1
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Han SI, Nakakuki M, Nakagawa Y, Wang Y, Araki M, Yamamoto Y, Tokiwa H, Takeda H, Mizunoe Y, Motomura K, Ohno H, Kainoh K, Murayama Y, Aita Y, Takeuchi Y, Osaki Y, Miyamoto T, Sekiya M, Matsuzaka T, Yahagi N, Sone H, Daitoku H, Sato R, Kawano H, Shimano H. Rhomboid protease RHBDL4/RHBDD1 cleaves SREBP-1c at endoplasmic reticulum monitoring and regulating fatty acids. PNAS Nexus 2023; 2:pgad351. [PMID: 37954160 PMCID: PMC10637267 DOI: 10.1093/pnasnexus/pgad351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023]
Abstract
The endoplasmic reticulum (ER)-embedded transcription factors, sterol regulatory element-binding proteins (SREBPs), master regulators of lipid biosynthesis, are transported to the Golgi for proteolytic activation to tune cellular cholesterol levels and regulate lipogenesis. However, mechanisms by which the cell responds to the levels of saturated or unsaturated fatty acids remain underexplored. Here, we show that RHBDL4/RHBDD1, a rhomboid family protease, directly cleaves SREBP-1c at the ER. The p97/VCP, AAA-ATPase complex then acts as an auxiliary segregase to extract the remaining ER-embedded fragment of SREBP-1c. Importantly, the enzymatic activity of RHBDL4 is enhanced by saturated fatty acids (SFAs) but inhibited by polyunsaturated fatty acids (PUFAs). Genetic deletion of RHBDL4 in mice fed on a Western diet enriched in SFAs and cholesterol prevented SREBP-1c from inducing genes for lipogenesis, particularly for synthesis and incorporation of PUFAs, and secretion of lipoproteins. The RHBDL4-SREBP-1c pathway reveals a regulatory system for monitoring fatty acid composition and maintaining cellular lipid homeostasis.
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Affiliation(s)
- Song-Iee Han
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masanori Nakakuki
- Pharmaceutical Research Center, Mochida Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8524, Japan
| | - Yoshimi Nakagawa
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Division of Complex Biosystem Research, Department of Research and Development, Institute of Natural Medicine, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Yunong Wang
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masaya Araki
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hiroaki Tokiwa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu 501-1196, Japan
| | - Hiroyuki Takeda
- Division of Proteo Drug Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Yuhei Mizunoe
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kaori Motomura
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroshi Ohno
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenta Kainoh
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuki Murayama
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuichi Aita
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshinori Takeuchi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshinori Osaki
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Motohiro Sekiya
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Naoya Yahagi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hirohito Sone
- Department of Internal Medicine, Faculty of Medicine, Niigata University, Niigata, Niigata 951-8510, Japan
| | - Hiroaki Daitoku
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryuichiro Sato
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, Nutri-Life Science Laboratory, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hiroyuki Kawano
- Pharmaceutical Research Center, Mochida Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8524, Japan
| | - Hitoshi Shimano
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-0004, Japan
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2
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Maekawa K, Ishizawa M, Ikawa T, Sajiki H, Matsumoto T, Tokiwa H, Makishima M, Yamada S. Syntheses of 25-Adamantyl-25-alkyl-2-methylidene-1α,25-dihydroxyvitamin D 3 Derivatives with Structure-Function Studies of Antagonistic and Agonistic Active Vitamin D Analogs. Biomolecules 2023; 13:1082. [PMID: 37509118 PMCID: PMC10377034 DOI: 10.3390/biom13071082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
The active form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3], is a major regulator of calcium homeostasis through activation of the vitamin D receptor (VDR). We have previously synthesized vitamin D derivatives with large adamantane (AD) rings at position 24, 25, or 26 of the side chain to study VDR agonist and/or antagonist properties. One of them-ADTK1, with an AD ring and 23,24-triple bond-shows a high VDR affinity and cell-selective VDR activity. In this study, we synthesized novel vitamin D derivatives (ADKM1-6) with an alkyl group substituted at position 25 of ADTK1 to develop more cell-selective VDR ligands. ADKM2, ADKM4, and ADKM6 had VDR transcriptional activity comparable to 1,25(OH)2D3 and ADTK1, although their VDR affinities were weaker. Interestingly, ADKM2 has selective VDR activity in kidney- and skin-derived cells-a unique phenotype that differs from ADTK1. Furthermore, ADKM2, ADKM4, and ADKM6 induced osteoblast differentiation in human dedifferentiated fat cells more effectively than ADTK1. The development of vitamin D derivatives with bulky modifications such as AD at position 24, 25, or 26 of the side chain is useful for increased stability and tissue selectivity in VDR-targeting therapy.
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Affiliation(s)
- Kazuki Maekawa
- Department of Chemistry, Faculty of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Michiyasu Ishizawa
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | - Takashi Ikawa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-Nishi, Gifu 501-1196, Japan
| | - Hironao Sajiki
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-Nishi, Gifu 501-1196, Japan
| | - Taro Matsumoto
- Department of Functional Morphology, Division of Cell Regeneration and Transplantation, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiroaki Tokiwa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University 1-25-4 Daigaku-Nishi, Gifu 501-1196, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | - Sachiko Yamada
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
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3
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Sekiya M, Kainoh K, Sugasawa T, Yoshino R, Hirokawa T, Tokiwa H, Nakano S, Nagatoishi S, Tsumoto K, Takeuchi Y, Miyamoto T, Matsuzaka T, Shimano H. The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis. Nat Commun 2021; 12:6315. [PMID: 34728642 PMCID: PMC8563733 DOI: 10.1038/s41467-021-26638-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/15/2021] [Indexed: 01/19/2023] Open
Abstract
Biological systems to sense and respond to metabolic perturbations are critical for the maintenance of cellular homeostasis. Here we describe a hepatic system in this context orchestrated by the transcriptional corepressor C-terminal binding protein 2 (CtBP2) that harbors metabolite-sensing capabilities. The repressor activity of CtBP2 is reciprocally regulated by NADH and acyl-CoAs. CtBP2 represses Forkhead box O1 (FoxO1)-mediated hepatic gluconeogenesis directly as well as Sterol Regulatory Element-Binding Protein 1 (SREBP1)-mediated lipogenesis indirectly. The activity of CtBP2 is markedly defective in obese liver reflecting the metabolic perturbations. Thus, liver-specific CtBP2 deletion promotes hepatic gluconeogenesis and accelerates the progression of steatohepatitis. Conversely, activation of CtBP2 ameliorates diabetes and hepatic steatosis in obesity. The structure-function relationships revealed in this study identify a critical structural domain called Rossmann fold, a metabolite-sensing pocket, that is susceptible to metabolic liabilities and potentially targetable for developing therapeutic approaches.
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Affiliation(s)
- Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Kenta Kainoh
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takehito Sugasawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryunosuke Yoshino
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo, 171-8501, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshinori Takeuchi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
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4
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Ikawa T, Yamamoto Y, Heguri A, Fukumoto Y, Murakami T, Takagi A, Masuda Y, Yahata K, Aoyama H, Shigeta Y, Tokiwa H, Akai S. Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical Biphenylenes. J Am Chem Soc 2021; 143:10853-10859. [PMID: 34197100 DOI: 10.1021/jacs.1c05434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In recent years, London dispersion interactions, which are the attractive component of the van der Waals potential, have been found to play an important role in controlling the regio- and/or stereoselectivity of various reactions. Particularly, the dispersion interactions between substrates and catalysts (or ligands) are dominant in various selective catalyzes. In contrast, repulsive steric interactions, rather than the attractive dispersion interactions, between bulky substituents are predominant in most of the noncatalytic reactions. Herein, we demonstrate the first example of London dispersion-controlled noncatalytic (2 + 2) cyclodimerization of substituted benzynes to selectively afford proximal biphenylenes in high yields and regioselectivities, depending on the extent of dispersion interactions in the substituents. This method can be applied for the synthesis of novel helical biphenylenes, which would be fascinating for chemists as these compounds are potential skeletons for ligands, catalysts, and medicines.
