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Kaori Fukuzawa

Section

Graduate School of Engineering

Job title

Specially Appointed Professor(Research)

Degree

修士（理学）（立教大学）
博士（工学）（東京大学）

researchmap

https://researchmap.jp/kaori.fukuzawa

J-GLOBAL ID

201401043647568067

Research History 7

2022/04 - Present

Osaka University　Graduate School of Pharmaceutical Sciences　Professor
2020/04 - Present

Tohoku University　Graduate School of Engineering
2016/10 - 2022/03

Hoshi University　Hoshi University
2018/04 - 2019/03

Kobe University　Institute of Promoting Academic Research Programs
2014/04 - 2018/03

Kobe University　Center for Collaborative Research and Technology Development　visiting associate professor
2014/07 - 2016/09

Nihon University　School of Dentistry at Matsudo　Assistant Professor
2000/04/01 - 2014/06/30

Mizuho Information and Research Institute, Inc.　Science Solutions Division　Manager

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Education 3

Rikkyo University　Faculty of Science　Department of Chemistry

1997/04/01 - 2000/03/31
Rikkyo University　Faculty of Science　Department of Chemistry

1995/04/01 - 1997/03/31
Rikkyo University　Faculty of Science　Department of Chemistry

1991/04/01 - 1995/03/31

Committee Memberships 11

一般社団法人 HPCIコンソーシアム　理事

2024/06 - Present
大阪大学教育研究評議会　評議員

2024/04 - Present
CBIジャーナル　編集委員長

2024/04 - Present
文部科学省 HPCI計画推進委員会　委員

2023/04 - Present
日本薬学会構造活性相関部会　幹事

2019/04 - Present
CBI学会FMO研究会　主査

2016/08 - Present
FMO創薬コンソーシアム　代表

2014/11 - Present
CBI学会　評議員

2014 - Present
分子科学会　編集委員

2014/11 - 2022/08
FMO研究会　幹事

2012/04 - 2016/07
日本コンピュータ化学会　理事

2022/04 -

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Professional Memberships 6

THE JAPAN SOCIETY OF DRUG DELIVERY SYSTEM
SOCIETY OF COMPUTER CHEMISTRY, JAPAN
THE PHARMACEUTICAL SOCIETY OF JAPAN
分子科学会
日本化学会
CBI学会

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Research Interests 7

BioStation
ABINIT-MP
FMO創薬
Fragment molecular orbital method
quantum chemistry
computational structural biology
計算生命科学

Research Areas 5

Nanotechnology/Materials / Basic physical chemistry /
Life sciences / Structural biochemistry /
Nanotechnology/Materials / Biochemistry /
Nanotechnology/Materials / Molecular biochemistry /
Informatics / Computational science /

Awards 5

第11回 HPCI利用研究課題優秀成果賞

2024/10
大谷賞

2019/05　星薬科大学
第５回「京を中核とする」HPCIシステム利用研究課題優秀成果賞

2018/11
第4回「京を中核とする」HPCIシステム利用研究課題優秀成果賞

2017/11
第８回資生堂女性研究者サイエンスグラント

2017/06

Papers 188

The Effectiveness of Local Fine-Tuned LLMs: Assessment of the Japanese National Examination for Pharmacists Peer-reviewed

Hiroto Asano, Daisuke Takaya, Asuka Hatabu, Minako Ohishi, Kaori Fukuzawa, Kenji Ikeda, Yu-Shi Tian

2025/04/15

DOI： 10.21203/rs.3.rs-6444534/v1 　
The seventh blind test of crystal structure prediction: structure generation methods Peer-reviewed

Lily M. Hunnisett, Jonas Nyman, Nicholas Francia, Nathan S. Abraham, Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, Mubarak Almehairbi, Andrea Anelli, Dylan M. Anstine, John E. Anthony, Joseph E. Arnold, Faezeh Bahrami, Michael A. Bellucci, Rajni M. Bhardwaj, Imanuel Bier, Joanna A. Bis, A. Daniel Boese, David H. Bowskill, James Bramley, Jan Gerit Brandenburg, Doris E. Braun, Patrick W. V. Butler, Joseph Cadden, Stephen Carino, Eric J. Chan, Chao Chang, Bingqing Cheng, Sarah M. Clarke, Simon J. Coles, Richard I. Cooper, Ricky Couch, Ramon Cuadrado, Tom Darden, Graeme M. Day, Hanno Dietrich, Yiming Ding, Antonio DiPasquale, Bhausaheb Dhokale, Bouke P. van Eijck, Mark R. J. Elsegood, Dzmitry Firaha, Wenbo Fu, Kaori Fukuzawa, Joseph Glover, Hitoshi Goto, Chandler Greenwell, Rui Guo, Jürgen Harter, Julian Helfferich, Detlef W. M. Hofmann, Johannes Hoja, John Hone, Richard Hong, Geoffrey Hutchison, Yasuhiro Ikabata, Olexandr Isayev, Ommair Ishaque, Varsha Jain, Yingdi Jin, Aling Jing, Erin R. Johnson, Ian Jones, K. V. Jovan Jose, Elena A. Kabova, Adam Keates, Paul F. Kelly, Dmitry Khakimov, Stefanos Konstantinopoulos, Liudmila N. Kuleshova, He Li, Xiaolu Lin, Alexander List, Congcong Liu, Yifei Michelle Liu, Zenghui Liu, Zhi-Pan Liu, Joseph W. Lubach, Noa Marom, Alexander A. Maryewski, Hiroyuki Matsui, Alessandra Mattei, R. Alex Mayo, John W. Melkumov, Sharmarke Mohamed, Zahrasadat Momenzadeh Abardeh, Hari S. Muddana, Naofumi Nakayama, Kamal Singh Nayal, Marcus A. Neumann, Rahul Nikhar, Shigeaki Obata, Dana O'Connor, Artem R. Oganov, Koji Okuwaki, Alberto Otero-de-la-Roza, Constantinos C. Pantelides, Sean Parkin, Chris J. Pickard, Luca Pilia, Tatyana Pivina, Rafał Podeszwa, Alastair J. A. Price, Louise S. Price, Sarah L. Price, Michael R. Probert, Angeles Pulido, Gunjan Rajendra Ramteke, Atta Ur Rehman, Susan M. Reutzel-Edens, Jutta Rogal, Marta J. Ross, Adrian F. Rumson, Ghazala Sadiq, Zeinab M. Saeed, Alireza Salimi, Matteo Salvalaglio, Leticia Sanders de Almada, Kiran Sasikumar, Sivakumar Sekharan, Cheng Shang, Kenneth Shankland, Kotaro Shinohara, Baimei Shi, Xuekun Shi, A. Geoffrey Skillman, Hongxing Song, Nina Strasser, Jacco van de Streek, Isaac J. Sugden, Guangxu Sun, Krzysztof Szalewicz, Benjamin I. Tan, Lu Tan, Frank Tarczynski, Christopher R. Taylor, Alexandre Tkatchenko, Rithwik Tom, Mark E. Tuckerman, Yohei Utsumi, Leslie Vogt-Maranto, Jake Weatherston, Luke J. Wilkinson, Robert D. Willacy, Lukasz Wojtas, Grahame R. Woollam, Zhuocen Yang, Etsuo Yonemochi, Xin Yue, Qun Zeng, Yizu Zhang, Tian Zhou, Yunfei Zhou, Roman Zubatyuk, Jason C. Cole

Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials　80　(6)　2024/12/01
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2052520624007492 　

eISSN： 2052-5206

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A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.
Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method Peer-reviewed

Daisuke Takaya, Shu Ohno, Toma Miyagishi, Sota Tanaka, Koji Okuwaki, Chiduru Watanabe, Koichiro Kato, Yu-Shi Tian, Kaori Fukuzawa

Scientific Data　2024/10/23

DOI： 10.1038/s41597-024-03999-2 　
Effects of Glass Bead Size on Dissolution Profiles in Flow-through Dissolution Systems (USP 4) Peer-reviewed

Hiroyuki Yoshida, Keita Teruya, Yasuhiro Abe, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Ken-ichi Izutsu

AAPS PharmSciTech　25　(8)　2024/10/22
Publisher: Springer Science and Business Media LLC
DOI： 10.1208/s12249-024-02972-x 　

eISSN： 1530-9932
New Catalytic Residues and Catalytic Mechanism of the RNase T1 Family Peer-reviewed

Katsuki Takebe, Mamoru Suzuki, Yumiko Hara, Takuya Katsutani, Naomi Motoyoshi, Tadashi Itagaki, Shuhei Miyakawa, Kuniaki Okamoto, Kaori Fukuzawa, Hiroko Kobayashi

ACS Bio & Med Chem Au　2024/09/20
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acsbiomedchemau.4c00046 　

ISSN： 2694-2437

eISSN： 2694-2437
Docosahexaenoic acid enhances the treatment efficacy for castration-resistant prostate cancer by inhibiting autophagy through Atg4B inhibition. International-journal Peer-reviewed

Yudai Kudo, Kana Nakamura, Honoka Tsuzuki, Kotaro Hirota, Mina Kawai, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma, Yuta Yoshino, Mitsuhiro Nakamura, Masaki Shiota, Naohiro Fujimoto, Akira Ikari, Satoshi Endo

Archives of biochemistry and biophysics　760　110135-110135　2024/08/23

DOI： 10.1016/j.abb.2024.110135 　

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Autophagy induction in cancer is involved in cancer progression and the acquisition of resistance to anticancer agents. Therefore, autophagy is considered a potential therapeutic target in cancer therapy. In this study, we found that long-chain fatty acids (LCFAs) have inhibitory effects on Atg4B, which is essential for autophagosome formation, through screening based on the pharmacophore of 21f, a recently developed Atg4B inhibitor. Among these fatty acids, docosahexaenoic acid (DHA), a polyunsaturated fatty acid, exhibited the most potent Atg4B inhibitory activity. DHA inhibited autophagy induced by androgen receptor signaling inhibitors (ARSI) in LNCaP and 22Rv1 prostate cancer cells and significantly increased apoptotic cell death. Furthermore, we investigated the effect of DHA on resistance to ARSI by establishing darolutamide-resistant prostate cancer 22Rv1 (22Rv1/Dar) cells, which had developed resistance to darolutamide, a novel ARSI. At baseline, 22Rv1/Dar cells showed a higher autophagy level than parental 22Rv1 cells. DHA significantly suppressed Dar-induced autophagy and sensitized 22Rv1/Dar cells by inducing apoptotic cell death through mitochondrial dysfunction. These results suggest that DHA supplementation may improve prostate cancer therapy with ARSI.
Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins

Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama, Akifumi Kato, Yuji Mochizuki, Tatsuya Nakano, Teruki Honma, Kaori Fukuzawa

2024/07/24
Publisher: American Chemical Society (ACS)
DOI： 10.26434/chemrxiv-2024-t9m7z 　

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The frozen domain (FD) approximation with fragment molecular orbital (FMO) method is efficient for partial geometry optimization of large systems. We implemented the FD formulation (FD and frozen domain dimer [FDD] methods) already proposed by Fedorov, D. G. et al. (J. Phys. Chem. Lett. 2011, 2 (4), 282–288.); proposed a variation of it, namely frozen domain and partial dimer (FDPD) method; and applied it to several protein-ligand complexes. The computational time for geometry optimization at the FDPD/HF/6-31G* level for the active site (six fragments) of the largest β2-adrenergic G protein-coupled receptor (440 residues) was almost half that of the conventional partial geometry optimization method. In the human estrogen receptor, the crystal structure was refined by FDPD geometry optimization of estradiol, surrounding hydrogen-bonded residues and a water molecule. The rather polarized ligand binding site of influenza virus neuraminidase was also optimized by FDPD optimization, which relaxed steric repulsion around the ligand in the crystal structure and optimized hydrogen bonding. For Serine-Threonine Kinase Pim1 and six inhibitors, the structures of the ligand binding site, Lys67, Glu121, Arg122, and benzofuranone ring and indole/azaindole ring of the ligand, were optimized at FDPD/HF/6-31G* and the ligand binding energy was estimated at the FMO-MP2/6-31G* level. As a result, the correlation coefficient between pIC50 and ligand binding energy was considerably improved as compared to results from both molecular mechanics- and quantum mechanics/molecular mechanics-optimized geometries. Thus, this approach is promising as a high-precision structure refinement method for structure-based drug discovery.
A machine learning model for predicting quantum chemistry based protein-drug molecule interactions Peer-reviewed

Ryosuke KITA, Chiduru WATANABE, Masateru OHTA, Naoki TANIMURA, Koji OKUWAKI, Mitsunori IKEGUCHI, Kaori FUKUZAWA, Teruki HONMA, Tsuyohiko FUJIGAYA, Koichiro KATO

The 38th Annual Conference of the Japanese Society for Artificial Intelligence　38　2024/05

DOI： 10.11517/pjsai.JSAI2024.0_4Q3IS2d05 　
Characterization and drug solubilization of arginine-based ionic liquids – Impact of counterions and stoichiometry Peer-reviewed

Siran Wang, Qihui Xu, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

International Journal of Pharmaceutics　124228-124228　2024/05
Publisher: Elsevier BV
DOI： 10.1016/j.ijpharm.2024.124228 　

ISSN： 0378-5173
Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path Peer-reviewed

Aaron J. Nessler, Okimasa Okada, Yuya Kinoshita, Koki Nishimura, Hiroomi Nagata, Kaori Fukuzawa, Etsuo Yonemochi, Michael J. Schnieders

Crystal Growth & Design　2024/04/17

DOI： 10.1021/acs.cgd.3c01358 　
The Development and Characterization of Novel Ionic Liquids Based on Mono- and Dicarboxylates with Meglumine for Drug Solubilizers and Skin Permeation Enhancers Peer-reviewed

