Takeshi Ishikawa, Ph. D.

Department of Chemistry, Biotechnology, and Chemical Engineering,
Research Field in Engineering, Science and Engineering Area,
Research and Education Assembly, Kagoshima University
Tel: +81-99-285-8334
E-mail: ishi [at] cb.kagoshima-u.ac.jp



Japanese


Education

Mar 1999B.S. Hokkaido University
Mar 2001M.S. Hokkaido University
Mar 2005Ph. D.Hokkaido University


Professional Experience

Apr 2005Postdoctoral Researcher of Japan Science and Technology Agency (JST)
Mar 2008Assistant Professor at Gifu University
Apr 2012Assistant Professor at Tohoku University
Feb 2013Associate Professor at Nagasaki University
Oct 2018Professor at Kagoshima University


Membership

The Chemical Society of Japan
Chem-Bio Informatics Society
The Biophysical Society of Japan
The Pharmaceutical Society of Janan

Publication

Google Scholar
ORCiD

[50] T. Ishikawa, K. Sakakura, Y. Mochizuki, RI-MP3 calculations of biomolecules based on the fragment molecular orbital method, J. Comput. Chem. online published (DOI: 10.1002/jcc.25368)
[49] T. Ishikawa, S. Mizuta, O. Kaneko, K. Yahata, Fragment Molecular Orbital Study of the Interaction Between Sarco/Endoplasmic Reticulum Ca2+-ATPase and Its Inhibitor Thapsigargin Toward Anti-Malarial Development, J. Phys. Chem. B, 122 (2018) 7970-7977 (DOI: 10.1021/acs.jpcb.8b04509)
[48] Y. Miyazaki, T. Ishikawa, Y. O. Kamatari, T. Nakagaki, H. Takatsuki, D. Ishibashi, K. Kuwata, N. Nishida, R. Atarashi, Identification of alprenolol hydrochloride as an anti-prion compound using surface plasmon resonance imaging, Mol. Neurobiol., online published (DOI: 10.1007/s12035-018-1088-7)
[47] T. Ishikawa, Ab initio quantum chemical calculation of electron density, electrostatic potential, and electric field of biomolecule based on fragment molecular orbital method, Int. J. Quantum Chem., 118 (2018) e25535 (DOI: 10.1002/qua.25535)
[46] S. Yamaguchi, N. Horie, K. Satoh, T. Ishikawa, T. Mori, H. Maeda, Y. Fukuda, S. Ishizaka, T. Hiu, Y. Morofuji, T. Izumo, N. Nishida, T. Matsuo, Age of Donor of Human Mesenchymal Stem Cells Affects Structural and Functional Recovery after Cell Therapy Following Ischaemic Stroke, J. Cerebr. Blood. F. Met., in press online published (DOI: 10.1177/0271678X17731964)
[45] K. Watanabe, T. Ishikawa, H. Otaki, S. Mizuta, T. Hamada, T. Nakagaki, D. Ishibashi, S. Urata, J. Yasuda, Y. Tanaka, N. Nishida, Structure-based drug discovery for combating influenza virus by targeting the PA-PB1 interaction, Sci. Rep., 7 (2017) 9500 (DOI: 10.1038/s41598-017-10021-w)
[44] T. Ishikawa, H. Otaki, S. Mizuta, M. Kuriyama, O. Onomura, N. Higfuchi, M. N. Nakashima, M. Nakashima and K. Ohyama, Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase, Drug Metabolism and Pharmacokinetics, 32 (2017) 201-207 (DOI: 10.1016/j.dmpk.2017.04.002)
[43] J. N. Makau, K. Watanabe, T. Ishikawa, S. Mizuta, T. Hamada, N. Kobayashi, N. Nishida, Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches, PLoS ONE, 12 (2017) e0173582 (DOI: 10.1371/journal.pone.0173582)
[42] S. Nakano, K. Yasukawa, T. Tokiwa, T. Ishikawa, E. Ishitsubo, N. Matsuo, S. Ito, H. Tokiwa, Y. Asano, Origin of Stereoselectivity and Substrate/ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase, J. Chem. Phys. B, 120 (2016) 10736-10743 (DOI: 10.1021/acs.jpcb.6b09328)
