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Wakimoto Toshiyuki

Faculty of Pharmaceutical Sciences　Molecular Pharmaceutical Sciences　Chemistry and Medicinal ChemistryProfessor

Researcher basic information

■ Degree
  • Ph.D., University of Tokyo
■ URL
researchmap URLホームページURL■ Various IDs
J-Global ID■ Research Keywords and Fields
Research Keyword
  • チョコガタイシカイメン
  • 蛍光プローブ
  • タンパク質脱リン酸化酵素
  • ミドリイガイ
  • 海綿
  • カリクリン
  • フラン脂肪酸
  • 抗炎症活性
  • Calyculin A
  • 二次代謝酵素
  • 機能制御
  • 酵素工学
  • 海洋生物資源
  • 物質生産
  • 生合成
Research Field
  • Life Science, Environmental and natural pharmaceutical resources
  • Life Science, Bioorganic chemistry
  • Life Science, Aquatic life science
■ Educational Organization

Career

■ Career
Career
  • 2015 - Present
    北海道大学大学院, 薬学研究院, 教授
  • 2013 - 2015
    東京大学大学院, 薬学系研究科, 准教授
  • 2010 - 2013
    東京大学大学院, 薬学系研究科, 講師
  • 2009 - 2010
    University of Shizuoka, School of Pharmaceutical Sciences, 講師
  • 2007 - 2009
    University of Shizuoka, School of Pharmaceutical Sciences, 助教
  • 2003 - 2007
    University of Shizuoka, School of Pharmaceutical Sciences, 助手
  • 2001 - 2003
    日本学術振興会海外特別研究員, ピッツバーグ大学化学科, 博士研究員
Educational Background
  • 2001, 東京大学大学院農学生命科学研究科
  • 1996, 東京大学農学部
Position History
  • 薬学部附属薬用植物園長, 2022年4月1日 - 2024年3月31日
  • 薬学部附属薬用植物園長, 2024年4月1日 - 2026年3月31日

Research activity information

■ Awards
  • Mar. 2021, 日本薬学会, 学術振興賞
    脇本 敏幸
  • Sep. 2014, 日本生薬学会, 学術貢献賞
    脇本 敏幸
  • Sep. 2013, 長瀬科学技術振興財団, 長瀬研究奨励賞
    脇本 敏幸
  • Sep. 2012, 日本生薬学会, 学術奨励賞
    脇本 敏幸
  • May 2008, 新規素材探索研究会, 最優秀ポスター賞
    脇本 敏幸
■ Papers
  • Stigmatellamines A–D: Bacterial Membrane Vesicle-Induced N -Alkylpyridinium Alkaloids from Stigmatella aurantiaca
    Teruhisa Manome; Aya Yoshimura; Keiko Konuma; Yui Numata; Kumi Kawaji; Eiichi N. Kodama; Toshiyuki Wakimoto
    Journal of Natural Products, 89, 4, 1362, 1369, American Chemical Society (ACS), 15 Apr. 2026
    Scientific journal
  • An atypical non-ribosomal peptide cyclase catalyzing homochiral coupling with cyclic amine nucleophile
    Mitsuo Aono; Yuito Yamada; Kenichi Matsuda; Toshiyuki Wakimoto
    The Journal of Antibiotics, Springer Science and Business Media LLC, 17 Dec. 2025
    Scientific journal
  • Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges
    Maria Dell; Masato Kogawa; Alena B. Streiff; Taro Shiraishi; Alessandro Lotti; Christoph M. Meier; Michelle A. Schorn; Christopher Field; Jackson K. B. Cahn; Hiromi Yokoyama; Yuito Yamada; Eike Peters; Yoko Egami; Yu Nakashima; Karen Co Tan; Christian Rückert; Mohammad Alanjary; Jörn Kalinowski; Tomohisa Kuzuyama; Paco Cardenas; Shirley Pomponi; Detmer Sipkema; Amy Wright; Kentaro Takada; Ikuro Abe; Toshiyuki Wakimoto; Haruko Takeyama; Jörn Piel
    Nature Chemical Biology, Springer Science and Business Media LLC, 13 Nov. 2025
    Scientific journal, Abstract

    Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, ‘ Candidatus Entotheonella’ members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 ‘Entotheonella’ candidate species and a member of a sister lineage named ‘ Candidatus Proxinella’. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.
  • Non-ribosomal peptide cyclase-directed chemoenzymatic synthesis of lariat lipopeptides.
    Masakazu Kobayashi; Kenichi Matsuda; Yuito Yamada; Rintaro Ichihara; Naho Onozawa; Hanako Fukano; Yoshihiko Hoshino; Aki Hirabayashi; Masato Suzuki; Akira Katsuyama; Satoshi Ichikawa; Toshiyuki Wakimoto
    Nature chemistry, 04 Nov. 2025, [International Magazine]
    English, Scientific journal, Lariat-shaped lipopeptides are important antimicrobial agents; however, their complex structures pose synthetic challenges that hamper efficient structural diversification. Here we report a new chemoenzymatic approach that facilitates access to lariat-shaped macrocycles. Unprotected, branched peptides bearing multiple nucleophiles, including a native amino terminus and a pseudo-amino terminus, were site-selectively cyclized using versatile non-ribosomal peptide cyclases, generating an array of lariat peptides with diverse sequences and ring sizes. The generality of this strategy was demonstrated using two penicillin-binding protein-type thioesterases, SurE and WolJ, as well as one type-I thioesterase, TycC thioesterase. Furthermore, the remaining nucleophile, which was not involved in the cyclization process, was exploited as a reactive handle for subsequent diversification via a site-selective acylation reaction (that is, Ser/Thr ligation). The tandem cyclization-acylation strategy enabled the one-pot, modular synthesis of lariat-shaped lipopeptides equipped with various acyl groups. Biological screening revealed that the site-selective acylation endowed the macrocyclic scaffolds with antimycobacterial activity and led to the identification of lipopeptides that inhibit 50% of growth at concentrations of 8-16 µg ml-1.
  • Diol as a New Pantetheine Surrogate for Chemoenzymatic Synthesis of Cyclic Peptides via Nonribosomal Peptide Cyclases
    Kei Fujita; Rintaro Ichihara; Masakazu Kobayashi; Kenichi Matsuda; Toshiyuki Wakimoto
    Methods in Molecular Biology, 105, 121, Springer US, 19 Jun. 2025
    In book
  • Arginine-N,N′-bisprenyltransferases: Switchable Catalysis in Consecutive Guanidine-N-prenylation
    Kei Fujita; Yuito Yamada; Tomo Taniguchi; Daisuke Fujinami; Takahiro Mori; Kenichi Matsuda; Ikuro Abe; Toshiyuki Wakimoto
    Journal of the American Chemical Society, 147, 28, 24766, 24773, American Chemical Society (ACS), 13 Jun. 2025
    Scientific journal
  • Facile Synthesis of 15N-Labeled Amino Acids Using 15N-Ammonium Salt
    Kuga Arima; Kenichi Matsuda; Toshiyuki Wakimoto
    Tetrahedron Letters, 157, 155490, 155490, Elsevier BV, Feb. 2025, [Peer-reviewed]
    Scientific journal
  • Enzymatic Peptide Macrocyclization via Indole-N-Acylation
    Hiroto Maruyama; Yuito Yamada; Yasuhiro Igarashi; Kenichi Matsuda; Toshiyuki Wakimoto
    Chemical Science, Royal Society of Chemistry (RSC), 2025, [Peer-reviewed]
    Scientific journal, Indole N-acylation is chemically challenging, due to the low nucleophilicity of the indole nitrogen. Although a few similar transformations have been proposed in the biosynthesis of indole-containing natural products, their...
  • Doubly Homologated Tyrosine-Containing Peptides from the Cyanobacterium Microcystis aeruginosa NIES-4285 and Their Biosynthesis
    Chin-Soon Phan; Zhengyi Ling; Jakia Jerin Mehjabin; Kenichi Matsuda; Nurcahyo Iman Prakoso; Taiki Umezawa; Toshiyuki Wakimoto; Tatsufumi Okino
    Journal of Natural Products, American Chemical Society (ACS), 30 Oct. 2024, [Peer-reviewed]
    Scientific journal
  • Synthesis and Cytotoxicity of Cyclic Octapeptide Surugamides with Varied <i>N</i>-Acyl Moieties
    Kenichi Matsuda; Shinya Niikura; Rintaro Ichihara; Kei Fujita; Anna M. Strasser; Rokusuke Yoshikawa; Jiro Yasuda; Yoshiki Hiramatsu; Hironori Hayashi; Eiichi N. Kodama; Toshiyuki Wakimoto
    Chemical and Pharmaceutical Bulletin, 72, 9, 826, 830, Pharmaceutical Society of Japan, 20 Sep. 2024, [Peer-reviewed]
    Scientific journal
  • Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials
    Kenichi Matsuda; Toshiyuki Wakimoto
    Current Opinion in Chemical Biology, Jun. 2024, [Peer-reviewed]
    Scientific journal
  • Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides
    Masakazu Kobayashi; Naho Onozawa; Kenichi Matsuda; Toshiyuki Wakimoto
    Communications Chemistry, 7, 1, Springer Science and Business Media LLC, 28 Mar. 2024, [Peer-reviewed]
    Scientific journal, Abstract

    Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
  • Bacterial hydrazine biosynthetic pathways featuring cupin/methionyl tRNA synthetase-like enzymes.
    Kenichi Matsuda; Toshiyuki Wakimoto
    ChemBioChem, e202300874, 08 Mar. 2024, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Nitrogen-Nitrogen (N-N) bond-containing functional groups in natural products and synthetic drugs play significant roles in exerting biological activities. The mechanisms of N-N bond formation in natural organic molecules have garnered increasing attention over the decades. Recent advances have illuminated various enzymatic and nonenzymatic strategies, and our understanding of natural N-N bond construction is rapidly expanding. A group of didomain proteins with zinc-binding cupin/methionyl-tRNA synthetase (MetRS)-like domains, also known as hydrazine synthetases, generates amino acid-based hydrazines, which serve as key biosynthetic precursors of diverse N-N bond-containing functionalities such as hydrazone, diazo, triazene, pyrazole, and pyridazinone groups. In this review, we summarize the current knowledge on hydrazine synthetase mechanisms and the various pathways employing this unique bond-forming machinery.
  • Phylogeny‐guided Characterization of Bacterial Hydrazine Biosynthesis Mediated by Cupin/methionyl tRNA Synthetase‐like Enzymes
    Kenichi Matsuda; Yuto Nakahara; Atina Rizkiya Choirunnisa; Kuga Arima; Toshiyuki Wakimoto
    ChemBioChem, Wiley, 25 Feb. 2024, [Peer-reviewed]
    Scientific journal, Cupin/methionyl‐tRNA synthetase (MetRS)‐like didomain enzymes catalyze nitrogen‐nitrogen (N–N) bond formation between Nw‐hydroxylamines and amino acids to generate hydrazines, key biosynthetic intermediates of various natural products containing N–N bonds. While the combination of these two building blocks leads to the creation of diverse hydrazine products, the full extent of their structural diversity remains largely unknown. To explore this, we herein conducted phylogeny‐guided genome‐mining of related hydrazine biosynthetic pathways consisting of two enzymes: flavin‐dependent Nw‐hydroxylating monooxygenases (NMOs) that produce Nw‐hydroxylamine precursors and cupin/MetRS‐like enzymes that couple the Nw‐hydroxylamines with amino acids via N–N bonds. A phylogenetic analysis identified the largely unexplored sequence spaces of these enzyme families. The biochemical characterization of NMOs demonstrated their capabilities to produce various Nw‐hydroxylamines, including those previously not known as precursors of N–N bonds. Furthermore, the characterization of cupin/MetRS‐like enzymes identified five new hydrazine products with novel combinations of building blocks, including one containing non‐amino acid building blocks: 1,3‐diaminopropane and putrescine. This study substantially expanded the variety of N–N bond forming pathways mediated by cupin/MetRS‐like enzymes.
  • Actinobacterial chalkophores: the biosynthesis of hazimycins
    Kenichi Matsuda; Hiroto Maruyama; Kumiko Imachi; Haruo Ikeda; Toshiyuki Wakimoto
    The Journal of Antibiotics, 20 Feb. 2024, [Peer-reviewed]
    Scientific journal
  • FlkO, a penicillin-binding protein-type thioesterase in cyclofaulknamycin biosynthesis
    Kenichi Matsuda; Rintaro Ichihara; Toshiyuki Wakimoto
    Organic & Biomolecular Chemistry, Royal Society of Chemistry (RSC), 2024, [Peer-reviewed]
    Scientific journal, In vitro studies of FlkO, a new penicillin-binding protein thioesterase, demonstrated its peptide-cyclizing activity and substrate scope.