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Affiliation(s)
- Takashi Ikawa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu 501-1196, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Akito Heguri
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yutaka Fukumoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomonari Murakami
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuto Masuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenzo Yahata
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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Seki F, Yamamoto Y, Fukuhara H, Ohishi K, Maruyama T, Maenaka K, Tokiwa H, Takeda M. Measles Virus Hemagglutinin Protein Establishes a Specific Interaction With the Extreme N-Terminal Region of Human Signaling Lymphocytic Activation Molecule to Enhance Infection. Front Microbiol 2020; 11:1830. [PMID: 32922371 PMCID: PMC7457132 DOI: 10.3389/fmicb.2020.01830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Received: 06/14/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022] Open
Abstract
Measles virus (MV) is a human pathogen that is classified in the genus Morbillivirus in the family Paramyxoviridae together with several non-human animal morbilliviruses. They cause severe systemic infections by using signaling lymphocytic activation molecule (SLAM) and poliovirus receptor-like 4 expressed on immune and epithelial cells, respectively, as receptors. The viral hemagglutinin (H) protein is responsible for the receptor-binding. Previously determined structures of MV-H and SLAM complexes revealed a major binding interface between the SLAM V domain and MV-H with four binding components (sites 1–4) in the interface. We studied the MV-H and human SLAM (hSLAM) complex structure in further detail by in silico analyses and determined missing regions or residues in the previously determined complex structures. These analyses showed that, in addition to sites 1–4, MV-H establishes a unique interaction with the extreme N-terminal region (ExNTR) of hSLAM. The first principles calculation-based fragment molecular orbital computation method revealed that methionine at position 29 (hSLAM-Met29) is the key residue for the interaction. hSLAM-Met29 was predicted to establish a CH-π interaction with phenylalanine at position 549 of MV-H (MVH-Phe549). A cell-cell fusion assay showed that the hSLAM-Met29 and MVH-Phe549 interaction is important for hSLAM-dependent MV membrane fusion. Furthermore, Jurkat cell lines expressing hSLAM with or without Met29 and recombinant MV possessing the H protein with or without Phe549 showed that the hSLAM-Met29 and MVH-Phe549 interaction enhanced hSLAM-dependent MV infection by ~10-fold. We speculate that in the evolutionary history of morbilliviruses, this interaction may have contributed to MV adaptation to humans because this interaction is unique for MV and only MV uses hSLAM efficiently among morbilliviruses.
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Affiliation(s)
- Fumio Seki
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Tokyo, Japan
| | - Hideo Fukuhara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kazue Ohishi
- Faculty of Engineering, Tokyo Polytechnic University, Atsugi, Japan
| | | | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Tokyo, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
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6
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Matsuzaka T, Kuba M, Koyasu S, Yamamoto Y, Motomura K, Arulmozhiraja S, Ohno H, Sharma R, Shimura T, Okajima Y, Han SI, Aita Y, Mizunoe Y, Osaki Y, Iwasaki H, Yatoh S, Suzuki H, Sone H, Takeuchi Y, Yahagi N, Miyamoto T, Sekiya M, Nakagawa Y, Ema M, Takahashi S, Tokiwa H, Shimano H. Hepatocyte ELOVL Fatty Acid Elongase 6 Determines Ceramide Acyl-Chain Length and Hepatic Insulin Sensitivity in Mice. Hepatology 2020; 71:1609-1625. [PMID: 31529722 DOI: 10.1002/hep.30953] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/09/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Dysfunctional hepatic lipid metabolism is a cause of nonalcoholic fatty liver disease (NAFLD), the most common chronic liver disorder worldwide, and is closely associated with insulin resistance and type 2 diabetes. ELOVL fatty acid elongase 6 (Elovl6) is responsible for converting C16 saturated and monounsaturated fatty acids (FAs) into C18 species. We have previously shown that Elovl6 contributes to obesity-induced insulin resistance by modifying hepatic C16/C18-related FA composition. APPROACH AND RESULTS To define the precise molecular mechanism by which hepatic Elovl6 affects energy homeostasis and metabolic disease, we generated liver-specific Elovl6 knockout (LKO) mice. Unexpectedly, LKO mice were not protected from high-fat diet-induced insulin resistance. Instead, LKO mice exhibited higher insulin sensitivity than controls when consuming a high-sucrose diet (HSD), which induces lipogenesis. Hepatic patatin-like phospholipase domain-containing protein 3 (Pnpla3) expression was down-regulated in LKO mice, and adenoviral Pnpla3 restoration reversed the enhancement in insulin sensitivity in HSD-fed LKO mice. Lipidomic analyses showed that the hepatic ceramide(d18:1/18:0) content was lower in LKO mice, which may explain the effect on insulin sensitivity. Ceramide(d18:1/18:0) enhances protein phosphatase 2A (PP2A) activity by interfering with the binding of PP2A to inhibitor 2 of PP2A, leading to Akt dephosphorylation. Its production involves the formation of an Elovl6-ceramide synthase 4 (CerS4) complex in the endoplasmic reticulum and a Pnpla3-CerS4 complex on lipid droplets. Consistent with this, liver-specific Elovl6 deletion in ob/ob mice reduced both hepatic ceramide(d18:1/18:0) and PP2A activity and ameliorated insulin resistance. CONCLUSIONS Our study demonstrates the key role of hepatic Elovl6 in the regulation of the acyl-chain composition of ceramide and that C18:0-ceramide is a potent regulator of hepatic insulin signaling linked to Pnpla3-mediated NAFLD.
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Affiliation(s)
- Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motoko Kuba
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Saori Koyasu
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Toshima, Tokyo, Japan
| | - Kaori Motomura
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Hiroshi Ohno
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Rahul Sharma
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuya Shimura
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuka Okajima
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Song-Iee Han
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuichi Aita
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuhei Mizunoe
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshinori Osaki
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hitoshi Iwasaki
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shigeru Yatoh
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroaki Suzuki
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hirohito Sone
- Department of Internal Medicine, Faculty of Medicine, Niigata University, Niigata, Japan
| | - Yoshinori Takeuchi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Naoya Yahagi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
| | - Satoru Takahashi
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Toshima, Tokyo, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan
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7
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Takeda M, Seki F, Yamamoto Y, Nao N, Tokiwa H. Animal morbilliviruses and their cross-species transmission potential. Curr Opin Virol 2020; 41:38-45. [PMID: 32344228 DOI: 10.1016/j.coviro.2020.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 02/01/2023]
Abstract
Like measles virus (MV), whose primary hosts are humans, non-human animal morbilliviruses use SLAM (signaling lymphocytic activation molecule) and PVRL4 (nectin-4) expressed on immune and epithelial cells, respectively, as receptors. PVRL4's amino acid sequence is highly conserved across species, while that of SLAM varies significantly. However, non-host animal SLAMs often function as receptors for different morbilliviruses. Uniquely, human SLAM is somewhat specific for MV, but canine distemper virus, which shows the widest host range among morbilliviruses, readily gains the ability to use human SLAM. The host range for morbilliviruses is also modulated by their ability to counteract the host's innate immunity, but the risk of cross-species transmission of non-human animal morbilliviruses to humans could occur if MV is successfully eradicated.
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Affiliation(s)
- Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama, Tokyo 208-0011, Japan.
| | - Fumio Seki
- Department of Virology 3, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama, Tokyo 208-0011, Japan
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Naganori Nao
- Department of Virology 3, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama, Tokyo 208-0011, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan
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8
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Kawasaki M, Kambe A, Yamamoto Y, Arulmozhiraja S, Ito S, Nakagawa Y, Tokiwa H, Nakano S, Shimano H. Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations. Int J Mol Sci 2020; 21:E361. [PMID: 31935812 PMCID: PMC6981837 DOI: 10.3390/ijms21010361] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 01/05/2023] Open
Abstract
The selective PPARα modulator (SPPARMα) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMα bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMα at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMα character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARα than to PPARγ. The crystal structure of PPARα-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 Å resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARα in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARα; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARα compared with the interaction between fenofibrate and PPARα.
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Affiliation(s)
- Mayu Kawasaki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
| | - Akira Kambe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
| | - Sundaram Arulmozhiraja
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
- Research Center for Smart Molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
| | - Hitoshi Shimano
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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9
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Yamada S, Kawasaki M, Fujihara M, Watanabe M, Takamura Y, Takioku M, Nishioka H, Takeuchi Y, Makishima M, Motoyama T, Ito S, Tokiwa H, Nakano S, Kakuta H. Competitive Binding Assay with an Umbelliferone-Based Fluorescent Rexinoid for Retinoid X Receptor Ligand Screening. J Med Chem 2019; 62:8809-8818. [PMID: 31483660 DOI: 10.1021/acs.jmedchem.9b00995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ligands for retinoid X receptors (RXRs), "rexinoids", are attracting interest as candidates for therapy of type 2 diabetes and Alzheimer's and Parkinson's diseases. However, current screening methods for rexinoids are slow and require special apparatus or facilities. Here, we created 7-hydroxy-2-oxo-6-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)-2H-chromene-3-carboxylic acid (10, CU-6PMN) as a new fluorescent RXR agonist and developed a screening system of rexinoids using 10. Compound 10 was designed based on the fact that umbelliferone emits strong fluorescence in a hydrophilic environment, but the fluorescence intensity decreases in hydrophobic environments such as the interior of proteins. The developed assay using 10 enabled screening of rexinoids to be performed easily within a few hours by monitoring changes of fluorescence intensity with widely available fluorescence microplate readers, without the need for processes such as filtration.
