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Biological Data Science Research Group

Project

Project1:Biological data science based on moleulcar profile
Member:Kazuhiko Fukui, Kenichiro Imai, Harumi Kagiwada, Kazutaka Araki

We are working on research to understand the relationship between drug-disease-side effect as a systematic biological network based on expression profile and genome variants/variations by federating and integrating multi-layer omics data. In addition, we aim to build a data infrastructure that leads to knowledge inference using a knowledge graph based on ontology.

Biological Data Science Research Group02

Project

Project2:Structure-based drug design, chemoinformatics and its applications
Member:Takatsugu Hirokawa, Chie Motono, Yuta Kajiwara

The purpose of this research project is to design a drug molecule based on the three-dimensional structure and interaction information of the target receptor protein. We are searching for and optimizing drug candidate compounds by in silico screening through development of molecular modeling method of target proteins, docking calculation with compounds, and joint research with pharmaceutical companies.

Biological Data Science Research Group03

Project

Project3:Protein network dynamics analysis
Member:Harumi Kagiwada, Kazutaka Araki

Protein phosphorylation is one of the representative mechanisms of post-translational modification which regulates enzyme activities and transduces signaling pathways. Here we developed a novel and convenient system for a series of phosphorylation analyses. By our system, the active pathways can be visualized to facilitate biological interpretation depending on the different cases such as disease-control and drug treatment.
In addition, we are promoting the development of target discovery technologies such as target identification and quantification of proteostasis states using advanced mass spectrometry, evaluation technology by integrating structural dynamics analyses, and the development of middle molecules and antibodies.

Biological Data Science Research Group04

Project

Project4:Disease associated variants-guided search for novel drug target
Member:Kenichiro Imai, Chie Motono, Yuta Kajiwara

Protein phosphorylation is one of the representative mechanisms of post-translational modification which regulates enzyme activities and transduces signaling pathways. Here we developed a novel and convenient system for a series of phosphorylation analyses. By our system, the active pathways can be visualized to facilitate biological interpretation depending on the different cases such as disease-control and drug treatment.
In addition, we are promoting the development of target discovery technologies such as target identification and quantification of proteostasis states using advanced mass spectrometry, evaluation technology by integrating structural dynamics analyses, and the development of middle molecules and antibodies.

Biological Data Science Research Group04

Member

Name Position
FUKUI Kazuhiko Research Group Leader
HIROKAWA Takatsugu Chief Senior Researcher
MOTONO Chie Senior Researcher
KAGIWADA Harumi Senior Researcher
IMAI Kenichiro Senior Researcher
ARAKI Kazutaka Senior Researcher
KAJIWARA Yuta Researcher

