1
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Shinya S, Katahira R, Furuita K, Sugiki T, Lee YH, Hattori Y, Takeshita K, Nakagawa A, Kokago A, Akagi KI, Oouchi M, Hayashi F, Kigawa T, Takimoto-Kamimura M, Fujiwara T, Kojima C. 19F chemical library and 19F-NMR for a weakly bound complex structure. RSC Med Chem 2022; 13:1100-1111. [PMID: 36324497 PMCID: PMC9491350 DOI: 10.1039/d2md00170e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/18/2022] [Indexed: 07/24/2023] Open
Abstract
Fragment-based drug discovery (FBDD), which involves small compounds <300 Da, has been recognized as one of the most powerful tools for drug discovery. In FBDD, the affinity of hit compounds tends to be low, and the analysis of protein-compound interactions becomes difficult. In an effort to overcome such difficulty, we developed a 19F-NMR screening method optimizing a 19F chemical library focusing on highly soluble monomeric molecules. Our method was successfully applied to four proteins, including protein kinases and a membrane protein. For FKBP12, hit compounds were carefully validated by protein thermal shift analysis, 1H-15N HSQC NMR spectroscopy, and isothermal titration calorimetry to determine dissociation constants and model complex structures. It should be noted that the 1H and 19F saturation transfer difference experiments were crucial to obtaining highly precise model structures. The combination of 19F-NMR analysis and the optimized 19F chemical library enables the modeling of the complex structure made up of a weak binder and its target protein.
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Affiliation(s)
- Shoko Shinya
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Ritsuko Katahira
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute Chungbuk 28119 South Korea
- Bio-Analytical Science, University of Science and Technology Daejeon 34113 South Korea
- Graduate School of Analytical Science and Technology, Chungnam National University Daejeon 34134 South Korea
| | - Yoshikazu Hattori
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Kohei Takeshita
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Aoi Kokago
- Graduate School of Engineering Science, Yokohama National University Tokiwadai 79-5, Hodogaya-ku Yokohama 2408501 Japan
| | - Ken-Ichi Akagi
- National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito Asagi Ibaraki-city Osaka 567-0085 Japan
| | - Muneki Oouchi
- RIKEN Spring-8 Center 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Fumiaki Hayashi
- RIKEN Spring-8 Center 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Takanori Kigawa
- RIKEN Center for Biosystems Dynamics Research 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Midori Takimoto-Kamimura
- Quantum-Structural Life Science Laboratories, CBI Research Institute 3-11-1 Shibaura, Minato-ku Tokyo 108-0023 Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita Osaka 565-0871 Japan
- Graduate School of Engineering Science, Yokohama National University Tokiwadai 79-5, Hodogaya-ku Yokohama 2408501 Japan
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2
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Saito R, Imai K, Takimoto D, Ezawa T, Sugiyama S, Takimoto-Kamimura M, Kurita N. Water molecule-mediated selective inhibition of bacterial zinc metalloproteinases by non-hydroxamate compounds: Ab initio molecular simulations. J Mol Graph Model 2022; 114:108200. [DOI: 10.1016/j.jmgm.2022.108200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
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3
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Nakamura S, Saito R, Yamamoto S, Kobayashi I, Takeda R, Suzuki R, Kawai K, Takimoto-Kamimura M, Kurita N. Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations. J Mol Graph Model 2021; 105:107873. [PMID: 33640786 DOI: 10.1016/j.jmgm.2021.107873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/19/2022]
Abstract
The androgen receptor (AR), a family of nuclear receptor proteins, stimulates the transcription of androgen-responsive genes. As its abnormal activation can cause the progression of prostate cancer, numerous types of ligands for AR have been developed as promising antagonists for the treatment of prostate cancer. We previously investigated the specific interactions between AR and nine types of existing non-steroidal ligands, using molecular simulations based on molecular mechanics and ab initio fragment molecular orbital methods. The results were confirmed to be comparable to the binding affinities of these ligands observed in experiments. We here propose novel ligands as potent inhibitors against AR and investigate their binding properties to AR, using the same molecular simulations. The results indicate that the most promising ligand binds stronger to AR than the existing non-steroidal ligands, and that our proposed ligand binds strongly to a mutant-type AR, which has drug resistance to the existing non-steroidal ligands.
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Affiliation(s)
- Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ittetsu Kobayashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ryosuke Takeda
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Rie Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo, 191-8512, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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4
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Fukushima K, Furuya M, Kamimura T, Takimoto-Kamimura M. Structure of macrophage migration inhibitory factor in complex with methotrexate. Acta Crystallogr D Struct Biol 2021; 77:293-299. [PMID: 33645533 DOI: 10.1107/s2059798321000474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022]
Abstract
Methotrexate (MTX) is an anticancer and anti-rheumatoid arthritis drug that is considered to block nucleotide synthesis and the cell cycle mainly by inhibiting the activity of dihydrofolate reductase (DHFR). Using affinity-matrix technology and X-ray analysis, the present study shows that MTX also interacts with macrophage migration inhibitory factor (MIF). Fragment molecular-orbital calculations quantified the interaction between MTX and MIF based on the structure of the complex and revealed the amino acids that are effective in the interaction of MTX and MIF. It should be possible to design new small-molecule compounds that have strong inhibitory activity towards both MIF and DHFR by structure-based drug discovery.
