Updated on 2024/06/21

写真a

 
ISHIKAWA Takeshi
 
Organization
Research Field in Engineering, Science and Engineering Area Graduate School of Science and Engineering (Engineering) Department of Engineering Chemistry and Biotechnology Program Professor
Title
Professor

Degree

  • 博士(理学) ( 2005.3   北海道大学 )

Research Interests

  • インシリコ創薬

  • 理論化学

  • 計算化学

  • 生命計算化学

  • 理論化学

  • 分子軌道法

  • フラグメント分子軌道法

  • PAICS

  • 量子化学

  • 計算化学

  • 抗体医薬品

  • プリオン病創薬

  • タンパク間相互作用(PPI)解析

  • タンパクータンパクドッキング

Research Areas

  • Life Science / Biophysics

  • Nanotechnology/Materials / Fundamental physical chemistry  / Computational Chemistry

  • Informatics / Computational science

  • Life Science / Pharmaceutical analytical chemistry and physicochemistry

Education

  • Hokkaido University

    2001.4 - 2005.3

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    Country: Japan

  • Hokkaido University

    1999.4 - 2001.3

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    Country: Japan

  • Hokkaido University

    1996.4 - 1999.3

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    Country: Japan

  • Hokkaido University

    1994.4 - 1996.3

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    Country: Japan

Research History

  • Kagoshima University   Research Field in Engineering, Science and Engineering Area Graduate School of Science and Engineering (Engineering) Department of Engineering Chemistry and Biotechnology Program   Professor

    2020.4

  • 鹿児島大学 学術研究院 理工学域工学系 工学専攻 化学生命工学プログラム 教授

    2020.4

  • Kagoshima University   Research Field in Engineering, Science and Engineering Area Graduate School of Science and Engineering (Engineering) Chemistry, Biotechnology, and Chemical Engineering Course   Professor

    2018.10 - 2020.3

  • Kagoshima University   Professor

    2018.10 - 2020.3

  • Nagasaki University   Graduate School of Biomedical Sciences   Associate Professor

    2013.2 - 2018.9

  • Tohoku University   Assistant Professor

    2012.4 - 2013.1

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    Country:Japan

  • Gifu University   Assistant Professor

    2008.3 - 2012.3

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    Country:Japan

  • 独立行政法人科学技術振興機構(勤務地:立教大学)   理学部化学科   研究員

    2005.4 - 2008.2

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    Country:Japan

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Professional Memberships

  • THE PHARMACEUTICAL SOCIETY OF JAPAN

  • THE BIOPHYSICAL SOCIETY OF JAPAN

  • THE CHEMICAL SOCIETY OF JAPAN

  • CHEM-BIO INFORMATICS SOCIETY

Committee Memberships

  • CBI学会   年会実行委員  

    2018.4 - 2019.3   

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    Committee type:Academic society

  • 情報計算化学生物(CBI)学会   CBI学会評議員  

    2014.4   

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    Committee type:Academic society

  • CBI学会   評議員  

    2014.4   

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    Committee type:Academic society

  • 情報計算化学生物(CBI)学会   CBI学会プログラム委員  

    2013.4   

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    Committee type:Academic society

  • 情報計算化学生物(CBI)学会   CBIジャーナル編集委員(第一分野長)  

    2013.4   

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    Committee type:Academic society

  • CBI学会   ジャーナル編集委員(第一分野長)  

    2013.4   

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    Committee type:Academic society

  • CBI学会   年会プログラム委員  

    2013.4   

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    Committee type:Academic society

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Papers

  • Wataru Imamura, Tomohiro Yamasaki, Hikaru Kato, Takeshi Ishikawa .  Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain .  Carbohydrate Polymer Technologies and Applications7   100473 - 100473   2024.6Reviewed

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

    DOI: 10.1016/j.carpta.2024.100473

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  • Activity of Regional Branch .  Seibutsu Butsuri64 ( 2 ) 112 - 113   2024Activity of Regional Branch

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    Language:Japanese   Publisher:The Biophysical Society of Japan General Incorporated Association  

    DOI: 10.2142/biophys.64.112

  • Kousaka S., Ishikawa T. .  Quantum Chemistry-Based Protein-Protein Docking without Empirical Parameters .  Journal of Chemical Theory and Computation   2024Reviewed

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    Authorship:Last author, Corresponding author   Language:English   Publisher:Journal of Chemical Theory and Computation  

    This study developed a novel protein-protein docking approach based on quantum chemistry. To judge the appropriateness of complex structures, we introduced two criterion values, EV1 and EV2, computed using the fragment molecular orbital method without any empirical parameters. These criterion values enable us to search complex structures in which patterns of the electrostatic potential of the two proteins are optimally aligned at their interface. The performance of our method was validated using 53 complexes in a benchmark set provided for protein-protein docking. When employing bound state structures, docking success rates reached 64% for EV1 and 76% for EV2. On the other hand, when employing unbound state structures, docking success rates reached 13% for EV1 and 17% for EV2.

    DOI: 10.1021/acs.jctc.4c00531

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  • Satoshi Mizuta, Tomoko Yamaguchi, Takeshi Ishikawa .  Nucleophilic fluorine substitution reaction of α-carbonyl benzyl bromide, phenylthiofluoroalkyl bromide, and 2-bromo-2-phenoxyacetonitrile .  RSC Advances14 ( 27 ) 19062 - 19066   2024Reviewed

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Royal Society of Chemistry (RSC)  

    This manuscript discloses the nucleophilic fluorination of various alkylbromides using EtN<sub>3</sub>·3HF, producing monofluorinated compounds including tertiary benzylfluoride.

    DOI: 10.1039/d4ra03085k

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  • Satoshi Mizuta, Masahiro Tabira, Naoki Shichiro, Tomoko Yamaguchi, Jun Ishihara, Takeshi Ishikawa .  Reaction Mechanism and Origin of Stereoselectivity in the Fluorination and Trifluoromethylthiolation of 2‐Bromoamides with AgF and AgSCF3 .  European Journal of Organic Chemistry   2023.11Reaction Mechanism and Origin of Stereoselectivity in the Fluorination and Trifluoromethylthiolation of 2‐Bromoamides with AgF and AgSCF3Reviewed

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    Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    Reactions of chiral α‐bromoamides with AgF readily gave the corresponding 2‐fluorinated amide with retention of configuration. The mechanism and origin of the stereochemistry were rationalised using density functional theory calculations, which suggested a double‐inversion pathway via the formation of an aziridinone intermediate. The computed reaction pathway is consistent with the experimental results. In addition, the stereochemistry in base‐promoted trifluoromethylthiolation of α‐bromoamides using AgSCF3 was examined. The experimental results showed that the reaction proceeds through the generation of a neutral aziridinone intermediate, following the attack of a trifluoromethylthiolate anion at C‐3. The stereoselectivity of C‐3 attack on the aziridinone depended on the steric bulk of substitutes on the α‐position and nitrogen of the amide. The study results show the potential utility of AgF and AgSCF3 in the synthesis of chiral 2‐functionalized amide derivatives and provide mechanistic insights for nucleophilic substitution of 2‐bromoamides.

    DOI: 10.1002/ejoc.202301100

  • Touya Toyomoto, Katsuhiko Ono, Tomoo Shiba, Kenta Momitani, Tianli Zhang, Hiroyasu Tsutsuki, Takeshi Ishikawa, Kanae Hoso, Koma Hamada, Azizur Rahman, Liping Wen, Yosuke Maeda, Keiichi Yamamoto, Masao Matsuoka, Kenjiro Hanaoka, Takuro Niidome, Takaaki Akaike, Tomohiro Sawa .  Alkyl gallates inhibit serine O-acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics .  Frontiers in Microbiology14   1276447   2023.10Reviewed

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Frontiers Media SA  

    A principal concept in developing antibacterial agents with selective toxicity is blocking metabolic pathways that are critical for bacterial growth but that mammalian cells lack. Serine O-acetyltransferase (CysE) is an enzyme in many bacteria that catalyzes the first step in l-cysteine biosynthesis by transferring an acetyl group from acetyl coenzyme A (acetyl-CoA) to l-serine to form O-acetylserine. Because mammalian cells lack this l-cysteine biosynthesis pathway, developing an inhibitor of CysE has been thought to be a way to establish a new class of antibacterial agents. Here, we demonstrated that alkyl gallates such as octyl gallate (OGA) could act as potent CysE inhibitors in vitro and in bacteria. Mass spectrometry analyses indicated that OGA treatment markedly reduced intrabacterial levels of l-cysteine and its metabolites including glutathione and glutathione persulfide in Escherichia coli to a level similar to that found in E. coli lacking the cysE gene. Consistent with the reduction of those antioxidant molecules in bacteria, E. coli became vulnerable to hydrogen peroxide-mediated bacterial killing in the presence of OGA. More important, OGA treatment intensified susceptibilities of metallo-β-lactamase-expressing Gram-negative bacteria (E. coli and Klebsiella pneumoniae) to carbapenem. Structural analyses showed that alkyl gallate bound to the binding site for acetyl-CoA that limits access of acetyl-CoA to the active site. Our data thus suggest that CysE inhibitors may be used to treat infectious diseases caused by drug-resistant Gram-negative bacteria not only via direct antibacterial activity but also by enhancing therapeutic potentials of existing antibiotics.

    DOI: 10.3389/fmicb.2023.1276447

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  • Wataru Imamura, Tomohiro Yamasaki, Hikaru Kato, Takeshi Ishikawa .  Insights into the molecular interaction of cyclodextran with a guest molecule: A computational study .  Carbohydrate Polymers301 ( Pt A ) 120315 - 120315   2023.2Reviewed

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

    DOI: 10.1016/j.carbpol.2022.120315

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  • Hiroki Ozono, Kento Mimoto, Takeshi Ishikawa .  Quantification and Neutralization of the Interfacial Electrostatic Potential and Visualization of the Dispersion Interaction in Visualization of the Interfacial Electrostatic Complementarity .  The Journal of Physical Chemistry B126 ( 42 ) 8415 - 8426   2022.10Reviewed

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    Authorship:Last author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.2c05033

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  • Yudai Kudo, Satoshi Endo, Mei Fujita, Atsumi Ota, Yuji O Kamatari, Yoshimasa Tanaka, Takeshi Ishikawa, Hayato Ikeda, Takuya Okada, Naoki Toyooka, Naohiro Fujimoto, Toshiyuki Matsunaga, Akira Ikari .  Correction to "Discovery and Structure-Based Optimization of Novel Atg4B Inhibitors for the Treatment of Castration-Resistant Prostate Cancer". .  Journal of medicinal chemistry65 ( 11 ) 8062 - 8063   2022.6Correction to "Discovery and Structure-Based Optimization of Novel Atg4B Inhibitors for the Treatment of Castration-Resistant Prostate Cancer".International journal

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    DOI: 10.1021/acs.jmedchem.2c00749

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  • Mizuta S, Kitamura K, Morii Y, Ishihara J, Yamaguchi T, Ishikawa T .  Correction to "Trifluoromethylthiolation of Hindered α-Bromoamides with Nucleophilic Trifluoromethylthiolating Reagents". .  The Journal of organic chemistry87 ( 7 ) 5035   2022.4Correction to "Trifluoromethylthiolation of Hindered α-Bromoamides with Nucleophilic Trifluoromethylthiolating Reagents".

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    DOI: 10.1021/acs.joc.2c00508

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  • Yudai Kudo, Satoshi Endo, Mei Fujita, Atsumi Ota, Yuji O. Kamatari, Yoshimasa Tanaka, Takeshi Ishikawa, Hayato Ikeda, Takuya Okada, Naoki Toyooka, Naohiro Fujimoto, Toshiyuki Matsunaga, Akira Ikari .  Discovery and Structure-Based Optimization of Novel Atg4B Inhibitors for the Treatment of Castration-Resistant Prostate Cancer .  Journal of Medicinal Chemistry65 ( 6 ) 4878 - 4892   2022.3Reviewed International journal

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

    Autophagy inhibition is an attractive target for cancer therapy. In this study, we discovered inhibitors of Atg4B essential for autophagosome formation and evaluated their potential as therapeutics for prostate cancer. Seventeen compounds were identified as candidates after in silico screening and a thermal shift assay. Among them, compound 17 showed the most potent Atg4B inhibitory activity, inhibited autophagy induced by anti-castration-resistant prostate cancer (CRPC) drugs, and significantly enhanced apoptosis. Although 17 has been known as a phospholipase A2 (PLA2) inhibitor, other PLA2 inhibitors had no effect on Atg4B and autophagy. We then performed structural optimization based on molecular modeling and succeeded in developing 21f (by shortening the alkyl chain of 17), which was a potent competitive inhibitor for Atg4B (Ki = 3.1 μM) with declining PLA2 inhibitory potency. Compound 21f enhanced the anticancer activity of anti-CRPC drugs via autophagy inhibition. These findings suggest that 21f can be used as an adjuvant drug for therapy with anti-CRPC drugs.

    DOI: 10.1021/acs.jmedchem.1c02113

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  • Shuzo Urata, Olaposi Idowu Omotuyi, Ayako Izumisawa, Takeshi Ishikawa, Satoshi Mizuta, Yasuteru Sakurai, Tatsuaki Mizutani, Hiroshi Ueda, Yoshimasa Tanaka, Jiro Yasuda .  Identification of novel chemical compounds targeting filovirus VP40-mediated particle production .  Antiviral Research199   105267 - 105267   2022.2Identification of novel chemical compounds targeting filovirus VP40-mediated particle productionReviewed International journal

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

    The central role of Ebola virus (EBOV) VP40 in nascent virion assembly and budding from infected host cells makes it an important therapeutic target. The mechanism of dimerization, following oligomerization of VP40 leading to the production of virus-like particles (VLP) has never been investigated for the development of therapeutic candidates against Ebola disease. Molecular dynamics-based computational screening targeted VP40 dimer with 40,000,000 compounds selected 374 compounds. A novel in vitro screening assay selected two compounds, NUSU#1 and NUSU#2. Conventional VLP assays consistently showed that both compounds inhibited EBOV VP40-mediated VLP production. Intriguingly, NUSU#1 inhibited the VP40-mediated VLP production in other ebolavirus species and the Marburg virus, but did not inhibit Lassa virus Z-mediated VLP production. These results strongly suggested that the selected compounds are potential lead drug candidates against Filovirus disease via disruption of VP40-mediated particle production.

    DOI: 10.1016/j.antiviral.2022.105267

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  • Satoshi Mizuta, Hiroki Otaki, Takeshi Ishikawa, Juliann Nzembi Makau, Tomoko Yamaguchi, Takuya Fujimoto, Nobuyuki Takakura, Nobuki Sakauchi, Shuji Kitamura, Hikaru Nono, Ryota Nishi, Yoshimasa Tanaka, Kohsuke Takeda, Noriyuki Nishida, Ken Watanabe .  Lead Optimization of Influenza Virus RNA Polymerase Inhibitors Targeting PA–PB1 Interaction .  Journal of Medicinal Chemistry65 ( 1 ) 369 - 385   2021.12Reviewed International journal

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

    Influenza viruses are responsible for contagious respiratory illnesses in humans and cause seasonal epidemics and occasional pandemics worldwide. Previously, we identified a quinolinone derivative PA-49, which inhibited the influenza virus RNA-dependent RNA polymerase (RdRp) by targeting PA-PB1 interaction. This paper reports the structure optimization of PA-49, which resulted in the identification of 3-((dibenzylamino)methyl)quinolinone derivatives with more potent anti-influenza virus activity. During the optimization, the hit compound 89, which was more active than PA-49, was identified. Further optimization and scaffold hopping of 89 led to the most potent compounds 100 and a 1,8-naphthyridinone derivative 118, respectively. We conclusively determined that compounds 100 and 118 suppressed the replication of influenza virus and exhibited anti-influenza virus activity against both influenza virus types A and B in the range of 50% effective concentration (EC50) = 0.061-0.226 μM with low toxicity (50% cytotoxic concentration (CC50) >10 μM).

