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動的創薬モダリティ研究グループ

研究概要

バイオ計測とITを融合させた最先端技術の開発により、創薬標的タンパク質をはじめとする生体高分子、細胞、個体など、ミクロからマクロまで多様かつ動的な対象に対して、その機能を制御する適切なモダリティの提供を行う基盤技術の開発と創薬への応用を推進します。

動的創薬モダリティ研究グループ

研究課題

研究課題1:多様な創薬モダリティを活用した動的構造創薬技術の開発
研究担当者:竹内 恒、徳永 裕二、今清水 正彦

近年、発展の著しい高分子バイオ医薬や、今後の発展が期待される中分子医薬など、新たな創薬モダリティに着目し、それらの動的構造評価と高機能化を行う技術を確立することで、創薬の可能性を広げる研究を行います。特に溶液NMR法を用いた、動的構造創薬技術の確立により、高分子バイオ医薬の高次構造解析、中分子医薬の高機能化、リード最適化などに取り組み、新たな創薬の仕組みを確立します。

動的創薬モダリティ研究グループ2

研究課題

研究課題2:動的な分子認識を利用した新規医薬品・医療技術のための理論計算基盤の開発
研究担当者:福西 快文

新規創薬モダリティは、静的な立体構造に加えて、その分子運動により機能を発揮します。一方、このように動的な創薬モダリティを解析するための理論計算ツールは、いまだ十分に開発されていません。私たちは、国内40社以上の製薬・IT企業と、共同で培ってきた計算技術を、創薬ソフトウェア群myPrestoに実装し、生命活動を調整する生体分子の運動と相互認識機構を解明する理論的ツールの開発と提供を行います。

動的創薬モダリティ研究グループ3

研究課題

研究課題3:動的生体プロファイリング・実験自動化技術の開発
研究担当者:足達 俊吾、茂木 克雄、前田 史雄

質量分析やProximity Extension Assay技術、AIを用いたデータ解析により、生体や細胞の状態を俯瞰的に捉え、その特徴から未来の状態をも予想可能とする技術を開発するとともに、ウイルスの機能を活用した細胞制御技術を開発します。また、自動培養装置、自動液滴操作、双腕ロボットを利用した実験自動化技術を開発し、実験プロトコルの最適化、標準化を容易にすることで、知識集約型のライフサイエンス研究を実現します。

動的創薬モダリティ研究グループ4

研究課題

研究課題4:遺伝学的情報とは異なるアプローチによる細胞の理解を目指した解析基盤の確立
研究担当者:小林 慎、福田 枝里子

細胞内ではエピジェネティクスや分子間相互作用など、単純な遺伝情報を超えた様々なイベントが起きています。我々はエピジェネティックな状態変化をライブイメージングする技術や、約2万種のヒトタンパク質を搭載したプロテインアレイによる分子間相互作用解析の技術などを用いることで、遺伝学的情報を超えた細胞の動的な状態を研究し、生物の理解や創薬に繋げる研究を推進します。 