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Affiliation(s)
- Kei Fukushima
- Pharmaceutical Discovery Research Laboratories, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Minoru Furuya
- Pharmaceutical Discovery Research Laboratories, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takashi Kamimura
- Veritas In Silico Inc., 1-11-1 Nishigotanda, Shinagawa, Tokyo 141-0031, Japan
| | - Midori Takimoto-Kamimura
- Pharmaceutical Discovery Research Laboratories, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
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5
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Takaya D, Watanabe C, Nagase S, Kamisaka K, Okiyama Y, Moriwaki H, Yuki H, Sato T, Kurita N, Yagi Y, Takagi T, Kawashita N, Takaba K, Ozawa T, Takimoto-Kamimura M, Tanaka S, Fukuzawa K, Honma T. FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. J Chem Inf Model 2021; 61:777-794. [PMID: 33511845 DOI: 10.1021/acs.jcim.0c01062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
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Affiliation(s)
- Daisuke Takaya
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shunpei Nagase
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshio Okiyama
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Sato
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yoichiro Yagi
- Graduate School of Engineering, Okayama University of Science, Okayama, 1-1 Ridai-cho, Okayama 700-0005, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norihito Kawashita
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Kenichiro Takaba
- Pharmaceutical Research Center, Laboratory for Medicinal Chemistry, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Tomonaga Ozawa
- Kissei Pharmaceutical Co., LTD., Frontier Technology Research Lab., Research Div. 4365-1 Hotaka Kashiwabara, Azumino, Nagano 399-8304, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Biomedical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Kobe, Hyogo 657-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Sendai, Miyagi 980-8579, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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6
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Nakamura S, Saito R, Yamamoto S, Terauchi Y, Kittaka A, Takimoto-Kamimura M, Kurita N. Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, molecular mechanics and ab initio molecular orbital simulations. Biophys Chem 2021; 270:106540. [PMID: 33418104 DOI: 10.1016/j.bpc.2020.106540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
The specific binding of active vitamin-D to the vitamin-D receptor (VDR) is closely related to the onset of immunological diseases. To inhibit the binding, various compounds have been developed as potent inhibitors against VDR. Among them, a compound NS-54c, which was developed based on the first VDR antagonist TEI-9647 (25-dehydro-1α-hydroxyvitamin D3-26,23-lactone), was revealed to posse almost 1000-fold improved antagonistic activity over the original TEI-9647. However, the reason for this significant improvement has not been elucidated. In the present study, we investigated the specific interactions between VDR and these inhibitors, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results simulated, we furthermore proposed novel inhibitors and investigated their binding properties to VDR. The results elucidate that the replacement of propyl group at the 24th site of NS-54c by a phenethyl group can enhance the binding affinity of the inhibitor to VDR. This finding provides useful information for developing novel potent inhibitors against VDR.
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Affiliation(s)
- Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yuta Terauchi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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7
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Sawada D, Kakuda S, Takeuchi A, Kawagoe F, Takimoto-Kamimura M, Kittaka A. Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor. Org Biomol Chem 2019; 16:2448-2455. [PMID: 29560490 DOI: 10.1039/c8ob00158h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both 2α- and 2β-hydroxypropyl substituted 14-epi-1α,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand binding domain of hVDR by X-ray co-crystallographic analysis. In conjunction with our previous results on 14-epi-19-nortachysterol, 2-methylidene-, 2α-methyl-, 2β-methyl, and 2α-hydroxypropoxy-14-epi-19-nortachysterol, we propose a variety of effects of substitution at the C2 position in the 14-epi-19-nortachysterol skeleton on biological activities.
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Affiliation(s)
- Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi, Tokyo 173-8605, Japan.
| | - Shinji Kakuda
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, Hino, Tokyo 191-8512, Japan
| | - Akiko Takeuchi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, Hino, Tokyo 191-8512, Japan
| | - Fumihiro Kawagoe
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi, Tokyo 173-8605, Japan.
| | | | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi, Tokyo 173-8605, Japan.
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8
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Terauchi Y, Suzuki R, Takeda R, Kobayashi I, Kittaka A, Takimoto-Kamimura M, Kurita N. Ligand chirality can affect histidine protonation of vitamin-D receptor: ab initio molecular orbital calculations in water. J Steroid Biochem Mol Biol 2019; 186:89-95. [PMID: 30278216 DOI: 10.1016/j.jsbmb.2018.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 12/19/2022]
Abstract
Vitamin D is recognized to play important roles in the onset of immunological diseases as well as the regulation of the amount of Ca in the blood. Since these physiological actions caused by active vitamin D are triggered by the specific interaction between the vitamin D receptor (VDR) and active vitamin D, many types of compounds have been developed as potent ligands against VDR. It was found that the binding affinity between VDR and its ligand depends significantly on the chirality of the ligand. However, the reason for the dependence has, thus far, not been elucidated. In the present study, we investigated the specific interactions between VDR and some ligands with different chirality, using ab initio fragment molecular orbital (FMO) calculations. The FMO results reveal that two histidine residues of VDR contribute significantly to the binding between VDR and ligand and that their protonation states can affect the specific interactions between VDR and ligand. We therefore considered other possible protonation states of these histidine residues and determined their most stable states, using the ab initio FMO calculations. The results illustrate the possibility that the difference in the chirality of a ligand can induce the change in protonation states of the histidine residues of VDR existing near the ligand. This finding provides an important warning that the protonation states of histidine residues existing near the ligand should be considered more precisely in the molecular simulations for investigating the specific interactions between protein and ligand.