    DOI: 10.1021/acs.jmedchem.1c01527

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  • Satoshi Mizuta, Kanami Kitamura, Yuki Morii, Jun Ishihara, Tomoko Yamaguchi, Takeshi Ishikawa .  Trifluoromethylthiolation of Hindered α-Bromoamides with Nucleophilic Trifluoromethylthiolating Reagents .  The Journal of Organic Chemistry86 ( 24 ) 18017 - 18029   2021.12Reviewed

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    DOI: 10.1021/acs.joc.1c02316

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  • Takeshi Ishikawa, Hiroki Ozono, Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki .  Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity .  The Journal of Physical Chemistry Letters12 ( 46 ) 11267 - 11272   2021.11Reviewed

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpclett.1c02788

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  • Hiroki Ozono, Takeshi Ishikawa .  Visualization of the Interfacial Electrostatic Complementarity: A Method for Analysis of Protein–Protein Interaction Based on Ab Initio Quantum Chemical Calculations .  Journal of Chemical Theory and Computation17 ( 9 ) 5600 - 5610   2021.8Reviewed

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    Authorship:Last author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jctc.1c00475

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  • M. M. N. Tun, K. Morita, T. Ishikawa, S. Urata .  The antiviral effect of the chemical compounds targeting DED/EDh motifs of the viral proteins on Lymphocytic Choriomeningitis virus and SARS-CoV-2 .  Viruses13   1220   2021.6The antiviral effect of the chemical compounds targeting DED/EDh motifs of the viral proteins on Lymphocytic Choriomeningitis virus and SARS-CoV-2Reviewed

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    DOI: 10.3390/v13071220

  • Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa .  The ABINIT-MP Program .  Recent Advances of the Fragment Molecular Orbital Method (Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa (eds.))   53 - 67   2021.2

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    Publishing type:Part of collection (book)   Publisher:Springer Singapore  

    DOI: 10.1007/978-981-15-9235-5_4

  • Satoshi Mizuta, Kanami Kitamura, Ayako Kitagawa, Tomoko Yamaguchi, Takeshi Ishikawa .  Silver‐Promoted Fluorination Reactions of α‐Bromoamides .  Chemistry – A European Journal27 ( 19 ) 5930 - 5935   2020.12Reviewed

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    Language:Japanese   Publisher:Wiley  

    DOI: 10.1002/chem.202004769

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  • Takeshi Ishikawa .  A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method .  Chemical Physics Letters761 ( 16 ) 138103 - 138103   2020.10Reviewed

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

    DOI: 10.1016/j.cplett.2020.138103

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  • Makoto Sumiyoshi, Taiga Miyazaki, Juliann Nzembi Makau, Satoshi Mizuta, Yoshimasa Tanaka, Takeshi Ishikawa, Koichi Makimura, Tatsuro Hirayama, Takahiro Takazono, Tomomi Saijo, Hiroyuki Yamaguchi, Shintaro Shimamura, Kazuko Yamamoto, Yoshifumi Imamura, Noriho Sakamoto, Yasushi Obase, Koichi Izumikawa, Katsunori Yanagihara, Shigeru Kohno, Hiroshi Mukae .  Novel and potent antimicrobial effects of caspofungin on drug-resistant Candida and bacteria .  Scientific Reports10 ( 1 ) 17745 - 17745   2020.10Reviewed International journal

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>
    Echinocandins, including caspofungin, micafungin, and anidulafungin, are first-line antifungal agents for the treatment of invasive candidiasis. They exhibit fungicidal activity by inhibiting the synthesis of β-1,3-<sc>d</sc>-glucan, an essential component of the fungal cell wall. However, they are active only against proliferating fungal cells and unable to completely eradicate fungal cells even after a 24 h drug exposure in standard time-kill assays. Surprisingly, we found that caspofungin, when dissolved in low ionic solutions, had rapid and potent antimicrobial activities against multidrug-resistant (MDR) <italic>Candida</italic> and bacteria cells even in non-growth conditions. This effect was not observed in 0.9% NaCl or other ion-containing solutions and was not exerted by other echinocandins. Furthermore, caspofungin dissolved in low ionic solutions drastically reduced mature biofilm cells of MDR <italic>Candida auris</italic> in only 5 min, as well as <italic>Candida</italic>-bacterial polymicrobial biofilms in a catheter-lock therapy model. Caspofungin displayed ion concentration-dependent conformational changes and intracellular accumulation with increased reactive oxygen species production, indicating a novel mechanism of action in low ionic conditions. Importantly, caspofungin dissolved in 5% glucose water did not exhibit increased toxicity to human cells. This study facilitates the development of new therapeutic strategies in the management of catheter-related biofilm infections.

    DOI: 10.1038/s41598-020-74749-8

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    Other Link: http://www.nature.com/articles/s41598-020-74749-8

  • Daisuke Ishibashi, Takeshi Ishikawa, Satoshi Mizuta, Hiroya Tange, Takehiro Nakagaki, Tsuyoshi Hamada, Noriyuki Nishida .  Novel Compounds Identified by Structure-Based Prion Disease Drug Discovery Using In Silico Screening Delay the Progression of an Illness in Prion-Infected Mice .  Neurotherapeutics17 ( 4 ) 1836 - 1849   2020.8Reviewed

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    DOI: 10.1007/s13311-020-00903-9

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    Other Link: http://link.springer.com/article/10.1007/s13311-020-00903-9/fulltext.html

  • Juliann Nzembi Makau, Ken Watanabe, Hiroki Otaki, Satoshi Mizuta, Takeshi Ishikawa, Yuji O. Kamatari, Noriyuki Nishida .  A quinolinone compound inhibiting the oligomerization of nucleoprotein of influenza A virus prevents the selection of escape mutants .  Viruses12 ( 3 ) 337   2020.3Reviewed

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    © 2020 by the authors. Licensee MDPI, Basel, Switzerland. The emergence of resistance to currently available anti-influenza drugs has heightened the need for antivirals with novel mechanisms of action. The influenza A virus (IAV) nucleoprotein (NP) is highly conserved and essential for the formation of viral ribonucleoprotein (vRNP), which serves as the template for replication and transcription. Recently, using in silico screening, we identified an antiviral compound designated NUD-1 (a 4-hydroxyquinolinone derivative) as a potential inhibitor of NP. In this study, we further analyzed the interaction between NUD-1 and NP and found that the compound interferes with the oligomerization of NP, which is required for vRNP formation, leading to the suppression of viral transcription, protein synthesis, and nuclear export of NP. We further assessed the selection of resistant variants by serially passaging a clinical isolate of the 2009 H1N1 pandemic influenza virus in the presence of NUD-1 or oseltamivir. NUD-1 did not select for resistant variants after nine passages, whereas oseltamivir selected for resistant variants after five passages. Our data demonstrate that NUD-1 interferes with the oligomerization of NP and less likely induces drug-resistant variants than oseltamivir; hence, it is a potential lead compound for the development of novel anti-influenza drugs.

    DOI: 10.3390/v12030337

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  • ISHII Seiichiro, SEKIGUCHI Masahiro, YOSHIDA Hisae, MASUKAWA Keisuke, ISHIKAWA Takeshi, SAKAMOTO Taiichi, YAMAGISHI Kenji .  Elucidation of the Role of Ca<sup>2+</sup> in the Formation of an RNA Aptamer/Human Immunoglobulin G Complex Using Molecular Dynamics Simulation .  Journal of Computer Chemistry, Japan18 ( 5 ) 208 - 210   2020.3Reviewed

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Society of Computer Chemistry, Japan  

    <p>An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca<sup>2+</sup> ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca<sup>2+</sup> ions. To elucidate the role of Ca<sup>2+</sup> ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca<sup>2+</sup> ions in a solvent. In the presence of Ca<sup>2+</sup> ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 Å from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca<sup>2+</sup> ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca<sup>2+</sup> ions play a role in maintaining the conformation of the RNA aptamer to the binding form.</p>

    DOI: 10.2477/jccj.2019-0051

  • 石川岳志 .  ソフトウェア紹介「生体分子量子化学計算プログラム「PAICS」の紹介」 .  アンサンブル22 ( 4 ) 345 - 349   2020ソフトウェア紹介「生体分子量子化学計算プログラム「PAICS」の紹介」Reviewed

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    Language:Japanese  

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  • SOMEKAWA Kenichi, UEDA Takehiko, YOSHIDOME Toshifumi, ISHIKAWA Takeshi, NISHIKORI Hisashi .  Molecular Simulation Analysis of Novel and Chiral Diels-Alder Reactions by Basic Catalysts .  Journal of Computer Chemistry, Japan19 ( 4 ) 175 - 177   2020

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Society of Computer Chemistry, Japan  

    <p>The reaction process and steric situations of novel basic and chiral catalyst Diels-Alder reactions by Kagan et al. were speculated by IRC of PM7 simulation for the three molecules reactions clearly. The addition reactions of enolic dienes (<b>1</b>) with dienophiles (<b>2</b>) by amines (<b>3</b>) such as (<i>S</i>)-(+)-prolinol / (<i>R</i>)-(−)-prolinol proceeded via lower energy reaction complexes (RC) and transition states (TS) of two steps. The steric shapes by IRC (Figure 2 ∼ 6) showed the clear interactions between the reaction points, and of OH with amine moieties in the <b>1·3, 1·3·2</b> and TS complexes, to give high stereoselective adducts. IRC of some reactions also guesses right the Michael reaction selectivity. The handy PM7 simulation is recommended for usual chemical growth.</p>

    DOI: 10.2477/jccj.2021-0011

  • H. Yoshida, K. Sato, T. Ishikawa, T. Sakamoto, K. Yamagishi .  Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation .  Chemical Physics Letters738   136854   2019.10Reviewed

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

    DOI: 10.1016/j.cplett.2019.136854

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  • Fumika Mi-Ichi, Takeshi Ishikawa, Vo Kha Tam, Sharmina Deloer, Shinjiro Hamano, Tsuyoshi Hamada, Hiroki Yoshida .  Characterization of Entamoeba histolytica adenosine 5'-phosphosulfate (APS) kinase; validation as a target and provision of leads for the development of new drugs against amoebiasis. .  PLoS neglected tropical diseases13 ( 8 ) e0007633 - e0007633   2019.8Reviewed International journal

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    BACKGROUND: Amoebiasis, caused by Entamoeba histolytica infection, is a global public health problem. However, available drugs to treat amoebiasis are currently limited, and no effective vaccine exists. Therefore, development of new preventive measures against amoebiasis is urgently needed. METHODOLOGY/PRINCIPAL FINDINGS: Here, to develop new drugs against amoebiasis, we focused on E. histolytica adenosine 5'-phosphosulfate kinase (EhAPSK), an essential enzyme in Entamoeba sulfolipid metabolism. Fatty alcohol disulfates and cholesteryl sulfate, sulfolipids synthesized in Entamoeba, play important roles in trophozoite proliferation and cyst formation. These processes are closely associated with clinical manifestation and severe pathogenesis of amoebiasis and with disease transmission, respectively. We validated a combination approach of in silico molecular docking analysis and an in vitro enzyme activity assay for large scale screening. Docking simulation ranked the binding free energy between a homology modeling structure of EhAPSK and 400 compounds. The 400 compounds were also screened by a 96-well plate-based in vitro APSK activity assay. Among fifteen compounds identified as EhAPSK inhibitors by the in vitro system, six were ranked by the in silico analysis as having high affinity toward EhAPSK. Furthermore, 2-(3-fluorophenoxy)-N-[4-(2-pyridyl)thiazol-2-yl]-acetamide, 3-phenyl-N-[4-(2-pyridyl)thiazol-2-yl]-imidazole-4-carboxamide, and auranofin, which were identified as EhAPSK inhibitors by both in silico and in vitro analyses, halted not only Entamoeba trophozoite proliferation but also cyst formation. These three compounds also dose-dependently impaired the synthesis of sulfolipids in E. histolytica. CONCLUSIONS/SIGNIFICANCE: Hence, the combined approach of in silico and in vitro-based EhAPSK analyses identified compounds that can be evaluated for their effects on Entamoeba. This can provide leads for the development of new anti-amoebic and amoebiasis transmission-blocking drugs. This strategy can also be applied to identify specific APSK inhibitors, which will benefit research into sulfur metabolism and the ubiquitous pathway terminally synthesizing essential sulfur-containing biomolecules.

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  • S. Urata, T. Ishikawa, J. Yasuda .  Roles of YIGL sequence of Ebola virus VP40 on genome replication and particle production .  J. Gen. Virol.100 ( 7 ) 1099 - 1111   2019.6Roles of YIGL sequence of Ebola virus VP40 on genome replication and particle productionReviewed

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    DOI: 10.1099/jgv.0.001286

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  • Keiichi Yamaguchi, Yuji O Kamatari, Fumiko Ono, Hiroaki Shibata, Takayuki Fuse, Abdelazim Elsayed Elhelaly, Mayuko Fukuoka, Tsutomu Kimura, Junji Hosokawa-Muto, Takeshi Ishikawa, Minoru Tobiume, Yoshinori Takeuchi, Yutaka Matsuyama, Daisuke Ishibashi, Noriyuki Nishida, Kazuo Kuwata .  A designer molecular chaperone against transmissible spongiform encephalopathy slows disease progression in mice and macaques. .  Nature biomedical engineering3 ( 3 ) 206 - 219   2019.2Reviewed International journal

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    Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases that lack therapeutic solutions. Here, we show that the molecular chaperone (N,N'-([cyclohexylmethylene]di-4,1-phenylene)bis(2-[1-pyrrolidinyl]acetamide)), designed via docking simulations, molecular dynamics simulations and quantum chemical calculations, slows down the progress of TSEs. In vitro, the designer molecular chaperone stabilizes the normal cellular prion protein, eradicates prions in infected cells, prevents the formation of drug-resistant strains and directly inhibits the interaction between prions and abnormal aggregates, as shown via real-time quaking-induced conversion and in vitro conversion NMR. Weekly intraperitoneal injection of the chaperone in prion-infected mice prolonged their survival, and weekly intravenous administration of the compound in macaques infected with bovine TSE slowed down the development of neurological and psychological symptoms and reduced the concentration of disease-associated biomarkers in the animals' cerebrospinal fluid. The de novo rational design of chaperone compounds could lead to therapeutics that can bind to different prion protein strains to ameliorate the pathology of TSEs.

    DOI: 10.1038/s41551-019-0349-8

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  • Koutaroh Okada, Mitsugu Araki, Takuya Sakashita, Biao Ma, Ryo Kanada, Noriko Yanagitani, Atsushi Horiike, Sumie Koike, Tomoko Oh-Hara, Kana Watanabe, Keiichi Tamai, Makoto Maemondo, Makoto Nishio, Takeshi Ishikawa, Yasushi Okuno, Naoya Fujita, Ryohei Katayama .  Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance. .  EBioMedicine41   105 - 119   2019.1Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance.Reviewed International journal

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    BACKGROUND: Alectinib has shown a greater efficacy to ALK-rearranged non-small-cell lung cancers in first-line setting; however, most patients relapse due to acquired resistance, such as secondary mutations in ALK including I1171N and G1202R. Although ceritinib or lorlatinib was shown to be effective to these resistant mutants, further resistance often emerges due to ALK-compound mutations in relapse patients following the use of ceritinib or lorlatinib. However, the drug for overcoming resistance has not been established yet. METHODS: We established lorlatinib-resistant cells harboring ALK-I1171N or -G1202R compound mutations by performing ENU mutagenesis screening or using an in vivo mouse model. We performed drug screening to overcome the lorlatinib-resistant ALK-compound mutations. To evaluate these resistances in silico, we developed a modified computational molecular dynamic simulation (MP-CAFEE). FINDINGS: We identified 14 lorlatinib-resistant ALK-compound mutants, including several mutants that were recently discovered in lorlatinib-resistant patients. Some of these compound mutants were found to be sensitive to early generation ALK-TKIs and several BCR-ABL inhibitors. Using our original computational simulation, we succeeded in demonstrating a clear linear correlation between binding free energy and in vitro experimental IC50 value of several ALK-TKIs to single- or compound-mutated EML4-ALK expressing Ba/F3 cells and in recapitulating the tendency of the binding affinity reduction by double mutations found in this study. Computational simulation revealed that ALK-L1256F single mutant conferred resistance to lorlatinib but increased the sensitivity to alectinib. INTERPRETATION: We discovered lorlatinib-resistant multiple ALK-compound mutations and an L1256F single mutation as well as the potential therapeutic strategies for these ALK mutations. Our original computational simulation to calculate the binding affinity may be applicable for predicting resistant mutations and for overcoming drug resistance in silico. FUND: This work was mainly supported by MEXT/JSPS KAKENHI Grants and AMED Grants.

    DOI: 10.1016/j.ebiom.2019.01.019

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  • T. Tokiwa, S. Nakano, Y. Yamamoto, T. Ishikawa, S. Ito, V. Sladek, K. Fukuzawa, Y. Mochizuki, H. Tokiwa, F. Misaizu, Y. Shigeta .  Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations .  J. Chem. Inf. Model.59 ( 1 ) 25 - 39   2018.12Reviewed

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    In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard. However, the physical complexity and the number of the interactions within a protein-ligand complex renders analysis of the results somewhat complicated. This situation prompted us to develop the 3D-visualization of interaction energies in protein (3D-VIEP) method; the toolkit AnalysisFMO, which should enable a more efficient and convenient workflow with FMO data generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate units, RbAnalysisFMO, and the PyMOL plugins. The former can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output files generated by the aforementioned quantum-chemical packages. The PyMOL plugins enable visualization of IFIEs or PIEs in the protein structure in PyMOL. We demonstrate the use of this tool on a lectin protein from Burkholderia cenocepacia in which FMO analysis revealed the existence of a new interaction between G1y84 and fucose. Moreover, we found that second-shell interactions are crucial in forming the sugar binding site. In the case of bilirubin oxidase from Myrothecium verrucaria (MvBO), we predict that interactions between Asp105 and three His residues (His401, His403, and His136) are essential for optimally positioning the His residues to coordinate Cu atoms to form one Type 2 and two Type 3 Cu ions.