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Affiliation(s)
- Shoya Yamada
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan.,Research Fellowship Division , Japan Society for the Promotion of Science , Sumitomo-Ichibancho FS Bldg., 8 Ichibancho , Chiyoda-ku, Tokyo 102-8472 , Japan
| | - Mayu Kawasaki
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan.,AIBIOS Co. Ltd. , Tri-Seven Roppongi 8F 7-7-7 Roppongi , Minato-ku, Tokyo 106-0032 Japan
| | - Masaki Watanabe
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Yuta Takamura
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Maho Takioku
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Hiromi Nishioka
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Yasuo Takeuchi
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences , Nihon University School of Medicine , 30-1 Oyaguchi-kamicho , Itabashi-ku, Tokyo 173-8610 , Japan
| | - Tomoharu Motoyama
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | | | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences , Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
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10
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Ito S, Kitamura T, Arulmozhiraja S, Manabe K, Tokiwa H, Suzuki Y. Total Synthesis of Termicalcicolanone A via Organocatalysis and Regioselective Claisen Rearrangement. Org Lett 2019; 21:2777-2781. [DOI: 10.1021/acs.orglett.9b00731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Saki Ito
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Taiki Kitamura
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sundaram Arulmozhiraja
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Research Center for Smart Molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Kei Manabe
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Research Center for Smart Molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yumiko Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
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11
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Miyashita Y, Numoto N, Arulmozhiraja S, Nakano S, Matsuo N, Shimizu K, Shibahara O, Fujihara M, Kakuta H, Ito S, Ikura T, Ito N, Tokiwa H. Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα). FEBS Lett 2018; 593:242-250. [DOI: 10.1002/1873-3468.13301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Yurina Miyashita
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED-CREST; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Nobutaka Numoto
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Sundaram Arulmozhiraja
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
| | - Shogo Nakano
- School of Food and Nutritional Sciences; University of Shizuoka; Japan
| | - Naoya Matsuo
- Department of Chemistry; Rikkyo University; Tokyo Japan
| | | | - Osamu Shibahara
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Michiko Fujihara
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Hiroki Kakuta
- Division of Pharmaceutical Sciences; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Japan
| | - Sohei Ito
- School of Food and Nutritional Sciences; University of Shizuoka; Japan
| | - Teikichi Ikura
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Nobutoshi Ito
- Department of Structural Biology; Medical Research Institute; Tokyo Medical and Dental University (TMDU); Japan
| | - Hiroaki Tokiwa
- Department of Chemistry; Rikkyo University; Tokyo Japan
- AMED-CREST; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- AMED; Japan Agency for Medical Research and Development (AMED); Tokyo Japan
- Research Center for Smart Molecules; Rikkyo University; Tokyo Japan
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12
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Tokiwa T, Nakano S, Yamamoto Y, Ishikawa T, Ito S, Sladek V, Fukuzawa K, Mochizuki Y, Tokiwa H, Misaizu F, Shigeta Y. Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. J Chem Inf Model 2018; 59:25-30. [PMID: 30517784 DOI: 10.1021/acs.jcim.8b00649] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard. However, the physical complexity and the number of the interactions within a protein-ligand complex renders analysis of the results somewhat complicated. This situation prompted us to develop the 3D-visualization of interaction energies in protein (3D-VIEP) method; the toolkit AnalysisFMO, which should enable a more efficient and convenient workflow with FMO data generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate units, RbAnalysisFMO, and the PyMOL plugins. The former can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output files generated by the aforementioned quantum-chemical packages. The PyMOL plugins enable visualization of IFIEs or PIEs in the protein structure in PyMOL. We demonstrate the use of this tool on a lectin protein from Burkholderia cenocepacia in which FMO analysis revealed the existence of a new interaction between Gly84 and fucose. Moreover, we found that second-shell interactions are crucial in forming the sugar binding site. In the case of bilirubin oxidase from Myrothecium verrucaria (MvBO), we predict that interactions between Asp105 and three His residues (His401, His403, and His136) are essential for optimally positioning the His residues to coordinate Cu atoms to form one Type 2 and two Type 3 Cu ions.
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Affiliation(s)
- Takaki Tokiwa
- Department of Chemistry, Graduate School of Science , Tohoku University , 6-3, Aoba, Aramaki , Aoba-ku, Sendai , Miyagi 980-8578 , Japan.,Department of Physics, Graduate School of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8571 , Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Yuta Yamamoto
- Department of Chemistry , Rikkyo University , 3-34-1 Nishi-Ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences , Nagasaki University , 1-12-4 Sakamoto , Nagasaki 852-8523 , Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Vladimir Sladek
- Institute of Chemistry-Centre for Glycomics , Dubravska cesta 9 , 84538 Bratislava , Slovakia
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences , Hoshi University , 2-4-41 Ebara , Shinagawa-Ku, Tokyo 142-8501 , Japan.,Institute of Industrial Science , The University of Tokyo , 4-6-1, Komaba , Meguro-ku, Tokyo 153-8505 Japan
| | - Yuji Mochizuki
- Department of Chemistry , Rikkyo University , 3-34-1 Nishi-Ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan.,Institute of Industrial Science , The University of Tokyo , 4-6-1, Komaba , Meguro-ku, Tokyo 153-8505 Japan
| | - Hiroaki Tokiwa
- Department of Chemistry , Rikkyo University , 3-34-1 Nishi-Ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science , Tohoku University , 6-3, Aoba, Aramaki , Aoba-ku, Sendai , Miyagi 980-8578 , Japan
| | - Yasuteru Shigeta
- Department of Physics, Graduate School of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8571 , Japan.,Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
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13
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Abstract
Protein residue networks (PRN) from energetic and geometric data are probably not identical. PRNs constructed from ab initio pair interaction energies are analyzed for the first time and compared to PRN based on center of mass separation. We use modern, previously unused algorithms such as global and local efficiencies to quantitatively confirm that both types of PRNs do exhibit small-world character. The main novelty finding is that interaction energy-based PRNs preserve small-world character even when clustered. A node hierarchy independent of the cutoff energy used for the edge creation is characteristic for them. Efficiency centrality identifies hubs responsible for such behavior. The interaction energy-based PRNs seem to comply with the scale-free network model with respect to efficiency centrality distribution as opposed to distance based PRNs. Community detection is introduced into protein network research as an extension beyond cluster analysis to study tertiary and quaternary structures.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry - Centre for Glycomics , Dubravska cesta 9 , 84538 Bratislava , Slovakia.,Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan
| | - Hiroaki Tokiwa
- Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan.,Department of Chemistry , Rikkyo University , Nishi-Ikebukuro , Toshima, Tokyo 171-8501 , Japan
| | - Hitoshi Shimano
- Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan.,Department of Internal Medicine, Faculty of Medicine , University of Tsukuba , 1-1-1 Tennodai , Tsukuba, Ibaraki 305-8575 , Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences , University of Tsukuba , Tennodai 1-1-1 , Tsukuba, Ibaraki 305-8577 , Japan
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14
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Otero R, Ishizawa M, Numoto N, Ikura T, Ito N, Tokiwa H, Mouriño A, Makishima M, Yamada S. 25 S-Adamantyl-23-yne-26,27-dinor-1α,25-dihydroxyvitamin D 3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J Med Chem 2018; 61:6658-6673. [PMID: 29989817 DOI: 10.1021/acs.jmedchem.8b00427] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Both 25 R- and 25 S-25-adamantyl-23-yne-26,27-dinor-1α,25-dihydroxyvitamin D3 (4a and 4b) were stereoselectively synthesized by a Pd(0)-catalyzed ring closure and Suzuki-Miyaura coupling between enol-triflate 7 and alkenyl-boronic ester 8. The 25 S isomer (4b) showed high vitamin D receptor (VDR) affinity (50% of that of the natural hormone 1α,25-dihydroxyvitamin D3, 1) and transactivation potency (kidney HEK293, 90%). In endogenous gene expression, it showed high cell-type selectivity for kidney cells (HEK293, CYP24A1 160% of 1), bone cells (MG63, osteocalcin 64%), and monocytes (U937, CAMP 96%) over intestine (SW480, CYP24A1 8%) and skin (HaCaT, CYP24A1 7%) cells. The X-ray crystal structural analysis of 4b in complex with rat VDR-ligand binding domain (LBD) showed the highest Cα positional shift from the 1/VDR-LBD complex at helix 11. Helix 11 of the 4b and 1 VDR-LBD complexes also showed significant differences in surface properties. These results suggest that 4b should be examined further as another candidate for a mild preventive osteoporosis agent.
