1
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Bashore F, Annor-Gyamfi J, Du Y, Katis V, Nwogbo F, Flax RG, Frye SV, Pearce KH, Fu H, Willson TM, Drewry DH, Axtman AD. Fused Tetrahydroquinolines Are Interfering with Your Assay. J Med Chem 2023; 66:14434-14446. [PMID: 37874947 PMCID: PMC10641811 DOI: 10.1021/acs.jmedchem.3c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Tricyclic tetrahydroquinolines (THQs) have been repeatedly reported as hits across a diverse range of high-throughput screening (HTS) campaigns. The activities of these compounds, however, are likely due to reactive byproducts that interfere with the assay. As a lesser studied class of pan-assay interference compounds, the mechanism by which fused THQs react with protein targets remains largely unknown. During HTS follow-up, we characterized the behavior and stability of several fused tricyclic THQs. We synthesized key analogues to pinpoint the cyclopentene ring double bond as a source of reactivity of fused THQs. We found that these compounds degrade in solution under standard laboratory conditions in days. Importantly, these observations make it likely that fused THQs, which are ubiquitously found within small molecule screening libraries, are unlikely the intact parent compounds. We urge deprioritization of tricylic THQ hits in HTS follow-up and caution against the investment of resources to follow-up on these problematic compounds.
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Affiliation(s)
- Frances
M. Bashore
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joel Annor-Gyamfi
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yuhong Du
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Vittorio Katis
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Centre for Medicines
Discovery, Nuffield Department of Medicine Research Building, Old
Road Campus, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Felix Nwogbo
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Raymond G. Flax
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Haian Fu
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Timothy M. Willson
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David H. Drewry
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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2
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Hatano A, Matsuzaka R, Shimane G, Wakana H, Suzuki K, Nishioka C, Kojima A, Kidowaki M. Introduction of pseudo-base benzimidazole derivatives into nucleosides via base exchange by a nucleoside metabolic enzyme. Bioorg Med Chem 2023; 91:117411. [PMID: 37451053 DOI: 10.1016/j.bmc.2023.117411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
In alternate organic synthesis, biocatalysis using enzymes provides a more stereoselective and cost-effective approach. Synthesis of unnatural nucleosides by nucleoside base exchange reactions using nucleoside-metabolizing enzymes has previously shown that the 5-position recognition of pyrimidine bases on nucleoside substrates is loose and can be used to introduce functional molecules into pyrimidine nucleosides. Here we explored the incorporation of purine pseudo bases into nucleosides by the base exchange reaction of pyrimidine nucleoside phosphorylase (PyNP), demonstrating that an imidazole five-membered ring is an essential structure for the reaction. In the case of benzimidazole, the base exchange proceeded to give the deoxyribose form in 96 % yield, and the ribose form in 23 % yield. The reaction also proceeded with 1H-imidazo[4,5-b]phenazine, a benzimidazole analogue with an additional ring, although the yield of nucleoside was only 31 %. Docking simulations between 1H and imidazo[4,5-b]phenazine nucleoside and the active site of PyNP (PDB 1BRW) supported our observation that 1H-imidazo[4,5-b]phenazine can be used as a substrate by PyNP. Thus, the enzymatic substitution reaction using PyNP can be used to incorporate many purine pseudo bases and benzimidazole derivatives with various functional groups into nucleoside structures, which have potential utility as diagnostic or therapeutic agents.
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Affiliation(s)
- Akihiko Hatano
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Riki Matsuzaka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Genki Shimane
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hiroyuki Wakana
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kou Suzuki
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Nishioka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Aoi Kojima
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Masatoshi Kidowaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-7-5, Toyosu, Koto-ku, Tokyo 135-8548, Japan
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3
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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4
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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. A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Sci Rep 2019; 9:19585. [PMID: 31863054 PMCID: PMC6925144 DOI: 10.1038/s41598-019-55069-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
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.
