Updated on 2024/10/19

写真a

 
KIMURA Yasuaki
 
Organization
Graduate School of Science Associate professor
Graduate School
Graduate School of Science
Undergraduate School
School of Science Department of Chemistry
Title
Associate professor
External link

Degree 1

  1. 博士(薬学) ( 2013.3   東京大学 ) 

Research Interests 5

  1. RNA

  2. 核酸化学

  3. ケミカルバイオロジー

  4. 創薬化学

  5. 核酸医薬

Research Areas 4

  1. Life Science / Pharmaceutical chemistry and drug development sciences

  2. Life Science / Bioorganic chemistry

  3. Nanotechnology/Materials / Bio chemistry

  4. Nanotechnology/Materials / Chemical biology

Research History 9

  1. Nagoya University   Graduate School of Science

    2020.7 - 2022.5

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  2. Nagoya University   Graduate School of Science   Associate professor

    2022.6

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  3. Nagoya University

    2020.7 - 2022.5

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  4. Nagoya University   Institute for Advanced Research

    2017.6 - 2020.6

  5. Nagoya University   Nagoya University

    2017.6 - 2020.6

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  6. 名古屋大学大学院   理学研究科   助教

    2015.7 - 2020.6

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  7. 東京大学大学院   薬学系研究科   特任助教

    2015.4 - 2015.6

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  8. ERATO金井触媒分子生命プロジェクト特任研究員   東京大大学院薬学系研究科

    2013.4 - 2015.6

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  9. 日本学術振興会特別研究員(DC1)

    2010.4 - 2013.3

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Education 1

  1. 東京大学大学院   薬学系研究科   分子薬学専攻

    2008.4 - 2013.3

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Professional Memberships 5

  1. NUCLEIC ACIDS THERAPEUTICS SOCIETY OF JAPAN

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  2. The Japan Society of Nucleic Acids Chemistry

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  3. THE CHEMICAL SOCIETY OF JAPAN

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  4. JAPANESE SOCIETY FOR CHEMICAL BIOLOGY

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  5. THE PHARMACEUTICAL SOCIETY OF JAPAN

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Awards 2

  1. 日本核酸化学会 大塚賞

    2018.11  

    木村康明

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  2. 大津会議アワードフェロー

    2011.10   公益財団法人MSD生命科学財団  

    木村康明

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Papers 51

  1. Development of hydrophobic tag purifying monophosphorylated RNA for chemical synthesis of capped mRNA and enzymatic synthesis of circular mRNA.

    Ototake M, Inagaki M, Kimura S, Onda K, Tada M, Kawaguchi D, Murase H, Fukuchi K, Gao Y, Kokubo K, Acharyya S, Meng Z, Ishida T, Kawasaki T, Abe N, Hashiya F, Kimura Y, Abe H

    Nucleic acids research     2024.10

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    DOI: 10.1093/nar/gkae847

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  2. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures Reviewed

    Inagaki, M; Abe, N; Li, ZM; Nakashima, Y; Acharyya, S; Ogawa, K; Kawaguchi, D; Hiraoka, H; Banno, A; Meng, ZY; Tada, M; Ishida, T; Lyu, P; Kokubo, K; Murase, H; Hashiya, F; Kimura, Y; Uchida, S; Abe, H

    NATURE COMMUNICATIONS   Vol. 14 ( 1 ) page: 2657   2023.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Nature Communications  

    Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80–90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.

    DOI: 10.1038/s41467-023-38244-8

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  3. Development of Chemical Capping Reaction for Complete Chemical Synthesis of mRNA

    Abe Hiroshi, Ogawa Kazuya, Abe Naoko, Kimura Yasuaki

    MEDCHEM NEWS   Vol. 33 ( 2 ) page: 75 - 78   2023.5

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:The Pharmaceutical Society of Japan  

    Recently, mRNA vaccines have been used with great success in SARS-CoV2 infections. However, mRNA vaccines are subject to reduced activity due to the <i>in vivo</i> instability of mRNA and other factors. Therefore, it is effective to introduce chemical modifications to mRNA that are expected to improve its stability, but there is no general synthetic method to achieve this. In this study, we developed a method for complete chemical synthesis of mRNA that avoids the enzymatic method, which is a barrier to the introduction of chemical modifications to mRNA. This method enables the introduction of site-specific chemical modifications to mRNA, and the appropriate chemical modification pattern that maximizes translational activity and stability. This paper describes the development of the complete chemical synthesis method, the structure-activity relationship of chemically modified mRNAs by the complete chemical synthesis method, and the therapeutic effects of mRNA cancer vaccines synthesized by this method.

    DOI: 10.14894/medchem.33.2_75

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  4. SYNTHESIS AND BIOLOGICAL EVALUATION OF NMDI14 DERIVATIVES AS ANTI-MESOTHELIOMA AGENTS International journal

    Hong Nhung Nguyen, Suzuki Koya, Kimura Yasuaki, Hirokawa Takatsugu, Murakami-Tonami Yuko, Abe Hiroshi

    HETEROCYCLES   Vol. 100 ( 2 ) page: 253 - 266   2020.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Heterocycles  

    Mesothelioma is a severe tumor formed in pleura and peritoneum, for which no useful molecular-targeting therapy is available. We synthesized several derivatives of NMDI14, which is a reported inhibitor for non-sense mediated mRNA decay, and evaluated the activity of the NMDI14 derivatives as potential anti-mesothelioma agents. Some of the synthesized compounds showed promising activity in terms of cytotoxicity toward mesothelioma model cells and promotion of GAS5 expression selectively in mesothelioma cells. These results indicate that the NMDI14 derivatives may be useful for further developing clinically effective anti-mesothelioma drugs.

    DOI: 10.3987/COM-19-14191

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  5. Intracellular Delivery of Antisense DNA and siRNA with Amino Groups Masked with Disulfide Units International journal

    Shu Zhaoma, Ota Azumi, Takayama Yukiya, Katsurada Yuri, Kusamori Kosuke, Abe Naoko, Nakamoto Kosuke, Tomoike Fumiaki, Tada Seiichi, Ito Yoshihiro, Nishikawa Makiya, Kimura Yasuaki, Abe Hiroshi

    CHEMICAL & PHARMACEUTICAL BULLETIN   Vol. 68 ( 2 ) page: 129 - 132   2020.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

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  6. Intracellular Delivery of Antisense DNA and siRNA with Amino Groups Masked with Disulfide Units International journal

    Shu Zhaoma, Ota Azumi, Takayama Yukiya, Katsurada Yuri, Kusamori Kosuke, Abe Naoko, Nakamoto Kosuke, Tomoike Fumiaki, Tada Seiichi, Ito Yoshihiro, Nishikawa Makiya, Kimura Yasuaki, Abe Hiroshi

    Chemical and Pharmaceutical Bulletin   Vol. 68 ( 2 ) page: 129 - 132   2020

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:The Pharmaceutical Society of Japan  

    <p>Efficient methods for delivery of antisense DNA or small interfering RNA (siRNA) are highly needed. Cationic materials, which are conventionally used for anionic oligonucleotide delivery, have several drawbacks, including aggregate formation, cytotoxicity and a low endosome escape efficiency. In this report a bio-reactive mask (<i>i.e.</i>, disulfide unit) for cationic amino groups was introduced, and the mask was designed such that it was removed at the target cell surface. Insolubility and severe cellular toxicity caused by exposed cationic groups are avoided when using the mask. Moreover, the disulfide unit used to mask the cationic group enabled direct delivery of oligonucleotides to the cell cytosol. The molecular design reported is a promising approach for therapeutic applications.</p>

