Updated on 2024/05/16


Graduate School of Science Department of Biological Chemistry Lecturer
School of Science Department of Biological Chemistry
Institute of Science


  • Graduate School of Science Department of Biological Chemistry 

    Lecturer  2022.04 - Now

  • School of Science Department of Biological Chemistry 

    Lecturer  2022.04 - Now


  • 博士(理学) ( Others )

Research Areas

  • Nanotechnology/Materials / Chemical biology

  • Nanotechnology/Materials / Chemistry and chemical methodology of biomolecules

  • Nanotechnology/Materials / Bio chemistry  / 生体関連化学

  • Life Science / Pharmaceutical chemistry and drug development sciences  / Chemical Biology

  • Nanotechnology/Materials / Chemistry and chemical methodology of biomolecules

  • Life Science / Applied biochemistry

  • Nanotechnology/Materials / Chemical biology

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Research subject summary

  • 進化分子工学を用いた特異的プロテインキナーゼ阻害剤創製法の確立

  • 細胞内プロテインネットワークの制御・機能解析法の確立

  • 立体構造規制ペプチドライブラリーを用いた分子標的ペプチドの創出

Research Career

  • Selection of Molecular-Targeting Ligands by Conformationally Constrained Peptide Libraries

    Directed Evolution, Peptide, Protein-Protein Interaction 

  • Regulation of Intracellular protein-protein interactions with molecular-targeting ligands

    Chemical Biology, Peptide, Protein-Protein Interactiion 

  • Generation of Highly Specific Protein Kinase Inhibitor

    Directed Evolution, Protein Kinase, Inhibitor 

Professional Memberships

  • Japan Society for Bioscience, Biotechnology, and Agrochemistry

    2019.04 - Now   Domestic

  • バイオインタラクション研究会

    2018.04 - Now   Domestic

  • 日本薬学会

    2017.04 - Now   Domestic

  • 日本生物工学会

    2014 - Now

  • 日本分子生物学会

    2011 - Now

  • 日本蛋白質科学会

    2011 - Now

  • 日本化学会

    2011 - Now

  • 日本ペプチド学会

    2011 - Now


  • Protein Science Society of Japan

  • The Pharmaceutical Society of Japan, Division of Medicinal Chemistry

  • The Pharmaceutical Society of Japan

  • The Society for Biotechnology, Japan

  • The Chemical Society of Japan


  • The Japanese Peptide Society

  • バイオインタラクション研究会

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  • メディシナルケミストリー シンポジウム優秀賞

    2017.10   日本薬学会 医薬化学部会  

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Job Career (off-campus)

  • Osaka Metropolitan University   Graduate School of Science

    2022.04 - Now


  • Extracellular Microvesicles Modified with Arginine-Rich Peptides for Active Macropinocytosis Induction and Delivery of Therapeutic Molecules

    Kenta Morimoto, Jojiro Ishitobi, Kosuke Noguchi, Ryoichi Kira, Yukiya Kitayama, Yuto Goto, Daisuke Fujiwara, Masataka Michigami, Atsushi Harada, Tomoka Takatani-Nakase, Ikuo Fujii, Shiroh Futaki, Masamitsu Kanada, Ikuhiko Nakase

    ACS Applied Materials & Interfaces   16 ( 14 )   17069 - 17079   2023( ISSN:19448244

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/acsami.3c14592


  • Generation of molecular-targeting helix-loop-helix peptides for inhibition of the interaction between cytotoxic T-lymphocyte-associated protein 4 and B7 in the dog Reviewed


    Journal of Veterinary Medical Science   84 ( 8 )   1101 - 1107   2022.06( ISSN:0916-7250

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1292/jvms.21-0318


  • 細胞内タンパク質間相互作用を制御する医薬品の創出に向けて

    藤原 大佑

    ファルマシア   58 ( 11 )   1075_1 - 1075_1   2022( ISSN:00148601

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    DOI: 10.14894/faruawpsj.58.11_1075_1

  • Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation Reviewed

    Setsu Nakae, Maho Kitamura, Daisuke Fujiwara, Masaaki Sawa, Tsuyoshi Shirai, Ikuo Fujii, Toshiji Tada

    Acta Crystallographica Section F Structural Biology Communications   77 ( 12 )   459 - 464   2021.12

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    Publishing type:Research paper (scientific journal)   International / domestic magazine:International journal  

    Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38–381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.

