A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Shuntaro Chiba; Masahito Ohue; Anastasiia Gryniukova; Petro Borysko; Sergey Zozulya; Nobuaki Yasuo; Ryunosuke Yoshino; Kazuyoshi Ikeda; Woong Hee Shin; Daisuke Kihara; Mitsuo Iwadate; Hideaki Umeyama; Takaaki Ichikawa; Reiji Teramoto; Kun Yi Hsin; Vipul Gupta; Hiroaki Kitano; Mika Sakamoto; Akiko Higuchi; Nobuaki Miura; Kei Yura; Masahiro Mochizuki; Chandrasekaran Ramakrishnan; A. Mary Thangakani; D. Velmurugan; M. Michael Gromiha; Itsuo Nakane; Nanako Uchida; Hayase Hakariya; Modong Tan; Hironori K. Nakamura; Shogo D. Suzuki; Tomoki Ito; Masahiro Kawatani; Kentaroh Kudoh; Sakurako Takashina; Kazuki Z. Yamamoto; Yoshitaka Moriwaki; Keita Oda; Daisuke Kobayashi; Tatsuya Okuno; Shintaro Minami; George Chikenji; Philip Prathipati; Chioko Nagao; Attayeb Mohsen; Mari Ito; Kenji Mizuguchi; Teruki Honma; Takashi Ishida; Takatsugu Hirokawa; Yutaka Akiyama; Masakazu Sekijima

doi:10.1038/s41598-019-55069-y

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki MiuraKei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

School of Advanced Science and Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.

Original language	English
Article number	19585
Journal	Scientific reports
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41598-019-55069-y
Publication status	Published - 2019 Dec 1

ASJC Scopus subject areas

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Chiba, S., Ohue, M., Gryniukova, A., Borysko, P., Zozulya, S., Yasuo, N., Yoshino, R., Ikeda, K., Shin, W. H., Kihara, D., Iwadate, M., Umeyama, H., Ichikawa, T., Teramoto, R., Hsin, K. Y., Gupta, V., Kitano, H., Sakamoto, M., Higuchi, A., ... Sekijima, M. (2019). A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific reports, 9(1), [19585]. https://doi.org/10.1038/s41598-019-55069-y

A prospective compound screening contest identified broader inhibitors for Sirtuin 1. / Chiba, Shuntaro; Ohue, Masahito; Gryniukova, Anastasiia; Borysko, Petro; Zozulya, Sergey; Yasuo, Nobuaki; Yoshino, Ryunosuke; Ikeda, Kazuyoshi; Shin, Woong Hee; Kihara, Daisuke; Iwadate, Mitsuo; Umeyama, Hideaki; Ichikawa, Takaaki; Teramoto, Reiji; Hsin, Kun Yi; Gupta, Vipul; Kitano, Hiroaki; Sakamoto, Mika; Higuchi, Akiko; Miura, Nobuaki; Yura, Kei; Mochizuki, Masahiro; Ramakrishnan, Chandrasekaran; Thangakani, A. Mary; Velmurugan, D.; Gromiha, M. Michael; Nakane, Itsuo; Uchida, Nanako; Hakariya, Hayase; Tan, Modong; Nakamura, Hironori K.; Suzuki, Shogo D.; Ito, Tomoki; Kawatani, Masahiro; Kudoh, Kentaroh; Takashina, Sakurako; Yamamoto, Kazuki Z.; Moriwaki, Yoshitaka; Oda, Keita; Kobayashi, Daisuke; Okuno, Tatsuya; Minami, Shintaro; Chikenji, George; Prathipati, Philip; Nagao, Chioko; Mohsen, Attayeb; Ito, Mari; Mizuguchi, Kenji; Honma, Teruki; Ishida, Takashi; Hirokawa, Takatsugu; Akiyama, Yutaka; Sekijima, Masakazu.

In: Scientific reports, Vol. 9, No. 1, 19585, 01.12.2019.

Research output: Contribution to journal › Article › peer-review

Chiba, S, Ohue, M, Gryniukova, A, Borysko, P, Zozulya, S, Yasuo, N, Yoshino, R, Ikeda, K, Shin, WH, Kihara, D, Iwadate, M, Umeyama, H, Ichikawa, T, Teramoto, R, Hsin, KY, Gupta, V, Kitano, H, Sakamoto, M, Higuchi, A, Miura, N, Yura, K, Mochizuki, M, Ramakrishnan, C, Thangakani, AM, Velmurugan, D, Gromiha, MM, Nakane, I, Uchida, N, Hakariya, H, Tan, M, Nakamura, HK, Suzuki, SD, Ito, T, Kawatani, M, Kudoh, K, Takashina, S, Yamamoto, KZ, Moriwaki, Y, Oda, K, Kobayashi, D, Okuno, T, Minami, S, Chikenji, G, Prathipati, P, Nagao, C, Mohsen, A, Ito, M, Mizuguchi, K, Honma, T, Ishida, T, Hirokawa, T, Akiyama, Y & Sekijima, M 2019, 'A prospective compound screening contest identified broader inhibitors for Sirtuin 1', Scientific reports, vol. 9, no. 1, 19585. https://doi.org/10.1038/s41598-019-55069-y