[41] T. Ishikawa, Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation, J. Comput. Aid. Mol. Des., 30 (2016) 875-887 (DOI: 10.1007/s10822-016-9967-3)
[40] D. Ishibashi, T. Nakagaki, T. Ishikawa, R. Atarashi, K. Watanabe, F. Cruz, T. Hamada, N. Nishida, Structurebased drug discovery for prion disease by using a novel binding simulation, EBioMedicine, 9 (2016) 238-249 (DOI: 10.1016/j.ebiom.2016.06.010)
[39] N. Sriwilaijaroen, S. Magesh, A. Imamura, H. Ando, H. Ishida, M. Sakai, E. Ishitsubo, T. Hori, S. Moriya, T. Ishikawa, K. Kuwata, T. Odagiri, M. Tashiro, A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-inhibitor Interactions, H. Hiramatsu, K. Tsukamoto, T. Miyagi, H. Tokiwa, M. Kiso, and Y. Suzuki, J. Med. Chem., 59 (2016) 4563-4577 (DOI: 10.1021/acs.jmedchem.5b01863)
[38] K. Pandey, P. Ferreira, T. Ishikawa, T. Nagai, O. Kaneko, K. Yahata, Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor, Sci. Rep., 6 (2016) 23454 (DOI: 10.1038/srep23454)
[37] D. Morita, Y. Yamamoto, T. Mizutani, T. Ishikawa, J. Suzuki, T. Igarashi, N. Mori, T. Shiina, H. Inoko, H. Fujita, K. Iwai, Y. Tanaka, B. Mikami, M. Sugita, Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex, Nat. Comm., 7 (2016) 10356 (DOI: 10.1038/ncomms10356)
[36] N. Kawashita, H. Yamasaki, T. Miyao, K. Kawai, Y. Sakae, T. Ishikawa, K. Mori, S. Nakamura, H. Kaneko, A Mini-review on Chemoinformatics Approaches for Drug Discovery, J. Comput. Aided Chem., 16 (2015) 15-29 (DOI: 10.2751/jcac.16.15)
[35] Y. Higuchi, T. Ishikawa, N. Ozawa, L. Chazeau, J.-Y. Cavaille, M. Kubo, Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation, Chem. Phys., 459 (2015) 96-101 (DOI: 10.1016/j.chemphys.2015.08.007)
[34] H. Oku, M. Inafuku, T. Ishikawa, T. Takamine, M. Ishmael, M. Fukuta, Molecular cloning and biochemical characterization of isoprene synthases from the tropical trees Ficus virgata, Ficus septica, and Casuarina equisetifolia, J. Plant Research, 128 (2015) 849-861 (DOI: 10.1007/s10265-015-0740-9)
[33] L. Chang, T. Ishikawa, K. Kuwata, S. Takada, Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions, J. Comput. Chem., 34 (2013) 1251-1257 (DOI: 10.1002/jcc.23250)
[32] T. Ishikawa, R. R. Burri, Yuji O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao, K. Kuwata, Theoretical study of the two binding modes　between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method, Phys. Chem. Chem. Phys., 15 (2031) 3646-3654 (DOI: 10.1039/C3CP42761G)
[31] K. Takemura, R. R. Burri, T. Ishikawa, T. Ishikura, S. Sakuraba, N. Matubayasi, K. Kuwata, A. Kitao, Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, Chem. Phys. Lett., 559 (2013) 94-98 (DOI:10.1016/j.cplett.2012.12.063)
[30] T. Okamoto, T. Ishikawa, Y. Koyano, N. Yamamoto, K. Kuwata, and M. Nagaoka, A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation, Bull. Chem. Soc. Jap., 86 (2013) 210-222 (DOI: 10.1246/bcsj.20120216)
[29] T. Ishikawa and K. Kuwata, RI-MP2 Gradient Calculation of Large Molecules using the Fragment Molecular Orbital Method, J. Phys. Chem. Lett., 3 (2012) 375-379 (DOI: 10.1021/jz201697x)
[28] T. Ishikawa, N. Yamamoto, and K. Kuwata, Partial energy gradient based on the fragment molecular orbital method: application to geometry optimization, Chem. Phys. Lett., 500 (2010) 149-154 (DOI: 10.1016/j.cplett.2010.09.071)