    DOI: 10.1107/s2053230x21011687


  • Chemical Modification of Phage‐Displayed Helix‐Loop‐Helix Peptides to Construct Kinase‐Focused Libraries Reviewed

    Daisuke Fujiwara, Kousuke Mihara, Ryo Takayama, Yusuke Nakamura, Mitsuhiro Ueda, Takeshi Tsumuraya, Ikuo Fujii

    ChemBioChem   22 ( 24 )   3406 - 3409   2021.10( ISSN:1439-4227

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   International / domestic magazine:International journal  

    Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target-focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase-focused library by chemically modifying helix-loop-helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip-3 retained the α-helical structure and bound to AurA with a KD value of 13.7 μM. Bip-3 and the adenosine-tethered peptide Bip-3-Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip-3-Adc bivalently inhibited AurA. In addition, the selectivity of Bip-3-Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase-focused library of phage-displayed HLH peptides.

    DOI: 10.1002/cbic.202100450


  • Generation of inhibitory peptides for IKKε from a kinase-focused phage library of helix-loop-helix peptides Reviewed

    Kousuke Mihara, Natsumi Nakajima, Ikuo Fujii, Daisuke Fujiwara

    Peptide Science   e24253   2021.10

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pep2.24253

  • Macropinocytosis-Inducible Extracellular Vesicles Modified with Antimicrobial Protein CAP18-Derived Cell-Penetrating Peptides for Efficient Intracellular Delivery. Reviewed

    Kosuke Noguchi, Momoko Obuki, Haruka Sumi, Merlin Klußmann, Kenta Morimoto, Shinya Nakai, Takuya Hashimoto, Daisuke Fujiwara, Ikuo Fujii, Eiji Yuba, Tomoka Takatani-Nakase, Ines Neundorf, Ikuhiko Nakase

    Molecular pharmaceutics   18 ( 9 )   3290 - 3301   2021.09( ISSN:1543-8384

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    Publishing type:Research paper (scientific journal)   International / domestic magazine:International journal  

    The antimicrobial protein CAP18 (approximate molecular weight: 18 000), which was first isolated from rabbit granulocytes, comprises a C-terminal fragment that has negatively charged lipopolysaccharide binding activity. In this study, we found that CAP18 (106-121)-derived (sC18)2 peptides have macropinocytosis-inducible biological functions. In addition, we found that these peptides are highly applicable for use as extracellular vesicle (exosomes, EV)-based intracellular delivery, which is expected to be a next-generation drug delivery carrier. Here, we demonstrate that dimerized (sC18)2 peptides can be easily introduced on EV membranes when modified with a hydrophobic moiety, and that they show high potential for enhanced cellular uptake of EVs. By glycosaminoglycan-dependent induction of macropinocytosis, cellular EV uptake in targeted cells was strongly increased by the peptide modification made to EVs, and intriguingly, our herein presented technique is efficiently applicable for the cytosolic delivery of the biologically cell-killing functional toxin protein, saporin, which was artificially encapsulated in the EVs by electroporation, suggesting a useful technique for EV-based intracellular delivery of biofunctional molecules.