    DOI: 10.1248/cpb.c19-00811

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  7. Disulfide-Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA International journal

    Zhaoma Shu, Iku Tanaka, Azumi Ota, Daichi Fushihara, Dr. Naoko Abe, Saki Kawaguchi, Dr. Kosuke, Nakamoto, Dr. Fumiaki Tomoike, Dr. Seiichi Tada, Prof. Yoshihiro Ito, Dr, Yasuaki Kimura, Prof. Hiroshi Abe

    Angew. Chem., Int. Ed.   Vol. 58 ( 20 ) page: 6611 - 6615   2019.5

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    Development of intracellular delivery methods for antisense DNA and siRNA is important. Previously reported methods using liposomes or receptor-ligands take several hours or more to deliver oligonucleotides to the cytoplasm due to their retention in endosomes. Oligonucleotides modified with low molecular weight disulfide units at a terminus reach the cytoplasm 10 minutes after administration to cultured cells. This rapid cytoplasmic internalization of disulfide-modified oligonucleotides suggests the existence of an uptake pathway other than endocytosis. Mechanistic analysis revealed that the modified oligonucleotides are efficiently internalized into the cytoplasm through disulfide exchange reactions with the thiol groups on the cellular surface. This approach solves several critical problems with the currently available methods for enhancing cellular uptake of oligonucleotides and may be an effective approach in the medicinal application of antisense DNA and siRNA.

    DOI: 10.1002/anie.201900993

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  8. Nano structure design for RNA interference

    Shu Zhaoma, Abe Naoko, Tomoike Fumiaki, Kimura Yasuaki, Ito Yoshihiro, Abe Hiroshi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   Vol. 255   page: .   2018.3

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  9. Synthesis of 2′-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs

    Kohei Nomura, Seongjin An, Yoshiaki Kobayashi, Jiro Kondo, Ting Shi, Hirotaka Murase, Kosuke Nakamoto, Yasuaki Kimura, Naoko Abe, Kumiko Ui-Tei, Hiroshi Abe

    Nucleic Acids Research   Vol. 52 ( 18 ) page: 10754 - 10774   2024.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    In this study, we report the synthesis of 2′-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5–11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced its thermodynamic stability, but X-ray crystallography and CD spectrum analysis confirmed that the RNA maintained its natural A-form structure. Although the introduction of the 2′-formamidonucleoside derivative at the 2nd position in the guide strand of the siRNA led to a slight decrease in the on-target RNAi activity, the siRNAs with different sequences incorporating 2′-formamidonucleoside with four kinds of nucleobases into any position other than 2nd position in the seed region revealed a significant suppression of off-target activity while maintaining on-target RNAi activity. This indicates that 2′-formamidonucleosides represent a promising approach for mitigating off-target effects in siRNA therapeutics.

    DOI: 10.1093/nar/gkae741

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  10. Intracellular delivery of antisense oligonucleotides by tri-branched cyclic disulfide units. International journal

    Fangjie Lyu, Hayase Hakariya, Haruka Hiraoka, Zhenmin Li, Noriaki Matsubara, Yonghao Soo, Fumitaka Hashiya, Naoko Abe, Zhaoma Shu, Kosuke Nakamoto, Yasuaki Kimura, Hiroshi Abe

    ChemMedChem   Vol. 19 ( 20 ) page: e202400472   2024.8

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    Therapeutic oligonucleotides, such as antisense DNA, show promise in treating previously untreatable diseases. However, their applications are still hindered by the poor membrane permeability of naked oligonucleotides. Therefore, it is necessary to develop efficient methods for intracellular oligonucleotide delivery. Previously, our group successfully developed disulfide-based Membrane Permeable Oligonucleotides (MPON), which achieved enhanced cellular uptake and gene silencing effects through an endocytosis-free uptake mechanism.  Herein, we report a new molecular design for the next generation of MPON, called trimer MPON. The trimer MPON consists of a tri-branched backbone, three α-lipoic acid units, and a spacer linker between the oligonucleotides and tri-branched cyclic disulfide unit. We describe the design, synthesis, and functional evaluation of the trimer MPON, offering new insights into the molecular design for efficient oligonucleotide delivery.

    DOI: 10.1002/cmdc.202400472

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  11. 2′-β-Methylselenyl nucleos(t)ide analogs as reverse transcriptase inhibitors against diverse HIV mutants Reviewed

    Yuki Yoshida, Yushi Niimi, Daichi Fushihara, Hideo Katakura, Ryusuke Fukui, Hirotaka Murase, Fumiaki Tomoike, Fumitaka Hashiya, Tsutomu Murakami, Eiichi N. Kodama, Tetsuro Suzuki, Kiyoshi Yasukawa, Yasuaki Kimura, Hiroshi Abe

    Bioorganic &amp; Medicinal Chemistry   Vol. 110   page: 117813 - 117813   2024.8

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bmc.2024.117813

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  12. Position-Specific Nucleoside Sugar Modifications in mRNA ORF: Enhancing Translational Function through Complete Chemical Synthesis of mRNA

    Hiroto Iwai, Yasuaki Kimura, Masakazu Honma, Kosuke Nakamoto, Keiichi Motosawa, Takayuki Atago, Kana Asano, Fumitaka Hashiya, Naoko Abe, Keiko Kobayashi, Ryoko Ogisu, Atushi Hashimoto, Keiko Hiraishi, Seiji Saito, Junichiro Yamamoto, Hiroshi Abe

        2024.4

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    DOI: 10.26434/chemrxiv-2024-bwpx6

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  13. Development of PCR Primer Enabling the Design of Flexible Sticky Ends for Efficient Concatenation of Long DNA Fragments Reviewed

    Kohei Nomura, Kaoru Onda, Hirotaka Murase, Fumitaka Hashiya, Yukiteru Ono, Goro Terai, Natsuhisa Oka, Kiyoshi Asai, Daisuke Suzuki, Naho Takahashi, Haruka Hiraoka, Masahito Inagaki, Yasuaki Kimura, Yoshihiro Shimizu, Naoko Abe, Hiroshi Abe

    RSC Chemical Biology   Vol. 5 ( 4 ) page: 360 - 371   2024.4

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    We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups...

    DOI: 10.1039/d3cb00212h

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  14. Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction Reviewed

    Sana Ohashi, Mayu Nakamura, Susit Acharyya, Masahito Inagaki, Naoko Abe, Yasuaki Kimura, Fumitaka Hashiya, Hiroshi Abe

    ACS Omega   Vol. 9 ( 8 ) page: 9300 - 9308   2024.2

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    DOI: 10.1021/acsomega.3c08516

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  15. Topological capture of mRNA for silencing gene expression Reviewed

    Lyu, F., Tomita, T., Abe, N., Hiraoka, H., Hashiya, F., Nakashima, Y., Kajihara, S., Tomoike, F., Shu, Z., Onizuka, K., Kimura, Y., Abe, H.

