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  1. Article ; Online: Four distinct network patterns of supramolecular/polymer composite hydrogels controlled by formation kinetics and interfiber interactions

    Keisuke Nakamura / Ryou Kubota / Takuma Aoyama / Kenji Urayama / Itaru Hamachi

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: Synthetic hydrogels composed of covalent polymers and supramolecular fibers have been investigated for controlled delivery of biopharmaceuticals, but characterisation of the structures and properties can be challenging. Here, the authors report an ... ...

    Abstract Synthetic hydrogels composed of covalent polymers and supramolecular fibers have been investigated for controlled delivery of biopharmaceuticals, but characterisation of the structures and properties can be challenging. Here, the authors report an imaging study for the composite network, categorizing into four distinct patterns controlled by network formation kinetics and interactions between
    Keywords Science ; Q
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Fluorescence imaging of drug target proteins using chemical probes

    Hao Zhu / Itaru Hamachi

    Journal of Pharmaceutical Analysis, Vol 10, Iss 5, Pp 426-

    2020  Volume 433

    Abstract: Fluorescence imaging can provide valuable information on the expression, distribution, and activity of drug target proteins. Chemical probes are useful small-molecule tools for fluorescence imaging with high structural flexibility and biocompatibility. ... ...

    Abstract Fluorescence imaging can provide valuable information on the expression, distribution, and activity of drug target proteins. Chemical probes are useful small-molecule tools for fluorescence imaging with high structural flexibility and biocompatibility. In this review, we briefly introduce two classes of fluorescent probes for the visualization of drug target proteins. Enzymatically activatable probes make use of the specific enzymatic transformations that generally produce a fluorogenic response upon reacting with target enzymes. Alternatively, specific imaging can be conferred with a ligand that drives the probes to target proteins, where the labeling relies on noncovalent binding, covalent inhibition, or traceless labeling by ligand-directed chemistry.
    Keywords Fluorescence imaging ; Drug target ; Chemical probe ; Ligand-directed chemistry ; Therapeutics. Pharmacology ; RM1-950
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Naturally occurring quercetin and myricetin as potent inhibitors for human ectonucleotide pyrophosphatase/phosphodiesterase 1

    Peeradon Duangiad / Bodee Nutho / Thawatchai Chaijarasphong / Noppawan Phumala Morales / Thunyarat Pongtharangkul / Itaru Hamachi / Akio Ojida / Jirarut Wongkongkatep

    Scientific Reports, Vol 14, Iss 1, Pp 1-

    2024  Volume 13

    Abstract: Abstract Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto ... ...

    Abstract Abstract Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto Green, a rapid chemical sensor of pyrophosphate, was employed to screen for effective ENPP1 inhibitors among five representative flavonoids (quercetin, myricetin, morin, kaempferol, and quercetin-3-glucoside), five nucleosides (adenosine, guanosine, inosine, uridine, and cytidine), and five deoxynucleosides (2′- and 3′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxyinosine, and 2′-deoxyuridine). Conventional colorimetric, fluorescence, and bioluminescence assays revealed that ENPP1 was effectively inhibited by quercetin (K i ~ 4 nM) and myricetin (K i ~ 32 nM) when ATP was used as a substrate at pH 7.4. In silico analysis indicated that the presence of a chromone scaffold, particularly one containing a hydroxyl group at the 3′ position on the B ring, may promote binding to the active site pocket of ENPP1 and enhance inhibition. This study demonstrated that the naturally derived quercetin and myricetin could effectively inhibit ENPP1 enzymatic activity and may offer health benefits in arthritis management.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Orthogonal Activation of Metabotropic Glutamate Receptor Using Coordination Chemogenetics

    Akinobu Senoo / Yutaro Yamada / Kento Ojima / Tomohiro Doura / Itaru Hamachi / Shigeki Kiyonaka

    Frontiers in Chemistry, Vol

    2022  Volume 9

    Abstract: Cell-surface receptors play a pivotal role as transducers of extracellular input. Although different cell types express the same receptor, the physiological roles of the receptor are highly dependent on cell type. To understand each role, tactics for ... ...

