Publications

van Nes, J.G.H., Smit, V.T.H.B.M., Putter, H., Kuppen, P.J., Kim, S.J., Daito, M., Ding, J., Shibayama, M., Numada, S., Gohda, K., Matsushima, T., Ishihara, H., Noguchi, S., and van de Velde, C.J.H. (2009) 
Validation study of the prognostic value of Cyclin-Dependent Kinase (CDK)-based risk in Caucasian breast cancer patients. British J. Can. in press.

Nakayama, S., Torikoshi, Y., Takahashi, T., Yoshida, T., Sudo, T., Matsushima, T., Kawasaki, Y., Katayama, A., Gohda, K., Hortobagyi, G.N., Noguchi, S., Sakai, T., Ishihara, H., and Ueno, N.T. (2009) 
Prediction of paclitaxel sensitivity by CDK1 and CDK2 activity in human breast cancer cells. Breast Can. Res. in press.

Tada, S., Tsutsumi, K., Ishihara, H., Suzuki, K., Gohda, K., and Teno, N. (2008) 
Species differences between human and rat in the substrate specificity of cathepsin K. J. Biochem. 144, 499-506.

Gohda, K. and Hakoshima, T. (2008) 
A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation. J. Comput.-Aided Mol. Design 22, 789-797.

Teno, N., Irie, O., Miyake, T., Gohda, K., Horiuchi, M., Tada, S., Nonomura, K., Kometani, M., Iwasaki, G., and Betschart, C. (2008) 
New chemotypes for cathepsin K inhibitors. Bioorg. & Med. Chem. Let. 18, 2599-2603.  

Teno, N., Miyake, T., Ehara, T., Irie, O., Sakaki, J., Ohmori, O., Gunji, H., Matsuura, N., Masuya, K., Hitomi, Y., Nonomura, K., Horiuchi, M., Gohda, K., Iwasaki, A., Umemura, I., Tada, S., Kometani, M., Iwasaki, G., Cowan-Jacob, S.W., Missbach, M., Lattmann, R., and Betschart, C. (2007) 
Novel scaffold for cathepsin K inhibitors. Bioorg. & Med. Chem. Let. 17, 6096-6100.

Shimamoto, S., Yoshida, T., Inui, T., Gohda, K., Kobayashi, Y., Fujimori, K., Tsurumura, T., Aritake, K., Urade, Y. and Ohkubo, T. (2007) 
NMR solution structure of lipocalin-type prostaglandin D synthase: Evidence for partial overlapping of catalytic pocket and retinoic acid-binding pocket within the central cavity. J. Biol. Chem. 282, 31373-31379

Gohda, K. and Hakoshima, T. (2007) 
P-loop pliability of Rho-kinase for inhibitor binding. Drug Design Research Perspectives, Kaplan, SP. (ed.), Nova Science Publishers, NY, pp39-55.

Gohda, K. (2006) 
A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: contribution of conformational flexibility to the inhibitory activity. J. Enz. Inh. and Med. Chem. 21, 609-615.

Sakurai, Y., Mizuno, T., Hiroaki, H., Gohda, K., Oku, J., and Tanaka, T. (2005) 
Extraordinary high thermal stability by a designed tandem Arg-Trp stretch in an a-helical coiled-coil. Angewandte Chemie Int. Ed. 44, 6180-6183.

Hiramoto, T., Nonaka, Y., Inoue, K., Yamamoto, T., Omatsu-Kanbe, M., Matsuura, H., Gohda, K., and Fujita, N. (2004) 
Identification of endogenous surrogate ligands for human P2Y receptors through an in silico search. J. Pharmacol. Sci. 95, 81-93.

Urata, H., Miyagoshi, H., Kumashiro, T., Yumoto, T., Mori, K., Shoji, K., Gohda, K., and Akagi, M. (2004)

Synthesis and hybridization properties of L-oligodeoxynucleotide analogues in a low anti glycosyl conformation. Org. Biomol. Chem. 2, 183-189.

Gohda, K., Ohta, D., Kozaki, A., Fujimori, K., Mori, I., and Kikuchi, T. (2001)

Identification of novel potent inhibitors for ATP-phosphoribosyl transferase using three-dimensional structural database search technique. Quant. Struct. Act. Relat. 20, 143-147.

Kanaori, K., Shibayama, N., Gohda, K., Tajima, K., and Makino, K. (2001)

Multiple Four-Stranded Conformations of Human Telomere Sequence d(CCCTAA) in Solution. Nucleic Acids Res. 29, 831-840.

Gohda, K., Ohta, D., Iwasaki, G., Ertl, P., and Jacob, O. (2001) 

Computational modeling of a binding conformation of the intermediate L-histidinal to histidinol dehydrogenase. J. Chem. Inf. Comp. Sci. 41, 196-201.

Gohda, K., Mori, I., Ohta, D., and Kikuchi, T. (2000) 

A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method. J. Comput.-Aided Mol. Design 14, 265-275.

Hanessian, S., Lu, P. -P., Sanceau, J. -Y., Chemla, P., Gohda, K., Fonne-Pfister, R., Prade, L., and Cowan-Jacob, S. W. (1999) 

An enzyme-bound bisubstrate hybrid inhibitor of adenylosuccinate synthetase. Angewandte Chemie Int. Ed. 38, 3160-3162.

Fukushima, K., and Gohda, K. (1999) 

Molecular surface structure of 4,4',7,7'-tetrachlorothioindigo crystal observed by atomic force microscopy. J. Phys. Chem. B 103, 3582-3586.