    Chemical Communications   Vol. 59 ( 77 ) page: 11564 - 11567   2023.9

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    DOI: 10.1039/d2cc06189a

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  16. The effect of γ phosphate modified deoxynucleotide substrates on PCR activity and fidelity. Reviewed International journal

    Fumitaka Hashiya, Hirotaka Murase, Akash Chandela, Haruka Hiraoka, Masahito Inagaki, Yuko Nakashima, Naoko Abe, Mayu Nakamura, Goro Terai, Yasuaki Kimura, Kaori Ando, Natsuhisa Oka, Kiyoshi Asai, Hiroshi Abe

    ChemBioChem   Vol. 24 ( 14 ) page: e202200572   2023.7

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    Controlling PCR fidelity is an important issue for molecular biology and high-fidelity PCR is essential for gene cloning. In general, fidelity control is achieved by protein engineering of polymerases. In contrast, only a few studies have reported controlling fidelity using chemically modified nucleotide substrates. In this report, we synthesized nucleotide substrates possessing a modification on Pγ and evaluated the effect of this modification on PCR fidelity. One of the substrates, nucleotide tetraphosphate, caused a modest decrease in Taq DNA polymerase activity and the effect on PCR fidelity was dependent on the type of mutation. The use of deoxyadenosine tetraphosphate enhanced the A:T→G:C mutation dramatically, which is common when using Taq polymerase. Conversely, deoxyguanosine tetraphosphate (dG4P) suppressed this mutation but increased the G:C→A:T mutation during PCR. Using an excess amount of dG4P suppressed both mutations successfully and total fidelity was improved.

    DOI: 10.1002/cbic.202200572

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  17. Synthesis of nucleoside oligophosphates by electrophilic activation of phosphorothioate Reviewed

    Shogo Hasegawa, Masahito Inagaki, Shunichi Kato, Zhenmin Li, Yasuaki Kimura, Hiroshi Abe

    Organic & Biomolecular Chemistry   Vol. 21 ( 19 ) page: 3997 - 4001   2023.5

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    We herein report a new synthetic method of nucleoside oligophosphates based on an electrophilic activation of 5'-phosphorothioate nucleotides. Treatment of the phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently afforded the key activated...

    DOI: 10.1039/d2ob02260e

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  18. A 2'-modified uridine analog, 2'-O-(methylthiomethoxy)methyl uridine, for siRNA applications Reviewed

    Lyu Fangjie, Seongjin An, Yoshiaki Kobayashi, Kohei Nomura, Rintaro Baba, Naoko Abe, Haruka Hiraoka, Fumitaka Hashiya, Zhaoma Shu, Kumiko Ui-Tei, Yasuaki Kimura, Hiroshi Abe

    Bioorganic & Medicinal Chemistry Letters   Vol. 74   page: 128939 - 128939   2022.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bmcl.2022.128939

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  19. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures.

    Masahito Inagaki, Naoko Abe, Zhenmin Li, Yuko Nakashima, Susit Acharyya, Kazuya Ogawa, Daisuke Kawaguchi, Haruka Hiraoka, Ayaka Banno, Zheyu Meng, Mizuki Tada, Tatsuma Ishida, Pingxue Lyu, Kengo Kokubo, Hirotaka Murase, Fumitaka Hashiya, Yasuaki Kimura, Satoshi Uchida, Hiroshi Abe

        2022.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    Removing immunogenic uncapped mRNA from in vitro transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide a maximum capping efficiency of around 80-90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. Herein, we developed hydrophobic photocaged tag-modified cap analogs, which separated capped mRNA from uncapped mRNA by reversed-phase HPLC. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provided 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. The Cap-2-type mRNA showed up to 3 to 4-fold higher translational activity in cultured cells and animals than mRNA prepared by the standard capping method. Notably, the purification process simultaneously removed immunogenic double-stranded mRNA, another major contaminant of in vitro transcribed mRNA, drastically reducing mRNA immunogenicity in cultured cells.

    DOI: 10.26434/chemrxiv-2022-vfjt6

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  20. Development of Fluorophosphoramidate as a Biocompatibly Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. Reviewed International journal

    Yuki Yoshida, Ti Zheng, Wataru Tanabe, Fumiaki Tomoike, Fumitaka Hashiya, Tetsuro Suzuki, Shuto Hirota, Yuriko Saiki, Akira Horii, Akiyoshi Hirayama, Tomoyosi Soga, Yasuaki Kimura, Hiroshi Abe

    ChemMedChem   Vol. 17 ( 17 ) page: e202200188   2022.9

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    Synthetic phosphate-derived functional groups are important for controlling the function of bioactive molecules in vivo. Herein we describe the development of a new type of biocompatible phosphate analog, a fluorophosphoramidate (FPA) functional group that has characteristic P-F and P-N bonds. We found that FPA with a primary amino group was relatively unstable in aqueous solution and was converted to a monophosphate, while FPA with a secondary amino group was stable. Furthermore, by improving the molecular design of FPA, we developed a reaction in which a secondary amino group is converted to a primary amino group in the intracellular environment and clarified that the FPA group functions as a phosphate prodrug of nucleoside. Various FPA-gemcitabine derivatives were synthesized and their toxicity to cancer cells were evaluated. One of the FPA-gemcitabine derivatives showed superior toxicity compared with gemcitabine and its ProTide prodrug, which methodology is widely used in various nucleoside analogs, including anti-cancer and anti-virus drugs.

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  21. Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. Reviewed International journal

    Naoko Abe, Akihiro Imaeda, Masahito Inagaki, Zhenmin Li, Daisuke Kawaguchi, Kaoru Onda, Yuko Nakashima, Satoshi Uchida, Fumitaka Hashiya, Yasuaki Kimura, Hiroshi Abe

    ACS Chemical Biology   Vol. 17 ( 6 ) page: 1308 - 1314   2022.6

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    Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5'-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2'-O-methylated nucleotides at the 5' end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.

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  22. Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization Reviewed International journal

    Haruka Hiraoka, Zhaoma Shu, Bao Tri Le, Keiko Masuda, Kosuke Nakamoto, Lyu Fangjie, Naoko Abe, Fumitaka Hashiya, Yasuaki Kimura, Yoshihiro Shimizu, Rakesh N. Veedu, Hiroshi Abe

    ChemBioChem   Vol. 22 ( 24 ) page: 3437 - 3442   2021.12

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    We have found that antisense oligonucleotides and siRNA molecules modified with repeat structures of disulfide units can be directly introduced into the cytoplasm and exhibit a suppressive effect on gene expression. In this study, we analyzed the mechanism of cellular uptake of these membrane-permeable oligonucleotides (MPONs). Time-course analysis by confocal microscopy showed that the uptake of MPONs from the plasma membrane to the cytoplasm reached 50 % of the total uptake in about 5 min. In addition, analysis of the plasma membrane proteins to which MPONs bind, identified several proteins, including voltage-dependent anion channel. Next, we analyzed the behavior of MPONs in the cell and found them to be abundant in the nucleus as early as 24 h after addition with the amount increasing further after 48 and 72 h. The amount of MPONs was 2.5-fold higher than that of unmodified oligonucleotides in the nucleus after 72 h. We also designed antisense oligonucleotides and evaluated the effect of MPONs on mRNA exon skipping using DMD model cells; MPONs caused exon skipping with 69 % efficiency after 72 h, which was three times higher than the rate of the control. In summary, the high capacity for intracytoplasmic and nuclear translocation of MPONs is expected to be useful for therapeutic strategies targeting exon skipping.