[27] T. Ishikawa and K. Kuwata, Acceleration of monomer self-consistent charge process in fragment molecular orbital method, C.B.I.J., 10 (2010) 24-31 (DOI: 10.1273/cbij.10.24)
[26] T. Ishikawa and K. Kuwata, Interaction analysis of the native structure of prion protein with quantum chemical calculations, J. Chem. Theor. Comput., 6 (2010) 538-547 (DOI: 10.1021/ct900456v)
[25] T. Ishikawa, T. Ishikura, and K. Kuwata, Theoretical study of the prion protein based on the fragment molecular orbital method, J. Comput. Chem., 30 (2009) 2594-2601 (DOI: 10.1002/jcc.21265)
[24] T. Ishikawa and K. Kuwata, Fragment molecular orbital calculation using the RI-MP2 method, Chem. Phys. Lett., 474 (2009) 195-198 (DOI: 10.1016/j.cplett.2009.04.045)
[23] shikawa, M. Sakurai, and S. Tanaka, Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits), N. Taguchi, Y. Mochizuki, T. Nakano, S. Amarai, K. Fukuzawa, T. IJ. Phys. Chem. B, 113 (2009) 1153-1161 (DOI: 10.1021/jp808151c)
[22] Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, and S. Tanaka, Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Toward an improvement of foce fields for classical molecular dynamics simulations, Chem. Phys. Lett., 467 (2009) 417-423 (DOI: 10.1016/j.cplett.2008.11.044)
[21] Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, and T. Nakano, Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit salvation, J. Comput. Chem., 30 (2009) 40-50 (DOI: 10.1002/jcc.21025)
[20] M. Ito, K. Fukuzawa, T. Ishikawa, Y. Mochizuki, T. Nakano, and S. Tanaka, Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information Transmission, J. Phys. Chem. B., 112 (2008) 12081-12094 (DOI: 10.1021/jp803369x)
[19] T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, S. Tanaka, and K. Tanaka, An application of fragment interaction analysis based on local MP2, Chem. Phys. Lett. 463 (2008) 189-194 (DOI: 10.1016/j.cplett.2008.08.022)
[18] M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki, T. Ishikawa, and T. Nakano, How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion, J. Am. Chem. Soc. Comm. 130 (2008) 2396-2397 (DOI: 10.1021/ja710038c)
[17] N. Taguchi, Y. Mochizuki, T. Ishikawa, and K. Tanaka, Multi-reference calculations of nitric oxide dimer, Chem. Phys. Lett. 451 (2008) 31-36 (DOI: 10.1016/j.cplett.2007.11.084)
[16] T. Ishikawa and K. Tanaka, Theoretical study on the structure of the ground state and photo-induced metastable states of [M(CN)5NO]2- (M=Ru,Fe) and mechanism of the photo-rearrangement among them, Z. Kristal. 223 (2008) 334-342 (DOI: 10.1524/zkri.2008.0033)
[15] Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, S. Tanaka, and K. Ebina, Application of the fragment molecular orbital method for determination of atomic charges on polypeptides, Chem. Phys. Lett. 449 (2007) 329-335 (DOI: 10.1016/j.cplett.2007.10.066)
[14] T. Ishiskawa, Y. Mochizuki, S. Amarai, T. Nakano, H. Tokiwa, S. Tanaka, and K. Tanaka, Fragment interaction analysis based on local MP2, Theor. Chem. Acc. 118 (2007) 937-945 (DOI: 10.1007/s00214-007-0374-7)
[13] Y. Mochizuki, K. Tanaka, K. Yamashita, T. Ishikawa, T. Nakano, S. Amari, K. Segawa, T. Murase, H. Tokiwa, and M. Sakurai, Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme, Theor. Chem. Acc. 117 (2007) 541-553 (DOI: 10.1007/s00214-006-0181-6)