  • Animal-associated marine Acidobacteria with a rich natural-product repertoire
    Stefan Leopold-Messer; Clara Chepkirui; Mathijs F.J. Mabesoone; Joshua Meyer; Lucas Paoli; Shinichi Sunagawa; Agustinus R. Uria; Toshiyuki Wakimoto; Jörn Piel
    Chem, Elsevier BV, Dec. 2023, [Peer-reviewed]
    Scientific journal
  • Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
    Masakazu Hoshino; Guillaume Cossard; Fabian B. Haas; Emma I. Kane; Kazuhiro Kogame; Takahiro Jomori; Toshiyuki Wakimoto; Susana M. Coelho
    Nature Ecology & Evolution, Cold Spring Harbor Laboratory, 12 Sep. 2023, [Peer-reviewed]
    Abstract

    Sexual reproduction is widespread among eukaryotes, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of taxa. Despite extensive research on the evolution of asexuality from sexual ancestors, the molecular changes underpinning the switch to asexual reproduction remain elusive, particularly in organisms with haploid sexual systems such as bryophytes, and red and brown algae in which males and females are haploid and multicellular. Here, we investigate independent events in which asexuality has emerged from sexual ancestor lineages in species of the brown algalScytosiphon, we examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that individuals from asexual, female-only (‘Amazon’) populations lose their ability to produce and sex pheromone and, consequently, are unable to attract and fuse with male gametes, whereas they gain the ability to trigger parthenogenic (asexual) development from large, unfertilized eggs. This independent and convergent decline in pheromone production and optimization of asexual traits is accompanied by convergent changes in gene expression, including de-feminization and masculinization of the Amazon gamete transcriptomes. These data are consistent with the idea that decay of female functions, rather than relaxation of sexual antagonism, is the dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we identify a locus on an autosomal protein-coding gene that is associated with the switch to asexuality. We propose that the sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
  • Membrane‐Vesicle‐Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production
    Aya Yoshimura; Rio Saeki; Ryusuke Nakada; Shota Tomimoto; Takahiro Jomori; Keisuke Suganuma; Toshiyuki Wakimoto
    Angewandte Chemie International Edition, Wiley, 14 Jul. 2023, [Peer-reviewed]
    Scientific journal
  • Carrier Protein Mediated Formation of the Dihydropyridazinone Ring in Actinopyridazinone Biosynthesis
    Kuga Arima; Satoko Akiyama; Kazuo Shin-ya; Kenichi Matsuda; Toshiyuki Wakimoto
    Angewandte Chemie International Edition, Wiley, 17 May 2023, [Peer-reviewed]
    Scientific journal
  • Streamlined Chemoenzymatic Synthesis of Cyclic Peptides by Non-ribosomal Peptide Cyclases
    Masakazu Kobayashi; Kei Fujita; Kenichi Matsuda; Toshiyuki Wakimoto
    Journal of the American Chemical Society, 13 Jan. 2023, [Peer-reviewed]
    Scientific journal
  • Chemo-Enzymatic Synthesis of Non-ribosomal Macrolactams by a Penicillin-Binding Protein-Type Thioesterase.
    Masakazu Kobayashi; Kei Fujita; Kenichi Matsuda; Toshiyuki Wakimoto
    Methods in Molecular Biology, 2670, 127, 144, 2023, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Penicillin-binding protein-type thioesterases (PBP-type TEs) are an emerging family of non-ribosomal peptide cyclases. PBP-type TEs exhibit distinct substrate scopes from the well-exploited ribosomal peptide cyclases and traditional non-ribosomal peptide cyclases. Their unique properties, as well as their stand-alone nature, highlight PBP-type TEs as valuable candidates for development as biocatalysts for peptide macrocyclization. Here in this chapter, we describe the scheme for the chemoenzymatic synthesis of non-ribosomal macrolactam by SurE, a representative member of PBP-type TEs.
  • Characterization of the surugamide biosynthetic gene cluster of TUA-NKU25, a Streptomyces diastaticus strain isolated from Kusaya and its effects on salt-dependent growth
    Aoi Takeuchi; Asahi Hirata; Aiko Teshima; Miu Ueki; Takumi Satoh; Kenichi Matsuda; Toshiyuki Wakimoto; Kenji Arakawa; Morio Ishikawa; Toshihiro Suzuki
    Bioscience, Biotechnology, and Biochemistry, Oxford University Press (OUP), 10 Dec. 2022, [Peer-reviewed]
    Scientific journal, Abstract

    Kusaya, a traditional Japanese fermented fish product, is known for its high preservability, as it contains natural antibiotics derived from microorganisms, and therefore molds and yeasts do not colonize it easily. In this study, the Streptomyces diastaticus strain TUA-NKU25 was isolated from Kusaya; its growth as well as the production of antibiotics were investigated. Strain TUA-NKU25 showed advantageous growth characteristics in the presence, but not in the absence of NaCl. Antimicrobial assay, high-performance liquid chromatography, and electrospray ionization-mass spectrometry analysis showed that this strain produced surugamide A and uncharacterized antimicrobial compound(s) during growth in the presence of NaCl, suggesting that biosynthesis of these compounds was upregulated by NaCl. Draft genomic analysis revealed that strain TUA-NKU25 possesses a surugamide biosynthetic gene cluster (sur BGC), although it is incomplete, lacking surB/surC. Phylogenetic analysis of strain TUA-NKU25 and surugamide-producing Streptomyces showed that sur BGC formed a clade distinct from other known groups.
  • New Theonellapeptolides from Indonesian Marine Sponge Theonella swinhoei as Anti-austerity Agents
    Jabal Haedar; Agustinus Uria; Subehan Lallo; Dya Fita Dibwe; Toshiyuki Wakimoto
    Marine Drugs, 20, 11, 661, 661, MDPI AG, 25 Oct. 2022, [Peer-reviewed]
    Scientific journal, We reported three new members of the theonellapeptolide family from theonellapeptolide II series, namely theonellapeptolides IIb (1), IIa (2), IIc (3), and three known members—IId (4), IIe (5), and Id (6)—from Kodingarengan marine sponge Theonella swinhoei collected in Makassar, Indonesia. The structures of tridecadepsipeptides 1–3, including the absolute configurations of their amino acids, were determined by the integrated NMR and tandem MS analyses followed by Marfey’s analysis. To the best of our knowledge, 1 and 2 are the first theonellapeptolide-type compounds to have a valine residue with D configuration at residue position 6. The isolated theonellapeptolide-type compounds 1–6 showed selective cytotoxic activity against human pancreatic MIA PaCa-2 cancer cells in a nutrient-deprived medium. Among them, the most potent preferential cytotoxicity was observed in new theonellapeptolide IIc (3) and known IId (4), IIe (5), and Id (6).
  • New azodyrecins identified by a genome mining-directed reactivity-based screening
    Atina Rizkiya Choirunnisa; Kuga Arima; Yo Abe; Noritaka Kagaya; Kei Kudo; Hikaru Suenaga; Junko Hashimoto; Manabu Fujie; Noriyuki Satoh; Kazuo Shin-ya; Kenichi Matsuda; Toshiyuki Wakimoto
    Beilstein Journal of Organic Chemistry, 18, 1017, 1025, Beilstein Institut, 10 Aug. 2022, [Peer-reviewed]
    Scientific journal, Only a few azoxy natural products have been identified despite their intriguing biological activities. Azodyrecins D–G, four new analogs of aliphatic azoxides, were identified from two Streptomyces species by a reactivity-based screening that targets azoxy bonds. A biological activity evaluation demonstrated that the double bond in the alkyl side chain is important for the cytotoxicity of azodyrecins. An in vitro assay elucidated the tailoring step of azodyrecin biosynthesis, which is mediated by the S-adenosylmethionine (SAM)-dependent methyltransferase Ady1. This study paves the way for the targeted isolation of aliphatic azoxy natural products through a genome-mining approach and further investigations of their biosynthetic mechanisms.
  • A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme
    Kenichi Matsuda; Kuga Arima; Satoko Akiyama; Yuito Yamada; Yo Abe; Hikaru Suenaga; Junko Hashimoto; Kazuo Shin-ya; Makoto Nishiyama; Toshiyuki Wakimoto
    Journal of the American Chemical Society, American Chemical Society (ACS), 30 Jun. 2022, [Peer-reviewed]
    Scientific journal
  • Insights into Phosphatase-activated Chemical Defense in a Marine Sponge Holobiont
    Takahiro Jomori; Kenichi Matsuda; Yoko Egami; Ikuro Abe; Akira Takai; Toshiyuki Wakimoto
    RSC Chemical Biology, 2, 6, 1600, 1607, Royal Society of Chemistry (RSC), Oct. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Marine sponges often contain potent cytotoxic compounds, which in turn evokes the principle question of how marine sponges avoid self-toxicity. In a marine sponge Discodermia calyx, the highly toxic calyculin...
  • Geographical parthenogenesis in the brown alga Scytosiphon lomentaria (Scytosiphonaceae): Sexuals in warm waters and parthenogens in cold waters
    Masakazu Hoshino; Shimpei F. Hiruta; Maria Emilia Croce; Mitsunobu Kamiya; Takahiro Jomori; Toshiyuki Wakimoto; Kazuhiro Kogame
    Molecular Ecology, 30, 22, 5814, 5830, Wiley, 06 Sep. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Geographical parthenogenesis, a phenomenon where parthenogens and their close sexual relatives inhabit distinct geographical areas, has been considered an interesting topic in evolutionary biology. Reports of geographical parthenogenesis from land and freshwater are numerous, but this occurrence has been rarely reported from the sea. Brown algae are mostly marine and are thought to include numerous obligate parthenogens; still, little is known about the distribution, origin and evolution of parthenogens in this group. Here we report a novel pattern of geographical parthenogenesis in the isogamous brown alga Scytosiphon lomentaria. Sex ratio investigation demonstrated that, in Japan, sexual populations grew in the coast along warm ocean currents, whereas female-dominant parthenogenetic populations grew mainly in the coast along a cold ocean current. In the two localities where sexual and parthenogenetic populations were parapatric, parthenogens grew in more wave-exposed areas than sexuals. Population genetic and phylogenetic analyses, including those based on genome-wide single nucleotide polymorphism data, indicated that parthenogens have initially evolved at least twice and subsequent hybridizations between the parthenogens and sexuals have generated multiple new parthenogenetic lineages. The origin of the initial parthenogens is not clear, except that it would not be interspecies hybridization. Interestingly, we found that the production of sex pheromones, which attract male gametes, has been independently lost in the initial two parthenogenetic lineages. This parallel loss of the sexual trait may represent the direct origin of parthenogens, or the regressive evolution of a useless trait under asexuality.
  • Argicyclamides A–C Unveil Enzymatic Basis for Guanidine Bis-prenylation
    Chin-Soon Phan; Kenichi Matsuda; Nandani Balloo; Kei Fujita; Toshiyuki Wakimoto; Tatsufumi Okino
    Journal of the American Chemical Society, American Chemical Society (ACS), 28 Jun. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Guanidine prenylation is an outstanding modification in alkaloid and peptide biosynthesis, but its enzymatic basis has remained elusive. We report the isolation of argicyclamides, a new class of cyanobactins with unique mono- and bis-prenylations on guanidine moieties, from Microcystis aeruginosa NIES-88. The genetic basis of argicyclamide biosynthesis was established by the heterologous expression and in vitro characterization of biosynthetic enzymes including AgcF, a new guanidine prenyltransferase. This study provides important insight into the biosynthesis of prenylated guanidines and offers a new toolkit for peptide modification.
  • PenA, a penicillin-binding protein-type thioesterase specialized for small peptide cyclization.
    Kenichi Matsuda; Kei Fujita; Toshiyuki Wakimoto
    Journal of Industrial Microbiology & Biotechnology, 48, 3-4, 04 Jun. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified group of peptide cyclases that catalyze head-to-tail macrolactamization of nonribosomal peptides. PenA, a new member of this group, is involved in the biosyntheses of cyclic pentapeptides. In this study, we demonstrated the enzymatic activity of PenA in vitro, and analyzed its substrate scope with a series of synthetic substrates. A comparison of the reaction profiles between PenA and SurE, a representative PBP-type TE, showed that PenA is more specialized for small peptide cyclization. A computational model provided a possible structural rationale for the altered specificity for substrate chain lengths.
  • Ascidian-associated photosymbionts from Manado, Indonesia: secondary metabolites, bioactivity simulation, and biosynthetic insight
    Inneke F. M. Rumengan; Vera I. Y. Roring; Jabal R. Haedar; Mayse S. Siby; Aldian H. Luntungan; Beivy J. Kolondam; Agustinus R. Uria; Toshiyuki Wakimoto
    Symbiosis, Springer Science and Business Media LLC, 22 Apr. 2021, [Peer-reviewed]
    Scientific journal
  • Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue
    Takefumi Kuranaga; Kenichi Matsuda; Masachika Takaoka; Chisato Tachikawa; Ayae Sano; Kosei Itoh; Ayumu Enomoto; Kei Fujita; Ikuro Abe; Toshiyuki Wakimoto
    ChemBioChem, 21, 23, 3329, 3332, Wiley, Dec. 2020, [Peer-reviewed]
    Scientific journal
  • Heterochiral coupling in non-ribosomal peptide macrolactamization
    Kenichi Matsuda; Rui Zhai; Takahiro Mori; Mazakazu Kobayashi; Ayae Sano; Ikuro Abe; Wakimoto Toshiyuki
    Nature Catalysis, 32, May 2020, [Peer-reviewed]
    Scientific journal
  • Polyketides Biosynthesis in Marine Sponges of the Family Theonellidae
    Agustinus Robert Uria; Toshiyuki Wakimoto
    Topics in Heterocyclic Chemistry, 389, 413, Springer Berlin Heidelberg, 2020, [Peer-reviewed]
    In book
  • Crystal Structures of Flavone C-Glycosides from Oolong Tea Leaves: Chafuroside A Dihydrate and Chafuroside B Monohydrate.
    Yasunori Iwao; Hitoshi Ishida; Shin-Ichiro Kimura; Toshiyuki Wakimoto; Hiromu Kondo; Shigeru Itai; Shuji Noguchi
    Chemical & Pharmaceutical Bulletin, 67, 9, 935, 939, 2019, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal, Chafuroside A and chafuroside B are flavone C-glycosides isolated from oolong tea leaves. They have a number of beneficial pharmacological activities related to antiinflammation at various concentrations. However, no crystallographic study of chafurosides has yet been reported. In the present study, the crystal structures of chafuroside A and chafuroside B were investigated using single-crystal X-ray diffraction. The asymmetric unit of the chafuroside A crystal consists of one chafuroside A and two water molecules, and that of chafuroside B contains one chafuroside B and one water molecule. The flavone moiety of chafuroside A is curved, i.e., the angle between the best-fit planes of the chromene and phenyl rings is 18.9°, whereas the chafuroside B flavone moiety is relatively flat. A comparison of the curvatures of the flavone moieties of various C-glycosides showed that the curvature of chafuroside A is significantly larger than those of the others. This structural feature might contribute to the differences between the strengths of the pharmacological activities of chafurosides A and B.
