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Structure-based Molecular Design Team _Publication List

Structure-based Molecular Design Team

1

Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase.

Balogun EO, Inaoka DK, Shiba T, Kido Y, Tsuge C, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PA, Kita K, Harada S.
Mol Microbiol, 94(6), 1315-1329 (2014).
2

Crystal structures of the S6K1 kinase domain in complexes with inhibitors.

Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S.
J Struct Funct Genomics, 15(3), 153-164 (2014).
3

A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity.

Okada-Iwabu M, Yamauchi T, Iwabu M, Honma T, Hamagami K, Matsuda K, Yamaguchi M, Tanabe H, Kimura-Someya T, Shirouzu M, Ogata H, Tokuyama K, Ueki K, Nagano T, Tanaka A, Yokoyama S, Kadowaki T.
Nature, 503(7477), 493-499 (2013).
4

Biochemical characterization of highly active Trypanosoma brucei gambiense glycerol kinase, a promising drug target.

Balogun EO, Inaoka DK, Shiba T, Kido Y, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PAM, Harada S, Kita K.
J Biochem, 154(1), 77-84 (2013).
5

A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo

Saito Y, Yuki H, Kuratani M, Hashizume Y, Takagi S, Honma T, Tanaka A, Shirouzu M, Mikuni J, Handa N, Ogahara I, Sone A, Najima Y, Tomabechi Y, Wakiyama M, Uchida N, Tomizawa-Murasawa M, Kaneko A, Tanaka S, Suzuki N, Kajita H, Aoki Y, Ohara O, Shultz LD, Fukami T, Goto T, Taniguchi S, Yokoyama S, Ishikawa F.
Sci Transl Med, 5(181), 181ra52 (2013).
6

Structure of the trypanosome cyanide-insensitive alternative oxidase.

Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, Kita K.
Proc Natl Acad Sci U S A, 110(12), 4580-4585 (2013).
7

Prediction of ligand-induced structural polymorphism of receptor interaction sites using machine learning.

Takaya D, Sato T, Yuki H, Sasaki S, Tanaka A, Yokoyama S, Honma T.
J Chem Inf Model, 53(3), 704-716 (2013).
8

Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase.

Murayama Y, Sekine S, Yokoyama S.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 69(Pt2), 174-177 (2013).
9

Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.

Sato T, Watanabe H, Tsuganezawa K, Yuki H, Mikuni J, Yoshikawa S, Kukimoto-Niino M, Fujimoto T, Terazawa Y, Wakiyama M, Kojima H, Okabe T, Nagano T, Shirouzu M, Yokoyama S, Tanaka A, Honma T.
Bioorg Med Chem, 20(12), 3756-3767 (2012).
10

Structure-activity relationship studies of novel glycosphingolipids that stimulate natural killer T-cells.

Tashiro T.
Biosci Biotechnol Biochem, 76(6), 1055-1067 (2012).
11

Blockade of inflammatory responses by a small-molecule inhibitor of the Rac activator DOCK2.

Nishikimi A, Uruno T, Duan X, Cao Q, Okamura Y, Saitoh T, Saito N, Sakaoka S, Du Y, Suenaga A, Kukimoto-Niino M, Miyano K, Gotoh K, Okabe T, Sanematsu F, Tanaka Y, Sumimoto H, Honma T, Yokoyama S, Nagano T, Kohda D, Kanai M, Fukui Y.
Chem Biol, 19(4), 288-297 (2012).
12

A novel Pim-1 kinase inhibitor targeting residues that bind the substrate peptide.

Tsuganezawa K, Watanabe H, Parker L, Yuki H, Taruya S, Nakagawa Y, Kamei D, Mori M, Ogawa N, Tomabechi Y, Handa N, Honma T, Yokoyama S, Kojima H, Okabe T, Nagano T, Tanaka A.
J Mol Biol, 417(3), 240-252 (2012).
13

Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.

Yuki H, Honma T, Hata M, Hoshino T.
Bioorg Med Chem, 20(2), 775-783 (2012).
14

A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors.

Takaya D, Yamashita A, Kamijo K, Gomi J, Ito M, Maekawa S, Enomoto N, Sakamoto N, Watanabe Y, Arai R, Umeyama H, Honma T, Matsumoto T, Yokoyama S.
Bioorg Med Chem, 19(22), 6892-6905 (2011).
15

A fluorescence correlation spectroscopy-based assay for fragment screening of slowly inhibiting protein-peptide interaction inhibitors.

Mikuni J, Kato M, Taruya S, Tsuganezawa K, Mori M, Ogawa N, Honma T, Yokoyama S, Kojima H, Okabe T, Nagano T, Tanaka A.
Anal Biochem, 402(1), 26-31 (2010).
16

Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei.

