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生物データサイエンスグループ

研究概要

独自の計測・解析技術により得られたオミクスデータと、有用な公共データ、リアルワールドデータ等と連携し、創薬、診断に資する、マルチモーダルなデータを構築します。得られたマルチモーダルなデータを活用し、グループ内で創出される多様なインシリコ解析技術(配列解析、複合体予測、分子動力学計算、パスウェイネットワーク解析、機械学習等)と組み合わせることで、創薬・診断に繋がる基盤技術の構築に取り組んでいます。

生物データサイエンス研究グループ

研究課題

研究課題1:マルチモーダルデータ解析による疾患メカニズム推定のためのデータサイエンス
研究担当者:今井 賢一郎、足達 俊吾

臨床検体の多層オミックスデータを計測・解析し、診断画像解析データとの連携からマルチモーダルなデータ解析を行い、早期診断に繋がる、疾患発症に係わる分子メカニズムの推定や患者層別化を行う基盤技術開発に取り組んでいます。また、レセプトデータなどのリアルワールドデータを活用し、得られた発症メカニズムの検証にも取り組んでいます。

生物データサイエンスグループ2

研究課題

研究課題2:新規医薬品・医療技術のためのRNA・DNAなどの新規標的への分子シミュレーションの基礎技術開発
研究担当者:福西 快文

新規創薬モダリティとしてRNA/DNAが注目されていますが、特にRNAは静的な配列情報・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。核酸の理論計算技術はタンパク質に比して未整備であり、精度・信頼性は未知です。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、核酸用に再構築し、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。

生物データサイエンスグループ3

研究課題

研究課題3:オミクス修飾を利用した疾患新規診断、治療法の開発
研究担当者:今野 雅允

RNA修飾は様々な疾患で変化していることが知られています。しかしその計測技術が未熟であり、診断治療への応用は実現していません。そこで私たちは、RNAを中心としたオミクスの修飾情報を計測する新規技術の開発を進めています。またこの技術を用いて計測したオミクスの修飾情報解析を進め、がんをはじめとした様々な疾患の早期診断技術開発、新規治療法開発に取り組んでいます。

生物データサイエンスグループ4

研究課題

研究課題4:疾患関連変異情報を利用した新規創薬標的探索法の構築
研究担当者:本野 千恵、今井 賢一郎

近年、多くの疾患関連変異情報が得られていますが、それらの多くは、生物学的解釈が難しく、従来とは異なる視点での利活用法や解析技術が求められています。本研究では、疾患関連変異をタンパク質の立体構造上でのクラスタという単位でとらえ、それらを基点としたタンパク質の未発見の機能部位の網羅的探索法を開発しています。疾患関連変異は、タンパク質構造上で機能部位近辺に集積する傾向がある一方、既知の機能部位に紐づかないクラスタは、未発見の機能部位を指し示す可能性があります。また、未発見の機能制御部位は、単純なポケットではなく、動的に生じるリガンド結合部位(クリプトサイト)やアロステリック制御部位の可能性があります。そこで、配列解析や分子動力学計算などを組み合わせることで、新規の機能部位、ひいては、新規創薬標的部位を予測する技術開発を行っています。

生物データサイエンスグループ5

研究課題

研究課題5:細胞内制御ネットワークの動的特性を解析する基盤技術の構築
研究担当者:川田 健太郎

細胞内には多種多様な分子が存在し、これらが互いに情報をやり取りすることで細胞の状態が決定されます。本研究では、細胞内分子が情報を伝えるネットワークが、細胞の分化や外部環境への適応に伴ってどのように変化するのか、ネットワークの変化が細胞の状態にどのように影響を与えるかを高精度で解析する基盤技術を開発しています。また、これらの研究を通じて多能性幹細胞などにおける分化制御の高精度化を推進しています。

生物データサイエンスグループ6

研究課題

研究課題6:タンパク質群ネットワーク動態の解析基盤の構築
研究担当者:鍵和田 晴美、新木 和孝

細胞外部からの刺激(シグナル)の多くはリン酸化経路によって伝えられ、細胞の挙動を決定しています。たんぱく質アレイを用い高度リン酸化解析のハイスループットを実現します。また、質量分析技術の高度化によるターゲット同定や翻訳後修飾を中心とする複合体ダイナミクス計測技術融合によるターゲット制御技術の開発を推進しています。