    DOI: 10.1002/cbic.202100413

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  23. Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells

    Kazuki Yamaoka, Ryota Oikawa, Naoko Abe, Kosuke Nakamoto, Fumiaki Tomoike, Fumitaka Hashiya, Yasuaki Kimura, Hiroshi Abe

    ChemBioChem   Vol. 22 ( 23 ) page: 3273 - 3276   2021.12

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    DOI: 10.1002/cbic.202100312

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  24. Structure, Synthesis and Inhibition Mechanism of Nucleoside Analogues as HIV‐1 Reverse Transcriptase Inhibitors (NRTIs) Reviewed International journal

    Yuki Yoshida, Masakazu Honma, Yasuaki Kimura, Hiroshi Abe

    ChemMedChem   Vol. 16 ( 5 ) page: 743 - 766   2021.3

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    Acquired immunodeficiency syndrome (AIDS) is caused by infection with the human immunodeficiency virus (HIV). Although treatments against HIV infection are available, AIDS remains a serious disease that causes many deaths annually. Although a variety of anti-HIV drugs have been synthesized and marketed to treat HIV-infected patients, nucleoside analogue reverse transcriptase inhibitors (NRTIs), which mimic nucleosides, are used extensively and remain a subject of interest to medicinal chemists. However, HIV has acquired drug resistance against NRTIs, and thus the struggle to find novel therapies continues. In this review, we trace the trajectory of NRTIs, focusing on the synthesis, mechanisms of action and applications of NRTIs that have been developed.

    DOI: 10.1002/cmdc.202000695

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    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cmdc.202000695

  25. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis Reviewed International journal

    Daisuke Kawaguchi, Ayumi Kodama, Naoko Abe, Kei Takebuchi, Fumitaka Hashiya, Fumiaki Tomoike, Kosuke Nakamoto, Yasuaki Kimura, Yoshihiro Shimizu, Hiroshi Abe

    Angewandte Chemie International Edition   Vol. 59 ( 40 ) page: 17403 - 17407   2020.9

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    Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.

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  26. Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters. Reviewed International journal

    Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai

    Journal of chemical theory and computation   Vol. 16 ( 9 ) page: 5923 - 5935   2020.9

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    Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases.

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  27. Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation Reviewed International journal

    Nakamoto, K., Abe, N., Tsuji, G., Kimura, Y., Tomoike, F., Shimizu, Y., Abe, H.

    Chemical Communications   Vol. 56 ( 46 ) page: 6217 - 6220   2020.6

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    <p>Circular RNA without a stop codon enables rolling circle translation. we carried out one-pot chemical synthesis of circular RNA from RNA fragments. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.</p>

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  28. Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes Reviewed International journal

    Hirotaka Fujita, Ryota Oikawa, Mayu Hayakawa, Fumiaki Tomoike, Yasuaki Kimura, Hiroyuki Okuno, Yoshiki Hatashita, Carolina Fiallos Oliveros, Haruhiko Bito, Toshio Ohshima, Satoshi Tsuneda, Hiroshi Abe, Takafumi Inoue

    Journal of Biological Chemistry   Vol. 295 ( 23 ) page: 7923 - 7940   2020.6

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    RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and inositol 1,4,5-trisphosphate receptor type 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF-FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.

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  29. Translational control by secondary-structure formation in mRNA in a eukaryotic system Reviewed International journal

    Daisuke Kawaguchi, Saaya Shimizu, Naoko Abe, Fumitaka Hashiya, Fumiaki Tomoike, Yasuaki Kimura, Hiroshi Abe

    Nucleosides, Nucleotides & Nucleic Acids   Vol. 39 ( 1-3 ) page: 195 - 203   2020.2

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    Eukaryotic mRNA has a cap structure at the 5' end and a poly(A) tail at the 3' end. The cap and poly(A) tail form a complex with multiple translation factors, and mRNA forms a circularized structure called a closed-loop model. This circularized structure reportedly not only stabilizes mRNA but also promotes ribosome recycling during translation, which improves translation efficiency. We designed an artificial mRNA that forms a circularized structure without a cap structure and poly(A) tail and found that its translational efficiency was improved compared with that of a sequence without the circularized structure in a eukaryotic translation system.

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  30. A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs. Reviewed International journal

    Shen Tian, Goro Terai, Yoshiaki Kobayashi, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai, Kumiko Ui-Tei

    RNA biology   Vol. 17 ( 2 ) page: 264 - 280   2020.2

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    MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in the regulation of gene function by a mechanism known as RNA silencing. In a previous study, we revealed that miRNA-mediated silencing efficacy is correlated with the combinatorial thermodynamic properties of the miRNA seed-target mRNA duplex and the 5´-terminus of the miRNA duplex, which can be predicted using 'miScore'. In this study, a robust refined-miScore was developed by integrating the thermodynamic properties of various miRNA secondary structures and the latest thermodynamic parameters of wobble base-pairing, including newly established parameters for I:C base pairing. Through repeated random sampling and machine learning, refined-miScore models calculated with either melting temperature (Tm) or free energy change (ΔG) values were successfully built and validated in both wild-type and adenosine-to-inosine edited miRNAs. In addition to the previously reported contribution of the seed-target duplex and 5´-terminus region, the refined-miScore suggests that the central and 3´-terminus regions of the miRNA duplex also play a role in the thermodynamic regulation of miRNA-mediated silencing efficacy.

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  31. Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors Reviewed International journal

    Yasuaki Kimura, Zhaoma Shu, Mika Ito, Naoko Abe, Kosuke Nakamoto, Fumiaki Tomoike, Satoshi Shuto, Yoshihiro Ito, Hiroshi Abe

    Chemical Communications   Vol. 56 ( 3 ) page: 466 - 469   2020.1

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    We herein report a new approach for RNA interference, so-called "build-up RNAi" approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors. The advantages of using these circular RNA formats for RNAi were presented in aspects of immunogenicity and cellular uptake.

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  32. SYNTHESIS AND BIOLOGICAL EVALUATION OF NMDI14 DERIVATIVES AS ANTI-MESOTHELIOMA AGENTS Reviewed International journal

    Hong Nhung Nguyen, Suzuki Koya, Kimura Yasuaki, Hirokawa Takatsugu, Murakami-Tonami Yuko, Abe Hiroshi

    Heterocycles   Vol. 100 ( 2 ) page: 253 - 266   2020.1

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  33. N6-methyl adenosine in siRNA evades immune response without reducing RNAi activity Reviewed International journal

    Akihiro Imaeda, Fumiaki Tomoike, Mayu Hayakawa, Kosuke Nakamoto, Yasuaki Kimura, Naoko Abe, Hiroshi Abe

    Nucleosides, Nucleotides and Nucleic Acids   Vol. 38 ( 12 ) page: 972 - 979   2019.12

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    PMID: 31298608

    DOI: 10.1080/15257770.2019.1641205

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  34. Intracellular delivery of Antisense DNA and siRNA with amino groups masked with disulfide units Reviewed International journal

    Zhaoma Shu, Azumi Ota, Yukiya Takayama, Yuri Katsurada, Kosuke Kusamori, Naoko Abe, Kosuke Nakamoto, Fumiaki Tomoike, Seiichi Tada, Yoshihiro Ito, Makiya Nishikawa, Yasuaki Kimura, Hiroshi Abe

      Vol. 68 ( 2 ) page: 129 - 132   2019.12

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  35. Disulfide‐Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA Reviewed International journal

