xiaohong Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Wen Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Wenqi Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Ye Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
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6
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Constructing conformational library for amyloid-β42 dimers as the smallest toxic oligomers using two CHARMM force fields. J Mol Graph Model 2022; 115:108207. [DOI: 10.1016/j.jmgm.2022.108207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/19/2022]
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7
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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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8
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Kageyama Y, Irie Y, Matsushima Y, Segawa T, Bellier JP, Hidaka K, Sugiyama H, Kaneda D, Hashizume Y, Akatsu H, Miki K, Kita A, Walker DG, Irie K, Tooyama I. Characterization of a Conformation-Restricted Amyloid β Peptide and Immunoreactivity of Its Antibody in Human AD brain. ACS Chem Neurosci 2021; 12:3418-3432. [PMID: 34464082 DOI: 10.1021/acschemneuro.1c00416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Characterization of amyloid β (Aβ) oligomers, the transition species present prior to the formation of Aβ fibrils and that have cytotoxicity, has become one of the major topics in the investigations of Alzheimer's disease (AD) pathogenesis. However, studying pathophysiological properties of Aβ oligomers is challenging due to the instability of these protein complexes in vitro. Here, we report that conformation-restricted Aβ42 with an intramolecular disulfide bond at positions 17 and 28 (SS-Aβ42) formed stable Aβ oligomers in vitro. Thioflavin T binding assays, nondenaturing gel electrophoresis, and morphological analyses revealed that SS-Aβ42 maintained oligomeric structure, whereas wild-type Aβ42 and the highly aggregative Aβ42 mutant with E22P substitution (E22P-Aβ42) formed Aβ fibrils. In agreement with these observations, SS-Aβ42 was more cytotoxic compared to the wild-type and E22P-Aβ42 in cell cultures. Furthermore, we developed a monoclonal antibody, designated TxCo-1, using the toxic conformation of SS-Aβ42 as immunogen. X-ray crystallography of the TxCo-1/SS-Aβ42 complex, enzyme immunoassay, and immunohistochemical studies confirmed the recognition site and specificity of TxCo-1 to SS-Aβ42. Immunohistochemistry with TxCo-1 antibody identified structures resembling senile plaques and vascular Aβ in brain samples of AD subjects. However, TxCo-1 immunoreactivity did not colocalize extensively with Aβ plaques identified with conventional Aβ antibodies. Together, these findings indicate that Aβ with a turn at positions 22 and 23, which is prone to form Aβ oligomers, could show strong cytotoxicity and accumulated in brains of AD subjects. The SS-Aβ42 and TxCo-1 antibody should facilitate understanding of the pathological role of Aβ with toxic conformation in AD.
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Affiliation(s)
- Yusuke Kageyama
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Yumi Irie
- Division of Food Science & Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yuka Matsushima
- Division of Food Science & Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Tatsuya Segawa
- Immuno-Biological Laboratories Co., Ltd., Fujioka-Shi, Gunma 375-0005, Japan
| | - Jean-Pierre Bellier
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daita Kaneda
- Choju Medical Institute, Fukushimura Hospital, 19-14 Noyoricho, Yamanaka, Aichi 441-8124, Japan
| | - Yoshio Hashizume
- Choju Medical Institute, Fukushimura Hospital, 19-14 Noyoricho, Yamanaka, Aichi 441-8124, Japan
| | - Hiroyasu Akatsu
- Choju Medical Institute, Fukushimura Hospital, 19-14 Noyoricho, Yamanaka, Aichi 441-8124, Japan
- Department of Community-Based Medical Education, Nagoya City University Graduate School of Medicine, Nagoya, Aichi 467-8601, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
| | - Douglas G. Walker
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Kazuhiro Irie
- Division of Food Science & Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
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9