    Abstract Cell-surface receptors play a pivotal role as transducers of extracellular input. Although different cell types express the same receptor, the physiological roles of the receptor are highly dependent on cell type. To understand each role, tactics for cell-specific activation of the target receptor are in high demand. Herein, we developed an orthogonal activation method targeting metabotropic glutamate receptor 1 (mGlu1), a G-protein coupled receptor. In this method, direct activation via coordination-based chemogenetics (dA-CBC) was adopted, where activation of mGlu1 was artificially induced by a protein conformational change in response to the coordination of a metal ion or metal-ion complex. Our structure-based protein design and screening approach identified mGlu1 mutants that were directly activated by the coordination of Cu2+ or Zn2+, in addition to our previous Pd-complex-sensitive mGlu1 mutant. Notably, the activation of the mutants was mutually orthogonal, resulting in cell-type selective activation in a model system using HEK293 cells.
    Keywords chemogenetics ; coordination chemistry ; orthogonal activation ; class C GPCR ; metabotropic glutamate receptor ; Chemistry ; QD1-999
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems

    Tamura, Tomonori / Itaru Hamachi

    Journal of the American Chemical Society. 2018 Dec. 28, v. 141, no. 7

    2018  

    Abstract: Chemical modification of proteins provides powerful tools to realize a broad range of exciting biological applications, including the development of new classes of biopharmaceuticals and functional studies of individual proteins in complex biological ... ...

    Abstract Chemical modification of proteins provides powerful tools to realize a broad range of exciting biological applications, including the development of new classes of biopharmaceuticals and functional studies of individual proteins in complex biological systems. Numerous strategies for linking desired chemical probes with target proteins have been developed in the last two decades, with most exploiting genetic protein engineering and/or bio-orthogonal chemistry that utilizes unnatural amino acids incorporated into proteins. Modification of native proteins in test tubes and biological contexts by site-specific and target-selective approaches remains challenging because appropriate organic chemistry to carry out such modifications is currently limited. Nonetheless, a variety of promising strategies have appeared recently that address this grand challenge in chemical biology. These new chemistries yield native protein-based well-defined bioconjugations, specific labeling of endogenous proteins in various biological crude milieus, and the establishment of chemical proteomics as a new research area in protein science. In this Perspective, we focus on recent remarkable progress in chemistry for native protein modification. We survey chemical characteristics of the methods and describe briefly these advanced applications to address unsolved biological issues. Current limitations and future directions of this research field are also discussed.
    Keywords amino acids ; biopharmaceuticals ; organic chemistry ; physicochemical properties ; proteins ; proteomics ; surveys
    Language English
    Dates of publication 2018-1228
    Size p. 2782-2799.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.8b11747
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Control of seed formation allows two distinct self-sorting patterns of supramolecular nanofibers

    Ryou Kubota / Kazutoshi Nagao / Wataru Tanaka / Ryotaro Matsumura / Takuma Aoyama / Kenji Urayama / Itaru Hamachi

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: Regulation of self-sorted nanofiber network patterns in double network hydrogels comprising supramolecular nanofibers is considered as key for potential applications. Here, the authors describe a selective construction of two distinct self-sorting ... ...

    Abstract Regulation of self-sorted nanofiber network patterns in double network hydrogels comprising supramolecular nanofibers is considered as key for potential applications. Here, the authors describe a selective construction of two distinct self-sorting network patterns, by controlling the kinetics of seed formation with dynamic covalent chemistry.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The Power of Confocal Laser Scanning Microscopy in Supramolecular Chemistry

    Dr. Ryou Kubota / Keisuke Nakamura / Shogo Torigoe / Prof. Dr. Itaru Hamachi

    ChemistryOpen, Vol 9, Iss 1, Pp 67-

    In situ Real‐time Imaging of Stimuli‐Responsive Multicomponent Supramolecular Hydrogels

    2020  Volume 79

    Abstract: Abstract Multicomponent supramolecular hydrogels are promising scaffolds for applications in biosensors and controlled drug release due to their designer stimulus responsiveness. To achieve rational construction of multicomponent supramolecular hydrogel ... ...