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Affiliation(s)
- Shuntaro Chiba
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan
| | | | - Petro Borysko
- Bienta/Enamine Ltd., 78 Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., 78 Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Nobuaki Yasuo
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Research Fellow of the Japan Society for the Promotion of Science DC1, Tokyo, Japan
| | - Ryunosuke Yoshino
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8575, Japan
| | - Kazuyoshi Ikeda
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Woong-Hee Shin
- Department of Biological Science, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, Indiana, 47907, USA.,Department of Computer Science, Purdue University, Indiana, 47907, USA
| | - Mitsuo Iwadate
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Hideaki Umeyama
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Takaaki Ichikawa
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Reiji Teramoto
- Discovery technology research department, Research division, Chugai Pharmaceutical Co.,Ltd., 200, Kajiwara, Kamakura, Kanagawa, 247-8530, Japan
| | - Kun-Yi Hsin
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan
| | - Vipul Gupta
- The Systems Biology Research Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Hiroaki Kitano
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan.,The Systems Biology Research Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan.,Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Mika Sakamoto
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Akiko Higuchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Nobuaki Miura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.,Center for Simulation Science and Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.,School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masahiro Mochizuki
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,IMSBIO Co., Ltd., Level 6 OWL TOWER, 4-21-1 Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan
| | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - A Mary Thangakani
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - D Velmurugan
- CAS in Crystallography and Biophysics and Bioinformatics Facility, University of Madras, Chennai, 600025, Tamilnadu, India
| | - M Michael Gromiha
- Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - Itsuo Nakane
- Okazaki City Hall, 2-9 Juo-cho Okazaki, Aichi, 444-8601, Japan
| | - Nanako Uchida
- IQVIA Services Japan K.K., 4-10-18 Takanawa Minato-ku, Tokyo, 108-0074, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Training Program of Leaders for Integrated Medical System (LIMS), Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Modong Tan
- Department of Chemistry & Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hironori K Nakamura
- Biomodeling Research Co., Ltd., 1-704-2 Uedanishi, Tenpaku-ku, Nagoya, 468-0058, Japan
| | - Shogo D Suzuki
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tomoki Ito
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Masahiro Kawatani
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Kentaroh Kudoh
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Sakurako Takashina
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Kazuki Z Yamamoto
- Isotope Science Center, The University of Tokyo, 2-11- 16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Keita Oda
- Google Japan Inc., 6-10-1 Roppongi, Minato-ku, Tokyo, 106-6126, Japan.,Otemachi Bldg. 3F, 1-6-1, Preferred Networks, Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Daisuke Kobayashi
- Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tatsuya Okuno
- Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Shintaro Minami
- Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - George Chikenji
- Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Philip Prathipati
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Chioko Nagao
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Attayeb Mohsen
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Mari Ito
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Teruki Honma
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takashi Ishida
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8575, Japan.,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan
| | - Yutaka Akiyama
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan
| | - Masakazu Sekijima
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan. .,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan. .,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan.
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5
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Hatano A, Kanno Y, Kondo Y, Sunaga Y, Umezawa H, Fukui K. Use of a deoxynojirimycin-fluorophore conjugate as a cell-specific imaging probe targeting α-glucosidase on cell membranes. Bioorg Med Chem 2019; 27:859-864. [PMID: 30712980 DOI: 10.1016/j.bmc.2019.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 11/26/2022]
Abstract
Molecules designed for cell-specific imaging were studied, taking advantage of an enzyme-inhibitor interaction. 1-Deoxynojirimycin (DNJ) can be actively captured by cells which express the surface membrane protein α-glucosidase. New probes composed of DNJ for recognition linked to a fluorophore signal portion were prepared (DNJ-CF31, DNJ-Dans 2 and DNJ-DEAC 3). Docking simulations revealed that the inhibitors acarbose and miglitol and the inhibitor portion of the probes bind at the same position in the pocket of α-glucosidase (human-derived PDB: 3TON). The ability of probes 1-3 to detect the difference between HeLa cells (from human cervical cancer tissue), Neuro-2a cells (from a mouse neuroblastoma C1300 tumor), N1E-115 cells (from a mouse brain neuroblastoma C1300 tumor), A1 cells (from the astrocyte of a newborn mouse brain), and Caco-2 cells (from a human colon carcinoma) was evaluated, and cell-specific fluorescence imaging was possible for conjugate probes 1 and 2. Caco-2 cells treated with probes 1 and 2 showed blue and green fluorescence, respectively, from the cell membrane, and did not stain the Caco-2 cells inside. These results show that DNJ-CF31 and DNJ-Dans 2 recognize an α-glucosidase protein on the surface of Caco-2 cells. Probes 1 and 2 did not stain any part of the other cells. This cell-specific imaging strategy is applicable for a variety of therapeutic agents for many diseases.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Yuichi Kanno
