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Yamashita S, O Kamatari Y, Honda R, Niwa A, Tomiata H, Hara A, Kuwata K. Monomeric a-synuclein (aS) inhibits amyloidogenesis of human prion protein (hPrP) by forming a stable aS-hPrP hetero-dimer. Prion 2021; 15:37-43. [PMID: 33849375 PMCID: PMC8049198 DOI: 10.1080/19336896.2021.1910176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Intermolecular interaction between hPrP and αS was investigated using high-speed atomic force microscopy, dynamic light scattering, and nuclear magnetic resonance. We found that hPrP spontaneously gathered and naturally formed oligomers. Upon addition of monomer αS with a disordered conformation, poly-dispersive property of hPrP was lost, and hetero-dimer formation started quite coherently, and further oligomerization was not observed. Solution structure of hPrP-αS dimer was firstly characterized using hetero-nuclear NMR spectroscopy. In this hetero-dimeric complex, C-terminal helical region of hPrP was in the molten-globule like state, while specific sites including hot spot and C-terminal region of αS selectively interacted with hPrP. Thus αS may suppress amyloidogenesis of hPrP by trapping the hPrP intermediate by the formation of a stable hetero-dimer with hPrP. Abbreviations: hPrP, human prion protein of amino acid residues of 23-231; PrPC, cellular form of prion protein; PrPSc, scrapie form of prion protein, HS-AFM; high speed atomic force microscopy; αS, α-synuclein; DLS, dynamic light scattering
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Affiliation(s)
- Satoshi Yamashita
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan
| | - Yuji O Kamatari
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Gifu, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan
| | - Ayumi Niwa
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Hiroyuki Tomiata
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan.,Department of Gene and Development, Gifu University School of Medicine, Tokai National Higher Education and Research System, Gifu, Japan
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2
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Shimizu J, Kuwata H, Kuwata K. Differences in fractal patterns and characteristic periodicities between word salads and normal sentences: Interference of meaning and sound. PLoS One 2021; 16:e0247133. [PMID: 33600483 PMCID: PMC7891721 DOI: 10.1371/journal.pone.0247133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 11/19/2022] Open
Abstract
Fractal dimensions and characteristic periodicities were evaluated in normal sentences, computer-generated word salads, and word salads from schizophrenia patients, in both Japanese and English, using the random walk patterns of vowels. In normal sentences, the walking curves were smooth with gentle undulations, whereas computer-generated word salads were rugged with mechanical repetitions, and word salads from patients with schizophrenia were unreasonably winding with meaningless repetitive patterns or even artistic cohesion. These tendencies were similar in both languages. Fractal dimensions between normal sentences and word salads of schizophrenia were significantly different in Japanese [1.19 ± 0.09 (n = 90) and 1.15 ± 0.08 (n = 45), respectively] and English [1.20 ± 0.08 (n = 91), and 1.16 ± 0.08 (n = 42)] (p < 0.05 for both). Differences in long-range (>10) periodicities between normal sentences and word salads from schizophrenia patients were predominantly observed at 25.6 (p < 0.01) in Japanese and 10.7 (p < 0.01) in English. The differences in fractal dimension and characteristic periodicities of relatively long-range (>10) presented here are sensitive to discriminate between schizophrenia and healthy mental state, and could be implemented in social robots to assess the mental state of people in care.
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Affiliation(s)
- Jun Shimizu
- United Graduate School of Drug Discovery and Medical Information Sciences, Tokai National Higher Education and Research System, Gifu University, Gifu, Japan
| | - Hiromi Kuwata
- Dept. of Pediatric Nursing, Shiga University of Medical Science, Otsu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Tokai National Higher Education and Research System, Gifu University, Gifu, Japan
- * E-mail:
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3
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Amato J, Mashima T, Kamatari YO, Kuwata K, Novellino E, Randazzo A, Giancola C, Katahira M, Pagano B. Improved Anti-Prion Nucleic Acid Aptamers by Incorporation of Chemical Modifications. Nucleic Acid Ther 2020; 30:414-421. [PMID: 32991255 DOI: 10.1089/nat.2020.0899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nucleic acid aptamers are innovative and promising candidates to block the hallmark event in the prion diseases, that is the conversion of prion protein (PrP) into an abnormal form; however, they need chemical modifications for effective therapeutic activity. This communication reports on the development and biophysical characterization of a small library of chemically modified G-quadruplex-forming aptamers targeting the cellular PrP and the evaluation of their anti-prion activity. The results show the possibility of enhancing anti-prion aptamer properties through straightforward modifications.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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4
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Shida T, Kamatari YO, Yoda T, Yamaguchi Y, Feig M, Ohhashi Y, Sugita Y, Kuwata K, Tanaka M. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nat Chem Biol 2020; 16:756-765. [PMID: 32284601 DOI: 10.1038/s41589-020-0516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Soluble prion proteins contingently encounter foreign prion aggregates, leading to cross-species prion transmission. However, how its efficiency is regulated by structural fluctuation of the host soluble prion protein remains unsolved. In the present study, through the use of two distantly related yeast prion Sup35 proteins, we found that a specific conformation of a short disordered segment governs interspecies prion transmissibility. Using a multidisciplinary approach including high-resolution NMR and molecular dynamics simulation, we identified critical residues within this segment that allow interspecies prion transmission in vitro and in vivo, by locally altering dynamics and conformation of soluble prion proteins. Remarkably, subtle conformational differences caused by a methylene group between asparagine and glutamine sufficed to change the short segment structure and substantially modulate the cross-seeding activity. Thus, our findings uncover how conformational dynamics of the short segment in the host prion protein impacts cross-species prion transmission. More broadly, our study provides mechanistic insights into cross-seeding between heterologous proteins.
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Affiliation(s)
- Toshinobu Shida
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.,Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan.,RIKEN-Max Planck Joint Research Center, Wako, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yumiko Ohhashi
- Graduate School of Science, Kobe University, Kobe, Japan.,Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Motomasa Tanaka
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan. .,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan.
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5
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Yamashita S, Honda R, Fukuoka M, Kimura T, Hosokawa-Muto J, Kuwata K. Discovery of a multipotent chaperone, 1-(2,6-Difluorobenzylamino)-3-(1,2,3,4-tetrahydrocarbazol-9-yl)-propan-2-ol with the inhibitory effects on the proliferation of prion, cancer as well as influenza virus. Prion 2020; 14:42-46. [PMID: 31971853 PMCID: PMC6984644 DOI: 10.1080/19336896.2020.1714372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We previously discovered three carbazole derivatives, GJP14 (1-piperidinylmethyl-2-(1-oxo-6-methyl-1,2,3,4-tetrahydrocarbazol-9-yl)-ethan-1-ol) with anti-prion activity, GJC29 (benzylamino-3-(1,2,3,4-tetrahydrocarbazol-9-yl)-propan-2-ol) with anti-cancer activity, and THC19 (1-piperidinylmethyl-2-(1,2,3,4-tetrahydrocarnazol-9-yl)-ethan-1-ol) with anti-influenza virus activity. During optimization of GJP14 for the anti-prion activity, we discovered a compound, 1-(2,6-difluorobenzylamino)-3-(1,2,3,4-tetrahydrocarbazol-9-yl)-propan-2-ol, termed 5Y, had the most strong anti-prion activity among a series of newly synthesized derivatives. Intriguingly, we noticed that 5Y had also the most strong anti-colon cancer as well as the anti-influenza virus activities among derivatives. No significant toxicity of 5Y was observed. These results demonstrate that 5Y is a multipotent lead compound with unusually wide spectrum, and may be applicable to therapeutics targeting multiple diseases.Abbreviations: MoPrP: mouse prion protein of amino acid residues of 23-231; PrPC: cellular form of prion protein; PrPSc: scrapie form of prion protein.