Results

  • Manabe T, Yasuda H, Terai H, Kagiwada H, Hamamoto J, Ebisudani T, Kobayashi K, Masuzawa K, Ikemura S, Kawada I, Hayashi Y, Fukui K, Horimoto K, Fukunaga K, Soejima K
    IGF2 Autocrine-Mediated IGF1R Activation Is a Clinically Relevant Mechanism of Osimertinib Resistance in Lung Cancer
    Molecular Cancer Res. 18 18: 549-559 (2020) doi: 10.1158/1541-7786
  • Koiwai K, Inaba K, Morohashi K, Enya S, Arai R, Kojima H, Okabe T, Fujikawa Y, Inoue H, Yoshino R, Hirokawa T, Kato K, Fukuzawa K, Shimada-Niwa Y, Nakamura A, Yumoto F, Senda T, Niwa R
    An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo
    J Biol Chem. 0: 0 (2020) doi: 10.1074/jbc.RA119.011463
  • Kagamu H, Kitano S, Yamaguchi O, Yoshimura K, Horimoto K, Kitazawa M, FFukui K, Shiono A, Mouri A, Nishihara F, Miura Y, Hashimoto K, Murayama Y, Kaira K, Kobayashi K
    CD4(+) T-cell Immunity in the Peripheral Blood Correlates with Response to Anti-PD-1 Therapy
    Cancer Immunology Res. 8 8: 334-344 (2020) doi: 10.1158/2326-6066
  • Adachi K, Yamada T, Ishizuka H, Oki M, Tsunogae S, Shimada N, Chiba O, Orihara T, Hidaka M, Hirokawa T, Odagi M, Konoki K, Yotsu-Yamashita M, Nagasawa K
    Synthesis of C12-Keto Saxitoxin Derivatives with Unusual Inhibitory Activity Against Voltage-Gated Sodium Channels
    Chemistry. 26: 2025-2033 (2020) doi: 10.1002/chem.201904184
  • 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
  • Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin WH, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin KY, Gupta V, Kitano H, Sakamoto M, Higuchi A, Miura N, Yura K, Mochizuki M, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Nakane I, Uchida N, Hakariya H, Tan M, Nakamura HK, Suzuki SD, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto KZ, Moriwaki Y, Oda K, Kobayashi D, Okuno T, Minami S, Chikenji G, Prathipati P, Nagao C, Mohsen A, Ito M, Mizuguchi K, Honma T, Ishida T, Hirokawa T, Akiyama Y, Sekijima M
    A prospective compound screening contest identified broader inhibitors for Sirtuin 1
    Sci Rep. 9: 19585 (2019) doi: 10.1038/s41598-019-55069-y
  • Araiso Y, Tsutsumi A, Qiu J, Imai K, Shiota T, Song J, Lindau C, Wenz LS, Sakaue H, Yunoki K, Kawano S, Suzuki J, Wischnewski M, Schutze C, Ariyama H, Ando T, Becker T, Lithgow T, Wiedemann N, Pfanner N, Kikkawa M, Endo T
    Structure of the mitochondrial import gate reveals distinct preprotein paths
    Nature.575: 395-401 (2019) doi: 10.1038/s41586-019-1680-7
  • Shiba-Ishii A, Hong J, Hirokawa T, Kim Y, Nakagawa T, Sakashita S, , Sakamoto N, Kozuma Y, Sato Y, Noguchi M
    Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis
    Clinical Cancer Res. 25: 2809-2820 (2019) doi: 10.1158/1078-0432.CCR-18-3631
  • Yamasaki S, Amemiya T, Yabuki Y, Horimoto K, Fukui K
    ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow
    J. Computer-Aided Molecular Design 33: 497-507 (2019) doi: 10.1007/s10822-019-00195-y
  • Santos HJ, Imai K, Makiuchi T, Tomii K, Horton P, Nozawa A, Okada K, Tozawa Y, Nozaki T
    Novel lineage-specific transmembrane beta-barrel proteins in the endoplasmic reticulum of Entamoeba histolytica
    FEBS J. 65: 164-170 (2019) doi: 10.1111/febs.14870
  • Yamada K, Nakazawa M, Matsumoto K, Tagami U, Hirokawa T, Homma K, Mori S, Matsumoto R, Saikawa W, Kitajima S
    Unnatural Tripeptides as Potent Positive Allosteric Modulators of T1R2/T1R3
    Acs Medicinal Chemistry Letters10: 800-805 (2019) doi: 10.1021/acsmedchemlett.9b00051
  • Santos HJ, Hanadate Y, Imai K, Nozaki T
    An Entamoeba-Specific Mitosomal Membrane Protein with Potential Association to the Golgi Apparatus
    Genes 10: 10 (2019) doi: 10.3390/genes10050367
  • Shawki HH, Ishikawa-Yamauchi Y, Kawashima A, Katoh Y, Matsuda M, Al-Soudy AS, Minisy FM, Kuno A, Gulibaikelamu X, Hirokawa T, Takahashi S, Oishi H
    EFCAB2 is a novel calcium-binding protein in mouse testis and sperm
    PloS One. 14: 0 (2019) doi: 10.1371/journal.pone.0214687
  • Parasuraman P, Selvin JFA, Gromiha MM, Fukui K, Veluraja K