  • The Revised Structure of the Cyclic Octapeptide Surugamide A
    Kenichi Matsuda; Takefumi Kuranaga; Ayae Sano; Akihiro Ninomiya; Kentaro Takada; Toshiyuki Wakimoto
    Chemical & Pharmaceutical Bulletin, 67, 5, 476, 480, 2019, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal, Surugamides are a group of non-ribosomal peptides isolated from marine-derived Streptomyces. Surugamide A (1) and its closely related derivatives, surugamides B-E (2-5), are D-amino acid containing cyclic octapeptides with cathepsin B inhibitory activity. The D-isoleucine (Ile), the nonproteinogenic amino acid residue embedded in 1, is less common in natural peptides because a rare Cβ-epimerization is required for its biosynthesis. Taking advantage of the synthetic route of 2 previously established by our group, we synthesized the cyclic octapeptide 1 containing D-Ile by solid phase peptide synthesis. The structure of 1 actually contains D-allo-Ile in place of D-Ile, which was corroborated by chemical syntheses and chromatographic comparisons.
  • A new cyclase family catalyzing head-to-tail macrolactamization of non-ribosomal peptides
    Kenichi Matsuda; Takefumi Kuranaga; Toshiyuki Wakimoto
    J. Synth. Org. Chem. Jpn., 77, 1106, 1115, 2019, [Peer-reviewed]
  • Scrobiculosides A and B from the Deep-Sea Sponge Pachastrella scrobiculosa
    Takahiro Jomori; Shuji Shiroyama; Yuji Ise; Hisanori Kohtsuka; Kenichi Matsuda; Takefumi Kuranaga; Toshiyuki Wakimoto
    J. Nat. Med., 73, 4, 814, 819, 2019, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal, Two new steroidal saponins, scrobiculosides A and B, were isolated from the deep-sea sponge Pachastrella scrobiculosa, collected at a depth of 200 m off Miura Peninsula, Japan. The aglycones of scrobiculosides A and B feature a vinylic cyclopropane and a ∆24,25 exomethylene on the side chains, respectively. Both saponins have a common sugar moiety composed of β-D-galactopyranosyl-(1 → 2)-6-acetyl-β-D-glucopyranoside, with the exception of an acetyl group on C6″ in scrobiculoside A. Scrobiculoside A exhibited cytotoxicity against HL-60 and P388 cells, with IC50 values of 52 and 61 μM, respectively.
  • SurE is a trans-acting thioesterase cyclizing two distinct non-ribosomal peptides.
    Matsuda, K; Kobayashi, M; Kuranaga, T; Takada, K; Ikeda, H; Matsunaga, S; Wakimoto, T
    Org. Biomol. Chem., 17, 1058, 1061, Jan. 2019, [Peer-reviewed]
    English, Scientific journal
  • Palmitoyl lactic acid induces adipogenesis and a brown fat-like phenotype in 3T3-L1 preadipocytes.
    Yuka Unno; Hirona Yamamoto; Shuto Takatsuki; Yoshinori Sato; Takefumi Kuranaga; Kazunaga Yazawa; Yasuo Ono; Toshiyuki Wakimoto
    Biochimica et Biophysica Acta. Molecular and Cell Biology of Lipids, 1863, 7, 772, 782, Jul. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Brown adipose tissue is specialized to generate heat by dissipating chemical energy and may provide novel strategies for obesity treatment in humans. Recently, advances in understanding the pharmacological and dietary agents that contribute to the browning of white adipose tissue have been made to alleviate obesity by promoting energy expenditure. Krill oil is widely used as a health supplement in humans. In this study, the components from krill oil that promote adipogenesis of 3T3-L1 cells were screened to reveal palmitoyl lactic acid (PLA) as a promoter of adipogenesis. The PLA-induced adipocytes contained large number of small lipid droplets. Moreover, similar to the peroxisome proliferator-activated receptor (PPAR)γ agonists, pioglitazone and rosiglitazone, PLA significantly enhances adipogenesis in the presence of dexamethasone compared with PLA alone. Treatment with PLA causes a brown fat-like phenotype in 3T3-L1 cells by enhanced expression of various brown/beige cell-specific genes, such as PR domain containing 16 (Prdm16) and peroxisome proliferative activated receptor, gamma, coactivator 1 alpha (Pgc1a), as well as adiponectin gene. The expression profile of the brown/beige cell-specific genes induced by PLA was similar to that of the PPARγ agonist in 3T3-L1 cells. Our findings suggest that PLA induces a brown fat-like phenotype and, thus, likely has therapeutic potential in treating obesity.
  • Discovery of Unprecedented Hydrazine-Forming Machinery in Bacteria.
    Matsuda K; Tomita T; Shin-Ya K; Wakimoto T; Kuzuyama T; Nishiyama M
    Journal of the American Chemical Society, 140, 29, 9083, 9086, Jul. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Recent studies described several different routes that facilitate nitrogen-nitrogen bond formation in natural product biosynthesis. We report herein the identification of unprecedented machinery for hydrazine formation involved in the biosynthesis of s56-p1, a dipeptide natural product with a unique hydrazone unit. The gene cassette comprising this machinery is widespread across several bacterial phyla, highlighting the overlooked potential of bacteria to synthesize hydrazine.
  • Biosynthetic Insights of Calyculin- and Misakinolide-Type Compounds in “Candidatus Entotheonella sp.”
    Agustinus R. Uria; Jörn Piel; Toshiyuki Wakimoto
    Methods in Enzymology, 604, 287, 330, Academic Press Inc., 01 Jan. 2018, [Peer-reviewed]
    English, In book
  • Diastereoselective total synthesis and structural confirmation of surugamide F
    Takefumi Kuranaga; Atsuki Fukuba; Akihiro Ninomiya; Kentaro Takada; Shigeki Matsunaga; Toshiyuki Wakimoto
    Chemical and Pharmaceutical Bulletin, 66, 6, 637, 641, Pharmaceutical Society of Japan, 2018, [Peer-reviewed]
    English, Scientific journal
  • Total Synthesis of the Non-Ribosomal Peptide Surugamide B and Identification of a New Offloading Cyclase Family
    Takefumi Kuranaga; Kenichi Matsuda; Ayae Sano; Masakazu Kobayashi; Akihiro Ninomiya; Kentaro Takada; Shigeki Matsunaga; Toshiyuki Wakimoto
    Angew. Chem. Int. Ed., 57, 30, 9447, 9451, 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, The cathepsin B inhibitor surugamide B (2), along with structurally related derivatives (A and C-E), has previously been isolated from the marine actinomycete Streptomyces sp. JAMM992. The biosynthetic genes are unexpectedly part of a cluster of four non-ribosomal peptide synthetase (NRPS) genes, two of which are responsible for the biosynthesis of the additional linear decapeptide surugamide F. However, the thioesterase domain required for the later stage of the biosynthesis of the cyclic peptides surugamides A-E is not present in any module architecture of the surugamide NRPSs. Herein, we report the first total synthesis of surugamide B (2) through the macrocyclization at the biomimetic position, which not only alleviated the Cα epimerization in the macrolactamization process, but also efficiently provided 2 in 34 % yield for 18 steps. Furthermore, both the chemical and enzymatic studies with the biosynthetic precursor mimics revealed that the stand-alone enzyme SurE, which belongs to the penicillin-binding protein family, is responsible for macrocyclization of the tethered octapeptidyl intermediate.
  • Protein phosphatases 1 and 2A and their naturally occurring inhibitors: current topics in smooth muscle physiology and chemical biology
    Akira Takai; Masumi Eto; Katsuya Hirano; Kosuke Takeya; Toshiyuki Wakimoto; Masaru Watanabe
    Journal of Physiological Sciences, 68, 1, Springer Tokyo, 01 Jan. 2018, [Peer-reviewed]
    English
  • Toward the Dark Matter of Natural Products
    Toshiyuki Wakimoto
    Chemical Record, 17, 11, 1124, 1134, Nov. 2017, [Peer-reviewed]
    English, Scientific journal
  • Identification of Pyridinium with Three Indole Moieties as an Antimicrobial Agent
    Masahiro Okada; Tomotoshi Sugita; Chin Piow Wong; Toshiyuki Wakimoto; Ikuro Abe
    Journal of Natural Products, 80, 4, 1205, 1209, Apr. 2017, [Peer-reviewed]
    English, Scientific journal
  • Total Synthesis of Theonellapeptolide Id
    Takefumi Kuranaga; Ayumu Enomoto; Hui Tan; Kazuto Fujita; Toshiyuki Wakirnoto
    Organic Letters, 19, 6, 1366, 1369, Mar. 2017, [Peer-reviewed]
    English, Scientific journal
  • Characterization of Giant Modular PKSs Provides Insight into Genetic Mechanism for Structural Diversification of Aminopolyol Polyketides
    Lihan Zhang; Takuya Hashimoto; Bin Qin; Junko Hashimoto; Ikuko Kozone; Teppei Kawahara; Masahiro Okada; Takayoshi Awakawa; Takuya Ito; Yoshinori Asakawa; Masashi Ueki; Shunji Takahashi; Hiroyuki Osada; Toshiyuki Wakimoto; Haruo Ikeda; Kazuo Shin-ya; Ikuro Abe
    Angew. Chem. Int. Ed., 56, 7, 1740, 1745, Feb. 2017, [Peer-reviewed]
    English, Scientific journal
  • Characterization of Giant Modular PKSs Provides Insight into Genetic Mechanism for Structural Diversification of Aminopolyol Polyketides
    Lihan Zhang; Takuya Hashimoto; Bin Qin; Junko Hashimoto; Ikuko Kozone; Teppei Kawahara; Masahiro Okada; Takayoshi Awakawa; Takuya Ito; Yoshinori Asakawa; Masashi Ueki; Shunji Takahashi; Hiroyuki Osada; Toshiyuki Wakimoto; Haruo Ikeda; Kazuo Shin‐ya; Ikuro Abe
    Angewandte Chemie, 129, 7, 1766, 1771, Wiley, 11 Jan. 2017
    Scientific journal, Abstract

    Polyketides form many clinically valuable compounds. However, manipulation of their biosynthesis remains highly challenging. An understanding of gene cluster evolution provides a rationale for reprogramming of the biosynthetic machinery. Herein, we report characterization of giant modular polyketide synthases (PKSs) responsible for the production of aminopolyol polyketides. Heterologous expression of over 150 kbp polyketide gene clusters successfully afforded their products, whose stereochemistry was established by taking advantage of bioinformatic analysis. Furthermore, phylogenetic analysis of highly homologous but functionally diverse domains from the giant PKSs demonstrated the evolutionary mechanism for structural diversification of polyketides. The gene clusters characterized herein, together with their evolutionary insights, are promising genetic building blocks for de novo production of unnatural polyketides.