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Affiliation(s)
- Satoshi Yamashita
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Tsutomu Kimura
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, Tokyo, Japan
| | - Junji Hosokawa-Muto
- First Department of Forsenic Science, National Research Institute of Police Science, Chiba, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan
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6
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Shirasaka M, Kuwata K, Honda R. α-Synuclein chaperone suppresses nucleation and amyloidogenesis of prion protein. Biochem Biophys Res Commun 2020; 521:259-264. [DOI: 10.1016/j.bbrc.2019.10.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 11/29/2022]
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Kakuda K, Niwa A, Honda R, Yamaguchi KI, Tomita H, Nojebuzzaman M, Hara A, Goto Y, Osawa M, Kuwata K. A DISC1 point mutation promotes oligomerization and impairs information processing in a mouse model of schizophrenia. J Biochem 2019; 165:369-378. [PMID: 30561706 DOI: 10.1093/jb/mvy116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/14/2018] [Indexed: 12/15/2022] Open
Abstract
Disrupted-in-schizophrenia 1 (DISC1) is strongly associated with schizophrenia, but it remains elusive how the modification of the intermolecular interaction of DISC1 affects the information processing in brain. We show that a DISC1 point mutation alters intermolecular cohesiveness promoting the phase separation, and disrupts sensorimotor gating monitored by the prepulse inhibition in a mouse model of schizophrenia. Although the conformation of DISC1 partial peptide with the schizophrenia-related mutation L607F in human or the corresponding L604F in mouse was essentially indistinguishable from the wild type (WT) as long as monitored by fluorescence, circular dichroism, ultracentrifugation, dynamic light scattering and nuclear magnetic resonance, the atomic force microscopy was able to detect their morphological distinctions. The WT peptides were round and well dispersed, while mutants were inhomogeneous and disrupted to form dimer to trimer that aligned along one direction without apparent aggregate formation. Homozygous L604F mutant mice created by CRISPR exhibited the significant decrease in DISC1 level in the immunohistopathology at the hippocampal region compared to the WTs. The ratio of prepulse inhibition of the homozygous mutant mice was significantly impaired compared to WTs. Altered DISC1 distribution or function caused by aberrant intermolecular interactions may contribute to information processing characteristics in schizophrenia.
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Affiliation(s)
- Kyosuke Kakuda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu
| | - Ayumi Niwa
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu
| | - Kei-Ichi Yamaguchi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu
| | - Md Nojebuzzaman
- Division of Regeneration Technology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka
| | - Masatake Osawa
- Division of Regeneration Technology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu
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8
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Yamaguchi K, Kamatari YO, Ono F, Shibata H, Fuse T, Elhelaly AE, Fukuoka M, Kimura T, Hosokawa-Muto J, Ishikawa T, Tobiume M, Takeuchi Y, Matsuyama Y, Ishibashi D, Nishida N, Kuwata K. A designer molecular chaperone against transmissible spongiform encephalopathy slows disease progression in mice and macaques. Nat Biomed Eng 2019; 3:206-219. [PMID: 30948810 DOI: 10.1038/s41551-019-0349-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/07/2019] [Indexed: 01/10/2023]
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases that lack therapeutic solutions. Here, we show that the molecular chaperone (N,N'-([cyclohexylmethylene]di-4,1-phenylene)bis(2-[1-pyrrolidinyl]acetamide)), designed via docking simulations, molecular dynamics simulations and quantum chemical calculations, slows down the progress of TSEs. In vitro, the designer molecular chaperone stabilizes the normal cellular prion protein, eradicates prions in infected cells, prevents the formation of drug-resistant strains and directly inhibits the interaction between prions and abnormal aggregates, as shown via real-time quaking-induced conversion and in vitro conversion NMR. Weekly intraperitoneal injection of the chaperone in prion-infected mice prolonged their survival, and weekly intravenous administration of the compound in macaques infected with bovine TSE slowed down the development of neurological and psychological symptoms and reduced the concentration of disease-associated biomarkers in the animals' cerebrospinal fluid. The de novo rational design of chaperone compounds could lead to therapeutics that can bind to different prion protein strains to ameliorate the pathology of TSEs.
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Affiliation(s)
- Keiichi Yamaguchi
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuji O Kamatari
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Life Science Research Center, Gifu University, Gifu, Japan
| | - Fumiko Ono
- Faculty of Animal Crisis Management, Chiba Institute of Science, Choshi, Japan.,Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Hiroaki Shibata
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, Shimotsuke, Japan
| | - Takayuki Fuse
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Abdelazim Elsayed Elhelaly
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Suez Canal University, Ismalia, Egypt
| | - Mayuko Fukuoka
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Tsutomu Kimura
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Chemistry, Faulty of Science Division II, Tokyo University of Science, Tokyo, Japan
| | - Junji Hosokawa-Muto
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,First Department of Forsenic Science, National Research Institute of Police Science, Kashiwa, Japan
| | - Takeshi Ishikawa
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Minoru Tobiume
- Department of Pathology, National Institute of Infectious Disease, Tokyo, Japan
| | - Yoshinori Takeuchi
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Matsuyama
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Ishibashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuo Kuwata
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan.
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9
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Kakuda K, Yamaguchi KI, Kuwata K, Honda R. A valine-to-lysine substitution at position 210 induces structural conversion of prion protein into a β-sheet rich oligomer. Biochem Biophys Res Commun 2018; 506:81-86. [PMID: 30336980 DOI: 10.1016/j.bbrc.2018.10.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases associated with structural conversion of α-helical prion protein (PrP) into its β-sheet rich isoform (PrPSc). Previous genetic analyses have indicated that several amino acid residues involved in the hydrophobic core of PrP (such as V180, F198, and V210) play a critical role in the development of prion diseases. To understand how these hydrophobic residues would contribute to the α-to-β conversion process of PrP, we substituted the V210 residue with bulkier (V210F, V210I, and V210L), smaller (V210A), and charged amino acids (V210K) and characterized its effects. Interestingly, although most of the mutations had little or no effect on the biochemical properties of PrP, the V210K mutation induced structural conversion of PrP into a β-structure. The β-inducing effect was prominent and observed even under a physiological condition (i.e., in the absence of denaturant, acidic pH, reducing agent, and high temperature) in contrast to the disease-associated mutations in the PrP gene. We also examined structural features of V210K PrP using guanidine-hydrochloride unfolding, dynamic light scattering, 8-anilino-1-naphthalene sulfonate fluorescence, and electron microscopy, and revealed that V210K PrP assembles into a non-fibrillar β-rich oligomer. Thus, the α-to-β conversion can be induced by introduction of a charged residue into the hydrophobic core, which provide novel insight into the structural dynamics of PrP.
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Affiliation(s)
- Kyosuke Kakuda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kei-Ichi Yamaguchi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan; Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan.
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10
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Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of lethal neurodegenerative diseases involving the structural conversion of cellular prion protein (PrPC) into the pathogenic isoform (PrPSc) for which no effective treatment is currently available. Previous studies have implicated that a polymeric molecule with a repeating unit, such as pentosane polysulfate and polyamidoamide dendrimers, exhibits a potent anti-prion activity, suggesting that poly-(amino acid)s could be a candidate molecule for inhibiting prion propagation. Here, by screening a series of poly-(amino acid)s in a prion-infected neuroblastoma cell line (GTFK), we identified poly-L-His as a novel anti-prion compound with an IC50 value of 1.8 µg/mL (0.18 µM). This potent anti-prion activity was specific to a high-molecular-weight poly-L-His and absent in monomeric histidine or low-molecular-weight poly-L-His. Solution NMR data indicated that poly-L-His directly binds to the loop region connecting Helix 2 and Helix 3 of PrPC and sterically blocks the structural conversion toward PrPSc. Poly-L-His, however, did not inhibit prion propagation in a prion-infected mouse when administered intraperitoneally, suggesting that the penetration of blood-brain barrier and/or the chemical stability of this polypeptide must be addressed before its application in vivo. Taken together, this study revealed the potential use of poly-L-His as a novel treatment against TSEs. (203 words).