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  • T. Ishikawa, K. Sakakura, Y. Mochizuki .  RI-MP3 calculations of biomolecules based on the fragment molecular orbital method .  J. Comput. Chem.39 ( 24 ) 1970 - 1978   2018.9RI-MP3 calculations of biomolecules based on the fragment molecular orbital methodReviewed

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  • T. Ishikawa, S. Mizuta, O. Kaneko, K. Yahata .  Fragment molecular orbital study of the interaction between sarco/endoplasmic reticulum Ca<sup>2+</sup>-ATPase and its inhibitor thapsigargin toward anti-malarial development .  J. Phys. Chem. B122 ( 33 ) 7970 - 7977   2018.8Fragment molecular orbital study of the interaction between sarco/endoplasmic reticulum Ca<sup>2+</sup>-ATPase and its inhibitor thapsigargin toward anti-malarial developmentInvited Reviewed

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    DOI: 10.1021/acs.jpcb.8b04509

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  • Yukiko Miyazaki, Takeshi Ishikawa, Yuji O Kamatari, Takehiro Nakagaki, Hanae Takatsuki, Daisuke Ishibashi, Kazuo Kuwata, Noriyuki Nishida, Ryuichiro Atarashi .  Identification of Alprenolol Hydrochloride as an Anti-prion Compound Using Surface Plasmon Resonance Imaging. .  Molecular neurobiology56 ( 1 ) 367 - 377   2018.4Identification of Alprenolol Hydrochloride as an Anti-prion Compound Using Surface Plasmon Resonance Imaging.Reviewed International journal

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    Prion diseases are transmissible neurodegenerative disorders of humans and animals, which are characterized by the aggregation of abnormal prion protein (PrPSc) in the central nervous system. Although several small compounds that bind to normal PrP (PrPC) have been shown to inhibit structural conversion of the protein, an effective therapy for human prion disease remains to be established. In this study, we screened 1200 existing drugs approved by the US Food and Drug Administration (FDA) for anti-prion activity using surface plasmon resonance imaging (SPRi). Of these drugs, 31 showed strong binding activity to recombinant human PrP, and three of these reduced the accumulation of PrPSc in prion-infected cells. One of the active compounds, alprenolol hydrochloride, which is used clinically as a β-adrenergic blocker for hypertension, also reduced the accumulation of PrPSc in the brains of prion-infected mice at the middle stage of the disease when the drug was administered orally with their daily water from the day after infection. Docking simulation analysis suggested that alprenolol hydrochloride fitted into the hotspot within mouse PrPC, which is known as the most fragile structure within the protein. These findings provide evidence that SPRi is useful in identifying effective drug candidates for neurodegenerative diseases caused by abnormal protein aggregation, such as prion diseases.

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  • Takeshi Ishikawa .  Ab initio quantum chemical calculation of electron density, electrostatic potential, and electric field of biomolecule based on fragment molecular orbital method .  International Journal of Quantum Chemistry118 ( 8 ) e25535 - 1212   2017.11Ab initio quantum chemical calculation of electron density, electrostatic potential, and electric field of biomolecule based on fragment molecular orbital methodReviewed

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    Efficient quantum chemical calculations of electrostatic properties, namely, the electron density (EDN), electrostatic potential (ESP), and electric field (EFL), were performed using the fragment molecular orbital (FMO) method. The numerical errors associated with the FMO scheme were examined at the HF, MP2, and RI-MP2 levels of theory using 4 small peptides. As a result, the FMO errors in the EDN, ESP, and EFL were significantly smaller than the magnitude of the electron correlation effects, which indicated that the FMO method provides sufficiently accurate values of electrostatic properties. In addition, an attempt to reduce the computational effort was proposed by combining the FMO scheme and a point charge approximation. The error due to this approximation was examined using 2 proteins, prion protein and human immunodeficiency virus type 1 protease. As illustrative examples, the ESP values at the molecular surface of these proteins were calculated at the MP2 level of theory.

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  • Susumu Yamaguchi, Nobutaka Horie, Katsuya Satoh, Takeshi Ishikawa, Tsuyoshi Mori, Hajime Maeda, Yuhtaka Fukuda, Shunsuke Ishizaka, Takeshi Hiu, Yoichi Morofuji, Tsuyoshi Izumo, Noriyuki Nishida, Takayuki Matsuo .  Age of donor of human mesenchymal stem cells affects structural and functional recovery after cell therapy following ischaemic stroke. .  Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism38 ( 7 ) 1199 - 1212   2017.9Age of donor of human mesenchymal stem cells affects structural and functional recovery after cell therapy following ischaemic stroke.Reviewed International journal

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    Cell transplantation therapy offers great potential to improve impairments after stroke. However, the importance of donor age on therapeutic efficacy is unclear. We investigated the regenerative capacity of transplanted cells focusing on donor age (young vs. old) for ischaemic stroke. The quantities of human mesenchymal stem cell (hMSC) secreted brain-derived neurotrophic factor in vitro and of monocyte chemotactic protein-1 at day 7 in vivo were both significantly higher for young hMSC compared with old hMSC. Male Sprague-Dawley rats subjected to transient middle cerebral artery occlusion that received young hMSC (trans-arterially at 24 h after stroke) showed better behavioural recovery with prevention of brain atrophy compared with rats that received old hMSC. Histological analysis of the peri-infarct cortex showed that rats treated with young hMSC had significantly fewer microglia and more vessels covered with pericytes. Interestingly, migration of neural stem/progenitor cells expressing Musashi-1 positively correlated with astrocyte process alignment, which was more pronounced for young hMSC. Aging of hMSC may be a critical factor that affects cell therapy outcomes, and transplantation of young hMSC appears to provide better functional recovery through anti-inflammatory effects, vessel maturation, and neurogenesis potentially by the dominance of trophic factor secretion.

    DOI: 10.1177/0271678X17731964

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  • Ken Watanabe, Takeshi Ishikawa, Hiroki Otaki, Satoshi Mizuta, Tsuyoshi Hamada, Takehiro Nakagaki, Daisuke Ishibashi, Shuzo Urata, Jiro Yasuda, Yoshimasa Tanaka, Noriyuki Nishida .  Structure-based drug discovery for combating influenza virus by targeting the PA-PB1 interaction .  SCIENTIFIC REPORTS7 ( 1 ) 9500   2017.8Structure-based drug discovery for combating influenza virus by targeting the PA-PB1 interactionReviewed

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    Influenza virus infections are serious public health concerns throughout the world. The development of compounds with novel mechanisms of action is urgently required due to the emergence of viruses with resistance to the currently-approved anti-influenza viral drugs. We performed in silico screening using a structure-based drug discovery algorithm called Nagasaki University Docking Engine ( NUDE), which is optimised for a GPU-based supercomputer (DEstination for Gpu Intensive MAchine; DEGIMA), by targeting influenza viral PA protein. The compounds selected by NUDE were tested for anti-influenza virus activity using a cell-based assay. The most potent compound, designated as PA-49, is a mediumsized quinolinone derivative bearing a tetrazole moiety, and it inhibited the replication of influenza virus A/WSN/33 at a half maximal inhibitory concentration of 0.47 mu M. PA-49 has the ability to bind PA and its anti-influenza activity was promising against various influenza strains, including a clinical isolate of A(H1N1) pdm09 and type B viruses. The docking simulation suggested that PA-49 interrupts the PAPB1 interface where important amino acids are mostly conserved in the virus strains tested, suggesting the strain independent utility. Because our NUDE/DEGIMA system is rapid and efficient, it may help effective drug discovery against the influenza virus and other emerging viruses.

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  • Takeshi Ishikawa, Hiroki Otaki, Satoshi Mizuta, Masami Kuriyama, Osamu Onomura, Norihide Higuchi, Mihoko N. Nakashima, Mikiro Nakashima, Kaname Ohyama .  Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase .  DRUG METABOLISM AND PHARMACOKINETICS32 ( 4 ) 201 - 207   2017.4Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolaseReviewed

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    The efficacy of the antiepileptic drug VPA is decreased by co-administered carbapenems (CBPMs). The mechanism of CBPM selective inhibition of acylpeptide hydrolase (APEH) hydrolysis of VPA-glucuronide (VPA-G) to VPA is unclear due to the lack of APEH structural information. Here we performed homology modeling of the three-dimensional structure of APEH and subsequent docking simulations with a modeled structure to understand this mechanism. Docking simulations indicated that four groups of binding structures were involved in the binding of VPA-G, panipenem, and meropenem to APEH, but only one or two binding structures were involved in the binding of meropenem with an open beta-lactam ring structure and other antibiotics involving ampicillin. One of the four VPA-G binding structures was close enough to the APEH catalytic triad to facilitate VPA-G hydrolysis. This binding structure was also the most stable binding structure for panipenem, suggesting potential inhibition of VPA-G hydrolysis by panipenem. Fragment molecular orbital calculations of interaction energies of amino acid residues of APEH with VPA-G, panipenem, and meropenem indicated that the binding structure for panipenem closest to the catalytic triad is stabilized upon APEH interaction. These data suggest that APEH binding characteristics with CBPMs may help explain the selective inhibition of APEH by CBPMs. (C) 2017 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

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  • Juliann Nzembi Makau, Ken Watanabe, Takeshi Ishikawa, Satoshi Mizuta, Tsuyoshi Hamada, Nobuyuki Kobayashi, Noriyuki Nishida .  Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches .  PLOS ONE12 ( 3 ) e0173582   2017.3Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approachesReviewed

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    Influenza viruses have acquired resistance to approved neuraminidase-targeting drugs, increasing the need for new drug targets for the development of novel anti-influenza drugs. Nucleoprotein (NP) is an attractive target since it has an indispensable role in virus replication and its amino acid sequence is well conserved. In this study, we aimed to identify new inhibitors of the NP using a structure-based drug discovery algorithm, named Nagasaki University Docking Engine (NUDE), which has been established especially for the Destination for GPU Intensive Machine (DEGIMA) supercomputer. The hit compounds that showed high binding scores during in silico screening were subsequently evaluated for anti-influenza virus effects using a cell-based assay. A 4-hydroxyquinolinone compound, designated as NUD-1, was found to inhibit the replication of influenza virus in cultured cells. Analysis of binding between NUD-1 and NP using surface plasmon resonance assay and fragment molecular orbital calculations confirmed that NUD-1 binds to NP and could interfere with NP-NP interactions essential for virus replication. Time-of-addition experiments showed that the compound inhibited the mid-stage of infection, corresponding to assembly of the NP and other viral proteins. Moreover, NUD-1 was also effective against various types of influenza A viruses including a clinical isolate of A(H1N1)pdm09 influenza with a 50% inhibitory concentration range of 1.8-2.1 mu M. Our data demonstrate that the combined use of NUDE system followed by the cell-based assay is useful to obtain lead compounds for the development of novel anti-influenza drugs.

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  • S. Nakano, K. Yasukawa, T. Tokiwa, T. Ishikawa, E. Ishitsubo, N. Matsuo, S. Ito, H. Tokiwa, Y. Asano .  Origin of Stereoselectivity and Substrate/ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase .  The Journal of Physical Chemistry B120 ( 41 ) 10736 - 10743   2016.9Origin of Stereoselectivity and Substrate/ligand Recognition in an FAD-Dependent R-Selective Amine OxidaseReviewed

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    DOI: 10.1021/acs.jpcb.6b09328

  • T. Ishikawa .  Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation .  Journal of Computer-Aided Molecular Design30 ( 10 ) 875 - 887   2016.9Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulationReviewed

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    DOI: 10.1007/s10822-016-9967-3

  • D. Ishibashi, T. Nakagaki, T. Ishikawa, R. Atarashi, K. Watanabe, F. Cruz, T. Hamada, N. Nishida .  Structure-based drug discovery for prion disease by using a novel binding simulation .  EBioMedicine9   238 - 249   2016.6Structure-based drug discovery for prion disease by using a novel binding simulationReviewed

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    DOI: 10.1016/j.ebiom.2016.06.010

  • N. Sriwilaijaroen, S. Magesh, A. Imamura, H. Ando, H. Ishida, M. Sakai, E. Ishitsubo, T. Hori, S. Moriya, T. Ishikawa, K. Kuwata, T. Odagiri, M. Tashiro, H. Hiramatsu, K. Tsukamoto, T. Miyagi, H. Tokiwa, M. Kiso, and Y. Suzuki .  A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-inhibitor Interactions .  Journal of Medicinal Chemistry59 ( 10 ) 4563 - 4577   2016.4A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-inhibitor InteractionsReviewed

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    DOI: 10.1021/acs.jmedchem.5b01863

  • K. Pandey, P. E. Ferreira, T. Ishikawa, T. Nagai, O. Kaneko, K. Yahata .  Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor .  Scientific Reports6   23454   2016.3Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensorReviewed

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    DOI: 10.1038/srep23454

  • D. Morita, Y. Yamamoto, T. Mizutani, T. Ishikawa, J. Suzuki, T. Igarashi, N. Mori, T. Shiina, H. Inoko, H. Fujita, K. Iwai, Y. Tanaka, B. Mikami, M. Sugita .  Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex .  Nature Communications7   10356   2016.1Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complexReviewed

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    DOI: 10.1038/ncomms10356

  • 石川岳志 .  フラグメント分子軌道法の新規薬剤開発への応用 .  YAKUGAKU ZASSI136 ( 1 ) 121 - 130   2016.1フラグメント分子軌道法の新規薬剤開発への応用Reviewed

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    DOI: 10.1248/yakushi.15-00230-5

  • N. Kawashita, H. Yamasaki, T. Miyano, K. Kawai, Y. Sakae, T. Ishikawa, K. Mori, S. Nakamura, H. Kaneko .  A Mini-review on Chemoinformatics Approaches for Drug Discovery .  Journal of Computer Aided Chemistry16   15 - 29   2015.10A Mini-review on Chemoinformatics Approaches for Drug DiscoveryReviewed

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    DOI: 10.2751/jcac.16.15

  • Y. Higuchi, T. Ishikawa, N. Ozawa, L. Chazeau, J.-Y. Cavaille, M. Kubo .  Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation .  Chemical Physics459   96 - 101   2015.8Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulationReviewed

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    DOI: 10.1016/j.chemphys.2015.08.007

  • H. Oku, M. Inafuku, T. Ishikawa, T. Takamine, M. Ishmael, M. Fukuta .  Molecular cloning and biochemical characterization of isoprene synthases from the tropical trees Ficus virgata, Ficus septica, and Casuarina equisetifolia .  Journal of Plant Research128 ( 5 ) 849 - 861   2015.6Molecular cloning and biochemical characterization of isoprene synthases from the tropical trees Ficus virgata, Ficus septica, and Casuarina equisetifoliaReviewed

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    DOI: 10.1007/s10265-015-0740-9

  • 鷹觜順平, 小橋創介, 石川岳志, 坂本健作, 山岸賢司 .  ハロゲン原子導入によるタンパク質の構造安定化メカニズムの解明 .  Journal of Computer Chemistry, Japan13 ( 6 ) 308 - 309   2014.12ハロゲン原子導入によるタンパク質の構造安定化メカニズムの解明Reviewed

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    DOI: 10.2477/jccj.2014-0056

  • 石川岳志 .  フラグメント分子軌道法に基づくQM/MM分子動力学計算: AMBER-PAICSインターフェースの構築 .  日本化学会情報化学部会誌31 ( 3 ) 71 - 77   2013.10フラグメント分子軌道法に基づくQM/MM分子動力学計算: AMBER-PAICSインターフェースの構築Reviewed

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    DOI: 10.11546/cicsj.31.71

  • L. Chang, T. Ishikawa, K. Kuwata, S. Takada .  Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions .  Journal of Computational Chemistry34 ( 14 ) 1251 - 1257   2013.2Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactionsReviewed

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    DOI: 10.1002/jcc.23250

  • T. Okamoto, T. Ishikawa, Y. Koyano, N. Yamamoto, K. Kuwata, and M. Nagaoka .  A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation .  Bulletin of the Chemical Society of Japan86 ( 2 ) 210 - 222   2013.2A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD SimulationReviewed

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    DOI: 10.1246/bcsj.20120216

  • T. Ishikawa, R. R. Burri, Yuji O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao, K. Kuwata .  A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method .  Physical Chemistry Chemical Physics15 ( 10 ) 3646 - 3654   2013.1A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital methodReviewed

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    DOI: 10.1039/C3CP42761G

  • K. Takemura, R. R. Burri, T. Ishikawa, T. Ishikura, S. Sakuraba, N. Matubayasi, K. Kuwata, A. Kitao .  Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation .  Chemical Physics Letters559   94 - 98   2013.1Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representationReviewed

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

    DOI: 10.1016/j.cplett.2012.12.063

  • T. Ishikawa, K. Kuwata .  RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital Method .  The Journal of Physical Chemistry Letters3 ( 3 ) 375 - 379   2012.2RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital MethodReviewed

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

    DOI: 10.1021/jz201697x

  • 石川岳志, 石倉孝和, 桑田一夫 .  フラグメント分子軌道法プログラム「PAICS」と統合創薬プログラム「NAGARA」 .  Molecular Science5 ( 1 ) NP0015   2011.6フラグメント分子軌道法プログラム「PAICS」と統合創薬プログラム「NAGARA」Reviewed

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

  • T. Ishikawa, N. Yamamoto, K. Kuwata .  Partial energy gradient based on the fragment molecular orbital method: application to geometry optimization .  Chemical Physics Letters500 ( 1-3 ) 149 - 154   2010.10Partial energy gradient based on the fragment molecular orbital method: application to geometry optimizationReviewed

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    DOI: 10.1016/j.cplett.2010.09.071

  • T. Ishikawa, K. Kuwata .  Acceleration of monomer self-consistent charge process in fragment molecular orbital method .  Chem. Bio. Info. J.10   24 - 31   2010.2Acceleration of monomer self-consistent charge process in fragment molecular orbital methodReviewed

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

    DOI: 10.1273/cbij.10.24

  • T. Ishikawa, K. Kuwata .  Interaction analysis of the native structure of prion protein with quantum chemical calculations .  Journal of Chemical Theory and Computation6 ( 2 ) 538 - 547   2009.12Interaction analysis of the native structure of prion protein with quantum chemical calculationsReviewed

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

    DOI: 10.1021/ct900456v

  • T. Ishikawa, K. Tanaka .  Theoretical study on the structure of the ground state and photo-induced metastable states of [M(CN)5NO]2-, (M=Ru, Fe) and mechanism of the photo-rearrangement among them .  Z. Kristal.223 ( 4-5 ) 334 - 342   2009.9Theoretical study on the structure of the ground state and photo-induced metastable states of [M(CN)5NO]2-, (M=Ru, Fe) and mechanism of the photo-rearrangement among themReviewed