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yuya Kondo
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yuta Sunaga
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hatsumi Umezawa
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Koji Fukui
- Department of Bioscience and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
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6
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Hatano A, Wakana H, Terado N, Kojima A, Nishioka C, Iizuka Y, Imaizumi T, Uehara S. Bio-catalytic synthesis of unnatural nucleosides possessing a large functional group such as a fluorescent molecule by purine nucleoside phosphorylase. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01063g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unnatural nucleosides are attracting interest as potential diagnostic tools, medicines, and functional molecules.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Hiroyuki Wakana
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Nanae Terado
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Aoi Kojima
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Chisato Nishioka
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Yu Iizuka
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Takuya Imaizumi
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Sanae Uehara
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
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7
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Fukunishi Y, Yamasaki S, Yasumatsu I, Takeuchi K, Kurosawa T, Nakamura H. Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction. Mol Inform 2017; 36:1600013. [PMID: 28001004 PMCID: PMC5297997 DOI: 10.1002/minf.201600013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/01/2016] [Indexed: 01/26/2023]
Abstract
In order to improve docking score correction, we developed several structure-based quantitative structure activity relationship (QSAR) models by protein-drug docking simulations and applied these models to public affinity data. The prediction models used descriptor-based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. The binding free energy that corresponded to the docking score was approximated by a weighted average of docking scores for multiple proteins, and we tried linear, weighted linear and polynomial regression models considering the compound similarities. In addition, we tried a combination of these regression models for individual data sets such as IC50 , Ki , and %inhibition values. The cross-validation results showed that the weighted linear model was more accurate than the simple linear regression model. Thus, the QSAR approaches based on the affinity data of public databases should improve docking scores.
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Affiliation(s)
- Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Satoshi Yamasaki
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Isao Yasumatsu
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takashi Kurosawa
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Hitachi Solutions East Japan, 12-1 Ekimaehoncho, Kawasaki-ku, Kanagawa, 210-0007, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Hatano A, Kanno Y, Kondo Y, Sunaga Y, Umezawa H, Okada M, Yamada H, Iwaki R, Kato A, Fukui K. Synthesis and characterization of novel, conjugated, fluorescent DNJ derivatives for α-glucosidase recognition. Bioorg Med Chem 2017; 25:773-778. [DOI: 10.1016/j.bmc.2016.11.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/17/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
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9
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Abstract
Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
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10
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Pressor mechanism evaluation for phytochemical compounds using in silico compound–protein interaction prediction. Regul Toxicol Pharmacol 2013; 67:115-24. [DOI: 10.1016/j.yrtph.2013.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 01/30/2023]
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11
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Hatano A, Kurosu M, Yonaha S, Okada M, Uehara S. One-pot approach to functional nucleosides possessing a fluorescent group using nucleobase-exchange reaction by thymidine phosphorylase. Org Biomol Chem 2013; 11:6900-5. [DOI: 10.1039/c3ob41605d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Peragovics Á, Simon Z, Tombor L, Jelinek B, Hári P, Czobor P, Málnási-Csizmadia A. Virtual affinity fingerprints for target fishing: a new application of Drug Profile Matching. J Chem Inf Model 2012; 53:103-13. [PMID: 23215025 DOI: 10.1021/ci3004489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We recently introduced Drug Profile Matching (DPM), a novel virtual affinity fingerprinting bioactivity prediction method. DPM is based on the docking profiles of ca. 1200 FDA-approved small-molecule drugs against a set of nontarget proteins and creates bioactivity predictions based on this pattern. The effectiveness of this approach was previously demonstrated for therapeutic effect prediction of drug molecules. In the current work, we investigated the applicability of DPM for target fishing, i.e. for the prediction of biological targets for compounds. Predictions were made for 77 targets, and their accuracy was measured by Receiver Operating Characteristic (ROC) analysis. Robustness was tested by a rigorous 10-fold cross-validation procedure. This procedure identified targets (N = 45) with high reliability based on DPM performance. These 45 categories were used in a subsequent study which aimed at predicting the off-target profiles of currently approved FDA drugs. In this data set, 79% of the known drug-target interactions were correctly predicted by DPM, and additionally 1074 new drug-target interactions were suggested. We focused our further investigation on the suggested interactions of antipsychotic molecules and confirmed several interactions by a review of the literature.