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Affiliation(s)
- Ryo Honda
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | | | - Abdelazim Elsayed Elhelaly
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | - Mitsuhiko Fuji
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | - Kazuo Kuwata
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan.,c Department of Gene and Development , Graduate School of Medicine, Gifu University , Gifu , Japan
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11
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Yamaguchi KI, Honda RP, Elhelaly AE, Kuwata K. Acceleration of nucleation of prion protein during continuous ultrasonication. J Biochem 2018; 163:503-513. [PMID: 29409004 DOI: 10.1093/jb/mvy015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/25/2017] [Indexed: 01/31/2023] Open
Abstract
Although pulsatile irradiation of ultrasonication is frequently used for generating amyloid fibrils in vitro, the potential for inducing amyloid fibrillation of proteins during continuous ultrasonication is unknown. In this study, we implemented a continuous irradiation system and measured far-ultraviolet circular dichroism in a real-time manner. During the continuous ultrasonication, the conformation of full-length mouse prion protein (mPrP) was rapidly altered without a lag time and electron microscopy revealed that distorted fibrils, β-oligomers and amorphous aggregates were formed at pH 2.2, 4.0 and 9.1, respectively. Similarly, hen egg white lysozyme formed distorted fibrils and small and large amorphous aggregates at pH 2.2 and 7.1 and 11.9, respectively, without a lag time. The concentration dependencies of the initial rates were different between the two systems. The aggregate formation of mPrP followed a first-order reaction, whereas that of lysozyme followed the zeroth-order reaction. Importantly, the reactions were immediately stopped by switching off ultrasonication, and restarted instantaneously when ultrasonication was restarted. Thus, the continuous ultrasonication significantly accelerates the nucleations of mPrP and lysozyme aggregates by the interaction between monomer and cavitation bubble. These cavitation bubbles may act as catalysts that decrease the activation free energy for nucleation, which is low in mPrP and high in lysozyme.
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Affiliation(s)
- Kei-Ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine
| | - Abdelazim Elsayed Elhelaly
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu 501-1193, Japan
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12
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Kawada Y, Goshima T, Sawamura R, Yokoyama SI, Yanase E, Niwa T, Ebihara A, Inagaki M, Yamaguchi K, Kuwata K, Kato Y, Sakurada O, Suzuki T. Daidzein reductase of Eggerthella sp. YY7918, its octameric subunit structure containing FMN/FAD/4Fe-4S, and its enantioselective production of R-dihydroisoflavones. J Biosci Bioeng 2018; 126:301-309. [PMID: 29699942 DOI: 10.1016/j.jbiosc.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 12/29/2022]
Abstract
S-Equol is a metabolite of daidzein, a type of soy isoflavone, and three reductases are involved in the conversion of daidzein by specific intestinal bacteria. S-Equol is thought to prevent hormone-dependent diseases. We previously identified the equol producing gene cluster (eqlABC) of Eggerthella sp. YY7918. Daidzein reductase (DZNR), encoded by eqlA, catalyzes the reduction of daidzein to dihydrodaidzein (the first step of equol synthesis), which was confirmed using a recombinant enzyme produced in Escherichia coli. Here, we purified recombinant DZNR to homogeneity and analyzed its enzymological properties. DZNR contained FMN, FAD, and one 4Fe-4S cluster per 70-kDa subunit as enzymatic cofactors. DZNR reduced the CC bond between the C-2 and C-3 positions of daidzein, genistein, glycitein, and formononetin in the presence of NADPH. R-Dihydrodaidzein and R-dihydrogenistein were highly stereo-selectively produced from daidzein and genistein. The Km and kcat for daidzein were 11.9 μM and 6.7 s-1, and these values for genistein were 74.1 μM and 28.3 s-1, respectively. This enzyme showed similar kinetic parameters and wide substrate specificity for isoflavone molecules. Thus, this enzyme appears to be an isoflavone reductase. Gel filtration chromatography and chemical cross-linking analysis of the active form of DZNR suggested that the enzyme consists of an octameric subunit structure. We confirmed this by small-angle X-ray scattering and transmission electron microscopy at a magnification of ×200,000. DZNR formed a globular four-petal cloverleaf structure with a central vertical hole. The maximum particle size was 173 Å.
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Affiliation(s)
- Yuika Kawada
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Tomoko Goshima
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Rie Sawamura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shin-Ichiro Yokoyama
- Department of Food Technology, Industrial Technology Center, Gifu Prefectural Government, 47 Kitaoyobi, Kasamatsu, Hashima, Gifu 501-6064, Japan
| | - Emiko Yanase
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Toshio Niwa
- Faculty of Health and Nutrition, Shubun University, 6 Nikko-cho, Ichinomiya, Aichi 491-0938, Japan
| | - Akio Ebihara
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Mizuho Inagaki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keiichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuta Kato
- Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Osamu Sakurada
- Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Tohru Suzuki
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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13
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Abstract
Amyloid fibrils formed from prion protein (PrP) are associated with prion diseases. In this review we discuss a number of extrinsic and intrinsic experimental factors related to the formation of PrP amyloid fibrils in vitro. We first examined the effects of ultrasonic power on the induction of amyloid fibrillation from PrP. The most important conclusion drawn from the results is that an applied ultrasonic power of approximately 2 W enhanced the nucleation of amyloid fibrils efficiently but that more powerful ultrasonication led to retardation of growth. We also reviewed evidence on the amyloidogenic regions of PrP based on peptide screening throughout the polypeptide sequence. These results showed that helix 2 (H2) peptides of PrP were capable of both the fibrillation and propagation of straight, long fibrils. Moreover, the conformation of preformed H2 fibrils changed reversibly depending on the pH of the solution, implying that interactions between side-chains modulated the conformation of amyloid fibrils. The evidence discussed in this review relates specifically to PrP but may be relevant to other amyloidogenic proteins.
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Affiliation(s)
- Kei-ichi Yamaguchi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
- Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
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14
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Endo S, Xia S, Suyama M, Morikawa Y, Oguri H, Hu D, Ao Y, Takahara S, Horino Y, Hayakawa Y, Watanabe Y, Gouda H, Hara A, Kuwata K, Toyooka N, Matsunaga T, Ikari A. Correction to Synthesis of Potent and Selective Inhibitors of Aldo-Keto Reductase 1B10 and Their Efficacy against Proliferation, Metastasis, and Cisplatin Resistance of Lung Cancer Cells. J Med Chem 2018; 61:1380. [PMID: 29323483 DOI: 10.1021/acs.jmedchem.7b01911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Abstract
Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.
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Affiliation(s)
- Ryo Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan
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16
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Abstract
We investigated the dissociation process of tri-N-acetyl-d-glucosamine from hen egg white lysozyme using parallel cascade selection molecular dynamics (PaCS-MD), which comprises cycles of multiple unbiased MD simulations using a selection of MD snapshots as the initial structures for the next cycle. Dissociation was significantly accelerated by PaCS-MD, in which the probability of rare event occurrence toward dissociation was enhanced by the selection and rerandomization of the initial velocities. Although this complex was stable during 1 μs of conventional MD, PaCS-MD easily induced dissociation within 100-101 ns. We found that velocity rerandomization enhances the dissociation of triNAG from the bound state, whereas diffusion plays a more important role in the unbound state. We calculated the dissociation free energy by analyzing all PaCS-MD trajectories using the Markov state model (MSM), compared the results to those obtained by combinations of PaCS-MD and umbrella sampling (US), steered MD (SMD) and US, and SMD and the Jarzynski equality, and experimentally determined binding free energy. PaCS-MD/MSM yielded results most comparable to the experimentally determined binding free energy, independent of simulation parameter variations, and also gave the lowest standard errors.