    Zhaoma Shu, Iku Tanaka, Azumi Ota, Daichi Fushihara, Naoko Abe, Saki Kawaguchi, Kosuke Nakamoto, Fumiaki Tomoike, Seiichi Tada, Yoshihiro Ito, Yasuaki Kimura, Hiroshi Abe

    Angewandte Chemie   Vol. 131 ( 20 ) page: 6683   2019.5

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  36. A Covalent Inhibitor for Glutathione S-Transferase Pi (GSTP1-1 ) in Human Cells. Reviewed International journal

    Yuko Shishido, Fumiaki Tomoike, Keiko Kuwata, Haruka Fujikawa, Yoshitaka Sekido, Yuko Murakami-Tonami, Tomoshi Kameda, Naoko Abe, Yasuaki Kimura, Satoshi Shuto, Hiroshi Abe

    Chembiochem : a European journal of chemical biology   Vol. 20 ( 7 ) page: 900 - 905   2019.4

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    Glutathione S-transferase π (GSTP1-1 ) is overexpressed in many types of cancer and is involved in drug resistance. Therefore, GSTP1-1 is an important target in cancer therapy, and many GST inhibitors have been reported. We had previously developed an irreversible inhibitor, GS-ESF, as an effective GST inhibitor; however, its cellular permeability was too low for it to be used in inhibiting intracellular GST. We have now developed new irreversible inhibitors by introducing sulfonyl fluoride (SF) into chloronitrobenzene (CNB). The mechanism of action was revealed to be that CNBSF first reacts with glutathione (GSH) through an aromatic substitution in the cell, then the sulfonyl group on the GSH conjugate with CNBSF reacts with Tyr108 of GST to form a sulfonyl ester bond. Our new inhibitor irreversible inhibited GSTP1-1 both in vitro and in cellulo with a long duration of action.

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  37. 膜透過性を有するGST共有結合性阻害剤の開発

    友池 史明, 宍戸 裕子, 藤川 遥加, 木村 康明, 桑田 啓子, 村上 優子, 福井 健二, 関戸 好孝, 矢野 貴人, 亀田 倫史, 周東 智, 阿部 洋

    日本薬学会年会要旨集   Vol. 139年会 ( 2 ) page: 80 - 80   2019.3

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  38. Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach Reviewed International journal

    Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai

        2018.10

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    <title>Abstract</title>In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosine-cytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existing parameters for canonical RNAs. A duplex with an internal inosine-cytosine pair is 0.9 kcal/mol more unstable than the same duplex with an internal guanine-cytosine pair, and is as stable as the one with an internal adenine-uracil pair (only 0.1 kcal/mol more stable) on average.

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  39. Chemical ligation reaction for oligonucleotides based on electrophilic phosphorothioester

    Kimura Yasuaki, Maruyama Hideto, Oikawa Ryota, Hayakawa Mayu, Abe Naoko, Tsuji Genichiro, Matsuda Akira, Shuto Satoshi, Ito Yoshihiro, Abe Hiroshi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   Vol. 255   page: .   2018.3

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  40. Development of glutathione S-transferase (GST) covalent inhibitor

    Shishido Yuko, Tomoike Fumiaki, Kimura Yasuaki, Kuwata Keiko, Yano Takato, Fukui Kenji, Fujikawa Haruka, Sekido Yoshitaka, Murakami-Tonami Yuko, Kameda Tomoshi, Shuto Satoshi, Abe Hiroshi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   Vol. 255   page: .   2018.3

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  41. Chemical ligation reaction for oligonucleotides based on electrophilic phosphorothioester Reviewed International journal

    Kimura Yasuaki, Maruyama Hideto, Oikawa Ryota, Hayakawa Mayu, Abe Naoko, Tsuji Genichiro, Matsuda Akira, Shuto Satoshi, Ito Yoshihiro, Abe Hiroshi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   Vol. 255   2018.3

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  42. Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications

    Abe Hiroshi, Kimura Yasuaki

    CHEMICAL & PHARMACEUTICAL BULLETIN   Vol. 66 ( 2 ) page: 117-122   2018.2

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  43. Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications Reviewed International journal

    Hiroshi Abe, Yasuaki Kimura

    Chemical and Pharmaceutical Bulletin   Vol. 66 ( 2 ) page: 117 - 122   2018

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    Chemical ligation of oligonucleotides (ONs) is the key reaction for various ON-based technologies. We have tried to solve the problems of RNA interference (RNAi) technology by applying ON chemical ligation to RNAi. We designed a new RNAi system, called intracellular buildup RNAi (IBR-RNAi), where the RNA fragments are built up into active small-interference RNA (siRNA) in cells through a chemical ligation reaction. Using the phosphorothioate and iodoacetyl groups as reactive functional groups for the ligation, we achieved RNAi effects without inducing immune responses. Additionally, we developed a new chemical ligation for IBR-RNAi, which affords a more native-like structure in the ligated product. The new ligation method should be useful not only for IBR-RNAi but also for the chemical synthesis of biofunctional ONs.

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  44. A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP(1-1)) Reviewed International journal

    Yuko Shishido, Fumiaki Tomoike, Yasuaki Kimura, Keiko Kuwata, Takato Yano, Kenji Fukui, Haruka Fujikawa, Yoshitaka Sekido, Yuko Murakami-Tonami, Tomoshi Kameda, Satoshi Shuto, Hiroshi Abe

    CHEMICAL COMMUNICATIONS   Vol. 53 ( 81 ) page: 11138 - 11141   2017.10

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    We herein report the first covalent G-site-binding inhibitor for GST, GS-ESF (1), which irreversibly inhibited the GSTP1-1 function. LC-MS/MS and X-ray structure analyses of the covalently linked GST-inhibitor complex suggested that 1 reacted with Tyr108 of GSTP1-1. The mechanism of covalent bond formation was discussed based on MD simulation results.

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  45. Chemical ligation of oligonucleotides using an electrophilic phosphorothioester Reviewed International journal

    Hideto Maruyama, Ryota Oikawa, Mayu Hayakawa, Shono Takamori, Yasuaki Kimura, Naoko Abe, Genichiro Tsuji, Akira Matsuda, Satoshi Shuto, Yoshihiro Ito, Hiroshi Abe

    NUCLEIC ACIDS RESEARCH   Vol. 45 ( 12 ) page: 7042 - 7048   2017.7

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    We developed a new approach for chemical ligation of oligonucleotides using the electrophilic phosphorothioester (EPT) group. A nucleophilic phosphorothioate group on oligonucleotides was converted into the EPT group by treatment with Sanger's reagent (1-fluoro-2,4-dinitrobenzene). EPT oligonucleotides can be isolated, stored frozen, and used for the ligation reaction. The reaction of the EPT oligonucleotide and an amino-modified oligonucleotide took place without any extra reagents at pH 7.0-8.0 at room temperature, and resulted in a ligation product with a phosphoramidate bond with a 39-85% yield. Thismethod has potential uses in biotechnology and chemical biology.