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Affiliation(s)
- Ágnes Peragovics
- Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
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13
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Peragovics Á, Simon Z, Brandhuber I, Jelinek B, Hári P, Hetényi C, Czobor P, Málnási-Csizmadia A. Contribution of 2D and 3D Structural Features of Drug Molecules in the Prediction of Drug Profile Matching. J Chem Inf Model 2012; 52:1733-44. [PMID: 22697495 DOI: 10.1021/ci3001056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ágnes Peragovics
- Department of Biochemistry,
Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány
1/C, H-1117 Budapest, Hungary
- Drugmotif Ltd., Szent Erzsébet
krt. 14, H-2112 Veresegyház, Hungary
| | - Zoltán Simon
- Drugmotif Ltd., Szent Erzsébet
krt. 14, H-2112 Veresegyház, Hungary
| | | | - Balázs Jelinek
- Department of Biochemistry,
Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány
1/C, H-1117 Budapest, Hungary
- Drugmotif Ltd., Szent Erzsébet
krt. 14, H-2112 Veresegyház, Hungary
| | - Péter Hári
- Drugmotif Ltd., Szent Erzsébet
krt. 14, H-2112 Veresegyház, Hungary
| | - Csaba Hetényi
- HAS-ELTE Molecular Biophysics Research Group, Pázmány Péter sétány.
1/C, H-1117 Budapest, Hungary
| | - Pál Czobor
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa utca 6, H-1083 Budapest,
Hungary
| | - András Málnási-Csizmadia
- Department of Biochemistry,
Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány
1/C, H-1117 Budapest, Hungary
- HAS-ELTE Molecular Biophysics Research Group, Pázmány Péter sétány.
1/C, H-1117 Budapest, Hungary
- Drugmotif Ltd., Szent Erzsébet
krt. 14, H-2112 Veresegyház, Hungary
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14
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Takashima Y, Mizohata E, Krungkrai SR, Fukunishi Y, Kinoshita T, Sakata T, Matsumura H, Krungkrai J, Horii T, Inoue T. The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase. J Biochem 2012; 152:133-8. [PMID: 22740703 DOI: 10.1093/jb/mvs070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) catalyses the final step in the de novo synthesis of uridine 5'-monophosphate (UMP) from orotidine 5'-monophosphate (OMP). A defective PfOMPDC enzyme is lethal to the parasite. Novel in silico screening methods were performed to select 14 inhibitors against PfOMPDC, with a high hit rate of 9%. X-ray structure analysis of PfOMPDC in complex with one of the inhibitors, 4-(2-hydroxy-4-methoxyphenyl)-4-oxobutanoic acid, was carried out to at 2.1 Å resolution. The crystal structure revealed that the inhibitor molecule occupied a part of the active site that overlaps with the phosphate-binding region in the OMP- or UMP-bound complexes. Space occupied by the pyrimidine and ribose rings of OMP or UMP was not occupied by this inhibitor. The carboxyl group of the inhibitor caused a dramatic movement of the L1 and L2 loops that play a role in the recognition of the substrate and product molecules. Combining part of the inhibitor molecule with moieties of the pyrimidine and ribose rings of OMP and UMP represents a suitable avenue for further development of anti-malarial drugs.