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

    DOI: 10.1524/zkri.2008.0033

  • T. Ishikawa, T. Ishikura, K. Kuwata .  Theoretical study of the prion protein based on the fragment molecular orbital method .  Journal of Computational Chemistry30 ( 16 ) 2594 - 2601   2009.4Theoretical study of the prion protein based on the fragment molecular orbital methodReviewed

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

    DOI: 10.1002/jcc.21265

  • T. Ishikawa, K. Kuwata .  Fragment molecular orbital calculation using the RI-MP2 method .  Chemical Physics Letters474 ( 1-3 ) 195 - 198   2009.4Fragment molecular orbital calculation using the RI-MP2 methodReviewed

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

    DOI: 10.1016/j.cplett.2009.04.045

  • N. Taguchi, Y. Mochizuki, T. Nakano, S. Amari, K. Fukuzawa, T. Ishikawa, M. Sakurai, S. Tanaka .  Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits) .  The Journal of Physical Chemistry B113 ( 4 ) 1153 - 1161   2009.1Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits)Reviewed

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

    DOI: 10.1021/jp808151c

  • Y. Okiyama, H. Watanabe*, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, S. Tanaka .  Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Toward an improvement of force fields for classical molecular dynamics simulations .  Chemical Physics Letters467 ( 4-6 ) 417 - 423   2008.11Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Toward an improvement of force fields for classical molecular dynamics simulationsReviewed

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

    DOI: 10.1016/j.cplett.2008.11.044

  • M. Ito, K. Fukuzawa, T. Ishikawa, Y. Mochizuki, T. Nakano, S. Tanaka .  Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information Transmission .  The Journal of Physical Chemistry B112 ( 38 ) 12081 - 12094   2008.8Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information TransmissionReviewed

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

    DOI: 10.1021/jp803369x

  • T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, S. Tanaka, K. Tanaka .  An application of fragment interaction analysis based on local MP2 .  Chemical Physics Letters463 ( 1-3 ) 189 - 194   2008.8An application of fragment interaction analysis based on local MP2Reviewed

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

    DOI: 10.1016/j.cplett.2008.08.022

  • Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, T. Nakano .  Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit salvation .  Journal of Computational Chemistry30 ( 1 ) 40 - 50   2008.3Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit salvationReviewed

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

    DOI: 10.1002/jcc.21025

  • M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki, T. Ishikawa, T. Nakano .  How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion .  Journal of the American Chemical Society130 ( 8 ) 2396 - 2397   2008.2How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium IonReviewed

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

    DOI: 10.1021/ja710038c

  • N. Taguchi, Y. Mochizuki, T. Ishikawa, K. Tanaka .  Multi-reference calculations of nitric oxide dimer .  Chemical Physics Letters451 ( 1-3 ) 31 - 36   2007.12Multi-reference calculations of nitric oxide dimerReviewed

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

    DOI: 10.1016/j.cplett.2007.11.084

  • Y. Okiyama, H. Watanabe*, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, S. Tanaka, K. Ebina .  Application of the fragment molecular orbital method for determination of atomic charges on polypeptides .  Chemical Physics Letters449 ( 4-6 ) 329 - 335   2007.10Application of the fragment molecular orbital method for determination of atomic charges on polypeptidesReviewed

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

    DOI: 10.1016/j.cplett.2007.10.066

  • T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, H. Tokiwa, S. Tanaka, K. Tanaka .  Fragment interaction analysis based on local MP2 .  Theoretical Chemistry Accounts118 ( 5-6 ) 937 - 945   2007.7Fragment interaction analysis based on local MP2Reviewed

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

    DOI: 10.1007/s00214-007-0374-7

  • Y. Mochizuki, K. Komeiji, T. Ishikawa, T. Nakano, H. Yamataka .  A fully quantum mechanical simulation study on the lowers n-π* state of hydrated formaldehyde .  Chemical Physics Letters437 ( 1-3 ) 66 - 72   2007.2A fully quantum mechanical simulation study on the lowers n-π* state of hydrated formaldehydeReviewed

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

    DOI: 10.1016/j.cplett.2007.02.016

  • Y. Mochizuki, K. Tanaka, K. Yamashita, T. Ishikawa, T. Nakano, S. Amari, K. Segawa, T. Murase, H. Tokiwa, M. Sakurai .  Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme .  Theoretical Chemistry Accounts117 ( 4 ) 541 - 553   2006.11Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital schemeReviewed

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

    DOI: 10.1007/s00214-006-0181-6

  • Y. Mochizuki, T. Nakano, S. Amari, T. Ishikawa, K. Tanaka, M. Sakurai, S. Tanaka .  Fragment molecular orbital calculations on red fluorescent protein (DsRed) .  Chemical Physics Letters433 ( 4-6 ) 360 - 367   2006.11Fragment molecular orbital calculations on red fluorescent protein (DsRed)Reviewed

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

    DOI: 10.1016/j.cplett.2006.11.088

  • K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, H. Tokiwa .  A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs .  Theoretical Chemistry Accounts117 ( 3 ) 397 - 405   2006.10A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphsReviewed

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

    DOI: 10.1007/s00214-006-0171-8

  • T. Ishikawa, Y. Mochizuki, K. Imamura, T. Nakano, H. Mori, H. Tokiwa, K. Tanaka, E. Miyoshi, S. Tanaka .  Application of fragment molecular orbital scheme to silicon-containing systems .  Chemical Physics Letters430 ( 4-6 ) 361 - 366   2006.9Application of fragment molecular orbital scheme to silicon-containing systemsReviewed

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    DOI: 10.1016/j.cplett.2006.09.015

  • T. Ishikawa, Y. Mochizuki, T. Nakano, S. Amari, H. Mori, H. Honda, T. Fujita, H. Tokiwa, S. Tanaka, Y. Komeiji, K. Fukuzawa, K. Tanaka, E. Miyoshi .  Fragment molecular orbital calculation on large scale systems containing heavy metal atom .  Chemical Physics Letters427 ( 1-3 ) 159 - 165   2006.7Fragment molecular orbital calculation on large scale systems containing heavy metal atomReviewed

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

    DOI: 10.1016/j.cplett.2006.06.103

  • Y. Mochizuki, T. Ishikawa, K. Tanaka, H. Tokiwa, T. Nakano, S. Tanaka .  Dynamic polarizability calculation with fragment molecular orbital scheme .  Chemical Physics Letters418 ( 4-6 ) 414 - 418   2005.11Dynamic polarizability calculation with fragment molecular orbital schemeReviewed

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

    DOI: 10.1016/j.cplett.2005.11.014

  • T. Ishikawa, K. Tanaka .  Response to “Comment on ‘Theoretical study of the photoinduced transfer among the ground state and two metastable state in [Fe(CN)5NO]2-’” [J. Chem. Phys. 122. 074314 (2005)], .  The Journal of Chemical Physics123 ( 4 ) 047102   2005.8Response to “Comment on ‘Theoretical study of the photoinduced transfer among the ground state and two metastable state in [Fe(CN)5NO]2-’” [J. Chem. Phys. 122. 074314 (2005)],Reviewed

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

    DOI: 10.1063/1.1989318

  • T. Ishikawa, K. Tanaka .  Electronic structures and the stabilities of metastable states in [Ru(CN)5NO]2-: A theoretical study .  Chemical Physics Letters412 ( 1-3 ) 164 - 170   2005.7Electronic structures and the stabilities of metastable states in [Ru(CN)5NO]2-: A theoretical studyReviewed

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

    DOI: 1016/j.cplett.2005.06.117

  • T. Ishikawa, K. Tanaka .  Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2- .  The Journal of Chemical Physics122 ( 7 ) 074314   2005.2Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2-Reviewed

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

    DOI: 10.1063/1.1851975

  • T. Ishikawa, K. Tanaka .  Theoretical study of lower electronic excitation spectra of [(Re6S8)Cl6]3- .  Chemical Physics Letters395 ( 1-3 ) 166 - 170   2004.8Theoretical study of lower electronic excitation spectra of [(Re6S8)Cl6]3-Reviewed

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

    DOI: 10.1016/j.cplett.2004.07.055

  • T. Ishikawa, T. Noro, T. Shoda .  Theoretical study on the photoisomerization of azobenzene .  The Journal of Chemical Physics115 ( 16 ) 7503 - 7512   2001.10Theoretical study on the photoisomerization of azobenzeneReviewed

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

    DOI: 10.1063/1.1406975

  • T. Suzuki, M. Kurahashi, Y. Yamauchi, T. Ishikawa, T. Noro .  Spin Polarized Metastable He* (23S, 1s2s) stimulated Desorption of H+ Ions .  Physical Review Letters86 ( 16 ) 3654 - 3657   2001.4Spin Polarized Metastable He* (23S, 1s2s) stimulated Desorption of H+ IonsReviewed

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    DOI: 10.1103/PhysRevLett.86.3654

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Books

  • The ABINIT-MP Program

    Mochizuki Y., Nakano T., Sakakura K., Okiyama Y., Watanabe H., Kato K., Akinaga Y., Sato S., Yamamoto J.I., Yamashita K., Murase T., Ishikawa T., Komeiji Y., Kato Y., Watanabe N., Tsukamoto T., Mori H., Okuwaki K., Tanaka S., Kato A., Watanabe C., Fukuzawa K.

    Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability  2021.1  ( ISBN:9789811592348

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    Language:Japanese

    We have been developing the ABINIT-MP program system as an original code for the fragment molecular orbital (FMO) calculations. ABINIT-MP has several unique features such as a variety of efficient correlated methods and hybrid parallelism. Additionally, an associated graphical user interface (named as BioStation Viewer) has been provided for end-users. In this chapter, we summarize the current features of the ABINIT-MP program. Plans and activities of future developments are addressed as well.

    DOI: 10.1007/978-981-15-9235-5_4

    Scopus

  • Recent Advances of the Fragment Molecular Orbital Method. FMO interfaced with Molecular Dynamics simulation (Chapter 19 : 373-389)

    Y. Komeji, T. Ishikawa

    Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability  2021.1  ( ISBN:9789811592348

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    Language:Japanese

    Three ways to combine FMO and MD are described: FMO-MD, FMO-QM/MM-MD, and MM-MD/FMO. FMO-MD is an ab initio MD in which force is updated on-the-fly by FMO. FMO-QM/MM-MD is a QM/MM-MD method in which the QM part is calculated by FMO. MM-MD/FMO is a simulation protocol in which FMO calculation is performed for molecular configurations generated by MM-MD. The methodology and application of these methods are described and compared.

    DOI: 10.1007/978-981-15-9235-5_19

    Scopus

  • Recent Advances of the Fragment Molecular Orbital Method. The ABINIT-MP Program (Chapter 4 : 53-67)

    Y. Mochizuki, T. Nakano, K. Sakakura, Y. Okiyama, H. Watanabe, K. Kato, Y. Akinaga, S. Sato, J. Yamamoto, K. Yamashita, T. Murase, T. Ishikawa, Y. Komeiji, Y. Kato, N. Watanabe, T. Tsukamoto, H. Mori, K. Okuwaki, S. Tanaka, A. Kato, C. Watanabe, K. Fukuzawa

    2021.1 

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  • Recent Advances of the Fragment Molecular Orbital Method. PAICS: Development of an Open-Source Software of Fragment Molecular Orbital Method for Biomolecule (Chapter 5 : 69-76)

    T. Ishikawa

    Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability  2021.1  ( ISBN:9789811592348

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    Language:Japanese

    PAICS is an open-source software available for fragment molecular orbital (FMO) calculation. A notable characteristic of PAICS is the capability to use the resolution of the identity (RI) approximation with the FMO scheme. Second-order Møller–Plesset perturbation theory with the RI approximation (RI-MP2) was implemented in PAICS, demonstrating that electron correlation energy of biomolecules could be efficiently calculated. Recently, third-order Møller–Plesset perturbation theory with the RI approximation (RI-MP3) was implemented, which enables us to calculate higher order electron correlation energy of biomolecules in a reasonable computational time. This chapter introduces the development of PAICS, by focusing on the FMO-RI-MP2 and MP3.

    DOI: 10.1007/978-981-15-9235-5_5

    Scopus

MISC

  • Characterization of Entamoeba histolytica adenosine 5′-phosphosulfate (APS) kinase

    見市文香, 石川岳志, TAM Vo kha, DELOER Sharmina, 濱野真二郎, 吉田裕樹

    日本寄生虫学会大会プログラム・抄録集   89th   2020

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  • AML1アプタマーの動的構造と結合親和性との相関

    田中淳, 増川恵介, 吉田尚恵, 吉田尚恵, 石川岳志, 坂本泰一, 山岸賢司

    日本細胞生物学会大会(Web)   71st   2019

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  • 抗体に結合するアプタマーと金属イオンの相互作用解析

    古峰真樹, 吉田尚恵, 関口真裕, 石川岳志, 山岸賢司, 坂本泰一

    日本分子生物学会年会プログラム・要旨集(Web)   42nd   2019

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  • 分子シミュレーションによるRNAアプタマー-IgG複合体の相互作用解析および複合体形成におけるCa<sup>2+</sup>の影響

    石井清一郎, 吉田尚恵, 吉田尚恵, 増川恵介, 石川岳志, 坂本泰一, 山岸賢司

    日本コンピュータ化学会年会講演予稿集   2019   2019

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  • RNAアプタマーと標的分子の結合メカニズムの解明

    増川恵介, 吉田尚恵, 吉田尚恵, 田中淳, 石井清一郎, 矢田部優貴, 石川岳志, 坂本泰一, 山岸賢司

    日本細胞生物学会大会(Web)   71st   2019

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  • 長崎大学における感染症インシリコ創薬の試み

    石川岳志

    CBI学会大会   2017   2017

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  • バルプロン酸とカルバペネム系抗菌薬の相互作用機序の計算化学的考察

    水田賢志, 石川岳志, 大滝大樹, 栗山正巳, 尾野村治, 樋口則英, 中嶋弥穂子, 中嶋幹郎, 大山要

    日本薬学会年会要旨集(CD-ROM)   137th   2017

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  • Identification of novel chemical compounds which inhibited filovirus VP40-mediated virus-like particle (VLP) production

    浦田秀造, 浦田秀造, OMOTUYI Olaposi Idowu, 石川岳志, 水田賢志, 櫻井康晃, 櫻井康晃, 水谷龍明, 植田弘師, 田中義正, 安田二朗, 安田二朗, 安田二朗

    日本薬学会年会要旨集(CD-ROM)   140th (Web)   2020

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  • 3-ヒドロキシ-2-ピリドン等の塩基触媒下,立体選択的Diels-Alder(DA)反応機構の分子軌道法シミュレーションによる解析と展開

    染川賢一, 上田岳彦, 吉留俊史, 石川岳志, 錦織寿, 岡村浩昭

    日本コンピュータ化学会年会講演予稿集   2019   2019

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  • 分子動力学計算によるIgGアプタマーの構造特性の解析

    石井清一郎, 吉田尚恵, 吉田尚恵, 増川恵介, 矢田部優貴, 秋田一雅, 猪股恵美礼, 石川岳志, 坂本泰一, 山岸賢司

    日本化学会春季年会講演予稿集(CD-ROM)   99th   2019

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  • フィロウイルスVP40による粒子形成を阻害する新規化合物の同定

    浦田秀造, 石川岳志, 水田賢志, OLAPOSI Omotuyi, 水谷龍明, 植田弘師, 田中義正, 安田二朗, 安田二朗

    日本ウイルス学会学術集会プログラム・予稿集(Web)   67th   2019

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  • カンジダ属および多剤耐性菌に対するカスポファンギンの新たな抗微生物活性

    住吉誠, 宮崎泰可, 宮崎泰可, 水田賢志, 田中義正, 石川岳志, 槇村浩一, 高園貴弘, 西條知見, 山本和子, 今村圭文, 泉川公一, 柳原克紀, 河野茂, 迎寛, 迎寛

    日本医真菌学会雑誌   60 ( Supplement 1 )   2019

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  • in silicoプリオン病創薬における薬効特異性の評価

    石橋 大輔, 中垣 岳大, 石川 岳志, 濱田 剛, 西田 教行

    生命科学系学会合同年次大会   2018   [1P - 1108]   2018

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    Language:English   Publisher:生命科学系学会合同年次大会運営事務局  

    J-GLOBAL

  • 新規作用機序をもつ抗インフルエンザウイルス薬の開発

    渡邊健, 石川岳志, 大滝大樹, 水田賢志, 濱田剛, 浦田秀造, 安田二朗, 田中義正, 西田教行, 西田教行

    日本薬学会年会要旨集(CD-ROM)   138th   2018

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  • 抗体に結合する化学修飾アプタマーの熱力学的解析

    矢田部優貴, 吉田尚恵, 関口真裕, 秋田一雅, 猪股恵美礼, 野村祐介, 石川岳志, 山岸賢司, 坂本泰一

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018

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  • FMO-QM/MM分子動力学計算と量子化学による創薬研究

    石川岳志

    CBI学会研究講演会   387th   2017

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  • 新たな作用機序をもつ抗インフルエンザウイルス薬の開発

    渡辺健, 石川岳志, 水田賢志, 中垣岳大, 大滝大樹, 濱田剛, 田中義正, 西田教行

    日本薬学会年会要旨集(CD-ROM)   137th   2017

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  • 抗マラリア化合物の開発をめざしたフラグメント分子軌道法によるSERCAとThapsigarginの分子間相互作用解析

    石川岳志, 水田賢志, 金子修, 矢幡一英

    日本薬学会年会要旨集(CD-ROM)   137th   2017

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  • 分子シミュレーションを用いたRNAアプタマーの設計手法の開発