Takayuki Furuishi, Sara Taguchi, Siran Wang, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutics　16　(3)　322-322　2024/02/26
Publisher: MDPI AG
DOI： 10.3390/pharmaceutics16030322 　

eISSN： 1999-4923

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In this study, we synthesized a family of novel ionic liquids (ILs) with meglumine (MGM) as cations and tartaric acid (TA), azelaic acid (AA), geranic acid (GA), and capric acid (CPA) as anions, using pharmaceutical additives via simple acid–base neutralization reactions. The successful synthesis was validated by attenuated total reflection–Fourier transform infrared (ATR-FTIR) and powder X-ray diffraction (PXRD). Thermal analysis using differential scanning calorimetry confirmed the glass transition temperature of MGM-ILs to be within the range of −43.4 °C–−13.8 °C. We investigated the solubilization of 15 drugs with varying pKa and partition coefficient (log P) values using these ILs and performed a comparative analysis. Furthermore, we present MGM-IL as a new skin permeation enhancer for the drug model flurbiprofen (FRP). We confirmed that AA/MGM-IL improves the skin permeation of FRP through hairless mouse skin. Moreover, AA/MGM-IL enhanced drug skin permeability by affecting keratin rather than stratum corneum lipids, as confirmed by ATR-FTIR. To conclude, MGM-ILs exhibited potential as drug solubilizer and skin permeation enhancers of drugs.
FMOe: Preprocessing and visualizing package of the fragment molecular orbital method for Molecular Operating Environment and its applications in covalent ligand and metalloprotein analyses Peer-reviewed

Hirotomo Moriwaki, Yusuke Kawashima, Chiduru Watanabe, Kikuko Kamisaka, Yoshio Okiyama, Kaori Fukuzawa, Teruki Honma

2024/02/08
Publisher: American Chemical Society (ACS)
DOI： 10.26434/chemrxiv-2024-2xk5n 　

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The fragment molecular orbital (FMO) method is an efficient quantum chemical calculation technique for large biomolecules, dividing each into smaller fragments and providing inter-fragment interaction energies (IFIEs) that support our understanding of molecular recognition. The ab initio fragment MO method program (ABINIT-MP), an FMO processing software, can automatically divide typical proteins and nucleic acids. In contrast, small molecules such as ligands and hetero systems must be manually divided. Thus, we developed a graphical user interface to easily handle such manual fragmentation as a library for Molecular Operating Environment (MOE) that preprocesses and visualizes FMO calculations. We demonstrated fragmentation with IFIE analyses for the two following cases: 1) covalent cysteine–ligand bonding inside the SARS-CoV-2 main protease (Mpro) and nirmatrelvir (Paxlovid) complex, and 2) the metal coordination inside a zinc-bound cyclic peptide. IFIE analysis successfully identified the key amino acid residues for the molecular recognition of nirmatrelrvir with Mpro and the details of their interactions (e.g., hydrogen bonds and CH/π interactions) via ligand fragmentation of functional group units. In metalloproteins, we found an efficient and accurate scheme for the fragmentation of Zn2+ ions with four histidines coordinated to the ion. FMOe simplifies manual fragmentation, allowing users to experiment with various fragmentation patterns and perform in-depth IFIE analysis with high accuracy. In the future, our findings will provide valuable insight into complicated cases, such as ligand fragmentation in modality drug discovery, especially for medium-sized molecules and metalloprotein fragmentation around metals.
Analysis of Moisture Stability in Amorphous Solid DispersionsUsing Molecular Dynamics and FMO Methods

Honoka MATSUMOTO, Koji OKUWAKI, Kenjirou HIGASHI, Takayuki FURUISHI, Kaori FUKUZAWA, Etsuo YONEMOCHI

Journal of Computer Chemistry, Japan　23　(4)　115-125　2024
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2024-0031 　

ISSN： 1347-1767

eISSN： 1347-3824
Probing RNA–Small Molecule Interactions Using Biophysical and Computational Approaches Peer-reviewed

Amiu Shino, Maina Otsu, Koji Imai, Kaori Fukuzawa, Ella Czarina Morishita

ACS Chemical Biology　2023/11/17

DOI： 10.1021/acschembio.3c00287 　
Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

Shintaro Iwasaki, Hironori Saito, Yuma Handa, Mingming Chen, Tilman Schneider-Poetsch, Yuichi Shichino, Mari Takahashi, Daniel Romo, Minoru Yoshida, Alois Furstner, Takuhiro Ito, Kaori Fukuzawa

2023/09/21

DOI： 10.1101/2023.09.21.558742 　
Crystal structure prediction with force field, DFT-D3 and FMO techniques

S. Obata, Y. Utsumi, Y. Ikabata, K. Okuwaki, K. Fukuzawa, N. Nakayama, E. Yonemochi, H. Goto

Acta Crystallographica Section A Foundations and Advances　79　(a2)　C890-C890　2023/08/22
Publisher: International Union of Crystallography (IUCr)
DOI： 10.1107/s2053273323087314 　

ISSN： 2053-2733
Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations Peer-reviewed

Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

2023/07/25
Publisher: American Chemical Society (ACS)
DOI： 10.26434/chemrxiv-2023-hrsvj 　

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COVID-19 remains a global pandemic, necessitating the urgent development of more effective therapeutics. By combining molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations, the binding structure and properties with Mpro were predicted for Nelfinavir (NLF), which was identified as a candidate compound through drug repositioning targeting the Main Protease (Mpro) produced by the causative virus, SARS-CoV-2. For the four docking poses selected by scoring using FMO energy, 100 structures each from the MD trajectory were sampled, and FMO calculations were performed and ranked based on binding energy. Besides the interaction between NLF and each Mpro residue, the desolvation effect of the pocket affected the ranking order. Furthermore, we identified several residues important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NLF. Asn142 was mentioned as a residue with hydrogen bonds or CH/π interaction with NLF; however, it was considered a transient interacting residue because of its unstable structure. Moreover, the tert-butyl group of NLF had no interaction with Mpro. Identifying weak interactions provides candidates for substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.
Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method Peer-reviewed

Koichiro Kato*, Ami Yamamoto, Chiduru Watanabe, Kaori Fukuzawa

Chem-Bio Informatics Journal　23　14-25　2023/07/20
Publisher: Chem-Bio Informatics Society
DOI： 10.1273/cbij.23.14 　

ISSN： 1347-6297

eISSN： 1347-0442
Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses Peer-reviewed

Katsuki Takebe, Mamoru Suzuki, Takao Kuwada-Kusunose, Satoko Shirai, Kaori Fukuzawa, Tomoko Takamiya, Narikazu Uzawa, Hiroshi Iijima

Journal of Chemical Information and Modeling　2023/07/12
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jcim.3c00331 　

ISSN： 1549-9596

eISSN： 1549-960X
Characterization of Co-amorphous Carvedilol–Maleic Acid System Prepared by Solvent Evaporation Peer-reviewed

Takayuki Furuishi, Nanami Sato-Hata, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutical Development and Technology　1-13　2023/03/22
Publisher: Informa UK Limited
DOI： 10.1080/10837450.2023.2194406 　

ISSN： 1083-7450

eISSN： 1097-9867
Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. International-journal Peer-reviewed

Koh Takeuchi, Miki Senda, Yoshiki Ikeda, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Mika Sasaki, Atsuo T Sasaki, Toshiya Senda

The FEBS journal　2023/03/01

DOI： 10.1111/febs.16763 　

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Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications, and recombination, have established de novo genes that translate into proteins with novel properties essential for high-order cellular functions. However, molecular processes through which a protein evolutionarily acquires a novel function are mostly speculative. Recently, we have provided evidence for a potential evolutionary mechanism underlying how, in mammalian cells, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) evolved into a GTP sensor from ATP-utilizing kinase. Mechanistically, PI5P4Kβ has acquired the guanine efficient association (GEA) motif by mutating its nucleotide base recognition sequence, enabling the evolutionary transition from an ATP-dependent kinase to a distinct GTP/ATP dual kinase with its KM for GTP falling into physiological GTP concentrations-the genesis of GTP sensing activity. Importantly, the GTP sensing activity of PI5P4Kβ is critical for the manifestation of cellular metabolism and tumorigenic activity in the multicellular organism. The combination of structural, biochemical, and biophysical analyses used in our study provides a novel framework for analyzing how a protein can evolutionarily acquire a novel activity, which potentially introduces a critical function to the cell.
Structure and Mechanism Analysis of Proteins by Fragment Molecular Orbital Calculations Invited Peer-reviewed

Kaori FUKUZAWA, Chiduru WATANABE, Koichiro KATO

Nihon Kessho Gakkaishi　65　(1)　17-25　2023/02/28
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.65.17 　

ISSN： 0369-4585

eISSN： 1884-5576
Promoting Activity of Terpenes on Skin Permeation of Famotidine Peer-reviewed

Qihui Xu, Yifan Wu, Hiroki Saito, Yuki Ofuchi, Haruna Setoyama, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Yasuko Obata

Chemical and Pharmaceutical Bulletin　71　(2)　111-119　2023/02/01
Publisher: Pharmaceutical Society of Japan
DOI： 10.1248/cpb.c22-00568 　

ISSN： 0009-2363

eISSN： 1347-5223
Physicochemical Properties and Transdermal Absorption of a Flurbiprofen and Lidocaine Complex in the Non-Crystalline Form Peer-reviewed

Qihui Xu, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutics　15　(2)　318　2023/01

DOI： 10.3390/pharmaceutics15020318 　

eISSN： 1999-4923
Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir (Xocova) Compared with Its Initial Screening Hit Peer-reviewed

Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma

2022/12/02
Publisher: American Chemical Society (ACS)
DOI： 10.26434/chemrxiv-2022-drwc0 　

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A non-covalent oral drug targeting severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) main protease (Mpro), ensitrelvir (brand name Xocova), has been developed by Unoh et al. (J. Med. Chem. 2022, 65, 9, 6499–6512) using structure-based drug design (SBDD). To elucidate the factors responsible for the enhanced inhibitory activities from in silico screening hit compound to ensitrelvir, we analyzed interaction energies between the inhibitor and each residue of Mpro using fragment molecular orbital (FMO) calculations. This analysis reveals that functional group conversion for P1’ and P1 parts in the two inhibitors increases the strength of existing interactions with Mpro and also provides novel interactions for ensitrelvir. Moreover, the associated slight changes in the conformation of Mpro induce further interactions for ensitrelvir in other parts, including hydrogen bonds, a halogen bond, and π-orbital interactions. Thus, we shed light on the promising strategies of SBDD for leading ensitrelvir to get higher inhibitory activity against Mpro by elucidating microscopic interactions through FMO-based analysis. These detailed mechanism findings, including water cross-linkings, will give a powerful tool for further improvement in SBDD.
Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti Peer-reviewed

Kazue Inaba, Kana Ebihara, Miki Senda, Ryunosuke Yoshino, Chisako Sakuma, Kotaro Koiwai, Daisuke Takaya, Chiduru Watanabe, Akira Watanabe, Yusuke Kawashima, Kaori Fukuzawa, Riyo Imamura, Hirotatsu Kojima, Takayoshi Okabe, Nozomi Uemura, Shinji Kasai, Hirotaka Kanuka, Takashi Nishimura, Kodai Watanabe, Hideshi Inoue, Yuuta Fujikawa, Teruki Honma, Takatsugu Hirokawa, Toshiya Senda, Ryusuke Niwa

BMC Biology　20　(1)　2022/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1186/s12915-022-01233-2 　

eISSN： 1741-7007

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<title>Abstract</title><sec> <title>Background</title> Mosquito control is a crucial global issue for protecting the human community from mosquito-borne diseases. There is an urgent need for the development of selective and safe reagents for mosquito control. Flavonoids, a group of chemical substances with variable phenolic structures, such as daidzein, have been suggested as potential mosquito larvicides with less risk to the environment. However, the mode of mosquito larvicidal action of flavonoids has not been elucidated. </sec><sec> <title>Results</title> Here, we report that several flavonoids, including daidzein, inhibit the activity of glutathione <italic>S</italic>-transferase Noppera-bo (Nobo), an enzyme used for the biosynthesis of the insect steroid hormone ecdysone, in the yellow fever mosquito <italic>Aedes aegypti</italic>. The crystal structure of the Nobo protein of <italic>Ae. aegypti</italic> (AeNobo) complexed with the flavonoids and its molecular dynamics simulation revealed that Glu113 forms a hydrogen bond with the flavonoid inhibitors. Consistent with this observation, substitution of Glu113 with Ala drastically reduced the inhibitory activity of the flavonoids against AeNobo. Among the identified flavonoid-type inhibitors, desmethylglycitein (4′,6,7-trihydroxyisoflavone) exhibited the highest inhibitory activity in vitro. Moreover, the inhibitory activities of the flavonoids correlated with the larvicidal activity, as desmethylglycitein suppressed <italic>Ae. aegypti</italic> larval development more efficiently than daidzein. </sec><sec> <title>Conclusion</title> Our study demonstrates the mode of action of flavonoids on the <italic>Ae. aegypti</italic> Nobo protein at the atomic, enzymatic, and organismal levels. </sec>
Fragment molecular orbital calculations containing Mg2+ ions: PPlase domain of Cyclophilin G Peer-reviewed

Masayasu Fujii, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

Chem-Bio Informatics Journal　22　55-62　2022/09/16
Publisher: Chem-Bio Informatics Society
DOI： 10.1273/cbij.22.55 　

ISSN： 1347-6297

eISSN： 1347-0442
Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives. International-journal Peer-reviewed

Chiaki Handa, Yuki Yamazaki, Shigeru Yonekubo, Noritaka Furuya, Takaki Momose, Tomonaga Ozawa, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

The Journal of steroid biochemistry and molecular biology　222　106152-106152　2022/09