動的創薬モダリティ研究グループ5

メンバー

名前 役職 主な研究テーマ
竹内 恒 TAKEUCHI Koh グループ長 ・NMRを用いた構造モダリティ研究
・創薬タンパク質の動的機能構造解析
・バイオ医薬の溶液中での構造評価
福西 快文 FUKUNISHI Yoshifumi 主任研究員 ・創薬分子設計のための計算化学ソフトウェア開発
・医薬分子を中心とした生物物理化学
・中分子・低分子の膜透過・脂溶性など物性予測
足達 俊吾 ADACHI Shungo 主任研究員 ・質量分析を用いた、タンパク質、RNA、細胞内シグナル経路解析技術の開発
・血液のマルチオミクス解析による生体プロファイリング技術の開発
・バイオ実験自動化装置の開発
小林 慎 KOBAYASHI Shin 主任研究員 ・哺乳類初期発生におけるエピジェネティクス制御の研究
・X染色体再活性化ライブイメージング技術を用いた幹細胞研究
・ヒト遺伝性疾患におけるエピジェネティクス研究
今清水 正彦 IMASHIMIZU Masahiko 主任研究員 ・熱運動を利用する生物反応を理解するための摂動手段の獲得
・THz光による水・生体高分子の運動変化の直接観測
・THz光の非熱的効果の検証
徳永 裕二 TOKUNAGA Yuji 主任研究員 ・抗体医薬の無侵襲な高次構造フィンガープリント技術
・動的構造解析によるリード化合物最適化技術
・創薬標的構造の探索を 指向したタンパク質の動的構造平衡
茂木 克雄 MOGI Katsuo 主任研究員 ・微小浮遊粒子のハンドリング技術
・微量液滴のハンドリング技術
・細胞分泌物質の電気計測装置の開発
福田 枝里子 FUKUDA Eriko 研究員 ・健康に関わる血中自己抗体の網羅的な検出と抗原同定
・ハイスループットなタンパク質発現・精製技術
・高密度・高機能プロテインアレイ作製技術
前田 史雄 MAEDA Fumio 研究員 ・HSVベクターの細胞標的能の最適化
・HSVベクターを利用した細胞間輸送システムの開発
・HSVベクター利用した細胞内情報取得技術の開発
五島 直樹 GOSHIMA Naoki 招聘研究員