    吉田尚恵, 吉田尚恵, 関口真裕, 秋田一雅, 猪股恵美礼, 野村祐介, 石川岳志, 坂本泰一, 山岸賢司

    日本蛋白質科学会年会プログラム・要旨集   17th   2017

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  • Theoretical study on the structure and dynamics of RNA aptamer to human immunoglobulin G

    吉田尚恵, 吉田尚恵, 関口真裕, 秋田一雅, 猪股恵美礼, 石川岳志, 坂本泰一, 山岸賢司

    化学系学協会東北大会プログラムおよび講演予稿集   2017   2017

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Presentations

  • T. Ishikawa   Development of a protein-ligand docking method based on molecular dynamics simulation and its application to anti-prion compounds  

    NDSU-KU 8th Annual Symposium 

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    Event date: 2023.11

    Language:English   Presentation type:Oral presentation (general)  

  • Ozora Kudo, Akari Endo, Masahiro Sekiguchi, Azumi ito, Takeshi Ishikawa, Taiichi Sakamoto, Kenji Yamagishi   Conformational behavior, dynamics, and affinity of A18-modified aptamers toward human Immunoglobulin G  

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    Event date: 2023.10

    Language:English   Presentation type:Poster presentation  

  • Drug Discovery Using Computational Chemistry: Method Development and Applications  

    2023.10 

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    Event date: 2023.10

    Language:English   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

  • 宮崎あんず、石川岳志、高松由基、浦田秀造   フニンウイルスNPエキソヌクレアーゼ活性部位のウイルス増殖における役割解明  

    第70回日本ウイルス学会学術集会 

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    Event date: 2023.9

    Language:Japanese   Presentation type:Poster presentation  

  • 遠藤朱梨,伊藤愛純,関口真裕,阪本智樹,片平正人,永田崇,石川岳志,山岸賢司,坂本泰一   抗体に結合するaptamerの改変体の結合能の解析  

    2023年度日本生化学会関東支部例会 

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    Event date: 2023.6

    Language:Japanese   Presentation type:Poster presentation  

  • 水田賢志、田平将大、森井優樹、石原淳、石川岳志   求核的トリフルオロメチルチオ化試薬を用いたα-SCF3化アミド類の合成法の開発  

    日本薬学会第143年会 

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    Event date: 2023.3

    Language:Japanese   Presentation type:Poster presentation  

  • アジリジノン中間体を経由するフッ化銀を用いたフッ化アミド類の合成法の開発  

    日本化学会第103春季年会 

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    Event date: 2023.3

    Language:Japanese   Presentation type:Poster presentation  

  • 石川岳志, 志々目裕太   バイオ医薬品開発の効率化を実現する生体分子量子化学計算プログラム「PAICS」  

    PARKS起業活動支援プログラム・Demo Day  2023.3 

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    Event date: 2023.3

    Language:Japanese   Presentation type:Oral presentation (general)  

  • 須藤正幸, 近藤智子, 石川岳志   SARS-CoV-2治療薬をめざしたインシリコ創薬  

    第16回桜ケ丘基礎系発表会  2023.3 

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    Event date: 2023.3

    Language:Japanese   Presentation type:Poster presentation  

  • 石川岳志   抗体医薬品開発を効率化する生体分子量子化学計算プログラム「PAICS」  

    KADAI STARTER‘S PITCH(KSP)  2023.1 

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    Event date: 2023.1

    Language:Japanese   Presentation type:Oral presentation (general)  

  • 工藤優大、藤田芽衣、吉野雄太、鎌足雄司、田中義正、石川岳志、藤本直浩、岡田卓哉、豊岡尚樹、遠藤智史、五十里彰   オートファゴソーム膜の形成を作用点とする新規オートファジー阻害剤の開発  

    第95回日本生化学会大会 

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    Event date: 2022.11

    Language:Japanese   Presentation type:Poster presentation  

  • Seiichiro ISHII, Ryoji YAMAZAKI, Ozora KUDO, Takeshi ISHIKAWA, Taiichi SAKAMOTO, Kenji YAMAGISHI   Conformational behavior and dynamics of G7A mutant IgG-aptamer  

    CBI学会2022年大会 

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    Event date: 2022.10

    Language:English   Presentation type:Poster presentation  

  • 石川岳志   抗体医薬品開発を加速するタンパク間相互作用(PPI)解析のためのインシリコ技術「VIINEC」  

    Bio Japan  2022.10 

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    Event date: 2022.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:横浜   Country:Japan  

  • T. Ishikawa   Development and Application of a Computational Method for Analyzing Protein-Protein Interaction   Invited International conference

    NDSU-KU 7th Annual Symposium  2022.10 

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    Event date: 2022.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:United States  

  • W. Imamura, T. Ishikawa   The molecular interaction of cyclodextran with a guest molecule using quantum chemical calculation and molecular dynamics simulation   International conference

    NDSU-KU 7th Annual Symposium  2022.10 

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    Event date: 2022.10

    Language:English   Presentation type:Poster presentation  

    Country:United States  

  • T. Ishikawa   Development and Application of a Computational Method for Analyzing Protein-Protein Interaction   Invited

    NDSU-KU 7th Annual Symposium  2022.10 

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    Event date: 2022.10

    Language:English   Presentation type:Oral presentation (invited, special)  

  • Ryoji Yamazaki,Azumi Ito,Tomoki Sakamoto,Masaki Komine,Takeshi Ishikawa, Masato Katahira,Takashi Nagata,Taiichi Sakamoto, Kenji Yamagihi   In silico approach for identification of the thermodynamic profiles of aptamer-IgG binding  

    2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  • A. Ito, Y. Yatabe, H. Yoshida, M. Sekiguchi, K. Akita, Y. Nakamura, Y. Nomura, T. Ishikawa, K. Yamagishi, T. Sakamoto   Effect of chemical modification on the aptamer that binds to IgG  

    2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  • T. Ishikawa   Development and Application of a Quantum Chemistry-Based Method for Analyzing Protein-Protein Interaction   Invited International conference

    The 20th Protein Island Matsuyama International Symposium  2022.9 

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    Event date: 2022.9

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  • T. Ishikawa   Development and Application of a Quantum Chemistry-Based Method for Analyzing Protein-Protein Interaction   Invited

    The 20th Protein Island Matsuyama International Symposium  2022.9 

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    Event date: 2022.9

    Language:English   Presentation type:Oral presentation (invited, special)  

  • 工藤優大, 藤田芽衣, 吉野雄太, 鎌足雄司, 田中義正, 石川岳志, 藤本直浩, 岡田卓哉, 豊岡尚樹, 遠藤智史, 五十里彰   がんアジュバント薬の開発を指向したオートファジー阻害剤の創製研究  

    第21回・次世代を担う若手のためのファーマ・バイオフォーラム2022  2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  • Kibet Ng’etich Japheth, Normalita Eka Pravitasari, Takeshi Ishikawa, Ayato Sato, Noriyuki Nishida, Takaya Sakura, Daniel Ken Inaoka   Application of AlphaFold2 to Predict Antimalarial Drug Targets and Phenotypic Validation  

    2022.8 

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    Event date: 2022.8

    Language:English   Presentation type:Oral presentation (general)  

  • W. Imamura, T. Ishikawa   Computational study on the inclusion mechanism of cyclodextran using quantum chemical calculation and molecular dynamics simulation  

    Joint Symposium of JTBW2021 and KNJS 2021  2021.11 

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    Event date: 2021.11

    Language:English   Presentation type:Poster presentation  

  • H. Ozono, T. Ishikawa   Development of visualization of the interfacial electrostatic complementarity (VIINEC) and an application to antibodies targeting PD-1/PD-L1 interaction  

    Joint Symposium of JTBW2021 and KNJS 2021  2021.11 

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    Event date: 2021.11

    Language:English   Presentation type:Poster presentation  

  • 石川岳志   フォーカストセッション「ペプチド創薬を指向した計算科学の最前線」, ドッキング計算を利用したヒト主要組織適合抗原とペプチドの結合親和性計算法の開発  

    CBI学会2021年大会  2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:遠隔   Country:Japan  

  • D. Arimura, T. Ishikawa   A computational study for the development of anti-prion compounds using the docking simulation  

    2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Poster presentation  

  • Visualization of the interfacial electrostatic complementarity: A method for analysis of protein-protein interaction based on fragment molecular orbital method  

    2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  • H. Ozono, T. Ishikawa   Application of visualization of the interfacial electrostatic complementarity (VIINEC) to antibodies targeting PD-1/PD-L1 interaction  

    2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Poster presentation  

  • 金田一樹,石井清一郎,坂本泰一,石川岳志,山岸賢司   分子シミュレーションを用いたヒト抗体(IgG)に特異的に結合する新規修飾アプタマーの分子設計  

    令和3年度化学系学協会東北大会  2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Poster presentation  

  • 山崎凌司, 金田一樹, 吉田尚恵, 坂本泰一, 石川岳志, 山岸賢司   デオキシリボヌクレオチドとリボヌクレオチドの違いによるIgGアプタマーの結合プロファイルの解析  

    令和3年度化学系学協会東北大会  2021.10 

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    Event date: 2021.10

    Language:Japanese   Presentation type:Poster presentation  

  • 今村亘, 山﨑智大, 日野志朗, 石川岳志   量子化学計算及び分子動力学計算による環状糖鎖の包接機構の理論的研究  

    第58回化学関連支部合同九州大会  2021.7 

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    Event date: 2021.7

    Language:Japanese   Presentation type:Poster presentation  

  • 佐藤啓子, 納屋昌実, 近藤好夫, 武部克希, 内藤真理子, 鈴木守, 今田勝巳, 石川岳志, 佐藤主税   歯周病細菌叢の病原性を抑える試み  

    第94回日本細菌学会総会  2021.3 

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    Event date: 2021.3

    Language:Japanese  

  • 大園紘貴, 石川岳志   抗体医薬品開発をめざしたFMO法に基づくタンパク質間相互作用解析法の開発と応用  

    日本化学会第101春季年会  2021.3 

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    Event date: 2021.3

    Language:Japanese   Presentation type:Poster presentation  

  • 石川岳志, 大園紘貴, 小原弘樹, 秋澤和輝, 畑田崚, 奥脇弘次, 望月祐志   フラグメント分子軌道法に基づく静電相互作用解析法の開発とSARS-CoV-2スパイクタンパク質への応用  

    第68回応用物理学会春季学術講演会  2021.3 

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    Event date: 2021.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:遠隔   Country:Japan  

  • 大園紘貴, 石川岳志   FMO法を用いたタンパク質間相互作用解析法の開発と免疫チェックポイント阻害剤への応用,  

    2020年日本化学会九州支部秋期研究発表会  2020.11 

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    Event date: 2020.11

    Language:Japanese   Presentation type:Poster presentation  

  • 石川岳志   生命科学を指向した量子化学計算プログラム「PAICS」の開発と応用   Invited

    日本コンピュータ化学会2020年秋季年会  2020.11 

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    Event date: 2020.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:鹿児島   Country:Japan  

  • 染川賢一, 上田岳彦, 吉留俊史, 石川岳志, 錦織寿, 岡村浩昭   塩基触媒による不斉Diels-Alder(DA)反応のMO法シミュレーションによる定量的解析と展開  

    日本コンピュータ化学会2020年秋季年会  2020.11 

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    Event date: 2020.11

    Language:Japanese   Presentation type:Poster presentation  

  • 石川岳志   医薬品開発を指向した量子化学プログラム「PAICS」の開発  

    イノベーション・ジャパン2020  2020.9 

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    Event date: 2020.9 - 2020.11

    Language:Japanese   Presentation type:Poster presentation  

    Venue:遠隔   Country:Japan  

  • 古峰真樹,吉田尚恵,関口真裕,石川岳志,山岸賢司,坂本泰一   抗体に結合するアプタマーと金属イオンの相互作用解析  

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese   Presentation type:Poster presentation  

  • 西田教行, 田中義正, 石川岳志, 水田賢志, 大滝大樹, 鎌足雄司, 渡邊健   薬剤耐性RNAウイルス出現予測法の確立と迅速制御のためのインシリコ創薬  

    J-PRIDE 研究成果発表会 「重症・難治性感染症の理解と予防・治療法の開発に向けて~若手研究者たちの挑戦~」 

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    Event date: 2019.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 浦田秀造, 石川岳志, 水田賢志, Omotuyi Olaposi, 水谷龍明, 植田弘師, 田中義正, 安田二朗   フィロウイルスVP40による粒子形成を阻害する新規化合物の同定  

    第67回日本ウイルス学会学術集会 

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    Event date: 2019.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 石井清一郎、吉田尚恵、増川恵介、石川岳志、坂本泰一、山岸賢司   分子シミュレーションによるRNAアプタマー- IgG複合体の相互作用解析および複合体形成におけるCa2+の影響  

    日本コンピュータ化学会2019年秋季年会 

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    Event date: 2019.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:広島  

  • Keisuke Masukawa, Hisae Yoshida, Seiichiro Ishii, Yuuki Yatabe, Takeshi Ishikawa, Taiichi Sakamoto, Kenji Yamagishi   Combined computational and experimental study on the binding mechanism of RNA aptamer to human Immunoglobulin G  

    2019年CBI学会 

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    Event date: 2019.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • T. Ishikawa   Quantum Chemical Calculation of biomolecule with Fragment Molecular Orbital Method: Program Development and Application to Drug Discovery   International conference

    NDSU KU Joint Symposium on Biotechnology, Nanomaterials and Polymers 

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    Event date: 2019.10

    Language:English   Presentation type:Oral presentation (general)  

    Venue: Fargo, USA  

  • 増川恵介, 吉田尚恵, 石井清一郎, 石川岳志, 坂本泰一, 山岸賢司   新規RNAアプタマーの設計を目指したRNAアプタマーと標的分子との結合メカニズム解析  

    RNAフロンティアミーティング2019 

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    Event date: 2019.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:静岡  

  • 石川岳志, 大滝大樹, J. N. Makaub, 渡邊健, 水田賢志, 鎌足雄司, 田中義正, 西田教行   計算化学を利用した薬剤耐性変異予測法の開発とオセルタミビル耐性インフルエンザウイルスでの検証  

    第72回日本細菌学会・第56回日本ウイルス学会九州支部総会 

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    Event date: 2019.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:熊本  

  • Keisuke MASUKAWA, Hisae YOSHIDA, Atsushi TANAKA, Seiichiro ISHII, Yuuki YATABE, Takeshi ISHIKAWA, Taiichi SAKAMOTO, Kenji YAMAGISHI   Binding mechanism between RNA aptamer and target molecule  

    第19回日本タンパク質科学会 

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    Event date: 2019.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:神戸  

  • Atsushi TANAKA, Keisuke MASUKAWA, Hisae YOSHIDA, Takeshi ISHIKAWAK, Taiichi SAKAMOTO, Kenji YAMAGISHI   Correlation between dynamic structure and binding affinity of AML1 aptamer  

    第19回日本タンパク質科学会 

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    Event date: 2019.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:神戸  

  • 染川賢一, 上田岳彦, 吉留俊史, 石川岳志, 錦織寿, 岡村浩昭   3-ヒドロキシ-2-ピリドン等の塩基触媒下, 立体選択的Diels-Alder(DA)反応機構の分子軌道法シミュレーションによる解析と展開  

    日本コンピュータ化学会2019年春季年会 

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    Event date: 2019.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 石井清一郎, 吉田尚恵, 増川恵介, 矢田部優貴, 秋田一雅, 猪股恵美礼, 石川岳志, 坂本泰一, 山岸賢司   分子動力学計算によるIgGアプタマーの構造特性の解析  

    日本化学会第99回春季大会 

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    Event date: 2019.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:神戸  

  • 石川岳志   FMOプログラム「PAICS」の開発と生命科学分野への応用   Invited

    第18回FMO研究会 

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    Event date: 2019.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

  • 矢田部優貴,吉田尚恵,関口真裕,秋田一雅,猪股恵美礼,中村義一,野村祐介,石川岳志,山岸賢司,坂本泰一   抗体に結合する化学修飾アプタマーの熱力学的解析  

    日本分子生物学会 

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    Event date: 2018.11

    Language:Japanese   Presentation type:Poster presentation  

    Venue:横浜  

  • T. Tokiwa, S. Nakano, Y. Yamamoto, T. Ishikawa, S. Ito, K. Fukuzawa, Y. Mochizuki, H. Tokiwa, Y. Shigeta   Data Analysis Toolkits of Fragment Molecular Orbital Calculations to Visualize Interaction Energies Using the GUI Plugin for PyMOL  

    2018年CBI学会 

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    Event date: 2018.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • T. Ishikawa, K. Sakakura, Y. Mochizuki   Efficient implementation of FMO-RI-MP3 method in PAICS  

    2018年CBI学会 

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    Event date: 2018.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • T. Ishikawa, K. Sakakura, Y. Mochizuki   Efficient implementation of FMO-RI-MP3 method in PAICS  

    2018年CBI学会 

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    Event date: 2018.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • T. Ishikawa, T. Ishikura, K. Kuwata   Theoretical Study of molecular interaction in prion protein based on fragment molecular orbital method  

    2008年CBI学会  

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    Event date: 2018.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • J. N. Makau, K. Watanabe, T. Ishikawa, S. Mizuta, N. Kobayashi, N. Nishida   Identification of influenza A virus inhibitors targeting viral nucleoprotein  

