Details of a Researcher - Nishimura, Takehiro

Papers - Nishimura, Takehiro

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Ester derivatives of Dictyostelium differentiation-inducing factors exhibit antibacterial activity, possibly via a prodrug-like function

Takahashi K., Kikuchi H., Nishimura T., Ishigaki H., Miura Y., Takahashi A., Kubohara Y.

BMC Research Notes 18 ( 1 ) 2025.12

Objective: Dictyostelium differentiation-inducing factors 1 and 3 [DIF-1 (1) and DIF-3 (2), respectively], along with their derivatives, such as Ph-DIF-1 (3) and Bu-DIF-3 (4), demonstrate antibacterial activity in vitro against Gram-positive bacteria, including methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), vancomycin-sensitive Enterococcus faecalis (VSE), and vancomycin-resistant Enterococcus faecium [VRE (VanA)]. This study investigates the therapeutic potential of DIF compounds against these Gram-positive bacteria. Results: In vitro tests revealed that the antibacterial activity of 3 and 4 was lost in the presence of human serum albumin (HSA), suggesting that HSA might inhibit their effectiveness. Further evaluation of less hydrophobic derivatives, DIF-1-NH2 (5) and NH2-Bu-DIF-3 (6), showed no antibacterial activity, even in the absence of HSA. However, ester derivatives Ph-DIF-1(AHA) (7) and Bu-DIF-3(2Ac) (8) exhibited antibacterial activity against the target bacteria in vitro, although this activity was also lost in the presence of HSA. We hypothesize that these ester derivatives may function as prodrugs, with their antibacterial activity possibly restored by hydrolysis through bacterial esterases. The results suggest that suitable ester modifications could enhance the in vivo antibacterial potential of DIF compounds, particularly if they can bypass HSA binding and be activated by bacterial enzymes.

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A new cannabigerolic acid derivative and its unprenylated precursor produced through the reconstitution of cannabinoid biosynthesis in Streptomyces

Kei Kudo, Takehiro Nishimura, Kei Miyako, Hikaru Suenaga, Kazuo Shin-ya

The Journal of Antibiotics (Nature Publishing Group) 78 ( 2 ) 126 - 130 2024.12

Research paper (scientific journal), Joint Work, Accepted, ISSN 00218820

A new derivative of cannabigerolic acid, designated as iso-cannabigerolic acid (iso-CBGA), a member of the cannabinoid family, and its precursor iso-olivetolic acid (iso-OA) were discovered from the culture of the engineered Streptomyces avermitilis heterologously expressing the genes responsible for cannabigerolic acid biosynthesis. Structural determination revealed an iso-pentyl moiety, which may arise from the biosynthetic precursor pool present in S. avermitilis. We describe herein the culture, isolation, structure determination and antibacterial activities of iso-CBGA and iso-OA.

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Compound–compound interaction analysis of baicalin and berberine derivatives in aqueous solution

Uekusa Y., Tanioka C., Nakamoto K., Tsutsumi R., Iida C., Enshu N., Nishimura T., Kiuchi F., Kikuchi H.

Journal of Natural Medicines 78 ( 3 ) 590 - 598 2024.06

ISSN 13403443

Baicalin and berberine are biologically active constituents of the crude drugs Scutellaria root and Coptis rhizome/Phellodendron bark, respectively. Baicalin and berberine are reported to combine together as a 1:1 complex that forms yellow precipitates by electrostatic interaction in decoctions of Kampo formulae containing these crude drugs. However, the structural basis and mechanism for the precipitate formation of this compound–compound interaction in aqueous solution remains unclarified. Herein, we searched for berberine derivatives in the Coptis rhizome that interact with baicalin and identified the chemical structures involved in the precipitation formation. Precipitation assays showed that baicalin formed precipitates with berberine and coptisine but not with palmatine and epiberberine. Thus, the 2,3-methylenedioxy structure may be crucial to the formation of the precipitates, and electrostatic interaction is necessary but is not sufficient. In this multicomponent system experiment, palmatine formed a dissociable complex with baicalin and may competitively inhibit the formation of berberine and coptisine precipitation with baicalin. Therefore, the precipitation formed by berberine and baicalin was considered to be caused by the aggregation of the berberine–baicalin complex, and the 2,3-methylenedioxy structure is likely crucial to the aggregation of the complex. Graphic abstract: (Figure presented.)

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Isolation and Structure Determination of New Pyrones from Dictyostelium spp. Cellular Slime Molds Coincubated with Pseudomonas spp.

Nishimura T., Murotani T., Sasaki H., Uekusa Y., Eguchi H., Ishigaki H., Takahashi K., Kubohara Y., Kikuchi H.