生物データサイエンスグループ7

研究課題

研究課題7:ヘルペスウイルスベクターの医薬モダリティとしての開発
研究担当者:前田 史雄

単純ヘルペスウイルスAmpliconベクターは、ウイルス粒子からウイルスゲノムを排除し、代わりにプラスミドをパッケージングしており、(1)極めて低い細胞毒性、(2)最大150kbpもの遺伝子積載容量、(3)幅広い種類の細胞への感染能を特徴としたウイルスベクターです。現在、効率的なベクター産生法の開発および特定の細胞を標的化した遺伝子導入技術の開発に取り組んでいます。またウイルスベクターにより高度な細胞制御を行うことで疾病モデル細胞株から非破壊的に分子情報取得し、低侵襲な疾患の診断に適した分子情報(バイオマーカー)や治療標的候補の探索に取り組んでいます。

生物データサイエンスグループ8

メンバー

名前 役職 主な研究テーマ
今井 賢一郎 IMAI Kenichiro グループ長 ・ミトコンドリアをターゲットとした創薬支援
・疾患関連変異のタンパク質構造上の分布をガイドとした新規創薬標的探索
・潜在疾患層別化マーカー探索
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
本野 千恵 MOTONO Chie 主任研究員 ・分子動力学計算による疾患メカニズム解明と創薬支援
・効率的な分子動力学計算の技術開発
・創薬向けタンパク質立体構造予測手法の開発
鍵和田 晴美 KAGIWADA Harumi 主任研究員 ・リン酸化活性プロファイリング測定系の構築
・リン酸化活性を用いた細胞応答の解析
・リン酸化活性を用いた組織を含む生体応答の解析
今野 雅允 KONNO Masamitsu 主任研究員 ・オミクス変化を利用した疾患新規診断、治療法の開発
・エピトランスクリプトームを中心としたトランスオミクス情報を取得解析する新規技術の開発
・生体制御修飾因子の機能解明と実用化
川田 健太郎 KAWATA Kentaro 主任研究員 ・多層オミクスデータによる細胞内ネットワーク構築
・細胞分化に伴う遺伝子制御ネットワークの動的特性解析
・逐次ネットワーク制御に基づく細胞機能制御法の開発支援
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