    第55回日本ウイルス学会九州支部総会 

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    Event date: 2018.9

    Language:English   Presentation type:Poster presentation  

    Venue:北九州  

  • 渡邊健, J. N. Makau, 石川岳志, 大滝大樹, 水田賢志, 中垣岳大, 石橋大輔, 浦田秀造, 安田二朗, 西田教行   インフルエンザウイルス複製を標的とした蛋白質-蛋白質相互作用阻害剤の開発  

    第55回日本ウイルス学会九州支部総会 

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    Event date: 2018.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:北九州  

  • 石橋大輔, 中垣岳大, 石川岳志, 水田賢志, 濱田剛, 西田教行   in silicoプリオン病創薬における薬効特異性の評価  

    生体機能と創薬シンポジウム2018 

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    Event date: 2018.8

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • 渡辺健, 石川岳志, 大滝大樹, 水田賢志, 濱田剛, 浦田秀造, 安田二朗, 田中義正, 西田教行   新規作用機序をもつ抗インフルエンザウイルス薬の開発  

    日本薬学会第138年会 

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    Event date: 2018.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:金沢  

  • Daisuke Ishibashi, Takehiro Nakagaki, Takeshi Ishikawa, Tsuyoshi Hamada, Noriyuki Nishida   in silico プリオン病創薬における薬効特異性の評価  

    2017年度生命科学系学会合同年次大会 (ConBio2017) 第40回日本分子生物学会年会 第90回日本生化学会大会 

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    Event date: 2017.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:神戸  

  • 石川岳志   フォーカストセッション「計算化学による感染症研究の最前線」, 長崎大学における感染症インシリコ創薬の試み  

    2017年CBI学会  

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    Event date: 2017.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:船堀  

  • H. Yoshida, M. Sekiguchi, K. Masukawa, S. Yamazaki, E. Inomata, K. Akita, T. Ishikawa, T. Sakamoto, K. Yamagishi   Structure and Dynamics of RNA Aptamer to Human Immunoglobulin G  

    2017年CBI学会 

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    Event date: 2017.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • T. Ishikawa   Efficient calculation of electrostatic potential of biomolecule based on fragment molecular orbital method  

    2017年CBI学会 

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    Event date: 2017.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • 吉田尚恵, 関口真裕, 秋田一雅, 猪股恵美礼, 石川岳志, 坂本泰一, 山岸賢司   Theoretical study on the structure and dynamics of RNA aptamer to human immunoglobulin G  

    日本化学会東北支部大会 

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    Event date: 2017.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:盛岡  

  • S. Urata, T. Ishikawa, J. Yasuda   YIGL motif in Ebola virus VP40 regulates virus-like particle production   International conference

    9th International Filovirus Symposium 

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    Event date: 2017.9

    Language:English   Presentation type:Poster presentation  

    Venue:Marburg, Germany  

  • 石川岳志   FMO-QM/MM分子動力学計算と量子化学による創薬研究   Invited

    第387回CBI学会研究講演会 「薬物-標的親和性計算の新潮流 ~古典MDから量子MDへ~」 

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    Event date: 2017.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:大阪  

  • H. Yoshida, M. Sekiguchi, K. Akita, E. Inomata, T. Ishikawa, T. Sakamoto, K. Yamagishi   IN SILICO DESIGN OF RNA APTAMER TO HUMAN IMMUNOGLOBULIN G   International conference

    EFMC-ASMC17: International Symposium on Advances in Synthetic and Medicinal Chemistry 

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    Event date: 2017.8

    Language:English   Presentation type:Poster presentation  

    Venue:Vienna, Austria  

  • J. N. Makau, K. Watanabe, T. Ishikawa, S. Mizuta, T. Hamada, N. Kobayashi, N. Nishida   Structure-based discovery of inhibitors targeting influenza A virus nucleoprotein   International conference

    The 17th International congress of virology 

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    Event date: 2017.7

    Language:English   Presentation type:Poster presentation  

    Venue:Singapore  

  • 吉田尚恵, 関口真裕, 秋田一雅, 猪股恵美礼, 野村祐介, 石川岳志, 坂本泰一, 山岸賢司   分子シミュレーションを用いたRNAアプタマーの設計手法の開発  

    第17回日本蛋白質科学会 

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    Event date: 2017.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • J. N. Makau, K. Watanabe, T. Ishikawa, S. Mizuta, T. Hamada, N. Kobayashi, N. Nishida   Targeting viral nucleoprotein in search for new influenza A virus inhibitors   International conference

    The 13th Nagasaki-Singapore Medical Symposium / Leading Program International Symposium 2017 

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    Event date: 2017.5

    Language:English   Presentation type:Poster presentation  

    Venue:Nagasaki, Japan  

  • 石川岳志, 水田賢志, 金子修, 矢幡一英   抗マラリア化合物の開発をめざしたフラグメント分子軌道法によるSERCAとThapsigarginの分子間相互作用解析  

    日本薬学会第137年会 

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    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 水田賢志, 石川岳志, 大滝大樹, 栗山正巳, 小野村治, 樋口則英, 中嶋 弥穂子, 中嶋 幹郎, 大山 要   バルプロン酸とカルパペネム系抗菌薬の相互作用機序の計算化学的考察  

    日本薬学会第137年会 

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    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 渡辺健, 石川岳志, 水田賢司, 中垣岳大, 大滝大樹, 濱田剛, 田中正義, 西田教行   新たな作用機序をもつ抗インフルエンザウイルス薬の開発  

    日本薬学会第137年会 

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    Event date: 2017.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 関口真裕, 吉田尚恵, 石川岳志, 山岸賢司   分子動力学計算を用いた修飾RNAアプタマーの立体構造解析  

    日本大学工学部学術研究報告会 

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    Event date: 2016.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:郡山  

  • 関口真裕,小野間優希,吉田尚恵,石川岳志,秋田一雅,猪股恵美礼,坂本泰一,山岸賢司   分子動力学計算を用いた修飾RNAアプタマーの構造解析  

    日本核酸医薬学会第2回年会 

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    Event date: 2016.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • Takeshi Ishikawa   Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation  

    2016年CBI学会 

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    Event date: 2016.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • H. Yoshida, T. Fukaya, M. Sekiguchi, E. Inomata, K. Akita, T. Ishikawa, T. Sakamoto, K. Yamagishi   Molecular Simulation Analysis of RNA Aptamer to Human Immunoglobulin G  

    2016年CBI学会 

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    Event date: 2016.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • H. Otaki, T. Ishikawa, S. Mizuta, K. Ohyama   Inhibition Mechanisms of Carbapenem Antibiotics on Acylpeptide Hydrolase: Docking Simulation Study  

    2016年CBI学会 

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    Event date: 2016.10

    Language:English   Presentation type:Poster presentation  

    Venue:東京  

  • D. Ishibashi, T. Nakagaki, T. Ishikawa, R. Atarashi, K. Watanabe, T. Hamada, N. Nishida   Structure-based drug discovery for prion disease by using a novel binding simulation on the graphics processing unit intensive supercomputer  

    第89回日本生化学会大会 

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    Event date: 2016.9

    Language:English   Presentation type:Poster presentation  

    Venue:仙台  

  • 関口真裕, 小野間優希, 深谷和紀, 八巻雷士, 吉田尚恵, 石川岳志, 秋田一雅, 猪股恵美礼, 坂本泰一, 山岸賢司   修飾RNAアプタマーに対する構造活性相関  

    第55回日本薬学会東北支部大会 

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    Event date: 2016.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:郡山  

  • J. N. Makau, K. Watanabe, T. Ishikawa, T. Hamada, N. Kobayashi, N. Nishida   Discovery of influenza virus inhibitors using in silico and in vitro approaches   International conference

    The 15th Awaji International Forum on Infection and Immunity 

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    Event date: 2016.9

    Language:English   Presentation type:Poster presentation  

    Venue:Awaji, Japan  

  • J. N. Makau, K. Watanabe, T. Ishikawa, T. Hamada, N. Kobayashi, N. Nishida   Discovery of influenza virus inhibitors using in silico and in vitro approaches   International conference

    第5回感染症若手フォーラム 

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    Event date: 2016.9

    Language:English   Presentation type:Oral presentation (general)  

    Venue:淡路島  

  • J. N. Makau, K. Watanabe, T. Ishikawa, T. Hamada, N. Kobayashi, N. Nishida   Drug discovery for influenza virus   International conference

    The 3rd International symposium for the Promotion of Science and Technology Innovation Cooperation between Africa and Japan 

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    Event date: 2016.7

    Language:English   Presentation type:Poster presentation  

    Venue:Tokyo, Japan  

  • N. Sriwilaijaroen, S. Magesh, A. Imamura, H. Ando, H. Ishida, M. Sakai, E. Ishitsubo, T. Hori, S. Moriya, T. Ishikawa, K. Kuwata, T. Odagiri, M. Tashiro, H. Hiramatsu, K. Tsukamoto, T. Miyagi, H. Tokiwa, M. Kiso, Y. Suzuki   A New Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases   International conference

    The 11th China-Japan International Conference of Virology 

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    Event date: 2016.7 - 2017.7

    Language:English   Presentation type:Oral presentation (general)  

    Venue:kannonji, Japan  

  • 関口真裕, 吉田尚恵, 石川岳志, 宮川伸, 坂本泰一, 山岸賢司   修飾RNAアプタマーに対するコンフォメーション解析  

    第16回日本蛋白質科学会年会  

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    Event date: 2016.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • 吉田尚恵, 石川岳志, 小橋創介, 鷹觜潤平, 春木満, 坂本健作, 山岸賢司   ハロゲン原子の導入によるタンパク質の構造安定化メカニズムの解明  

    第16回日本蛋白質科学会年会 

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    Event date: 2016.6

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 渡辺健, 石川岳志, 水田賢志, 大滝大樹, 濱田剛, 田中義正, 西田教行   In silico スクリーニングによる抗インフルエンザ化合物の探索  

    日本薬学会第136年会 

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    Event date: 2016.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:横浜  

  • 吉田尚恵, 関口真裕, 石川岳志, 宮川伸, 坂本泰一, 山岸賢司   分子シミュレーションを利用したRNAアプタマーと標的タンパク質との結合メカニズムの解析  

    日本化学会第96春季年会2016 

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    Event date: 2016.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:京都  

  • 吉田尚恵, 関口真裕, 石川岳志, 坂本泰一, 沼田靖, 山岸賢司   計算化学手法を用いた新規RNAアプタマー設計手法の開発  

    日本大学工学部学術研究報告会 

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    Event date: 2015.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:郡山  

  • 石川岳志   ワクチン開発をめざしたヒト主要組織適合抗原(HLA)とペプチドの結合親和性計算法の開発  

    琉球大学熱帯生物圏研究センター共同利用研究会「計算科学と感染症研究」 

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    Event date: 2015.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:沖縄  

  • 山口将, 堀江信貴, 佐藤克也, 石川岳志, 前田肇, 諸藤陽一, 出雲剛, 西田教行, 松尾孝之   脳梗塞に対する間葉系幹細胞移植の効果はドナーの年齢に依存する~内因性神経幹細胞遊走の違い~  

    第27回日本脳循環代謝学会総会 

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    Event date: 2015.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:富山  

  • K. Yahata, K. Pandey, P. E. Ferreira, T. Ishikawa, O. Kaneko   Calcium monitoring in Plasmodium falciparum through Yellow Cameleon-Nano Biosensors   International conference

    The 14th Awaji International Forum on Infection and Immunity 

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    Event date: 2015.9

    Language:English   Presentation type:Poster presentation  

    Venue:Awaji, Japan  

  • 石川岳志   シンポジウム「創薬・化学研究における化合物・相互作用情報の活用 ~ケモインフォマティクスからの試み~」, フラグメント分子軌道法の新規薬剤開発への応用   Invited

    第135回日本薬学会 

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    Event date: 2015.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:神戸  

  • 石川岳志   第8回FMO研究会 「ナノバイオ分子計算とデザイン」 FMO法を用いた最近の研究 -PAICSの開発と生命科学への応用-  

    2014年CBI学会 

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    Event date: 2014.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:船堀  

  • 小橋創介, 鷹觜潤平, 石川岳志, 春木満, 坂本健作, 山岸賢司   非天然型アミノ酸の導入によるタンパク質の耐熱化メカニズムの解明  

    第3回生命医薬情報学連合大会 

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    Event date: 2014.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 鷹觜潤平, 小橋創介, 石川岳志, 坂本健作, 山岸賢司   ハロゲン原子導入によるタンパク質の構造安定化メカニズムの解明  

    日本コンピュータ化学会2014年秋季年会 

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    Event date: 2014.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:郡山  

  • 石川岳志   ランチョンセミナー「今こそ高精度計算によるコンピュータ支援型創薬を」, 生体分子全電子計算プログラム「PAICS」の紹介   Invited

    第134回日本薬学会 

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    Event date: 2014.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:熊本  

  • 石川岳志   フォーカストセッション(第一分野) 「フラグメント分子軌道法の最近の展開: 実利用へ向けた開発と応用」 Application of FMO method to interaction analysis of biomolecules  

    2013年CBI学会 

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    Event date: 2013.10

    Language:Japanese   Presentation type:Oral presentation (general)  

  • Takeshi Ishikawa   Application of the Fragment Molecular Orbital Method to Drug Discovery   International conference

    Drug Discovery & Therapy World Congress 2013 

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    Event date: 2013.6

    Language:English   Presentation type:Oral presentation (general)  

    Venue:Boston  

  • 白珊丹, 小林康彦, 佐藤誠一亮, 石川岳志, 樋口祐次, 尾澤伸樹, 足立幸志, 久保百司   化学修飾したDLC膜におけるトライボケミカル反応プロセスの計算科学による解明  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 周康, 尾澤伸樹, 石川岳志, 樋口祐次, 久保百司   計算科学手法に基づいたシリカ砥粒によるサファイア表面の化学機械研磨プロセスの解析  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 河口健太郎, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   化学機械研磨によるシリコンウェハの平滑化メカニズムの量子分子動力学法による解析  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 佐藤誠一亮, 小林康彦, 白珊丹, 石川岳志, 樋口祐次, 尾澤伸樹, 足立幸志, 久保百司   計算科学シミュレーションによる窒化炭素膜の窒素原子が摩擦特性に及ぼす影響  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 小林康彦, 佐藤誠一亮, 白珊丹, 石川岳志, 樋口祐次, 尾澤伸樹, 足立幸志, 久保百司   量子分子動力学法を用いた水潤滑による炭化ケイ素の低摩擦化に関する研究  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 張琪, 刀東風, 白珊丹, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   ナノスクラッチされたグラフェンレイヤーの原子構造と機械特性の計算科学に基づく解明  

    トライポロジー会議2013春 

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    Event date: 2013.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京  

  • 樋口祐次,石川岳志,尾澤伸樹,久保百司   ポリエチレンの切断反応が半結晶高分子の耐久性に与える影響  

    日本物理学会第68回年次大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:広島  

  • 千枝繁樹, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   エチレングリコールを用いたアルカリ形燃料電池における酸化触媒反応の第一原理シミュレーション  

    電気化学会第80回大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 尾澤伸樹, 中村美穂, 河口健太郎, 石川岳志, 樋口祐次, 久保百司   第一原理計算を用いたペロブスカイト型酸化物砥粒におけるガラス研磨性能の検討と代替砥粒の理論的設計  

    2013年春期第60回応用物理学会学術講演会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川  

  • 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 寒川誠二, 久保百司   フルオロカーボンラジカルによるシリコン酸化膜SiO2エッチングプロセスへの量子分子動力学法アプローチ  

    2013年春期第60回応用物理学会学術講演会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川  

  • 柳谷一行, 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   量子分子動力学法を用いたGaNエッチング過程における反応メカニズムの解析  

    2013年春期第60回応用物理学会学術講演会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川  

  • 桑原卓哉, 伊藤寿, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   薄膜Si太陽電池のプラズマCVD プロセスにおけるラジカル種の影響に関する量子化学計算  

    2013年春期第60回応用物理学会学術講演会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川  

  • 中村耕輔, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   量子分子動力学シミュレーションによるリチウムイオン電池の劣化プロセスの解析  

    電気化学会第80回大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 坂之井遼太, 許競翔, 石川岳志, 樋口祐次, 尾澤伸樹, 佐藤一永, 橋田俊之, 久保百司   分子動力学法及び密度汎関数法によるSOFC用電解質の亀裂進展メカニズムの解析  

    電気化学会第80回大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 許競翔, 坂之井遼太, 石川岳志, 樋口祐次, 尾澤伸樹, 佐藤一永, 橋田俊之, 久保百司   分子動力学法を用いた固体酸化物形燃料電池アノードにおけるドーパントがシンタリングに及ぼす影響の解析  

    電気化学会第80回大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 小林顕, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   フッ素系高分子電解質における分解劣化プロセスの第一原理分子動力学シミュレーション  

    電気化学会第80回大会 

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    Event date: 2013.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • K. Kawaguchi, T. Ishikawa, Y. Higuchi, N. Ozawa, T. Shimazaki, and M. Kubo   Quantum Chemical Molecular Dynamics Simulations of Mechano-Chemical Reactions during Copper Chemical Mechanical Polishing Processes   International conference

    222nd ECS Meeting PRiME2012 

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    Event date: 2012.10

    Language:English   Presentation type:Poster presentation  

    Venue:Honolulu, Hawaii  

  • A. Kobayashi, T. Ishikawa, Y. Higuchi, N. Ozawa, T. Shimazaki, and M. Kubo   First-Principles Molecular Dynamics Simulation of the Chemical Degradation of Polymer Electrolyte Membranes   International conference