業績リスト

  • Mizukoshi Y, Takeuchi K, Tokunaga Y, Matsuo H, Imai M, Fujisaki M, Kamoshida H, Takizawa T, Hanzawa H, Shimada I
    Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium
    Sci Adv. 6(40):eabd0480. (2020) doi: 10.1126/sciadv.abd0480
  • Kato A, Adachi S, Kawano S, Takeshima K, Watanabe M, Kitazume S, Sato R, Kusano H, Koyanagi N, Maruzuru Y, Arii J, Hatta T, Natsume T, Kawaguchi Y
    Identification of a herpes simplex virus 1 gene encoding neurovirulence factor by chemical proteomics
    Nat Commun. 11(1):4894. (2020) doi: 10.1038/s41467-020-18718-9
  • Imashimizu M, Tokunaga Y, Afek A, Takahashi H, Shimamoto N, Lukatsky DB
    Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences
    Biomolecules. 10(9):E1299. (2020) doi: 10.3390/biom10091299
  • Maruyama Y, Koroku S, Imai M, Takeuchi K, Mitsutake A
    Mutation-induced change in chignolin stability from pi-turn to alpha-turn
    Rsc Advances 10 10: 22797-22808 (2020) doi: 10.1039/d0ra01148g
  • Dubey A, Takeuchi K, Reibarkh M, Arthanari H
    The role of NMR in leveraging dynamics and entropy in drug design
    J. Biomolecular Nmr 66: 0 (2020) doi: 10.1007/s10858-020-00335-9
  • Kitakaze T, Yoshikawa M, Kobayashi Y, Kimura N, Goshima N, Ishikawa T, Ogata Y, Yamashita Y, Ashida H, Harada N, Yamaji R
    Extracellular transglutaminase 2 induces myotube hypertrophy through G protein-coupled receptor 56
    Biochim Biophys Acta Mol Cell Res. 1867:118563 (2020) doi:10.1016/j.bbamcr.2019.118563
  • Tokunaga Y, Takeuchi K*, Okude J, Ori K, Torizawa T, Shimada I*
    Structural Fingerprints of an Intact Monoclonal Antibody Acquired under Formulated Storage Conditions via (15)N Direct Detection Nuclear Magnetic Resonance
    J Med Chem. 12: 0 (2020) doi:10.1021/acs.jmedchem.0c00231
  • Fukuda T, Hamaguchi M, Osaka T, Hashimoto Y, Ushigome E, Asano M, Yamazaki M, Fukuda E, Yamaguchi K, Ogawa K, Goshima N, Fukui M
    A Pilot Study on the Effect of Anti-Thrombopoietin Antibody on Platelet Count in Patients with Type 2 Diabetes
    Molecules. 25: 0 (2020) doi: 10.3390/molecules25071667
  • Murano K, Iwasaki YW, Ishizu H, Mashiko A, Shibuya A, Kondo S, Adachi S, Suzuki S, Saito K, Natsume T, Siomi MC, Siomi H
    Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing
    EMBO JOURNAL 0: 0 (2020) doi: 10.15252/embj.2019102870
  • Otsuka H, Fukao A, Tomohiro T, Adachi S, Suzuki T, Takahashi A, Funakami Y, Natsume T, Yamamoto T, Duncan KE, Fujiwara T
    ARE-binding protein ZFP36L1 interacts with CNOT1 to directly repress translation via a deadenylation-independent mechanism
    Biochimie. 9084: 30080-8 (2020) doi: 10.1016/j.biochi.2020.04.010
  • Goldshtein M, Mellul M, Deutch G, Imashimizu M, Takeuchi K, Meshorer E, Ram O, Lukatsky DB
    Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry
    Biophysical J. 118 118: 2015-2026 (2020) doi: 10.1016/j.bpj.2020.02.009
  • Tatebayashi K, Yamamoto K, Tomida T, Nishimura A, Takayama T, Oyama M, Kozuka-Hata H, Adachi-Akahane S, Tokunaga Y Saito H
    Osmostress enhances activating phosphorylation of Hog1 MAP kinase by mono-phosphorylated Pbs2 MAP2K
    EMBO JOURNAL 39 39: 0 (2020) doi: 10.15252/embj.2019103444
  • Yoshida M, Saito M, Ito S, Ogawa K, Goshima N, Nagata K, Doi T
    Structure-Activity Relationship Study on Col-003, a Protein-Protein Interaction Inhibitor between Collagen and Hsp47
    Chem Pharm Bull 68: 220-226 (2020) doi: 10.1248/cpb.c19-00634
  • Tokunaga Y, Viennet T, Arthanari H, Takeuchi K*
    Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR
    INTERNATIONAL J. Molecular Sciences 21 21: 0 (2020) doi: 10.3390/ijms21051829
  • Kitazawa M, Hatta T, Sasaki Y, Fukui K, Ogawa K, Fukuda E, Goshima N, Okita N, Yamada Y, Nakagama H, Natsume T, Horimoto K
    Promotion of the Warburg effect is associated with poor benefit from adjuvant chemotherapy in colorectal cancer
    Cancer Sci. 111: 658-666 (2020) doi: 10.1111/cas.14275
  • Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T
    LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation
    EMBO JOURNAL 39 39: 0 (2020) doi: 10.15252/embj.2019102729
  • Asano T, Noda Y, Tanaka KI, Yamakawa N, Wada M, Mashimo T, Fukunishi Y, Mizushima T, Takenaga M
    A2B adenosine receptor inhibition by the dihydropyridine calcium channel blocker nifedipine involves colonic fluid secretion
    Sci Rep. 10: 3555 (2020) doi: 10.1038/s41598-020-60147-7
  • Taniue K, Hayashi T, Kamoshida Y, Kurimoto A, Takeda Y, Negishi L, Iwasaki K, Kawamura Y, Goshima N, Akiyama T
    UHRF1-KAT7-mediated regulation of TUSC3 expression via histone methylation/acetylation is critical for the proliferation of colon cancer cells
    Oncogene 39 39: 1018-1030 (2020) doi: 10.1038/s41388-019-1032-y
  • Yasuda R, Adachi S, Okonogi A, Anzai Y, Kamiyama T, Katano K, Hoshi N, Mogi K, Natsume T
    Cell Stress Reduction by a Novel Perfusion-Culture System Using Commercial Culture Dish
    Applied Sciences-Basel 10 10: 0 (2020) doi: 10.3390/app10010095
  • Hia F, Yang SF, Shichino Y, Yoshinaga M, Murakawa Y, Vandenbon A, Fukao A, Fujiwara T, Landthaler M, Natsume T, Adachi S, Iwasaki S, Takeuchi O
    Codon bias confers stability to human mRNAs
    EMBO Rep. 20: 0 (2019) doi: 10.15252/embr.201948220
  • Fukuda E*, Mori M, Shiku H, Miyahara Y, Kawamura Y, Ogawa K, Ogura T, Goshima N
    Development of INSOL-tag for proteome-wide protein handling and its application in protein array analysis
    Genes Cells. 0: 0 (2019) doi: 10.1111/gtc.12735
  • Takeuchi K, Imai M, Shimada I
    Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR
    Proc Natl Acad Sci U S A. 116: 19963-19972 (2019) doi: 10.1073/pnas.1906129116
  • Arthanari H#*, Takeuchi K#*, Dubey A, Wagner G #
    Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins
    Current Opinion In Structural Biology 58 294-304 65: 455-458 (2019) doi: 10.1016/j.sbi.2019.06.005
  • Fukunishi Y, Mashimo T, Kurosawa T, Wakabayashi Y, Nakamura HK, Takeuchi K
    Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion
    Mol Inform. 15: 0 (2019) doi: 10.1002/minf.201900071
  • Sekine S, Kiyono T, Ryo E, Ogawa R, Wakai S, Ichikawa H, Suzuki, K, Arai S, Tsuta K, Ishida M, Sasajima Y, Goshima N, Yamazaki N, , Mori T
    Recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poroma and porocarcinoma
    J. Clinical Investigation 129: 3827-3832 (2019) doi: 10.1172/JCI126185
  • Naffouje R, Grover P, Yu H, Sendilnathan A, Wolfe K, Majd N, Smith EP, Takeuchi K, Senda T, Kofuji S, Sasaki AT
    Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story
    Cancers 11: 0 (2019) doi: 10.3390/cancers11091346
  • Takeuchi K, Baskaran K, Arthanari H
    Structure determination using solution NMR: Is it worth the effort
    J. Magnetic Resonance 189: 233-248 (2019) doi: 10.1016/j.jmr.2019.07.045
  • Ito S, Saito M, Yoshida M, Takeuchi K, Doi T, Nagata K
    A BRET-based assay reveals collagen-Hsp47 interaction dynamics in the endoplasmic reticulum and small-molecule inhibition of this interaction
    J Biol Chem. 0: 0 (2019) doi: 10.1074/jbc.RA119.010567