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Affiliation(s)
- Yuta Terauchi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Rie Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ryosuke Takeda
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ittetsu Kobayashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo, 173-8605, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo, 191-8512, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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9
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Takeda R, Kobayashi I, Suzuki R, Kawai K, Kittaka A, Takimoto-Kamimura M, Kurita N. Proposal of potent inhibitors for vitamin-D receptor based on ab initio fragment molecular orbital calculations. J Mol Graph Model 2018; 80:320-326. [DOI: 10.1016/j.jmgm.2018.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/31/2022]
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10
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Takeda R, Suzuki R, Kobayashi I, Kawai K, Kittaka A, Takimoto-Kamimura M, Kurita N. Specific interactions between vitamin D receptor and ligand depending on its chirality: ab initio fragment molecular orbital calculations. CBIJ 2018. [DOI: 10.1273/cbij.18.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ryosuke Takeda
- Department of Computer Science and Engineering, Toyohashi University of Technology,
| | - Rie Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology,
| | - Ittetsu Kobayashi
- Department of Computer Science and Engineering, Toyohashi University of Technology,
| | | | | | | | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology,
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11
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Takeda R, Kobayashi I, Shimamura K, Ishimura H, Kadoya R, Kawai K, Kittaka A, Takimoto-Kamimura M, Kurita N. Specific interactions between vitamin-D receptor and its ligands: Ab initio molecular orbital calculations in water. J Steroid Biochem Mol Biol 2017; 171:75-79. [PMID: 28242261 DOI: 10.1016/j.jsbmb.2017.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 10/20/2022]
Abstract
Vitamin D is recognized to play important roles not only in the bone metabolism and the regulation of Ca amount in the blood but also in the onset of immunological diseases. These physiological actions caused by vitamin D are triggered by the specific interaction between vitamin D receptor (VDR) and vitamin D. In the present study, we investigated the interactions between VDR and vitamin D derivatives using ab initio molecular simulation, in order to elucidate the reason for the significant difference in their effects on VDR activity. Based on the results simulated, we elucidated which parts of the derivatives and which residues of VDR mainly contribute to the specific binding between VDR and the derivatives at an electronic level. This finding will be helpful for proposing new vitamin D derivatives as a potent modulator or inhibitor against VDR.
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Affiliation(s)
- Ryosuke Takeda
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ittetsu Kobayashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Kanako Shimamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Hiromi Ishimura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Ryushi Kadoya
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Kentaro Kawai
- Drug Research Center, Kaken Pharmaceutical Co. Ltd, 14, Shinomiya, Minamigawara-cho, Yamashina-ku, Kyoto 607-8042, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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12
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Saitoh H, Watanabe H, Kakuda S, Takimoto-Kamimura M, Takagi K, Takeuchi A, Takenouchi K. Synthesis and biological activities of vitamin D3 derivatives with cyanoalkyl side chain at C-2 position. J Steroid Biochem Mol Biol 2015; 148:27-30. [PMID: 25500068 DOI: 10.1016/j.jsbmb.2014.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/02/2014] [Accepted: 12/07/2014] [Indexed: 11/21/2022]
Abstract
We synthesized and evaluated novel vitamin D3 derivatives with cyanoalkyl side chain at C-2 position on the basis of our previous research for 2α side chain which bears nitrogen atom-containing functional group. Through a study of X-ray co-crystal structures of human VDR and compound 3, we demonstrated that the 2α alkyl side chain in compound 3 shows a novel interaction in the complex of hVDR-LBD and ligand. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.
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Affiliation(s)
- Hiroshi Saitoh
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan.
| | - Hidekazu Watanabe
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kenichiro Takagi
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Akiko Takeuchi
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kazuya Takenouchi
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
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13
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Matsuo M, Hasegawa A, Takano M, Saito H, Kakuda S, Takagi K, Ochiai E, Horie K, Takimoto-Kamimura M, Takenouchi K, Sawada D, Kittaka A. Design and synthesis of 2α-(tetrazolylethyl)-1α,25-dihydroxyvitamin D3 as a high affinity ligand for vitamin D receptor. J Steroid Biochem Mol Biol 2014; 144 Pt A:201-3. [PMID: 24036313 DOI: 10.1016/j.jsbmb.2013.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 10/26/2022]
Abstract
X-ray cocrystallographic studies of the human vitamin D receptor (hVDR)-[2α-(3-hydroxypropyl)-1α,25-dihydroxyvitamin D3 (O1C3)] complex showed that the terminal hydroxy group of the 2α-functional group of O1C3 formed a hydrogen bond with Arg274 in the ligand binding domain (LBD) of hVDR to stabilize the complex; therefore, O1C3 showed 3-times greater binding affinity for VDR than the natural hormone. Here, the effects of a heteroaromatic ring on binding to hVDR instead of the terminal OH group of O1C3 and also on preliminary biological activities were studied. We synthesized 2α-[2-(tetrazol-2-yl)ethyl]-1α,25(OH)2D3 (1a) and its regioisomer 2α-[2-(tetrazol-1-yl)ethyl]-1α,25(OH)2D3 (1b), in which 1a showed much higher hVDR binding affinity and greater osteocalcin promoter transactivation activity in human osteosarcoma (HOS) cells than those of 1b. X-ray cocrystallographic analysis of the hVDR-1a complex showed new hydrogen bond formation between one of the nitrogen atoms of the tetrazole ring and Arg274. This article is part of a Special Issue entitled '16th Vitamin D Workshop'.