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Affiliation(s)
- Rocio Otero
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas , Universidad de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Michiyasu Ishizawa
- Department of Biomedical Sciences , Nihon University School of Medicine , Itabashi-ku, Tokyo 173-8610 , Japan
| | - Nobutaka Numoto
- Medical Research Institute , Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 113-8510 , Japan
| | - Teikichi Ikura
- Medical Research Institute , Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 113-8510 , Japan
| | - Nobutoshi Ito
- Medical Research Institute , Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 113-8510 , Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science , Rikkyo University , Toshima-ku, Tokyo 171-8501 , Japan
| | - Antonio Mouriño
- Departamento de Química Orgánica, Laboratorio de Investigación Ignacio Ribas , Universidad de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Makoto Makishima
- Department of Biomedical Sciences , Nihon University School of Medicine , Itabashi-ku, Tokyo 173-8610 , Japan
| | - Sachiko Yamada
- Department of Biomedical Sciences , Nihon University School of Medicine , Itabashi-ku, Tokyo 173-8610 , Japan
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15
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Nakano S, Motoyama T, Miyashita Y, Ishizuka Y, Matsuo N, Tokiwa H, Shinoda S, Asano Y, Ito S. Benchmark Analysis of Native and Artificial NAD +-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data. Biochemistry 2018; 57:3722-3732. [PMID: 29787243 DOI: 10.1021/acs.biochem.8b00339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full-consensus design (FCD) and ancestral-sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial l-threonine 3-dehydrogenases (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1, and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD+ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH); the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5 °C higher than that of CnTDH, respectively, and the dissociation constants toward NAD+ of FcTDH-N1 and AncTDH were 2- and 7-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.
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Affiliation(s)
- Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Tomoharu Motoyama
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Yurina Miyashita
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Yuki Ishizuka
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Naoya Matsuo
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Hiroaki Tokiwa
- Department of Chemistry , Rikkyo University , Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Suguru Shinoda
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Yasuhisa Asano
- Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan.,Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan.,Asano Active Enzyme Molecule Project , ERATO, JST , 5180 Kurokawa , Imizu, Toyama 939-0398 , Japan
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16
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Miyashita Y, Matsuo N, Yamamoto Y, Nakano S, Ito S, Numoto N, Ikura T, Ito N, Sekiya M, Shimano H, Tokiwa H. Computational design and molecular mechanism in oligomerization of C‐terminal binding protein 2. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.798.22] [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: 11/11/2022]
Affiliation(s)
- Yurina Miyashita
- AMED‐CRESTJapan Agency for Medical Research and Development (AMED)Chiyoda‐kuTokyoJapan
- Department of ChemistryRikkyo UniversityToshima‐kuTokyoJapan
| | | | | | - Shogo Nakano
- School of Food and Nutritional SciencesUniversity of ShizuokaSuruga‐kuShizuokaJapan
| | - Sohei Ito
- School of Food and Nutritional SciencesUniversity of ShizuokaSuruga‐kuShizuokaJapan
| | - Nobutaka Numoto
- Department of Structural BiologyMedical Research InstituteTokyo Medical and Dental University (TMDU)Bunkyo‐kuTokyoJapan
| | - Teikichi Ikura
- Department of Structural BiologyMedical Research InstituteTokyo Medical and Dental University (TMDU)Bunkyo‐kuTokyoJapan
| | - Nobutoshi Ito
- Department of Structural BiologyMedical Research InstituteTokyo Medical and Dental University (TMDU)Bunkyo‐kuTokyoJapan
| | - Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism)Faculty of MedicineUniversity of TsukubaTsukuba‐CityIbarakiJapan
| | - Hitoshi Shimano
- AMED‐CRESTJapan Agency for Medical Research and Development (AMED)Chiyoda‐kuTokyoJapan
- Department of Internal Medicine (Endocrinology and Metabolism)Faculty of MedicineUniversity of TsukubaTsukuba‐CityIbarakiJapan
| | - Hiroaki Tokiwa
- AMED‐CRESTJapan Agency for Medical Research and Development (AMED)Chiyoda‐kuTokyoJapan
- Department of ChemistryRikkyo UniversityToshima‐kuTokyoJapan
- Research Center for Smart MoleculesRikkyo UniversityToshima‐kuTokyoJapan
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17
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Motoyana T, Nakano S, Yamamoto Y, Tokiwa H, Asano Y, Ito S. Discovery of novel monomeric L‐threonine 3‐dehydrogenase and elucidation of product release mechanism. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.796.14] [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: 11/11/2022]
Affiliation(s)
- Tomoharu Motoyana
- Graduate Division of Nutritional and Environmental ScienceUniversity of ShizuokaShizuokaJapan
| | - Shogo Nakano
- ERATOJSTImizuJapan
- Graduate Division of Nutritional and Environmental ScienceUniversity of ShizuokaShizuokaJapan
| | | | - Hiroaki Tokiwa
- Department of ChemistryRikkyo UnivesityTokyoJapan
- Research Center for Smart MoleculesRikkyo UniversityTokyoJapan
| | - Yasuhisa Asano
- ERATOJSTImizuJapan
- Biotechnology Research Center and Department of BiotechnologyToyama Prefectural UniversityImizuJapan
| | - Sohei Ito
- ERATOJSTImizuJapan
- Graduate Division of Nutritional and Environmental ScienceUniversity of ShizuokaShizuokaJapan
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18
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Shimizu K, Miyashita Y, Matsuo N, Yamamoto Y, Nakano S, Ito S, Numoto N, Ikura T, Ito N, Kakuta H, Tokiwa H. What is the origin of partial agonist activity of CBt‐PMN for hRXRα? FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.530.22] [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: 11/11/2022]
Affiliation(s)
| | - Yurina Miyashita
- chemistryRikkyo universityTokyoJapan
- AMED‐CRESTJapan Agency for medical Research and Development (AMED)TokyoJapan
| | | | | | | | | | | | | | - Nobutoshi Ito
- Tokyo Medical and Dental University (TMDU)TokyoJapan
| | - Hiroki Kakuta
- Okayama University Graduate School of MedicineOkayamaJapan
| | - Hiroaki Tokiwa
- ChemistryRikkyo universityTokyoJapan
- AMED‐CRESTJapan Agency for medical Research and Development (AMED)TokyoJapan
- Research Center for Smart MoleculeRikkyo universityTokyoJapan
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19
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Nakano S, Motoyama T, Miyashita Y, Ishizuka Y, Matsuo N, Tokiwa H, Shinoda S, Asano Y, Ito S. How to design artificial protein surpassing native enzyme function ~ Design and multidisciplinary analysis of artificial L‐threonine 3‐dehydrogenase ~. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.798.4] [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: 11/11/2022]
Affiliation(s)
- Shogo Nakano
- Asano Active Enzyme Molecule ProjectERATO, JSTImizuJapan
- School of Food and Nutritional SciencesUniversity of ShizuokaShizuokaJapan
| | - Tomoharu Motoyama
- School of Food and Nutritional SciencesUniversity of ShizuokaShizuokaJapan
| | | | - Yuki Ishizuka
- School of Food and Nutritional SciencesUniversity of ShizuokaShizuokaJapan
| | - Naoya Matsuo
- Department of ChemistryRikkyo UniversityToshimakuJapan
| | - Hiroaki Tokiwa
- Department of ChemistryRikkyo UniversityToshimakuJapan
- Research Center for Smart MoleculesRikkyo UniversityToshimakuJapan
| | - Suguru Shinoda
- Asano Active Enzyme Molecule ProjectERATO, JSTImizuJapan
- Toyama Prefectural UniversityImizuJapan
| | - Yasuhisa Asano
- Asano Active Enzyme Molecule ProjectERATO, JSTImizuJapan
- Toyama Prefectural UniversityImizuJapan
| | - Sohei Ito
- Asano Active Enzyme Molecule ProjectERATO, JSTImizuJapan
- School of Food and Nutritional SciencesUniversity of ShizuokaShizuokaJapan
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20
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Yamamoto Y, Takei K, Arulmozhiraja S, Sladek V, Matsuo N, Han SI, Matsuzaka T, Sekiya M, Tokiwa T, Shoji M, Shigeta Y, Nakagawa Y, Tokiwa H, Shimano H. Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα. Biochem Biophys Res Commun 2018; 499:239-245. [PMID: 29567478 DOI: 10.1016/j.bbrc.2018.03.135] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 03/11/2018] [Accepted: 03/18/2018] [Indexed: 11/28/2022]
Abstract
Peroxisome proliferator-activated receptor-α (PPARα) is a ligand-activated transcription factor involved in the regulation of lipid homeostasis and improves hypertriglyceridemia. Pemafibrate is a novel selective PPARα modulator (SPPARMα) that activates PPARα transcriptional activity. Here, we computationally constructed the structure of the human PPARα in a complex with pemafibrate, along with that of hPPARα complexed with the classical fenofibrate, and studied their interactions quantitatively by using the first-principles calculations-based fragment molecular orbital (FMO) method. Comprehensive structural and protein-ligand binding elucidation along with the in vitro luciferase analysis let us to identify pemafibrate as a novel SPPARMα. Unlike known fibrate ligands, which bind only with the arm I of the Y-shaped ligand binding pocket, the Y-shaped pemafibrate binds to the entire cavity region. This lock and key nature causes enhanced induced fit in pemafibrate-ligated PPARα. Importantly, this selective modulator allosterically changes PPARα conformation to form a brand-new interface, which in turn binds to PPARα co-activator, PGC-1α, resulting in the full activation of PPARα. The structural basis for the potent effects of pemafibrate on PPARα transcriptional activity predicted by the in silico FMO methods was confirmed by in vitro luciferase assay for mutants. The unique binding mode of pemafibrate reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering cues for improving the binding affinity and selectivity of ligand for better clinical consequences. The findings explain the high affinity and efficacy of pemafibrate, which is expected to be in the clinical use soon.
