Publications (2006, 2007)

[Research Papers] [Presentations in Academic Meetings]

Research Papers

  1. Ishikawa, S., Hirota, S., Neya, S., Funasaki, N.: Molecular Motions of α-Cyclodextrin on a Dodecyl Chain Studied by Molecular Dynamics Simulations. Chem. Pharm. Bull., 54, 528-534 (2006)
  2. Yokoyama, T., Neya, S., Antonio, T., Yonetani, T., Park, S.-Y., Tame, J. R. H.: R-State Hemoglobin with Low Oxygen Affinity: Crystal Structures of Deoxy Human and Carbonmonoxy Horse Hemoglobin Bound to the Effector Molecule L35. J. Mol. Biol., 356, 790-801 (2006)
  3. Yamanaka, K., Okimoto, N., Neya, S., Hata, M., Hoshino, T.: Behavior of Water Molecules in ATPase Pocket of Myosin. J. Mol. Struct. (THEOCHEM), 758, 97-105 (2006)
  4. Mie, Y., Kishida, M., Neya, S., Funasaki, N., Mizutani, F., Nishiyama, K., Taniguchi, I.: Electrochemical Analysis of Heme Functions of Myoglobin Using Semi-Artificial Myoglobins. J. Electroanal. Chem., 588, 226-234 (2006)
  5. Neya, S., Imai, K., Hiramatsu, Y., Kitagawa, T., Hoshino, T., Hata, M., Funasaki, N.: Significance of the Molecular Shape of Iron Corrphycene in a Protein Pocket. Inorg. Chem., 45, 4238-4242 (2006)
  6. Ode, H., Neya, S., Hata, M., Sugiura, W., Hoshino, T.: Computational Simulations of HIV-1 Proteases-Multi-drug Resistance Due to Nonactive Site Mutation L90M. J. Am. Chem. Soc., 128, 7887-7895 (2006)
  7. Miyauchi, K., Curran, R., Matthews, E., Komano, J., Hoshino, T., Engelman, D. M., Matsuda, Z.: Mutations of Conserved Glycine Residues within the Membrane-Spanning Domain of Human Immunodeficiency Virus Type 1 gp41 Can Inhibit Membrane Fusion and Incorporation of Env onto Virions. Jpn. J. Infect. Dis., 59, 77-84 (2006)
  8. Nishiyama, K., Watanabe, T., Hoshino, T., Ohdomari, I.: Analysis of Interactions between Luciferase and Si Substrates Using Molecular Dynamics Simulations. Jpn. J. Appl. Phys., 45, 1021-1025 (2006)
  9. Nakajima, J., Sato, Y., Hoshino, T., Yamazaki, M., Saito, K.: Mechanistic Study on the Oxidation of Anthocyanidin Synthase by Quantum Mechanical Calculation. J. Biol. Chem., 281, 21387-21398 (2006)
  10. Funasaki, N., Uratsuji, I., Okuno, T., Hirota, S., Neya, S.: Masking Mechnism of Bitter Taste of Drugs. Studied with Ion Selective Electrodes. Chem. Pharm. Bull., 54, 1156-1161 (2006)
  11. Koyama, M., Neya, S., Mizutani, Y.: Role of Heme Propionates of Myoglobin in Vibrational Energy Relaxation. Chem. Phys. Lett., 430, 404-408 (2006)
  12. Hata, M., Marshall, G. R.: Do Benzodiazepines Mimic Reverse-turn Structures? J. Comput.-Aided Mol. Des. 20, 321-331 (2006)
  13. Neya, S., Quan, J., Hata, M., Hoshino, T., Funasaki, N.: A Novel and Efficient Synthesis of Porphine. Tetrahedron Lett., 47, 8731-8732 (2006)