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Affiliation(s)
- Yasuhide Takashima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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15
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Fukunishi Y, Mizukoshi Y, Takeuchi K, Shimada I, Takahashi H, Nakamura H. Protein–ligand docking guided by ligand pharmacophore-mapping experiment by NMR. J Mol Graph Model 2011; 31:20-7. [DOI: 10.1016/j.jmgm.2011.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 12/01/2022]
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Abstract
IMPORTANCE OF THE FIELD Structure-based in silico drug screening is now widely used in drug development projects. Structure-based in silico drug screening is generally performed using a protein-compound docking program and docking scoring function. Many docking programs have been developed over the last 2 decades, but their prediction accuracy remains insufficient. AREAS COVERED IN THIS REVIEW This review highlights the recent progress of the post-processing of protein-compound complexes after docking. WHAT THE READER WILL GAIN These methods utilize ensembles of docking poses of compounds to improve the prediction accuracy for the ligand-docking pose and screening results. While the individual docking poses are not reliable, the free energy surface or the most probable docking pose can be estimated from the ensemble of docking poses. TAKE HOME MESSAGE The protein-compound docking program provides an arbitral rather than a canonical ensemble of docking poses. When the ensemble of docking poses satisfies the canonical ensemble, we can discuss how these post-docking analysis methods work and fail. Thus, improvements to the docking software will be needed in order to generate well-defined ensembles of docking poses.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135 0064, Japan.
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17
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Semantic similarity for automatic classification of chemical compounds. PLoS Comput Biol 2010; 6. [PMID: 20885779 PMCID: PMC2944781 DOI: 10.1371/journal.pcbi.1000937] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 08/23/2010] [Indexed: 11/28/2022] Open
Abstract
With the increasing amount of data made available in the chemical field, there is a strong need for systems capable of comparing and classifying chemical compounds in an efficient and effective way. The best approaches existing today are based on the structure-activity relationship premise, which states that biological activity of a molecule is strongly related to its structural or physicochemical properties. This work presents a novel approach to the automatic classification of chemical compounds by integrating semantic similarity with existing structural comparison methods. Our approach was assessed based on the Matthews Correlation Coefficient for the prediction, and achieved values of 0.810 when used as a prediction of blood-brain barrier permeability, 0.694 for P-glycoprotein substrate, and 0.673 for estrogen receptor binding activity. These results expose a significant improvement over the currently existing methods, whose best performances were 0.628, 0.591, and 0.647 respectively. It was demonstrated that the integration of semantic similarity is a feasible and effective way to improve existing chemical compound classification systems. Among other possible uses, this tool helps the study of the evolution of metabolic pathways, the study of the correlation of metabolic networks with properties of those networks, or the improvement of ontologies that represent chemical information. Among the existing systems capable of computationally comparing chemical compounds, the majority use only structural and physicochemical properties. However, with the emergence of ChEBI and other chemical compound databases, it has become feasible to create a system that can use the relevance of compounds in a biological context as well. This setting enables the distinction of molecules with different roles in nature but similar structures, or similar roles and different structures. ChEBI is organized as an ontology that classifies chemical compounds, which we use to derive a semantic similarity measure that reflects the biological relevance of molecules. In an effort to use as much information as possible, we introduce Chym, a system that integrates structural and semantic information in a single hybrid metric, and we show the accuracy of the system in three distinct classification problems, which consist in deciding whether a compound crosses the blood brain barrier, is a P-glycoprotein substrate or an estrogen receptor ligand. Chym outperforms the previous attempts to solve these three problems, with a maximum accuracy of 90.0%.
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18
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A similarity search using molecular topological graphs. J Biomed Biotechnol 2009; 2009:231780. [PMID: 20037730 PMCID: PMC2796334 DOI: 10.1155/2009/231780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 07/26/2009] [Accepted: 09/19/2009] [Indexed: 11/22/2022] Open
Abstract
A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.