    Investigation on the binding specificity of Agrocybe cylindracea galectin towards alpha(2,6)-linked sialyllactose by molecular modeling and molecular dynamics simulations
    J. Carbohydrate Chemistry 250: 463-473 (2019) doi: 10.1080/07328303.2019.1631323
  • Nakagita T, Ishida A, Matsuya T, Kobayashi T, Narukawa M, Hirokawa T, Hashimoto M, Misaka T
    Structural insights into the differences among lactisole derivatives in inhibitory mechanisms against the human sweet taste receptor
    PloS One. 14: 0 (2019) doi: 10.1371/journal.pone.0213552
  • Sakaue H, Shiota T, Ishizaka N, Kawano S, Tamura Y, Tan KS, Imai K, Motono C, Hirokawa T, Taki K, Miyata N, Kuge O, Lithgow T, Endo T
    Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly
    Mol Cell. 73: 1044-1055 (2019) doi: 10.1016/j.molcel.2019.01.003
  • Yasuda S, Hayashi T, Kajiwara Y, Murata T, Kinoshita M
    Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability
    J. Chemical Physics 150: 10 (2019) doi: 10.1063/1.5082217
  • Amemiya T, Gromiha MM, Horimoto K, Fukui K
    Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses
    Scientific Reports 0: 0 (2019) doi: 10.1038/s41598-018-36636-1
  • Toyoda Y, Morimoto K, Suno R, Horita S, Yamashita K, Hirata K, Sekiguchi Y, Yasuda S, Shiroishi M, Shimizu T, Urushibata Y, Kajiwara Y, Inazumi T, Hotta Y, Asada H, Nakane T, Shiimura Y, Nakagita T, Tsuge K, Yoshida S, Kuribara T, Hosoya T, Sugimoto Y, Nomura N, Sato M, Hirokawa T, Kinoshita M, Murata T, Takayama K, Yamamoto M, Narumiya S, Iwata S, Kobayashi T
    Ligand binding to human prostaglandin E receptor EP4 at the lipid-bilayer interface
    Nat Chem Biol. 15: 18-26 (2019) doi: 10.1038/s41589-018-0131-3
  • Ma Y, Iida K, Sasaki S, Hirokawa T, Heddi B, Phan AT, Nagasawa K
    Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains
    Molecules. 24: 0 (2019) doi: 10.3390/molecules24020263
  • 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
  • Ma Y, Tsushima Y, Sakuma M, Sasaki S, Iida K, Okabe S, Seimiya H, Hirokawa T, Nagasawa K
    Development of G-quadruplex ligands for selective induction of a parallel-type topology
    Org Biomol Chem. 0: 0 (2018) doi: 10.1039/c8ob01702f
  • Toda Y, Nakagita T, Hirokawa T, Yamashita Y, Nakajima A, Narukawa M, Ishimaru Y, Uchida R, Misaka T
    Positive/Negative Allosteric Modulation Switching in an Umami Taste Receptor (T1R1/T1R3) by a Natural Flavor Compound, Methional
    Sci Rep. 8: 11796 (2018) doi: 10.1038/s41598-018-30315-x
  • Nakagita T, Ishida A, Kobayashi T, Hirokawa T, Hashimoto M, Misaka, T
    How do sweet taste inhibitors having the O-phenyllactic acid skeleton interact with transmembrane domain of T1R3
    Chemical Senses 43: (5):E137-E137; JUN 2018 doi: 10.1093/chemse/bjy010
  • Kawamura S, Ito Y, Hirokawa T, Hikiyama E, Yamada S, Shuto S
    Ligand-Phospholipid Conjugation: A Versatile Strategy for Developing Long-Acting Ligands That Bind to Membrane Proteins by Restricting the Subcellular Localization of the Ligand
    J Med Chem. 61: 4020-4029 (2018) doi: 10.1021/acs.jmedchem.8b00041
  • Nemoto K, Kagawa M, Nozawa A, Hasegawa Y, Hayashi M, Imai K, Tomii K, Sawasaki T
    Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system
    Sci Rep. 8: 4268 (2018) doi: 10.1038/s41598-018-22538-9
  • Caba C, Khan HA, Auld J, Ushioda R, Araki K, Nagata K, Mutus B
    Conserved Residues Lys(57 )and Lys(401) of Protein Disulfide Isomerase Maintain an Active Site Conformation for Optimal Activity: Implications for Post-Translational Regulation
    Frontiers In Molecular Biosciences 9: 92-100 (2018) doi: 10.3389/fmolb.2018.00018
  • Kitamura A, Ishida Y, Kubota H, Pack CG, Homma T, Ito S, Araki K, Kinjo M, Nagata K
    Detection of substrate binding of a collagen-specific molecular chaperone HSP47 in solution using fluorescence correlation spectroscopy
    Biochem.... And Biophysical Res. Communications 497: 279-284 (2018) doi: 10.1016/j.bbrc.2018.02.069
  • Kasahara K, Aoki H, Kiyono T, Wang S, Kagiwada H, Yuge M, Tanaka T, Nishimura Y, Mizoguchi A, Goshima N, Inagaki M