DOI： 10.1016/j.jsbmb.2022.106152 　

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Estrogen receptors (ERs) are ligand-activated transcription factors, with two subtypes ERα and ERβ. The endogenous ligand of ERs is the common 17β-estradiol, and the ligand-binding pocket of ERα and ERβ is very similar. Nevertheless, some ERβ-selective agonist ligands have been reported. DPN (diarylpropionitrile) is a widely used ERβ-selective agonist; however, the structure of the ERβ-DPN complex has not been solved. Therefore, the bound-state conformation of DPN and its enantioselectivity remain unresolved. In this report, we present the structures of the complexes of ERβ with DPN or its derivatives that include a chlorine atom by the X-ray crystallography. Additionally, we measured the binding affinity between ERβ and DPN or derivatives by isothermal titration calorimetry (ITC) and estimated the binding affinity by fragment molecular orbital (FMO) calculations. We also examined the correlation between the ITC data and results from the FMO calculations. FMO calculations showed that S-DPN interacts strongly with three amino acids (Glu305, Phe356, and His475) of ERβ, and ITC measurements confirmed that the chlorine atom of the DPN derivatives enhances binding affinity. The enthalpy change by ITC correlated strongly with the interaction energy (total IFIEs; inter-fragment interaction energies) calculated by FMO (R = 0.870). We propose that FMO calculations are a valuable approach for enhancing enthalpy contributions in drug design, and its scope of applications includes halogen atoms such as chlorine. This study is the first quantitative comparison of thermodynamic parameters obtained from ITC measurements and FMO calculations, providing new insights for future precise drug design.
Study of Orally Disintegrating Tablets Using Erythritol as an Excipient Produced by Moisture-Activated Dry Granulation (MADG) Peer-reviewed

Mizuki Yamada, Agata Ishikawa, Shun Muramatsu, Takayuki Furuishi, Yoshinori Onuki, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceuticals　15　(8)　1004-1004　2022/08/15
Publisher: MDPI AG
DOI： 10.3390/ph15081004 　

eISSN： 1424-8247

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Moisture-activated dry granulation (MADG) is an eco-friendly granulation method that uses a small amount of water and insoluble excipients to absorb moisture. MADG is expected to improve productivity and reduce costs. Erythritol, an excipient used for preparing orally disintegrating tablets (ODTs), has poor tabletability and is difficult to form into tablets by conventional methods, such as high-shear granulation (HSG) and direct compression. In this study, we optimized the manufacturing conditions for ODTs to improve the tabletability of erythritol using MADG. The disintegration time of tablets made using the MADG method was approximately one-tenth that of those made using the HSG method, and the hardness was approximately 1.4 times higher. Moreover, MADG could delay disintegration and improve tabletability. We further attempted to optimize the manufacturing conditions using MADG, particularly in terms of the amount of water used. The disintegration time increased as the amount of added water increased. Moreover, water absorption tests revealed that capillary wetting decreased as the amount of water added increased, but the initial wetting did not change. These results suggested that the disintegration time was prolonged because of the increase in granule density and decrease in capillary wetting with the increase in the amount of added water. The hardness of the tablets increased because of the easy deformation of the granules after the addition of up to 3% water; however, when more than 3% water was added, the hardness decreased because of the aggregation of the granules with the excess water. Finally, two-dimensional maps of the effect of the amount of added water and water activity indicated that tablets with a hardness of ≥80 N and a disintegration time of ≤15 s could be produced by adjusting the amount of added water to within the range of 2.2–3.3% and water activity to 0.3–0.53. These results indicate that MADG can improve the tabletability of erythritol and be used for the granulation of ODTs. Tablets with appropriate hardness and disintegration properties can be produced by adjusting the water content to approximately 2.7% and the water activity to approximately 0.4 when producing ODTs with MADG.
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy Peer-reviewed

Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki, Norihito Kawashita, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

Journal of Computational Chemistry　43　(20)　1362-1371　2022/07/30
Publisher: Wiley
DOI： 10.1002/jcc.26940 　

ISSN： 0192-8651

eISSN： 1096-987X
The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity. International-journal Peer-reviewed

Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hong Yang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki, Yu-Hua Lo, Doshun Ito, Natsuki Osaka, Yuki Fujii, Atsuo T Sasaki, Toshiya Senda

Structure (London, England : 1993)　30　(6)　886-899　2022/06/02

DOI： 10.1016/j.str.2022.04.004 　

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Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kβ has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128 G proteins has uncovered that most kinases and PI5P4Kβ use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kβ has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.
FMO calculations for zinc metalloprotease: Fragmentation of amino-acid residues coordinated to zinc ion Peer-reviewed

Imai, K., Takimoto, D., Saito, R., Watanabe, C., Fukuzawa, K., Kurita, N.

Chem-Bio Informatics Journal　22　21-25　2022/06

DOI： 10.1273/cbij.22.21 　

ISSN： 1347-0442 1347-6297
Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation. International-journal Peer-reviewed

Xiaohan Ma, Kenjirou Higashi, Kaori Fukuzawa, Keisuke Ueda, Kazunori Kadota, Yuichi Tozuka, Etsuo Yonemochi, Kunikazu Moribe

International journal of pharmaceutics　615　121477-121477　2022/03/05

DOI： 10.1016/j.ijpharm.2022.121477 　

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α-Glycosyl rutin (Rutin-G) consists of a flavonol skeleton and sugar groups and is a promising additive for amorphous formulations. In our previous study, experimental approaches suggested an interaction between the model drug carbamazepine (CBZ) and flavonol skeleton of Rutin-G that stabilizes amorphous formulations. In the present study, the formation and stabilization mechanisms of CBZ/Rutin-G amorphous formulation were investigated using a computational approach. The CBZ/Rutin-G amorphous formulation was obtained via molecular dynamics (MD) simulation, which mimicked the melt-quenching method. Root mean square deviation analysis revealed that the translational motion of CBZ during the cooling process was suppressed by adding Rutin-G. Monitoring the atomic distance during the cooling process revealed that hydrogen bonds via carboxamide oxygen of CBZ with hydroxyl hydrogen of Rutin-G were preferentially formed with flavonol skeletons than sugar groups. The simulated amorphous formulation was then calculated using fragment molecular orbital (FMO) method. The quantitative evaluation of multiple interactions revealed that the hydrogen bond energy was higher in CBZ-sugar groups than in CBZ-flavonol skeleton, while the π-type of interaction energy was higher in CBZ-flavonol skeleton than in CBZ-sugar groups. The computational approach combining MD simulation and FMO calculation provides information on various interactions that are difficult to detect using experimental approaches, which helps understand the formation and stabilization mechanism of amorphous formulations.
Fragment molecular orbital calculations for biomolecules Invited Peer-reviewed

Fukuzawa, K., Tanaka, S.

Current Opinion in Structural Biology　72　127-134　2022/02
Publisher: Elsevier {BV}
DOI： 10.1016/j.sbi.2021.08.010 　

ISSN： 1879-033X 0959-440X
Sulfated Hyaluronan Binds to Heparanase and Blocks Its Enzymatic and Cellular Actions in Carcinoma Cells Peer-reviewed

Shi, J., Kanoya, R., Tani, Y., Ishikawa, S., Maeda, R., Suzuki, S., Kawanami, F., Miyagawa, N., Takahashi, K., Oku, T., Yamamoto, A., Fukuzawa, K., Nakajima, M., Irimura, T., Higashi, N.

International Journal of Molecular Sciences　23　(9)　2022

DOI： 10.3390/ijms23095055 　

ISSN： 1422-0067 1661-6596
Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method Peer-reviewed

Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

Applied Physics Express　15　(1)　017001-017001　2022/01/01
Publisher: IOP Publishing
DOI： 10.35848/1882-0786/ac4300 　

ISSN： 1882-0778

eISSN： 1882-0786

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<title>Abstract</title> In large biomolecular systems such as protein complexes, there are huge numbers of combinations of inter-residue interactions whose comprehensive analyses are often beyond the intuitive processing by researchers. Here we propose a computational method to allow for a systematic analysis of these interactions based on the fragment molecular orbital calculations, in which the inter-fragment interaction energies are comprehensively processed by the singular value decomposition. For a trimer complex of SARS-CoV-2 spike protein, three-body interactions among residues belonging to three chains are analyzed to elicit a small number of essential interaction modes or networks crucial for the structural stability of the complex.
Altered Media Flow and Tablet Position as Factors of How Air Bubbles Affect Dissolution of Disintegrating and Non-disintegrating Tablets Using a USP 4 Flow-Through Cell Apparatus Peer-reviewed

Hiroyuki Yoshida, Keita Teruya, Yasuhiro Abe, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Ken-ichi Izutsu

AAPS PHARMSCITECH　22　(7)　2021/08

DOI： 10.1208/s12249-021-02117-4 　

ISSN： 1530-9932
Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method Peer-reviewed

Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

The Journal of Physical Chemistry B　125　(24)　6501-6512　2021/06/24
Publisher: American Chemical Society ({ACS})
DOI： 10.1021/acs.jpcb.1c03043 　

ISSN： 1520-6106

eISSN： 1520-5207
Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins Peer-reviewed

Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Ami Yamamoto, Kazuki Watanabe, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma

2021/06/18
Publisher: Cambridge University Press (CUP)
DOI： 10.33774/chemrxiv-2021-njqc8 　
Computational ab initio interaction analyses between neutralizing antibody and SARS-CoV-2 variant spike proteins using the fragment molecular orbital method Peer-reviewed

Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Kaori Fukuzawa, Tatsuya Takagi

Bulletin of the Chemical Society of Japan　2021/05/15
Publisher: The Chemical Society of Japan
DOI： 10.1246/bcsj.20210104 　

ISSN： 0009-2673

eISSN： 1348-0634
Manufacturability and Properties of Granules and Tablets Using the Eco-Friendly Granulation Method Green Fluidized Bed Granulation Compared to Direct Compression Peer-reviewed

Agata Ishikawa, Hiroshi Takasaki, Atsushi Sakurai, Takuma Katayama, Koichi Wada, Takayuki Furuishi, Kaori Fukuzawa, Yasuko Obata, Etsuo Yonemochi

Chemical and Pharmaceutical Bulletin　69　(5)　447-455　2021/05/01
Publisher: Pharmaceutical Society of Japan
DOI： 10.1248/cpb.c20-00970 　

ISSN： 0009-2363

eISSN： 1347-5223
Stabilization mechanism of amorphous carbamazepine by transglycosylated rutin, a non-polymeric amorphous additive with a high glass transition temperature. International-journal Peer-reviewed

Chisa Aoki, Xiaohan Ma, Kenjirou Higashi, Yuya Ishizuka, Keisuke Ueda, Kazunori Kadota, Kaori Fukuzawa, Yuichi Tozuka, Kohsaku Kawakami, Etsuo Yonemochi, Kunikazu Moribe

International journal of pharmaceutics　600　120491-120491　2021/05/01

DOI： 10.1016/j.ijpharm.2021.120491 　

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α-Glycosyl rutin (Rutin-G), composed of a flavonol skeleton and sugar groups, is a promising non-polymeric additive for stabilizing amorphous drug formulations. In this study, the mechanism of the stabilization of the amorphous state of carbamazepine (CBZ) by Rutin-G was investigated. In comparison with hypromellose (HPMC), which is commonly used as a crystallization inhibitor for amorphous drugs, Rutin-G significantly stabilized amorphous CBZ. Moreover, the dissolution rate and the resultant supersaturation level of CBZ were significantly improved in the CBZ/Rutin-G spray-dried samples (SPDs) owing to the rapid dissolution property of Rutin-G. Differential scanning calorimetry measurement demonstrated a high glass transition temperature (Tg) of 186.4°C corresponding to Rutin-G. The CBZ/Rutin-G SPDs with CBZ weight ratios up to 80% showed single glass transitions, indicating the homogeneity of CBZ and Rutin-G. A solid-state NMR experiment using 13C- and 15N-labeled CBZ demonstrated the interaction between the flavonol skeleton of Rutin-G and the amide group of CBZ. A 1H-13C two-dimensional heteronuclear correlation NMR experiment and quantum mechanical calculations confirmed the presence of a possible hydrogen bond between the amino proton in CBZ and the carbonyl oxygen in the flavonol skeleton of Rutin-G. This specific hydrogen bond could contribute to the strong interaction between CBZ and Rutin-G, resulting in the high stability of amorphous CBZ in the CBZ/Rutin-G SPD. Hence, Rutin-G, a non-polymeric amorphous additive with high Tg, high miscibility with drugs, and rapid and pH-independent dissolution properties could be useful in the preparation of amorphous formulations.
Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation Peer-reviewed

Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Tatsuya Takagi, Kaori Fukuzawa

The Journal of Physical Chemistry Letters　12　(16)　4059-4066　2021/04/29

DOI： 10.1021/acs.jpclett.1c00663 　

ISSN： 1948-7185
Crystal Structures of Antiarrhythmic Drug Disopyramide and Its Salt with Phthalic Acid Peer-reviewed

Majid Ismail Tamboli, Yushi Okamoto, Yohei Utsumi, Takayuki Furuishi, Siran Wang, Daiki Umeda, Okky Dwichandra Putra, Kaori Fukuzawa, Hidehiro Uekusa, Etsuo Yonemochi

Crystals　11　(4)　379-379　2021/04/06

DOI： 10.3390/cryst11040379 　

ISSN： 2073-4352
Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses dagger Peer-reviewed

Chiduru Watanabe, Yoshio Okiyama, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

CHEMICAL SCIENCE　12　(13)　2021/04

DOI： 10.1039/d0sc06528e 　

ISSN： 2041-6520

eISSN： 2041-6539
Crystal Structure of Novel Terephthalate Salt of Antiarrhythmic Drug Disopyramide Peer-reviewed

Majid Ismail Tamboli, Yohei Utusmi, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

Crystals　11　(4)　2021/03/31

DOI： 10.3390/cryst11040368 　

ISSN： 2073-4352

eISSN： 2073-4352
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method International-journal Peer-reviewed

Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama, Hirotomo Moriwaki, Hitomi Yuki, Tomohiro Sato, Noriyuki Kurita, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Kenichiro Takaba, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

Journal of Chemical Information and Modeling　61　(2)　777-794　2021/02/22
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jcim.0c01062 　

ISSN： 1549-9596

eISSN： 1549-960X

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We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation Peer-reviewed

Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Applied Physics Express　14　(2)　027003-027003　2021/02/01
Publisher: {IOP} Publishing
DOI： 10.35848/1882-0786/abdac6 　

ISSN： 1882-0778

eISSN： 1882-0786
Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method Peer-reviewed

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki

Bulletin of the Chemical Society of Japan　94　(1)　91-96　2021/01/15

DOI： 10.1246/bcsj.20200227 　

ISSN： 0009-2673

eISSN： 1348-0634
FMO Drug Design Consortium

Fukuzawa, K., Tanaka, S., Yagi, Y., Kurita, N., Kawashita, N., Takaba, K., Honma, T.

Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability　2021
Publisher: Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability
DOI： 10.1007/978-981-15-9235-5_8 　
Improving the Accuracy of Crystal Structure Prediction Using FMO Crystal Energy: An Example of Target XXIII Peer-reviewed

Yohei UTSUMI, Daiki UMEDA, Koji OKUWAKI, Shigeaki OBATA, Naofumi NAKAYAMA, Hitoshi GOTO, Takayuki FURUISHI, Kaori FUKUZAWA, Etsuo YONEMOCHI

Journal of Computer Chemistry, Japan　20　(3)　92-93　2021
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2021-0041 　

ISSN： 1347-1767

eISSN： 1347-3824
Estimation of Graph Convolutional Network in Ames Prediction of Drug Candidate Compounds Peer-reviewed

HANDA Chiaki, OZAWA Tomonaga, FUKUZAWA Kaori, YONEMOCHI Etsuo

Journal of Computer Chemistry, Japan　20　(1)　1-9　2021
Publisher: Society of Computer Chemistry, Japan
DOI： 10.2477/jccj.2020-0015 　

ISSN： 1347-1767

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Ames test to detect mutagenicity in vitro is of crucial importance in drug discovery and development as an early alerting system for potential carcinogenicity and/or teratogenicity for drug candidates. In the alerting system of machine learning approaches, which are the main approach of in silico prediction, there is a concept called Applicability domain (AD) that has a significant influence on prediction accuracy. In drug discovery, prediction of drug candidate compounds with low structural similarity to the training data may take place, while such compounds have a high probability of being out of the AD and tend to be less accurate. In this study, we evaluated the performance of several machine learning methods for a group of compounds with a high probability of being included in AD or not, respectively. The results showed that the performance of the graph convolutional networks (GCN) method which have achieved a superior performance in a wide range of tasks was better than conventional methods. In particular, the accuracy of the GCN method is significantly different from the conventional methods for the prediction of molecules with low structural similarity (Figure 4).
Modeling of Solid and Surface

Koichiro Kato, Aya Hashimoto, Eiichi Tamiya, Kaori Fukuzawa, Yuichiro Ishikawa, Yuji Mochizuki

Recent Advances of the Fragment Molecular Orbital Method　407-424　2021
Publisher: Springer Singapore
DOI： 10.1007/978-981-15-9235-5_21 　
The ABINIT-MP Program

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

Recent Advances of the Fragment Molecular Orbital Method　53-67　2021
Publisher: Springer Singapore
DOI： 10.1007/978-981-15-9235-5_4 　
How to Perform FMO Calculation in Drug Discovery

Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Tatsuya Nakano

Recent Advances of the Fragment Molecular Orbital Method　93-125　2021
Publisher: Springer Singapore
DOI： 10.1007/978-981-15-9235-5_7 　
Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations Peer-reviewed

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

RSC Advances　11　(6)　3272-3279　2021

DOI： 10.1039/D0RA09555A 　

eISSN： 2046-2069
Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method Peer-reviewed

Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi, Tadashi Maruyama

Journal of Molecular Graphics and Modelling　100　107650-107650　2020/11

DOI： 10.1016/j.jmgm.2020.107650 　

ISSN： 1093-3263

eISSN： 1873-4243
Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation Peer-reviewed

Kato, K., Honma, T., Fukuzawa, K.

Journal of Molecular Graphics and Modelling　100　107695-107695　2020/11
Publisher: Elsevier {BV}
DOI： 10.1016/j.jmgm.2020.107695 　

ISSN： 1873-4243 1093-3263
Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase - inhibitor complex Peer-reviewed

Shusuke Tokutomi, Kohei Shimamura, Kaori Fukuzawa, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　757　2020/10

DOI： 10.1016/j.cplett.2020.137883 　

ISSN： 0009-2614

eISSN： 1873-4448
Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery Peer-reviewed

Hiroki Tanaka, Tatsunari Takahashi, Manami Konishi, Nae Takata, Masaki Gomi, Daiki Shirane, Ryo Miyama, Shinya Hagiwara, Yuki Yamasaki, Yu Sakurai, Keisuke Ueda, Kenjirou Higashi, Kunikazu Moribe, Eiji Shinsho, Ruka Nishida, Kaori Fukuzawa, Etsuo Yonemochi, Koji Okuwaki, Yuji Mochizuki, Yuta Nakai, Kota Tange, Hiroki Yoshioka, Shinya Tamagawa, Hidetaka Akita

ADVANCED FUNCTIONAL MATERIALS　30　(34)　2020/08

DOI： 10.1002/adfm.201910575 　

ISSN： 1616-301X

eISSN： 1616-3028
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning Peer-reviewed

Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, Teruki Honma

Journal of Chemical Information and Modeling　60　(7)　3361-3368　2020/07/27
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jcim.0c00273 　

ISSN： 1549-9596

eISSN： 1549-960X
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) International-journal Peer-reviewed

Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Journal of Chemical Information and Modeling　60　(7)　3593-3602　2020/07/27
Publisher: American Chemical Society ({ACS})
DOI： 10.1021/acs.jcim.0c00283 　

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The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.
Activity-specificity trade-off gives PI5P4Kβ a nucleotide preference to function as a GTP-sensing kinase

Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hongyang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki, YuHua Lo, Atsuo T. Sasaki, Toshiya Senda

2020/06/10

DOI： 10.1101/2020.06.09.137430 　
Fragmentation at sp2 carbon atoms in fragment molecular orbital method Peer-reviewed

Yoshinobu Akinaga, Koichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki

Journal of Computational Chemistry　41　(15)　1416-1420　2020/06/05
Publisher: Wiley
DOI： 10.1002/jcc.26190 　

ISSN： 0192-8651

eISSN： 1096-987X
An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo Peer-reviewed

Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa

JOURNAL OF BIOLOGICAL CHEMISTRY　295　(20)　7154-7167　2020/05

DOI： 10.1074/jbc.RA119.011463 　

ISSN： 0021-9258

eISSN： 1083-351X
Crystal Structural Analysis of DL-Mandelate Salt of Carvedilol and Its Correlation with Physicochemical Properties Peer-reviewed

Nanami Hata, Takayuki Furuishi, Majid I. Tamboli, Momiji Ishizaki, Daiki Umeda, Kaori Fukuzawa, Etsuo Yonemochi

Crystals　2020/01/20

DOI： 10.3390/cryst10010053 　
Development Status of ABINIT-MP in 2020

Yuji MOCHIZUKI, Kota SAKAKURA, Hiromasa WATANABE, Koji OKUWAKI, Koichiro KATO, Naoki WATANABE, Yoshio OKIYAMA, Kaori FUKUZAWA, Tatsuya NAKANO

Journal of Computer Chemistry, Japan　19　(4)　142-145　2020
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2021-0015 　

ISSN： 1347-1767

eISSN： 1347-3824
Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method Peer-reviewed

Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI

Journal of Computer Chemistry, Japan　19　(1)　1-7　2020
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2019-0030 　

ISSN： 1347-1767

eISSN： 1347-3824
Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations Peer-reviewed

Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

Applied Physics Express　13　(1)　017002-017002　2020/01/01
Publisher: {IOP} Publishing
DOI： 10.7567/1882-0786/ab5e0a 　
Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method Peer-reviewed

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

Japanese Journal of Applied Physics　58　(12)　120906-120906　2019/12/01

DOI： 10.7567/1347-4065/ab5335 　

ISSN： 0021-4922

eISSN： 1347-4065
Crystal structure prediction of irsogladine maleate by experimental and computational methods Peer-reviewed

Chinatsu Sakata, Yushi Okamoto, Daiki Umeda, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

J. Comput. Chem. Jpn　18　156-158　2019/11
Effect of sulfobutyl ether-β-cyclodextrin and propylene glycol alginate on the solubility of clozapine Peer-reviewed

Takayuki Furuishi, Kohei Sekino, Mihoko Gunji, Kaori Fukuzawa, Hiromasa Nagase, Tomohiro Endo, Haruhisa Ueda, Etsuo Yonemochi

Pharmaceutical Development and Technology　24　(4)　479-486　2019/04

DOI： 10.1080/10837450.2018.1514521 　

ISSN： 1083-7450

eISSN： 1097-9867
Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules Peer-reviewed

Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma

Chem-Bio Informatics Journal　19　(0)　5-18　2019/03
Publisher: Chem-Bio Informatics Society
DOI： 10.1273/cbij.19.5 　

ISSN： 1347-0442
The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. International-journal Peer-reviewed

Shintaro Iwasaki, Wakana Iwasaki, Mari Takahashi, Ayako Sakamoto, Chiduru Watanabe, Yuichi Shichino, Stephen N Floor, Koichi Fujiwara, Mari Mito, Kosuke Dodo, Mikiko Sodeoka, Hiroaki Imataka, Teruki Honma, Kaori Fukuzawa, Takuhiro Ito, Nicholas T Ingolia

Molecular cell　73　(4)　738-748　2019/02/21

DOI： 10.1016/j.molcel.2018.11.026 　

ISSN： 1097-2765
Destabilization of DNA through interstrand crosslinking by UO₂²⁺ Peer-reviewed

Rossberg, A., Abe, T., Okuwaki, K., Barkleit, A., Fukuzawa, K., Nakano, T., Mochizuki, Y., Tsushima, S.

Chemical Communications　55　(14)　2015-2018　2019/02/18

DOI： 10.1039/c8cc09329f 　

ISSN： 1359-7345
Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies Peer-reviewed

Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

The Journal of Physical Chemistry B　123　(5)　957-973　2019/02/07

DOI： 10.1021/acs.jpcb.8b09326 　

ISSN： 1520-6106
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations Peer-reviewed

Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta

Journal of Chemical Information and Modeling　59　(1)　25-30　2019/01/28

DOI： 10.1021/acs.jcim.8b00649 　

ISSN： 1549-9596

eISSN： 1549-960X
X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明 Peer-reviewed

新庄永治, 奥脇弘次, 土居英男, 望月祐志, 古石誉之, 福澤薫, 米持悦生

J. Comp. Chem. Jpn.　17　(4)　172-179　2019/01
A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA) Peer-reviewed

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry　20　(0)　1-6　2019

DOI： 10.2751/jcac.20.1 　

ISSN： 1345-8647
Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules Peer-reviewed

Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma

CHEM-BIO INFORMATICS JOURNAL　19　5-18　2019

DOI： 10.1273/cbij.19.5 　

ISSN： 1347-6297

eISSN： 1347-0442
Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method Peer-reviewed

Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

Bulletin of the Chemical Society of Japan　91　(11)　1596-1605　2018/11

DOI： 10.1246/bcsj.20180150 　

ISSN： 0009-2673
Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening Peer-reviewed

Keiya Maruyama, Yinglei Sheng, Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka

Computational and Theoretical Chemistry　1132　23-34　2018/05/15

DOI： 10.1016/j.comptc.2018.04.001 　

ISSN： 2210-271X
Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study Peer-reviewed

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

The Journal of Physical Chemistry B　122　(16)　4457-4471　2018/04/26

DOI： 10.1021/acs.jpcb.8b01172 　

ISSN： 1520-6106
Development and Application of FMO Calculation − DPD Simulation Conbination Scheme Peer-reviewed

Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori

Journal of Computer Chemistry, Japan　17　(3)　144　2018

DOI： 10.2477/jccj.2018-0020 　
FMO計算-粗視化シミュレーション連携手法の開発と応用 Peer-reviewed

奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫

J. Comp. Chem. Jpn.　17　144-146　2018
Formation Mechanism of Lipid Membrane and Vesicle Using Small Angle X-ray Scattering and Dissipative Particle Dynamics (DPD) Method Peer-reviewed

Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

JOURNAL OF COMPUTER CHEMISTRY-JAPAN　17　(4)　172-179　2018

DOI： 10.2477/jccj.2018-0012 　

ISSN： 1347-1767

eISSN： 1347-3824
Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase Peer-reviewed

Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL　16　421-434　2018

DOI： 10.1016/j.csbj.2018.10.003 　

ISSN： 2001-0370
Analysis of ligand binding specificity of estrogen receptor by the fragment molecular orbital method Peer-reviewed

Yuya Seki, Tsukasa Kato, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yone

JOURNAL OF COMPUTER CHEMISTRY-JAPAN　17　(3)　160-162　2018

DOI： 10.2477/jccj.2018-0028 　

ISSN： 1347-1767

eISSN： 1347-3824
Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method Peer-reviewed

Nakano Tatsuya, Fukuzawa Kaori, Okiyama Yoshio, Watanabe Chiduru, Komeiji Yuto, Mochizuki Yuji

CHEM-BIO INFORMATICS JOURNAL　18　119-122　2018

DOI： 10.1273/cbij.18.119 　

ISSN： 1347-6297

eISSN： 1347-0442
Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO plus MM-PBSA) Approach Peer-reviewed

Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma

JOURNAL OF CHEMICAL INFORMATION AND MODELING　57　(12)　2996-3010　2017/12

DOI： 10.1021/acs.jcim.7b00110 　

ISSN： 1549-9596

eISSN： 1549-960X
Epalrestat tetrahydrofuran monosolvate: crystal structure and phase transition Peer-reviewed

Daiki Umeda, Okky Dwichandra Putra, Mihoko Gunji, Kaori Fukuzawa, Etsuo Yonemochi

ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS　73　941-+　2017/07

DOI： 10.1107/S2056989017007976 　

ISSN： 2056-9890
Solubility improvement of epalrestat by layered structure formation via cocrystallization Peer-reviewed

Okky Dwichandra Putra, Daiki Umeda, Yuda Prasetya Nugraha, Takayuki Furuishi, Hiromasa Nagase, Kaori Fukuzawa, Hidehiro Uekusa, Etsuo Yonemochi

CRYSTENGCOMM　19　(19)　2614-2622　2017/05

DOI： 10.1039/c7ce00284j 　

ISSN： 1466-8033
Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Moller-Plesset perturbation (MP2.5) scheme Peer-reviewed

Haruka Yamada, Yuji Mochizuki, Kaori Fukuzawa, Yoshio Okiyama, Yuto Komeiji

COMPUTATIONAL AND THEORETICAL CHEMISTRY　1101　46-54　2017/02

DOI： 10.1016/j.comptc.2016.12.008 　

ISSN： 2210-271X

eISSN： 1872-7999
Explicit solvation of a single-stranded DNA, a binding protein, and their complex: A suitable protocol for fragment molecular orbital calculation Peer-reviewed

Komeiji, Y., Okiyama, Y., Mochizuki, Y., Fukuzawa, K.