  • Corrigendum to: Biosynthetic Gene Cluster for Surugamide A Encompasses an Unrelated Decapeptide, Surugamide F (ChemBioChem, (2016), 17, 18, (1709-1712), 10.1002/cbic.201600350)
    Ninomiya A; Katsuyama Y; Kuranaga T; Miyazaki M; Nogi Y; Okada S; Wakimoto T; Ohnishi Y; Matsunaga S; Takada K
    ChemBioChem, 18, 17, 2017, [Peer-reviewed]
  • Concise Synthesis of Anserine: Efficient Solvent Tuning in Asymmetric Hydrogenation Reaction
    Megumi Yamashita; Keita Shimizu; Yasuaki Koizumi; Toshiyuki Wakimoto; Yoshitaka Hamashima; Tomohiro Asakawa; Makoto Inai; Toshiyuki Kan
    Synlett, 27, 19, 2734, 2736, 01 Dec. 2016, [Peer-reviewed]
    Scientific journal
  • Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'
    Yu Nakashima; Yoko Egami; Miki Kimura; Toshiyuki Wakimoto; Ikuro Abe
    PLOS ONE, 11, 10, e0164468, Oct. 2016, [Peer-reviewed]
    English, Scientific journal
  • Biosynthetic Gene Cluster for Surugamide A Encompasses an Unrelated Decapeptide, Surugamide F
    Akihiro Ninomiya; Yohei Katsuyama; Takefumi Kuranaga; Masayuki Miyazaki; Yuichi Nogi; Shigeru Okada; Toshiyuki Wakimoto; Yasuo Ohnishi; Shigeki Matsunaga; Kentaro Takada
    ChemBioChem, 17, 18, 1709, 1712, 15 Sep. 2016, [Peer-reviewed]
    English, Scientific journal
  • Sulfoureido Lipopeptides from the Marine Sponge Discodermia kiiensis
    Karen Co Tan; Toshiyuki Wakimoto; Ikuro Abe
    Journal of Natural Products, 79, 9, 2418, 2422, Sep. 2016, [Peer-reviewed]
    English, Scientific journal
  • Structural Diversification of Lyngbyatoxin A by Host-Dependent Heterologous Expression of the tleABC Biosynthetic Gene Cluster
    Lihan Zhang; Shotaro Hoshino; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    ChemBioChem, 17, 15, 1407, 1411, Aug. 2016, [Peer-reviewed]
    English, Scientific journal
  • Synthesis of chemical-biology tools enabling in vivo imaging and analysis of epigallocatechin gallate
    Tomohiro Asakawa; Atsushi Yoshida; Yasuo Hirooka; Takashi Suzuki; Kunihiko Itoh; Kosuke Shimizu; Naoto Oku; Takumi Furuta; Toshiyuki Wakimoto; Makoto Inai; Toshiyuki Kan
    Heterocycles, 93, 1, 218, 242, Apr. 2016, [Peer-reviewed]
    English, Scientific journal
  • Syntheses of methylated catechins and theaflavins using 2-nitrobenzenesulfonyl group to protect and deactivate phenol
    Tomohiro Asakawa; Yusuke Kawabe; Atsushi Yoshida; Yoshiyuki Aihara; Tamiko Manabe; Yoshitsugu Hirose; Asuka Sakurada; Makoto Inai; Yoshitaka Hamashima; Takumi Furuta; Toshiyuki Wakimoto; Toshiyuki Kan
    Journal of Antibiotics, 69, 4, 299, 312, Apr. 2016, [Peer-reviewed]
    English, Scientific journal
  • 複合培養法を用いた新規macrolactam類の単離構造決定
    星野 翔太郎; 岡田 正弘; 張 恵平; 林 文晶; 脇本 敏幸; 尾仲 宏康; 阿部 郁朗
    日本薬学会年会要旨集, 136年会, 2, 112, 112, (公社)日本薬学会, Mar. 2016
    Japanese
  • An Unusual Chimeric Diterpene Synthase from Emericella variecolor and Its Functional Conversion into a Sesterterpene Synthase by Domain Swapping
    Bin Qin; Yudai Matsuda; Takahiro Mori; Masahiro Okada; Zhiyang Quan; Takaaki Mitsuhashi; Toshiyuki Wakimoto; Ikuro Abe
    Angew. Chem. Int. Ed., 55, 5, 1658, 1661, Jan. 2016, [Peer-reviewed]
    English, Scientific journal
  • Calyculin: Nature's way of making the sponge-derived cytotoxin
    Toshiyuki Wakimoto; Yoko Egami; Ikuro Abe
    Natural Product Reports, 33, 6, 751, 760, 2016, [Peer-reviewed]
    English
  • Niizalactams A-C, Multicyclic Macrolactams Isolated from Combined Culture of Streptomyces with Mycolic Acid-Containing Bacterium
    Shotaro Hoshino; Masahiro Okada; Toshiyuki Wakirnoto; Huiping Zhang; Fumiaki Hayashi; Hiroyasu Onaka; Ikuro Abe
    Journal of Natural Products, 78, 12, 3011, 3017, Dec. 2015, [Peer-reviewed]
    English, Scientific journal
  • Dietziamides, novel tetramic acid dimers from Dietzia timorensis MZ-3 with antioxidative activity
    Shotaro Hoshino; Toshiyuki Wakimoto; Huiping Zhang; Fumiaki Hayashi; Masahiro Okada; Ikuro Abe
    Bioorganic & Medicinal Chemistry Letters, 25, 18, 3953, 3955, Sep. 2015, [Peer-reviewed]
    English, Scientific journal
  • Structural Basis for beta-Carboline Alkaloid Production by the Microbial Homodimeric Enzyme McbB
    Takahiro Mori; Shotaro Hoshino; Shusaku Sahashi; Toshiyuki Wakimoto; Takashi Matsui; Hiroyuki Morita; Ikuro Abe
    CHEMISTRY & BIOLOGY, 22, 7, 898, 906, Jul. 2015, [Peer-reviewed]
    English, Scientific journal
  • Arcyriaflavin E, a new cytotoxic indolocarbazole alkaloid isolated by combined-culture of mycolic acid-containing bacteria and Streptomyces cinnamoneus NBRC 13823
    Shotaro Hoshino; Lihan Zhang; Takayoshi Awakawa; Toshiyuki Wakimoto; Hiroyasu Onaka; Ikuro Abe
    Journal of Antibiotics, 68, 5, 342, 344, May 2015, [Peer-reviewed]
    English, Scientific journal
  • Uncovering the Unusual D-Ring Construction in Terretonin Biosynthesis by Collaboration of a Multifunctional Cytochrome P450 and a Unique Isomerase
    Yudai Matsuda; Taiki Iwabuchi; Toshiyuki Wakimoto; Takayoshi Awakawa; Ikuro Abe
    Journal of the American Chemical Society, 137, 9, 3393, 3401, Mar. 2015, [Peer-reviewed]
    English, Scientific journal
  • Chojalactones A-C, Cytotoxic Butanolides Isolated from Streptomyces sp Cultivated with Mycolic Acid Containing Bacterium
    Shotaro Hoshino; Toshiyuki Wakimoto; Hiroyasu Onaka; Ikuro Abe
    Organic Letters, 17, 6, 1501, 1504, Mar. 2015, [Peer-reviewed]
    English, Scientific journal
  • Cytotoxic cyclic peptides from the marine sponges
    Toshiyuki Wakimoto; Karen Co Tan; Hiroki Tajima; Ikuro Abe
    Handbook of Anticancer Drugs from Marine Origin, 113, 144, Springer International Publishing, 01 Jan. 2015, [Peer-reviewed]
    English, In book
  • Production of indole antibiotics induced by exogenous gene derived from sponge metagenomes
    Yuya Takeshige; Yoko Egami; Toshiyuki Wakimoto; Ikuro Abe
    Molecular Biosystems, 11, 5, 1290, 1294, 2015, [Peer-reviewed]
    English, Scientific journal
  • Phosphocalyculin C as a pyrophosphate protoxin of calyculin C in the marine sponge Discodermia calyx
    Yoko Egami; Toshiyuki Wakimoto; Ikuro Abe
    Bioorganic & Medicinal Chemistry Letters, 24, 22, 5150, 5153, Nov. 2014, [Peer-reviewed]
    English, Scientific journal
  • Complete Biosynthetic Pathway of Anditomin: Nature's Sophisticated Synthetic Route to a Complex Fungal Meroterpenoid
    Yudai Matsuda; Toshiyuki Wakimoto; Takahiro Mori; Takayoshi Awakawa; Ikuro Abe
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136, 43, 15326, 15336, Oct. 2014, [Peer-reviewed]
    English, Scientific journal
  • Calyculin biogenesis from a pyrophosphate protoxin produced by a sponge symbiont
    Toshiyuki Wakimoto; Yoko Egami; Yu Nakashima; Yukihiko Wakimoto; Takahiro Mori; Takayoshi Awakawa; Takuya Ito; Hiromichi Kenmoku; Yoshinori Asakawa; Joern Piel; Ikuro Abe
    Nature Chemical Biology, 10, 8, 648, U193, Aug. 2014, [Peer-reviewed]
    English, Scientific journal
  • A Methyltransferase Initiates Terpene Cyclization in Teleocidin B Biosynthesis
    Takayoshi Awakawa; Lihan Zhang; Toshiyuki Wakimoto; Shotaro Hoshino; Takahiro Mori; Takuya Ito; Jun Ishikawa; Martin E. Tanner; Ikuro Abe
    Journal of the American Chemical Society, 136, 28, 9910, 9913, Jul. 2014, [Peer-reviewed]
    English, Scientific journal
  • Three Acyltetronic Acid Derivatives: Noncanonical Cryptic Polyketides from Aspergillus niger Identified by Genome Mining
    Xiao-Long Yang; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    ChemBioChem, 15, 11, 1578, 1583, Jul. 2014, [Peer-reviewed]
    English, Scientific journal
  • ミコール酸含有微生物Tsukamurella pulmonisとの複合培養による、放線菌Streptomyces属由来新規生物活性物質の探索
    星野 翔太郎; 張 驪駻; 淡川 孝義; 脇本 敏幸; 尾仲 宏康; 阿部 郁朗
    日本放線菌学会大会講演要旨集, 29回, 48, 48, 日本放線菌学会, Jun. 2014
    Japanese
  • Lipodiscamides A-C, New Cytotoxic Lipopeptides from Discodermia kiiensis
    Karen Co Tan; Toshiyuki Wakimoto; Ikuro Abe
    Organic Letters, 16, 12, 3256, 3259, Jun. 2014, [Peer-reviewed]
    English, Scientific journal
  • An environmental bacterial taxon with a large and distinct metabolic repertoire (vol 506, pg 58, 2014)
    Micheal C. Wilson; Tetsushi Mori; Christian Rueckert; Agustinus R. Uria; Maximilian J. Helf; Kentaro Takada; Christine Gernert; Ursula A. E. Steffens; Nina Heycke; Susanne Schmitt; Christian Rinke; Eric J. N. Helfrich; Alexander O. Brachmann; Cristian Gurgui; Toshiyuki Wakimoto; Matthias Kracht; Max Cruesemann; Ute Hentschel; Ikuro Abe; Shigeki Matsunaga; Joern Kalinowski; Haruko Takeyama; Joern Piel
    Nature, 507, 7491, Mar. 2014, [Peer-reviewed]
    English
  • Enantioselective Synthesis of SB-203207
    Yasuo Hirooka; Kazutada Ikeuchi; Yuichiro Kawamoto; Yusuke Akao; Takumi Furuta; Tomohiro Asakawa; Makoto Inai; Toshiyuki Wakimoto; Tohru Fukuyama; Toshiyuki Kan
    Organic Letters, 16, 6, 1646, 1649, Mar. 2014, [Peer-reviewed]
    English, Scientific journal
  • An environmental bacterial taxon with a large and distinct metabolic repertoire
    Micheal C. Wilson; Tetsushi Mori; Christian Rueckert; Agustinus R. Uria; Maximilian J. Helf; Kentaro Takada; Christine Gernert; Ursula A. E. Steffens; Nina Heycke; Susanne Schmitt; Christian Rinke; Eric J. N. Helfrich; Alexander O. Brachmann; Cristian Gurgui; Toshiyuki Wakimoto; Matthias Kracht; Max Cruesemann; Ute Hentschel; Ikuro Abe; Shigeki Matsunaga; Joern Kalinowski; Haruko Takeyama; Joern Piel
    Nature, 506, 7486, 58, +, Feb. 2014, [Peer-reviewed]
    English, Scientific journal
  • Erratum: An environmental bacterial taxon with a large and distinct metabolic repertoire (Nature (2014) 506 (58-62) DOI: 10.1038/nature12959))
    Micheal C. Wilson; Tetsushi Mori; Christian Rückert; Agustinus R. Uria; Maximilian J. Helf; Kentaro Takada; Christine Gernert; Ursula A E Steffens; Nina Heycke; Susanne Schmitt; Christian Rinke; Eric J N Helfrich; Alexander O. Brachmann; Cristian Gurgui; Toshiyuki Wakimoto; Matthias Kracht; Max Crüsemann; Ute Hentschel; Ikuro Abe; Shigeki Matsunaga; Jörn Kalinowski; Haruko Takeyama; Jörn Piel
    Nature, 507, 262, 01 Jan. 2014
  • Revised Structure of Cyclolithistide A, a Cyclic Depsipeptide from the Marine Sponge Discodermia japonica
    Hiroki Tajima; Toshiyuki Wakimoto; Kentaro Takada; Yuji Ise; Ikuro Abe
    Journal of Natural Products, 77, 1, 154, 158, Jan. 2014, [Peer-reviewed]
    English, Scientific journal
  • Pyranonigrin E: A PKS-NRPS Hybrid Metabolite from Aspergillus niger Identified by Genome Mining
    Takayoshi Awakawa; Xiao-Long Yang; Toshiyuki Wakimoto; Ikuro Abe
    ChemBioChem, 14, 16, 2095, 2099, Nov. 2013, [Peer-reviewed]
    English, Scientific journal
  • Induced production of novel prenyldepside and coumarins in endophytic fungi Pestalotiopsis acaciae
    Xiao-Long Yang; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    Tetrahedron Letters, 54, 43, 5814, 5817, Oct. 2013, [Peer-reviewed]
    English, Scientific journal
  • Ergot alkaloid from the sea slug Pleurobranchus forskalii
    Toshiyuki Wakimoto; Karen Co Tan; Ikuro Abe
    Toxicon, 72, 1, 4, Sep. 2013, [Peer-reviewed]
    English, Scientific journal
  • Induced biosyntheses of a novel butyrophenone and two aromatic polyketides in the plant pathogen Stagonospora nodorum
    Xiao Long Yang; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    Natural Products and Bioprospecting, 3, 4, 141, 144, 01 Aug. 2013
    Scientific journal
  • Cycloforskamide, a cytotoxic macrocyclic peptide from the sea slug Pleurobranchus forskalii
    Karen Co Tan; Toshiyuki Wakimoto; Kentaro Takada; Takashi Ohtsuki; Nahoko Uchiyama; Yukihiro Goda; Ikuro Abe
    Journal of Natural Products, 76, 7, 1388, 1391, 26 Jul. 2013, [Peer-reviewed]
    English, Scientific journal
  • Induced production of the novel glycolipid ustilagic acid C in the plant pathogen Ustilago maydis
    Xiao-Long Yang; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    Tetrahedron Letters, 54, 28, 3655, 3657, 10 Jul. 2013, [Peer-reviewed]
    English, Scientific journal
  • Indole-porphyrin hybrids produced by metagenomics
    Xiao-Long Yang; Toshiyuki Wakimoto; Yuya Takeshige; Rui He; Yoko Egami; Takayoshi Awakawa; Ikuro Abe
    Bioorganic & Medicinal Chemistry Letters, 23, 13, 3810, 3813, Jul. 2013, [Peer-reviewed]
    English, Scientific journal
  • Spiro-Ring Formation is Catalyzed by a Multifunctional Dioxygenase in Austinol Biosynthesis
    Yudai Matsuda; Takayoshi Awakawa; Toshiyuki Wakimoto; Ikuro Abe
    Journal of the American Chemical Society, 135, 30, 10962, 10965, Jul. 2013, [Peer-reviewed]
    English, Scientific journal
  • Epigenetic modifier-induced biosynthesis of novel fusaric acid derivatives in endophytic fungi from Datura stramonium L.