    222nd ECS Meeting PRiME2012 

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    Event date: 2012.10

    Language:English   Presentation type:Poster presentation  

    Venue:Honolulu, Hawaii  

  • S. Sato, S. Bai, T. Ishikawa, Y. Higuchi, N. Ozawa, T. Shimazaki, K. Adachi, J. Martin, and M. Kubo   Tight-Binding Quantum Chemical Molecular Dynamics and First-Principles Molecular Dynamics Studies of Super-Low Friction Mechanism on Carbon Nitride Coating   International conference

    222nd ECS Meeting PRiME2012 

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    Event date: 2012.10

    Language:English   Presentation type:Poster presentation  

    Venue:Honolulu, Hawaii  

  • K. Yanagiya, H. Ito, T. Kuwahara, T. Ishikawa, Y. Higuchi, N. Ozawa, M. Kubo   Quantum Chemical Molecular Dynamics Simulation of GaN Etching Processes by Cl Radical   International conference

    222nd ECS Meeting PRiME2012 

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    Event date: 2012.10

    Language:English   Presentation type:Poster presentation  

    Venue:Honolulu, Hawaii  

  • 佐藤誠一亮, 白珊丹, 石川岳志, 樋口裕次, 尾澤伸樹, 島崎智実, 足立幸志, 久保百司   量子分子動力学法による窒化炭素膜とダイヤモンドライクカーボン膜の低摩擦機構の研究  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 樋口祐次, 石川岳志, 尾澤伸樹, 久保百司   酸素と高分子の化学反応が耐久性に与える影響  

    2012年物理学会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:横浜  

  • 尾澤伸樹, 中村美穂, 河口健太郎, 石川岳志, 樋口祐次,久保百司   第一原理計算を用いたペロブスカイト型酸化物砥粒におけるCMP特性の検討  

    2012年度精密工学会秋季大会学術講演会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:小倉  

  • 樋口祐次, 石川岳志, 尾澤伸樹, 久保百司   第一原理分子動力学法と粗視化分子動力学法による化学反応で劣化した高分子の応力測定  

    2012年秋季第73回応用物理学会学術講演会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:松山  

  • 桑原卓哉, 伊藤寿, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   量子分子動力学法を用いた薄膜シリコン太陽電池のCVD プロセスにおけるSiHxの表面反応機構の検討  

    2012年秋季第73回応用物理学会学術講演会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:松山  

  • 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 寒川誠二, 久保百司   量子分子動力学シミュレーションを用いたCFxラジカルによるシリコン酸化膜SiO2のエッチングプロセス解析  

    2012年秋季第73回応用物理学会学術講演会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:松山  

  • 柳谷一行, 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   量子分子動力学法によるCl2プラズマガスを用いたGaNのエッチングシミュレーション  

    2012年秋季第73回応用物理学会学術講演会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:松山  

  • 尾澤伸樹, 中村美穂, 河口健太郎, 石川岳志, 樋口祐次, 久保百司   計算科学手法を用いたペロブスカイト型酸化物砥粒によるガラス表面の化学機械研磨プロセスの解析  

    トライボロジー会議2012秋 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:室蘭  

  • 河口健太郎, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   量子分子動力学法によるシリコンウェハの精密研磨プロセスの解析  

    トライボロジー会議2012秋 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:室蘭  

  • 白珊丹, 佐藤誠一亮, 石川岳志, 樋口祐次, 尾澤伸樹, 足立幸志, 久保百司   計算科学を用いた水素及びフッ素終端DLC膜におけるトライボケミカル反応メカニズムの解明  

    トライボロジー会議2012秋 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:室蘭  

  • 佐藤誠一亮, 白珊丹, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   第一原理分子動力学法とTight-Binding量子分子動力学法による窒化炭素膜の低摩擦メカニズムの解明  

    トライボロジー会議2012秋 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:室蘭  

  • 河口健太郎, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   砥粒の摩擦が促進するCu化学機械研磨プロセスの計算科学シミュレーション  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 柳谷一行, 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   ClラジカルによるGaNエッチング過程の量子分子動力学法に基づく解析  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 小林顕, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   第一原理分子動力学法による高分子電解質膜の化学的劣化機構の解析  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 桑原卓哉, 伊藤寿, 石川岳志, 樋口祐次, 尾澤伸樹, 久保百司   量子分子動力学法に基づく薄膜シリコン太陽電池の化学気相成長メカニズムの解明  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 伊藤寿, 桑原卓哉, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 寒川誠二, 久保百司   量子分子動力学シミュレーションを用いたフルオロカーボンラジカルCFxによるSiO2エッチングプロセスのメカニズム解明  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 尾澤伸樹, 小林顕, 冨士田実央, 石川岳志, 樋口祐次, 久保百司   第一原理計算に基づくアルカリ形燃料電池における高選択性エチレングリコール酸化触媒の高速スクリーニング  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 坂之井遼太, 許競翔, 石川岳志, 樋口祐次, 尾澤伸樹, 島崎智実, 久保百司   高耐久性SOFCの実現に向けた計算科学シミュレーションによる電解質の破壊特性評価  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • 樋口祐次, 石川岳志, 尾澤伸樹, 久保百司   酸化反応によるポリエチレンの劣化プロセス: 第一原理分子動力学法と粗視化分子動力学による解明  

    第110回触媒討論会 

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    Event date: 2012.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡  

  • Takeshi Ishikawa   Quantum Chemical Study of Biomolecules Using Fragment Molecular Orbital Method: An Application to Prion Protein   Invited International conference

    Institute for Protein Research Seminar -Impacts of Supersaturation on Protein Science 

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    Event date: 2012.6

    Language:English   Presentation type:Oral presentation (invited, special)  

  • 鎌足雄司, 石川岳志, 桑田一夫   ITCおよびSPR法から得られた蛋白質-リガンド結合の熱力学的パラメータの比較  

    第12回日本蛋白質科学会 

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    Event date: 2012.6

    Language:Japanese   Presentation type:Poster presentation  

    Venue:名古屋  

  • Takeshi Ishikawa   Quantum chemical study for condensed-phase system based on the fragment molecular orbital method: Applications to geometry optimization and molecular dynamics simulation   Invited International conference

    Multi-scale Simulation of Condensed-phase Reacting Systems 

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    Event date: 2012.5

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:名古屋  

  • 石川岳志   FMOプログラム「PAICS」の紹介  

    FMO研究会キックオフミーティング 

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    Event date: 2012.4

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神戸  

  • 酒井美帆, 石川岳志, 安藤弘宗, 石田秀治, 木曾真, 鈴木康夫, 常盤広明   FMO法を用いた新規阻害薬とNeuraminidase(NA)との理論的相互作用解析  

    第132回日本薬学会 

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    Event date: 2012.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:札幌  

  • N. Hanada, T. Ishikawa, H. Miyachi, K. Kuwata, and H. Tokiwa   Ab Initio Fragment Molecular Orbital Study of Nuclear Receptor Enhanceosome   International conference

    34th Annual Meeting of Molecular Biology Society of Japan 

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    Event date: 2011.12

    Language:English   Presentation type:Poster presentation  

    Venue:Yokohama, Japan  

  • M. Sakai, T. Ishikawa, H. Ando, H. Ishida, M. Kiso, K. Kuwata, Y. Suzuki, and H. Tokiwa   Theoretical Interaction Analysis between Novel Inhibitors and Influenza Virus Neuraminidases using Fragment Molecular Orbital Method   International conference

    8th AFMC International Medicinal Chemistry Symposium (AIMECS2011) 

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    Event date: 2011.11

    Language:English   Presentation type:Poster presentation  

    Venue:Tokyo, Japan  

  • 岡本拓也, 小谷野哲之, 石川岳志, 桑田一夫, 長岡正隆   FMO-QM/MM分子動力学シミュレーションに向けたAMBER-PAICSインターフェースの開発  

    分子科学討論会2011 

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    Event date: 2011.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:札幌  

  • S. Motoyoshi, T. Ishikawa, K. Yamagishi, K. Kuwata, H. Tokiwa   All-Electronic Calculations (AEC)-Docking Procedure Based on the FMO-ONIOM Method   International conference

    WATOC2011 

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    Event date: 2011.7

    Language:English   Presentation type:Poster presentation  

    Venue:Santiago, Spain  

  • Takeshi Ishikawa   シンポジウム「Prime Number and Life -New Paradigm for the 21th century-」, Fragment molecular orbital method and number theory   Invited

    第48回生物物理学会 

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    Event date: 2010.9

    Language:English   Presentation type:Oral presentation (invited, special)  

  • 石川岳志   「疾病と膜動態のタンパク質科学」 フラグメント分子軌道法による正常型プリオンタンパク質の内部相互作用の解析  

    大阪大学タンパク質研究所セミナー 

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    Event date: 2010.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:大阪  

  • 石川岳志   ランチョンセミナー「次世代創薬への挑戦」, 生体分子量子化学計算プログラム「PAICS」の開発と創薬への応用   Invited

    第130回日本薬学会 

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    Event date: 2010.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:岡山  

  • 石川岳志   「創薬の最前線」, フラグメント分子軌道法による生体分子の量子化学計算-プログラム開発と創薬への応用-,  

    HPCシステムズ主催 第二回生体分子計算化学セミナー 

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    Event date: 2010.1

    Language:Japanese   Presentation type:Oral presentation (general)  

  • Takeshi Ishikawa   Quantum chemical calculation of biomolecular systems based on fragment molecular orbital method   Invited International conference

    International Symposium on Multi-Scale Dynamics of Protein Complex Formations and Function 

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    Event date: 2009.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:東京  

  • 田口尚貴, 望月祐志, 石川岳志, 中野達也, 森寛敏, 三好永作, 田中成典   フラグメント分子軌道法によるポリシラン類の物性に関する理論的研究  

    日本化学会第89春季年会 

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    Event date: 2009.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:習志野  

  • 沖山佳生, 渡邉博文, 福澤薫, 中野達也, 望月祐志, 石川岳志, 蛯名邦禎, 田中成典   フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定と古典MDへの応用  

    スーパーコンピューターワークショップ2009「次世代理論化学の新展開と超並列計算への挑戦」 

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    Event date: 2009.1

    Language:Japanese   Presentation type:Poster presentation  

    Venue:岡崎  

  • 田口尚貴, 望月祐志, 石川岳志, 中野達也, 森寛敏, 三好永作, 田中成典   ポリシラン類の物性に関する理論的研究  

    スーパーコンピューターワークショップ2009「次世代理論化学の新展開と超並列計算への挑戦」 

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    Event date: 2009.1

    Language:Japanese   Presentation type:Poster presentation  

    Venue:岡崎  

  • 石川岳志   シンポジウム「レアイベントから創薬へ」, 量子化学計算に基づく創薬研究へのアプローチ -プログラム開発と生体分子への応用-   Invited

    第46回生物物理学会 

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    Event date: 2008.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:福岡  

  • 田口尚貴, 望月祐志, 中野達也, 甘利真司, 福澤薫, 石川岳志, 櫻井実, 田中成典   赤色蛍光タンパク質の励起状態に関する理論的研究  

    バイオスーパーコンピューティング・シンポジウム(BSCS) 

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    Event date: 2008.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Yuji Mochizuki, T. Ishikawa, K. Ebina, S. Tanaka   Determination of ESP charges on polypeptides using the fragment molecular orbital method and the applications for molecular simulations  

    2008年CBI学会 

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    Event date: 2008.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • N. Taguchi, Y. Mochizuki, T. Nakano, T. Ishikawa, K. Fukuzawa, M. Sakurai, S. Tanaka   Theoretical Study of the Excited States of DsRed Mutants by Fragment Molecular Orbital Method   International conference

    WATOC2008 

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    Event date: 2008.9

    Language:English   Presentation type:Poster presentation  

    Venue:Sydney, Australia  

  • 田口尚貴, 望月祐志, 石川岳志, 中野達也, 森寛敏, 三好永作, 田中成典   フラグメント分子軌道法によるポリシラン類の物性に関する理論的研究  

    第2回分子科学討論会 

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    Event date: 2008.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • 本田宏明, 田中皓, 吉村崇, 佐々木陽一, 石川岳志, 三好永作   6核錯体[(Tc6S8)Br6]4-の電子構造ならびに電子スペクトル: [(Re6S8)Br6]4-, [(Re6S8)Cl6]4-, [(Re6Cl8)Cl6]2-との比較検討  

    第2回分子科学討論会 

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    Event date: 2008.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • 石川岳志, 桑田一夫   量子化学計算によるプリオンタンパク質と低分子化合物との相互作用解析  

    プリオンシンポジウム2008 

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    Event date: 2008.8

    Language:English   Presentation type:Poster presentation  

    Venue:北海道  

  • 田口尚貴, 望月祐志, 中野達也, 甘利真司, 石川岳志, 福澤薫, 櫻井実, 田中成典   フラグメント分子軌道法によるDsRed類縁種の励起状態に関する理論的研究  

    日本化学会第88回春期年会 

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    Event date: 2008.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 佐藤真, 山高博, 古明地勇人, 望月祐志, 石川岳志, 中野達也   FMO-MD法によるメチルジアゾニウムカチオンの加水分解反応シミュレーション  

    日本化学会第88回春期年会 

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    Event date: 2008.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 石川岳志, 望月祐志, 甘利真司, 中野達也, 常盤広明, 田中成典, 田中皓   FMO法における局在化MP2法を用いた相互作用解析: FILMの開発と応用  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 望月祐志, 中野達也, 田中皓, 石川岳志, 三好永作, 古明地勇人, 山下勝美, 村瀬匡, 甘利真司, 福澤薫, 櫻井実, 田中成典   フラグメント分子軌道法における大規模Post-HF計算  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 田口尚貴, 望月祐志, 石川岳志, 田中皓   二量化した一酸化窒素分子の高度相関計算による研究  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 望月祐志, 古明地勇人, 石川岳志, 中野達也, 山高博, 山下勝美, 栗崎以久男, 田中成典   FMO-MD/MLFMO-CIS(D)法による水和分子の励起状態シミュレーション  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 沖山佳生, 渡邉博文, 福澤薫, 中野達也, 望月祐志, 石川岳志, 田中成典, 蛯名邦禎   フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 古明地勇人, 石川岳志, 望月祐志, 山高博, 中野達也   FMO-MD法の再実装と溶液計算への応用  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 佐藤真, 山高博, 古明地勇人, 望月祐志, 石川岳志, 中野達也   FMO-MD法によるジアゾニウムカチオンの加水分解反応シミュレーション  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • 田中皓, 望月祐志, 石川岳志, 山下勝美, 村瀬匡, 田口尚貴, 田中成典   スピン適合並列化中間状態駆動CASCIプログラムと応用計算  

    第1回分子科学討論会 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:仙台  

  • K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Ishikawa, A. Kato, T. Nakano, S. Tanaka   Intra- and Intermolecular interaction between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study  

    2006年CBI学会 

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    Event date: 2006.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 石川岳志, 望月祐志, 中野達也, 甘利真司, 森寛敏, 本田宏明, 藤田貴敏, 常盤広明, 田中成典, 古明地勇人, 福澤薫, 田中皓, 三好永作   FMO法へのMCPの導入と生体分子系への適用  

    平成18年度分子構造総合討論会 

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    Event date: 2006.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:静岡  

  • 伊藤三香, 福澤薫, 望月祐志, 石川岳志, 中野達也, 田中成典   レチノイドXレセプターのへリックス12に関する理論的研究  

    平成18年度分子構造総合討論会 

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    Event date: 2006.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:静岡  

  • Y. Mochizuki, K. Yamashita, T. Nakano, T. Ishikawa, S. Amari, K. Segawa, T. Murase, H. Tokiwa, M. Sakurai, K. Tanaka   A parallelized integral-direct CIS(D) method with multilayer fragment molecular orbital scheme   International conference

    International Conference of Quantum Chemistry 

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    Event date: 2006.5

    Language:English   Presentation type:Poster presentation  

    Venue:Kyoto, Japan  

  • K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, H. Tokiwa   An Efficient Algorithm for parallel processing of a spin adapted full configuration interaction   International conference

    International Conference of Quantum Chemistry 

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    Event date: 2006.5

    Language:English   Presentation type:Poster presentation  

    Venue:Kyoto, Japan  

  • 山岸賢司, 山本恵子, 石川岳志, 望月祐志, 中野達也, 山田幸子, 常盤広明   FMO法を基盤とした新規創薬手法の開発と応用  

    第126年会日本薬学会 

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    Event date: 2006.3

    Language:Japanese   Presentation type:Poster presentation  

    Venue:仙台  

  • 石川岳志, 田中皓   [Mn(CN)5NO]3-に関する理論的研究  

    平成17年度分子構造総合討論会 

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    Event date: 2005.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 田中皓, 石川岳志, 常盤広明, 望月祐志   グラフ表示の閉殻と開殻への分離によるCASCIの並列, ベクトル処理アルゴリズム  

    平成17年度分子構造総合討論会 

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    Event date: 2005.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 望月祐志, 中野達也, 石川岳志, 福澤薫, 加藤昭史, 田中皓, 常盤広明, 甘利真司, 北浦和夫, 田中成典   ABINIT-MPプログラムの最近の機能拡張  

    平成17年度分子構造総合討論会 

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    Event date: 2005.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 石川岳志, 田中皓   [Ru(CN)5NO]2-の安定および準安定構造と光誘起遷移過程の理論的研究  

    平成16年度分子構造総合討論会 

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    Event date: 2004.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:広島  

  • 石川岳志, 田中皓   [Fe(CN)5NO]2-の光誘起遷移過程の理論的研究  

    第8回理論化学討論会 

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    Event date: 2004.6

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:広島  

  • T. Ishikawa, K. Tanaka   Theoretical study on light-induced metastable state in Na2[Fe(CN)5NO]・2H2O   International conference