Chem-Bio Informatics Journal　17　(0)　72-84　2017
Publisher: Chem-Bio Informatics Society
DOI： 10.1273/cbij.17.72 　

ISSN： 1347-0442
Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning Peer-reviewed

Yuji MOCHIZUKI, Kota SAKAKURA, Yoshinobu AKINAGA, Kouichiro KATO, Hiromasa WATANABE, Yoshio OKIYAMA, Tatsuya NAKANO, Yuto KOMEIJI, Akira OKUSAWA, Kaori FUKUZAWA, Shigenori TANAKA

Journal of Computer Chemistry, Japan　16　(5)　119-122　2017
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2017-0051 　

ISSN： 1347-1767
FMOプログラムABINIT-MPの開発状況と機械学習との連携 Peer-reviewed

望月祐志, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人, 奥沢明, 福澤薫, 田中成典

J. Comp. Chem. Jpn.　16　119-122　2017
A new solvate of epalerstat, a drug for diabetic neuropathy Peer-reviewed

Okky Dwichandra Putra, Daiki Umeda, Kaori Fukuzawa, Mihoko Gunji, Etsuo Yonemochi

Acta Crystallographica Section E: Crystallographic Communications　73　1264-1267　2017

DOI： 10.1107/S2056989017010751 　

ISSN： 2056-9890

eISSN： 2056-9890
Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation Peer-reviewed

Komeiji Yuto, Okiyama Yoshio, Mochizuki Yuji, Fukuzawa Kaori

CHEM-BIO INFORMATICS JOURNAL　17　72-84　2017

DOI： 10.1273/cbij.17.72 　

ISSN： 1347-6297
A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA) Peer-reviewed

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry　18　(0)　143-148　2017

DOI： 10.2751/jcac.18.143 　

ISSN： 1345-8647
Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method Peer-reviewed

Kana Tokuda, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　69　144-153　2016/09

DOI： 10.1016/j.jmgm.2016.08.004 　

ISSN： 1093-3263

eISSN： 1873-4243
Fragment Molecular Orbital (FMO) Calculations of Peptoids Peer-reviewed

KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori

Journal of Computer Chemistry, Japan　15　(3)　51-52　2016
Publisher: Society of Computer Chemistry, Japan
DOI： 10.2477/jccj.2016-0032 　

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Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.
Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy Peer-reviewed

Masataka SAKAGUCHI, Yuji MOCHIZUKI, Chiduru WATANABE, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan　14　(5)　155-163　2015/12/03
Publisher: Journal of Computer Chemistry, Japan
DOI： 10.2477/jccj.2015-0033 　

ISSN： 1347-3824
Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein-ligand complexes and extended clustering techniques Peer-reviewed

Ryo Kurauchi, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

COMPUTATIONAL AND THEORETICAL CHEMISTRY　1061　12-22　2015/06

DOI： 10.1016/j.comptc.2015.02.016 　

ISSN： 2210-271X

eISSN： 1872-7999
Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method Peer-reviewed

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

CHEMICAL PHYSICS LETTERS　629　58-64　2015/06

DOI： 10.1016/j.cplett.2015.03.057 　

ISSN： 0009-2614

eISSN： 1873-4448
Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method Peer-reviewed

Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

Computational and Theoretical Chemistry　1054　29-37　2015/02

DOI： 10.1016/j.comptc.2014.11.020 　

ISSN： 2210-271X
Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems Peer-reviewed

Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan　14　(1)　1-9　2015
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2014-0039 　

ISSN： 1347-1767

eISSN： 1347-3824
フラグメント分子軌道法を用いたspin-component-scaled MP2法に基づくタンパク－リガンド相互作用クラスター解析

Shinji Amari, Yuji Mochizuki, Akifumi Kato, Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Tatsuya Nakano

2　(4)　17-25　2014/11/30
Publisher:
ISSN： 2189-7069
インシリコ創薬におけるFMO法と周辺基盤技術の進歩 Invited

福澤薫

SAR News No.27　2014/10
Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change Peer-reviewed

Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　53　48-58　2014/09

DOI： 10.1016/j.jmgm.2014.07.004 　

ISSN： 1093-3263

eISSN： 1873-4243
Charge Clamps of Lysines and Hydrogen Bonds Play Key Roles in the Mechanism to Fix Helix 12 in the Agonist and Antagonist Positions of Estrogen Receptor alpha: Intramolecular Interactions Studied by the Ab Initio Fragment Molecular Orbital Method Peer-reviewed

Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Sachiko Aida-Hyugaji

JOURNAL OF PHYSICAL CHEMISTRY B　118　(19)　4993-5008　2014/05

DOI： 10.1021/jp411627y 　

ISSN： 1520-6106
Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy Peer-reviewed

Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji

COMPUTATIONAL AND THEORETICAL CHEMISTRY　1034　7-16　2014/04

DOI： 10.1016/j.comptc.2014.02.002 　

ISSN： 2210-271X

eISSN： 1872-7999
Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems Peer-reviewed

Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　16　(22)　10310-10344　2014

DOI： 10.1039/c4cp00316k 　

ISSN： 1463-9076

eISSN： 1463-9084
Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations Peer-reviewed

Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki

Chemical Physics Letters　566　25-31　2013/04

DOI： 10.1016/j.cplett.2013.02.020 　

ISSN： 0009-2614
Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design Peer-reviewed

Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　41　31-42　2013/04

DOI： 10.1016/j.jmgm.2013.01.006 　

ISSN： 1093-3263
Device, system, method and program for producing fragment model Peer-reviewed

Mochizuki Yuji, Tsukamoto Takayuki, Fukuzawa Kaori

2013/03
Publisher: Google Patents

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US Patent App. 14/442,321
ABINIT-MP/BioStation によるFMO 法の創薬への適用 Invited Peer-reviewed

福澤薫, 渡邉千鶴

CICSJ Bulletin　31　(4)　89-89　2013
Publisher: 公益社団法人日本化学会・情報化学部会
DOI： 10.11546/cicsj.31.89 　

ISSN： 0913-3747
フラグメント分子軌道法によるインフルエンザウイルス表面タンパク質の大規模量子化学計算 Invited

福澤薫, 望月祐志, 中野達也, 田中成典

CBI学会誌　2013
Structure-based drug designを指向した新規フラグメント分割法に基づく4体補正フラグメント分子軌道(FMO4)計算 Invited

渡邉千鶴, 福澤薫, 沖山佳生, 望月祐志, 塚本貴志, 加藤昭史, 田中成典, 中野達也

CBI学会誌　1　(1)　2013

ISSN： 2189-7069
Interaction energy calculation system, method and program Peer-reviewed

Nakano Tatsuya, Mochizuki Yuji, Fukuzawa Kaori

2012/08
Publisher: Google Patents

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US Patent App. 14/356,744
Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage Peer-reviewed

Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano

CHEMICAL PHYSICS LETTERS　535　157-162　2012/05

DOI： 10.1016/j.cplett.2012.03.046 　

ISSN： 0009-2614

eISSN： 1873-4448
New fragmentation of fragment molecular orbital method applicable to fragment based drug design Peer-reviewed

Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji

2012
Continuous multipole methodによるfragment molecular orbital法の高速化

中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 渡邊千鶴, 福澤薫, 田中成典, 望月祐志

44-50　2012

DOI： 10.2751/jcac.13.44 　
Development of the four-body corrected fragment molecular orbital (FMO4) method Peer-reviewed

Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka

Chemical Physics Letters　523　128-133　2012/01

DOI： 10.1016/j.cplett.2011.12.004 　

ISSN： 0009-2614
Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation Peer-reviewed

Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS　130　(4-6)　1197-1202　2011/12

DOI： 10.1007/s00214-011-1048-z 　

ISSN： 1432-881X
Higher-order correlated calculations based on fragment molecular orbital scheme Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS　130　(2-3)　515-530　2011/10

DOI： 10.1007/s00214-011-1036-3 　

ISSN： 1432-881X

eISSN： 1432-2234
Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations Peer-reviewed

Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　30　110-119　2011/09

DOI： 10.1016/j.jmgm.2011.06.011 　

ISSN： 1093-3263
Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme Peer-reviewed

Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters　509　(1-3)　67-71　2011/06

DOI： 10.1016/j.cplett.2011.04.070 　

ISSN： 0009-2614
Sialic Acid Recognition of the Pandemic Influenza 2009 H1N1 Virus: Binding Mechanism Between Human Receptor and Influenza Hemagglutinin Peer-reviewed

Kaori Fukuzawa, Katsumi Omagari, Katsuhisa Nakajima, Eri Nobusawa, Shigenori Tanaka

PROTEIN AND PEPTIDE LETTERS　18　(5)　530-539　2011/05

DOI： 10.2174/092986611794927893 　

ISSN： 0929-8665
Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM　962　(1-3)　45-55　2010/12

DOI： 10.1016/j.theochem.2010.09.013 　

ISSN： 0166-1280
Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA) Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters　493　(4-6)　346-352　2010/06

DOI： 10.1016/j.cplett.2010.05.034 　

ISSN： 0009-2614
Theoretical Analysis of the Molecular Mechanism of Stabilization of Nova-RNA Complex System: Fragment Molecular Orbital Method Based Quantum Chemical Calculation For the Effect of the Complex Formation on the Electronic State of Biomacromolecular System Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL JOURNAL　98　(3)　74A-74A　2010/01

DOI： 10.1016/j.bpj.2009.12.419 　

ISSN： 0006-3495
Accuracy of fragmentation in ab initio calculations of hydrated sodium cation Peer-reviewed

Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　478　(4-6)　295-300　2009/08

DOI： 10.1016/j.cplett.2009.07.060 　

ISSN： 0009-2614

eISSN： 1873-4448
Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy Peer-reviewed

Toshio Watanabe, Yuichi Inadomi, Hiroaki Umeda, Kaori Fukuzawa, Shigenori Tanaka, Tatsuya Nakano, Umpei Nagashima

JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE　6　(6)　1328-1337　2009/06

DOI： 10.1166/jctn.2009.1182 　

ISSN： 1546-1955

eISSN： 1546-1963
Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding Peer-reviewed

Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　113　(15)　4991-4994　2009/04

DOI： 10.1021/jp810997c 　

ISSN： 1520-6106
Developments of FMO methodology and graphical user interface in ABINIT-MP Peer-reviewed

Nakano Tatsuya, Mochizuki Yuji, Kato Akifumi, Fukuzawa Kaori, Ishikawa Takeshi, Amari Shinji, Kurisaki Ikuo, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems　37-62　2009
Publisher: CRC Press: Boca Raton, FL
DOI： 10.1201/9781420078497-6 　
Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method Peer-reviewed

Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya

Annual Report of the Earth Simulator Center April　2010　2009
7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules Peer-reviewed

Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems　133-169　2009
Publisher: CRC Press
DOI： 10.1201/9781420078497-10 　
3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (Protein: Function, 2SP6 Towards Supercomputiong for Electronic Structures of Biological Peer-reviewed

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　49　(supplement)　S161　2009
Publisher: The Biophysical Society of Japan General Incorporated Association
2SP6-07 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules, The Peer-reviewed

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　49　(supplement)　S15　2009
Publisher: The Biophysical Society of Japan General Incorporated Association
Discovery of boron-conjugated 4-anilinoquinazoline as a prolonged inhibitor of EGFR tyrosine kinase Peer-reviewed

Hyun Seung Ban, Taikou Usui, Wataru Nabeyama, Hidetoshi Morita, Kaori Fukuzawa, Hiroyuki Nakamura

ORGANIC & BIOMOLECULAR CHEMISTRY　7　(21)　4415-4427　2009

DOI： 10.1039/b909504g 　

ISSN： 1477-0520
Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits) Peer-reviewed

Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　113　(4)　1153-1161　2009/01

DOI： 10.1021/jp808151c 　

ISSN： 1520-6106

eISSN： 1520-5207
Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations Peer-reviewed

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

Chemical Physics Letters　467　(4-6)　417-423　2009/01

DOI： 10.1016/j.cplett.2008.11.044 　

ISSN： 0009-2614
Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission Peer-reviewed

Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　112　(38)　12081-12094　2008/09

DOI： 10.1021/jp803369x 　

ISSN： 1520-6106
COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY　236　2008/08

ISSN： 0065-7727
Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method Peer-reviewed

Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

COMPUTATIONAL BIOLOGY AND CHEMISTRY　32　(3)　198-211　2008/06

DOI： 10.1016/j.compbiolchem.2008.03.006 　

ISSN： 1476-9271
Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site? Peer-reviewed

Bryan M. B. VanSchouwen, Heather L. Gordon, Stuart M. Rothstein, Yuto Komeiji, Kaori Fukuzawa, Shigenori Tanaka

COMPUTATIONAL BIOLOGY AND CHEMISTRY　32　(3)　149-158　2008/06

DOI： 10.1016/j.compbiolchem.2008.01.001 　

ISSN： 1476-9271

eISSN： 1476-928X
Large scale FMO-MP2 calculations on a massively parallel-vector computer Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　457　(4-6)　396-403　2008/05

DOI： 10.1016/j.cplett.2008.03.090 　

ISSN： 0009-2614
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; Part II: Influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions Peer-reviewed

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY A　112　(10)　1986-1998　2008/03

DOI： 10.1021/jp075430r 　

ISSN： 1089-5639
Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery Peer-reviewed

Bernhard Fischer, Kaori Fukuzawa, Wolfgang Wenzel

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　70　(4)　1264-1273　2008/03

DOI： 10.1002/prot.21607 　

ISSN： 0887-3585
Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL CHEMISTRY　130　(1-2)　1-9　2007/10

DOI： 10.1016/j.bpc.2007.06.011 　

ISSN： 0301-4622
Intra- and intermolecular interactions between Cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (vol 27, pg 948, 2006) Peer-reviewed

Kaori Fukuzawa, Yuto Komeiji, Yujj Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF COMPUTATIONAL CHEMISTRY　28　(13)　2237-2239　2007/10

DOI： 10.1002/jcc.20803 　

ISSN： 0192-8651
DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations Peer-reviewed

Toshio Watanabe, Yuichi Inadomi, Kaori Fukuzawa, Tatsuya Nakano, Shigenori Tanaka, Lennart Nilsson, Umpei Nagashima

JOURNAL OF PHYSICAL CHEMISTRY B　111　(32)　9621-9627　2007/08

DOI： 10.1021/jp071710v 　

ISSN： 1520-6106
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism Peer-reviewed

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　111　(13)　3525-3533　2007/04

DOI： 10.1021/jp070054w 　

ISSN： 1520-6106
Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948)) Peer-reviewed

Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.