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  46. Supramolecular Ligands for Histone Tails by Employing a Multivalent Display of Trisulfonated Calix[4]arenes Reviewed

    Yasuaki Kimura, Nae Saito, Kayo Hanada, Jiaan Liu, Takayoshi Okabe, Shigehiro A. Kawashima, Kenzo Yamatsugu, Motomu Kanai

    CHEMBIOCHEM   Vol. 16 ( 18 ) page: 2599 - 2604   2015.12

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    Post-translational modification of histone tails plays critical roles in gene regulation. Thus, molecules recognizing histone tails and controlling their epigenetic modification are desirable as biochemical tools to elucidate regulatory mechanisms. There are, however, only a few synthetic ligands that bind to histone tails with substantial affinity. We report CA2 and CA3, which exhibited sub-micromolar affinity to histone tails (especially tails with a trimethylated lysine). Multivalent display of trisulfonated calix[4] arene was important for strong binding. CA2 was applicable not only to synthetic tail peptides but also to endogenous histone proteins, and was successfully used to pull-down endogenous histones from nuclear extract. These findings indicate the utility of these supramolecular ligands as biochemical tools for studying chromatin regulator protein and as a targeting motif in ligand-directed catalysis to control epigenetic modifications.

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  47. Catalytic Anomeric Aminoalkynylation of Unprotected Aldoses Reviewed

    Yasuaki Kimura, Soichi Ito, Yohei Shimizu, Motomu Kanai

    ORGANIC LETTERS   Vol. 15 ( 16 ) page: 4130 - 4133   2013.8

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    A copper(I)-catalyzed anomeric aminoalkynylation reaction of unprotected aldoses was realized. Use of an electron-deficient phosphine ligand, boric acid to stabilize the iminium intermediate, and a protic additive (IPA) to presumably enhance reversible carbohydrate-boron complexation were all essential for efficient conversion. The reaction proceeded well even with a natural disaccharide substrate, suggesting that the developed catalytic reaction could be useful for the synthesis of glycoconjugates with minimum use of protecting groups.

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  48. Inhibition of MAO-A and stimulation of behavioural activities in mice by the inactive prodrug form of the anti-influenza agent oseltamivir Reviewed

    Miki Hiasa, Yumiko Isoda, Yasushi Kishimoto, Kenta Saitoh, Yasuaki Kimura, Motomu Kanai, Masakatsu Shibasaki, Dai Hatakeyama, Yutaka Kirino, Takashi Kuzuhara

    British Journal of Pharmacology   Vol. 169 ( 1 ) page: 115 - 129   2013.5

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    Background and Purpose Oseltamivir is the most widely prescribed anti-influenza medication. However, in rare instances, it has been reported to stimulate behavioural activities in adolescents. The goal of this study was to determine the molecular mechanism responsible for these behavioural activities. Experimental Approach We performed an in vitro assay of MAO-A, the enzyme responsible for neurotransmitter degradation, using either the active form - oseltamivir carboxylate (OC) or the inactive prodrug - oseltamivir ethyl ester (OEE). We also analysed the docking of MAO-A with OEE or OC in silico. Mouse behaviours after OEE or OC administration were monitored using automated video and computer analysis. Key Results OEE, but not OC, competitively and selectively inhibited human MAO-A. The estimated Ki value was comparable with the Km values of native substrates of MAO-A. Docking simulations in silico based on the tertiary structure of MAO-A suggested that OEE could fit into the inner pocket of the enzyme. Behavioural monitoring using automated video analysis further revealed that OEE, not OC, significantly enhanced spontaneous behavioural activities in mice, such as jumping, rearing, sniffing, turning and walking. Conclusions and Implications Our multilevel analyses suggested OEE to be the cause of the side effects associated with oseltamivir and revealed the molecular mechanism underlying the stimulated behaviours induced by oseltamivir in some circumstances. © 2013 The Authors. British Journal of Pharmacology © 2013 The British Pharmacological Society.

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  49. Design and Synthesis of Resin-Conjugated Tamiflu Analogs for Affinity Chromatography Reviewed

    Yasuaki Kimura, Kenzo Yamatsugu, Motomu Kanai, Noriko Echigo, Takashi Kuzuhara, Masakatsu Shibasaki

    BULLETIN OF THE KOREAN CHEMICAL SOCIETY   Vol. 31 ( 3 ) page: 588 - 594   2010.3

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    Two types of resin-conjugated Tamiflu analogs were synthesized by modifying our original synthetic route of oseltamivir phosphate (Tamiflu). The prepared resins bound to influenza virus neuraminidase, the main target of Tamiflu. The resins will be useful for isolating and identifying presumed endogenous vertebrate proteins that interact with Tamiflu, which might relate to the rarely observed abnormal behavior exhibited by some influenza patients treated with Tamiflu.

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  50. Design and synthesis of immobilized Tamiflu analog on resin for affinity chromatography Reviewed

    Yasuaki Kimura, Kenzo Yamatsugu, Motomu Kanai, Noriko Echigo, Takashi Kuzuhara, Masakatsu Shibasaki

    TETRAHEDRON LETTERS   Vol. 50 ( 26 ) page: 3205 - 3208   2009.7

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    A resin linked with the Tamiflu core was synthesized by modifying our original synthetic route Of oseltamivir phosphate (Tamiflu). The prepared resin bound to the influenza virus enzyme neuraminidase, the main target of Tamiflu. The immobilized Tamiflu analog will be useful for isolating and identifying presumed endogenous vertebrate proteins that interact with Tamiflu, which might relate to the abnormal behavior exhibited by some influenza patients treated with Tamiflu. (C) 2009 Elsevier Ltd. All rights reserved.

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  51. A Synthesis of Tamiflu by Using a Barium-Catalyzed Asymmetric Diels-Alder-Type Reaction Reviewed

    Kenzo Yamatsugu, Liang Yin, Shin Kamijo, Yasuaki Kimura, Motomu Kanai, Masakatsu Shibasaki

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   Vol. 48 ( 6 ) page: 1070 - 1076   2009

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MISC 9

  1. 新規2′修飾核酸によるsiRNAの標的特異性の向上

    馬場麟太郎, 野村浩平, 阿部奈保子, 安成鎮, 小林芳明, 程久美子, 橋谷文貴, 木村康明, 阿部洋, 阿部洋, 阿部洋

    中部化学関係学協会支部連合秋季大会講演予稿集   Vol. 52nd (CD-ROM)   2021

  2. ウイルスタンパク質の活性をトリガーとした新規不可逆阻害剤の開発

    福井竜介, 新美結士, 片倉秀雄, 鈴木哲郎, 村上努, 児玉栄一, 木村康明, 阿部洋

    日本薬学会年会要旨集(CD-ROM)   Vol. 139th ( 2 ) page: ROMBUNNO.23K‐pm11 - 103   2019.3

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  3. ウイルスポリメラーゼの不可逆阻害を目指した新規2′‐&βセレノ核酸アナログの創製

    村上努, 木村康明, 新美結士, 藤野真之, 片倉秀雄, 鈴木哲朗, 児玉栄一, 阿部洋

    日本エイズ学会誌   Vol. 20 ( 4 ) page: 468 - 468   2018.11

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  4. ウイルスポリメラーゼの不可逆阻害を目指した新規2'-&βセレノ核酸アナログの創製

    村上 努, 木村 康明, 新美 結士, 藤野 真之, 片倉 秀雄, 鈴木 哲朗, 児玉 栄一, 阿部 洋

    日本エイズ学会誌   Vol. 20 ( 4 ) page: 468 - 468   2018.11

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  5. Development of glutathione S-transferase (GST) covalent inhibitor International journal

    Shishido Yuko, Tomoike Fumiaki, Kimura Yasuaki, Kuwata Keiko, Yano Takato, Fukui Kenji, Fujikawa Haruka, Sekido Yoshitaka, Murakami-Tonami Yuko, Kameda Tomoshi, Shuto Satoshi, Abe Hiroshi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   Vol. 255   page: .   2018.3