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Affiliation(s)
- Miki Matsuo
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Asami Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Masashi Takano
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Hiroshi Saito
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kenichiro Takagi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Eiji Ochiai
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kyohei Horie
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kazuya Takenouchi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan.
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14
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Takimoto-Kamimura M, Kakuda S, Matsumoto Y. The inhibitory mechanism analysis of human chymase specific inhibitor TJK002. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314092833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Chymase is a mast cell specific serine protease that is stored within secretory granules and released together with heparin and histamine in response to allergen challenge or other stimuli. Recent study have shown that chymase possess processing activity for biological peptides and cytokines implicated in a variety of diseases. For example, the chymases of primateds and dogs have highly specific angiotensin II generating activity, and the results of animal studies suggest the chymase contributes to the pathogenesis of cardiovascular diseases via Ang II generation. Based on the results of these studies, inhibition of chymase is expected to provide therapeutic means for the treatment of these diseases. Recently, we have developed some novel benzimidazole derived in human chymase inhibitors and the crystal structure of human chymase complexed with a nobel benzimidazole inhibitor TJK002 was obtained at 2.8A. TJK002 showed potent inhibitory activity (Ki value 2.24nM) with respect to human chymase. X-ray crystallographic structure showed that THK002 forms an anon-covalent interaction with the catalytic domain of human chymase. 4-methylbenzothiophen-3-yl moiety of TJK002 occupies the S1 pocket. The carboxylic acid for hydrogen bonds with the imidazole N (e) atom of H57 and O (g) atoms of Ser195 at the catalytic site. The binding mode of TJK002 is very unique and attractive compared other cymase inhibitors. It depends on the binding mode of TJK002 and reflects to its biological function. Because by site-directed mutagenesis, human mast cell chymase are responsible for an acidic amino acid residue preference in the P2' position of substrates. Chymase inhibitors besides TJK002 have negatively charged p2' moiety. But TJK002 doesn't have such a moiety which binds to S2' site, but it still has a strong incisory activity. We clarify its strong inhibitory mechanism of TJK002 by Fragment molecular orbital (FMO) calculation. We discovered the stacking interaction between the benzimidazole ring and His57 is quite effective for the inhibitory activity of TJK002.
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15
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Fujino A, Fukushima K, Kubota T, Matsumoto Y, Takimoto-Kamimura M. Structure of the β-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1344-8. [PMID: 24316826 PMCID: PMC3855716 DOI: 10.1107/s1744309113030534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/07/2013] [Indexed: 06/02/2023]
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a previous report, it was shown that MK2 in complex with the selective inhibitor TEI-I01800 adopts an α-helical glycine-rich loop that is induced by the stable nonplanar conformer of TEI-I01800. To understand the mechanism of the structural change, the structure of MK2 bound to TEI-L03090, which lacks the key substituent found in TEI-I01800, was determined. MK2-TEI-L03090 has a β-sheet glycine-rich loop in common with other kinases, as predicted. This result suggests that a small compound can induce a drastic conformational change in the target protein structure and can be used to design potent and selective inhibitors.
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Affiliation(s)
- Aiko Fujino
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Kei Fukushima
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takaharu Kubota
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Yoshiyuki Matsumoto
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
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16
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Fujino A, Fukushima K, Kubota T, Kosugi T, Takimoto-Kamimura M. Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity. J Synchrotron Radiat 2013; 20:905-9. [PMID: 24121337 PMCID: PMC3795553 DOI: 10.1107/s0909049513020736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the MK2-TEI-I01800 complex has been reported; its Gly-rich loop was found to form an α-helix, not a β-sheet as has been observed for other Ser/Thr kinases. TEI-I01800 is 177-fold selective against MK2 compared with CDK2; in order to understand the inhibitory mechanism of TEI-I01800, the cyclin-dependent kinase 2 (CDK2) complex structure with TEI-I01800 was determined at 2.0 Å resolution. Interestingly, the Gly-rich loop of CDK2 formed a β-sheet that was different from that of MK2. In MK2, TEI-I01800 changed the secondary structure of the Gly-rich loop from a β-sheet to an α-helix by collision between Leu70 and a p-ethoxyphenyl group at the 7-position and bound to MK2. However, for CDK2, TEI-I01800 bound to CDK2 without this structural change and lost the interaction with the substituent at the 7-position. In summary, the results of this study suggest that the reason for the selectivity of TEI-I01800 is the favourable conformation of TEI-I01800 itself, making it suitable for binding to the α-form MK2.
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Affiliation(s)
- Aiko Fujino
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Kei Fukushima
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takaharu Kubota
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Tomomi Kosugi
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
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17
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Fukushima K, Kamimura T, Takimoto-Kamimura M. Structure basis 1/2SLPI and porcine pancreas trypsin interaction. J Synchrotron Radiat 2013; 20:943-7. [PMID: 24121345 PMCID: PMC3795561 DOI: 10.1107/s090904951302133x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/31/2013] [Indexed: 06/02/2023]
Abstract
SLPI (secretory leukocyte protease inhibitor) is a 107-residue protease inhibitor which inhibits various serine proteases, including elastase, cathepsin G, chymotrypsin and trypsin. SLPI is obtained as a multiple inhibitor in lung defense and in chronic airway infection. X-ray crystal structures have so far reported that they are full-length SLPIs with bovine α-chymotrypsin and 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58-Ala107) with HNE (human neutrophil elastase). To understand the role of this multiple inhibitory mechanism, the crystal structure of 1/2SLPI with porcine pancreas trypsin was solved and the binding modes of two other complexes compared. The Leu residue surprisingly interacts with the S1 site of trypsin, as with chymotrypsin and elastase. The inhibitory mechanism of 1/2SLPI using the wide primary binding site contacts (from P2' to P5) with various serine proteases is discussed. These inhibitory mechanisms have been acquired in the evolution of the protection system for acute inflammatory diseases.