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Affiliation(s)
- Yuta Yamamoto
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Kenta Takei
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Sundaram Arulmozhiraja
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan; Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Vladimir Sladek
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan; Institute of Chemistry - Centre for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda, Tokyo 100-0004, Japan
| | - Naoya Matsuo
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Song-Iee Han
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda, Tokyo 100-0004, Japan
| | - Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda, Tokyo 100-0004, Japan
| | - Takaki Tokiwa
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba, Sendai, Miyagi 980-8578, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan; Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda, Tokyo 100-0004, Japan.
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda, Tokyo 100-0004, Japan; International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan.
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21
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Ikawa T, Akai S, Kaneko H, Yamamoto Y, Arulmozhiraja S, Tokiwa H. 3-(Triflyloxy)benzynes Enable the Regiocontrolled Cycloaddition of Cyclic Ureas to Synthesize 1,4-Benzodiazepine Derivatives. Synlett 2018. [DOI: 10.1055/s-0036-1591924] [Citation(s) in RCA: 9] [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] [Indexed: 10/18/2022]
Abstract
A versatile synthesis of 1,4-benzodiazepine derivatives through the reaction of various 3-(trifluoromethanesulfonyloxy)benzynes with N-(p-toluenesulfonyl)imidazolidin-2-ones is reported. This reaction system provides a 1,4-benzodiazepine bearing a trifluoromethanesulfonyloxy group as a single regioisomer among the four possible regioisomers.
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Affiliation(s)
- Takashi Ikawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Hideki Kaneko
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yuta Yamamoto
- Department of Chemistry, Research Center for Smart Molecules, Rikkyo University
| | | | - Hiroaki Tokiwa
- Department of Chemistry, Research Center for Smart Molecules, Rikkyo University
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22
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Suzuki Y, Iwata N, Dobashi K, Takashima R, Arulmozhiraja S, Ishitsubo E, Matsuo N, Tokiwa H. Alkanoylation of quinazoline by nucleophilic aromatic substitution: Combined experimental and computational study. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Konishi H, Matsubara M, Mori K, Tokiwa T, Arulmozhiraja S, Yamamoto Y, Ishikawa Y, Hashimoto H, Shigeta Y, Tokiwa H, Manabe K. Mechanistic Insight into Weak Base-Catalyzed Generation of Carbon Monoxide from Phenyl Formate and Its Application to Catalytic Carbonylation at Room Temperature without Use of External Carbon Monoxide Gas. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hideyuki Konishi
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
| | - Mika Matsubara
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
| | - Keisuke Mori
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
| | - Takaki Tokiwa
- Center for Computational Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba, Ibaraki 305-8571 Japan
- Department of Chemistry, Graduate School of Science; Tohoku University; Aramaki, Aoba-ku, Sendai, Miyagi 980-8578 Japan
| | - Sundaram Arulmozhiraja
- Department of Chemistry; Rikkyo University; 3-34-1 Nishi-Ikebukuro, Toshima-ku Tokyo 171-8501 Japan
| | - Yuta Yamamoto
- Department of Chemistry; Rikkyo University; 3-34-1 Nishi-Ikebukuro, Toshima-ku Tokyo 171-8501 Japan
| | - Yoshinobu Ishikawa
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences; University of Tsukuba; 1-1-1 Tennodai Tsukuba, Ibaraki 305-8571 Japan
| | - Hiroaki Tokiwa
- Department of Chemistry; Rikkyo University; 3-34-1 Nishi-Ikebukuro, Toshima-ku Tokyo 171-8501 Japan
| | - Kei Manabe
- School of Pharmaceutical Sciences; University of Shizuoka; 52-1 Yada Suruga-ku, Shizuoka 422-8526 Japan
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24
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Motoyama T, Nakano S, Yamamoto Y, Tokiwa H, Asano Y, Ito S. Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase. Biochemistry 2017; 56:5758-5770. [DOI: 10.1021/acs.biochem.7b00832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomoharu Motoyama
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shogo Nakano
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano
Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yuta Yamamoto
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano
Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Sohei Ito
- Graduate
Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano
Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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25
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Sladek V, Kóňa J, Tokiwa H. In silico analysis of interaction pattern switching in ligand⋯receptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors. Phys Chem Chem Phys 2017; 19:12527-12537. [DOI: 10.1039/c7cp01200d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Different binding modes for charge-neutral and protonated inhibitor forms in Golgi α-mannosidase II active sites may influence their biological activities.
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Affiliation(s)
- V. Sladek
- Institute of Chemistry – Centre for Glycomics
- Slovak Academy of Sciences
- 845 38 Bratislava
- Slovakia
- Dept. of Chemistry
| | - J. Kóňa
- Institute of Chemistry – Centre for Glycomics
- Slovak Academy of Sciences
- 845 38 Bratislava
- Slovakia
| | - H. Tokiwa
- Dept. of Chemistry
- Rikkyo University
- Toshima
- Japan
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26
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Arulmozhiraja S, Matsuo N, Ishitsubo E, Okazaki S, Shimano H, Tokiwa H. Comparative Binding Analysis of Dipeptidyl Peptidase IV (DPP-4) with Antidiabetic Drugs - An Ab Initio Fragment Molecular Orbital Study. PLoS One 2016; 11:e0166275. [PMID: 27832184 PMCID: PMC5104442 DOI: 10.1371/journal.pone.0166275] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023] Open
Abstract
Dipeptidyl peptidase IV (DPP-4) enzyme is responsible for the degradation of incretins that stimulates insulin secretion and hence inhibition of DPP-4 becomes an established approach for the treatment of type 2 diabetics. We studied the interaction between DPP-4 and its inhibitor drugs (sitagliptin 1, linagliptin 2, alogliptin 3, and teneligliptin 4) quantitatively by using fragment molecular orbital calculations at the RI-MP2/cc-pVDZ level to analyze the inhibitory activities of the drugs. Apart from having common interactions with key residues, inhibitors encompassing the DPP-4 active site extensively interact widely with the hydrophobic pocket by their hydrophobic inhibitor moieties. The cumulative hydrophobic interaction becomes stronger for these inhibitors and hence linagliptin and teneligliptin have larger interaction energies, and consequently higher inhibitory activities, than their alogliptin and sitagliptin counterparts. Though effective interaction for both 2 and 3 is at [Formula: see text] subsite, 2 has a stronger binding to this subsite interacting with Trp629 and Tyr547 than 3 does. The presence of triazolopiperazine and piperazine moiety in 1 and 4, respectively, provides the interaction to the S2 extensive subsite; however, the latter's superior inhibitory activity is not only due to a relatively tighter binding to the S2 extensive subsite, but also due to the interactions to the S1 subsite. The calculated hydrophobic interfragment interaction energies correlate well with the experimental binding affinities (KD) and inhibitory activities (IC50) of the DPP-4 inhibitors.