Molecules 29 ( 9 ) 2024.05

Cellular slime molds are excellent model organisms in the field of cell and developmental biology because of their simple developmental patterns. During our studies on the identification of bioactive molecules from secondary metabolites of cellular slime molds toward the development of novel pharmaceuticals, we revealed the structural diversity of secondary metabolites. Cellular slime molds grow by feeding on bacteria, such as Klebsiella aerogenes and Escherichia coli, without using medium components. Although changing the feeding bacteria is expected to affect dramatically the secondary metabolite production, the effect of the feeding bacteria on the production of secondary metabolites is not known. Herein, we report the isolation and structure elucidation of clavapyrone (1) from Dictyostelium clavatum, intermedipyrone (2) from D. magnum, and magnumiol (3) from D. intermedium. These compounds are not obtained from usual cultural conditions with Klebsiella aerogenes but obtained from coincubated conditions with Pseudomonas spp. The results demonstrate the diversity of the secondary metabolites of cellular slime molds and suggest that widening the range of feeding bacteria for cellular slime molds would increase their application potential in drug discovery.

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Anti-trypanosomal Lignans Isolated from Salvadoran Peperomia pseudopereskiifolia

Castillo U.G., Uekusa Y., Nishimura T., Kiuchi F., Martínez M.L., Menjívar J., Nakajima-Shimada J., Núñez M.J., Kikuchi H.

Journal of Natural Products 87 ( 4 ) 1067 - 1074 2024.04

ISSN 01633864

A search for anti-trypanosomal natural compounds from plants collected in El Salvador, a country particularly endemic for Chagas disease, resulted in the isolation of five lignan-type compounds (1-5) from Peperomia pseudopereskiifolia. The lignan derivatives 1, 2, and 4 are new. Their absolute configuration was determined by chemical derivatization. Compounds 1, 5, 6, and 8 exhibited anti-trypanosomal activity against the amastigote form of T. cruzi comparable to that of the existing drug benznidazole.

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Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds

Kudo K., Nishimura T., Izumikawa M., Kozone I., Hashimoto J., Fujie M., Suenaga H., Ikeda H., Satoh N., Shin-ya K.

Journal of Antibiotics (Journal of Antibiotics) 77 ( 5 ) 288 - 298 2024

ISSN 00218820

The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.

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Isolation and Structure Elucidation of JBIR-157, a Skeletally Novel Aromatic Polyketide Produced by the Heterologous Expression of a Cryptic Gene Cluster

Nishimura T., Kudo K., Izumikawa M., Kozone I., Hashimoto J., Kagaya N., Suenaga H., Takeuchi K., Shin-Ya K.

Chemical and Pharmaceutical Bulletin 72 ( 5 ) 475 - 479 2024

ISSN 00092363

Heterologous expression of natural compound biosynthetic gene clusters (BGCs) is a robust approach for not only revealing the biosynthetic mechanisms leading to the compounds, but also for discovering new products from uncharacterized BGCs. We established a heterologous expression technique applicable to huge biosynthetic gene clusters for generating large molecular secondary metabolites such as type-I polyketides. As an example, we targeted concanamycin BGC from Streptomyces neyagawaensis IFO13477 (the cluster size of 99kbp), and obtained a bacterial artificial chromosome (BAC) clone with an insert size of 211kbp that contains the entire concanamycin BGC. Interestingly, heterologous expression for this BAC clone resulted in two additional aromatic polyketides, ent-gephyromycin, and a new compound designated as JBIR-157, together with the expected concanamycin. Bioinformatic and biochemical analyses revealed that a cryptic biosynthetic gene cluster in this BAC clone was responsible for the production of these type-II polyketide synthases (PKS) compounds. Here, we describe the production, isolation, and structure elucidation of JBIR-157, determined primarily by a series of NMR spectral analyses.

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Synthesis of a Library of Terpenoid Alkaloid–Like Compounds Containing Medium-Sized Rings via Reconstruction of the Humulene Skeleton

Nishimura T., Shiga K., Sekiya M., Sugawara A., Yonezawa T., Kikuchi H.

Chemistry - A European Journal 30 ( 48 ) 2024

ISSN 09476539

The construction of a chemical library based on natural products is a promising method for the synthesis of natural product-like compounds. In this study, we synthesized a terpenoid alkaloid-like compound library based on the humulene skeleton. Our strategy, which enables access to diverse ring systems such as 11-membered monocyclic, oxabicyclic, and medium-sized aza ring-containing scaffolds, involves the introduction of a nitrogen atom, an intermolecular C−O bond formation via Lewis acid-mediated epoxide-opening transannulation, and a ring-reconstruction strategy based on olefin metathesis. A cheminformatics analysis based on their structural and physicochemical properties revealed that the synthesized compounds have high three-dimensionality and high natural product likeness scores but with structural novelty. The usefulness of the terpenoid alkaloid-like compound library for drug discovery and the accessibility to structure-activity relationship studies were validated by performing an assay for osteoclast-specific tartrate-resistant acid phosphatase activity, resulting in the identification of a seed compound for bone-resorptive diseases such as osteoporosis.