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19
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McLean LR, Zhang Y, Li H, Li Z, Lukasczyk U, Choi YM, Han Z, Prisco J, Fordham J, Tsay JT, Reiling S, Vaz RJ, Li Y. Discovery of covalent inhibitors for MIF tautomerase via cocrystal structures with phantom hits from virtual screening. Bioorg Med Chem Lett 2009; 19:6717-20. [PMID: 19836948 DOI: 10.1016/j.bmcl.2009.09.106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 09/25/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Biochemical and X-ray crystallographic studies confirmed that hydroxyquinoline derivatives identified by virtual screening were actually covalent inhibitors of the MIF tautomerase. Adducts were formed by N-alkylation of the Pro-1 at the catalytic site with a loss of an amino group of the inhibitor.
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Affiliation(s)
- Larry R McLean
- Discovery Research, sanofi-aventis, Bridgewater, NJ 08807, USA.
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20
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FUKUNISHI Y, SUGIHARA Y, MIKAMI Y, SAKAI K, KUSUDO H, NAKAMURA H. Advanced in-silico drug screening to achieve high hit ratio. ACTA ACUST UNITED AC 2009. [DOI: 10.5571/syntheng.2.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Fukunishi Y, Nakamura H. A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method. J Mol Graph Model 2008; 27:628-36. [PMID: 19046907 DOI: 10.1016/j.jmgm.2008.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/13/2008] [Accepted: 10/15/2008] [Indexed: 11/28/2022]
Abstract
We developed a new molecular dynamics simulation method for molecular overlapping (alignment) and ligand-based in-silico drug screening based on molecular similarity. The molecular system consists of the query compound and the other compound(s) selected from a compound library. The newly introduced intermolecular interaction between compounds is proportional to the molecular overlap instead of the van der Waals and Coulomb interactions between atoms of different molecules. This method was able to achieve both conformer generation of molecules and molecular overlapping (alignment) at the same time. After an energy minimization and following short-time MD simulation, the molecules in the system were overlapped with each other and the similarity between compounds was measured by the volume of the overlap. We applied this MD simulation method to ligand-based in-silico drug screening and found that it worked well for several targets.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, Japan.
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22
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Omagari K, Mitomo D, Kubota S, Nakamura H, Fukunishi Y. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Adv Appl Bioinform Chem 2008; 1:19-28. [PMID: 21918604 PMCID: PMC3169939 DOI: 10.2147/aabc.s3767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We examined the procedures to combine two different in silico drug-screening results to achieve a high hit ratio. When the 3D structure of the target protein and some active compounds are known, both structure-based and ligand-based in silico screening methods can be applied. In the present study, the machine-learning score modification multiple target screening (MSM-MTS) method was adopted as a structure-based screening method, and the machine-learning docking score index (ML-DSI) method was adopted as a ligand-based screening method. To combine the predicted compound’s sets by these two screening methods, we examined the product of the sets (consensus set) and the sum of the sets. As a result, the consensus set achieved a higher hit ratio than the sum of the sets and than either individual predicted set. In addition, the current combination was shown to be robust enough for the structural diversities both in different crystal structure and in snapshot structures during molecular dynamics simulations.