    DOI: 10.1021/acs.molpharmaceut.1c00244


  • An Immune-Stimulatory Helix–Loop–Helix Peptide: Selective Inhibition of CTLA-4–B7 Interaction Reviewed

    Tharanga M.R. Ramanayake Mudiyanselage, Masataka Michigami, Zhengmao Ye, Atsuko Uyeda, Norimitsu Inoue, Kikuya Sugiura, Ikuo Fujii, Daisuke Fujiwara

    ACS Chemical Biology   15 ( 2 )   360 - 368   2020.02( ISSN:1554-8929

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    Authorship:Last author   Publishing type:Research paper (scientific journal)   International / domestic magazine:International journal  

    Molecular-targeting peptides and mini-proteins are promising alternatives to antibodies in a wide range of applications in bioscience and medicine. We have developed a helix-loop-helix (HLH) peptide as an alternative to antibodies to inhibit specific protein interactions. Cytotoxic T lymphocyte antigen-4 (CTLA-4) downregulates immune responses of cytotoxic T-cells by interaction with B7-1, a co-stimulatory molecule expressed on antigen presenting cells (APCs). To induce immune stimulatory activity, we used directed evolution methods to generate a HLH peptide that binds to CTLA-4, inhibiting the CTLA-4-B7-1 interaction and inducing immune stimulatory activity. Yeast-displayed libraries of HLH peptides were constructed and screened against CTLA-4 and identified the binding peptide Y-2, which exhibits a moderate affinity. The affinity of Y-2 was improved by in vitro affinity maturation to afford a stronger binder, ERY2-4. Peptide ERY2-4 specifically bound to CTLA-4 with a KD of 196.8 ± 2.3 nM, comparable to the affinity of the CTLA-4-B7-1 interaction. Furthermore, ERY2-4 inhibited the CTLA-4-B7-1 interaction with an IC50 of 1.1 ± 0.03 μM and blocked the interaction between CTLA-4 and dendritic cells (DCs) presenting B7 on their surface. Importantly, ERY2-4 showed no cross-reactivity against CD28, suggesting it does not suppress T-cell activation. Finally, in a mixed lymphocyte reaction assay with DCs and T cells, ERY2-4 enhanced an allogeneic lymphocyte response. Since CTLA-4 is a critical immune checkpoint for restricting the cancer immune response, this inhibitory HLH peptide represents a new class of drug candidates for immunotherapy.

    DOI: 10.1021/acschembio.9b00743


  • Intracellular target delivery of cell-penetrating peptide-conjugated dodecaborate for boron neutron capture therapy (BNCT). Reviewed

    Ikuhiko Nakase, Miku Katayama, Yoshihide Hattori, Miki Ishimura, Shunsuke Inaura, Daisuke Fujiwara, Tomoka Takatani-Nakase, Ikuo Fujii, Shiroh Futaki, Mitsunori Kirihata

    Chemical communications (Cambridge, England)   55 ( 93 )   13955 - 13958   2019.11( ISSN:1359-7345

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    Publishing type:Research paper (scientific journal)  

    In this study, we designed and synthesized organelle-targeted cell-penetrating peptide (CPP)-conjugated boron compounds to increase their cellular uptake and to control the intracellular locations for the induction of sophisticated anticancer biological activity in boron neutron capture therapy (BNCT), leading to anticancer effects with ATP reduction and apoptosis when irradiated with neutrons in an in vitro BNCT assay.

    DOI: 10.1039/c9cc03924d


  • Generation of Molecular-Targeting Peptides for Protein Kinase:A Phage-Displayed Library of Helix-Loop-Helix Peptides conjugated with Adenosine. Reviewed

    Fujiwara, D., Mihara, K., Nakamura, Y., Tsumuraya, T., and Fujii, I.

    Peptide Science 雑誌 日本ペプチド学会   2016   169 - 170   2017.04

  • A Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein-Protein Interactions by Epitope and Arginine Grafting Reviewed

    Fujiwara D., Kitada H., Oguri M., Nishihara T., Michigami M., Shiraishi K., Yuba E., Nakase I., Im H., Cho S., Joung JY., Kodama S., Kono K., Ham S., Fujii I.

    Angwe. Chem. Int. Ed. 雑誌 John Wiley & Sons, Inc.   2016.08

  • Macrocyclization and Labeling of Helix-Loop-Helix peptide with intramolecular bis-thioether linkage Reviewed

    Nishihara T., Kitada H., Fujiwara D., Fujii I.