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Affiliation(s)
- Kei Fukushima
- Medicinal Chemistry Technology Department, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Takashi Kamimura
- Medicinal Chemistry Technology Department, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Medicinal Chemistry Technology Department, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
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18
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Matsumoto Y, Kakuda S, Koizumi M, Mizuno T, Muroga Y, Kawamura T, Takimoto-Kamimura M. Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor. J Synchrotron Radiat 2013; 20:914-8. [PMID: 24121339 PMCID: PMC3795555 DOI: 10.1107/s0909049513020748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The X-ray crystallographic study shows that the benzimidazole inhibitor forms a non-covalent interaction with the catalytic domain of human chymase. The hydrophobic fragment of the inhibitor occupies the S1 pocket. The carboxylic acid group of the inhibitor forms hydrogen bonds with the imidazole N(ℇ) atom of His57 and/or the O(γ) atom of Ser195 which are members of the catalytic triad. This imidazole ring of His57 induces π-π stacking to the benzene ring of the benzimidazole scaffold as P2 moiety. Fragment molecular orbital calculation of the atomic coordinates by X-ray crystallography shows that this imidazole ring of His57 could be protonated with the carboxyl group of Asp102 or hydroxyl group of Ser195 and the stacking interaction is stabilized. A new drug design strategy is proposed where the stacking to the protonated imidazole of the drug target protein with the benzimidazole scaffold inhibitor causes unpredicted potent inhibitory activity for some enzymes.
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Affiliation(s)
- Yoshiyuki Matsumoto
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Masahiro Koizumi
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Tsuyoshi Mizuno
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Yumiko Muroga
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Takashi Kawamura
- Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
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19
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Matsuo M, Hasegawa A, Takano M, Saito H, Kakuda S, Chida T, Takagi KI, Ochiai E, Horie K, Harada Y, Takimoto-Kamimura M, Takenouchi K, Sawada D, Kittaka A. Synthesis of 2α-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo. ACS Med Chem Lett 2013; 4:671-4. [PMID: 24900728 DOI: 10.1021/ml400098w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/28/2013] [Indexed: 11/28/2022] Open
Abstract
2α-Heteroarylethyl-1α,25-dihydroxyvitamin D3 analogues, which were designed to form a hydrogen bond between Arg274 of human vitamin D receptor (hVDR) and a nitrogen atom of the heteroaromatic ring at the 2α-position, were synthesized. Among them, 2α-[2-(tetrazol-2-yl)ethyl]-1α,25-dihydroxyvitamin D3 showed higher osteocalcin promoter transactivation activity in human osteosarcoma (HOS) cells and a greater therapeutic effect in ovariectomized (OVX) rats, osteoporosis model animals, on enhancing bone mineral density than those of active vitamin D3. X-ray cocrystallographic analysis of the hVDR-ligand complex confirms that the new hydrogen bond formation stabilized the complex.
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Affiliation(s)
- Miki Matsuo
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Asami Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Masashi Takano
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hiroshi Saito
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Takayuki Chida
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Ken-ichiro Takagi
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Eiji Ochiai
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Kyohei Horie
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Yoshifumi Harada
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | | | - Kazuya Takenouchi
- Teijin Institute for Bio-medical
Research, Teijin Pharma Ltd., Hino-shi,
Tokyo 191-8512, Japan
| | - Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
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20
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Sawada D, Tsukuda Y, Saito H, Takagi K, Kakuda S, Takimoto-Kamimura M, Ochiai E, Takenouchi K, Kittaka A. Synthesis of 14-epi-2α-hydroxypropoxy-1α,25-dihydroxy-19-nortachysterol and its hVDR binding. J Steroid Biochem Mol Biol 2013; 136:27-9. [PMID: 23246987 DOI: 10.1016/j.jsbmb.2012.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 10/03/2012] [Accepted: 11/28/2012] [Indexed: 11/26/2022]
Abstract
Recently, we evaluated a novel skeleton in the vitamin D family, 14-epi-1α,25(OH)2-19-nortachysterol, and discovered its unique binding configuration in the human vitamin D receptor (VDR) with the C5,6- and C7,8-s-trans triene configuration. Because of its unprecedented form, this skeleton has a promising characteristic profile for clinical use, and also the synthesis of its derivatives should be versatile. Therefore, we synthesized the novel analog, 2α-hydroxypropoxy substituted 14-epi-1α,25(OH)2-19-nortachysterol, and evaluated its human VDR binding affinity. Although this substitution is one of the promising modification of vitamin D3 such as eldecalcitol (ED-71), it had negative effects on the binding affinity, and the compound showed lower affinity than 1α,25(OH)2D3 and its parent compound, 14-epi-1α,25(OH)2-19-nortachysterol. It was thought that the unprecedented binding configuration of this skeleton should not allow the terminal hydroxyl group of the 2α-substituent to construct effective hydrogen bond networks around the amino acid residues in the binding pocket. This article is part of a Special Issue entitled 'Vitamin D Workshop'.