業績リスト

  • Shimizu, R; Murai, K; Tanaka, K; Sato, Y; Takeda, N; Nakasyo, S; Shirasaki, T; Kawaguchi, K; Shimakami, T; Nio, K; Nakaya, Y; Kagiwada, H Horimoto, K; Mizokami, M; Kaneko, S; Murata, K; Yamashita, T; Honda, M.
    Nucleos(t)ide analogs for hepatitis B virus infection differentially regulate the growth factor signaling in hepatocytes.
    HEPATOL COMMUN. 2024 Jan 5;8(1):e0351. doi: 10.1097/HC9.0000000000000351
  • Fukuda, I; Moritsugu, K; Higo, J; Fukunishi, Y.
    A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems.
    J CHEM PHYS. 2023 Dec 21;159(23):234116. doi: 10.1063/5.0172270
  • Watanabe, Y; Iwasaki, Y; Sasaki, K; Motono, C; Imai, K; Suzuki, K.
    Atg15 is a vacuolar phospholipase that disintegrates organelle membranes.
    CELL REP. 2023 Dec 15:113567. doi: 10.1016/j.celrep.2023.113567
  • Maeda, F; Adachi, S; Natsume, T.
    Non-destructive and efficient method for obtaining miRNA information in cells by artificial extracellular vesicles.
    SCI REP. 2023 Dec 14;13(1):22231. doi: 10.1038/s41598-023-48995-5
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    RNA Modification Related Diseases and Sensing Methods.
    APPLIED SCIENCES-BASEL. 2023 13(11) 6376. doi: 10.3390/app13116376
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    Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.
    FRONT MOL BIOSCI. 2023 Feb 6;10:1110567. doi: 10.3389/fmolb.2023.1110567
  • Takeda, H; Busto, JV; Lindau, C; Tsutsumi, A; Tomii, K; Imai, K; Yamamori, Y; Hirokawa, T; Motono, C; Ganesan, I; Wenz, LS; Becker, T; Kikkawa, M; Pfanner, N; Wiedemann, N; Endo, T.
    A multipoint guidance mechanism for β-barrel folding on the SAM complex.
    NAT STRUCT MOL BIOL. 2023 Jan 5. doi: 10.1038/s41594-022-00897-2
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    Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method.
    J BIOL CHEM. 2022 Dec 20:102822. doi: 10.1016/j.jbc.2022.102822
  • Murotomi, K; Kagiwada, H; Hirano, K; Yamamoto, S; Numata, N; Matsumoto, Y; Kaneko, H; Namihira, M.
    Cyclo-glycylproline attenuates hydrogen peroxide-induced cellular damage mediated by the MDM2-p53 pathway in human neural stem cells.
    J CELL PHYSIOL. 2022 Dec 31. doi: 10.1002/jcp.30940
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    Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles.
    BIOPHYS REV. 2022 Nov 28:1-25. doi: 10.1007/s12551-022-01015-8
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    RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease.
    SCIENCE. 2022 Nov 25;378(6622):882-889. doi: 10.1126/science.add7347
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    Investigation on substrate specificity and catalytic activity of serine protease neuropsin.
    BIOPHYS PHYSICOBIOL. 2022 Sep 22;19:e190040. doi: 10.2142/biophysico.bppb-v19.0040
  • Tirta, YK; Adachi, S; Perez, CAG; Adhitama, N; Nong, QD; Natsume, T; Kato, Y; Watanabe, H.
    CELF1 represses Doublesex1 expression via its 5 UTR in the crustacean Daphnia magna.
    PLOS ONE. 2022 Oct 14;17(10):e0275526. doi: 10.1371/journal.pone.0275526
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    RNAapt3D: RNA aptamer 3D-structural modeling database.
    BIOPHYS J. 2022 Sep 22:S0006-3495(22)00773-1. doi: 10.1016/j.bpj.2022.09.023
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    Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover.
    MOL CELL. 2022 Sep 15;82(18):3424-3437.e8. doi: 10.1016/j.molcel.2022.08.018
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    Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements.
    DATABASE (Oxford). 2022 Aug 22;2022:baac072. doi: 10.1093/database/baac072
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    Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.
    SCI REP. 2022 Aug 13;12(1):13792. doi: 10.1038/s41598-022-17920-7
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    Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts.
    SCI REP. 2022 Jul 11;12(1):11757. doi: 10.1038/s41598-022-15038-4
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    Lack of Hikeshi activates HSF1 activity under normal conditions and disturbs the heat-shock response.
    LIFE SCI ALLIANCE. 2022 May 17;5(9):e202101241. doi: 10.26508/lsa.202101241
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    Role of the Orphan Transporter SLC35E1 in the Nuclear Egress of Herpes Simplex Virus 1.
    J VIROL. 2022 Apr 27:e0030622. doi: 10.1128/jvi.00306-22
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    Entamoeba histolytica EHD1 Is Involved in Mitosome-Endosome Contact.
    MBIO. 2022 Apr 11:e0384921. doi: 10.1128/mbio.03849-21
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    Role of the TOM Complex in Protein Import into Mitochondria: Structural Views.