    Biopolymer, Peptide Science 雑誌 John Wiley & Sons, Inc.   106   415 - 421   2016

  • Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Intracellular Protein-Protein Interaction Inhibitors Reviewed

    Fujiwara, D., Kitada, H., Oguri, M., Nishihara, T., Michigami, M., Shiraishi, K., Yuba, E., Nakase, I., Kodama, S., Kono, K., Ham, S., Fujii, I.

    Peptide Sci. 雑誌 日本ペプチド学会   85 - 86   2016

  • Poly-Arginine Conjugated Helix-Loop-Helix Peptide as an Inhibitor for p53-HDM2 interaction Reviewed

    Inaura, S., Kitada, H., Michigami, M., Fujiwara, D., Nakase, I., Fujii, I.

    Peptide Sci. 雑誌 日本ペプチド学会   259 - 260   2016

  • Molecular Design of Protien Kinase Inhibitors: Conjugation of ATP-Competitive Molecules with Kinase Surface-Targeted Peptides Reviewed

    Takayama R., Fujiwara, D., and Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   313 - 314   2015

  • Molecular characterization of a Penicillium chrysogenum exo-rhamnogalacturonan lyase that is structurally distinct from other polysaccharide lyase family proteins Reviewed

    Iwai, M., Kawakami, T., Ikemoto, T., Fujiwara, D., Takenaka, S., Nakazawa, M., Ueda, M., Sakamoto, T.

    Appl. Microbiol. Biotechnol. 雑誌 Springer   2015

  • Biochemical Charactarization of Overexpression of an Endo-rhamnogalacturonan Lyase from Penicillium Chrysogenum Reviewed

    Iwai, M., Yamada, H., Ikemoto, T., Matsumoto, S., Fujiwara, D., Takenaka, S., and Sakamoto, T.

    Mol. Biotechnol 雑誌 Springer   57   539 - 548   2015

  • Design of Helix-Loop-Helix Peptide Inhibitor for p53-HDM2 Interaction Reviewed

    Kitada, H., Oguri, M., Fujiwara, D., and Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   271 - 272   2015

  • Peptide-based immunoabsorbents: Molecular grafting of IgG-Fc-binding epitopes of Protein A onto a de novo-designed helix-loop-helix Reviewed

    Kawabata, K., Nagai, H., Konishi, N., Fujiwara, D., Sasaki, R., Ichikawa, T., Fujii, I.

    Bioorg. Med. Chem. 雑誌 ELSEVIER   22   1845 - 1849   2014

  • The crystal structure of multidrug-resistance regulator RamR with multiple drugs Reviewed

    Yamasaki, S., Nikaido, E., Nakashima, R., Sakurai, K., Fujiwara, D., Fujii, I., Nishino, K.

    Nat. Commun. 雑誌 Nature Publishing Group   4   2013

  • Chemical synthesis and modification of cyclic Helix-Loop-Helix peptides by click chemistry and intramolecular bi-thioether linkage Reviewed

    Nishihara, T., Kitada, H., Fujiwara, D. and Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   135 - 136   2013

  • Chemically modified phage-displayed peptide libraries: Tethering biotin to the displayed peptides Reviewed

    Nakamura, Y., Fujiwara, D., Nishihara, T., and Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   535 - 354   2013

  • Phage selection of peptide "Microantibodies" Reviewed

    Fujiwara, D., Fujii, I.

    Curr. Protoc. Chem. Biol. 雑誌 John Wiley & Sons, Inc.   2013

  • Isolation of human VEGF binding peptides from a conformationally constrained peptide library Reviewed

    Yamamoto, T., Ye Z., Fujiwara, D., Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   311 - 312   2012

  • Yeast-displayed peptide libraries to generate molecular-targeting peptides Reviewed

    Sekinishi, K., Fujiwara, D., Shibasaki, S., Ueda, A., Fujii, I.