    Han Jing Chen; Takayoshi Awakawa; Jie Yin Sun; Toshiyuki Wakimoto; Ikuro Abe
    Natural Products and Bioprospecting, 3, 1, 20, 23, 01 Feb. 2013
    Scientific journal
  • Allos-hemicalyculin A, a photochemically converted calyculin from the marine sponge Discodermia calyx
    Miki Kimura; Toshiyuki Wakimoto; Ikuro Abe
    Tetrahedron Letters, 54, 1, 114, 116, Jan. 2013, [Peer-reviewed]
    English, Scientific journal
  • Cyclodipeptides from metagenomic library of a Japanese marine sponge
    Rui He; Bochu Wang; Toshiyuki Wakimoto; Manyuan Wang; Liancai Zhu; Ikuro Abe
    Journal of the Brazilian Chemical Society, 24, 12, 1926, 1932, 2013, [Peer-reviewed]
    English, International conference proceedings
  • Stereocontrolled Total Synthesis of (-)-FR901483
    Shigeru Ieda; Akitaka Masuda; Mami Kariyama; Toshiyuki Wakimoto; Tomohiro Asakawa; Tohru Fukuyama; Toshiyuki Kan
    Heterocycles, 86, 2, 1071, 1092, Dec. 2012, [Peer-reviewed]
    English, Scientific journal
  • Heterologously expressed beta-hydroxyl fatty acids from a metagenomic library of a marine sponge
    Rui He; Toshiyuki Wakimoto; Yoko Egami; Hiromichi Kenmoku; Takuya Ito; Yoshinori Asakawa; Ikuro Abe
    BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 22, 24, 7322, 7325, Dec. 2012, [Peer-reviewed]
    English, Scientific journal
  • Whiskey Congeners Suppress LPS/IFN gamma-Induced NO Production in Murine Macrophage RAW 264 Cells by Inducing Heme Oxygenase-1 Expression
    Tomohiro Itoh; Masashi Ando; Yasuyuki Tsukamasa; Toshiyuki Wakimoto; Haruo Nukaya
    JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 60, 51, 12491, 12500, Dec. 2012, [Peer-reviewed]
    English, Scientific journal
  • Labile natural products
    Toshiyuki Wakimoto; Ikuro Abe
    MedChemComm, 3, 8, 866, 870, Aug. 2012, [Peer-reviewed]
    English
  • Terretonin Biosynthesis Requires Methylation as Essential Step for Cyclization
    Yudai Matsuda; Takayoshi Awakawa; Takayuki Itoh; Toshiyuki Wakimoto; Tetsuo Kushiro; Isao Fujii; Yutaka Ebizuka; Ikuro Abe
    ChemBioChem, 13, 12, 1738, 1741, Aug. 2012, [Peer-reviewed]
    English, Scientific journal
  • A heptaketide naphthaldehyde produced by a polyketide synthase from Nectria haematococca
    Takayoshi Awakawa; Takuya Kaji; Toshiyuki Wakimoto; Ikuro Abe
    Bioorganic & Medicinal Chemistry Letters, 22, 13, 4338, 4340, Jul. 2012, [Peer-reviewed]
    English, Scientific journal
  • Prenylation of a Nonaromatic Carbon of Indolylbutenone by a Fungal Indole Prenyltransferase
    Jing Chen; Hiroyuki Morita; Toshiyuki Wakimoto; Takahiro Mori; Hiroshi Noguchi; Ikuro Abe
    Organic Letters, 14, 12, 3080, 3083, Jun. 2012, [Peer-reviewed]
    English, Scientific journal
  • Calyxamides A and B, Cytotoxic Cyclic Peptides from the Marine Sponge Discodermia calyx
    Miki Kimura; Toshiyuki Wakimoto; Yoko Egami; Karen Co Tan; Yuji Ise; Ikuro Abe
    Journal of Natural Products, 75, 2, 290, 294, Feb. 2012, [Peer-reviewed]
    English, Scientific journal
  • Porphyrins from a metagenomic library of the marine sponge Discodermia calyx
    Rui He; Toshiyuki Wakimoto; Yuya Takeshige; Yoko Egami; Hiromichi Kenmoku; Takuya Ito; Bochu Wang; Yoshinori Asakawa; Ikuro Abe
    Molecular Biosystems, 8, 9, 2334, 2338, 2012, [Peer-reviewed]
    English, Scientific journal
  • Engineering of Plant Type III Polyketide Synthases
    Toshiyuki Wakimoto; Hiroyuki Morita; Ikuro Abe
    Natural Product Biosynthesis by Microorganisms and Plants, Part A, 515, 337, 358, 2012, [Peer-reviewed]
    English, In book
  • Stereocontrolled Total Synthesis of (+)-UCS1025A
    Kenji Uchida; Takahiro Ogawa; Yoshinori Yasuda; Hiraku Mimura; Teppei Fujimoto; Tohru Fukuyama; Toshiyuki Wakimoto; Tomohiro Asakawa; Yoshitaka Hamashima; Toshiyuki Kan
    Angew. Chem. Int. Ed., 51, 51, 12850, 12853, 2012, [Peer-reviewed]
    English, Scientific journal
  • Furan fatty acid as an anti-inflammatory component from the green-lipped mussel Perna canaliculus
    Toshiyuki Wakimoto; Hikaru Kondo; Hirohiko Nii; Kaori Kimura; Yoko Egami; Yusuke Oka; Masae Yoshida; Eri Kida; Yiping Ye; Saeko Akahoshi; Tomohiro Asakaw; Koichi Matsumura; Hitoshi Ishida; Haruo Nukaya; Kuniro Tsuji; Toshiyuki Kan; Ikuro Abe
    Proc. Natl. Acad. Sci. USA, 108, 42, 17533, 17537, Oct. 2011, [Peer-reviewed]
    English, Scientific journal
  • 16 Enzymatic Synthesis of Unnatural Novel Biologically Active Compounds by Engineered Plant Polyketide Synthases(Oral Presentation)
    Morita Hiroyuki; Mori Takahiro; Yamashita Makoto; Wakimoto Toshiyuki; Abe Ikuro
    Symposium on the Chemistry of Natural Products, symposium papers, 53, 91, 96, Symposium on the chemistry of natural products, 02 Sep. 2011
    Japanese, HsPKS1 from Huperzia serrata is a type III polyketide synthase (PKS) with remarkable substrate tolerance and catalytic potential. Here we present the synthesis of unnatural novel polyketide-alkaloid hybrid molecules by exploiting the enzyme reaction using precursor-directed and structure-based approaches. HsPKS1 produced novel pyridoisoindole (or benzopyridoisoindole) with the 6.5.6-fused (or 6.6.5.6-fused) ring system by the condensation of 2-carbamoylbenzoyl-CoA (or 3-carbamoyl-2-naphthoyl-CoA), a synthetic nitrogen-containing non-physiological starter substrate, with two molecules of malonyl-CoA. The structure-based S348G mutant not only extended the product chain length, but also altered the cyclization mechanism to produce a biologically active, ring-expanded 6.7.6-fused dibenzoazepine, by the condensation of 2-carbamoylbenzoyl-CoA with three malonyl-CoAs. Thus, the basic nitrogen atom and the structure-based mutagenesis enabled additional C-C and C-N bond formation to generate the novel polyketide-alkaloid scaffold. Benzalacetone synthase (BAS) from Rheum palmatum is a structurally simple, plant-specific type III PKS, which catalyzes the one-step decarboxylative condensation of malonyl-CoA with 4-coumaroyl-CoA. The type III PKS exhibits unusually broad substrate specificity and notable catalytic versatility. Here we report that R. palmatum BAS efficiently produces a series of unnatural, novel tetramic acid derivatives by the condensation of malonyl-CoA with aminoacyl-CoA thioesters, chemically synthesized from L- and D-amino acids. Remarkably, the novel tetramic acid dimer from D-phenylalanoyl-CoA, showed moderate antiproliferative activity against murine leukemia P388 cells.
  • Synthesis of unnatural alkaloid scaffolds by exploiting plant polyketide synthase
    Hiroyuki Morita; Makoto Yamashita; She-Po Shi; Toshiyuki Wakimoto; Shin Kondo; Ryohei Kato; Shigetoshi Sugio; Toshiyuki Kohno; Ikuro Abe
    Proc. Natl. Acad. Sci. USA, 108, 33, 13504, 13509, Aug. 2011, [Peer-reviewed]
    English, Scientific journal
  • Enantioselective Total Synthesis of Aperidine
    Toshiyuki Wakimoto; Kakeru Miyata; Hitoshi Ohuchi; Tomohiro Asakawa; Haruo Nukaya; Yoshihide Suwa; Toshiyuki Kan
    Organic Letters, 13, 10, 2789, 2791, May 2011, [Peer-reviewed]
    English, Scientific journal
  • Cytotoxic Tetramic Acid Derivative Produced by a Plant Type-III Polyketide Synthase
    Toshiyuki Wakimoto; Takahiro Mori; Hiroyuki Morita; Ikuro Abe
    Journal of the American Chemical Society, 133, 13, 4746, 4749, Apr. 2011, [Peer-reviewed]
    English, Scientific journal
  • Stereocontrolled Synthesis of (+)-Methoxyphenylkainic Acid and (+)-Phenylkainic Acid
    Takumi Higashi; Yoichiro Isobe; Hitoshi Ouchi; Hiroto Suzuki; Yuko Okazaki; Tomohiro Asakawa; Takumi Furuta; Toshiyuki Wakimoto; Toshiyuki Kan
    Organic Letters, 13, 5, 1089, 1091, Mar. 2011, [Peer-reviewed]
    English, Scientific journal
  • Proof of the Existence of an Unstable Amino Acid: Pleurocybellaziridine in Pleurocybella porrigens
    Toshiyuki Wakimoto; Tomohiro Asakawa; Saeko Akahoshi; Tomohiro Suzuki; Kaoru Nagai; Hirokazu Kawagishi; Toshiyuki Kan
    Angew. Chem. Int. Ed., 50, 5, 1168, 1170, 2011, [Peer-reviewed]
    English, Scientific journal
  • Concise synthesis of catechin probes enabling analysis and imaging of EGCg
    Atsushi Yoshida; Yasuo Hirooka; Yusuke Sugata; Mariko Nitta; Tamiko Manabe; Shunsuke Ido; Kouki Murakami; Repon Kumer Saha; Takashi Suzuki; Motohiro Ohshima; Akira Yoshida; Kunihiko Itoh; Kosuke Shimizu; Naoto Oku; Takumi Furuta; Tomohiro Asakawa; Toshiyuki Wakimoto; Toshiyuki Kan
    Chemical Communications, 47, 6, 1794, 1796, 2011, [Peer-reviewed]
    English, Scientific journal
  • PET imaging of nobiletin based on a practical total synthesis
    Tomohiro Asakawa; Aiki Hiza; Miho Nakayama; Makoto Inai; Dai Oyama; Hiroyuki Koide; Kosuke Shimizu; Toshiyuki Wakimoto; Norihiro Harada; Hideo Tsukada; Naoto Oku; Toshiyuki Kan
    Chemical Communications, 47, 10, 2868, 2870, 2011, [Peer-reviewed]
    English, Scientific journal
  • Proof of the Existence of an Unstable Amino Acid: Pleurocybellaziridine in Pleurocybella porrigens
    Toshiyuki Wakimoto; Tomohiro Asakawa; Saeko Akahoshi; Tomohiro Suzuki; Kaoru Nagai; Hirokazu Kawagishi; Toshiyuki Kan
    Angewandte Chemie, 123, 5, 1200, 1202, Wiley, 23 Dec. 2010
  • Search for toxic compounds from the mushroom Pleurocybella porrigens
    Suzuki Tomohiro; Fujita Motohiro; Amano Yuko; Asakawa Tomohiro; Akahoshi Saeko; Wakimoto Toshiyuki; Kobayashi Yuka; Morita Tatsuya; Arai Nobutaka; Nagai Kaoru; Tanaka Shigeyasu; Hirai Hirofumi; Kan Toshiyuki; Kawagishi Hirokazu
    Symposium on the Chemistry of Natural Products, symposium papers, 52, 655, 660, Symposium on the chemistry of natural products, 01 Sep. 2010
    Japanese, The mushroom Pleurocybela porrigens (Angel's wings in English; Sugihiratake in Japanese) is widespread and common throughout temperate regions of the world. It has been eaten for a lng time all over the world. However, in autumn 2004 in Japan, fifty-five people got poisoned by eating this mushroom, and seventeen peoplel among them died of acute encephalopaty. There had been no report regarding toxocity of the fruiting bodies until the incident. Under these circumstances, we tried to isolate teh principle(s) of the disease. Purification of a glycoprotein showing lethal activity against mouse The mushroom was extracted with water and boiling water. After repeated chromatography of the water-soluble fractions, a glycoprotein was purified. The substance showed lethal toxocity toward mice at a dose of 24mg/kg (i.p.). Purification, characterization, and cDNA cloning of a lectin (PPL) PPL was purified from this mushroom. The results of SDS-PAGE gel filtration and MALDI-TOF-mass of PPL indicated that its molecular mass was 56kDa, and it was composed of four 14kDa subunits with no disulfide bonds. The complete amino acid sequence was determined by amino acid sequencing. The cDNA of PPL was cloned from RNA extracted from the mushroom. The open reading frame of the cDNA of the protein consisted of 411 bp encoding 137 amino acids. Intravenous (i.v.) (50mg/kg) or intraperitoneal (i.p.) (150mg/kg) administration of PPL to mice did not show any toxocity. However, i.v. (9mg/kg) administration of the protein to rats exhibited lethal toxocity. Purification of unusual amino acids showing cytotoxicity against mouse cerebrum glial cells Six amino acid derivatives (1-6) including three novel ones (1-3) were isolated from the mushroom. These compounds were cytotoxic to mouse glial cells. The structural novelty and analogy of the amino acids is such that each acid has the β-hydroxyvaline unit adducted to endogenous molecules, which inspired us to conclude the occurrence of an aziridine-amino acid (7) as the common precursor of the six compounds. We synthesized this compound and proved its occurrence in this mushroom. Compound 7 showed toxocity against rat CG4-16 oligodendrocyte cells; 7 significantly reduced the cell viability at concentrations up to 10μg/ml (87μM). Mechanism of the acute encephalopathy We found that a mixture of the letnal glycoprotein and PPL showed protease activity and disrupted the blood-brain barrier (BBB) in mice. We speculated that compound 7 or its derivatives caused demyelinating symptom after disruption of BBB. Verfication of the hypothesis is now on progress.