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Affiliation(s)
- Duy Phuoc Tran
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Kazuhiro Takemura
- Institute of Molecular and Cellular Biosciences, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kazuo Kuwata
- Center for Emerging Infectious Diseases, Gifu University , 1-1 Yanagido, Gifu-shi, Gifu 501-1194, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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17
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Endo S, Xia S, Suyama M, Morikawa Y, Oguri H, Hu D, Ao Y, Takahara S, Horino Y, Hayakawa Y, Watanabe Y, Gouda H, Hara A, Kuwata K, Toyooka N, Matsunaga T, Ikari A. Synthesis of Potent and Selective Inhibitors of Aldo-Keto Reductase 1B10 and Their Efficacy against Proliferation, Metastasis, and Cisplatin Resistance of Lung Cancer Cells. J Med Chem 2017; 60:8441-8455. [PMID: 28976752 DOI: 10.1021/acs.jmedchem.7b00830] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aldo-keto reductase 1B10 (AKR1B10) is overexpressed in several extraintestinal cancers, particularly in non-small-cell lung cancer, where AKR1B10 is a potential diagnostic marker and therapeutic target. Selective AKR1B10 inhibitors are required because compounds should not inhibit the highly related aldose reductase that is involved in monosaccharide and prostaglandin metabolism. Currently, 7-hydroxy-2-(4-methoxyphenylimino)-2H-chromene-3-carboxylic acid benzylamide (HMPC) is known to be the most potent competitive inhibitor of AKR1B10, but it is nonselective. In this study, derivatives of HMPC were synthesized by removing the 4-methoxyphenylimino moiety and replacing the benzylamide with phenylpropylamide. Among them, 4c and 4e showed higher AKR1B10 inhibitory potency (IC50 4.2 and 3.5 nM, respectively) and selectivity than HMPC. The treatments with the two compounds significantly suppressed not only migration, proliferation, and metastasis of lung cancer A549 cells but also metastatic and invasive potentials of cisplatin-resistant A549 cells.
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Shuang Xia
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Miho Suyama
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Yoshifumi Morikawa
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Hiroaki Oguri
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Dawei Hu
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Yoshinori Ao
- Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Satoyuki Takahara
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Yoshihiro Hayakawa
- Division of Pathogenic Biochemistry, Institute of Natural Medicine, University of Toyama , Toyama 930-0194, Japan
| | - Yurie Watanabe
- School of Pharmacy, Showa University , Tokyo 142-8555, Japan
| | - Hiroaki Gouda
- School of Pharmacy, Showa University , Tokyo 142-8555, Japan
| | - Akira Hara
- Faculty of Engineering, Gifu University , Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , Gifu 501-1193, Japan
| | - Naoki Toyooka
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan.,Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Toshiyuki Matsunaga
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Akira Ikari
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
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18
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Endo S, Takada S, Honda RP, Müller K, Weishaupt JH, Andersen PM, Ludolph AC, Kamatari YO, Matsunaga T, Kuwata K, El-Kabbani O, Ikari A. Instability of C154Y variant of aldo-keto reductase 1C3. Chem Biol Interact 2017; 276:194-202. [DOI: 10.1016/j.cbi.2016.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/09/2016] [Accepted: 12/22/2016] [Indexed: 12/14/2022]
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19
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Kabir A, Endo S, Toyooka N, Fukuoka M, Kuwata K, Kamatari YO. Evaluation of compound selectivity of aldo-keto reductases using differential scanning fluorimetry. J Biochem 2017; 161:215-222. [PMID: 28003428 DOI: 10.1093/jb/mvw063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/11/2016] [Indexed: 02/03/2023] Open
Abstract
Inhibitors of AKR1B10 belonging to the aldo-keto reductase (AKR) superfamily are considered promising candidates for anti-cancer drugs. AKR1B1, a structurally similar isoform of AKR1B10, is involved in glucose metabolism. Thus, selective inhibition of AKR1B10 is required for the development of anti-cancer drugs. In this study, we first compared correlations between melting temperature and the 50% inhibition concentration obtained from differential scanning fluorimetry (DSF) and an enzyme inhibitory experiment, respectively, and a good correlation was found, except for compounds with low solubility. This result indicates that the DSF method is useful for drug screening for the AKR superfamily. We then evaluated their selectivity as inhibitors against all seven major human AKR1 family proteins and found that C18 is most specific for AKR1B10.
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Affiliation(s)
- Aurangazeb Kabir
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Satoshi Endo
- Labolatory of Biochemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi Gifu 501-1196, Japan
| | - Naoki Toyooka
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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20
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Tahoun A, Masutani H, El-Sharkawy H, Gillespie T, Honda RP, Kuwata K, Inagaki M, Yabe T, Nomura I, Suzuki T. Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages. Gut Pathog 2017; 9:27. [PMID: 28469711 PMCID: PMC5412050 DOI: 10.1186/s13099-017-0177-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/21/2017] [Indexed: 02/07/2023] Open
Abstract
Background Bifidobacterium longum 105-A produces markedly high amounts of capsular polysaccharides (CPS) and exopolysaccharides (EPS) that should play distinct roles in bacterial–host interactions. To identify the biological function of B. longum 105-A CPS/EPS, we carried out an informatics survey of the genome and identified the EPS-encoding genetic locus of B. longum 105-A that is responsible for the production of CPS/EPS. The role of CPS/EPS in the adaptation to gut tract environment and bacteria-gut cell interactions was investigated using the ΔcpsD mutant. Results A putative B. longum 105-A CPS/EPS gene cluster was shown to consist of 24 putative genes encoding a priming glycosyltransferase (cpsD), 7 glycosyltransferases, 4 CPS/EPS synthesis machinery proteins, and 3 dTDP-L-rhamnose synthesis enzymes. These enzymes should form a complex system that is involved in the biogenesis of CPS and/or EPS. To confirm this, we constructed a knockout mutant (ΔcpsD) by a double cross-over homologous recombination. Compared to wild-type, the ∆cpsD mutant showed a similar growth rate. However, it showed quicker sedimentation and formation of cell clusters in liquid culture. EPS was secreted by the ∆cpsD mutant, but had altered monosaccharide composition and molecular weight. Comparison of the morphology of B. longum 105-A wild-type and ∆cpsD by negative staining in light and electron microscopy revealed that the formation of fimbriae is drastically enhanced in the ∆cpsD mutant while the B. longum 105-A wild-type was coated by a thick capsule. The fimbriae expression in the ∆cpsD was closely associated with the disappearance of the CPS layer. The wild-type showed low pH tolerance, adaptation, and bile salt tolerance, but the ∆cpsD mutant had lost this survivability in gastric and duodenal environments. The ∆cpsD mutant was extensively able to bind to the human colon carcinoma Caco-2 cell line and was phagocytosed by murine macrophage RAW 264.7, whereas the wild-type did not bind to epithelial cells and totally resisted internalization by macrophages. Conclusions Our results suggest that CPS/EPS production and fimbriae formation are negatively correlated and play key roles in the survival, attachment, and colonization of B. longum 105-A in the gut. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0177-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amin Tahoun
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Faculty of Veterinary Medicine, Kafr El-Sheikh University, Kafr El-Sheikh, 33516 Egypt
| | - Hisayoshi Masutani
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Hanem El-Sharkawy
- Faculty of Veterinary Medicine, Kafr El-Sheikh University, Kafr El-Sheikh, 33516 Egypt.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Trudi Gillespie
- CALM_live Imaging Facility, Centre for Inflammation Research, University of Edinburgh, Edinburgh, 47 EH16 4TJ UK
| | - Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Mizuho Inagaki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Tomio Yabe
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Izumi Nomura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Tohru Suzuki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
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21
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Honda RP, Kuwata K. The native state of prion protein (PrP) directly inhibits formation of PrP-amyloid fibrils in vitro. Sci Rep 2017; 7:562. [PMID: 28373719 PMCID: PMC5429628 DOI: 10.1038/s41598-017-00710-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
The conversion of globular proteins into amyloid fibrils is associated with a wide variety of human diseases. One example is the prion protein (PrP), which adopts an α-helical structure in the native state but its amyloid form is implicated in the pathogenesis of prion diseases. Previous evidence has suggested that destabilization of the native state promotes amyloid formation, but the underlying mechanism remains unknown. In this study, we report that the native state of PrP serves as a potent inhibitor in the formation of PrP amyloid fibrils. By monitoring the time courses of thioflavin T fluorescence, the kinetics of amyloid formation was studied in vitro under various concentrations of pre-formed amyloid, monomer, and denaturant. Quantitative analysis of the kinetic data using various models of enzyme kinetics suggested that the native state of PrP is either an uncompetitive or noncompetitive inhibitor of amyloid formation. This study highlights the significant role of the native state in inhibiting amyloid formation, which provides new insights into the pathogenesis of misfolding diseases.
