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An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes.
Chiba, Shuntaro; Ishida, Takashi; Ikeda, Kazuyoshi; Mochizuki, Masahiro; Teramoto, Reiji; Taguchi, Y-H; Iwadate, Mitsuo; Umeyama, Hideaki; Ramakrishnan, Chandrasekaran; Thangakani, A Mary; Velmurugan, D; Gromiha, M Michael; Okuno, Tatsuya; Kato, Koya; Minami, Shintaro; Chikenji, George; Suzuki, Shogo D; Yanagisawa, Keisuke; Shin, Woong-Hee; Kihara, Daisuke; Yamamoto, Kazuki Z; Moriwaki, Yoshitaka; Yasuo, Nobuaki; Yoshino, Ryunosuke; Zozulya, Sergey; Borysko, Petro; Stavniichuk, Roman; Honma, Teruki; Hirokawa, Takatsugu; Akiyama, Yutaka; Sekijima, Masakazu.
Afiliação
  • Chiba S; Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, J3-23 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
  • Ishida T; Education Academy of Computational Life Sciences, Tokyo Institute of Technology, J3-141 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
  • Ikeda K; Advanced Computational Drug Discovery Unit, Institute of Innovative Research, Tokyo Institute of Technology, J3-23 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
  • Mochizuki M; Education Academy of Computational Life Sciences, Tokyo Institute of Technology, J3-141 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
  • Teramoto R; Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
  • Taguchi YH; Level Five Co. Ltd., Shiodome Shibarikyu Bldg., 1-2-3 Kaigan, Minato-ku, Tokyo, 105-0022, Japan.
  • Iwadate M; IMSBIO Co., Ltd., Level 6 OWL TOWER, 4-21-1 Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan.
  • Umeyama H; Forerunner Pharma Research, Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
  • Ramakrishnan C; Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
  • Thangakani AM; Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
  • Velmurugan D; Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
  • Gromiha MM; Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India.
  • Okuno T; CAS in Crystallography and Biophysics and Bioinformatics Facility, University of Madras, Chennai, 600025, Tamilnadu, India.
  • Kato K; CAS in Crystallography and Biophysics and Bioinformatics Facility, University of Madras, Chennai, 600025, Tamilnadu, India.
  • Minami S; Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India.
  • Chikenji G; Division of Neurogenetics, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, 466-8550, Japan.
  • Suzuki SD; Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa, Nagoya, 464-8603, Japan.
  • Yanagisawa K; Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.
  • Shin WH; Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa, Nagoya, 464-8603, Japan.
  • Kihara D; Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
  • Yamamoto KZ; Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
  • Moriwaki Y; Department of Biological Sciences, Purdue University, Indiana, 47907, USA.
  • Yasuo N; Department of Biological Sciences, Purdue University, Indiana, 47907, USA.
  • Yoshino R; Department of Computer Science, Purdue University, Indiana, 47907, USA.
  • Zozulya S; Isotope Science Center, The University of Tokyo, 2-11- 16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
  • Borysko P; Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
  • Stavniichuk R; Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
  • Honma T; Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
  • Hirokawa T; Global Scientific Information and Computing Center, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
  • Akiyama Y; Bienta/Enamine Ltd., 78 Chervonotkatska Street, Kyiv, 02660, Ukraine.
  • Sekijima M; National Taras Shevchenko University of Kyiv, 64/13 Volodymyrska Street, Kyiv, 01601, Ukraine.
Sci Rep ; 7(1): 12038, 2017 09 20.
Article em En | MEDLINE | ID: mdl-28931921
ABSTRACT
We propose a new iterative screening contest method to identify target protein inhibitors. After conducting a compound screening contest in 2014, we report results acquired from a contest held in 2015 in this study. Our aims were to identify target enzyme inhibitors and to benchmark a variety of computer-aided drug discovery methods under identical experimental conditions. In both contests, we employed the tyrosine-protein kinase Yes as an example target protein. Participating groups virtually screened possible inhibitors from a library containing 2.4 million compounds. Compounds were ranked based on functional scores obtained using their respective methods, and the top 181 compounds from each group were selected. Our results from the 2015 contest show an improved hit rate when compared to results from the 2014 contest. In addition, we have successfully identified a statistically-warranted method for identifying target inhibitors. Quantitative analysis of the most successful method gave additional insights into important characteristics of the method used.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Inibidores de Proteínas Quinases / Inibidores Enzimáticos / Proteínas Proto-Oncogênicas c-yes / Descoberta de Drogas / Ensaios de Triagem em Larga Escala Tipo de estudo: Diagnostic_studies / Prognostic_studies / Screening_studies Limite: Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Inibidores de Proteínas Quinases / Inibidores Enzimáticos / Proteínas Proto-Oncogênicas c-yes / Descoberta de Drogas / Ensaios de Triagem em Larga Escala Tipo de estudo: Diagnostic_studies / Prognostic_studies / Screening_studies Limite: Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article