  • Structure Function Studies on Coumaroyl-CoA Ligase
    Wanibuchi Kiyofumi; Mori Takahiro; Niwano Tomoko; Zhang Gang; Wakimoto Toshiyuki; Morita Hiroyuki; Abe Ikuro
    Symposium on the Chemistry of Natural Products, symposium papers, 52, 55, 60, Symposium on the chemistry of natural products, 01 Sep. 2010
    Japanese, 4-Coumareate:coenzyme A ligase (4CL) plays a key role in phenylpropanoid metabilism, providing precursors for a variety of plant secondary metabolites such as flavonoids and lignin. The enzyme catalyzes formation of 4-coumaroyl-CoA by initial activation of 4-coumaric acid with ATP to form an acyl-AMP intermediate, which is followed by thioester bond formation with CoASH and the concomitant release of AMP. The activation of the carboxylate substrate with ATP to form the acyl-AMP intermediate is a common mechanism for other adenylate-forming enzymes, including fatty acyl-CoA synthetase, the adenylation domains of the modular non-ribosomal peptide synthetase, and firefly luciferase (the ANL superfamily enzymes). Here we report that 4CL from Arabiaopsis thaliana (At4CL2) shows remarkable substrate promiscuity and novel catalytic functions. First, it was demonstrated that, in the absence of CoASH, the enzyme catalyzed amide bond forming reactions by condensation of 4-coumaric acid and the amino group fo D- and L- amino acids. Second, the enzyme generated a variety of biologically active amides including homoserine lactones and capsaicin by coupling the corresponding acids and amines. Finally, unexpectedly, structure-based 4CL site-directed mutants, Y253F and Q345A, catalyzed formation of dipeptides from a series of amino acids in the presence of ATP. Thus, the CoA ligase was functionally converted to dipeptide synthetase by the single amino acid substitutions in the substrate binding pocket.
  • Structural characteristics of green tea catechins for formation of protein carbonyl in human serum albumin
    Takeshi Ishii; Taiki Mori; Tatsuya Ichikawa; Maiko Kaku; Koji Kusaka; Yoshinori Uekusa; Mitsugu Akagawa; Yoshiyuki Aihara; Takumi Furuta; Toshiyuki Wakimoto; Toshiyuki Kan; Tsutomu Nakayama
    Bioorganic and Medicinal Chemistry, 18, 14, 4892, 4896, Jul. 2010, [Peer-reviewed]
    English, Scientific journal
  • Binding affinity of tea catechins for HSA: Characterization by high-performance affinity chromatography with immobilized albumin column
    Takeshi Ishii; Kanako Minoda; Min-Jung Bae; Taiki Mori; Yoshinori Uekusa; Tatsuya Ichikawa; Yoshiyuki Aihara; Takumi Furuta; Toshiyuki Wakimoto; Toshiyuki Kan; Tsutomu Nakayama
    Molecular Nutrition & Food Research, 54, 6, 816, 822, Jun. 2010, [Peer-reviewed]
    English, Scientific journal
  • Inhibitory Effects of Whisky Congeners on IgE-Mediated Degranulation in Rat Basophilic Leukemia RBL-2H3 Cells and Passive Cutaneous Anaphylaxis Reaction in Mice
    Tomohiro Itoh; Mariko Tsukane; Minako Koike; Chizu Nakamura; Kenji Ohguchi; Masafumi Ito; Yukihiro Akao; Sehchi Koshimizu; Yoshinori Nozawa; Toshiyuki Wakimoto; Haruo Nukaya; Yoshihide Suwa
    Journal of Agricultural and Food Chemistry, 58, 12, 7149, 7157, Jun. 2010, [Peer-reviewed]
    English, Scientific journal
  • Modified Julia-Kocienski Reaction Promoted by Means of m-NPT (Nitrophenyltetrazole) Sulfone
    Yuki Sakai; Kazutada Ikeuchi; Yuji Yamada; Toshiyuki Wakimoto; Toshiyuki Kan
    Synlett, 5, 827, 829, Mar. 2010, [Peer-reviewed]
    English, Scientific journal
  • Solid-Supported Synthesis of Artificial Phospholipids
    Takumi Furuta; Hitoshi Onuki; Masayoshi Mochizuki; Mai Ito; Makoto Inai; Toshiyuki Wakimoto; Toshiyuki Kan
    Synlett, 20, 3373, 3377, Dec. 2009, [Peer-reviewed]
    English, Scientific journal
  • Structure-activity relationship study on alpha(1) adrenergic receptor antagonists from beer
    Toshiyuki Wakimoto; Makoto Nitta; Kana Kasahara; Taketo Chiba; Ye Yiping; Kuniro Tsuji; Toshiyuki Kan; Haruo Nukaya; Masaji Ishiguro; Minako Koike; Yoshiaki Yokoo; Yoshihide Suwa
    BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 19, 20, 5905, 5908, Oct. 2009, [Peer-reviewed]
    English, Scientific journal
  • Formation Mechanism of Chafuroside A and B, Novel Anti-inflammatory Flavone C-Glycosides in Oolong Tealeaves
    Ishida Hitoshi; Wakimoto Toshiyuki; Nukaya Haruo
    Symposium on the Chemistry of Natural Products, symposium papers, 51, 521, 526, Symposium on the chemistry of natural products, 01 Sep. 2009
    Japanese, A procedure was developed for quantitative determination of chafuroside A1, a flavone C-glycoside with potent anti-inflammatory activity, and its regioisomer chafuroside B2, as well as isovitexin and vitexin, by selected reaction monitoring liquid chromatography-tandem mass spectrometry analysis. This method was successfully applied to commercial leaves of green tea, houji tea, oolong tea and black tea. High levels of chafuroside A and chafutoside B were found in oolong tea leaves that had been heated at over 140℃. Next, their precursors, prechafuroside A and prechafuroside B, were isolated frommethanol extract of oolong tea leaves prepared from Shizu 7132, Camellia sinensis (L.) O. Kuntze, by partiton with n-butanol and H_2O and chromatography on Diaion SP-825, Sephadex LH-20, and ODS C-18, guided by assay of chafuroside formation. Prechafuroside A and prechafutoside B gave chafuroside A and Chafuroside B, respectively, in good yields when heated at 160℃ for 0.5h. Hydrolysis of prechafuroside A and prechafuroside B with pyridine and dioxane quantitatively afforded isovitexin and vitexin, respectively. Based on these results and physicochemical data (MS, UV and NMR), prechafuroside A and prechafuroside B were concluded to be new flavone C-glycoside sulfates, isovitexin-2"-sulfate 5 and vitexin-2"-sulfate 6, respectively.
  • Regioselective synthesis of methylated epigallocatechin gallate via nitrobenzenesulfonyl (Ns) protecting group
    Yoshiyuki Aihara; Atsusi Yoshida; Takumi Furuta; Toshiyuki Wakimoto; Toshifumi Akizawa; Motomi Konishi; Toshiyuki Kan
    Bioorganic and Medicinal Chemistry Letters, 19, 15, 4171, 4174, Aug. 2009, [Peer-reviewed]
    English, Scientific journal
  • Quantitation of Chafurosides A and B in Tea Leaves and Isolation of Prechafurosides A and B from Oolong Tea Leaves
    Hitoshi Ishida; Toshiyuki Wakimoto; Yukiko Kitao; Shimako Tanaka; Toshio Miyase; Haruo Nukaya
    Journal of Agricultural and Food Chemistry, 57, 15, 6779, 6786, Aug. 2009, [Peer-reviewed]
    English, Scientific journal
  • Concise Synthesis of Chafurosides A and B
    Takumi Furuta; Miho Nakayama; Hirotaka Suzuki; Hiroko Tajimi; Makoto Inai; Haruo Nukaya; Toshiyuki Wakimoto; Toshiyuki Kan
    Organic Letters, 11, 11, 2233, 2236, Jun. 2009, [Peer-reviewed]
    English, Scientific journal
  • Stereocontrolled total synthesis of (-)-myriocin
    Makoto Inai; Toshihiro Goto; Takumi Furuta; Toshiyuki Wakimoto; Toshiyuki Kan
    Tetrahedron: Asymmetry, 19, 24, 2771, 2773, Dec. 2008, [Peer-reviewed]
    English, Scientific journal
  • Total Synthesis of (-)-Serotobenine
    Yasuaki Koizumi; Hideki Kobayashi; Toshiyuki Wakimoto; Takumi Furuta; Tohru Fukuyama; Toshiyuki Kan
    Journal of the American Chemical Society, 130, 50, 16854, +, Dec. 2008, [Peer-reviewed]
    English, Scientific journal
  • Isolation and identification of bioactive principles in beer
    Haruo Nukaya; Toshiyuki Wakimoto; Yoshiaki Yokoo; Yoshihide Suwa
    Yakugaku Zasshi, 127, 55, 57, 2007, [Peer-reviewed]
    Japanese, Scientific journal
  • Structural determination of two active compounds that bind to the muscarinic M-3 receptor in beer
    Nahoko Yamaji; Yoshiaki Yokoo; Takashi Iwashita; Asuka Nemoto; Minako Koike; Yoshihide Suwa; Toshiyuki Wakimoto; Kuniro Tsuji; Haruo Nukaya
    Alcoholism: Clinical and Experimental Research, 31, 9S, 14S, Jan. 2007, [Peer-reviewed]
    English, Scientific journal
  • Concise total synthesis of flavone C-glycoside having potent anti-inflammatory activity
    T Furuta; T Kimura; S Kondo; H Mihara; T Wakimoto; H Nukaya; K Tsuji; K Tanaka
    Tetrahedron, 60, 42, 9375, 9379, Oct. 2004, [Peer-reviewed]
    English, Scientific journal
  • Erratum: Crystal structure of the complex between calyculin A and the catalytic subunit of protein phosphatase 1 (Structure (May 2002) 10 (715-724))
    Akiko Kita; Akiko Kita; Shigeki Matsunaga; Shigeki Matsunaga; Akira Takai; Akira Takai; Hirotaka Kataiwa; Hirotaka Kataiwa; Toshiyuki Wakimoto; Toshiyuki Wakimoto; Nobuhiro Fusetani; Nobuhiro Fusetani; Minoru Isobe; Minoru Isobe; Kunio Miki; Kunio Miki
    Structure, 10, 1149, 29 Aug. 2002
  • Crystal structure of the complex between calyculin A and the catalytic subunit of protein phosphatase 1
    A Kita; S Matsunaga; A Takai; H Kataiwa; T Wakimoto; N Fusetani; M Isobe; K Miki
    Structure, 10, 5, 715, 724, May 2002, [Peer-reviewed]
    English, Scientific journal
  • Insight into binding of calyculin A to protein phosphatase 1: Isolation of hemicalyculin A and chemical transformation of calyculin A
    Toshiyuki Wakimoto; Shigeki Matsunaga; Akira Takai; Nobuhiro Fusetani
    Chemistry and Biology, 9, 3, 309, 319, 2002, [Peer-reviewed]
    English, Scientific journal
  • The solution structures of calyculin A and dephosphonocalyculin A by NMR.
    KE Volter; GK Pierens; RJ Quinn; T Wakimoto; S Matsunaga; N Fusetani
    Bioorganic & Medicinal Chemistry Letters, 9, 5, 717, 722, Mar. 1999, [Peer-reviewed]
    English, Scientific journal
  • Octa- and nonaprenylhydroquinone sulfates, inhibitors of alpha 1,3-fucosyltransferase VII, from an Australian marine sponge Sarcotragus sp.
    T Wakimoto; A Maruyama; S Matsunaga; N Fusetani; K Shinoda; PT Murphy
    BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 9, 5, 727, 730, Mar. 1999, [Peer-reviewed]
    English, Scientific journal
  • Erratum: Isolation of four new calyculins from the marine sponge Discodermia calyx (Journal of Organic Chemistry (1997) 62 (2640))
    S. Matsunaga; T. Wakimoto; N. Fusetani
    Journal of Organic Chemistry, 62, 9388, 01 Dec. 1997, [Peer-reviewed]
  • 31 Structure and Biological Activity of New Calyculins Isolated from the Marine Sponge Discodermia calyx
    Matsunaga Shigeki; Wakimoto Toshiyuki; Fusetani Nobuhiro
    Symposium on the Chemistry of Natural Products, symposium papers, 39, 181, 186, Symposium on the chemistry of natural products, 20 Jul. 1997
    Japanese, The calyculins [calyculin A (1)], unique polyketides bearing a variety of functionalities isolated from the Japanese marine sponge Discodermia calyx, exhibit antitumor, smooth muscle contractile, and tumor promotion activities, which are most likely to be attributable to inhibition of protein phosphatases 1 and 2A. Eight known calyculins A(1)-H, which differ in the presence or absence of methyl group on C32 and in the geometry of C2-C3 and C6-C7 double bonds, display similar inhibitory activity against protein phosphatases 2A. Further examination of D. calyx extracts led to isolation of five more calyculin derivatives, calyculin J(2), calyculinamide A(3), calyculinamide F(4), des-N-methyl-calyculin A(5), and dephosphonocalyculin A(6). Structures of 2-6 were assigned on the basis of spectral data and chemical transformation. Calyculin J(2) had a bromine atom and an additional tetrahydrofuran ring. The structure including the absolute stereochemistry has been established by chemical transformation of calyculin A. Calyculinamide A(3) was found to have a terminal amide group instead of the nitrite in 1 by analysis of spectral data. This was further substantiated by hydrolysis of 1. Dephosphonocalyculin A (6) behaved a more polar compound than other calyculins in both normal phase and reversed phase chromatographies. The FAB mass spectrum exhibited an (M+H)^+ ion at m/z929, 80 units smaller than that of calyculin A, whereas the gross structure of 6, which was identical with that of 1 except for the phosphate ester on the C17 oxygen function, was easily assigned on the basis of the COSY, HMQC, and HMBC spectra. The structure including the absolute stereochemistry has been confirmed by chemical transformation of 6 and 1 to a common compound. Compounds 3, 4, 6 showed inhibitory activity against protein phosphatase 2A similar to that of calyculin A. However, IC_<50> values of 2 and 5 were 100 and 150 times higher than that of calyculin A.