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Affiliation(s)
- Sundaram Arulmozhiraja
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
- Research Center for Smart molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
| | - Naoya Matsuo
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
| | - Erika Ishitsubo
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
| | - Seiji Okazaki
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
- Research Center for Smart molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), University of Tsukuba, Tsukuba 305–8575, Japan
- AMED-CREST, Tokyo, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
- Research Center for Smart molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171–8501, Japan
- AMED-CREST, Tokyo, Japan
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27
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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28
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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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29
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Watarai Y, Ishizawa M, Ikura T, Zacconi FCM, Uno S, Ito N, Mouriño A, Tokiwa H, Makishima M, Yamada S. Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds. J Med Chem 2015; 58:9510-21. [DOI: 10.1021/acs.jmedchem.5b00792] [Citation(s) in RCA: 11] [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: 01/31/2023]
Affiliation(s)
- Yusuke Watarai
- Department
of Chemistry, Faculty of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Michiyasu Ishizawa
- Department
of Biomedical Sciences, Nihon University School of Medicine, 30-1
Ohyaguchikami-machi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Teikichi Ikura
- Medical
Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Flavia C. M. Zacconi
- Departamento
de Química Orgánica, Laboratorio de Investigación
Ignacio Ribas, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Shigeyuki Uno
- Department
of Biomedical Sciences, Nihon University School of Medicine, 30-1
Ohyaguchikami-machi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Nobutoshi Ito
- Medical
Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Antonio Mouriño
- Departamento
de Química Orgánica, Laboratorio de Investigación
Ignacio Ribas, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Hiroaki Tokiwa
- Department
of Chemistry, Faculty of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Makoto Makishima
- Department
of Biomedical Sciences, Nihon University School of Medicine, 30-1
Ohyaguchikami-machi, Itabashi-ku, Tokyo 173-8610, Japan
| | - Sachiko Yamada
- Department
of Biomedical Sciences, Nihon University School of Medicine, 30-1
Ohyaguchikami-machi, Itabashi-ku, Tokyo 173-8610, Japan
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30
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Tokiwa H. [Possibility of New Medicinal Chemistry Based on "Wet-Dry" Interfaced Pharmaceutical Category]. YAKUGAKU ZASSHI 2015; 135:1001-2. [PMID: 26329543 DOI: 10.1248/yakushi.15-00175-f] [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: 11/22/2022]
Affiliation(s)
- Hiroaki Tokiwa
- Research Center for Smart Molecules, Department of Chemistry, Rikkyo University
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31
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Suhara Y, Hirota Y, Hanada N, Nishina S, Eguchi S, Sakane R, Nakagawa K, Wada A, Takahashi K, Tokiwa H, Okano T. Synthetic Small Molecules Derived from Natural Vitamin K Homologues that Induce Selective Neuronal Differentiation of Neuronal Progenitor Cells. J Med Chem 2015; 58:7088-92. [DOI: 10.1021/acs.jmedchem.5b00999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshitomo Suhara
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yoshihisa Hirota
- Department
of Hygienic Sciences, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Norika Hanada
- Department
of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shun Nishina
- Laboratory
of Environmental Sciences, Yokohama College of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Sachiko Eguchi
- Laboratory
of Environmental Sciences, Yokohama College of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Rie Sakane
- Department
of Bioscience and Engineering, College of Systems Engineering and
Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kimie Nakagawa
- Department
of Hygienic Sciences, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department
of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku,
Kobe 658-8558, Japan
| | - Kazuhiko Takahashi
- Laboratory
of Environmental Sciences, Yokohama College of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Toshio Okano
- Department
of Hygienic Sciences, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
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32
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Ikawa T, Kaneko H, Masuda S, Ishitsubo E, Tokiwa H, Akai S. Trifluoromethanesulfonyloxy-group-directed regioselective (3 + 2) cycloadditions of benzynes for the synthesis of functionalized benzo-fused heterocycles. Org Biomol Chem 2015; 13:520-6. [PMID: 25378144 DOI: 10.1039/c4ob01627k] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Highly regioselective (3 + 2) cycloadditions of (trifluoromethanesulfonyloxy)benzynes [(triflyloxy)benzynes] with 1,3-dipoles followed by cross-coupling reactions provided multisubstituted benzo-fused heterocycles. The triflyloxy group at the 3-position of benzynes, and even that at the remote 4-position, greatly affected the regiocontrol of the cycloaddition. These groups also served to install other substituents at their ipso-positions.
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Affiliation(s)
- Takashi Ikawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.
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33
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Onoda K, Sawada H, Morita D, Fujii K, Tokiwa H, Kuroda T, Miyachi H. Anti-MRSA activity of isoplagiochin-type macrocyclic bis(bibenzyl)s is mediated through cell membrane damage. Bioorg Med Chem 2015; 23:3309-16. [PMID: 25999206 DOI: 10.1016/j.bmc.2015.04.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 11/17/2022]
Abstract
We synthesized three geometrical isomers of a macrocyclic bis(bibenzyl) based on isoplagiochin, a natural product isolated from bryophytes, and evaluated their antibacterial activity towards methicillin-resistant Staphylococcus aureus (anti-MRSA activity). The isomer containing a 1,4-linked ring (5) showed only weak activity, whereas the isomers containing a 1,3-linked (6) or 1,2-linked (7) C ring showed potent anti-MRSA activity. Molecular dynamics calculations indicated that these differences are probably due to differences in the conformational flexibility of the macrocyclic ring; the active compounds 6 and 7 were more rigid than 5. In order to understand the action mechanism of anti-MRSA activity, we investigated the cellular flux of a fluorescent DNA-binder, ethidium bromide (EtBr), in the presence and absence of these macrocycles. The active compound 6 increased the levels of EtBr inflow and outflow in S. aureus cells, as did our potent anti-MRSA riccardin derivative (4), indicating that these compounds increased the permeability of the cytoplasmic membrane. Inactive 5 had no effect on EtBr inflow or outflow. Furthermore, compound 6 abrogated the normal intracellular concentration gradients of Na(+) and K(+) in S. aureus cells, increasing the intracellular Na(+) concentration and decreasing the K(+) concentration, while 5 had no such effect. These results indicate that anti-MRSA-active macrocyclic bis(bibenzyl) derivatives directly damage the gram-positive bacterial membrane, resulting in increased permeability.
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Affiliation(s)
- Kenji Onoda
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hiromi Sawada
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Daichi Morita
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kana Fujii
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Teruo Kuroda
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hiroyuki Miyachi
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
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34
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Kawata K, Morishita KI, Nakayama M, Yamada S, Kobayashi T, Furusawa Y, Arimoto-Kobayashi S, Oohashi T, Makishima M, Naitou H, Ishitsubo E, Tokiwa H, Tai A, Kakuta H. RXR partial agonist produced by side chain repositioning of alkoxy RXR full agonist retains antitype 2 diabetes activity without the adverse effects. J Med Chem 2014; 58:912-26. [PMID: 25486327 DOI: 10.1021/jm501863r] [Citation(s) in RCA: 15] [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] [Indexed: 11/28/2022]
Abstract
We previously reported RXR partial agonist CBt-PMN (1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)-1H-benzotriazole-5-carboxylic acid: 5, EC50 = 143 nM, Emax = 75%), which showed a potent glucose-lowering effect without causing serious adverse effects. However, it remains important to elucidate the structural requirements for RXR efficacy and the glucose-lowering effect because RXR-permissive heterodimers such as PPAR/RXR or LXR/RXR are reported to be activated differently depending upon the chemical structure of RXR agonists. In this work, we show that an RXR partial agonist, NEt-4IB (6-[ethyl-(4-isobutoxy-3-isopropylphenyl)amino]pyridine-3-carboxylic acid: 8b, EC50 = 169 nM, Emax = 55%), can be obtained simply by repositioning the side chains (interchanging the isobutoxy and isopropoxy groups) at the hydrophobic moiety of the RXR full agonist NEt-3IB (6-[ethyl-(3-isobutoxy-4-isopropylphenyl)amino]pyridine-3-carboxylic acid: 7b, EC50 = 19 nM). NEt-4IB (8b) showed antitype 2 diabetes activity without the above side effects upon repeated oral administration to mice at 10 mg/kg/day, similarly to 5.