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Affiliation(s)
- Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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22
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Kabir A, Honda RP, Kamatari YO, Endo S, Fukuoka M, Kuwata K. Effects of ligand binding on the stability of aldo-keto reductases: Implications for stabilizer or destabilizer chaperones. Protein Sci 2016; 25:2132-2141. [PMID: 27595938 PMCID: PMC5119574 DOI: 10.1002/pro.3036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 01/26/2023]
Abstract
Ligands such as enzyme inhibitors stabilize the native conformation of a protein upon binding to the native state, but some compounds destabilize the native conformation upon binding to the non-native state. The former ligands are termed "stabilizer chaperones" and the latter ones "destabilizer chaperones." Because the stabilization effects are essential for the medical chaperone (MC) hypothesis, here we have formulated a thermodynamic system consisting of a ligand and a protein in its native- and non-native state. Using the differential scanning fluorimetry and the circular dichroism varying the urea concentration and temperature, we found that when the coenzyme NADP+ was absent, inhibitors such as isolithocholic acid stabilized the aldo-keto reductase AKR1A1 upon binding, which showed actually the three-state folding, but destabilized AKR1B10. In contrast, in the presence of NADP+ , they destabilized AKR1A1 and stabilized AKR1B10. To explain these phenomena, we decomposed the free energy of stabilization (ΔΔG) into its enthalpy (ΔΔH) and entropy (ΔΔS) components. Then we found that in a relatively unstable protein showing the three-state folding, native conformation was stabilized by the negative ΔΔH in association with the negative ΔΔS, suggesting that the stabilizer chaperon decreases the conformational fluctuation of the target protein or increase its hydration. However, in other cases, ΔΔG was essentially determined by the delicate balance between ΔΔH and ΔΔS. The proposed thermodynamic formalism is applicable to the system including multiple ligands with allosteric interactions. These findings would promote the development of screening strategies for MCs to regulate the target conformations.
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Affiliation(s)
- Aurangazeb Kabir
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Ryo P. Honda
- Department of Molecular Pathobiochemistry, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
| | | | - Satoshi Endo
- Laboratory of BiochemistryGifu Pharmaceutical UniversityGifu501‐1196Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
- Department of Gene and Development, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
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23
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Ali F, Yamaguchi K, Fukuoka M, Elhelaly AE, Kuwata K. Logical design of an anti-cancer agent targeting the plant homeodomain in Pygopus2. Cancer Sci 2016; 107:1321-8. [PMID: 27324116 PMCID: PMC5021024 DOI: 10.1111/cas.12995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 12/29/2022] Open
Abstract
Pygopus2 (Pygo2) is a component of the Wnt signaling pathway, which is required for β-catenin mediated transcription. Plant homeodomain (PHD) finger in Pygo2 intercalates the methylated histone 3 (H3K4me) tail and HD1 domain of BCL9 that binds to β-catenin. Thus, PHD finger may be a potential target for the logical design of an anti-cancer drug. Here, we found that Spiro[2H-naphthol[1,2-b]pyran-2,4'-piperidine]-1'ethanol,3,4-dihydro-4-hydroxy-α-(6-methyl-1H-indol-3-yl)) termed JBC117 interacts with D339, A348, R356, V376 and A378 in PHD corresponding to the binding sites with H3K4me and/or HD1, and has strong anti-cancer effects. For colon (HCT116) and lung (A549) cancer cell lines, IC50 values were 2.6 ± 0.16 and 3.3 ± 0.14 μM, respectively, while 33.80 ± 0.15 μM for the normal human fibroblast cells. JBC117 potently antagonized the cellular effects of β-catenin-dependent activity and also inhibited the migration and invasion of cancer cells. In vivo studies showed that the survival time of mice was significantly prolonged by the subcutaneous injection of JBC117 (10 mg/kg/day). In conclusion, JBC117 is a novel anti-cancer lead compound targeting the PHD finger of Pygo2 and has a therapeutic effect against colon and lung cancer.
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Affiliation(s)
- Ferdausi Ali
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Keiichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.
- Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan.
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Mizusawa H, Kuwata K. PRION 2016 Tokyo Declaration. Prion 2016; 10:265-6. [PMID: 27565561 DOI: 10.1080/19336896.2016.1220242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Hidehiro Mizusawa
- a Congress President, Prion 2016 Tokyo President, National Center of Neurology and Psychiatry , Tokyo , Japan
| | - Kazuo Kuwata
- b Congress President, APPS 2016 Senior Professor, United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , Gifu , Japan
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25
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Sriwilaijaroen N, Magesh S, Imamura A, Ando H, Ishida H, Sakai M, Ishitsubo E, Hori T, Moriya S, Ishikawa T, Kuwata K, Odagiri T, Tashiro M, Hiramatsu H, Tsukamoto K, Miyagi T, Tokiwa H, Kiso M, Suzuki Y. A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-Inhibitor Interactions. J Med Chem 2016; 59:4563-77. [PMID: 27095056 DOI: 10.1021/acs.jmedchem.5b01863] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
People throughout the world continue to be at risk for death from influenza A virus, which is always creating a new variant. Here we present a new effective and specific anti-influenza viral neuraminidase (viNA) inhibitor, 9-cyclopropylcarbonylamino-4-guanidino-Neu5Ac2en (cPro-GUN). Like zanamivir, it is highly effective against N1-N9 avian and N1-N2 human viNAs, including H274Y oseltamivir-resistant N1 viNA, due to its C-6 portion still being anchored in the active site, different from the disruption of oseltamivir's C-6 anchoring by H274Y mutation. Unlike zanamivir, no sialidase inhibitory activity has been observed for cPro-GUN against huNeu1-huNeu4 enzymes. Broad efficacy of cPro-GUN against avian and human influenza viruses in cell cultures comparable to its sialidase inhibitory activities makes cPro-GUN ideal for further development for safe therapeutic or prophylactic use against both seasonal and pandemic influenza.
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Affiliation(s)
- Nongluk Sriwilaijaroen
- Department of Preclinical Sciences, Faculty of Medicine, Thammasat University , Pathumthani 12120, Thailand.,Health Science Hills, College of Life and Health Sciences, Chubu University , Aichi 487-8501, Japan
| | | | | | - Hiromune Ando
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Kyoto 606-8501, Japan
| | | | | | | | | | - Setsuko Moriya
- Division of Cancer Glycosylation Research, Institute of Molecular Biomembrane and Glycobiology, Tohoku Pharmaceutical University , Sendai 981-8558, Japan
| | | | | | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases , Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases , Tokyo 208-0011, Japan
| | - Hiroaki Hiramatsu
- Health Science Hills, College of Life and Health Sciences, Chubu University , Aichi 487-8501, Japan
| | - Kenji Tsukamoto
- Research Team for Zoonotic Diseases, National Institute of Animal Health , Ibaraki 305-0856, Japan
| | - Taeko Miyagi
- Division of Cancer Glycosylation Research, Institute of Molecular Biomembrane and Glycobiology, Tohoku Pharmaceutical University , Sendai 981-8558, Japan
| | | | - Makoto Kiso
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Kyoto 606-8501, Japan
| | - Yasuo Suzuki
- Health Science Hills, College of Life and Health Sciences, Chubu University , Aichi 487-8501, Japan
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Honda RP, Xu M, Yamaguchi KI, Roder H, Kuwata K. A Native-like Intermediate Serves as a Branching Point between the Folding and Aggregation Pathways of the Mouse Prion Protein. Structure 2015; 23:1735-1742. [PMID: 26256540 PMCID: PMC4640677 DOI: 10.1016/j.str.2015.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/08/2015] [Accepted: 07/01/2015] [Indexed: 12/30/2022]
Abstract
Transient folding intermediates and/or partially unfolded equilibrium states are thought to play a key role in the formation of protein aggregates. However, there is only indirect evidence linking accumulation of folding intermediates to aggregation, and the underlying mechanism remains to be elucidated. Here, we show that a partially unfolded state of the prion protein accumulates both as a stable equilibrium state at acidic pH (A-state) and as a late folding intermediate. With a time resolution of approximately 60 μs, we systematically studied the kinetics of folding and unfolding, starting from various initial conditions including the U-, N-, and A-states. Quantitative modeling showed that the observed kinetic data are completely consistent with a sequential four-state mechanism where the A-state is a late folding intermediate. Combined with previous evidence linking A-state accumulation to aggregation, the results indicate that this native-like state serves as a branching point between the folding and aggregation pathways.