  14. Ohgo, S., Neya, S., Uekusa, H., Nakamura, M.: An Isocyanide Probe for Heme Electronic Structure: Bis(tert-butylisocyanide) Complex od Diazaporphyrin Showing a Unique (dxy)2(dxz,dyz)3 Ground State. Chem. Commun. 4590-4592 (2006)
  15. Sato, Y., Hata, M., Neya, S., Hoshino, T.: Computational Analysis of the Proton Translocation from Asp96 to Schiff base in Bacteriorhodopsin. J. Phys. Chem. 110 22804-22812 (2006)
  16. Gulam, R. M., Neya, S., Teraoka, J.: Resonance Raman Spectra of Highly Reduced Iron Porphycenes. J. Porphyrins Phthalocyanines 10, 1271-1284 (2006)
  17. Yuki, H., Tanaka, Y., Hata, M., Ishikawa, H., Neya, S., Hoshino, T.: Implementation of pi-pi Interactions in Molecular Dynamics Simulation. J. Comput. Chem. 28, 1091-1099 (2007)
  18. Ode, H., Matsuyama, S., Hata, M., Hoshino, T., Kakizawa, J., Sugiura, W.: Mechanism of Drug Resistance Due to N88S in CRF01_AE HIV-1 Protease, Analyzed by Molecular Dynamics Simulations. J. Med. Chem. 50, 1768-1777 (2007)
  19. Torimoto, N., Ishii, I., Hata, M., Kobayashi, Y., Nakamura, H., Ariyoshi, N., Kitada, M.: Theoretical Calculation of Triazolam Hydroxylation and Endogenous Steroid Inhibition in the Active Site of CYP3A4. Biochim. Biophys. Acta, Proteins Proteomics 1774, 223-232 (2007)
  20. Torimoto, N., Ishii, I., Toyama, K., Hata, M., Tanaka, K., Shimomura, H., Nakamura, H., Ariyoshi, N., Ohmori, S., Kitada, M.: Helices F-G Are Important for the Substrate Specificities of CYP3A7. Drug Metab. Dispos. 35, 484-492 (2007)
  21. Ode, H., Matsuyama, S., Hata, M., Neya, S., Kakizawa, J., Sugiura, W., Hoshino, T.: Computational Characterization of Structural Role of the Non-active Site Mutation M36I of Human Immunodeficiency Virus Type 1 Protease. J. Mol. Biol. 370, 598-607 (2007)
  22. Neya, S., Takahashi, A., Ode, H., Hoshino, T., Hata, M., Ikezaki A., Ohgo, Y., Takahashi, M., Hiramatsu, H., Kitagawa, T., Furutani, Y., Kandori H., Funasaki, N., Nakamura, M.: Magnetic and Infrared Properties of the Azide Complex of 2,7,12,17-[Tetra propylporphycenato]iron(III): A Novel Admixing Mechanism of the S = 5/2 and S = 3/2 States. Eur. J. Inorg. Chem. 2007, 3188-3194 (2007)
  23. Kanari, Y., Shoji, Y., Ode, H., Miyake, T., Tanii, T., Hoshino, T., Ohdomari, I. : Protein Adsorption on Self-Assembled Monolayers Induced by Surface Water Molecule. Jpn. J. Appl. Phys. 46, 6303-6308 (2007)
  24. Takaoka, T., Mori, K., Okimoto, N., Neya, S., Hoshino, T : Prediction of the structure of complexes comprised of proteins and glycosaminoglycans using docking simulation and cluster analysis. J. Chem. Theor. Comput. 3, 2347-2356 (2007)
  25. Nishiyama, K., Watanabe, T., Hoshino, T., Ohdomari, I. : nalysis of binding energies between luciferin and luciferase adsorbed on Si surface by docking simulations. Chem. Phys. Lett. 439, 148-150 (2007)