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Wang K, Na L, Duan M. The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β. Curr Top Med Chem 2021; 21:151-167. [PMID: 32938351 DOI: 10.2174/1568026620666200916123000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liu Na
- School of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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10
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Uchino A, Tsukano C, Imamoto T, Irie K. Synthesis of Alkyl Bridged‐Tris‐α‐Amino Acids as C
3
‐Symmetric and Linear Linkers. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ayumi Uchino
- Division of Food Science and Biotechnology Graduate School of Agriculture Kyoto University Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
| | - Chihiro Tsukano
- Division of Food Science and Biotechnology Graduate School of Agriculture Kyoto University Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
| | - Tsuneo Imamoto
- Department of Chemistry Graduate School of Science Chiba University Yayoi-cho, Inage-ku, Chiba 263-8522 Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology Graduate School of Agriculture Kyoto University Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
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11
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 367] [Impact Index Per Article: 122.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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12
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Matsushima Y, Yanagita RC, Irie K. Control of the toxic conformation of amyloid β42 by intramolecular disulfide bond formation. Chem Commun (Camb) 2020; 56:4118-4121. [PMID: 32163091 DOI: 10.1039/d0cc01053g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a method to fix the conformation of Aβ42 to the toxic or non-toxic form by intramolecular disulfide bonds. We found that an Aβ42 analog crosslinked within the molecule at the 17th and 28th amino acid residues exhibited high aggregative ability and potent neurotoxicity comparable to those of E22P-Aβ42. This analog would be useful in the research of Aβ42 oligomers and to develop reliable antibodies for early diagnosis of Alzheimer's disease.
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Affiliation(s)
- Yuka Matsushima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, 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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13
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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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14
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Obata Y, Murakami K, Kawase T, Hirose K, Izuo N, Shimizu T, Irie K. Detection of Amyloid β Oligomers with RNA Aptamers in App NL-G-F/NL-G-F Mice: A Model of Arctic Alzheimer's Disease. ACS OMEGA 2020; 5:21531-21537. [PMID: 32905362 PMCID: PMC7469371 DOI: 10.1021/acsomega.0c02134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
RNA aptamers have garnered attention for diagnostic applications due to their ability to recognize diverse targets. Oligomers of 42-mer amyloid β-protein (Aβ42), whose accumulation is relevant to the pathology of Alzheimer's disease (AD), are among the most difficult molecules for aptamer recognition because they are prone to aggregate in heterogeneous forms. In addition to designing haptens for in vitro selection of aptamers, the difficulties involved in determining their effect on Aβ42 oligomerization impede aptamer research. We previously developed three RNA aptamers (E22P-AbD4, -AbD31, and -AbD43) with high affinity for protofibrils (PFs) derived from a toxic Aβ42 dimer. Notably, these aptamers recognized diffuse staining, which likely originated from PFs or higher-order oligomers with curvilinear structures in a knock-in AppNL-G-F/NL-G-F mouse, carrying the Arctic mutation that preferentially induced the formation of PFs, in addition to a PS2Tg2576 mouse. To determine which oligomeric sizes were mainly altered by the aptamer, ion mobility-mass spectrometry (IM-MS) was carried out. One aptamer, E22P-AbD43, formed adducts with the Aβ42 monomer and dimer, leading to suppression of further oligomerization. These findings support the utility of these aptamers as diagnostics for AD.