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Affiliation(s)
- Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi, Tokyo 173-8605, Japan
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21
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Saito H, Takagi K, Horie K, Kakuda S, Takimoto-Kamimura M, Ochiai E, Chida T, Harada Y, Takenouchi K, Kittaka A. Synthesis of novel C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation on bone. J Steroid Biochem Mol Biol 2013; 136:3-8. [PMID: 23416104 DOI: 10.1016/j.jsbmb.2013.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 01/18/2013] [Accepted: 02/05/2013] [Indexed: 11/20/2022]
Abstract
Up to the present, numerous vitamin D derivatives have been synthesized, but most of them have straight side chains, and there are few publications described about in vitro and in vivo evaluations on bone by vitamin D derivatives. In our previous paper, we reported the synthesis of various C-2 substituted vitamin D derivatives (2b-2i) with a 2,2-dimethylcyclopentanone unit in the CD-ring side chains, and that the derivatives have strong activity for enhancing bone growth. On the basis of results, this time, we report the synthesis of 2α-substituted vitamin D3 derivatives with chiral cyclopentanone (3-6 and 12-16). These derivatives were obtained by Pd-coupling reaction with A-ring precursor and CD-rings precursor. We evaluated novel derivatives in vitro assays, for affinities for VDR and transactivation assays by human osteosarcoma (HOS) cells. In this research, we demonstrated that some novel vitamin D derivatives (12-MP, 13-MP, 15-MP and 16-LP) have strong transactivation activities in spite of lower affinity for VDR than 1. In addition, we also demonstrated that these derivatives have strong activities for enhancing bone growth using OVX therapeutic rats. This article is part of a Special Issue entitled 'Vitamin D Workshop'.
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Affiliation(s)
- Hiroshi Saito
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Tokyo 191-8512, Japan.
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22
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Kosugi T, Mitchell DR, Fujino A, Imai M, Kambe M, Kobayashi S, Makino H, Matsueda Y, Oue Y, Komatsu K, Imaizumi K, Sakai Y, Sugiura S, Takenouchi O, Unoki G, Yamakoshi Y, Cunliffe V, Frearson J, Gordon R, Harris CJ, Kalloo-Hosein H, Le J, Patel G, Simpson DJ, Sherborne B, Thomas PS, Suzuki N, Takimoto-Kamimura M, Kataoka KI. Correction to Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAP-K2) as an Antiinflammatory Target: Discovery and in Vivo Activity of Selective Pyrazolo[1,5- a]pyrimidine Inhibitors Using a Focused Library and Structure-Based Optimization Approach. J Med Chem 2012. [DOI: 10.1021/jm3013954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Kosugi T, Mitchell DR, Fujino A, Imai M, Kambe M, Kobayashi S, Makino H, Matsueda Y, Oue Y, Komatsu K, Imaizumi K, Sakai Y, Sugiura S, Takenouchi O, Unoki G, Yamakoshi Y, Cunliffe V, Frearson J, Gordon R, Harris CJ, Kalloo-Hosein H, Le J, Patel G, Simpson DJ, Sherborne B, Thomas PS, Suzuki N, Takimoto-Kamimura M, Kataoka KI. Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) as an antiinflammatory target: discovery and in vivo activity of selective pyrazolo[1,5-a]pyrimidine inhibitors using a focused library and structure-based optimization approach. J Med Chem 2012; 55:6700-15. [PMID: 22746295 DOI: 10.1021/jm300411k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel class of mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) inhibitors was discovered through screening a kinase-focused library. A homology model of MAPKAP-K2 was generated and used to guide the initial SAR studies and to rationalize the observed selectivity over CDK2. An X-ray crystal structure of a compound from the active series bound to crystalline MAPKAP-K2 confirmed the predicted binding mode. This has enabled the discovery of a series of pyrazolo[1,5-a]pyrimidine derivatives showing good in vitro cellular potency as anti-TNF-α agents and in vivo efficacy in a mouse model of endotoxin shock.
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Affiliation(s)
- Tomomi Kosugi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd. , Hino, Tokyo 191-8512, Japan
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Kumagai G, Takano M, Shindo K, Sawada D, Saito N, Saito H, Kakuda S, Takagi KI, Takimoto-Kamimura M, Takenouchi K, Chen TC, Kittaka A. C15-functionalized 16-ene-1α,25-dihydroxyvitamin D3 is a new vitamin D analog with unique biological properties. Anticancer Res 2012; 32:311-317. [PMID: 22213321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Δ(16) structure as a vitamin D analog enhanced vitamin D receptor (VDR) binding affinity and induced significant cell differentiation, whereas its relative calcemic activity was reduced compared to 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3)). Methodologies available to introduce a double bond at C16-C17 of the D-ring on the seco-steroidal skeleton were limited; therefore, a new synthetic strategy was developed to obtain not only the Δ(16) structure, but also a new C15-functional group. Since C15-functionalization was unprecedented in vitamin D analog studies, the hybrid structure of Δ(16) and the C15-OH group at the D-ring may provide important information on the structure-activity relationship with vitamin D analogs. The synthesized 16-ene-2α-methyl-1α,15α,25-trihydroxyvitamin D(3) showed almost 3-times higher VDR binding affinity and an equipotent level of osteocalcin promoter transactivation activity in human osteosarcoma cells as compared to 1α,25(OH)(2)D(3).