    Abstract Abstract Multicomponent supramolecular hydrogels are promising scaffolds for applications in biosensors and controlled drug release due to their designer stimulus responsiveness. To achieve rational construction of multicomponent supramolecular hydrogel systems, their in‐depth structural analysis is essential but still challenging. Confocal laser scanning microscopy (CLSM) has emerged as a powerful tool for structural analysis of multicomponent supramolecular hydrogels. CLSM imaging enables real‐time observation of the hydrogels without the need of drying and/or freezing to elucidate their static and dynamic properties. Through multiple, selective fluorescent staining of materials of interest, multiple domains formed in supramolecular hydrogels (e. g. inorganic materials and self‐sorting nanofibers) can also be visualized. CLSM and the related microscopic techniques will be indispensable to investigate complex life‐inspired supramolecular chemical systems.
    Keywords confocal microscopy ; gels ; self-assembly ; stimulus response ; supramolecular chemistry ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Wiley-VCH
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Fluorescence Differentiation of ATP-Related Multiple Enzymatic Activities in Synovial Fluid as a Marker of Calcium Pyrophosphate Deposition Disease Using Kyoto Green

    Nattha Yongwattana / Nutsara Mekjinda / Tulyapruek Tawonsawatruk / Itaru Hamachi / Akio Ojida / Jirarut Wongkongkatep

    Molecules, Vol 25, Iss 5, p

    2020  Volume 1116

    Abstract: Calcium pyrophosphate deposition disease (CPPD) is a crystal induced inflammation in joints, and causes severe pain in elderly people. The accumulation of pyrophosphate (PPi) in synovial fluid (SF) results from several enzymatic reactions, especially the ...

    Abstract Calcium pyrophosphate deposition disease (CPPD) is a crystal induced inflammation in joints, and causes severe pain in elderly people. The accumulation of pyrophosphate (PPi) in synovial fluid (SF) results from several enzymatic reactions, especially the highly activated e-NPPs, which catalyze the conversion of ATP to PPi. This study demonstrates the detection of relative catalytic activity of 3 enzymes—ecto-nucleotide pyrophosphatase/phosphodiesterases (e-NPPs), tissue nonspecific alkaline phosphatase (TNAP), and ecto-nucleoside triphosphate diphosphohydrolases (e-NTPDases)—using a single molecular sensor called Kyoto Green. Kyoto Green exhibits excellent performance in sensing the catalytic activity of the commercial representatives of the e-NPPs, TNAP, and e-NTPDases, which are ENPP1, PPase, and apyrase, respectively, in both single-enzyme and multi-enzyme assays. Analysis of SF enzymes in 19 SF samples from human and swine revealed moderate activity of e-NPPs, high activity of e-NTPDases, and low activity of TNAP. Our newly developed method for analysis of multiple enzymatic activities using Kyoto Green in biological SF will assist improvement in accuracy of the CPPD prognosis/diagnosis, which will minimize unnecessary medical procedures.
    Keywords cppd ; pseudogout ; enpp1 ; ppase ; apyrase ; synovial fluid ; fluorescence detection ; molecular sensor ; Organic chemistry ; QD241-441
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Force generation by a propagating wave of supramolecular nanofibers

    Ryou Kubota / Masahiro Makuta / Ryo Suzuki / Masatoshi Ichikawa / Motomu Tanaka / Itaru Hamachi

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: The rational design of spatiotemporal patterns in artificial molecular systems remains at an early stage of development. Here, the authors design a reaction network to control the formation and degradation of nanofibers by orthogonal chemical stimuli and ...

    Abstract The rational design of spatiotemporal patterns in artificial molecular systems remains at an early stage of development. Here, the authors design a reaction network to control the formation and degradation of nanofibers by orthogonal chemical stimuli and describe force generation by a propagating wave of supramolecular nanofibers.
    Keywords Science ; Q
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Control of seed formation allows two distinct self-sorting patterns of supramolecular nanofibers

    Ryou Kubota / Kazutoshi Nagao / Wataru Tanaka / Ryotaro Matsumura / Takuma Aoyama / Kenji Urayama / Itaru Hamachi

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: Regulation of self-sorted nanofiber network patterns in double network hydrogels comprising supramolecular nanofibers is considered as key for potential applications. Here, the authors describe a selective construction of two distinct self-sorting ... ...

    Abstract Regulation of self-sorted nanofiber network patterns in double network hydrogels comprising supramolecular nanofibers is considered as key for potential applications. Here, the authors describe a selective construction of two distinct self-sorting network patterns, by controlling the kinetics of seed formation with dynamic covalent chemistry.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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