    Second Generation on Octahedral Metal Compounds: New development and Prospect 

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    Event date: 2004.5

    Language:English   Presentation type:Poster presentation  

    Venue:札幌  

  • 石川岳志, 田中皓   [Fe(CN)5NO]2-の安定および準安定構造と光誘起遷移過程の理論的研究  

    平成15年度分子構造総合討論会 

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    Event date: 2003.9

    Language:Japanese   Presentation type:Oral presentation (keynote)  

    Venue:京都  

  • 石川岳志, 田中皓   [Fe(CN)5NO]2-の光誘起準安定状態と遷移過程の理論的研究  

    分子研研究会高精度大規模計算が開く新しい分子科学 

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    Event date: 2002.11

    Language:Japanese   Presentation type:Poster presentation  

    Venue:岡崎  

  • 石川岳志, 田中皓   [Fe(CN)5NO]2-の基底状態および励起状態に関する理論的研究  

    年度分子構造総合討論会 

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    Event date: 2002.10

    Language:Japanese   Presentation type:Poster presentation  

    Venue:神戸  

  • 石川岳志, 野呂武, 庄田孝行   アゾベンゼンの光異性化の理論的研究  

    平成13年度分子構造総合討論会 

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    Event date: 2001.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:札幌  

  • 本田宏明, 石川岳志, 野呂武, 田中皓, 三好永作   結晶中のクラスター錯体[Re6S8Br4]4-と[Re6S8Cl6]3-の電子的励起スペクトルの理論的解析  

    平成13年度分子構造総合討論会 

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    Event date: 2001.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:札幌  

  • 石川岳志, 野呂武, 庄田孝行   アゾベンゼンの光異性化における理論的研究  

    平成12年度分子構造総合討論会 

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    Event date: 2000.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東京  

  • 石川岳志, 野呂武, 庄田孝行   アゾベンゼンの光異性化における電子状態  

    平成11年度分子構造総合討論会 

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    Event date: 1999.9

    Language:Japanese   Presentation type:Poster presentation  

    Venue:大阪  

  • 工藤 優大, 藤田 芽衣, 吉野 雄太, 鎌足 雄司, 田中 義正, 石川 岳志, 藤本 直浩, 岡田 卓哉, 豊岡 尚樹, 遠藤 智史, 五十里 彰   オートファゴソーム膜の形成を作用点とする新規オートファジー阻害剤の開発  

    日本生化学会大会プログラム・講演要旨集  2022.11  (公社)日本生化学会

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  • 佐藤 啓子, 納屋 昌実, 近藤 好夫, 武部 克希, 内藤 真理子, 鈴木 守, 今田 勝巳, 石川 岳志, 佐藤 主税   抗菌薬標的タンパク質の生化学 歯周病細菌叢の病原性を抑える試み  

    日本細菌学雑誌  2021.2  日本細菌学会

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  • 石川 岳志   第387回CBI学会研究講演会「薬物-標的親和性計算の新潮流 ~古典MDから量子MDへ~」 FMO-QM/MM分子動力学計算と量子化学による創薬研究   Invited

    第387回 CBI学会研究講演会  2017.9 

  • 石川岳志   第18回FMO研究会 FMOプログラム「PAICS」の開発と生命科学分野への応用  

    2019.3 

  • 石川岳志   日本コンピュータ化学会2020年秋季年会 生命科学を指向した量子化学計算プログラム「PAICS」の開発と応用   Invited

    日本コンピュータ化学会2020年秋季年会  2020.11 

  • 水田 賢志, 石川 岳志, 大滝 大樹, 栗山 正巳, 尾野村 治, 樋口 則英, 中嶋 弥穂子, 中嶋 幹郎, 大山 要   バルプロ酸とカルバペネム系抗菌薬の相互作用機序の計算化学的考察  

    日本薬学会年会要旨集  2017.3  (公社)日本薬学会

  • 渡邊 健, 石川 岳志, 大滝 大樹, 水田 賢志, 濱田 剛, 浦田 秀造, 安田 二朗, 田中 義正, 西田 教行   新規作用機序をもつ抗インフルエンザウイルス薬の開発  

    日本薬学会年会要旨集  2018.3  (公社)日本薬学会

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  • 渡辺 健, 石川 岳志, 水田 賢志, 中垣 岳大, 大滝 大樹, 濱田 剛, 田中 義正, 西田 教行   新たな作用機序をもつ抗インフルエンザウイルス薬の開発  

    日本薬学会年会要旨集  2017.3  (公社)日本薬学会

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    Language:Japanese  

  • 石川 岳志, 水田 賢志, 金子 修, 矢幡 一英   抗マラリア化合物の開発をめざしたフラグメント分子軌道法によるSERCAとThapsigarginの分子間相互作用解析  

    日本薬学会年会要旨集  2017.3  (公社)日本薬学会

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  • 住吉 誠, 宮崎 泰可, 水田 賢志, 田中 義正, 石川 岳志, 槇村 浩一, 高園 貴弘, 西條 知見, 山本 和子, 今村 圭文, 泉川 公一, 柳原 克紀, 河野 茂, 迎 寛   カンジダ属および多剤耐性菌に対するカスポファンギンの新たな抗微生物活性  

    日本医真菌学会雑誌  2019.10  (一社)日本医真菌学会

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  • 浦田 秀造, Omotuyi Olaposi Idowu, 石川 岳志, 水田 賢志, 櫻井 康晃, 水谷 龍明, 植田 弘師, 田中 義正, 安田 二朗   エボラウイルスVP40による粒子産生を標的とした新規化合物の同定  

    日本薬学会年会要旨集  2020.3  (公社)日本薬学会

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  • 石橋 大輔, 中垣 岳大, 石川 岳志, 濱田 剛, 西田 教行   in silicoプリオン病創薬における薬効特異性の評価  

    生命科学系学会合同年次大会  2017.12  生命科学系学会合同年次大会運営事務局

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    Language:English  

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Intellectual Property

  • 分子間相互作用解析装置、分子間相互作用解析法及びプログラム

    石川岳志

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    Application no:特願2023-25282  Date applied:2023.2

  • 分子間相互作用解析装置、分子間相互作用解析法及びプログラム

    石川岳志, 大園紘貴

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    Application no:特願2022-139395  Date applied:2022

  • プリオン病治療薬

    石橋大輔, 西田教行, 水田賢志, 石川岳志

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    Application no:特願2018-177224  Date applied:2018.9

    Country of applicant:Domestic  

  • キノリノン化合物および抗RNAウイルス薬

    水田賢志, 渡辺健, 西田教行, 濱田剛, 石川岳志, 田中義正, 大滝大樹, 安田二郎, 浦田秀造

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    Application no:PCT/JP2018/013592  Date applied:2018.3

    Country of applicant:Domestic  

  • キノリノン化合物および抗RNAウイルス治療薬

    水田賢志, 渡辺健, 西田教行, 濱田剛, 石川岳志, 田中義正, 大滝大樹

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    Application no:特願2017-72230  Date applied:2017.3

    Country of applicant:Domestic  

  • 核酸アプタマー, 固相担体, ヒトIgG精製用カラム, 及びヒトIgGの精製方法

    山岸賢司, 関口真裕, 吉田尚恵, 坂本泰一, 野村祐介, 石川岳志

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    Application no:特願2017-23175  Date applied:2017.2

    Announcement no:特開2018-126117  Date announced:2018.8

    Country of applicant:Domestic  

  • プリオン病予防・治療剤

    石橋大輔, 西田教行, 中垣岳大, 濱田剛, 石川岳志

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    Application no:特願2016-170349  Date applied:2016.8

    Announcement no:特開2018-35099  Date announced:2018.3

    Country of applicant:Domestic  

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Research Projects

  • 抗体医薬品の開発コストを軽減するインシリコ技術の社会実装

    2023.10 - 2024.9

    令和5年度 一般財団法人ふくおかフィナンシャルグループ企業育成財団研究開発助成金

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    Authorship:Principal investigator 

  • 化学シャペロンに有効なファーマコフォアモデルの構築法の開発と抗プリオン薬への応用

    2023.4 - 2025.3

    令和5年度 科学研究費助成事業 基盤研究(B)(一般)

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    Authorship:Principal investigator 

  • 抗体医薬品開発を加速する量子化学計算に基づいた次世代インシリコ創薬技術の開発

    2023.4 - 2024.3

    令和5年度 AMED 橋渡し研究プログラム 異分野融合型研究シーズ(シーズH)

  • バイオ医薬品開発の効率化を実現する生体分子量子化学計算プログラム「PAICS」

    2022.10 - 2023.3

    2022年度 JST大学発新産業創出プログラム(START)大学・エコシステム推進型「PARKS起業活動支援プログラム」

  • 熱帯樹木由来高活性イソプレン合成酵素の探索とハイブリッド型発酵用高機能酵素の開発

    Grant number:22K05195  2022.4 - 2025.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    屋 宏典, 石川 岳志, 堀谷 正樹, 稲福 征志

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

  • 分子シミュレーションによる新規RNAアプタマー設計の基盤技術の構築

    Grant number:21K12129  2021.4 - 2024.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    山岸 賢司, 坂本 泰一, 石川 岳志

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    Grant amount:\4030000 ( Direct Cost: \3100000 、 Indirect Cost:\930000 )

    RNAアプタマーは抗体に代わる次世代技術として、医薬品分野や診断薬分野などで注目されている。本研究は、申請者が蓄積してきたアプタマーに対する研究成果をもとに、RNAアプタマーが標的タンパク質をどのように認識し結合するのか、その分子認識メカニズムを計算化学手法により明らかにする。そして、アプタマー設計に、はじめて計算化学という手法を取り入れ、論理的な観点から新しいRNAアプタマーを設計する基盤技術の構築を目指すものである。
    当該年度は、抗体に結合するRNAアプタマーを解析の対象とし、アプタマーを構成するヌクレオチドが、RNA型かDNA型の違いによって、標的分子である抗体との結合プロファイルにどのような違いが引き起こされるか解析し、以下の結果を得た。
    まず、分子動力学計算を用いて、RNAアプタマーの構造ダイナミクスを解析した。その結果、標的分子に対する結合性が同じアプタマーでも、標的分子との結合に伴い、RNA型のアプタマーよりDNA型のアプタマーのほうが、アプタマーのダイナミクスが大きく抑制されることが明らかとなった。
    次に、研究分担者の石川により開発された、フラグメント分子軌道法に基づき生体分子間の静電的相補性を視覚的および定量的に解析できるVIINEC法を用いて、アプタマーと標的分子の分子間相互作用を解析した。その結果、相互作用エネルギーはRNA型アプタマーの方が大きいが、静電的相補性はDNA型のアプタマーの方が大きいことが示された。
    また、実験的な解析では、NMRを用いて塩基対部分のイミノプロトンシグナルの帰属を行い、さらに運動性についての情報を得た。RNA型およびDNA型のアプタマーのNOESYスペクトルにおいて、末端ステムの部分の21番目のU残基に由来するイミノプロトンに化学交換シグナルが観測されることから、末端ステムが閉じた構造と開いた構造があることが示唆された。

  • Construction of preemptive medicine for rheumatoid arthritis based on proteomics and artificial intelligence of a medical examination cohort

    Grant number:20K20617  2020.7 - 2023.3

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

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    Grant amount:\25870000 ( Direct Cost: \19900000 、 Indirect Cost:\5970000 )

  • 抗プリオン効果を生み出すファーマコフォアモデルの構築と新規治療薬の開発

    2020.4 - 2023.3

    科学研究費補助金  基盤研究(B)

  • 抗プリオン効果を生み出すファーマコフォアモデルの構築と新規治療薬の開発

    2020.4 - 2022.3

    令和2年度科学研究費助成事業基盤研究(B)(一般) 

    石川岳志, 石橋大輔, 水田賢司, 鎌足雄司

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    Authorship:Principal investigator 

  • Molecular Recognition Mechanism of RNA aptamer

    Grant number:18K11536  2018.4 - 2021.3

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

    YAMAGISHI Kenji

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    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

    We performed ab initio FMO calculation for the RNA aptamer-hFc1 complex to understand the high affinity and specificity of the RNA aptamer. We analyzed the intermolecular interactions between each nucleotide of the aptamer and each amino acid of hFc1 using FMO-IFIE analysis. The G7 nucleotide shows the strongest interaction energy with hFc1 among all groups. In particular, ionic interaction of the phosphate group of the G7 nucleotide with Lys340 results in a robust electrostatic interaction between the RNA aptamer and hFc1. We furthermore performed molecular dynamics simulation for the RNA aptamer-hFc1 complex with and without Ca2+ ions in a solvent. Only in the absence of Ca2+ ions, the RMSD increased and the structure of the aptamer changed from the initial structure. This result indicates that Ca2+ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
    This study provides physicochemical insights into the binding of the RNA aptamer to hFc1.

  • HLA-ペプチド親和性の網羅的計算法の開発とベーチェット病の病因解明への応用

    2016.4 - 2019.3

    科学研究費補助金  基盤研究(C)

  • HLA-ペプチド親和性の網羅的計算法の開発とベーチェット病の病因解明への応用

    2016.4 - 2019.3

    平成28年度 科学研究費助成事業 基盤研究(C)(一般) 

    石川岳志

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    Authorship:Principal investigator  Grant type:Competitive

  • 計算化学手法を用いた新規RNAアプタマーの設計手法の開発

    2015.10 - 2016.9

    その他省庁等  平成27年度 マッチングプラナープログラム「探索試験」 

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    Grant type:Competitive

  • 凝集系化学反応の遷移状態計算のための新規手法と汎用ソフトウエアの開発

    2015.5 - 2016.4

    民間財団等  平成27年度 第4回 公益社団法人新化学技術推進協会 新化学技術研究奨励賞 

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    Grant type:Competitive

  • 研究会「感染症と計算科学」の開催(2015年11月13日琉球大学)

    2015.4 - 2016.3

    琉球大学熱帯生物圏研究センター  平成27年度 琉球大学熱帯生物圏研究センター 共同利用研究会 

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    Grant type:Competitive

  • 新薬創成のためのモバイル端末を利用したシリアスゲームに関する調査研究

    2015.2 - 2016.1

    民間財団等  平成26年度 公益財団法人科学技術融合振興機構 調査研究助成 

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    Grant type:Competitive

  • 熱帯樹木のイソプレン生合成酵素と基質間の相互作用エネルギーの解析

    2014.4 - 2015.3

    琉球大学熱帯生物圏研究センター  平成26年度 琉球大学熱帯生物圏研究センター・共同利用研究 

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    Grant type:Competitive

  • 第一原理計算によるタンパク場を考慮した部分構造最適化システムの構築

    2009.4 - 2010.3

    岐阜大学  平成21年度 岐阜大学 大学活性化経費(大型科研チャレンジ枠) 

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    Grant type:Competitive

  • FMO法による体内揺らぎを考慮した相互作用解析法の構築とプリオンタンパクへの応用

    2008.4 - 2010.3

    科学研究費補助金  研究活動スタート支援

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Teaching Experience

  • Fundamentals of Physical Chemistry

    2022.4
    Institution:Kagoshima University

  • Advanced Lecture on Chemistry and Biotechnology(分担)

    2020.4
    Institution:鹿児島大学大学院理工学研究科工学専攻

  • 微分積分学Ⅰ

    2020.4
    Institution:鹿児島大学工学部共通

  • 生命工学(分担)

    2020.4
    Institution:鹿児島大学工学部先進工学科共通

  • フレッシュマンセミナー(分担)

    2020.4
    Institution:鹿児島大学工学部先進工学科化学生命工学プログラム

  • 線形代数学Ⅰ

    2020.4
    Institution:鹿児島大学工学部共通

  • 理論分子科学特論

    2020.4
    Institution:鹿児島大学大学院理工学研究科工学専攻

  • 量子物理化学

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • 化学生命工学セミナーⅠ(分担)

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • 卒業論文

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • 化学生命工学研究基礎

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • 化学生命工学特別研究Ⅱ

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • 化学生命工学特別研究Ⅰ

    2019.4
    Institution:鹿児島大学工学部化学生命工学科

  • Advanced Lecture on Applied Chemistry(分担)

    2019.4
    -
    2020.3
    Institution:鹿児島大学 大学院理工学研究科化学生命・化学工学専攻

  • 微分積分学AⅠ

    2019.4
    -
    2020.3
    Institution:鹿児島大学工学部化学生命工学科

  • フレッシュマンセミナー(分担)

    2019.4
    -
    2020.3
    Institution:鹿児島大学工学部化学生命工学科

  • 線形代数学Ⅰ

    2019.4
    -
    2020.3
    Institution:鹿児島大学工学部化学生命工学科

  • 理論分子科学特論

    2019.4
    -
    2020.3
    Institution:鹿児島大学大学院理工学研究科化学生命・化学工学専攻

  • アカデミア創薬学特論Ⅱ(分担)

    2018.4
    Institution:長崎大学大学院医歯薬学総合研究科

  • 化学生命工学セミナーⅡ

    2018.4
    Institution:鹿児島大学工学部化学生命工学科

  • 化学情報処理(2006年度~2007年度)

    Institution:立教大学

  • 感染系授業(分担)(2013年度~2016年度)

  • 生物医科学特論及び実習C(2017年度~2018度)

  • 生物医科学特論及び実習C-2(2013年度~2016年度)

  • 生物医科学特論及び実習C-1(2013年度~2016年度)

  • 生命を担う分子群のかたち(分担)(2008年度~2011年度)

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