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Affiliation(s)
- Kohei Kawata
- Division of Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , 1-1-1, Tsushima-naka, Kita-ku Okayama 700-8530, Japan
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35
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Tanaka Y, Gamo K, Oyama T, Ohashi M, Waki M, Matsuno K, Matsuura N, Tokiwa H, Miyachi H. Molecular dynamics study-guided identification of cyclic amine structures as novel hydrophobic tail components of hPPARγ agonists. Bioorg Med Chem Lett 2014; 24:4001-5. [PMID: 25017035 DOI: 10.1016/j.bmcl.2014.06.023] [Citation(s) in RCA: 3] [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: 05/17/2014] [Revised: 06/05/2014] [Accepted: 06/09/2014] [Indexed: 11/25/2022]
Abstract
We previously reported that a α-benzylphenylpropanoic acid-type hPPARγ-selective agonist with a piperidine ring as the hydrophobic tail part (3) exhibited sub-micromolar-order hPPARγ agonistic activity. In order to enhance the activity, we planned to carry out structural development based on information obtained from the X-ray crystal structure of hPPARγ ligand binding domain (LBD) complexed with 3. However, the shape and/or nature of the binding pocket surrounding the piperidine ring of 3 could not be precisely delineated because the structure of the omega loop of the LBD was poorly defined. Therefore, we constructed and inserted a plausible omega loop by means of molecular dynamics simulation. We then used the reconstructed LBD structure to design new mono-, bi- and tricyclic amine-bearing compounds that might be expected to show greater binding affinity for the LBD. Here, we describe synthesis and evaluation of α-benzylphenylpropanoic acid derivatives 8. As expected, most of the newly synthesized compounds exhibited more potent hPPARγ agonistic activity and greater hPPARγ binding affinity than 3. Some of these compounds also showed comparable aqueous solubility to 3.
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Affiliation(s)
- Yuta Tanaka
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kanae Gamo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takuji Oyama
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, 4-3-37 Takeda, Kofu City, Yamanashi 400-8510, Japan
| | - Masao Ohashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Minoru Waki
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kenji Matsuno
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Nobuyasu Matsuura
- Department of Life Science, Faculty of Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Hiroyuki Miyachi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
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36
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Suhara Y, Motoyoshi S, Hirota Y, Sawada N, Nakagawa K, Tokiwa H, Okano T. [Structure-activity relationship of novel vitamin K analogues as steroid and xenobiotic receptor (SXR) agonists]. YAKUGAKU ZASSHI 2014; 132:881-6. [PMID: 22864345 DOI: 10.1248/yakushi.132.881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Vitamin K2 is a ligand for a nuclear receptor, steroid and xenobiotic receptor (SXR), that induces the gene expressions of CYP3A4. We synthesized new vitamin K analogues with the same isoprene side chains symmetrically introduced at the 2 and 3 positions of 1,4-naphthoquinone and vitamin K2 analogues with hydroxyl or phenyl groups at the ω-terminal of the side chain. The upregulation of SXR-mediated transcription of the target gene by the analogues was dependent on the length of the side chain and the hydrophobicity of the ω-terminal residues. Phenyl analogue menaquinone-3 was as active as the known SXR ligand rifampicin.
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37
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Kudo T, Ishizawa M, Maekawa K, Nakabayashi M, Watarai Y, Uchida H, Tokiwa H, Ikura T, Ito N, Makishima M, Yamada S. Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. J Med Chem 2014; 57:4073-87. [DOI: 10.1021/jm401989c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Michiyasu Ishizawa
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | | | - Makoto Nakabayashi
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | | | - Hikaru Uchida
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | | | | | | | - Makoto Makishima
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | - Sachiko Yamada
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
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38
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Abe T, Sando A, Teraoka F, Otsubo T, Morita K, Tokiwa H, Ikeda K, Suzuki T, Hidari KIPJ. Computational design of a sulfoglucuronide derivative fitting into a hydrophobic pocket of dengue virus E protein. Biochem Biophys Res Commun 2014; 449:32-7. [PMID: 24796674 DOI: 10.1016/j.bbrc.2014.04.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 10/25/2022]
Abstract
We performed first-principles calculations based on the ab initio fragment molecular orbital method on dengue virus envelope protein with a hydrophobic ligand, octyl-β-D-glucose to develop an entry inhibitor. As several polar amino acid residues are present at the edge of the pocket, the glucose moiety was chemically modified with hydrophilic groups. Introduction of both sulfated and carboxylated groups on glucose enhanced not only binding affinity to the protein but also inhibition of dengue virus entry. Octyl-2-O-sulfo β-D-glucuronic acid may serve as a molecular probe to study the dengue virus entry process.
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Affiliation(s)
- Tomoko Abe
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan
| | - Ayumi Sando
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Fumiteru Teraoka
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Tadamune Otsubo
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Kiyoshi Ikeda
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan.
| | - Takashi Suzuki
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan
| | - Kazuya I P J Hidari
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan.
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39
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Nakano S, Okazaki S, Tokiwa H, Asano Y. Binding of NAD+ and L-threonine induces stepwise structural and flexibility changes in Cupriavidus necator L-threonine dehydrogenase. J Biol Chem 2014; 289:10445-10454. [PMID: 24558034 DOI: 10.1074/jbc.m113.540773] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Crystal structures of short chain dehydrogenase-like L-threonine dehydrogenase from Cupriavidus necator (CnThrDH) in the apo and holo forms were determined at 2.25 and 2.5 Å, respectively. Structural comparison between the apo and holo forms revealed that four regions of CnThrDH adopted flexible conformations when neither NAD(+) nor L-Thr were bound: residues 38-59, residues 77-87, residues 180-186, and the catalytic domain. Molecular dynamics simulations performed at the 50-ns time scale revealed that three of these regions remained flexible when NAD(+) was bound to CnThrDH: residues 80-87, residues 180-186, and the catalytic domain. Molecular dynamics simulations also indicated that the structure of CnThrDH changed from a closed form to an open form upon NAD(+) binding. The newly formed cleft in the open form may function as a conduit for substrate entry and product exit. These computational results led us to hypothesize that the CnThrDH reaction progresses by switching between the closed and open forms. Enzyme kinetics parameters of the L80G, G184A, and T186N variants also supported this prediction: the kcat/Km, L-Thr value of the variants was >330-fold lower than that of the wild type; this decrease suggested that the variants mostly adopt the open form when L-Thr is bound to the active site. These results are summarized in a schematic model of the stepwise changes in flexibility and structure that occur in CnThrDH upon binding of NAD(+) and L-Thr. This demonstrates that the dynamical structural changes of short chain dehydrogenase-like L-threonine dehydrogenase are important for the reactivity and specificity of the enzyme.
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Affiliation(s)
- Shogo Nakano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Seiji Okazaki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hiroaki Tokiwa
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Research Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Sawada H, Onoda K, Morita D, Ishitsubo E, Matsuno K, Tokiwa H, Kuroda T, Miyachi H. Structure–anti-MRSA activity relationship of macrocyclic bis(bibenzyl) derivatives. Bioorg Med Chem Lett 2013; 23:6563-8. [DOI: 10.1016/j.bmcl.2013.10.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/11/2013] [Accepted: 10/29/2013] [Indexed: 11/28/2022]
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Nakabayashi M, Tsukahara Y, Iwasaki-Miyamoto Y, Mihori-Shimazaki M, Yamada S, Inaba S, Oda M, Shimizu M, Makishima M, Tokiwa H, Ikura T, Ito N. Crystal Structures of Hereditary Vitamin D-Resistant Rickets-Associated Vitamin D Receptor Mutants R270L and W282R Bound to 1,25-Dihydroxyvitamin D3 and Synthetic Ligands. J Med Chem 2013; 56:6745-60. [DOI: 10.1021/jm400537h] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Makoto Nakabayashi
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | | | | | | | - Sachiko Yamada
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | - Satomi Inaba
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto 606-8522, Japan
| | - Masayuki Oda
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto 606-8522, Japan
| | | | - Makoto Makishima
- Department
of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Faculty of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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42
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Minami A, Ishibashi S, Ikeda K, Ishitsubo E, Hori T, Tokiwa H, Taguchi R, Ieno D, Otsubo T, Matsuda Y, Sai S, Inada M, Suzuki T. Catalytic preference of Salmonella typhimurium LT2 sialidase for N-acetylneuraminic acid residues over N-glycolylneuraminic acid residues. FEBS Open Bio 2013; 3:231-6. [PMID: 23772399 PMCID: PMC3678298 DOI: 10.1016/j.fob.2013.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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] [Received: 04/15/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 01/21/2023] Open
Abstract
In a comparison of sialidase activities toward N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), we found that Salmonella typhimurium LT2 sialidase (STSA) hardly cleaved 4-methylumbelliferyl Neu5Gc (4MU-Neu5Gc). The k cat/K m value of STSA for 4MU-Neu5Gc was found to be 110 times lower than that for 4-methylumbelliferyl Neu5Ac (4MU-Neu5Ac). Additionally, STSA had remarkably weak ability to cleave α2-3-linked-Neu5Gc contained in gangliosides and equine erythrocytes. In silico analysis based on first-principle calculations with transition-state analogues suggested that the binding affinity of Neu5Gc2en is 14.3 kcal/mol more unstable than that of Neu5Ac2en. The results indicated that STSA preferentially cleaves Neu5Ac residues rather than Neu5Gc residues, which is important for anyone using this enzyme to cleave α2-3-linked sialic acids.