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  6. RETFプローブを用いた生体内の核酸検出

    友池史明, 山岡和樹, 伊藤真央, 木村康明, 井上貴文, 阿部洋

    日本化学会春季年会講演予稿集(CD-ROM)   Vol. 98th   2018

  7. グルタチオン-S-トランスフェラーゼを標的とした共有結合性阻害剤の開発 International journal

    宍戸 裕子, 藤川 遥加, 友池 史明, 木村 康明, 桑田 啓子, 村上 優子, 福井 健二, 関戸 好孝, 矢野 貴人, 周東 智, 阿部 洋

    生命科学系学会合同年次大会   Vol. 2017年度   page: [3P - 0205]   2017.12

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  8. 共有結合型グルタチオンS-転移酵素阻害剤の創薬研究 International journal

    宍戸 裕子, 藤川 遥加, 木村 康明, 友池 史明, 桑田 啓子, 矢野 貴人, 福井 健二, 関戸 好孝, 村上 優子, 周東 智, 阿部 洋

    日本薬学会年会要旨集   Vol. 137年会 ( 2 ) page: 68 - 68   2017.3

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  9. オセルタミビルによるモノアミン酸化酵素(MAO)阻害活性の検討

    ISODA YUMIKO, HIASA MIKI, KISHIMOTO YASUSHI, SAITO KENTA, KIMURA YASUAKI, KANAI MOTOMU, SHIBASAKI MASAKATSU, KIRINO YUTAKA, HATAKEYAMA HIROSHI, KUZUHARA TAKASHI

    日本薬学会年会要旨集(CD-ROM)   Vol. 133rd ( 3 ) page: ROMBUNNO.29T-PM11S - 155   2013.3

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KAKENHI (Grants-in-Aid for Scientific Research) 11

  1. ジスルフィドを利用したオリゴ核酸デリバリー法の深化と技術拡張

    Grant number:23K23486  2022.4 - 2026.3

    科学研究費助成事業  基盤研究(B)

    木村 康明

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    Authorship:Principal investigator 

    Grant amount:\17160000 ( Direct Cost: \13200000 、 Indirect Cost:\3960000 )

    細胞内の標的mRNAの分解を誘発することによって疾病治療を行うオリゴ核酸医薬の開発が盛んに行われているが、オリゴ核酸分子を効率的に細胞内に送達する手法について様々な課題がある。 本研究ではジスルフィド構造に基づき、その送達効率の向上と送達の分子メカニズムの解明に取り組み、高活性な核酸医薬創出の基盤を構築する。
    アンチセンス核酸やsiRNAは標的mRNAの発現を抑制する遺伝子治療薬として有望であるが、その細胞内へのデリバリー法に関して課題がある。有用な手法としてLNPなどの高分子キャリアや、リガンドコンジュゲート法などが存在するが、細胞質への到達効率や細胞毒性等の観点から課題が残り、オリゴ核酸に適した新規のデリバリー技術の開発が重要である。こうした背景を踏まえ本研究ではジスルフィド構造をオリゴ核酸の末端に導入することで、その細胞内取り込みを促進する手法を開発する。
    今年度の研究では、酸化型を含む各種ジスルフィド部位の構造誘導体の合成とその活性評価を行った。分子設計おいてはジスルフィド部位の化学的反応性を考慮した一連の誘導体構造を設定し、合成においてはオリゴ核酸の合成と、反応性官能基導入過程を分離することで安定的に設計したオリゴ核酸を調製した。各種誘導体を導入したオリゴ核酸を細胞系で評価し、膜透過性・細胞毒性・免疫応答の観点から有望なジスルフィド構造や修飾パターンを見出しつつある。
    種々のジスルフィド誘導体について合成および活性評価を実施し、細胞膜透過性や細胞毒性の観点から有望な誘導体候補を見出しているため。
    引き続きジスルフィドおよびリンカー部位の構造活性相関を行い、更なる活性向上を目指す。また、アンチセンス核酸以外のモダリティへの導入も検討し、基盤技術の適用範囲の拡大を図る。有望な構造について細胞膜透過のメカニズム解析を行う。

  2. Dynamic Element-Effect Design for Unconventional Molecular Functions

    Grant number:22K21346  2022.12 - 2029.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Fund for the Promotion of Joint International Research (International Leading Research )

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  3. ジスルフィドを利用したオリゴ核酸デリバリー法の深化と技術拡張

    Grant number:22H02219  2022.4 - 2026.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    木村 康明

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    Authorship:Principal investigator 

    Grant amount:\17160000 ( Direct Cost: \13200000 、 Indirect Cost:\3960000 )

    アンチセンス法やRNA干渉法に基づく核酸医薬の開発が進んでいるが、そのデリバリー法には課題が残っている。例えば代表的なデリバリー法であるlipid nano-particle法では、オリゴ核酸の細胞質内への送達効率が低く、またキャリア分子に由来する免疫原性や分子組成の不均一性などの種々の課題がある。本研究では、申請者らがこれらの課題解決を目指し開発を進めてきたジスルフィド構造を基盤としたオリゴ核酸の新規デリバリー法について、取り込み過程の分子機構の理解、分子構造の最適化による機能向上、そして適用可能な核酸医薬モダリティの拡張を目指す。
    アンチセンス核酸やsiRNAは標的mRNAの発現を抑制する遺伝子治療薬として有望であるが、その細胞内へのデリバリー法に関して課題がある。有用な手法としてLNPなどの高分子キャリアや、リガンドコンジュゲート法などが存在するが、細胞質への到達効率や細胞毒性等の観点から課題が残り、オリゴ核酸に適した新規のデリバリー技術の開発が重要である。こうした背景を踏まえ本研究ではジスルフィド構造をオリゴ核酸の末端に導入することで、その細胞内取り込みを促進する手法を開発する。
    今年度の研究では、酸化型を含む各種ジスルフィド部位の構造誘導体の合成とその活性評価を行った。分子設計おいてはジスルフィド部位の化学的反応性を考慮した一連の誘導体構造を設定し、合成においてはオリゴ核酸の合成と、反応性官能基導入過程を分離することで安定的に設計したオリゴ核酸を調製した。各種誘導体を導入したオリゴ核酸を細胞系で評価し、膜透過性・細胞毒性・免疫応答の観点から有望なジスルフィド構造や修飾パターンを見出しつつある。
    種々のジスルフィド誘導体について合成および活性評価を実施し、細胞膜透過性や細胞毒性の観点から有望な誘導体候補を見出しているため。
    引き続きジスルフィドおよびリンカー部位の構造活性相関を行い、更なる活性向上を目指す。また、アンチセンス核酸以外のモダリティへの導入も検討し、基盤技術の適用範囲の拡大を図る。有望な構造について細胞膜透過のメカニズム解析を行う。

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  4. Molecular design strategy to avoid side effects of covalent drugs

    Grant number:20K21249  2020.7 - 2022.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

    Kimura Yasuaki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\6500000 ( Direct Cost: \5000000 、 Indirect Cost:\1500000 )

    Mechanistic analysis and structure-activity relationship studies of a reverse transcriptase inhibitor with a novel mechanism of action were conducted. In the mechanistic analysis, we verified the release of reactive species associated with the enzymatic reaction unique to this inhibitor and the inhibitory effect based on the release of reactive species. In the structure-activity relationship study, we found a molecular design guideline for further enhancement of activity and succeeded in developing a highly effective prodrug of phosphate-based on a novel chemical structure

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  5. Development of covalent drugs activatable by the target enzymes

    Grant number:18K14356  2018.4 - 2020.3

    Grant-in-Aid for Early-Career Scientists

    Kimura Yasuaki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

    A covalent drug is a drug molecule that forms a covalent bond with a target enzyme to inhibit its function, and has high inhibitory activity. Due to this property, covalent drugs targeting various enzymes have been developed in recent years. However, covalent drugs often form covalent bonds with non-targeting proteins, and side effects derived from them are a major issue in the development of covalent drugs. In this research, as a strategy to avoid such side effect problems, we developed a covalent drug that is activated by a target enzyme and developed an antiviral drug by using a nucleoside analog as an example. The developed nucleoside analog showed good pharmacological activity against HIV.