    EGF receptor kinase suppresses ciliogenesis through activation of USP8 deubiquitinase
    Nat Commun. 9: 758 (2018) doi: 10.1038/s41467-018-03117-y
  • Sakai Y, Kawaguchi A, Nagata K, Hirokawa T
    Analysis by metadynamics simulation of binding pathway of influenza virus M2 channel blockers
    Microbiol Immunol. 62: 34-43 (2018) doi: 10.1111/1348-0421.12561
  • Suno R, Kimura KT, Nakane T, Yamashita K, Wang J, Fujiwara T, Yamanaka Y, Im D, Horita S, Tsujimoto H, Tawaramoto MS, Hirokawa T, Nango E, Tono K, Kameshima T, Hatsui T, Joti Y, Yabashi M, Shimamoto K, Yamamoto M, Rosenbaum DM, Iwata S, Shimamura T, Kobayashi T
    Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA
    Structure. 26: 7-19 (2018) doi: 10.1016/j.str.2017.11.005
  • Ito S, Ogawa K, Takeuchi K, Takagi M, Yoshida M, Hirokawa T, Hirayama S, Shin-ya K, Shimada I, Doi T, Goshima N, Natsume T, Nagata K
    A small-molecule compound inhibits a collagen-specific molecular chaperone and could represent a potential remedy for fibrosis
    J. Biol. Chem. 292: 20076-20085 (2017) doi: 10.1074/jbc.M117.815936
  • Nemoto K, Ramadan A, Arimura GI, Imai K, Tomii K, Shinozaki K, Sawasaki T
    Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation
    Nat Commun. 8: 1004 (2017) doi: 10.1038/s41467-017-01005-5
  • Chiba S, Ishida T, Ikeda K, Mochizuki M, Teramoto R, Taguchi YH, Iwadate M, Umeyama H, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Okuno T, Kato K, Minami S, Chikenji G, Suzuki SD, Yanagisawa K, Shin WH, Kihara D, Yamamoto KZ, Moriwaki Y, Yasuo N, Yoshino R, Zozulya S, Borysko P, Stavniichuk R, Honma T, Hirokawa T, Akiyama Y, Sekijima M
    An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes
    Sci Rep. 7: 12038 (2017) doi:10.1038/s41598-017-10275-4
  • Okamoto N, Mizote K, Honda H, Saeki A, Watanabe Y, Yamaguchi-Miyamoto T, Fukui R, Tanimura N, Motoi Y, Akashi-Takamura S, Kato T, Fujishita S, Kimura T, Ohto U, Shimizu T, Hirokawa T, Miyake K, Fukase K, Fujimoto Y, Nagai Y, Takatsu K
    Funiculosin variants and phosphorylated derivatives promote innate immune responses via the Toll-like receptor 4/myeloid differentiation factor-2 complex
    J. Biol. Chem. 292: 15378-15394 (2017) doi: 10.1074/jbc.M117.791780
  • Shinohara Y, Koyama YM, Ukai-Tadenuma M, Hirokawa T, Kikuchi M, Yamada RG, Ukai H, Fujishima H, Umehara T, Tainaka K, Ueda HR
    Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
    Mol. Cell 67: 783- (2017) doi: 10.1016/j.molcel.2017.08.009
  • Shiga Y, Murata D, Sugimoto A, Oshima Y, Tada M, Ishii-Watabe A, Imai K, Tomii K, Takeuchi T, Kagaya S, Sato A
    Hinge-Deficient IgG1 Fc Fusion: Application to Human Lactoferrin
    Mol Pharm. 14: 3025-3035 (2017) doi: 10.1021/acs.molpharmaceut.7b00221
  • Fukasawa Y, Oda T, Tomii K, Imai K*
    Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages
    Mol Biol Evol. 34: 1574-1586 (2017) doi: 10.1093/molbev/msx096
  • Sayama M, Inoue A, Nakamura S, Jung SJ, Ikubo M, Otani Y, Uwamizu A, Kishi T, Makide K, Aoki J, Hirokawa T, Ohwada T
    Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS1 by Docking-Aided Structure-Activity Analysis
    J. Med. Chem. 60: 6384-6399 (2017) doi: 10.1021/acs.jmedchem.7b00693
  • Uegaki K, Kumanogoh H, Mizui T, Hirokawa T, Ishikawa Y, Kojima M
    BDNF Binds Its Pro-Peptide with High Affinity and the Common Val66Met Polymorphism Attenuates the Interaction
    Int J Mol Sci. 18: 0 (2017) doi: 10.3390/ijms18051042
  • Asamitsu K, Hirokawa T, Okamoto T
    MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding
    PloS One. 12: 0 (2017) doi: 10.1371/journal.pone.0171727
  • Wada Y, Nakano S, Morimoto A, Kasahara K, Hayashi T, Takada Y, Suzuki H, Niwa-Sakai M, Ohashi S, Mori M, Hirokawa T, Shuto S
    Discovery of Novel Indazole Derivatives as Orally Available beta(3)-Adrenergic Receptor Agonists Lacking Off-Target-Based Cardiovascular Side Effects
    J. Med. Chem. 60: 3252-3265 (2017) doi: 10.1021/acs.jmedchem.6b01197
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