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Key Words
- 4MU, 4-methylumbelliferone
- 4MU-Neu5Ac, 4-methylumbelliferyl N-acetylneuraminic acid
- 4MU-Neu5Gc
- 4MU-Neu5Gc, 4-methylumbelliferyl N-glycolylneuraminic acid
- AUSA, Arthrobacter ureafaciens sialidase
- Boc, tert-butoxycarbonyl
- CPSA, Clostridium perfingens sialidase
- DANA, 2,3-dehydro-2-deoxy-N-acetylneuraminic acid
- DMAP, 4-dimethylaminopyridine
- DMB, 1,2-diamino-4,5-methylenedioxybenzene
- Docking simulations
- E. coli, Escherichia coli
- HPLC, high-performance liquid chromatography
- MDSA, Macrobdella decora sialidase
- N-glycolylneuraminic acid
- N.D., not detected
- Neu5Ac, N-acetylneuraminic acid
- Neu5Gc, N-glycolylneuraminic acid
- PBS, phosphate buffered saline
- STSA, Salmonella typhimurium LT2 sialidase
- Salmonella typhimurium LT2 sialidase
- Sia, sialic acid
- Sialic acid
- Substrate specificity
- THF, tetrahydrofuran
- VCSA, Vibrio cholerae sialidase
- rt, room temperature
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Affiliation(s)
- Akira Minami
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sayaka Ishibashi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kiyoshi Ikeda
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Erika Ishitsubo
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Takanori Hori
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Risa Taguchi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Daisuke Ieno
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Tadamune Otsubo
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Yukino Matsuda
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Saki Sai
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Mari Inada
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Takashi Suzuki
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Katsuyama I, Chouthaiwale PV, Cui HL, Ito Y, Sando A, Tokiwa H, Tanaka F. Substituent-dependent reactivity in aldehyde transformations: 4-(phenylethynyl)benzaldehydes versus simple benzaldehydes. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Takagi A, Ikawa T, Kurita Y, Saito K, Azechi K, Egi M, Itoh Y, Tokiwa H, Kita Y, Akai S. Generation of 3-borylbenzynes, their regioselective Diels–Alder reactions, and theoretical analysis. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.016] [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: 10/27/2022]
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Ikawa T, Takagi A, Goto M, Aoyama Y, Ishikawa Y, Itoh Y, Fujii S, Tokiwa H, Akai S. Regiocomplementary cycloaddition reactions of boryl- and silylbenzynes with 1,3-dipoles: selective synthesis of benzo-fused azole derivatives. J Org Chem 2013; 78:2965-83. [PMID: 23428206 DOI: 10.1021/jo302802b] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Benzo-fused nitrogen-containing heterocycles are abundant in biologically active compounds. One of the most important methods for preparing such heterocycles is the (3 + 2) cycloaddition reaction of benzynes with 1,3-dipolar compounds. However, the reactions of unsymmetrically substituted benzynes generally show low selectivity and hence yield mixtures of two regioisomers. In this paper, we describe the synthesis of both regioisomers of multisubstituted benzo-fused azole derivatives such as benzotriazoles, 1H-indazoles, and benzo[d]isoxazoles through the regiocomplementary (3 + 2) cycloaddition reactions of 3-boryl- and 3-silylbenzynes with 1,3-dipoles. The improved generation of 3-borylbenzynes from new precursors was one of the most important results of this work, which produced the successful (3 + 2) cycloaddition reactions with exclusive and proximal selectivities. On the other hand, similar reactions of 3-silylbenzynes selectively afforded distal cycloadducts. Analysis of the reaction pathways of these amazing regioselectivities by density functional theory calculations revealed that the (3 + 2) cycloadditions of borylbenzynes are controlled by the electrostatic effect of the boryl group, while those of silylbenzynes are controlled mainly by the steric effect of the bulky silyl groups that produced electrostatically unfavorable adducts via anomalous transition states.
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Affiliation(s)
- Takashi Ikawa
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-ku, Shizuoka, Shizuoka 422-8526, Japan
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46
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Nakano Y, Watanabe Y, Ito Y, Yamada S, Tokiwa H. Novel homodimer model of the β-adrenergic receptor in complex with free fatty acids and cholesterol: first-principles calculation studies. Bioinformation 2012; 8:1245-8. [PMID: 23275728 PMCID: PMC3532008 DOI: 10.6026/97320630081245] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 11/23/2022] Open
Abstract
We propose a theoretical novel homodimer model of the β- adrenergic receptor (βAR) in complex with a heterogeneous mixture of free fatty acids (FFAs) and cholesterol based on first-principles calculations. We used the density-functional-based tight binding with dispersion (DFTB-D) method, which accurately evaluates van der Waals interactions between FFAs and amino acid residues in the receptor. The calculations suggest that a stable homodimer of bAR can form a complex with FFAs and cholesterol by extensive van der Waals interactions in the cell membrane, and that the heterogeneous composition of the FFAs is important for the stability of the homodimer complex. The stable van der Waals interactions propagate from one of the bAR to the other through the cholesterol and FFAs in the homodimer complex. The energy propagation in the complex has the potential to enhance molecular signaling in adipocytes, because the stability of the complex can influence anti-adiposity effects after oral treatment of the FFA components.
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Affiliation(s)
- Yuka Nakano
- Department of Chemistry, Rikkyo University,
Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuo Watanabe
- Nihon Pharmaceutical University, 10281 Komuro,
Ina-machi, Kitaadachi-gun, Saitama 362-0806, Japan
| | - Yoshihiko Ito
- School of Pharmaceutical Sciences, University of
Shizuoka, 52-1, Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Shizuo Yamada
- School of Pharmaceutical Sciences, University of
Shizuoka, 52-1, Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University,
Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
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Tokiwa H. Modern Chemistry & Multiscale Simulations That Support Current Drug Design. YAKUGAKU ZASSHI 2012; 132:861-2. [DOI: 10.1248/yakushi.132.861] [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: 11/22/2022]
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48
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Endo-Umeda K, Uno S, Fujimori K, Naito Y, Saito K, Yamagishi K, Jeong Y, Miyachi H, Tokiwa H, Yamada S, Makishima M. Differential Expression and Function of Alternative Splicing Variants of Human Liver X Receptor α. Mol Pharmacol 2012; 81:800-10. [DOI: 10.1124/mol.111.077206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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49
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Suhara Y, Hanada N, Okitsu T, Sakai M, Watanabe M, Nakagawa K, Wada A, Takeda K, Takahashi K, Tokiwa H, Okano T. Structure-activity relationship of novel menaquinone-4 analogues: modification of the side chain affects their biological activities. J Med Chem 2012; 55:1553-8. [PMID: 22250752 DOI: 10.1021/jm2013166] [Citation(s) in RCA: 18] [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] [Indexed: 01/13/2023]
Abstract
We synthesized new vitamin K analogues with demethylation or reduction of the double bonds of the side chain of menaquinone-4 (MK-4) and evaluated their SXR-mediated transcriptional activity as well as the extent of their conversion to MK-4. The results indicated that the analogue with the methyl group deleted at the 7' site of the side chain part affected conversion activity to MK-4. In contrast, a decrease in the number of the double bonds in the side chain moiety appeared to decrease the SXR-mediated transcriptional activity.
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Affiliation(s)
- Yoshitomo Suhara
- Laboratory of Environmental Sciences, Yokohama College of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
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50
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Ikawa T, Tokiwa H, Akai S. Experimental and Theoretical Studies on Regiocontrol of Benzyne Reactions Using Silyl and Boryl Directing Groups. J SYN ORG CHEM JPN 2012. [DOI: 10.5059/yukigoseikyokaishi.70.1123] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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