Journal of Computational Chemistry　28　(13)　2007

DOI： 10.1002/jcc.20803 　
2P058 Theoretical study on the sequence specific recognition mechanism of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method (Proteins-structure and structure-function relationship, Poster Presentations) Peer-reviewed

Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　47　(supplement)　S127　2007
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.47.S127_3 　
Comparison of epitope structures of H3HAs through protein modeling of influenza a virus hemagglutinin: Mechanism for selection of antigenic variants in the presence of a monoclonal antibody Peer-reviewed

Setsuko Nakajima, Katsuhisa Nakajima, Eri Nobusawa, Jin Zhao, Shigenori Tanaka, Kaori Fukuzawa

MICROBIOLOGY AND IMMUNOLOGY　51　(12)　1179-1187　2007

DOI： 10.1111/j.1348-0421.2007.tb04013.x 　

ISSN： 0385-5600
Application of the fragment molecular orbital method for determination of atomic charges on polypeptides Peer-reviewed

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina

Chemical Physics Letters　449　(4-6)　329-335　2007

DOI： 10.1016/j.cplett.2007.10.066 　

ISSN： 0009-2614
Effects of Point Mutations on the Binding Energies of Estrogen Receptor with Estradiol Peer-reviewed

K. Maeda, A. Schug, H. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka

J. Comput. Chem. Jpn.　6　(1)　33-46　2007
Publisher: 日本コンピュータ化学会
DOI： 10.2477/jccj.6.33 　

ISSN： 1347-1767

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We have studied the molecular mechanism for the binding between estrogen receptor and estradiol using ab initio methods. To examine the validity of in silico analysis of mutation effects, we made point mutations of receptor employed in experiments, and compared the calculated results for the binding energies with experimental data. We performed the calculations at the HF/STO-3G and MP2/STO-3G levels by using the Fragment Molecular Orbital (FMO) method. The calculated results for three of six mutants qualitatively agreed with experimental data. However, the other three examples failed to reproduce the experimental data. We discussed the reasons for these discrepancies.
Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules Invited

FUKUZAWA Kaori, NAKANO Tatsuya, KATO Akifumi, MOCHIZUKI Yuji, TANAKA Shigenori

Journal of Chemical Software　6　(3)　185-198　2007
Publisher: Society of Computer Chemistry, Japan
DOI： 10.2477/jccj.6.185 　

ISSN： 1347-1767

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This review introduces the application of the Fragment molecular orbital (FMO) method. The ABINIT-MP and BioStation Viewer programs have been used for such applications. The FMO method was applied for problems of transcriptional regulation, including interactions of nuclear receptor, ligand, transcription factor, and DNA. Detailed interactions between biomolecules and the roles of each amino acid residue were revealed through analyses of inter-fragment interaction energy (IFIE), charge distribution, and orbital configuration. Electrostatic and van der Waals dispersion interactions were found to be equally important in molecular recognition. It was found that the inclusion of electron correlation was essential to obtain appropriate pictures. Other applications such as the photo-excitation process are also introduced.
Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field Invited

NAKANO Tatsuya, MOCHIZUKI Yuji, AMARI Shinji, KOBAYASHI Masato, FUKUZAWA Kaori, TANAKA Shigenori

Journal of Computer Chemistry, Japan　6　(3)　173-184　2007
Publisher: Society of Computer Chemistry, Japan
DOI： 10.2477/jccj.6.173 　

ISSN： 1347-1767

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Kitaura et al. (Chem. Phys. Lett. 312, 319-324 (1999)) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the ab initio FMO method, a molecule or a molecular cluster is divided into fragments, and the MO calculations on the fragments (monomers) and the fragment pairs (dimers) are performed to obtain the total energy that is expressed as a summation of the fragment energies and inter-fragment interaction energies (IFIEs). In this paper, we provide a brief description of the ab initio FMO method and demonstrate recent applications in the nano-bio field.
フラグメント分子軌道法プログラムABINIT-MPによる受容体－リガンド相互作用解析 Invited

福澤薫, 中野達也

CBI学会ソリューションガイドモノグラフ「構造に基づく薬の設計法（SBDD）の進歩」＋ソリューションガイド　2007
Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006) Peer-reviewed

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B　110　(47)　24276-24276　2006/11

DOI： 10.1021/jp065705n 　

ISSN： 1520-6106
Advanced scientific computational methods and their applications to nuclear technologies - (6) Simulation methods in discretized systems, (2) Peer-reviewed

Seiichi Koshizuka, Kiyoshi Matsubara, Kaori Fukuzawa

JOURNAL OF THE ATOMIC ENERGY SOCIETY OF JAPAN　48　(9)　684-689　2006/09

DOI： 10.3327/jaesj.48.684 　

ISSN： 0004-7120
Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method Peer-reviewed

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B　110　(32)　16102-16110　2006/08

DOI： 10.1021/jp060770i 　

ISSN： 1520-6106
Fragment molecular orbital calculations on large scale systems containing heavy metal atom Peer-reviewed

Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

CHEMICAL PHYSICS LETTERS　427　(1-3)　159-165　2006/08

DOI： 10.1016/j.cplett.2006.06.103 　

ISSN： 0009-2614
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study Peer-reviewed

K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

JOURNAL OF COMPUTATIONAL CHEMISTRY　27　(8)　948-960　2006/06

DOI： 10.1002/jcc.20399 　

ISSN： 0192-8651
Drug discovery using grid technology Peer-reviewed

Hitoshi Goto, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada, Hiroshi Chuman

Modern Methods for Theoretical Physical Chemistry of Biopolymers　227-248　2006

DOI： 10.1016/B978-044452220-7/50076-9 　
Developments and applications of ABINIT-MP software based on the fragment molecular orbital method Peer-reviewed

Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

Modern Methods for Theoretical Physical Chemistry of Biopolymers　39-52　2006
Publisher: Elsevier
DOI： 10.1016/B978-044452220-7/50066-6 　
VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening Peer-reviewed

S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano

JOURNAL OF CHEMICAL INFORMATION AND MODELING　46　(1)　221-230　2006/01

DOI： 10.1021/ci050262q 　

ISSN： 1549-9596
量子化学計算（FMO法） Invited

中野達也, 望月祐志, 甘利真司, 福澤薫

東京大学情報基盤センター・スーパーコンピューティングニュース　2006
分子軌道法 Invited

松原聖, 福澤薫

原子力学会誌　2006
BioStation Viewer: Analysis and Visualization for Interactions of Bio-Macromolecules Invited

KATO Akifumi, FUKUZAWA Kaori, MOCHIZUKI Yuji, AMARI Shinji, NAKANO Tatsuya

Transactions of Visualization Society of Japan　26　(101)　124-129_1　2006
Publisher: The Visualization Society of Japan
DOI： 10.3154/jvs.26.124 　

ISSN： 0916-4731
1A configuration analysis for fragment interaction Peer-reviewed

Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS　410　(4-6)　247-253　2005/07

DOI： 10.1016/j.cplett.2005.05.079 　

ISSN： 0009-2614
Numerical methodology of sodium-water reaction with multiphase flow analysis Peer-reviewed

T Takata, A Yamaguchi, K Fukuzawa, K Matsubara

NUCLEAR SCIENCE AND ENGINEERING　150　(2)　221-236　2005/06

DOI： 10.13182/NSE05-A2511 　

ISSN： 0029-5639
Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands

FUKUZAWA, MOCHIZUKI, TANAKA, AMARI, KITAURA, AND, Nakano

Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa)　ES-P23,　2005
Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: An application of fragment molecular orbital method Peer-reviewed

K Fukuzawa, K Kitaura, M Uebayasi, K Nakata, T Kaminuma, T Nakano

JOURNAL OF COMPUTATIONAL CHEMISTRY　26　(1)　1-10　2005/01

DOI： 10.1002/jcc.20130 　

ISSN： 0192-8651
量子化学計算でみるエストロゲン受容体と化学物質の相互作用 Invited

福澤薫

バイオニクス　2　(7)　65-67　2005
Publisher: オーム社
ISSN： 1349-9343
Ab initio potential energy surfaces of the ion-molecule reaction: C2H2+O+ Peer-reviewed

K Fukuzawa, T Matsushita, K Morokuma

JOURNAL OF CHEMICAL PHYSICS　121　(7)　3117-3129　2004/08

DOI： 10.1063/1.1769360 　

ISSN： 0021-9606
非経験的フラグメント分子軌道法によるエストロゲン受容体とリガンドとの結合性予測 Invited

長嶋雲兵, 福澤薫, 中野達也

ファインケミカル　33　(4)　44-52　2004
Publisher: シーエムシー出版
ISSN： 0913-6150
Fragment molecular orbital study of the binding energy of ligands to the estrogen receptor Invited Peer-reviewed

K Fukuzawa, K Kitaura, K Nakata, T Kaminuma, T Nakano

PURE AND APPLIED CHEMISTRY　75　(11-12)　2405-2410　2003/11

DOI： 10.1351/pac200375112405 　

ISSN： 0033-4545
Fragment molecular orbital method: application to molecular dynamics simulation, 'ab initio FMO-MD' Peer-reviewed

Y Komeiji, T Nakano, K Fukuzawa, Y Ueno, Y Inadomi, T Nemoto, M Uebaysai, DG Fedorov, K Kitaura

CHEMICAL PHYSICS LETTERS　372　(3-4)　342-347　2003/04

DOI： 10.1016/S0009-2614(03)00430-5 　

ISSN： 0009-2614
DNA鎖の第一原理計算の現状と将来 Invited

田中成典, 福澤薫, 中野達也, 栗田典之

表面科学　2003

DOI： 10.1380/jsssj.24.664 　
Fragment molecular orbital method: use of approximate electrostatic potential Peer-reviewed

T Nakano, T Kaminuma, T Sato, K Fukuzawa, Y Akiyama, M Uebayasi, K Kitaura

CHEMICAL PHYSICS LETTERS　351　(5-6)　475-480　2002/01

DOI： 10.1016/S0009-2614(01)01416-6 　

ISSN： 0009-2614
An ab initio and experimental study of vibrational effects in low energy O++C2H2 charge-transfer collisions Peer-reviewed

K Fukuzawa, T Matsushita, K Morokuma, DJ Levandier, YH Chiu, RA Dressler, E Murad, A Midey, S Williams, AA Viggiano

JOURNAL OF CHEMICAL PHYSICS　115　(7)　3184-3194　2001/08

DOI： 10.1063/1.1385793 　

ISSN： 0021-9606
Ion-molecule reactions producing HC3NH+ in interstellar space: Forbiddenness of the reaction between cyclic C3H3+ and the N atom Peer-reviewed

N Takagi, K Fukuzawa, Y Osamura, HF Schaefer

ASTROPHYSICAL JOURNAL　525　(2)　791-798　1999/11

ISSN： 0004-637X
A molecular orbital study of the HC3NH+ + e(-) dissociative recombination and its role in the production of cyanoacetylene isomers in interstellar clouds Peer-reviewed

Y Osamura, K Fukuzawa, R Terzieva, E Herbst

ASTROPHYSICAL JOURNAL　519　(2)　697-704　1999/07

ISSN： 0004-637X
Are neutral-neutral reactions effective for the carbon-chain growth of cyanopolyynes and polyacetylenes in interstellar space? Peer-reviewed

K Fukuzawa, Y Osamura, HF Schaefer

ASTROPHYSICAL JOURNAL　505　(1)　278-285　1998/09

DOI： 10.1086/306168 　

ISSN： 0004-637X

eISSN： 1538-4357
Molecular orbital study of neutral-neutral reactions concerning HC3N formation in interstellar space Peer-reviewed

K Fukuzawa, Y Osamura

ASTROPHYSICAL JOURNAL　489　(1)　113-121　1997/11

DOI： 10.1086/304782 　

ISSN： 0004-637X

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Misc. 66

Interaction analysis between β-cyclodextrin and ibuprofen enantiomers using experimental methods and molecular simulations.