    ANNU REV BIOCHEM. 2022 Feb 14. doi: 10.1146/annurev-biochem-032620-104527
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    Unfolding is the driving force for mitochondrial import and degradation of Parkinsons disease-related protein DJ-1.
    J CELL SCI. 2021 Oct 22:jcs.258653. doi: 10.1242/jcs.258653
  • Kimura, M; Imai, K; Morinaka, Y; Hosono-Sakuma, Y; Horton, P; Imamoto, N.
    Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding.
    SCI REP. 2021 Aug 2;11(1):15649. doi: 10.1038/s41598-021-94948-1
  • Motono, C; Yanagida, S; Sato, M; Hirokawa, T.
    MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts.
    BIOINFORMATICS. 2021 Jul 21:btab538. doi: 10.1093/bioinformatics/btab538
  • Kagiwada, H; Kiboku, T; Matsuo, H; Kitazawa, M; Fukui, K; Horimoto, K.
    Assessing the activation/inhibition of tyrosine kinase-related pathways with a newly developed platform.
    PROTEOMICS. 2021 Jun 21:e2000251. doi: 10.1002/pmic.202000251
  • Amemiya, T; Horimoto, K; Fukui, K.
    Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses.
    SCI REP. 2021 May 12;11(1):10136. doi: 10.1038/s41598-021-89171-x
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    LSD1 defines erythroleukemia metabolism by controlling the lineage-specific transcription factors GATA1 and C/EBP
    Blood Adv. 2021 May 11;5(9):2305-2318. doi: 10.1182/bloodadvances.2020003521
  • Ohashi, H; Watashi, K; Saso, W; Shionoya, K; Iwanami, S; Hirokawa, T; Shirai, T; Kanaya, S; Ito, Y; Kim, KS; Nomura, T; Suzuki, T; Nishioka, K; Ando, S; Ejima, K; Koizumi, Y; Tanaka, T; Aoki, S; Kuramochi, K; Suzuki, T; Hashiguchi, T; Maenaka, K; Matano, T; Muramatsu, M; Saijo, M; Aihara, K; Iwami, S; Takeda, M; McKeating, JA; Wakita, T
    Potential anti-COVID-19 agents, Cepharanthine and Nelfinavir, and their usage for combination treatment.
    ISCIENCE. 2021 Mar 26:102367. doi: 10.1016/j.isci.2021.102367
  • Koiwai K, Morohashi K, Inaba K, Ebihara K, Kojima H, Okabe T, Yoshino R, Hirokawa T, Nampo T, Fujikawa Y, Inoue H, Yumoto F, Senda T, Niwa R
    Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S-transferase Noppera-bo
    J Pestic Sci. 2021 Feb 20;46(1):75-87. doi: 10.1584/jpestics.D20-072
  • Kojima W, Yamano K, Kosako H, Imai K, Kikuchi R, Tanaka K, Matsuda N
    Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy.
    AUTOPHAGY. 2021 Jan 26:1-26. doi: 10.1080/15548627.2021.1874133
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    Mitochondrial sorting and assembly machinery operates by β-barrel switching.
    NATURE. 2021 Jan 6. doi: 10.1038/s41586-020-03113-7
  • Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K
    Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex.
    RSC ADVANCES 10 (71) 43319-43323; doi: 10.1039/d0ra09413g DEC 7
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    Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.
    FRONT GENET 2020 Nov 25;11:607812. doi: 10.3389/fgene.2020.607812. eCollection
  • Sakamoto K, Masutani T, Hirokawa T
    Generation of KS-58 as the first K-Ras(G12D)-inhibitory peptide presenting anti-cancer activity in vivo.
    SCI REP. 10(1):21671 (2020) doi: 10.1038/s41598-020-78712-5
  • Araiso Y, Imai K, Endo T
    Structural snapshot of the mitochondrial protein import gate
    FEBS J. 2020 Dec 10. doi: 10.1111/febs.15661
  • Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D
    Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs
    Adv Appl Bioinform Chem. 2020 Nov 12;13:11-25. doi: 10.2147/AABC.S235542
  • Nguyen HN, Suzuki K, Kimura Y, Hirokawa T, Murakami-Tonami Y, Abe H
    SYNTHESIS AND BIOLOGICAL EVALUATION OF NMDI14 DERIVATIVES AS ANTI-MESOTHELIOMA AGENTS
    HETEROCYCLES 100 (2) 253-266; (2020) doi: 10.3987/COM-19-14191
  • Santos HJ, Chiba Y, Makiuchi T, Arakawa S, Murakami Y, Tomii K, Imai K, Nozaki T
    Import of Entamoeba histolytica Mitosomal ATP Sulfurylase Relies on Internal Targeting Sequences
    Microorganisms. 8(8):1229. (2020) doi: 10.3390/microorganisms8081229
  • Nakagita T, Taketani C, Narukawa M, Hirokawa T, Kobayashi T, Misaka T
    Ibuprofen, a nonsteroidal anti-inflammatory drug, is a potent inhibitor of the human sweet taste receptor
    Chem Senses. bjaa057 (2020) doi: 10.1093/chemse/bjaa057
  • Tomonari T, Sato Y, Tanaka H, Tanaka T, Fujino Y, Mitsui Y, Hirao A, Taniguchi T, Okamoto K, Sogabe M, Miyamoto H, Muguruma N, Kagiwada H, Kitazawa M, Fukui K, Horimoto K, Takayama T
    Potential use of lenvatinib for patients with unresectable hepatocellular carcinoma including after treatment with sorafenib: Real-world evidence and in vitro assessment via protein phosphorylation array
    Oncotarget. 11: 2531-2542 (2020) doi: 10.18632/oncotarget.27640
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