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Affiliation(s)
- Ryo P Honda
- Department of Molecular Pathobiochemistry, Gifu University Graduate School of Medicine, Yanagido 1-1, Gifu 501-1193, Japan
| | - Ming Xu
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kei-Ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Heinrich Roder
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan; Department of Gene Development, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
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Abstract
An abnormal form of prion protein (PrP) is considered to be the pathogen in prion diseases. However, the structural details of this abnormal form are not known. To characterize the non-native structure of PrP, we synthesized position-specific double-fluorescent labeled PrP for a fluorescence resonance energy transfer (FRET) experiment. Using FRET, we observed a conformational change in the labeled PrP associated with amyloid fibril formation. The FRET analysis indicated that the distance between fluorescent labeled N- and C-terminal sites of PrP increased upon the formation of amyloid fibrils compared with that of the native state. This approach using FRET analysis is useful for elucidating the structure of abnormal PrP.
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Affiliation(s)
| | - Kei-ichi Yamaguchi
- a Center for Emerging Infectious Diseases , Gifu University.,b United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University
| | - Yuji O Kamatari
- a Center for Emerging Infectious Diseases , Gifu University.,c Life Science Research Center , Gifu University
| | - Kazuo Kuwata
- a Center for Emerging Infectious Diseases , Gifu University.,b United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University.,d Department of Gene Development, Graduate School of Medicine , Gifu University , Gifu , Japan
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Nakagaki T, Satoh K, Ishibashi D, Fuse T, Sano K, Kamatari YO, Kuwata K, Shigematsu K, Iwamaru Y, Takenouchi T, Kitani H, Nishida N, Atarashi R. FK506 reduces abnormal prion protein through the activation of autolysosomal degradation and prolongs survival in prion-infected mice. Autophagy 2014; 9:1386-94. [DOI: 10.4161/auto.25381] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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29
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Honda RP, Yamaguchi KI, Kuwata K. Acid-induced molten globule state of a prion protein: crucial role of Strand 1-Helix 1-Strand 2 segment. J Biol Chem 2014; 289:30355-30363. [PMID: 25217639 DOI: 10.1074/jbc.m114.559450] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conversion of a cellular prion protein (PrP(C)) to its pathogenic isoform (PrP(Sc)) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP(C) is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP(C) and discovered a unique acid-induced molten globule state at pH 2.0 termed the "A-state." We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp(144), Asp(147), and Glu(196), followed by disruption of key salt bridges in PrP(C). Moreover, the initial population of the A-state at low pH (pH 2.0-5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases.
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Affiliation(s)
- Ryo P Honda
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kei-Ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Kazuo Kuwata
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan; Department of Gene and Development, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan and.
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30
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Kuwata K. Logical Design of Medical Chaperone for Prion Diseases. Curr Top Med Chem 2013; 13:2432-40. [DOI: 10.2174/15680266113136660171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/09/2013] [Accepted: 08/22/2013] [Indexed: 11/22/2022]
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31
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Yamaguchi KI, Kamatari YO, Fukuoka M, Miyaji R, Kuwata K. Nearly Reversible Conformational Change of Amyloid Fibrils as Revealed by pH-Jump Experiments. Biochemistry 2013; 52:6797-806. [DOI: 10.1021/bi400698u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kei-ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Reiji Miyaji
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
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32
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Kimura T, Sako T, Siqin, Hosokawa-Muto J, Cui YL, Wada Y, Kataoka Y, Doi H, Sakaguchi S, Suzuki M, Watanabe Y, Kuwata K. Synthesis of an (11) C-labeled antiprion GN8 derivative and evaluation of its brain uptake by positron emission tomography. ChemMedChem 2013; 8:1035-9. [PMID: 23712919 DOI: 10.1002/cmdc.201300167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 11/10/2022]
Abstract
A radiolabeled PET! A (11) C-labeled derivative of N,N'-(methylenedi-4,1-phenylene)bis[2-(1-pyrrolidinyl) acetamide] (GN8), an antiprion agent currently under development, was synthesized by palladium-catalyzed rapid methylation of aryltributylstannane and assessed for brain penetration and organ distribution in rats by positron emission tomography (PET).
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Affiliation(s)
- Tsutomu Kimura
- Center for Emerging Infectious Diseases, United Graduate School of Drug Discovery & Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
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33
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Okamoto T, Ishikawa T, Koyano Y, Yamamoto N, Kuwata K, Nagaoka M. A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation. BCSJ 2013. [DOI: 10.1246/bcsj.20120216] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuya Okamoto
- Graduate School of Information Science, Nagoya University
| | - Takeshi Ishikawa
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
| | | | | | - Kazuo Kuwata
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
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34
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Ishikawa T, Burri RR, Kamatari YO, Sakuraba S, Matubayasi N, Kitao A, Kuwata K. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method. Phys Chem Chem Phys 2013; 15:3646-54. [DOI: 10.1039/c3cp42761g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Mashima T, Nishikawa F, Kamatari YO, Fujiwara H, Saimura M, Nagata T, Kodaki T, Nishikawa S, Kuwata K, Katahira M. Anti-prion activity of an RNA aptamer and its structural basis. Nucleic Acids Res 2012. [PMID: 23180780 PMCID: PMC3553944 DOI: 10.1093/nar/gks1132] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrPC) of PrP into an abnormal form (PrPSc) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrPC is expected to block this conversion and to thereby prevent prion diseases. Here, we show that an RNA aptamer comprising only 12 residues, r(GGAGGAGGAGGA) (R12), reduces the PrPSc level in mouse neuronal cells persistently infected with the transmissible spongiform encephalopathy agent. Nuclear magnetic resonance analysis revealed that R12, folded into a unique quadruplex structure, forms a dimer and that each monomer simultaneously binds to two portions of the N-terminal half of PrPC, resulting in tight binding. Electrostatic and stacking interactions contribute to the affinity of each portion. Our results demonstrate the therapeutic potential of an RNA aptamer as to prion diseases.
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Affiliation(s)
- Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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36
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Kamatari YO, Hayano Y, Yamaguchi KI, Hosokawa-Muto J, Kuwata K. Characterizing antiprion compounds based on their binding properties to prion proteins: implications as medical chaperones. Protein Sci 2012; 22:22-34. [PMID: 23081827 DOI: 10.1002/pro.2180] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 01/21/2023]
Abstract
A variety of antiprion compounds have been reported that are effective in ex vivo and in vivo treatment experiments. However, the molecular mechanisms for most of these compounds remain unknown. Here we classified antiprion mechanisms into four categories: I, specific conformational stabilization; II, nonspecific stabilization; III, aggregation; and IV, interaction with molecules other than PrP(C). To characterize antiprion compounds based on this classification, we determined their binding affinities to PrP(C) using surface plasmon resonance and their binding sites on PrP(C) using NMR spectroscopy. GN8 and GJP49 bound specifically to the hot spot in PrP(C), and acted as "medical chaperones" to stabilize the native conformation. Thus, mechanisms I was predominant. In contrast, quinacrine and epigallocathechin bound to PrP(C) rather nonspecifically; these may stabilize the PrP(C) conformation nonspecifically including the interference with the intermolecular interaction following mechanism II. Congo red and pentosan polysulfate bound to PrP(C) and caused aggregation and precipitation of PrP(C), thus reducing the effective concentration of prion protein. Thus, mechanism III was appropriate. Finally, CP-60, an edarabone derivative, did not bind to PrP(C). Thus these were classified into mechanism IV. However, their antiprion activities were not confirmed in the GT + FK system, whose details remain to be elucidated. This proposed antiprion mechanisms of diverse antiprion compounds could help to elucidate their antiprion activities and facilitate effective antiprion drug discovery.