Kido Y, Shiba T, Inaoka DK, Sakamoto K, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Moore A, Harada S, Kita K.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 66(pt3), 275-278 (2010).
17

Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase

Balogun Emmanuel Oluwadare; Inaoka Daniel Ken; Kido Yasutoshi; Shiba Tomoo; Nara Takeshi; Aoki Takashi; Honma Teruki; Tanaka Akiko; Inoue Masayuki; Matsuoka Shigeru; Michels Paul A. M, Harada Shigeharu; Kita Kiyoshi.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 66(Pt3), 304-308 (2010).
18

Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening.

Sato T, Honma T, Yokoyama S.
J Chem Inf Model, 50(1), 170-185 (2010).
19

In silico functional profiling of small molecules and its applications.

Sato T, Matsuo Y, Honma T, Yokoyama S.
J Med Chem, 51(24), 7705-7716 (2008).
20

Predicting human liver microsomal stability with machine learning techniques.

Sakiyama Y, Yuki H, Moriya T, Hattori K, Suzuki M, Shimada K, Honma T.
J Mol Graph Model, 26(6), 907-915 (2008).
21

Recent advances in de novo design strategy for practical lead identification

Honma T.
Med Res Rev, 23(5), 606-632 (2003).
22

Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design.

Honma T, Hayashi K, Aoyama T, Hashimoto N, Machida T, Fukasawa K, Iwama T, Ikeura C, Ikuta M, Suzuki-Takahashi I, Iwasawa Y, Hayama T, Nishimura S, Morishima H.
J Med Chem, 44(26), 4615-4627 (2001).
23

A Novel Approach for the Development of Selective Cdk4 Inhibitors:  Library Design Based on Locations of Cdk4 Specific Amino Acid Residues

Honma T, Yoshizumi T, Hashimoto N, Hayashi K, Kawanishi N, Fukasawa K, Takaki T, Ikeura C, Ikuta M, Suzuki-Takahashi I, Hayama T, Nishimura S, Morishima H.
J Med Chem, 44(26), 4628-4640 (2001).
24

Crystallographic Approach to Identification of Cyclin-dependent Kinase 4 (CDK4)-specific Inhibitors by Using CDK4 Mimic CDK2 Protein

Ikuta M, Kamata K, Fukasawa K, Honma T, Machida T, Hirai H, Suzuki-Takahashi I, Hayama T, Nishimura S.
J Biol Chem, 276(29), 27548-27554 (2001).
25

Synthesis and biological activities of NB-506 analogues modified at the glucose group.

Ohkubo M, Nishimura T, Kawamoto H, Nakano M, Honma T, Yoshinari T, Arakawa H, Suda H, Morishima H, Nishimura S.
Bioorg Med Chem Lett, 10(5), 419-422 (2000).
26

Synthesis and biological activities of NB-506 analogues: Effects of the positions of two hydroxyl groups at the indole rings.

Ohkubo M, Nishimura T, Honma T, Nishimura I, Ito S, Yoshinari T, Suda HA, Morishima H, Nishimura S.
Bioorg Med Chem Lett, 9(23), 3307-3312 (1999).
27

Total Synthesis of (+)-Obtusenyne.

Fujiwara K, Awakura D, Tsunashima M, Nakamura A, Honma T, Murai A.
J Org Chem, 64(8), 2616-2617 (1999).
28

Biogenetic intermediates, (3e and 3z,12z)-laurediols and (3e and 3z)-12,13- dihydrolaurediols, isolated from Laurencia nipponica.

Fukuzawa, A.; Honma, T.; Takasugi, Y.; Murai, A.
Phytochemistry, 32(6), 1435-1438 (1999).
29

Structural basis for chemical inhibition of human blood coagulation factor Xa.

Kamata K, Kawamoto H, Honma T, Iwama T, Kim SH.
Proc Natl Acad Sci U S A, 95(12), 6630-6635 (1998).
30

Synthesis of dissymmetric indolocarbazole glycosides using the Mitsunobu reaction at the glycosylation step.

Ohkubo, M.; Nishimura, T.; Jona, H.; Honma, T.; Ito, S.; Morishima, H.
Tetrahedron, 53(17), 5937-5950 (1997).
31

Practical Synthesis of Indolopyrrolocarbazoles

Ohkubo M, Nishimura T, Jona H, Honma T, Morishima H.
Tetrahedron, 52(24), 8099-8112 (1996).
32

Novel synthesis of a dihydroxyethylene isostere of renin inhibitors.

Atsuumi S, Ikeura C, Honma T, Morishima H.
Chem Pharm Bull, 42(10), 2164-2166 (1994).

和文論文

1

機械学習による薬物のヒト肝ミクロゾーム安定性の予測

嵜山陽二郎, 幸瞳, 本間光貴.
CBI学会誌,（2）,1-5,2009.

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Structure-based Molecular Design Team, please visit the following websites.


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