Reviews

  1. Hata, M., Fujii, Y., Tanaka, Y., Ishikawa, H., Ishii, M., Neya, S., Tsuda, M., Hoshino, T.: Substrate Deacylation Mechanisms of Serine-β-lactamases. Biol. Pharm. Bull. 29, 2151-2159 (2006)

Presentations in Academic Meetings

  1. Neya, S., Hoshino, T., Hata, M.: Control of Oxygen Binding to Heme Iron by Porphyrin Variants. The 14th Takeda Science Foundation Symposium of Bioscience; The 50th Anniversary of Oxygenases. Advances and Reflections, Kyoto, Japan, Program & Abstracts, 93 (2006)
  2. Neya, S., Hoshino, T., Hata, M.: Biological Significance of Molecular Shape of Iron Corrphycene in Protein Cavity. The 16th Symposium on Role of Metals in Biological Reactions, Biology and Medicine (SMS 2006), Tokyo, Japan, Yakugaku Zasshi 126(suppl. 1), O-11 (2006)
  3. Neya, S., Hoshino T., Hata, M.: Functional Regulation of Myoglobin with Chemically Modified Corrphycenes. 4th International Conference on Porphyrins and Phthalocyanines, Rome, Italy, J. Porphyrins Phthalocyanines, 10, 796 (2006)
  4. Ode, H., Matsuyama, S., Neya, S., Hata, M., Sugiura, W., Hoshino, T. : NFV-Resistant Mechanism due to Non-active Site Mutation N88S on Subtype AE HIV-1 PRs. 2006 Annual Meeting of CBI Society, Tokyo, Japan, Proceedings, 54 (2006)
  5. Iwamoto, K., Neya, S., Hoshino, T. : Evaluation of the Binding Affinity of Antibodies from Antigen Binding Energy and VH-VL Interaction Energy Calculated by the MM-GBSA Method. 2006 Annual Meeting of CBI Society, Tokyo, Japan, Proceedings, 55 (2006)
  6. Takaoka, T., Okimoto, N., Mori, K., Neya, S., Hoshino, T. : Prediction of Complex Structure Comprised of a Protein and a Glycosaminoglycan Using Docking Simulation and Cluster Analysis. 2006 Annual Meeting of CBI Society, Tokyo, Japan, Proceedings, 56 (2006)
  7. Koyama, M., Neya, S., Mizutani, Y. : Effect of Heme Propionates on Dynamics of Myoglobin. 20th International Conference on Raman Spectroscopy (ICORS2006), Yokohama, Japan, Abstracts, 177 (2006)
  8. Ando, S., Hata, M., Tozuka, Y., Moribe, K., Yamamoto, K.: Equimolar Complex Formation of Ethenzamide or 2-Methoxybenzamide with Ureal Compounds: Investigation of Complexation Mechanism by Theoretical Calculation. Asian Pharmaceutics Graduate Congress: The Science of Product Design and Pharmaceutical Technology, Singapore, Singapore (2006)
  9. Fuji, H., Tatsumi, J., Komano, J., Hoshino, T.: Development of HIV-1 RNaseH inhibitor by Computer-Assisted Drug Design. Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, Okinawa, Japan, Program, 442 (2006)
  10. Ohgo, Y., Neya, S., Uekusa, H., Nakamura, M..: Bis(tert-butylisocyanide) Complex of Diazaporphyrin Showing a Unique (dxy)2(dxz, dyz)3 Ground State. 233rd ACS National Meeting, Chicago, United States (2007)
  11. Hoshino, T., Mori, K. : Investigation on the binding of amyloid peptides to a GM1 cluster through the moleculardynamics simulations of GM1-containing membranes. 1st International Symposium on Nanomedicine -from Basic to Applications- (ISNM2007) & 2nd Molecule-Based Information Transmission and Reception (MB-ITR2007), Okazaki, Japan, Proceedings, 33 (2007)
  12. Nakamura, M., Ohgo, Y,. Ikazaki, A., Eguchi, E., Neya, S. : Unsusual electronic and magnetic properties in iron(III) porphyrinoids 1st Georgian Bay International Conference on Bioinorganic Chemistry. Parry Sound, Canada, (2007)
  13. Nakamura, M., Ohgo, Y,. Ikazaki, A., Eguchi, E., Neya, S. : Formation of iron(III) porphyrinates with unusual electronic and magnetic properties 13th International conference of biological inorganic chemistry, Vienna, Austria, (2007)
  14. Ohgo, Y., Neya, S., Nakamura, M.: Change in Nonplanarity of heme as electron transfer switch 13th International conference of biological inorganic chemistry, Vienna, Austria, (2007)
  15. Neya, S., Hoshino, T. : Pursuit of the biological function of a novel porphyrinoid replaced with a pyridine ring. The 17th symposium on the role of metals in biological reactions, biology, and medicine (SRM2007). Yakugaku Zasshi, 127, 17, (2007)
  16. Hoshino, T. : Computational design, organic chemical synthesis, and biological assay of an inhibitor against HIV-1 protease. The 2nd Workshop on Biological Applications of Plasma/Photon Processing, (2007)
  17. Ode, H., Matsuo, Y., Neya, S., Hoshino, T. : Development of AMBER Force Field for Nucleic Acids. 2007 Annual Meeting of CBI Society, Hiroshima, Japan, Proceedings, 66 (2007)
  18. Matsuo, Y., Ode, H., Hirohashi, Y., Torigoe, T., Sato, N., Neya, S., Hoshino, T. : Computational and Biochemical Investigation on the Binding Affinities of Peptides with HLAs. 2007 Annual Meeting of CBI Society, Hiroshima, Japan, Proceedings, 73 (2007)
  19. Okimoto, N., Futatsugi, N., Suenaga, A., Fuji, H., Yanai, R., Ohno, Y., Narumi, T., Taiji, M. : Virtual screening by combining molecular docking and molecular dynamics simulation. 2007 Annual Meeting of CBI Society, Hiroshima, Japan, Proceedings, 88 (2007)
  20. Hisatomi, H., Katagiri, D., Neya, S., Hoshino, T. : Novel ab initio Secondary Structure Prediction Method. 2007 Annual Meeting of CBI Society, Hiroshima, Japan, Proceedings, 115 (2007)
  21. Futatsugi, N., Okimoto, N., Suenaga, A., Fuji, H., Narumi, T., Ohno, Y., Yanai, R., Taiji, M. : In Silico Prediction of Side Effects on Drug Development. 2007 Annual Meeting of CBI Society, Hiroshima, Japan, Proceedings, 136 (2007)
  22. Neya, S., Hoshino, T.: Infrared and Magnetic Properties of Nonplanaer Iron(III) Porphyrin Azide:Proposal of a Novel Mechanism of Spin Admixing. International Symposium on Metallomics 2007, Chemical Society of Japan, Nagoya, Japan. Abstract p. 140, (November 28-December 1, 2007)
Top Page
Copyright © Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University