  6. 標的酵素で活性化される共有結合医薬の開発

    2018.4 - 2020.3

    日本学術振興会  科学研究費補助金 若手研究 

    木村康明

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  7. Improvement of catalytic turnover based on transition state control of oligonucleotide template chemical reaction

    Grant number:16KT0052  2016.7 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Abe Hiroshi

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    The fluorescence reaction based on the oligonucleotide (ON) template reaction is one of the most basic working principles of the RNA detection probe. In this method, an ON probe having a reactive functional group and an ON probe having a fluorescent precursor whose fluorescence is suppressed by a protecting group are associated on the target RNA, and then the protective group is removed and fluorescence signal is generated. Since this fluorescence reaction specifically occurs in the presence of target RNA, it can be the working principle RNA detection probe. In order to detect intracellular RNA highly sensitively, we worked on (1) accelerating ON template reaction and (2) development of a new method of intracellular administration of ON probe without lipofection. Prospective results were obtained in (1) by appropriately selecting the nucleophile for the reaction, and in (2) by use of phosphorothioate in the ON probe.

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  8. mRNAの化学合成を可能にするRNAライゲーション反応の開発

    2016.4 - 2018.3

    科学研究費補助金  若手研究(B)

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    Authorship:Principal investigator 

  9. Development of Chemical Ligation Reaction of RNA for Chemical Synthesis of mRNA

    Grant number:16K21091  2016.4 - 2018.3

    Kimura Yasuaki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\3900000 ( Direct Cost: \3000000 、 Indirect Cost:\900000 )

    We developed chemical ligation reaction for oligonucleotides (ONs) that enables the synthesis of long ONs such as mRNA etc. In the ON synthesis for ON medicines, chemical synthesis is optimal because high molecular homogeneity and tolerance for unnatural structure are required, but the current solid phase synthesis has an upper limit on the length of the products. Therefore, it is necessary to couple the fragments obtained by the solid phase synthesis by chemical reaction. We developed new chemical ligation reactions for ONs, which afford ligated strands having a linkage structure similar to that of natural ONs.

  10. mRNAの化学合成を可能にするRNAライゲーション反応の開発

    2016.4 - 2018.3

    日本学術振興会  科学研究費補助金 若手研究(B) 

    木村康明

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  11. 環境調和型触媒的不斉炭素-炭素結合形成反応の開発と重要医薬品合成への応用

    Grant number:10J07619  2010.4 - 2013.3

    日本学術振興会  特別研究員奨励費 (DC1)  特別研究員奨励費

    木村康明

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    Authorship:Principal investigator  Grant type:Competitive

    オリゴ糖や複合糖鎖は、細胞分化や免疫応答などの重要な生命現象に関与していることが知られている。そのため合成糖類縁体は、医薬化学や分子生物学の研究領域において最も重要な分子種の一つである。従来の糖類縁体の合成においては、多くの反応を阻害する水酸基を保護することが一般的であった。保護基の使用により高い確実性をもって様々な化学変換を行うことが可能になったが、保護基の着脱に纏わる煩雑な操作のために、合成効率が大きく低下する例も多い。そのような問題点に対し、保護基フリーの糖に対して適用可能な触媒的炭素-炭素結合形成反応を開発することで、保護基の使用を最小限に抑えた効率的な糖誘導体合成法の確立することを目標に据え、研究を行った。前年渡までに、一価銅触媒による末端アルキンと二級アミンを基質とした無保護のアルドースに対するアミノアルキニル化反応においては、各々のアルキン及び単糖基質に最適な反応条件を見出し、本反応が効率的な糖誘導体合成に有用であることが示されたが、今年度は本反応の高い官能基許容性を生かし、bioconjugationを指向した反応の開発に取り組んだ。具体的には、二糖などの多数の水酸基を持つ糖基質や、biotin等生物学的に有用な構造を有するアルキンを基質として、目的のアミノアルキニル化が進行することを見出した。この結果は、本反応が効率的な物質生産のみならず、chemical biology等における有用な方法論を提供するものであることを示しているといえる。
    また、本触媒反応を基盤として、抗インフルエンザ薬:ザナミビル(商品名リレンザ)の合成研究も行った。現在までに合成中後半に至る合成経路が確立しており、鍵反応であるザナミビルの中心六員環形成反応の開発を行っている。今後は、アミノアルキニル化反応の高い官能基許容性を最大限活用し、多様な置換基構造を有するザナミビル誘導体合成にも展開していく予定である。

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Industrial property rights 6

  1. 核酸モノマー

    阿部 洋, 阿部 奈保子, 木村 康明, 野村 浩平, 程 久美子, 小林 芳明, 安 成鎮

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    Applicant:国立大学法人東海国立大学機構

    Application no:特願2020-159793  Date applied:2020.9

    Announcement no:特開2022-053148  Date announced:2022.4

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  2. マイクロRNAプロセシング活性の検出方法及びその応用

    辻村 啓太, 尾崎 紀夫, 阿部 洋, 木村 康明

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    Applicant:国立大学法人東海国立大学機構

    Application no:特願2020-547024  Date applied:2020.1

    Publication no:WO2020-183941  Date published:2020.9

    Patent/Registration no:特許第6869587号  Date registered:2021.4 

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  3. マイクロRNAプロセシング活性の検出方法及びその応用

    辻村 啓太, 尾崎 紀夫, 阿部 洋, 木村 康明

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    Applicant:国立大学法人東海国立大学機構

    Application no:JP2020002568  Date applied:2020.1

    Publication no:WO2020-183941  Date published:2020.9

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  4. マイクロRNAプロセシング活性の検出方法及びその応用

    辻村 啓太, 尾崎 紀夫, 阿部 洋, 木村 康明

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    Applicant:国立大学法人東海国立大学機構

    Application no:特願2020-547024  Date applied:2020.1

    Patent/Registration no:特許第6869587号  Date registered:2021.4 

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  5. β修飾リン酸化合物前駆体、β修飾リン酸化合物、反応阻害剤及びこれを含む医薬並びに反応阻害方法

    阿部 洋, 木村 康明

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    Applicant:国立研究開発法人科学技術振興機構

    Application no:JP2019009213  Date applied:2019.3

    Publication no:WO2019-172394  Date published:2019.9

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  6. β修飾リン酸化合物前駆体、β修飾リン酸化合物、反応阻害剤及びこれを含む医薬並びに反応阻害方法

    阿部 洋, 木村 康明

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    Applicant:国立研究開発法人科学技術振興機構

    Application no:JP2019009213  Date applied:2019.3

    Patent/Registration no:特許第7266896号  Date registered:2023.4 

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