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Affiliation(s)
- Go Kumagai
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan
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25
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Sawada D, Katayama T, Tsukuda Y, Saito N, Saito H, Kakuda S, Takimoto-Kamimura M, Takenouchi K, Kittaka A. The difference between 14-epi-previtamin D3 and 14-epi-19-norprevitamin D3: their synthesis and binding affinity for human VDR. Anticancer Res 2012; 32:319-326. [PMID: 22213322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The synthesis of 14-epi-1α,25(OH)(2)previtamin D(3), 14-epi-19-nor-1α,25(OH)(2)previtamin D(3), and their 2-substituted analogs is described. The vitamin D receptor (VDR) binding affinity was further evaluated and 2α-methyl substituted 14-epi-1α,25(OH)(2)previtamin D(3) had 17-fold more potent affinity than 14-epi-1α,25(OH)(2)previtamin D(3).In the comparison of these compounds, the effects of thermal equilibrium, with or without 19-carbon at the A-ring, and their CD-ring structures are discussed.
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Affiliation(s)
- Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan.
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26
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Shindo K, Kumagai G, Takano M, Sawada D, Saito N, Saito H, Kakuda S, Takagi KI, Ochiai E, Horie K, Takimoto-Kamimura M, Ishizuka S, Takenouchi K, Kittaka A. New C15-Substituted Active Vitamin D3. Org Lett 2011; 13:2852-5. [DOI: 10.1021/ol200828s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kanako Shindo
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Go Kumagai
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Masashi Takano
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Nozomi Saito
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Hiroshi Saito
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Ken-ichiro Takagi
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Eiji Ochiai
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Kyohei Horie
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Seiichi Ishizuka
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Kazuya Takenouchi
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Sagamihara, Kanagawa 252-5195, Japan, and Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
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27
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Sawada D, Tsukuda Y, Saito H, Kakuda S, Takimoto-Kamimura M, Ochiai E, Takenouchi K, Kittaka A. Development of 14-epi-19-Nortachysterol and Its Unprecedented Binding Configuration for the Human Vitamin D Receptor. J Am Chem Soc 2011; 133:7215-21. [DOI: 10.1021/ja201481j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daisuke Sawada
- Faculty of Pharmaceutical Sciences, Teikyo University, 1091-1, Suwarashi, Midori-ku, Sagamihara, Kanagawa 252-5195, Japan
| | - Yuya Tsukuda
- Faculty of Pharmaceutical Sciences, Teikyo University, 1091-1, Suwarashi, Midori-ku, Sagamihara, Kanagawa 252-5195, Japan
| | - Hiroshi Saito
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Shinji Kakuda
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | | | - Eiji Ochiai
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Kazuya Takenouchi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Hino, Tokyo 191-8512, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 1091-1, Suwarashi, Midori-ku, Sagamihara, Kanagawa 252-5195, Japan
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Kakuda S, Ishizuka S, Eguchi H, Mizwicki MT, Norman AW, Takimoto-Kamimura M. Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1α-hydroxyvitamin D3-26,23-lactone. Acta Crystallogr D Biol Crystallogr 2010; 66:918-26. [DOI: 10.1107/s0907444910020810] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 06/01/2010] [Indexed: 11/10/2022]
Abstract
TEI-9647 antagonizes vitamin D receptor (VDR) mediated genomic actions of 1α,25(OH)2D3in human cells but is agonistic in rodent cells. The presence of Cys403, Cys410 or of both residues in the C-terminal region of human VDR (hVDR) results in antagonistic action of this compound. In the complexes of TEI-9647 with wild-type hVDR (hVDRwt) and H397F hVDR, TEI-9647 functions as an antagonist and forms a covalent adduct with hVDR according to MALDI–TOF MS. The crystal structures of complexes of TEI-9647 with rat VDR (rVDR), H305F hVDR and H305F/H397F hVDR showed that the agonistic activity of TEI-9647 is caused by a hydrogen-bond interaction with His397 or Phe397 located in helix 11. Both biological activity assays and the crystal structure of H305F hVDR complexed with TEI-9647 showed that the interaction between His305 and TEI-9647 is crucial for antagonist activity. This study indicates the following stepwise mechanism for TEI-9647 antagonism. Firstly, TEI-9647 forms hydrogen bonds to His305, which promote conformational changes in hVDR and draw Cys403 or Cys410 towards the ligand. This is followed by the formation of a 1,4-Michael addition adduct between the thiol (–SH) group of Cys403 or Cys410 and theexo-methylene group of TEI-9647.
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Fujino A, Fukushima K, Namiki N, Kosugi T, Takimoto-Kamimura M. Structural analysis of an MK2-inhibitor complex: insight into the regulation of the secondary structure of the Gly-rich loop by TEI-I01800. Acta Crystallogr D Biol Crystallogr 2009; 66:80-7. [PMID: 20057052 DOI: 10.1107/s0907444909046411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 11/04/2009] [Indexed: 11/10/2022]
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the complex of human MK2 (residues 41-364) with the potent MK2 inhibitor TEI-I01800 (pK(i) = 6.9) was determined at 2.9 A resolution. The MK2 structure in the MK2-TEI-I01800 complex is composed of two domains, as observed for other Ser/Thr kinases; however, the Gly-rich loop in the N-terminal domain forms an alpha-helix structure and not a beta-sheet. TEI-I01800 binds to the ATP-binding site as well as near the substrate-binding site of MK2. Both TEI-I01800 molecules have a nonplanar conformation that differs from those of other MK2 inhibitors deposited in the Protein Data Bank. The MK2-TEI-I01800 complex structure is the first active MK2 with an alpha-helical Gly-rich loop and TEI-I01800 regulates the secondary structure of the Gly-rich loop.