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JBIR-155, a Specific Class D β-Lactamase Inhibitor of Microbial Origin

Nishimura T., Kawahara T., Kagaya N., Ogura Y., Takikawa H., Suenaga H., Adachi M., Hirokawa T., Doi T., Shin-Ya K.

Organic Letters (Organic Letters) 23 ( 11 ) 4415 - 4419 2021

Research paper (scientific journal), Joint Work, Lead author, Accepted, ISSN 15237060

We discovered JBIR-155 as a novel specific class D β-lactamase inhibitor from Streptomyces polymachus SoB100815Hv02. JBIR-155 consists of a 6-oxabicyclo[3.2.0]heptan-7-one skeleton and a long unsaturated alkyl chain moiety of which absolute configuration was determined by spectroscopic data, modified Mosher's method, and analyses of the relative configuration of chemically modified derivative. JBIR-155 specifically exhibited inhibitory activity against the class D β-lactamase, with an IC50 value of 0.36 μM.

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Hemiacetal-less rapamycin derivatives designed and produced by genetic engineering of a type I polyketide synthase

Kudo K., Nishimura T., Kozone I., Hashimoto J., Kagaya N., Suenaga H., Ikeda H., Shin-ya K.

Scientific Reports (Scientific Reports) 11 ( 1 ) 9944 2021

Research paper (scientific journal), Joint Work, Accepted

Engineering polyketide synthases is one of the most promising ways of producing a variety of polyketide derivatives. Exploring the undiscovered chemical space of this medicinally important class of middle molecular weight natural products will aid in the development of improved drugs in the future. In previous work, we established methodology designated ‘module editing’ to precisely manipulate polyketide synthase genes cloned in a bacterial artificial chromosome. Here, in the course of investigating the engineering capacity of the rapamycin PKS, novel rapamycin derivatives 1–4, which lack the hemiacetal moiety, were produced through the heterologous expression of engineered variants of the rapamycin PKS. Three kinds of module deletions in the polyketide synthase RapC were designed, and the genetically engineered vectors were prepared by the in vitro module editing technique. Streptomyces avermitilis SUKA34 transformed with these edited PKSs produced new rapamycin derivatives. The planar structures of 1–4 established based on 1D and 2D NMR, ESI–TOF–MS and UV spectra revealed that 2 and 3 had skeletons well-matched to the designs, but 1 and 4 did not. The observations provide important insights into the mechanisms of the later steps of rapamycin skeletal formation as well as the ketone-forming oxygenase RapJ.

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A novel oxazole-containing tetraene compound, JBIR-159, produced by heterologous expression of the cryptic trans-AT type polyketide synthase biosynthetic gene cluster

Hashimoto T., Hashimoto J., Kagaya N., Nishimura T., Suenaga H., Nishiyama M., Kuzuyama T., Shin-ya K.

The Journal of Antibiotics (Journal of Antibiotics) 74 ( 5 ) 354 - 358 2021

Research paper (scientific journal), Joint Work, Accepted, ISSN 00218820

Using genome mining approach, we identified a novel biosynthetic gene cluster containing trans-AT type PKS genes from Streptomyces versipellis 4083-SVS6. A bacterial artificial chromosome (BAC) clone, pKU503JL68_PN1_P10-C12, accommodating the entire biosynthetic gene cluster was obtained from a BAC library. Heterologous expression of the biosynthetic gene cluster in Streptomyces lividans TK23 led to the production of a novel polyene compound, JBIR-159. We report herein the biosynthetic gene cluster for JBIR-159, and the heterologous expression, isolation, structure determination and a brief biological activity.

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In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives

Nature Communications 11 ( 1 ) 4022 2020

Research paper (scientific journal), Joint Work, Accepted

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Removal of the E-Olefin Barrier of Humulene Leading to Unnatural Terpenoid-like Skeletons

Organic Letters 20 ( 22 ) 7317 - 7320 2018

Research paper (scientific journal), Joint Work, Lead author, Accepted

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Development of a Terpenoid Alkaloid-like Compound Library Based on the Humulene Skeleton

Chemistry–A European Journal 22 ( 44 ) 15819 - 15825 2016

Research paper (scientific journal), Joint Work, Accepted

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