[12] Y. Mochizuki, K. Komeiji, T. Ishikawa, T. Nakano, and H. Yamataka, A fully quantum mechanical simulation study on the lowes n-π* state of hydrated formaldehyde, Chem. Phys. Lett. 437 (2007) 66-72 (DOI: 10.1016/j.cplett.2007.02.016)
[11] Y. Mochizuki, T. Nakano, S. Amari, T. Ishikawa, K. Tanaka, M Sakurai, and S. Tanaka, Fragment molecular orbital calculations on red fluorescent protein (DsRed), Chem. Phys. Lett. 433 (2007) 360-367 (DOI: 10.1016/j.cplett.2006.11.088)
[10] K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, and H. Tokiwa, A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs, Theor. Chem. Acc. 117 (2007) 397-405 (DOI: 10.1007/s00214-006-0171-8)
[09] T. Ishikawa, Y. Mochizuki, K. Imamura, T. Nakano, H. Mori, H. Tokiwa, K. Tanaka, E. Miyoshi, and S. Tanaka, Application of fragment molecular orbital scheme to silicon-containing systems, Chem. Phys. lett. 430 (2006) 361-366 (DOI: 10.1016/j.cplett.2006.09.015)
[08] T. Ishikawa, Y. Mochizuki, T. Nakano, S. Amari, H. Mori, H. Honda, T. Fujita, H. Tokiwa, S. Tanaka, Y. Komeiji, K. Fukuzawa, K. Tanaka, and E. Miyoshi, Fragment molecular orbital calculation on large scale systems containing heavy metal atom, Chem. Phys. lett. 427 (2006) 159-165 (DOI: 10.1016/j.cplett.2006.06.103)
[07] Y. Mochzuki, T. Ishikawa, K. Tanaka, H. Tokiwa, T. Nakano, and S. Tanaka, Dynamic polarizability calculation with fragment molecular orbital scheme, Chem. Phys. Lett. 418 (2005) 414-418 (DOI: 10.1016/j.cplett.2005.11.014)
[06] T. Ishikawa and K. Tanaka, Electronic structures and the stabilities of metastable states in [Ru(CN)5NO]2-: A theoretical study, Chem. Phys. Lett. 412 (2005) 164-170 (DOI: 10.1016/j.cplett.2005.06.117)
[05] T. Ishikawa and K. Tanaka, Response to “Comment on Theoretical study of the photoinduced transfer among the ground state and two metastable state in [Fe(CN)5NO]2-.” [J. Chem. Phys. 122. 074314 (2005)], J. Chem. Phys. 123 (2005) 047102 (DOI: 10.1063/1.1989318)
[04] T. Ishikawa and K. Tanaka, Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2-, J. Chem. Phys. 122 (2005) 074314 (DOI: 10.1063/1.1851975)
[03] T. Ishikawa and K. Tanaka, Theoretical study of lower electronic excitation spectra of [(Re6S8)Cl6]3-, Chem. Phys. Lett. 395 (2004) 166-170 (DOI: 10.1016/j.cplett.2004.07.055)
[02] T. Suzuki, M. Kurahashi, Y. Yamauchi, T. Ishikawa and T. Noro, Spin Polarized Metastable He* (23S, 1s2s) stimulated Desorption of H+ Ions, Phys. Rev. Lett. 86 (2001) 3654-3657 (DOI: 10.1103/PhysRevLett.86.3654)
[01] T. Ishikawa, T. Noro, and T. Shoda, Theoretical study on the photoisomerization of azobenzene, J. Chem. Phys. 115 (2001) 7503-7512 (DOI: 10.1063/1.1406975)

Proceeding

[1] Ab initio FMO-MD method reimplemented and applied to pure water, Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, and T. Nakano, Computation in Modern Science and Engineering - Proc. ICCMSE2007 (Simos T. E. and Maroulis G. eds, AIP) 1261-1264

Book

[1] The FRAGMENT MOLECULAR ORBIAL METHOD: Practical Applications to Large Molecular Systems; D. G. Fedorov and K. Kitaura Eds, CRC Press, Boca Raton, FL, 2009, Developments of FMO Methodology and Graphical User Interface in ABINIT-MP (Chapter 3 : 37-62), T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S. Amaari, I. Kurisaki, S. Tanaka