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Affiliation(s)
- Yayoi Obata
- 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
| | | | | | - Naotaka Izuo
- Department
of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba 260-8670, 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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15
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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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16
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Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease. Chem Commun (Camb) 2020; 56:4627-4639. [PMID: 32300761 PMCID: PMC7254607 DOI: 10.1039/d0cc01551b] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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17
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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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18
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Murakami K, Yoshimura M, Nakagawa S, Kume T, Kondo T, Inoue H, Irie K. Evaluation of Toxic Amyloid 42 Oligomers in Rat Primary Cerebral Cortex Cells and Human iPS-derived Neurons Treated with 10-Me-Aplog-1, a New PKC Activator. Int J Mol Sci 2020; 21:ijms21041179. [PMID: 32053979 PMCID: PMC7072833 DOI: 10.3390/ijms21041179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Amyloid β42 (Aβ42), a causative agent of Alzheimer’s disease (AD), is derived extracellularly from Aβ precursor protein (APP) following the latter’s cleavage by β-secretase, but not α-secretase. Protein kinase Cα (PKCα) activation is known to increase α-secretase activity, thereby suppressing Aβ production. Since Aβ42 oligomer formation causes potent neurotoxicity, APP modulation by PKC ligands is a promising strategy for AD treatment. Although bryostatin-1 (bryo-1) is a leading compound for this strategy, its limited natural availability and the difficulty of its total synthesis impedes further research. To address this limitation, Irie and colleagues have developed a new PKC activator with few side effects, 10-Me-Aplog-1, (1), which decreased Aβ42 in the conditioned medium of rat primary cerebral cortex cells. These results are associated with increased α-secretase but not PKCε-dependent Aβ-degrading enzyme. The amount of neuronal embryonic lethal abnormal vision (nELAV), a known β-secretase stabilizer, was reduced by treatment with 1. Notably, 1 prevented the formation of intracellular toxic oligomers. Furthermore, 1 suppressed toxic oligomerization within human iPS-derived neurons such as bryo-1. Given that 1 was not neurotoxic toward either cell line, these findings suggest that 1 is a potential drug lead for AD therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
- Correspondence: (K.M.); (K.I.); Tel.: +81-75-753-6282 (K.M.); +81-75-753-6281 (K.I.)
| | - Mayuko Yoshimura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
| | - Shota Nakagawa
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan; (S.N.); (T.K.)
| | - Toshiaki Kume
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan; (S.N.); (T.K.)
- Department of Applied Pharmacology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takayuki Kondo
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; (T.K.); (H.I.)
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto 619-0237, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; (T.K.); (H.I.)
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto 619-0237, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
- Correspondence: (K.M.); (K.I.); Tel.: +81-75-753-6282 (K.M.); +81-75-753-6281 (K.I.)
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19
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Shinoda K, Kanai M, Sohma Y. Design, Synthesis, and Properties of a Chemically Tethered Amyloid-β Segment Trimer Resistant to Intertrimer Mis-aggregation. J Org Chem 2020; 85:1635-1643. [PMID: 31829587 DOI: 10.1021/acs.joc.9b02612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The oligomer species of amyloid-β peptide (Aβ) may be relevant to the development of Alzheimer's disease. Isolating specific oligomer species of Aβ (i.e., dimers, trimers, tetramers, etc.), however, is difficult due to the transient, labile property of the oligomers. Here, we improved the resistance to intertrimer mis-aggregation of chemically tethered Aβ25-35 trimers by introducing charged structures to the cyclic peptide tether that is covalently attached to the Aβ chain. The resistance to aggregation of the chemically tethered trimers positively correlated with the number of negative charges at the tether. Thus, a chemical trimer possessing three malonic acids at the tether exhibited high resistance because of the attenuated self-association by anionic repulsion. In addition, the malonic acid trimer possessed amyloidogenic properties such as cross-β-sheet structures, seeding activity, and cytotoxicity. This is the first study demonstrating that chemical modifications at the non-Aβ component enhance the resistance to aggregation of chemically tethered Aβ oligomers, by which the structural integrity of Aβ is maintained. Biological/biophysical evaluations of the intertrimer aggregation-resistant trimer may offer new, useful insights into the pathological functions of Aβ oligomers.
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Affiliation(s)
- Kiyomichi Shinoda
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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20
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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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21
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Irie K. Synthesis and Structure-Function Analyses of the Toxic Dimer and Trimer Models of Amyloid β. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.1201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Three Structural Features of Functional Food Components and Herbal Medicine with Amyloid β42 Anti-Aggregation Properties. Molecules 2019; 24:molecules24112125. [PMID: 31195683 PMCID: PMC6600243 DOI: 10.3390/molecules24112125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 01/29/2023] Open
Abstract
Aggregation of amyloid β42 (Aβ42) is one of the hallmarks of Alzheimer's disease (AD). There are numerous naturally occurring products that suppress the aggregation of Aβ42, but the underlying mechanisms remain to be elucidated. Based on NMR and MS spectroscopic analysis, we propose three structural characteristics found in natural products required for the suppressive activity against Aβ42 aggregation (i.e., oligomerization by targeting specific amino acid residues on this protein). These characteristics include (1) catechol-type flavonoids that can form Michael adducts with the side chains of Lys16 and 28 in monomeric Aβ42 through flavonoid autoxidation; (2) non-catechol-type flavonoids with planarity due to α,β-unsaturated carbonyl groups that can interact with the intermolecular β-sheet region in Aβ42 aggregates, especially aromatic rings such as those of Phe19 and 20; and (3) carboxy acid derivatives with triterpenoid or anthraquinoid that can generate a salt bridge with basic amino acid residues such as Lys16 and 28 in the Aβ42 dimer or trimer. Here, we summarize the recent body of knowledge concerning amyloidogenic inhibitors, particularly in functional food components and Kampo medicine, and discuss their application in the treatment and prevention of AD.