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Affiliation(s)
- Yuji O Kamatari
- Life Science Research Center, Gifu University, Gifu 501-1194, Japan
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37
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Okamoto K, Okamoto I, Hatashita E, Kuwata K, Yamaguchi H, Kita A, Yamanaka K, Ono M, Nakagawa K. Overcoming Erlotinib Resistance in EGFR Mutation-Positive Non-Small-Cell Lung Cancer Cells by Targeting Survivin. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)32199-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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38
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Kuwata K. [Non-commutative geometrical drug discovery--the principle of geometrical regulation]. YAKUGAKU ZASSHI 2012; 132:873-9. [PMID: 22864344 DOI: 10.1248/yakushi.132.873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We developed a theoretical framework for the regulation of biological macromolecules using the logically designed compounds. According to the cohomology theory, algebraic objects can be translated into geometrical ones. Successfully established quantum theory at 20th century, which essentially deals with the non-commutative nature of the space, also suggests the non-commutative topology of biological space. Arithmetic geometrical representation of the molecules as well as the macroscopic membranous structures would uncover their structural groups in Hilbert space. In order to construct the concrete image of biological space, here we combined quantum chemical (QC) model, all-atom (AA) model and coarse grained (CG) model, into one program designated 'NAGARA'. These three models can be arranged in an arbitrary manner to yield the desired statistical ensemble. For example, QC model was applied to the optimization of the chemical structure of anti-prion lead compound GN8. Arithmetic geometrical representation of these algebraic models is in progress.
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Affiliation(s)
- Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Japan.
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39
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Sanghera N, Correia BEFS, Correia JRS, Ludwig C, Agarwal S, Nakamura HK, Kuwata K, Samain E, Gill AC, Bonev BB, Pinheiro TJT. Deciphering the molecular details for the binding of the prion protein to main ganglioside GM1 of neuronal membranes. ACTA ACUST UNITED AC 2012; 18:1422-31. [PMID: 22118676 DOI: 10.1016/j.chembiol.2011.08.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 10/15/2022]
Abstract
The prion protein (PrP) resides in lipid rafts in vivo, and lipids modulate misfolding of the protein to infectious isoforms. Here we demonstrate that binding of recombinant PrP to model raft membranes requires the presence of ganglioside GM1. A combination of liquid- and solid-state NMR revealed the binding sites of PrP to the saccharide head group of GM1. The binding epitope for GM1 was mapped to the folded C-terminal domain of PrP, and docking simulations identified key residues in the C-terminal region of helix C and the loop between strand S2 and helix B. Crucially, this region of PrP is linked to prion resistance in vivo, and structural changes caused by lipid binding in this region may explain the requirement for lipids in the generation of infectious prions in vitro.
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Affiliation(s)
- Narinder Sanghera
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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40
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Yamada K, Koyama H, Hagiwara K, Ueda A, Sasaki Y, Kanesashi SN, Ueno R, Nakamura HK, Kuwata K, Shimizu K, Suzuki M, Aida Y. Identification of a novel compound with antiviral activity against influenza A virus depending on PA subunit of viral RNA polymerase. Microbes Infect 2012; 14:740-7. [PMID: 22441116 DOI: 10.1016/j.micinf.2012.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
Abstract
Influenza viruses have developed resistance to current drugs, creating a need for new antiviral targets and new drugs to treat influenza virus infections. In this study, computational and experimental screening of an extensive compound library identified THC19, which was able to suppress influenza virus replication. This compound had no cytotoxic effects and did not disrupt cell cycle progression or induce apoptosis in MDCK cells as confirmed by WST-1 assays, flow cytometry analysis, and caspase-3 assays. Time-of-addition experiments showed that THC19 acts at a relatively early stage of the viral lifecycle. Subsequent mini-genome assays revealed that THC19 inhibited viral genome replication and/or transcription, suggesting that it interferes with one or more of the viral components that form the ribonucleoprotein complexes, namely polymerase basic 2 (PB2), polymerase basic 1 (PB1), polymerase acidic (PA), nucleoprotein (NP) and viral RNA. Finally, mini-genome assays where PB2, PB1, PA or NP from A/WSN/33 (H1N1) virus were replaced with those from A/Udorn/307/1972 (H3N2) virus effectively demonstrated that THC19 inhibited viral multiplication in a manner dependent upon the PA subunit. Taken together, these results suggest that influenza virus PA protein is a potential target for, and may aid the development of, novel compounds that inhibit influenza A virus replication.
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Affiliation(s)
- Kazunori Yamada
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Abstract
The second-order Møller-Plesset perturbation theory (MP2) gradient using resolution of the identity approximation (RI-MP2 gradient) was combined with the fragment molecular orbital (FMO) method to evaluate the gradient including electron correlation for large molecules. In this study, we adopted a direct implementation of the RI-MP2 gradient, in which a characteristic feature of the FMO scheme was utilized. Test calculations with a small peptide presented a computational advantage of the RI-MP2 gradient over the canonical MP2 gradient. In addition, it was shown that the error of the RI-MP2 gradient, caused by RI approximation, was negligible. As an illustrative example, we performed gradient calculations for two biomolecules-a prion protein with GN8 and a human immunodeficiency virus type 1 (HIV1) protease with lopinavir (LPV). These calculations demonstrated that the gradient including the correlation effect could be evaluated with only about twice the computational effort of the Hartree-Fock (HF) gradient.
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Affiliation(s)
- Takeshi Ishikawa
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuo Kuwata
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Tanizaki J, Okamoto I, Takezawa K, Sakai K, Azuma K, Kuwata K, Yamaguchi H, Hatashita E, Nishio K, Janne PA, Nakagawa K. Combined effect of ALK and MEK inhibitors in EML4-ALK-positive non-small-cell lung cancer cells. Br J Cancer 2012; 106:763-7. [PMID: 22240786 PMCID: PMC3322944 DOI: 10.1038/bjc.2011.586] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background: Although most non-small-cell lung cancer (NSCLC) patients with the echinoderm microtubule-associated protein-like 4 (EML4) – anaplastic lymphoma kinase (ALK) fusion gene – benefit from ALK tyrosine kinase inhibitors (ALK-TKIs), the efficacy of these drugs varies greatly among individuals. Methods: The antitumour action of ALK-TKIs in EML4–ALK-positive NSCLC cell lines was evaluated from their effects on cell proliferation, signal transduction, and apoptosis. Results: The ALK-TKI TAE684 inhibited cell proliferation and induced apoptosis, in association with inhibition of STAT3 and ERK phosphorylation, in EML4–ALK-positive H3122 cells. TAE684 inhibited STAT3 phosphorylation, but not ERK phosphorylation, and it showed little effect on cell proliferation or apoptosis, in EML4–ALK-positive H2228 cells. The combination of TAE684 and a MEK inhibitor-induced marked apoptosis accompanied by inhibition of STAT3 and ERK pathways in H2228 cells. Such dual interruption of STAT3 and ERK pathways induced downregulation of the antiapoptotic protein survivin and upregulation of the proapoptotic protein BIM. Conclusion: Our results indicate that interruption of both STAT3-survivin and ERK–BIM pathways is required for induction of apoptosis in NSCLC harbouring EML4–ALK, providing a rationale for combination therapy with ALK and MEK inhibitors in EML4–ALK-positive NSCLC patients for whom ALK inhibitors alone are ineffective.