Chiba, Shuntaro ; Ohue, Masahito ; Gryniukova, Anastasiia ; Borysko, Petro ; Zozulya, Sergey ; Yasuo, Nobuaki ; Yoshino, Ryunosuke ; Ikeda, Kazuyoshi ; Shin, Woong Hee ; Kihara, Daisuke ; Iwadate, Mitsuo ; Umeyama, Hideaki ; Ichikawa, Takaaki ; Teramoto, Reiji ; Hsin, Kun Yi ; Gupta, Vipul ; Kitano, Hiroaki ; Sakamoto, Mika ; Higuchi, Akiko ; Miura, Nobuaki ; Yura, Kei ; Mochizuki, Masahiro ; Ramakrishnan, Chandrasekaran ; Thangakani, A. Mary ; Velmurugan, D. ; Gromiha, M. Michael ; Nakane, Itsuo ; Uchida, Nanako ; Hakariya, Hayase ; Tan, Modong ; Nakamura, Hironori K. ; Suzuki, Shogo D. ; Ito, Tomoki ; Kawatani, Masahiro ; Kudoh, Kentaroh ; Takashina, Sakurako ; Yamamoto, Kazuki Z. ; Moriwaki, Yoshitaka ; Oda, Keita ; Kobayashi, Daisuke ; Okuno, Tatsuya ; Minami, Shintaro ; Chikenji, George ; Prathipati, Philip ; Nagao, Chioko ; Mohsen, Attayeb ; Ito, Mari ; Mizuguchi, Kenji ; Honma, Teruki ; Ishida, Takashi ; Hirokawa, Takatsugu ; Akiyama, Yutaka ; Sekijima, Masakazu. / A prospective compound screening contest identified broader inhibitors for Sirtuin 1. In: Scientific reports. 2019 ; Vol. 9, No. 1.

@article{d36d6ac5bf5e4c0782f5b3527674ac71,

title = "A prospective compound screening contest identified broader inhibitors for Sirtuin 1",

abstract = "Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.",

author = "Shuntaro Chiba and Masahito Ohue and Anastasiia Gryniukova and Petro Borysko and Sergey Zozulya and Nobuaki Yasuo and Ryunosuke Yoshino and Kazuyoshi Ikeda and Shin, {Woong Hee} and Daisuke Kihara and Mitsuo Iwadate and Hideaki Umeyama and Takaaki Ichikawa and Reiji Teramoto and Hsin, {Kun Yi} and Vipul Gupta and Hiroaki Kitano and Mika Sakamoto and Akiko Higuchi and Nobuaki Miura and Kei Yura and Masahiro Mochizuki and Chandrasekaran Ramakrishnan and Thangakani, {A. Mary} and D. Velmurugan and Gromiha, {M. Michael} and Itsuo Nakane and Nanako Uchida and Hayase Hakariya and Modong Tan and Nakamura, {Hironori K.} and Suzuki, {Shogo D.} and Tomoki Ito and Masahiro Kawatani and Kentaroh Kudoh and Sakurako Takashina and Yamamoto, {Kazuki Z.} and Yoshitaka Moriwaki and Keita Oda and Daisuke Kobayashi and Tatsuya Okuno and Shintaro Minami and George Chikenji and Philip Prathipati and Chioko Nagao and Attayeb Mohsen and Mari Ito and Kenji Mizuguchi and Teruki Honma and Takashi Ishida and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima",