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Affiliation(s)
- Katsumi Omagari
- Japan Biological Informatics Consortium (JBiC), Koto-ku, Tokyo, Japan
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23
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INOUE T, ADACHI H, MURAKAMI S, TAKANO K, MATSUMURA H, MORI Y, FUKUNISHI Y, NAKAMURA H, KINOSHITA T, NAKANISHI I, OKUNO Y, MINAKATA S, SHIMOJO S, SAKATA T. New Progressing Crystallization Technology of Membrane Protein and Introduction of Pharamaceutical Innovation Value Chain. YAKUGAKU ZASSHI 2008; 128:497-505. [DOI: 10.1248/yakushi.128.497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tsuyoshi INOUE
- Graduate School of Engineering Osaka University
- NPO BioGrid Center Kansai
| | | | - Satoshi MURAKAMI
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University
| | | | | | - Yusuke MORI
- Graduate School of Engineering Osaka University
| | | | - Haruki NAKAMURA
- NPO BioGrid Center Kansai
- Research Center of Structural and Functional Proteomics, Institute for Protein Research, Osaka University
| | - Takayoshi KINOSHITA
- Department of Applied Biochemistry, Graduate School of Agriculture and Life Sciences, Osaka Prefecture University
| | - Isao NAKANISHI
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Yasushi OKUNO
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | | | - Shinji SHIMOJO
- NPO BioGrid Center Kansai
- Cybermedia Center, Osaka University
| | - Tsuneaki SAKATA
- NPO BioGrid Center Kansai
- Cybermedia Center, Osaka University
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24
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Zhou JZ. Structure-directed combinatorial library design. Curr Opin Chem Biol 2008; 12:379-85. [PMID: 18328830 DOI: 10.1016/j.cbpa.2008.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 02/11/2008] [Indexed: 11/30/2022]
Abstract
In recent years pharmaceutical companies have utilized structure-based drug design and combinatorial library design techniques to speed up their drug discovery efforts. Both approaches are routinely used in the lead discovery and lead optimization stages of the drug discovery process. Fragment-based drug design, a new power tool in the drug design toolbox, is also gaining acceptance across the pharmaceutical industry. This review will focus on the interplay between these three design techniques and recent developments in computational methodologies that enhance their integration. Examples of successful synergistic applications of these three techniques will be highlighted. Opinion regarding possible future directions of the field will be given.
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Affiliation(s)
- Joe Zhongxiang Zhou
- Department of Structural and Computational Biology, Pfizer Global Research & Development, La Jolla Laboratories, San Diego, CA 92121, USA.
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25
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Fukunishi Y, Nakamura H. Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. J Chem Inf Model 2008; 48:148-56. [DOI: 10.1021/ci700306s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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26
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Murali S, Hojo S, Tsujishita H, Nakamura H, Fukunishi Y. In-silico drug screening method based on the protein–compound affinity matrix using the factor selection technique. Eur J Med Chem 2007; 42:966-76. [PMID: 17307278 DOI: 10.1016/j.ejmech.2006.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 12/14/2006] [Accepted: 12/21/2006] [Indexed: 11/25/2022]
Abstract
We have developed a new in-silico drug screening method, a modified version of a docking score index (DSI) method, based on a protein-compound docking affinity matrix. By using this method, the docking scores are converted to the docking score indexes by the principal component analysis (PCA) method and each compound is projected into a PCA space. In this study, we propose a method to select a set of suitable principal component axes and evaluate the database enrichment for 12 target proteins. This method selects the new active compounds or hits, which are close to the known active compounds, thereby enhancing the database enrichment.
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Affiliation(s)
- Sukumaran Murali
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan
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27
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Xie L, Bourne PE. A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 2007; 8 Suppl 4:S9. [PMID: 17570152 PMCID: PMC1892088 DOI: 10.1186/1471-2105-8-s4-s9] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will lead to improved methods for protein-ligand docking and binding site analysis. Most current shape descriptors characterize only the local properties of protein structure using an all-atom representation and are slow to compute. We need new shape descriptors that have the ability to capture both local and global structural information, are robust for application to models and low quality structures and are computationally efficient to permit high throughput analysis of protein structures. Results We introduce a new shape description that requires only the Cα atoms to represent the protein structure, thus making it both fast and suitable for use on models and low quality structures. The notion of a geometric potential is introduced to quantitatively describe the shape of the structure. This geometric potential is dependent on both the global shape of the protein structure as well as the surrounding environment of each residue. When applying the geometric potential for binding site prediction, approximately 85% of known binding sites can be accurately identified with above 50% residue coverage and 80% specificity. Moreover, the algorithm is fast enough for proteome-scale applications. Proteins with fewer than 500 amino acids can be scanned in less than two seconds. Conclusion The reduced representation of the protein structure combined with the geometric potential provides a fast, quantitative description of protein-ligand binding sites with potential for use in large-scale predictions, comparisons and analysis.