  • Yamashita Y, Tanaka K, Yamakawa N, Asano T, Kanda Y, Takafuji A, , Kawahara M, Takenaga M, Fukunishi Y, Mizushima T
    Chemical modification-mediated optimisation of bronchodilatory activity of mepenzolate, a muscarinic receptor antagonist with anti-inflammatory activity
    Bioorganic 27: 3339-3346 (2019) doi: 10.1016/j.bmc.2019.06.016
  • Sato T, Higashioka K, Sakurai H, Yamamoto T, Goshima N, Ueno M, Sotozono C
    Core Transcription Factors Promote Induction of PAX3-Positive Skeletal Muscle Stem Cells
    Stem Cell Reports. 13: 352-365 (2019) doi: 10.1016/j.stemcr.2019.06.006
  • Aly MK, Ninomiya K, Adachi S, Natsume T, Hirose T
    Two distinct nuclear stress bodies containing different sets of RNA-binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure
    Biochem.... And Biophysical Res. Communications 516: 419-423 (2019) doi: 10.1016/j.bbrc.2019.06.061
  • Ghani FI, Dendo K, Watanabe R, Yamada K, Yoshimatsu Y, Yugawa T, , Nakahara T, Tanaka K, Yoshida H, Yoshida M, Ishikawa M, Goshima N, , Kato T, Kiyono T
    An Ex-Vivo Culture System of Ovarian Cancer Faithfully Recapitulating the Pathological Features of Primary Tumors
    Cells 8: 10 (2019) doi: 10.3390/cells8070644
  • Higo J, Kasahara K, Wada M, Dasgupta B, Kamiya N, Hayami T, Fukuda I, Fukunishi Y, Nakamura H
    Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism
    Protein Engineering Design 32: 297-308 (2019) doi: 10.1093/protein/gzz029
  • Mogi K*, Adachi S, Takada N, Inoue T, Natsume T
    Electrowetting on Dielectric (EWOD) Device with Dimple Structures for Highly Accurate Droplet Manipulation
    Applied Sciences-Basel 9: 10 (2019) doi: 10.3390/app9122406
  • Imashimizu M, Kireeva ML, Lubkowska L, Kashlev M, Shimamoto N
    The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase
    J. Molecular Biology 431: 2528-2542 (2019) doi: 10.1016/j.jmb.2019.04.020
  • Boeszoermenyi A, Chhabra S, Dubey A, Radeva DL, Burdzhiev NT, Chanev CD, Petrov OI, Gelev VM, Zhang M, Anklin C, Kovacs H, Wagner G, Kuprov I, Takeuchi K*, Arthanari H*
    Aromatic (19)F-(13)C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics
    Nat Methods. 16: 333-340 (2019) doi: 10.1038/s41592-019-0334-x
  • Takeuchi F, Ikeda S, Tsukamoto Y, Iwasawa Y, Qihao C, Otakaki Y, Ryota O, Yao WL, Narita R, Makoto H, Watashi K, Wakita T, Takeuchi K, Chayama K, Kogure A, Kato H, Fujita T
    Screening for inhibitor of episomal DNA identified dicumarol as a hepatitis B virus inhibitor
    PloS One. 14: 0 (2019) doi: 10.1371/journal.pone.0212233
  • Yasuda R, Adachi S, Okonogi A, Anzai Y, Kamiyama T, Katano K, , Hoshi N, Natsume T, Mogi K*
    Fabrication of a Novel Culture Dish Adapter with a Small Recess Structure for Flow Control in a Closed Environment
    Applied Sciences-Basel 9: 10 (2019) doi: 10.3390/app9020269
  • Adachi S, Anzai Y, Nishimura F, Yasuda R, Okonogi A, Kamiyamna T, Kotera H, Natsume T
    Development of an ANSI/SBS Standard Size Culture Medium Auto-Exchanger
    JSDE, 54: 391-398 (2018) doi: 10.14953/jjsde.2018.2829
  • Inoko A, Yano T, Miyamoto T, Matsuura S, Kiyono T, Goshima N, Inagaki M, Hayashi Y
    Albatross/FBF1 contributes to both centriole duplication and centrosome separation
    Genes Cells. 23: 1023-1042 (2018) doi: 10.1111/gtc.12648
  • Ohsawa K, Yoshida M, Izumikawa M, Takagi M, Shin-Ya K, Goshima N, Hirokawa T, Natsume T, Doi T
    Synthesis and biological evaluation of thielocin B1 analogues as protein-protein interaction inhibitors of PAC3 homodimer
    Bioorg Med Chem. 10 185 (2018) doi: 10.1016/j.bmc.2018.11.001