古石誉之, 古石誉之, 伊野希, 奥脇弘次, 池上眞由美, 遠藤朋宏, 米持悦生, 米持悦生, 福澤薫

シクロデキストリンシンポジウム講演要旨集　40th　2024
COMT-Ligand Molecular Interactions Based on Crystal Structures and Quantum Chemical Calculations

福澤薫, 福澤薫, 白井智子, 武部克希, 高谷大輔, 飯島洋, 飯島洋

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Interaction Analysis Between Xanthine Oxidoreductase and Inhibitors Using the Fragment Molecular Orbital Calculation

TIAN Yu-Shi, MARTIN, MARTIN, NASUTION Mochammad Arfin Fardiansyah, 高谷大輔, 水口賢司, 水口賢司, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
実験及び計算手法を併用したEudragit Eによる薬物可溶化機構の解明

齊藤智輝, 植田圭祐, 東顕二郎, 奥脇弘次, 奥脇弘次, 古石誉之, 福澤薫, 米持悦生, 森部久仁一

日本薬剤学会年会講演要旨集(CD-ROM)　39th　2024
トルブタミドとメグルミンからなるイオン液体含有口腔内崩壊フィルム製剤の設計

古石誉之, 土井優月, 井上元基, 福澤薫, 米持悦生

日本薬剤学会年会講演要旨集(CD-ROM)　39th　2024
Study of novel inhibitors of m-Glu5 using fragment molecular orbital method

小田島大貴, 宮川柊兵, 半田佑磨, 古石誉之, 米持悦生, 佐藤朋広, 幸瞳, 本間光貴, 高谷大輔, 上村みどり, 上村みどり, 福澤薫, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Molecular dynamics and quantum chemical calculations for the RNA sequence specificity of eIF4A inhibitors

半田佑磨, 半田佑磨, 斉藤大寛, 斉藤大寛, 奥脇弘次, 古石誉之, 米持悦生, 加藤幸一郎, 渡邉千鶴, 本間光貴, 伊藤拓宏, 岩崎信太郎, 岩崎信太郎, 福澤薫, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Application of computational chemistry to the evaluation of molecular states and intermolecular interactions of drugs in tocophersolan solid dispersions

米持悦生, 小林千夏, 奥脇弘次, 古石誉之, 東顕二郎, 山下雄史, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Structure and interaction analysis of ssPalm lipid nanoparticle containing nucleic acids using molecular simulation

小浪なおこ, 佐々木香純, 奥脇弘次, 奥脇弘次, 奥脇弘次, 田中浩揮, 秋田英万, 古石誉之, 福澤薫, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Drug Solubilizing Ability of Ionic Liquids Composed of Citric Acid and Arginine

田中菜緒, 岡部華奈, 古石誉之, 山下雄史, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Crystal structure analysis of novel complexes of Famotidine and Saccharin

市川高弘, LI Ye, 古石誉之, 山下雄史, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Characterization of ionizable lipid nanoparticles by experimental methods and molecular simulations

小倉由未佳, 奥脇弘次, 古石誉之, 山下雄史, 福澤薫, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Analysis of PI5P4Kβ: Elucidation of GTP specificity by computational approach

宮川柊兵, 奥脇弘次, 奥脇弘次, 奥脇弘次, 古石誉之, 米持悦生, 千田美紀, 千田俊哉, 竹内恒, 福澤薫, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Molecular dynamic simulation and fragment molecular orbital methods on the moecular complex of norephedrine enantiomers with β-cyclodextrin

古石誉之, 奈良友里衣, 遠藤朋宏, 奥脇弘次, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Molecular design based on interaction analysis between IL-10 receptor complexes using FMO calculations

上村憲汰, 半田佑磨, 半田佑磨, 宮岸澄真, 古石誉之, 米持悦生, 遠藤真弓, 上村みどり, TIAN Yushi, 高谷大輔, 福澤薫, 福澤薫

日本薬学会年会要旨集(Web)　144th　2024

ISSN： 0918-9823
Structure and interaction analysis of complexes between BzDANP and bulged RNAs using NMR and dynamical FMO calculation

OHNO Shu, FUJIWARA Aina, KAWAI Gota, NAKATANI Kazuhiko, HANDA Yuma, HANDA Yuma, TIAN Yu-Shi, TAKAYA Daisuke, FUKUZAWA Kaori

CBI学会大会(CD-ROM)　2023　2023
Interaction analysis of IL-10 receptor complex using MD and FMO calculations

MIYAGISHI Toma, KAMIMURA Kenta, HANDA Yuma, HANDA Yuma, TAKIMOTO-KAMIMURA Midori, TAKIMOTO-KAMIMURA Midori, ENDO Mayumi, OKUWAKI Koji, MORI Yoshiharu, TANAKA Shigenori, TIAN Yu-Shi, TAKAYA Daisuke, FUKUZAWA Kaori

CBI学会大会(CD-ROM)　2023　2023
Applicabilities of Neural Network Potential to Predict ligand-RNA Interactions

ASANO Hiroto, MATSUMOTO Hiromu, OHNO Shu, HANDA Yuma, HANDA Yuma, HATABU Asuka, TAKAYA Daisuke, IKEDA Kenji, TIAN Yu-Shi, FUKUZAWA Kaori, KATO Koichiro

CBI学会大会(CD-ROM)　2023　2023
Computational Interaction analysis between Interleukin-10 and Interleukin-10 receptor Using the Fragment Molecular Orbital Method

KAMIMURA Kenta, HANDA Yuma, HANDA Yuma, FURUISHI Takayuki, YONEMOTI Etuto, TIAN Yu-shi, TAKAYA Daisuke, FUKUZAWA Kaori, FUKUZAWA Kaori, MIYAGISHI Toma, TAKIMOTO-KAMIMURA Midori, ENDO Mayumi

CBI学会大会(CD-ROM)　2023　2023
フラグメント分子軌道法を活用した代謝型グルタミン酸受容体5阻害剤の分子設計

小田島大貴, 宮川柊兵, 半田佑磨, 古石誉之, 米持悦生, 佐藤朋広, 幸瞳, 本間光貴, 高谷大輔, 上村みどり, 上村みどり, 福澤薫, 福澤薫

構造活性相関シンポジウム講演要旨集(CD-ROM)　51st　2023
分子動力学法を用いたトコフェルソラン固体分散体中の薬物の分散状態および分子間相互作用の評価

小林千夏, 奥脇弘次, 古石誉之, 東顕二郎, 山下雄史, 福澤薫, 福澤薫, 米持悦生

日本薬学会関東支部大会講演要旨集(CD-ROM)　67th　2023
ファモチジンの新規複合体作製と計算科学を用いた安定性の評価

市川高弘, LI Ye, 古石誉之, 福澤薫, 福澤薫, 山下雄史, 米持悦生

日本薬学会関東支部大会講演要旨集(CD-ROM)　67th　2023
クエン酸とアルギニンによるイオン液体の作製と薬物可溶化能評価

田中菜緒, 岡部華奈, 古石誉之, 山下雄史, 福澤薫, 福澤薫, 米持悦生

日本薬学会関東支部大会講演要旨集(CD-ROM)　67th　2023
分子動力学計算を用いたEudragit Eによる薬物可溶化機構の解明

齊藤智輝, 植田圭祐, 東顕二郎, 奥脇弘次, 古石誉之, 福澤薫, 福澤薫, 米持悦生, 森部久仁一

日本薬学会関東支部大会講演要旨集(CD-ROM)　67th　2023
Structure and interaction evaluation of ssPalm lipid nanoparticle using computational chemistry

小浪なおこ, 氏家かれん, 佐々木香純, 奥脇弘次, 田中浩揮, 秋田英万, 古石誉之, 福澤薫, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　143rd　2023

ISSN： 0918-9823
Application of in silico simulation to evaluation of hygroscopic behavior of solid dispersion formulations

米持悦生, 松本穂香, 奥脇弘次, 古石誉之, 福澤薫, 福澤薫

日本薬学会年会要旨集(Web)　143rd　2023

ISSN： 0918-9823
Characterization of lipid nanoparticle-nucleic acid complexes by experimental methods and molecular simulations

佐々木香純, 奥脇弘次, 古石誉之, 東顕二郎, 福澤薫, 福澤薫, 米持悦生

日本薬学会年会要旨集(Web)　143rd　2023

ISSN： 0918-9823
処方設計への応用に向けた計算科学を用いたイオン性脂質ナノ粒子の構造予測

小倉由未佳, 奥脇弘次, 古石誉之, 山下雄史, 米持悦生, 福澤薫

製剤と粒子設計シンポジウム講演要旨集　40th　2023
Molecular dynamic simulation and fragment molecular orbital methods on the inclusion complexation of norephedrine enantiomers with β-cyclodextrin

奈良友里衣, 古石誉之, 奥脇弘次, 遠藤朋宏, 福澤薫, 福澤薫, 米持悦生

シクロデキストリンシンポジウム講演要旨集　39th　2023
イオン化脂質のプロトン化による脂質ナノ粒子の構造変化に関する研究

小倉由未佳, 奥脇弘次, 古石誉之, 福澤薫, 米持悦生

日本DDS学会学術集会プログラム予稿集　39th　2023
トルブタミドとメグルミンからなるイオン液体含有口腔内崩壊フィルム製剤の開発

古石誉之, 古石誉之, 土井優月, 福澤薫, 米持悦生

日本DDS学会学術集会プログラム予稿集　39th　2023
Structural evaluation of ionizable lipid nanoparticles using experimental methods and molecular simulations

小倉由未佳, 奥脇弘次, 古石誉之, 福澤薫, 米持悦生

日本薬剤学会年会講演要旨集(CD-ROM)　38th　2023
Citric acid/Arginine ionic liquid: Characterization and drug solubilization

古石誉之, 岡部華奈, 田中菜緒, 福澤薫, 米持悦生

日本薬剤学会年会講演要旨集(CD-ROM)　38th　2023
Mechanism of functional expression and conditions for formulation optimization of molecular complexes of arginine and asparagine as binder for formulation

加藤里佳, 佐藤瑠莉, 村松駿, 古石誉之, 福澤薫, 米持悦生

日本薬剤学会年会講演要旨集(CD-ROM)　38th　2023
インシリコスクリーニング(LBDD)のための最近のフィンガープリントの性能検討

高谷大輔, 田雨時, 福澤薫

構造活性相関シンポジウム講演要旨集(CD-ROM)　50th　2022
実験手法と分子シミュレーションを用いた脂質ナノ粒子-核酸複合体の構造解析に基づく処方設計

佐々木香純, 奥脇弘次, 古石誉之, 米持悦生, 福澤薫, 東顕二郎

製剤と粒子設計シンポジウム講演要旨集　39th　2022
Ready-to-Use型mRNA内封脂質ナノ粒子製剤の物性評価

山川拓真, 田中浩揮, 萩原伸哉, 櫻井遊, 佐々木香純, 米持悦生, 福澤薫, 中井悠太, 丹下耕太, 秋田英万, 秋田英万

遺伝子・デリバリー研究会シンポジウム要旨集　21st (CD-ROM)　2022
Development of Ready-to-Use type LNPs

田中浩揮, 萩原伸哉, 山川拓真, 櫻井遊, 米持悦生, 福澤薫, 中井悠太, 丹下耕太, 秋田英万, 秋田英万

日本核酸医薬学会年会講演要旨集(CD-ROM)　7th　2022
Evaluation of Physical Properties of Ready-to-Use Formulations of Lipid Nanoparticles Enclosed in mRNA

山川拓真, 田中浩揮, 萩原伸哉, 櫻井遊, 佐々木香純, 米持悦生, 福澤薫, 中井悠太, 丹下耕太, 秋田英万, 秋田英万

日本核酸医薬学会年会講演要旨集(CD-ROM)　7th　2022
Study of structural change mechanism of RNA-containing nanoparticles

米持悦生, 古石誉之, 福澤薫

KEK Progress Report (Web)　(2022-5)　2022

ISSN： 1344-6320
FMO計算を用いたIL10-IL10受容体複合体間の相互作用解析

上村憲汰, 半田佑磨, 古石誉之, 米持悦生, 上村みどり, 遠藤真弓, 田雨時, 高谷大輔, 福澤薫, 福澤薫

日本薬学会関東支部大会講演要旨集　66th (CD-ROM)　2022
セラミドの立体配置が角層細胞間脂質の構造変化に及ぼす影響

荒井梨絵, 古石誉之, 福澤薫, 米持悦生, 小幡誉子, 石田賢哉

日本薬学会関東支部大会講演要旨集　66th (CD-ROM)　2022
リポプレックス生成過程における脂質二重膜に及ぼすCholesterolの影響

田中渓, 佐々木香純, 古石誉之, 福澤薫, 福澤薫, 米持悦生

日本薬学会関東支部大会講演要旨集　66th (CD-ROM)　2022
FMODBデータ収集:高分解能X線結晶構造データに対する量子化学計算

渡邉千鶴, 渡邉千鶴, 神坂紀久子, 今井恭平, 滝本大地, 斎藤涼祐, 栗田典之, 岡山友樹, 宮嶋起徳, 吉本耀, 原田一真, 川下理日人, 藤井真靖, 森義治, 田中成典, 本間光貴, 福澤薫

日本蛋白質科学会年会プログラム・要旨集　22nd (Web)　2022
FMO法を用いたSARS-CoV-2メインプロテアーゼ-阻害薬S-217622結合メカニズムの解明

渡邉千鶴, 田中成典, 沖山佳生, 大山達也, 神坂紀久子, 幸瞳, 高谷大輔, 福澤薫, 本間光貴

構造活性相関シンポジウム講演要旨集　50th (CD-ROM)　2022
FMO計算によるSARS-CoV-2変異株RBD-中和抗体間の相互作用解析

渡邉一樹, 渡邉一樹, 渡邉千鶴, 渡邉千鶴, 本間光貴, 田雨時, 川嶋裕介, 川下理日人, 星野忠次, 西田紀貴, 福澤薫, 福澤薫, 高木達也

日本薬学会関東支部大会講演要旨集　65th　2021
Computational Ab Initio Interaction Analyses between Neutralizing Antibody and SARS-CoV-2 Variant Spike Proteins Using the Fragment Molecular Orbital Method

Watanabe Kazuki, Watanabe Chiduru, Watanabe Chiduru, Honma Teruki, Tian Yu-Shi, Kawashima Yusuke, Kawashita Norihito, Fukuzawa Kaori, Fukuzawa Kaori, Takagi Tatsuya

Bulletin of the Chemical Society of Japan (Web)　94　(6)　2021

ISSN： 1348-0634
New formulation strategy pioneered by computational chemistry-Application to LNP and solid dispersion formulations-

米持悦生, 福澤薫

Pharm Tech Japan　37　(8)　2021

ISSN： 0910-4739
Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability

Mochizuki, Y., Tanaka, S., Fukuzawa, K.

Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability　2021
Publisher: Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability
DOI： 10.1007/978-981-15-9235-5 　
COMT/阻害剤複合体の結晶構造解析及び,量子化学計算による相互作用解析

武部克希, 福澤薫, 鈴木守, 桑田(楠瀬)隆生, 鵜澤成一, 飯島洋

構造活性相関シンポジウム講演要旨集(CD-ROM)　48th　2020
Effects of cholesterol derivative on membrane stability of positively charged lipoplexes

米持悦生, 古石誉之, 福澤薫

KEK Progress Report (Web)　(2020-6)　2020

ISSN： 1344-6320
Taking Water into Account with the Fragment Molecular Orbital Method. International-journal

Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

Methods in molecular biology (Clifton, N.J.)　2114　105-122　2020

DOI： 10.1007/978-1-0716-0282-9_7 　

More details Close

This chapter describes the current status of development of the fragment molecular orbital (FMO) method for analyzing the electronic state and intermolecular interactions of biomolecular systems in solvent. The orbital energies and the inter-fragment interaction energies (IFIEs) for a specific molecular structure can be obtained directly by performing FMO calculations by exposing water molecules and counterions around biomolecular systems. Then, it is necessary to pay attention to the thickness of the water shell surrounding the biomolecules. The single-point calculation for snapshots from MD trajectory does not incorporate the effects of temperature and configurational fluctuation, but the SCIFIE (statistically corrected IFIE) method is proposed as a many-body correlated method that partially compensates for this deficiency. Furthermore, implicit continuous dielectric models have been developed as effective approaches to incorporating the screening effect of the solvent in thermal equilibrium, and we illustrate their usefulness for theoretical evaluation of IFIEs and ligand-binding free energy on the basis of the FMO-PBSA (Poisson-Boltzmann surface area) method and other computational methods.
Current Status of ABINIT-MP Open Series Invited Peer-reviewed

Yuji MOCHIZUKI, Yoshinobu AKINAGA, Kota SAKAKURA, Hiromasa WATANABE, Kouichiro KATO, Naoki WATANABE, Koji OKUWAKI, Tatsuya NAKANO, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan　18　(3)　129-131　2019
Publisher: Society of Computer Chemistry Japan
DOI： 10.2477/jccj.2019-0016 　

ISSN： 1347-1767

eISSN： 1347-3824
Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method

中野達也, 福澤薫, 福澤薫, 沖山佳生, 渡邉千鶴, 古明地勇人, 望月祐志, 望月祐志

Chem-Bio Informatics Journal (Web)　18　2018

ISSN： 1347-0442
脂質・遺伝子ナノ複合体の溶液中における生成機構

米持悦生, 古石誉之, 福澤薫

KEK Progress Report (Web)　(2018-7)　2018

ISSN： 1344-6320
Protein-ligand interactions based on the fragment molecular orbital method

149　(5)　240-246　2017/05
Publisher: 日本薬理学会
ISSN： 0015-5691
FMO創薬を加速する大規模データ解析

TANAKA SHIGENORI, 福澤薫, 本間光貴

CICSJ Bull.　35　(No. 3)　205-209　2017
Analysis of Biological Interaction by Fragment Molecular Orbital (FMO) Method : Analyses of the interactions between measles virus hemagglutinin and their receptors

丸山正, 嶋根康弘, 岩沢美佐子, 秦田勇二, 吉田尊雄, 高木善弘, 大石和恵, 田中成典, 渡邉博文, 徐逢祺, 望月祐志, 福澤薫, 古明地勇人

Annual report of the earth simulator　251-257　2016/04
Publisher: Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology
ISSN： 2189-6917
Implementation of Pair Interaction Energy Decomposition Analysis and Its Applications to Protein-Ligand Systems

塚本貴志, 加藤幸一郎, 加藤昭史, 中野達也, 中野達也, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 福澤薫

Journal of Computer Chemistry, Japan (Web)　14　(1)　2015

ISSN： 1347-3824
Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors Invited

T. Maruyama, Y. Shimane, K. Ohishi, M. Iwasawa, Y. Hatada, Y. Takaki, T. Yoshida, TANAKA SHIGENORI, S. Anzaki, Y. Komeiji, Y. Mochizuki, K. Fukuzawa

Annual Report of the Earth Simulator Center　April 2014 – March 2015　131-135　2015
Publisher: Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology
ISSN： 2189-6917
医薬品候補化合物とタンパク質の相互作用解析 Invited

福澤薫

JST 産学官連携ジャーナル　2014/05/15
Large-Scale Electronic-State Calculations of Protein-Ligand Systems for Drug Design with Fragment Molecular Orbital Method

TANAKA SHIGENORI, Y. Mochizuki, K. Yamashita, Y. Okiyama, K. Fukuzawa, T. Nakano

Annual Report of the Earth Simulator Center, April 2011 – March 2012　185-190　2012
Publisher: Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology
ISSN： 1348-5822
Large-Scale Electronic-State Calculations of Influenza Viral Proteins with Fragment Molecular Orbital Method and Applications to Mutation Prediction

TANAKA SHIGENORI, A. Yoshioka, Y. Mochizuki, K. Fukuzawa, K. Yamashita, T. Nakano

Annual Report of the Earth Simulator Center, April 2010 – March 2011　187-191　2011
DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method

WATANABE Toshio, WATANABE Toshio, INADOMI Yuichi, FUKUZAWA Kaori, TANAKA Shigenori, NAKANO Tatsuya, NILSSON Lennart, NAGASHIMA Umpei

生物物理　46　(Supplement 2)　S108　2006/10/01

ISSN： 0582-4052
Bio-imaging

ABE Yukinobu, FUKUZAWA Kaori

26　(101)　123-123　2006/04/01

ISSN： 0916-4731
FMO-MD: a new ab initio molecular dynamics simulation method applicable to proteins

Y Komeiji, T Nakano, K Fukuzawa, Y Ueno, T Nemoto, DG Fedorov, M Uebayasi, K Kitaura

BIOPHYSICAL JOURNAL　84　(2)　465A-465A　2003/02

ISSN： 0006-3495

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Books and Other Publications 5

In silico創薬におけるスクリーニングの高速化・効率化技術

福澤薫

技術情報協会　2018/01
The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems

Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

Taylor & Francis/ CRC Press　2009/05/18
プログラムで実践する生体分子量子化学計算

佐藤文俊, 中野達也, 望月祐志, 福澤薫, 甘利真司

森北出版　2008/10/10
Modern Methods for Theoretical Physical Chemistry of Biopolymers

T. Nakano, Y. Mochizuki, K. Fukuzawa, S. Amari, S. Tanaka

Elsevier Science　2006/09/27
フラグメント分子軌道法入門‐ABINIT-MPによるタンパク質の非経験的量子化学計算‐

中野達也, 谷森奏一郎, 加藤昭史, 小池上繁, 雨宮克樹, 福澤薫

アドバンスソフト株式会社　2004/07/10

Presentations 31

HPCIを活用したFMO創薬プラットフォームの構築 Invited

福澤薫

日本薬学会第139年会 FMOデータベース公開記念シンポジウム　2019/03/21
フラグメント分子軌道法に基づく創薬基盤の構築 Invited

福澤薫

第46回構造活性相関シンポジウム　2018/12/06
第5回「京」を中核とするHPCIシステム利用研究課題成果報告会

福澤薫

2018/11/02
HPCIを活用したFMO創薬技術の開発 Invited

福澤薫

サイエンティフィック・システム研究会科学技術計算分科会　2018/10/25
フラグメント分子軌道法に基づく創薬プラットフォームの構築 Invited

福澤薫

兵庫県立大学第１１回医工連携セミナー　2018/07/17
In silico Drug Discovery Based on the Fragment Molecular Orbital method Invited

FUKUZAWA Kaori

Symposium on Streamlining Drug Discovery　2018/06/05
HPCIを活用したFMO創薬プラットフォームの構築

福澤薫

第４回「京」を中核とするHPCIシステム利用研究課題成果報告会　2017/11/02
FMO創薬コンソーシアムにおける活動

福澤薫

FMODD・KBDD合同公開シンポジウム　2017/10/04
Towards realizing FMO based drug design

福澤薫

構造科学と計算科学の融合ワークショップ　2017/03/28
フラグメント分子軌道法による生体高分子およびナノバイオ系の量子化学計算 Invited

福澤薫

日本表面科学会関東支部セミナー　2016/11/26
FMO創薬の実現に向けた取り組み Invited

福澤薫

CBI学会2016年次大会　2016/10/26
創薬分子設計におけるFMO法の役割

福澤薫

第10回分子科学討論会　2016/09/14
FMO創薬コンソーシアムFMO創薬コンソーシアムにおけるタンパク質－リガンド相互作用の高精度解析と創薬への応用 Invited

福澤薫

バイオグリッド研究会2016　2016/05/28
Application of fragment molecular orbital method for structure-based drug design International-presentation

Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Hirofumi Watanabe, Teruki Honma, Yuji Mochizuki, Satoshi Anzaki, Shigenori Tanaka

Pacifichem 2015　2015/12
フラグメント分子軌道法の創薬への応用～FMO創薬の実現に向けて～ Invited

福澤薫

第43回構造活性相関シンポジウム SAR2015　2015/09/29
Fragment Molecular Orbital Study Concerning Influenza Viral Surface Proteins Invited

Kaori Fukuzawa

2015/05/13
ペプチド結合における新規フラグメント分割方法の検証および精度評価

坂口正貴, 福澤薫, 渡邉千鶴, 望月祐志

日本化学会第95春季年会 (2015)　2015/03/29
アパタイト結晶に対するフラグメント分子軌道法の試み＃２

加藤幸一郎, 福澤薫, 望月祐志

2015年春季学術講演会　2015/03/13
フラグメント分子軌道法でナノ－バイオ界面を見る Invited

望月祐志, 福澤薫

2015年春季学術講演会　2015/03/12
フラグメント分子軌道法プログラムABINIT-MPの創薬への適用 Invited

福澤薫

第6回ProteinDF, ABINIT-MPユーザ会「生体分子量子化学研究会～state of the arts 生体分子シミュレーションの今～」　2015/03/04
フラグメント分子軌道法のインシリコ創薬への応用

福澤薫, 渡邉千鶴, 沖山佳生, 渡邉博文, 本間光貴, 望月祐志, 田中成典

日本化学会第95春季年会 (2015)　2015/03
FMO法の実際と創薬への応用可能性 Invited

福澤薫

第３回先進科学技術活用力養成講座ＦＭＯ計算法の創薬への活用　2015/02/10
フラグメント分子軌道法と応用事例～創薬、ウイルス感染症、そしてナノバイオ分子設計 Invited

福澤薫

NTT物性科学基礎研究所BBL-Seminar　2015/01/09
構造ベース創薬におけるFMO計算法の活用 Invited

福澤薫

第５回神戸大学研究拠点サロン「構造ベース創薬の現状と新しい取り組み」　2014/11/17
Benchmark for new fragmentation breaking peptide bonds International-presentation

K. Fukuzawa, M. Sakaguchi, C. Watanabe, Y. Mochizuki

Chem-Bio Informatics Society(CBI) Annual Meeting 2014　2014/10
FMO-based analysis on DsRed chromophore

M. Sakaguchi, Y. Mochizuki, C. Watanabe, K. Fukuzawa

Chem-Bio Informatics Society(CBI) Annual Meeting 2014　2014/10
Prediction of activity cliff among Pim1 inhibitors using FMO and MM-PBSA calculations International-presentation

Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Yuji Mochizuki, Lorien J. Parker, Hitomi Yuki, Teruki Honma

Chem-Bio Informatics Society(CBI) Annual Meeting 2014　2014/10
Theoretical calculations on proteins with fragment molecular orbital method International-presentation

Y. Mochizuki, K. Fukuzawa, Y. Okiyama, C. Watanabe, T. Honma, S. Tanaka

Chem-Bio Informatics Society(CBI) Annual Meeting 2014　2014/10
フラグメント分子軌道法(FMO法)を用いた、酵素NylBの誘導適合過程における残基間相互作用エネルギー変化の統計的解析

安東寛之, 馬場剛史, 重田育照, 渡邉千鶴, 沖山佳生, 福澤薫, 望月祐志, 中野雅由

分子科学討論会　2014/09
フラグメント分子軌道法の概要と超分解能解析への展開 Invited

福澤薫

「FMO法を用いた超分解能結晶構造解析の実現に向けて」セミナー　2014/08/28
ナノバイオ複合系の分子シミュレーション―FMO 計算によるタンパク質と固体表面の相互作用モデリング― Invited

福澤薫

FOCUS事例集　2014

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Industrial Property Rights 4

フラグメントモデル作成装置、フラグメントモデル作成システム、フラグメントモデル作成方法、及び、フラグメントモデル作成プログラム

望月祐志, 塚本貴志, 福澤薫

5357320

Property Type: Patent
フラグメントモデルを作成するための装置、システム、方法、及びプログラム

望月祐志, 塚本貴志, 福澤薫

Property Type: Patent
相互作用エネルギー算出システム、方法、及びプログラム

中野達也, 望月祐志, 福澤薫

Property Type: Patent
相互作用エネルギー算出システム、相互作用エネルギー算出方法及び相互作用エネルギー算出プログラム

中野達也, 望月祐志, 福澤薫

5067682

Property Type: Patent

Research Projects 6

Elucidation of destabilization mechanism of drug amorphous nanosuspension for middle-molecule drug development

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Chiba University

2024/04/01 - 2028/03/31
Design of heparanase inhibitors focusing on molecular bending and competitive interaction: aiming to suppress skin inflammatory diseases

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Hoshi University

2022/04/01 - 2025/03/31
構造インフォマティクスとFMO計算を融合したインシリコスクリーニング支援研究 Competitive

本間光貴

Offer Organization: 日本医療研究開発機構

System: 創薬等ライフサイエンス研究支援基盤事業

2017/04 - 2022/03
女性ホルモン受容体に対する植物エストロゲンの特異的作用の解明と評価手法の開発 Competitive

福澤薫

Offer Organization: 公益財団法人小柳財団

System: 研究助成金

2017/04 - 2018/03
量子化学計算に基づく生体高分子の超分解能構造解析技術の開発と創薬への応用 Competitive

福澤薫

System: 科研費基盤研究 (C)

2015/04 - 2018/03
フラグメント分子軌道法による核内受容体のサブタイプ特異的薬剤のデザイン Competitive

Offer Organization: 資生堂

System: 女性研究者サイエンスグラント

2015/06/01 - 2016/05/31

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Teaching Experience 10

計算生命科学の基礎　神戸大学
機能分子薬学特論Ⅰ　星薬科大学
総合薬学演習II　星薬科大学
総合薬学演習I　星薬科大学
化学実験　日本大学松戸歯学部
化学２　日本大学松戸歯学部
化学１　日本大学松戸歯学部
薬学英語　星薬科大学
臨床分析の基礎と応用　星薬科大学
物理化学I　星薬科大学

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