note = "Funding Information: We gratefully acknowledge the financial support of The Japan Biological Informatics Consortium (JBIC), Schr{\"o}dinger K.K., Namiki Shoji Co., Ltd., Microsoft Japan Co., Ltd., DataDirect Networks Japan, Inc., Fast Track Initiative, Inc., NEC Corporation, HPCTECH Corporation, IMSBIO Co., Ltd., DiscoveResource, Inc., Biomodeling Research Co., Ltd., Lisit, Co., Ltd., Leave a Nest Co., Ltd., Level Five Co., Ltd., Research Organization for Information Science and Technology (RIST), Teijin Pharma Limited, DELL, NVIDIA Corporation, and Innovations and Future Creation Inc. (MIRAI SOUZOU) which made it possible to complete our contest. We are deeply grateful to Tokyo Institute of Technology, Ministry of Economy, Trade and Industry (METI), Japan Pharmaceutical Manufacturers Association (JPMA), Information Processing Society of Japan (IPSJ), Japanese Society of Bioinformatics (JSBi), Chem-Bio Informatics (CBI) Society, The Japan DataScientist Society, The Science News Ltd., and Nikkan Kogyo Shimbun Ltd. We would like to offer our special thanks to Mr. Toshiaki Miyaki and Ms. Kanako Ozeki. This work is partially supported by the Research Complex Program “Wellbeing Research Campus: Creating new values through technological and social innovation” from Japan Science and Technology Agency (JST) and the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP19am0101112j0003.",

year = "2019",

month = dec,

day = "1",

doi = "10.1038/s41598-019-55069-y",

language = "English",

volume = "9",

journal = "Scientific Reports",

issn = "2045-2322",

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T1 - A prospective compound screening contest identified broader inhibitors for Sirtuin 1

AU - Chiba, Shuntaro

AU - Ohue, Masahito

AU - Gryniukova, Anastasiia

AU - Borysko, Petro

AU - Zozulya, Sergey

AU - Yasuo, Nobuaki

AU - Yoshino, Ryunosuke

AU - Ikeda, Kazuyoshi

AU - Shin, Woong Hee

AU - Kihara, Daisuke

AU - Iwadate, Mitsuo

AU - Umeyama, Hideaki

AU - Ichikawa, Takaaki

AU - Teramoto, Reiji

AU - Hsin, Kun Yi

AU - Gupta, Vipul

AU - Kitano, Hiroaki

AU - Sakamoto, Mika

AU - Higuchi, Akiko

AU - Miura, Nobuaki

AU - Yura, Kei

AU - Mochizuki, Masahiro

AU - Ramakrishnan, Chandrasekaran

AU - Thangakani, A. Mary

AU - Velmurugan, D.

AU - Gromiha, M. Michael

AU - Nakane, Itsuo

AU - Uchida, Nanako

AU - Hakariya, Hayase

AU - Tan, Modong

AU - Nakamura, Hironori K.

AU - Suzuki, Shogo D.

AU - Ito, Tomoki

AU - Kawatani, Masahiro

AU - Kudoh, Kentaroh

AU - Takashina, Sakurako

AU - Yamamoto, Kazuki Z.

AU - Moriwaki, Yoshitaka

AU - Oda, Keita

AU - Kobayashi, Daisuke

AU - Okuno, Tatsuya

AU - Minami, Shintaro

AU - Chikenji, George

AU - Prathipati, Philip

AU - Nagao, Chioko

AU - Mohsen, Attayeb

AU - Ito, Mari

AU - Mizuguchi, Kenji

AU - Honma, Teruki

AU - Ishida, Takashi

AU - Hirokawa, Takatsugu

AU - Akiyama, Yutaka

AU - Sekijima, Masakazu

N1 - Funding Information: We gratefully acknowledge the financial support of The Japan Biological Informatics Consortium (JBIC), Schrödinger K.K., Namiki Shoji Co., Ltd., Microsoft Japan Co., Ltd., DataDirect Networks Japan, Inc., Fast Track Initiative, Inc., NEC Corporation, HPCTECH Corporation, IMSBIO Co., Ltd., DiscoveResource, Inc., Biomodeling Research Co., Ltd., Lisit, Co., Ltd., Leave a Nest Co., Ltd., Level Five Co., Ltd., Research Organization for Information Science and Technology (RIST), Teijin Pharma Limited, DELL, NVIDIA Corporation, and Innovations and Future Creation Inc. (MIRAI SOUZOU) which made it possible to complete our contest. We are deeply grateful to Tokyo Institute of Technology, Ministry of Economy, Trade and Industry (METI), Japan Pharmaceutical Manufacturers Association (JPMA), Information Processing Society of Japan (IPSJ), Japanese Society of Bioinformatics (JSBi), Chem-Bio Informatics (CBI) Society, The Japan DataScientist Society, The Science News Ltd., and Nikkan Kogyo Shimbun Ltd. We would like to offer our special thanks to Mr. Toshiaki Miyaki and Ms. Kanako Ozeki. This work is partially supported by the Research Complex Program “Wellbeing Research Campus: Creating new values through technological and social innovation” from Japan Science and Technology Agency (JST) and the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP19am0101112j0003.

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Y1 - 2019/12/1

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AB - Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.

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A prospective compound screening contest identified broader inhibitors for Sirtuin 1

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