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23
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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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24
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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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25
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Zhang H, Dong X, Liu F, Zheng J, Sun Y. Ac-LVFFARK-NH 2 conjugation to β-cyclodextrin exhibits significantly enhanced performance on inhibiting amyloid β-protein fibrillogenesis and cytotoxicity. Biophys Chem 2018; 235:40-47. [DOI: 10.1016/j.bpc.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/12/2018] [Accepted: 02/04/2018] [Indexed: 11/16/2022]
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26
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Hanaki M, Murakami K, Katayama S, Akagi KI, Irie K. Mechanistic analyses of the suppression of amyloid β42 aggregation by apomorphine. Bioorg Med Chem 2018; 26:1538-1546. [PMID: 29429575 DOI: 10.1016/j.bmc.2018.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/05/2023]
Abstract
(R)-Apomorphine (1) has the potential to reduce the accumulation of amyloid β-protein (Aβ42), a causative agent of Alzheimer's disease (AD). Although the inhibition of Aβ42 aggregation by 1 is ascribable to the antioxidative effect of its phenol moiety, its inhibitory mechanism at the molecular level remains to be fully elucidated. LC-MS and UV analyses revealed that 1 is autoxidized during incubation to produce an unstable o-quinone form (2), which formed a Michael adduct with Lys 16 and 28 of Aβ42. A further autoxidized form of 1 (3) with o-quinone and phenanthrene moieties suppressed Aβ42 aggregation comparable to 1, whereas treating 1 with a reductant, tris(2-carboxyethyl)phosphine diminished its inhibitory activity. 1H-15N SOFAST-HMQC NMR studies suggested that 1 interacts with Arg5, His13,14, Gln15, and Lys16 of the Aβ42 monomer. These regions form intermolecular β-sheets in Aβ42 aggregates. Since 3 did not perturb the chemical shift of monomeric Aβ42, we performed aggregation experiments using 1,1,1,3,3,3-hexafluoro-2-propanol-treated Aβ42 to investigate whether 3 associates with Aβ42 oligomers. Compounds 1 and 3 delayed the onset of the oligomer-driven nucleation phase. Despite their cytotoxicity, they did not exacerbate Aβ42-mediated neurotoxicity in SH-SY5Y neuroblastoma cells. These results demonstrate that extension of the conjugated system in 1 by autoxidation can promote its planarity, which is required for intercalation into the β-sheet of Aβ42 nuclei, thereby suppressing further aggregation.
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Affiliation(s)
- 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
| | - Sumie Katayama
- 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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27
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Meier BH, Riek R, Böckmann A. Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR. Trends Biochem Sci 2017; 42:777-787. [PMID: 28916413 DOI: 10.1016/j.tibs.2017.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 11/28/2022]
Abstract
Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered structural studies by classical approaches. Progress in sample preparation, as well as solid-state NMR methods, recently enabled the determination of high-resolution 3D structures of fibrils such as the amyloid-β fibril, which is involved in Alzheimer's disease. Notably, the simultaneous but independent structure determination of Aβ1-42, a peptide that forms fibrillar deposits in the brain of Alzheimer patients, by two independent laboratories, which yielded virtually identical results, has highlighted how structures can be obtained that allow further functional investigation.
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Affiliation(s)
- Beat H Meier
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Roland Riek
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon,7 passage du Vercors, 69367 Lyon, France.
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