  • Nagai T, Mukoyama S, Kagiwada H, Goshima N, Mizuno K
    Cullin-3-KCTD10-mediated CEP97 degradation promotes primary cilium formation
    J Cell Sci. 131: 0 (2018) doi: 10.1242/jcs.219527
  • Freilich R, Betegon M, Tse E, Mok SA, Julien O, Agard DA, Southworth DR, Takeuchi K, Gestwicki JE
    Competing protein-protein interactions regulate binding of Hsp27 to its client protein tau
    Nat Commun. 9: 4563 (2018) doi: 10.1038/s41467-018-07012-4
  • Zhai L, Wang S, Nara M, Takeuchi K, Shimada I, Otani Y, Ohwada T
    Application of C-Terminal 7-Azabicyclo[2.2.1]heptane to Stabilize beta-Strand-like Extended Conformation of a Neighboring alpha-Amino Acid
    J Org Chem. 83: 13063-13079 (2018) doi: 10.1021/acs.joc.8b01756
  • Hosoi Y, Soma M, Shiura H, Sado T, Hasuwa H, Abe K, Kohda T, Ishino F, Kobayashi S*
    Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype
    Nat Commun. 9: 3829 (2018) doi: 10.1038/s41467-018-06327-6
  • Kurita JI, Hirao Y, Nakano H, Fukunishi Y, Nishimura Y
    Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities
    Sci Rep. 8: 13763 (2018) doi: 10.1038/s41598-018-31852-1
  • Sadahiro T, Isomi M, Muraoka N, Kojima H, Haginiwa S, Kurotsu S, Tamura F, Tani H, Tohyama S, Fujita J, Miyoshi H, Kawamura Y, Goshima N, Iwasaki YW, Murano K, Saito K, Oda M, Andersen P, Kwon C, Uosaki H, Nishizono H, Fukuda K, Ieda M
    Tbx6 Induces Nascent Mesoderm from Pluripotent Stem Cells and Temporally Controls Cardiac versus Somite Lineage Diversification
    Cell Stem Cell. 23: 382-395 (2018) doi: 10.1016/j.stem.2018.07.001
  • Fukunishi Y, Yamashita Y, Mashimo T, Nakamura H
    Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications
    Mol Inform. 28: 741-753 (2018) doi: 10.1002/minf.201700120
  • Sugiki T, Egawa D, Kumagai K, Kojima C, Fujiwara T, Takeuchi K, Shimada I, Hanada K, Takahashi H
    Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif
    J Biol Chem. 293: 11206-11217 (2018) doi: 10.1074/jbc.RA118.002465
  • Yanagita K, Nagashio R, Jiang SX, Kuchitsu Y, Hachimura K, Ichinoe M, Igawa S, Fukuda E, Goshima N, Satoh Y, Murakumo Y, Saegusa M, Sato Y
    Cytoskeleton-Associated Protein 4 Is a Novel Serodiagnostic Marker for Lung Cancer
    Am J Pathol. 188: 1328-1333 (2018) doi: 10.1016/j.ajpath.2018.03.007
  • Mogi K*, Hayashida K, Yamamoto T
    Damage-less Handling of Exosomes Using an Ion-depletion Zone in a Microchannel
    Anal Sci. 34: 875-880 (2018) doi: 10.2116/analsci.17P462
  • Noguchi A, Adachi S, Yokota N, Hatta T, Natsume T, Kawahara H
    ZFP36L2 is a cell cycle-regulated CCCH protein necessary for DNA lesion-induced S-phase arrest
    Biology Open 7: 10 (2018) doi: 10.1242/bio.031575
  • Kobayashi S*
    Live Imaging of X-Chromosome Inactivation and Reactivation Kinetics
    Methods Mol Biol. 35: 301-305 (2018) doi: 10.1007/978-1-4939-8766-5_7
  • Takahashi S, Kobayashi S*, Hiratani I*
    Epigenetic differences between naive and primed pluripotent stem cells
    Cell Mol Life Sci. 75: 1191-1203 (2018) doi: 10.1007/s00018-017-2703-x
  • Tanaka KI, Yamakawa N, Yamashita Y, Asano T, Kanda Y, Takafuji A, Kawahara M, Takenaga M, Fukunishi Y, Mizushima T
    Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity
    Front Pharmacol. 0: 0 (2018) doi: 10.3389/fphar.2018.00344
  • Mogi K*
    A Visualization Technique of a Unique pH Distribution around an Ion Depletion Zone in a Microchannel by Using a Dual-Excitation Ratiometric Method
    Micromachines 9: 0 (2018) doi: 10.3390/mi9040167
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