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Affiliation(s)
- J Tanizaki
- Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
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Yamaguchi KI, Matsumoto T, Kuwata K. Proper calibration of ultrasonic power enabled the quantitative analysis of the ultrasonication-induced amyloid formation process. Protein Sci 2011; 21:38-49. [PMID: 22095682 DOI: 10.1002/pro.755] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/02/2011] [Accepted: 10/07/2011] [Indexed: 12/12/2022]
Abstract
To elucidate the mechanisms of ultrasonication on the amyloid fibril formation, we quantitatively determined the ultrasonic power using both calorimetry and potassium iodide (KI) oxidation, and under the properly calibrated ultrasonic power, we investigated the ultasonication-induced amyloid formation process of the mouse prion protein (mPrP(23-231)). These methods revealed that the ultrasonic power in our system ranged from 0.3 to 2.7 W but entirely dependent on the positions of the ultrasonic stage. Intriguingly, the nucleation time of the amyloid fibrils was found to be shortened almost proportionally to the ultrasonic power, indicating that the probability of the occurrence of nucleus formation increases proportionally to the ultrasonic power. Moreover, mPrP(23-231) formed two types of aggregates: rigid fibrils and short fibrils with disordered aggregates, depending on the ultrasonic power. The nucleation of rigid fibrils required an ultrasonic power larger than 1.5 W. While at the strong ultrasonic power larger than 2.6 W, amyloid fibrils were formed early, but simultaneously fine fragmentation of fibrils occurred. Thus, an ultrasonic power of approximately 2.0 W would be suitable for the formation of rigid mPrP(23-231) fibrils under the conditions utilized (ultrasonication applied for 30 s every 9 min). As ultrasonication has been widely used to amplify the scrapie form of the prion protein, or other amyloids in vitro, the calorimetry and KI oxidation methods proposed here might help determining the adequate ultrasonic powers necessary to amplify them efficiently.
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Affiliation(s)
- Kei-ichi Yamaguchi
- Center for Emerging Infectious Diseases, Gifu University, Yanagido 1-1, Gifu, Japan
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Fukuoka M, Minakuchi M, Kawaguchi A, Nagata K, Kamatari YO, Kuwata K. Structure-based discovery of anti-influenza virus A compounds among medicines. Biochim Biophys Acta Gen Subj 2011; 1820:90-5. [PMID: 22108550 DOI: 10.1016/j.bbagen.2011.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 12/26/2022]
Abstract
BACKGROUND Influenza A virus (IAV) infection is nowadays a major public health concern, in particular since the 2009 H1N1 flu pandemic. The outbreak of IAV strains resistant to currently available drugs, such as oseltamivir or zanamivir targeting the neuraminidase, is a real threat for humans as well as for animals. Thus the development of anti-IAV drugs with a novel action mechanism may be an urgent theme. METHODS We performed a docking simulation targeting the interface of PA interacting with PB1 using a drug database including ~4000 compounds. We then conducted cell viability assay and plaque assay using IAV/WSN/33. Finally we examined their anti-IAV mechanism by surface plasmon resonance and IAV replicon assay. RESULTS We found that benzbromarone, diclazuril, and trenbolone acetate had strong anti-IAV activities. We confirmed that benzbromarone and diclazuril bound with PA subunit, and decreased the transcriptional activity of the viral RNA polymerase. CONCLUSIONS Benzbromarone and diclazuril had strong anti-IAV activities with novel action mechanism, i.e. inhibition of viral RNA polymerase. GENERAL SIGNIFICANCE Since benzbromarone and diclazuril are already used in public as medicines, these could be the candidates for alternatives in case of an outbreak of IAV which is resistant to pre-existing anti-IAV drugs.
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Affiliation(s)
- Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1Yanagido, Gifu 501-1193, Japan
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Hosokawa-Muto J, Kimura T, Kuwata K. Respiratory and cardiovascular toxicity studies of a novel antiprion compound, GN8, in rats and dogs. Drug Chem Toxicol 2011; 35:264-71. [DOI: 10.3109/01480545.2011.598533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Kato Z, Stern JNH, Nakamura HK, Miyashita N, Kuwata K, Kondo N, Strominger JL. The autoimmune TCR-Ob.2F3 can bind to MBP85-99/HLA-DR2 having an unconventional mode as in TCR-Ob.1A12. Mol Immunol 2011; 48:314-20. [PMID: 20810170 DOI: 10.1016/j.molimm.2010.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/30/2010] [Accepted: 07/18/2010] [Indexed: 11/18/2022]
Abstract
The generation of T cell receptor (TCR) sequence diversity can produce 'forbidden' clones able to recognize self-antigens. Here, the structure of the complex between a myelin basic protein peptide (MBP85-99), human leukocyte antigen (HLA)-DR2 (DRB1*1501/DRA) and TCR-Ob.2F3, the dominant autoimmune clone obtained from a multiple sclerosis (MS) patient, has been determined using structural docking simulation and dynamics in silico and compared to the structure of TCR-Ob.1A12 complexes with the same MHC/peptide determined by X-ray crystallography. The two TCRs differ by three amino acids in the CDR3 α and β loops. As the result different hydrogen bonds are formed between the two CDR3β loops and the peptide in the complexes of the simulated structures, with three hydrogen bonds seen in the TCR-Ob.2F3 complex and five in the TCR-Ob.1A12 complex. The two TCRs, each located near the N-terminal end of the HLA-DR2 binding groove and both had an orthogonal binding axis but they deviated by about 10°. Simulation methods, such as structural docking and molecular dynamics as used here, provide an avenue to understand molecular binding mode efficiently and more rapidly than obtaining multiple crystal structures when a large structural database is already available.
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Affiliation(s)
- Zenichiro Kato
- Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02193, USA.
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Ishikawa T, Yamamoto N, Kuwata K. Partial energy gradient based on the fragment molecular orbital method: Application to geometry optimization. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.09.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Iwasa T, Okamoto I, Takezawa K, Yamanaka K, Nakahara T, Kita A, Koutoku H, Sasamata M, Hatashita E, Yamada Y, Kuwata K, Fukuoka M, Nakagawa K. Marked anti-tumour activity of the combination of YM155, a novel survivin suppressant, and platinum-based drugs. Br J Cancer 2010; 103:36-42. [PMID: 20517311 PMCID: PMC2905296 DOI: 10.1038/sj.bjc.6605713] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Survivin, a member of the inhibitor of apoptosis protein family, is an attractive target for cancer therapy. We have now investigated the effects of the combination of YM155, a novel small-molecule inhibitor of survivin expression, and platinum compounds (cisplatin and carboplatin) on human non-small cell lung cancer (NSCLC) cell lines. METHODS The anti-cancer efficacy of YM155 in combination with platinum compounds was evaluated on the basis of cell death and progression of tumour xenografts. Platinum compound-induced DNA damage was evaluated by immunofluorescence analysis of histone gamma-H2AX. RESULTS Immunofluorescence analysis of histone gamma-H2AX showed that YM155 delayed the repair of double-strand breaks induced in nuclear DNA by platinum compounds. The combination of YM155 and platinum compounds also induced synergistic increases both in the number of apoptotic cells and in the activity of caspase-3. Finally, combination therapy with YM155 and platinum compounds delayed the growth of NSCLC tumour xenografts in nude mice to an extent greater than that apparent with either treatment modality alone. CONCLUSION These results suggest that YM155 sensitises tumour cells to platinum compounds both in vitro and in vivo, and that this effect is likely attributable to the inhibition of DNA repair and consequent enhancement of apoptosis.
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Affiliation(s)
- T Iwasa
- Department of Medical Oncology, Kinki University School of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
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Endo S, Matsunaga T, Kuwata K, Zhao HT, El-Kabbani O, Kitade Y, Hara A. Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10. Bioorg Med Chem 2010; 18:2485-90. [DOI: 10.1016/j.bmc.2010.02.050] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Revised: 02/20/2010] [Accepted: 02/23/2010] [Indexed: 01/25/2023]
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