  • Isolation of dephosphonocalyculin A from the marine sponge, Discodermia calyx
    S Matsunaga; T Wakimoto; N Fusetani; M Suganuma
    Tetrahedron Letters, 38, 21, 3763, 3764, May 1997, [Peer-reviewed]
    English, Scientific journal
  • Isolation of four new calyculins from the marine sponge Discodermia calyx
    S. Matsunaga; T. Wakimoto; N. Fusetani
    Journal of Organic Chemistry, 62, 8, 2640, 2642, 1997, [Peer-reviewed]
    English, Scientific journal
■ Other Activities and Achievements
■ Books and other publications
■ Syllabus
  • 卒業研究準備実習Ⅰ, 2024年, 学士課程, 薬学部
  • 生命医薬科学概論, 2024年, 修士課程, 生命科学院
  • 卒業研究準備実習Ⅱ, 2024年, 学士課程, 薬学部
  • 天然物化学特論, 2024年, 修士課程, 生命科学院
  • 薬学論文講読演習Ⅰ, 2024年, 学士課程, 薬学部
  • 薬学英語Ⅱ, 2024年, 学士課程, 薬学部
  • 薬学論文講読演習Ⅱ, 2024年, 学士課程, 薬学部
  • 有機構造解析, 2024年, 学士課程, 薬学部
  • 薬学論文講読演習Ⅲ, 2024年, 学士課程, 薬学部
  • 機器分析学, 2024年, 学士課程, 薬学部
  • 薬学総合演習, 2024年, 学士課程, 薬学部
  • 生薬学・漢方医学, 2024年, 学士課程, 薬学部
  • 薬学卒業研究, 2024年, 学士課程, 薬学部
  • 天然物化学, 2024年, 学士課程, 薬学部
  • 薬科学演習, 2024年, 学士課程, 薬学部
  • 薬科学論文講読演習, 2024年, 学士課程, 薬学部
  • 薬科学卒業研究, 2024年, 学士課程, 薬学部
  • 生命科学研究, 2024年, 修士課程, 生命科学院
  • 生命科学実習, 2024年, 修士課程, 生命科学院
  • 生命科学論文講読Ⅰ, 2024年, 修士課程, 生命科学院
  • 生命科学論文講読Ⅱ, 2024年, 修士課程, 生命科学院
  • 生命科学特別研究, 2024年, 博士後期課程, 生命科学院
  • 生命科学文献講読, 2024年, 博士後期課程, 生命科学院
■ Research Themes
  • Molecules that regulates mating behavior of crustaceans: diversity of pheromones and their functions
    Grants-in-Aid for Scientific Research
    01 Apr. 2023 - 31 Mar. 2027
    神尾 道也; 脇本 敏幸; 和田 哲; 千葉 晋; 山家 秀信
    2023年度は実験設備の整備を含んだ研究全体の準備を行った。クリガニに関しては5月に北海道大学臼尻実験所にて採集を行い、十分な数の脱皮前メスとそれをを抱いたオスの交尾前ガードペア、脱皮後交尾し交尾栓を持ちながら単独で歩行する交尾後メス、そして単独のオスを捕獲した。これらを実験所にて一時飼育しながら採尿を行い、オス尿約300ml、メス尿約1300mlを採取し、求愛フェロモン精製を開始するための十分な試料を得た。この試料を、脱塩装置で処理した。さらに、東京海洋大学品川キャンパスに冷却水槽を増設し、飼育可能数を拡充した。この飼育設備を用いて飼育したオスを用いて、抱卵メス尿の活性試験、NAGLの活性試験を行った。また、交尾済みのメスも品川にて飼育し、産卵、抱卵させ、抱卵メスの尿を採集した。東京農業大学オホーツクキャンパスにも冷却器を備えた飼育施設を設置しクリガニとトゲクリガニ間の種特異性を検証するための行動実験の準備を整えた。
    タラバエビ類の研究においては、研究用水槽システムの構築とフェロモンに対する反応を観察するための行動実験の条件検討を行った。
    ヤドカリ類においては、行動実験用設備の構築と、それを用いたフェロモン検出のための行動実験の条件検討、フェロモンを用いた個体間の相互作用の観察を行った。
    フェロモンの生合成酵素を探索するための基盤として、クリガニの求愛フェロモン産生器官と考えられているメスの触覚腺の摘出法の検討を行った。また、交尾フェロモン放出期間と考えられている鰓周辺の解剖と、分別方法の検討を進めた。
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Tokyo University of Marine Science and Technology, 23K27002
  • 予知生合成科学・研究総括班
    科学研究費助成事業
    16 Jun. 2022 - 31 Mar. 2027
    葛山 智久; 内山 真伸; 丸山 千登勢; 寺田 透; 渡辺 賢二; 勝山 陽平; 山崎 真巳; 脇本 敏幸; 大栗 博毅; 淡川 孝義; 荘司 長三
    日本学術振興会, 学術変革領域研究(A), 東京大学, 22H05119
  • 新規ペプチド修飾酵素の機能拡張による大環状複雑骨格の創出
    Grants-in-Aid for Scientific Research Grant-in-Aid for Transformative Research Areas (A)
    Jun. 2022 - Mar. 2027
    脇本 敏幸; 松田 研一
    Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), Hokkaido University, 22H05128
  • 化学酵素合成法を用いた環状ペプチド農薬の開発
    2024 - 2026
    脇本 敏幸
    農産物の安定供給の維持において農薬は重要な役割を果たしてきた。一方で、農薬使用量の増加に伴い、潜在的な健康被害や環境負荷の問題が顕在化しており、特に欧米において既存農薬の使用規制の強化が進んでいる。そのため、効果の持続性と生分解性を兼ね備えた次世代農薬の開発が世界的な急務となっている。そこで、本研究課題では新たな農薬モダリティとして環状ペプチドを活用することで、これらの課題の克服を目指す。独自に構築した環状ペプチドの効率的化学酵素合成法を用いて、環状ペプチドを基盤とする農薬シーズ候補化合物を探索し、環境負荷を軽減しつつ、効果的かつ安全なペプチド農薬シーズを創製する。
    科学技術振興機構, 産学が連携した研究開発成果の展開/研究成果展開事業/研究成果最適展開支援プログラム(A-STEP)/ステージI(育成フェーズ), 24032287
  • Search for new natural products derived from rare microorganisms
    Grants-in-Aid for Scientific Research
    25 Apr. 2023 - 31 Mar. 2024
    脇本 敏幸; LIU MIAOMIAO
    微生物から見出された生物活性天然物は抗生物質をはじめ、抗がん剤や免疫抑制剤などとして臨床上重要な医薬品として用いられている。とりわけ近年では薬剤耐性菌出現への対処として、新しい作用機序を有する新規抗生物質の開発が急務となっている。さらに、最近のゲノム配列解読技術の発展に伴い、微生物のゲノムにコードされる天然物生合成遺伝子が次々に明らかにされてきた。その過程で、微生物ゲノムに含まれる生合成遺伝子の数は、単離された天然物の数よりも数倍多いことが分かってきた。したがって、これら休眠遺伝子を活性化できれば未開拓な天然物が獲得できる。
    実際に、これまでに国内外の研究者が様々な休眠遺伝子活性化方法を検討してきた。例えば、低濃度の抗生物質や異種細菌を特定の細菌培養液に添加することで、新規天然物の生産を誘導する例が報告されている。これらの知見は、同じ細菌種であっても、異なる培養条件では異なる天然物を生産できる可能性を示している。OSMAC (One Strain - Many Compounds)として知られている微生物の潜在的な天然物生産能を実験的に示した概念である。培養条件を工夫する方策はさまざまな手法が考えられるが、細菌が生息する本来の自然環境を模倣することで、休眠遺伝子を活性化できる可能性がある。そこで我々は細菌が放出する細胞外膜小胞（MVs）に着目した。多くの細菌が生産するMVsは海水など様々な環境中から検出されている。MVsはタンパク質、DNA断片や小分子化合物を内包する小胞で、細菌間相互作用の媒体として機能することが示唆されている。本研究では、OSMAC による新規天然物の取得を目指し、特にMVsを細菌培養液に添加して細菌間相互作用を模倣することで休眠遺伝子の活性化を試みた。その結果複数の新規天然物の検出に成功した。
    Japan Society for the Promotion of Science, Grant-in-Aid for JSPS Fellows, Hokkaido University, 23KF0001
  • 希少微生物株のゲノムマイニングによる天然医薬品資源の探索
    科学研究費助成事業
    01 Apr. 2021 - 31 Mar. 2024
    脇本 敏幸
    本研究では従来の天然物探索事例の少ない微生物株についてゲノム情報を取得し、ゲノム情報を起点とした新規天然物の探索を実施する。特に放線菌以外の菌株、中でも物質生産に秀でたグラム陰性菌を見出し、重点的に探索を進める。原位置培養方法を駆使して、未培養微生物株を収集するとともに、海綿動物や植物に共生する微生物株を重点的に探索標的とする。環境中より収集した菌株は16S rRNA配列によって系統解析し、放線菌以外で有望な微生物株を選別する。それらのゲノム解析を実施し、二次代謝物の生合成遺伝子を解析する。塩基配列と天然物の構造情報は現時点で完全には一致していないが、多くの代謝経路について経路を担う酵素や責任遺伝子が明らかになってきている。天然物の設計図である生合成遺伝子クラスターがゲノム上になければ、二次代謝産物が生産されることはないことを考えると、生合成遺伝子クラスターの有無は極めて重要な新規天然物探索の指標となる。本研究では新規微生物培養方法や次世代シークエンサーを駆使し、最先端の新規微生物二次代謝産物の探索を展開する。生合成遺伝子クラスターを起点とすることで様々なアドバンテージがある。第１に休眠遺伝子である場合はトランスポゾン変異などを導入して活性化を施すことができる。第２にひとたび新規天然物が得られれば、生合成遺伝子クラスターが紐づいてくるために、生合成経路の解析へ容易に展開できる。新規の二次代謝酵素が見出されれば生体触媒としての応用展開が期待できる。第３に生合成遺伝子クラスターには化合物の生合成経路のみならず、自己耐性機構が含まれている場合があるため、自己耐性機構から該当化合物の作用機序を明らかにすることができる。このように本研究では次世代型の新規天然物探索手法を最大限活用し、これまでにない包括的な探索研究を実施し、新規抗生物質や細胞毒性物質の発見を目指す。
    日本学術振興会, 基盤研究(B), 北海道大学, 21H02635
  • Redesigning Biosynthetic Machineries (International Activity Support Team)
    Grants-in-Aid for Scientific Research
    30 Jun. 2016 - 31 Mar. 2022
    Abe Ikuro
    In this project, we have made a dramatic development from simply learning biosynthetic machineries to designing new blueprints for producing desired natural products. We established a new world-leading technology platform for creation of complex functional molecules by rational reconstruction of biosynthetic machineries as a new academic field. In order to strongly promote joint research with foreign countries, the International Activity Support Group invited outstanding foreign researchers and held lecture meetings on a regular basis. Furthermore, international symposiums were held with the aim of strengthening cooperation and exchange with the U.S., Germany, China, and other countries. We strategically promoted joint research with foreign countries, focusing on medium-term support for young researchers. Many of the results of joint research with foreign countries resulted in excellent co-authored papers.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 16K21725
  • 環状ペプチドの効率的合成方法の開発
    2020 - 2022
    脇本 敏幸
    本課題はペプチドを環状にする新規合成技術を開発する。従来の技術では困難であった、10アミノ酸残基以下の短鎖環状ペプチド合成を可能とする要素技術の確立を目指す。我々はこれまでに放線菌から新しいペプチド環化酵素を発見し短鎖環状ペプチドの効率的合成に成功した（PCT/JP2019/017707）。本課題では、幅広い種類の短鎖ペプチド基質に適用可能な環化酵素群をもとに、高効率かつ大量合成に適した生体触媒を開発する。本技術を確立することで、従来合成ができなかった短鎖環状ペプチドを低コストかつ大量製造できるようになるため、創薬開発での活用が期待される製造基盤技術である。
    科学技術振興機構, 産学が連携した研究開発成果の展開/研究成果展開事業/研究成果最適展開支援プログラム(A-STEP)/産学共同(育成型), 20349208
  • Biosynthetic gene cluster of bioactive natural products from marine invertebrates
    Grants-in-Aid for Scientific Research
    01 Apr. 2018 - 31 Mar. 2021
    WAKIMOTO Toshiyuki
    Marine sponges are sessile animals harboring vast array of symbiont microorganisms. They inhabit in global oceans and the number of species are estimated to be 10,000. More than 20,000 bioactive natural products have been isolated from the marine sponges thus far. The search based on the randam screening is so common that cytotoxic compounds has been dominated and some of them exhibit significantly potent cytotoxicity with pM range of concentration. However, due to the scarcity and highly complex structure, most of them had not been developed to clinically useful anti-cancer agents. On the other hand, it has been suggested that many sponge-derived cytotoxins are produced by symbiont bacteria. In this study, we implanted the search for biosynthetic gene cluster of sponge-derived bioactive molecules and detailed analysis of biosynthetic pathway, and identification of producer symbiont.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 18H02581
  • Production of rare bioactive natural products originating from uncultured bacteria
    Grants-in-Aid for Scientific Research
    30 Jun. 2016 - 31 Mar. 2021
    WAKIMOTO Toshiyuki
    Marine sponges often contain potent cytotoxic compounds, which usually target molecules that are likely to be shared with the sponge itself. This fact in turn evokes the principle question of how marine sponges avoid self-toxicity. We previously identified an intriguing mechanism to prevent self-toxicity by the phosphorylation of the highly toxic calyculin A in the sponge holobiont, which is catalyzed by the phosphotransferase CalQ of a producer symbiont, “Candidatus Entotheonella” sp. However, the activating mechanism to dephosphorylate the stored phosphocalyculin A remains elusive. Here we show that the phosphatase specific to phosphocalyculin A is CalL, which is also encoded in the calyculin biosynthetic gene cluster. CalL represents a new clade and unprecedently coordinates the heteronuclear metals Cu and Zn. The CalL is localized in the periplasmic space of the sponge symbiont, where it is ready for the on-demand production of calyculin A in response to sponge tissue disruption.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, 16H06448
  • Redesigning Biosynthetic Machineries (Project Team)
    Grants-in-Aid for Scientific Research
    30 Jun. 2016 - 31 Mar. 2021
    Abe Ikuro
    In this project, we have made a dramatic development from simply learning biosynthetic machineries to designing new blueprints for producing desired natural products. Based on the detailed analyses of the structural diversity of natural products from the viewpoint of genes, enzymes, and reactions, we established a new world-leading technology platform for creation of complex functional molecules by rational reconstruction of biosynthetic machineries as a new academic field. In order to facilitate the research plan, the project team formulated a research policy and provided a forum to actively promote exchanges, collaborations, and joint research among individual research promoters. Researchers from various fields collaborated and complemented each other in their areas of expertise to conduct joint research and create a new academic field.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 16H06442
  • Biosynthetic study on bioactive compounds from marine sponges
    Grants-in-Aid for Scientific Research
    26 Jul. 2017 - 31 Mar. 2019
    脇本 敏幸; URIA AGUSTINUS