Gohda, K., Kimura Y., Mori, I., Ohta, D., and Kikuchi, T. (1998) 

Theoretical evidence of the existence of a diazafulvene intermediate in the reaction pathway of imidazoleglycerol phosphate dehydratase: design of a novel and potent heterocycle structure for the inhibitor on the basis of the electronic structure-activity relationship study. Biochim. Biophys. Acta, 1385, 107-114.

Fukushima, K., Nakatsu, K., Takahashi, R., Yamamoto, H., Gohda, K., and Homma, S. (1998) 

Crystal Structures and Photocarrier Generation of Thioindigo Derivatives. J. Phys. Chem. B 102, 5985-5990.

Kikuchi, T., Okamoto, M., Geiser, M., Schmitz, A., Gohda, K., Takai, M., Morita, T., and Fujita, N. (1997) 

Prediction of the biologically active sites in eclosion hormone from the silkworm, Bombyx mori. Protein Engineering 10, 217-222.

Gohda, K., Matsuo, N., Oda, Y., Ikehara, M., and Uesugi, S. (1997) 

Effects of 2'-substituents of the first deoxyguanosine residue in the recognition sequence on EcoRI restriction endonuclease activity. J. Biochem. 121, 219-224.

Gohda, K., Oka, K., Tomita, K., and Hakoshima, T. (1994) 

Crystal structure of RNase T1 complexed with the product nucleotide 3'-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2'-hydroxyl group of the ribose. J. Biol. Chem. 269, 17531-17536.

Gohda, K., Itoh, T., Hiramatsu, Y., Tomita, K., Nishikawa, S., Uesugi, S., Morioka, H., Otsuka, E., Ikehara, M., and Hakoshima, T. (1993) 

Crystal structure of RNase T1(Y45W) complexes with 3'AMP and GflpA. J. Biochem. 114, 842-848.

Hakoshima, T., Itoh, T., Tomita, K., Goda, K., Nishikawa, S., Morioka, H., Uesugi, S., Ohtsuka, E., and Ikehara, M. (1992) 

Three-dimensional structure of a mutant ribonuclease T1(Y45W) complexed with non-cognizable ribonucleotide, 2'-AMP, and its comparison with a specific complex with 2'-GMP. J. Mol. Biol. 223, 1013-1028.

Hakoshima, T., Itoh, T., Gohda, K., Tomita, K., Uesugi, S., Nishikawa, S., Morioka, H., Ohtsuka, E., and Ikehara, M. (1991) 

Non-cognizable ribonucleotide, 2'-AMP, binds to a mutant ribonuclease T1(Y45W) at a new base-binding site but not at the guanine-recognition site. FEBS Lett. 290, 216-20.

Hakoshima, T., Oka, K., Toda, S., Tanaka, M., Goda, K., Higo, T., Itoh, T., Minami, H., Tomita, K., Nishikawa, S., Morioka, H., Imura, J., Uesugi, S., Ohtsuka, E., and Ikehara, M. (1990) 

Crystallographic characterization of wild-type and mutant ribonuclease T1 complexes with several ribonucleotides. J. Biochem. 108, 695-698.

Proceedings in Int'l Nat'l Conferences

Inoue, K., Inui, T., Ohkubo, T., Gohda, K., Urade, Y., and Yagi, N. (2005) 

Structural and functional studies of lipocalin-type prostaglandin D synthase complexed with lipophilic small ligands by x-ray small angle scattering. The 30th Federation of European Biochemical Societies (FEBS) Congress - 9th International Union of Biochemistry and Molecular Biology (IUBMB) Conference, Budapest, Hungary, July 2 - 7.

Inoue, K., Inui, T., Ohkubo, T., Gohda, K., Urade, Y., and Yagi, N. (2004) 
Structural studies of lipocalin-type prostaglandin D synthase complexed with lipophilic small ligands by x-ray small angle scattering. The 5th International Conference on Biological Physics (ICBP2004), Gothenburg, Sweden, August 23 - 27.

Doi, M., Kobayashi, Y., Kyogoku, Y., Takimoto, M., and Goda, K. (1990) 

Structure study of human calcitonin. Pept.: Chem., Struct., Biol., Proc. Am. Pept. Symp., 11th pp.165-167.

Invited Lectures

Gohda, K. A Study of CP-CoMFA Analysis for a Set of IGPD Inhibitors with Different Conformational Flexibility. 98' TRIPOS Users Meeting, Kobe, Dec.7-8, 1998.

Patents

Altmann, E., Betschart, C., Gohda, K., Horiuchi, M., Lattmann, R., Missbach, M., Sakaki, J., Takai, M., Teno, N., Cowen, S. D., Greenspan, P. D., McQuire, L. W., Tommasi, R. A., Van D., John H. (1999) Synthesis of dipeptide nitriles as inhibitors of cysteine cathepsins.  WO 9924460.

Seminars & Lectures
Gohda, K.  Rho kinase inhibitors. Graduated School Seminar, College of Agriculture, Osaka Prefectural University, Sakai, October 26, 2007.

Gohda, K.  Drug discovery by methods of computational chemistry.　Graduated School Seminar, College of Agriculture, Osaka Prefectural University, Sakai, June 28, 2004.

Gohda, K. Changing research and development of new drugs by computer. Open Lecture, Tsu City College, Tsu, September 20, 2003.

Gohda, K. Computer and Chemistry. Educational Lecture, Tsu City College, Tsu, July 19, 2002.

Gohda, K. Computer-aided molecular modeling technique-driven, structure-based discovery of a novel ligand molecule specifically bound to a target protein. Graduated School Seminar, Dept. Science & Engineering, Ritsumeikan University, Kusatsu, June 29, 2002.