    Pept. Sci. 雑誌 日本ペプチド学会   313 - 314   2012

  • Selection of Inhibitory Peptides for Aurora-A Kinase from a Phage-displayed Library of Helix-Loop-Helix Peptides Reviewed

    Fujiwara D., Ye Z., Gouda, M., Yokota, K., Tsumuraya T., Fujii I.

    Bioorg. Med. Chem. Lett. 雑誌 Science Direct   20   1776 - 1778   2010

  • A phage displayed library of constrained loop peptides Reviewed

    Fujiwara D., Ye Z., Tsumuraya T., Fujii I.

    Pept. Sci. 雑誌 日本ペプチド学会   2007

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Books and Other Publications

  • 新規モダリティ医薬品のための新しいDDS技術と製剤化

    中瀬生彦, 藤原大佑( Role: Joint author ,  第4章 エクソソームのDDSキャリアの活用とその設計 第2節 細胞膜透過性ペプチド修飾型エクソソームを基盤とした薬物送達技術の開発)

    株式会社技術情報協会  2023.01 

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    Total pages:10  


  • ポスト抗体医薬:免疫チェックポイントを制御するヘリックス-ループ-ヘリックスペプチド—マイクロ抗体—


    日本ペプチド学会 Peptide Newsletter Japan   ( 121 )   8 - 11   2021.07

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  • ポスト抗体医薬:免疫チェックポイントを制御するヘリックス-ループ-ヘリックスペプチド—マイクロ抗体—


    酵素工学ニュース   84   9 - 12   2020.12

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  • 分子標的 HLH ペプチドを基盤とした新しい創薬モダリティー


    Drug Delivery System   35   2020.07

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  • 【中分子創薬とDDS】分子標的HLHペプチドを基盤とした新しい創薬モダリティー

    藤井 郁雄, 藤原 大佑, 道上 雅孝

    Drug Delivery System   35 ( 3 )   212 - 221   2020.07( ISSN:0913-5006

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  • タンパク質-タンパク質相互作用(PPI)阻害活性を有する立体構造規制ペプチド「マイクロ抗体」の概要と安定性

    藤原大佑, 藤井郁雄

    株式会社情報機構 医薬品開発における中分子領域 (核酸医薬・ペプチド医薬品)における開発戦略   2019.10

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  • ヘリックス‐ループ‐ヘリックスペプチド「マイクロ抗体」を基盤とした中分子創薬


    日本農芸化学会関西支部講演会講演要旨集   509th   4‐5   2019.07

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  • ホウ素中性子捕捉療法(BNCT)における膜透過性ペプチドを用いたホウ素薬剤の細胞内局在制御と細胞死誘導促進

    中瀬生彦, 片山未来, 服部能英, 石村美紀, 稲浦峻亮, 藤原大佑, 中瀬朋夏, 藤井郁雄, 二木史朗, 切畑光統

    日本DDS学会学術集会プログラム予稿集   35th   130   2019.06

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  • ポスト抗体医薬品:立体構造規制ペプチド「マイクロ抗体」を土台とした中分子創薬

    藤原大佑, 弓場英司, 白石一乗, 中瀬生彦, 藤井郁雄

    日本薬学会医薬化学部会 MDCHEM NEWS   28   83 - 87   2018.04

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  • ポスト抗体医薬:高機能化分子標的ペプチドの設計と創出

    藤原大佑, 藤井郁雄

    株式会社化学工業社 化学工業   67   861 - 867   2016.11

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Industrial Property Rights

  • プロテインキナーゼ阻害剤


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    Patent/Registration no:P170014560 

  • 抗腫瘍ペプチド化合物


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Outline of collaborative research (seeds)

  • 次世代型ファージ表層提示ペプチドライブラリーの構築と分子標的リガンドの獲得

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  • プロテインキナーゼ特異的阻害剤の創製

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Charge of on-campus class subject

  • Experiment in Biological Science II

    2021   Practical Training  

  • Protein Chemistry


  • Fundamental Experiments of Biology

    2021   Practical Training  

  • Chemical Biology