    海綿動物は多種多様な共生微生物を宿す付着性の多細胞動物である。世界中の海に生息し、１万種が現存するといわれる海綿動物からは、これまで２万以上の生理活性物質が単離、報告されてきた。ランダムスクリーニングに由来するため細胞毒性物質の数が多く、pM程度の濃度で強力な細胞毒性を示す化合物も少なくない。しかしながら、それらの多くが稀少かつ複雑な構造を有するために、抗がん剤として研究開発がなされた化合物は極めて少ない。一方で、それら海綿由来細胞毒性物質のほとんどは共生微生物によって生産されることが示唆されている。本研究では医薬品資源として有望な海綿由来稀少生理活性物質の生合成遺伝子および生産菌を同定し、可培養化や異種生産を目指した基礎的知見を得る。昨年度より海綿動物から微量成分として見出されたspongistatinの生合成遺伝子の特定を進めてきた。Spongistatinはtrans AT型PKSによる生合成経路が予想される化合物であり、その生合成遺伝子には特徴的な配列を有するketosynthase (KS)が含まれる。したがってKSの縮重プライマーを用いたtrans AT型PKSの探索を重点的に行った。その結果、海綿メタゲノムDNAよりtrans AT型PKSに属するKS配列を得た。さらに海綿メタゲノムライブラリーを構築し、得られたtrans AT型KS配列に基づくスクリーニングを行った。その結果、複数のヒットクローンを得ることに成功した。現在詳細なシークエンス解析を進めている。また、海綿共生微生物の可培養化を目指し、沖縄産海綿Theonella swinhoeiから様々な組成の培地を用いた培養を試みた。その結果、既知微生物と相同性が低い微生物を含む数百種類の微生物を単離した。その中にはPKSやNRPS遺伝子を有する微生物群も数多く含まれており今後さらに物質生産能の検証を進める。
    Japan Society for the Promotion of Science, Grant-in-Aid for JSPS Fellows, Hokkaido University, 17F17114
  • Bioactive secondary metabolites produced by sponge symbiont Entotheonella
    Grants-in-Aid for Scientific Research
    01 Apr. 2015 - 31 Mar. 2018
    WAKIMOTO Toshiyuki; KURANAGA Takefumi; EGAMI Yoko
    Marine sponges are prolific sources of bioactive molecules as well as highly complex consortia, including significantly large populations of symbiotic bacteria. The symbiotic bacteria often cannot be cultured under normal laboratory conditions. To access the gene clusters responsible for the biosynthesis of sponge-derived bioactive natural products, homology-based screening of the sponge metagenome library has been implemented. We successfully obtained the biosynthetic gene clusters of cytotoxic compounds, calyculins isolated from the Japanese sponge Discodermia calyx by a metagenome mining approach. The single cell analysis revealed that all these gene clusters were encoded by the same filamentous bacterium, which was identified as Candidatus “Entotheonella sp.” based on the 16S rRNA sequence. In this study, we investigated new metabolites as well as other gene clusters responsible for the biosynthesis of bioactive peptides derived from Discodermia kiiensis and Theonella swinhoei.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 15H03112
  • Collection and survey of biosynthetic genes of spore-derived biologically active substances and clarification of biosynthetic machinery
    Grants-in-Aid for Scientific Research
    01 Apr. 2014 - 31 Mar. 2018
    Abe Ikuro
    By collecting sponges in the Pacific region and isolating and comparing biosynthesis genes, we elucidated its biosynthetic machinery and searched for origin of structural diversity of natural products. At the same time, we investigated the possibility of producing bacteria common to these sponges and investigated the universality of the distribution of symbiotic bacteria excelling in substance production. As a result, the importance of marine biological resources in the Pacific region was demonstrated, and great contribution was expected to future drug development.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), The University of Tokyo, 26303005
  • The mechanism regulating the function of a natural cytotoxin
    Grants-in-Aid for Scientific Research
    01 Apr. 2015 - 31 Mar. 2017
    WAKIMOTO Toshiyuki; EGAMI Yoko
    Marine sponges are prolific sources of highly potent cytotoxic compounds, some of which are promising as anticancer drugs. However, the potent cytotoxicity would be harmful to the host sponge, because marine sponges are also animals. Therefore, it is possible that the self-resistance and activated defense systems underlie their biosynthetic mechanism. Wound-activated chemical defense systems are prevalent among terrestrial plants. The precursor molecule and the activating enzyme are compartmentalized in the tissue, which is readily disrupted by wounding to accomplish chemical defense. The similar activated defense strategy has also been found in a few marine sponges. In previous study, we obtained calyculin biosynthetic gene cluster from the metagenomic DNA of Japanese marine sponge Discodermia calyx and the deactivating enzyme was also clustered. The aim of this work is to identify the as-yet unknown enzyme involved in the activating process of the precursor molecule.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Hokkaido University, 15K12740
  • Calyculin A生合成機構の解析
    科学研究費助成事業
    01 Apr. 2013 - 31 Mar. 2015
    脇本 敏幸
    本研究では伊豆半島産チョコガタイシカイメンに含まれる細胞毒性物質カリクリンAの生合成経路の解明を目指した。カリクリンAはタンパク質脱リン酸化酵素1および2Aを特異的に阻害し、各種がん細胞に対してpMオーダーで増殖阻害活性を示す。我々はカリクリンAの生合成遺伝子クラスターの探索を進め、チョコガタイシカイメンよりメタゲノムライブラリーを作成、ポリケタイド合成酵素遺伝子に保存性の高い配列を足掛かりとしてスクリーニングを行った。その結果、全長150 kbpに及ぶ長大な生合成遺伝子クラスターの取得に至った。予想通り、本遺伝子クラスターはⅠ型ポリケタイド合成酵素と非リボソーム型ペプチド合成酵素をコードしており、それらのモジュールやドメインの構成はカリクリンAの構造と良い一致を示した。さらに、いくつかの推定修飾酵素について機能解析を試みた。遺伝子クラスター上流には３つのリン酸基転移酵素がコードされており、それらを大腸菌において異種発現し、酵素反応を試みた。その結果、３つのうち１つ（CalQ）がカリクリンAを基質として受け入れ、二リン酸化体を生成することを明らかにした。このことには海綿メタゲノムより同定した遺伝子クラスターがカリクリンA生合成遺伝子であることを支持している。カリクリンAの二リン酸体の生物活性を調べたところ、細胞毒性は1,000倍、PP2A阻害活性は20倍と著しく減弱しており、カリクリンAのプロドラッグ体であることが示唆された。したがって、カリクリン生合成における最終産物はカリクリンAではなく、本研究で見出されたホスホカリクリンAであることが明らかとなった。
    日本学術振興会, 新学術領域研究(研究領域提案型), 東京大学, 25108705
  • Identification and genome analysis of bacterial symbiont producing sponge-derived secondary metabolites
    Grants-in-Aid for Scientific Research
    01 Apr. 2013 - 31 Mar. 2015
    WAKIMOTO Toshiyuki
    In this study, we tried to identify the bacterial symbiont producing sponge-derived secondary metabolites. Theonellidae family sponges are well known to contain diverse secondary metabolites. However, the real producer of them had been unknown, though it had been supposed to be symbiont bacteria. The identification of such bacteria could be a key issue to pave the way for the supply limitation of medicinally important sponge-derived compounds. Three Theonellidae sponge species were therefore subjected to genetic evaluation, cell separation and single cell analysis. As a result, the Entotheonella was identified to be the real producer of almost all secondary metabolites of three sponge spieces. Our findings provide not only the proof of a sponge-specific molecule synthesized by the unique and uncultured bacterium rather than sponge itself, but also useful insights into the supply of sponge-derived medicinally important compounds.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, The University of Tokyo, 25560399
  • Enzyme engineering for natural product biosynthesis
    Grants-in-Aid for Scientific Research
    01 Apr. 2011 - 31 Mar. 2015
    ABE IKURO; WAKIMOTO Toshiyuki; AWAKAWA Takayoshi; MATSUDA Yudai; MORITA Hiroyuki; SUGIO Shigetoshi; NOGUCHI Hiroshi; KUSHIRO Testuo
    Several enzymes involved in the biosynthesis of natural products, such as plant polyketide synthase and CoA-ligase, exhibit remarkable catalytic versatility and substrate promiscuity. This makes the enzymes an excellent platform for enzyme engineering and further production of structurally divergent molecules. In this study, on the basis of the X-ray crystal structures of the enzymes, we succeeded in production of chemically and structurally divergent unnatural natural products, by structure-based enzyme engineering and precursor directed biosynthesis. In addition, we succeeded in elucidation of biosynthetic machinery of complex natural products including calyculin, teleocidin, and antimycin.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), The University of Tokyo, 23241068
  • Studies on biosynthetic assembly line of meroterpenoids
    Grants-in-Aid for Scientific Research
    01 Apr. 2010 - 31 Mar. 2015
    ABE IKURO; MATSUDA Yudai; WAKIMOTO Toshiyuki; AWAKAWA Takayoshi; MORITA Hiroyuki
    Meroterpenoids are hybrid natural products of both terpenoid and polyketide origin. We identified several biosynthetic gene clusters of pharmaceutically important fungal meroterpenoids, which includes that is responsible for the production of pyripyropene A, terretonin, anditomin, and andrastin, through reconstituted biosynthesis in a heterologous fungal expression system. Interestingly, the biosynthetic assembly lines are rich sources for interesting enzymes and chemistry, such as previously unknown membrane-bound terpene cyclases and multifunctional oxygenases, for the generation of structurally divergent complex fungal meroterpenoids.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 22108004
  • Development of selective phosphatase inhibitor based on calyculin A
    Grants-in-Aid for Scientific Research
    2011 - 2012
    TOSHIYUKI Wakimoto
    Many marine natural products exhibit highly potent cytotoxicity. They selectively inhibit the functions of either intracellular or membrane-bound target molecules, leading to cell death. These specific biological activities can provide valuable information on the biochemical research field. Therefore, we initiated this program aimed at the development of functionalized calyculin A, a protein phosphatase inhibitor, which was originally isolated from the marine sponge, Discodermia calyx. Based on the insights into the structural moieties essential for biological activity, the synthetic process toward library construction and fluorescent probe were developed.
    Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), The University of Tokyo, 23710250
  • Research for useful marineorganisms in Asia and Pacific regions
    Grants-in-Aid for Scientific Research
    2009 - 2011
    NAKAO Yoichi; HORI Kanji; SAKAI Ryuichi; FUSETANI Nobuhiro; MATSUOKA Shunji; FUKUZAWA Seketsu; WAKIMOTO Toshiyuki; FUJITA Masaki; TAKADA Kentarou
    In this project, a total 515 marine organisms were collected from 3 countries and preserved as the extract-, microbe-, and genome-libraries. Currently, evaluation for bioactivities of these extracts are being carried out. At the same time, thight collaborative relationship among the researchers of these countries and our group was founded, through this project.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Waseda University, 21404010
  • Studies on the biological activity of furan fatty acids
    Grants-in-Aid for Scientific Research
    2007 - 2009
    WAKIMOTO Toshiyuki
    Furan fatty acid is known as naturally occurring in various organisms but rare fatty acid. The elucidation of biological activity of furan fatty acid has been limited to antioxidant activity in vitro due to paucity of this fatty acid. In this study, isolation and semi-synthesis of this fatty acid were established, which enable us to disclose more potent anti-inflammatory activity of furan fatty acid than that of EPA.
    Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), University of Shizuoka, 19780162