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Affiliation(s)
- Lei Xie
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Philip E Bourne
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Fukunishi Y, Kubota S, Nakamura H. Finding ligands for G protein-coupled receptors based on the protein–compound affinity matrix. J Mol Graph Model 2007; 25:633-43. [PMID: 16777448 DOI: 10.1016/j.jmgm.2006.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Revised: 04/27/2006] [Accepted: 05/02/2006] [Indexed: 11/18/2022]
Abstract
We developed a novel method of identifying new active ligands based on information related to known active compounds using protein-compound docking simulations, even when the tertiary structure of the actual target receptor protein is unknown. This method was used to find ligands of G protein-coupled receptors (GPCRs), i.e., agonists and antagonists of histamine, adrenaline, serotonin and dopamine receptors. The principal component analysis (PCA) method was applied to the protein-compound affinity matrix, which was given by thorough docking calculations between sets of many protein pockets and chemical compounds. The set of protein pockets did not necessary include the target protein. Each compound was depicted as a point in the PCA space. Compounds in a sphere, whose center was set to the known active compound in the multi-dimensional PCA space or to the average position of several known active compounds, were selected as candidate-hit compounds. Our method was found to be effective for finding the ligands of GPCRs based on known native ligands, even when only the soluble protein structures were used in the docking simulations.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Tokyo 135-0064, Japan.
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29
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Fukunishi Y, Kubota S, Nakamura H. Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening. J Chem Inf Model 2006; 46:2071-84. [PMID: 16995738 DOI: 10.1021/ci060152z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a new method to improve the accuracy of molecular interaction data using a molecular interaction matrix. This method was applied to enhance the database enrichment of in silico drug screening and in silico target protein screening using a protein-compound affinity matrix calculated by a protein-compound docking software. Our assumption was that the protein-compound binding free energy of a compound could be improved by a linear combination of its docking scores with many different proteins. We proposed two approaches to determine the coefficients of the linear combination. The first approach is based on similarity among the proteins, and the second is a machine-learning approach based on the known active compounds. These methods were applied to in silico screening of the active compounds of several target proteins and in silico target protein screening.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan.
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31
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Fukunishi Y, Hojo S, Nakamura H. An Efficient in Silico Screening Method Based on the Protein−Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands. J Chem Inf Model 2006; 46:2610-22. [PMID: 17125201 DOI: 10.1021/ci600334u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method has been developed to design a focused library based on available active compounds using protein-compound docking simulations. This method was applied to the design of a focused library for cytochrome P450 (CYP) ligands, not only to distinguish CYP ligands from other compounds but also to identify the putative ligands for a particular CYP. Principal component analysis (PCA) was applied to the protein-compound affinity matrix, which was obtained by thorough docking calculations between a large set of protein pockets and chemical compounds. Each compound was depicted as a point in the PCA space. Compounds that were close to the known active compounds were selected as candidate hit compounds. A machine-learning technique optimized the docking scores of the protein-compound affinity matrix to maximize the database enrichment of the known active compounds, providing an optimized focused library.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan.
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32
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Fukunishi Y, Kubota S, Kanai C, Nakamura H. A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening. J Comput Aided Mol Des 2006; 20:237-48. [PMID: 16897580 DOI: 10.1007/s10822-006-9047-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2006] [Accepted: 04/25/2006] [Indexed: 11/28/2022]
Abstract
We developed a new structure-based in-silico screening method using a negative image of a ligand-binding pocket and a multi-protein-compound interaction matrix. Based on the structure of the ligand pocket of the target protein, we designed a negative image, which consists of virtual atoms whose radii are close to those of carbon atoms. The virtual atoms fit the pocket ideally and achieve an optimal Coulomb interaction. A protein-compound docking program calculates the protein-compound interaction matrix for many proteins and many compounds including the negative image, which can be treated as a virtual compound. With specific attention to a vector of docking scores for a single compound with many proteins, we selected a compound whose score vector was similar to that of the negative image as a candidate hit compound. This method was applied to representative target proteins and showed high database enrichment with a relatively quick procedure.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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