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Affiliation(s)
- Aiko Fujino
- Teijin Institute for Biomedical Research, Japan
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30
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Kakuda S, Okada K, Eguchi H, Takenouchi K, Hakamata W, Kurihara M, Takimoto-Kamimura M. Structure of the ligand-binding domain of rat VDR in complex with the nonsecosteroidal vitamin D3 analogue YR301. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:970-3. [PMID: 18997319 PMCID: PMC2581693 DOI: 10.1107/s1744309108026754] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 08/19/2008] [Indexed: 11/10/2022]
Abstract
Vitamin D receptor (VDR) is a ligand-inducible hormone receptor that mediates 1alpha,25(OH)(2)D(3) action, regulating calcium and phosphate metabolism, induces potent cell differentiation activity and has immunosuppressive effects. Analogues of 1alpha,25(OH)(2)D(3) have been used clinically for some years. However, the risk of potential side effects limits the use of these substances. LG190178 is a novel nonsecosteroidal ligand for VDR. (2S)-3-[4-(3-{4-[(2R)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-2-methylphenoxy] propane-1,2-diol (YR301) is the only one of the four evaluated stereoisomers of LG190178 to have strong activity. To understand the strong activity of YR301, the crystal structure of YR301 complexed with the rat VDR ligand-binding domain (VDR LBD) was solved at 2.0 A resolution and compared with the structure of the VDR LBD-1alpha,25(OH)(2)D(3) complex. YR301 and 1alpha,25(OH)(2)D(3) share the same position and the diethylmethyl group occupies a similar space to the C and D rings of 1alpha,25(OH)(2)D(3). YR301 has two characteristic hydroxyl groups which contribute to its potent activity. The first is 2'-OH, which forms hydrogen bonds to the NE2 atoms of both His301 and His393. The other is 2-OH, which interacts with Ser233 OG and Arg270 NH1. These two hydroxyl groups of YR301 correspond exactly to 25-OH and 1-OH, respectively, of 1alpha,25(OH)(2)D(3). The terminal hydroxyl group (3-OH) of YR301 is directly hydrogen bonded to Arg270 and also interacts indirectly with Tyr232 OH and the backbone NH of Asp144 via water molecules. Additional derivatization of the terminal hydroxyl group using the positions of the water molecules might be useful for the design of more potent compounds.
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31
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Kakuda S, Okada K, Eguchi H, Takenouchi K, Hakamata W, Kurihara M, Takimoto-Kamimura M. Structure of the LBD of rat VDR in complex with a non-seco-steroidal vitamin D3 analogue YR301. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308089046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Kitamura M, Hara T, Adachi K, Takimoto-Kamimura M. Polymorphism and crystal structure of BPT propyl ester in various solvents. Acta Crystallogr A 2008. [DOI: 10.1107/s010876730808121x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Koizumi M, Fujino A, Fukushima K, Kamimura T, Takimoto-Kamimura M. Complex of human neutrophil elastase with 1/2SLPI. J Synchrotron Radiat 2008; 15:308-11. [PMID: 18421166 PMCID: PMC2394824 DOI: 10.1107/s0909049507060670] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 11/19/2007] [Indexed: 05/16/2023]
Abstract
SLPI (secretory leukocyte protease inhibitor) is a 107-residue non-glycosylated protease inhibitor, which inhibits a wide range of serine proteases, trypsin, chymotrypsin, neutrophil elastase, chymase and cathepsin G. X-ray crystallographic analyses have shown that SLPI comprises two separate domains of similar architecture [Grütter, Fendrich, Huber & Bode (1988), EMBO J. 7, 345-351] and the C-terminal domain interacts with bovine alpha-chymotrypsin. In order to understand SLPI's multiple functions against various serine proteases, the complex HNE (human neutrophil elastase) has been co-crystallized with 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58-Ala107), which has a biological activity similar to full SLPI. The 1/2SLPI and HNE complex structure was solved at 1.7 A resolution, and compared with the interaction mechanism of elafin, which is a specific inhibitor of elastase. It was found that P1 Leu72i and six hydrogen bonds between the main chains in the primary contact region have sufficient ability to inhibit HNE and PPE (porcine pancreatic elastase), and P5 Tyr68i is important in increasing the selectivity of 1/2SLPI against HNE. The mechanisms of the functions of SLPI are relatively unknown, but the current study could help understand the selectivity of SLPI against HNE and PPE.
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Affiliation(s)
- Masahiro Koizumi
- Teijin Institute for Bio-medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Aiko Fujino
- Teijin Institute for Bio-medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Kay Fukushima
- Teijin Institute for Bio-medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Takashi Kamimura
- Teijin Institute for Bio-medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan
- Correspondence e-mail:
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Suzuki K, Misaki S, Shiromizu I, Takimoto-Kamimura M, Bando M, Kunishima N, Nodake Y, Sugahara M, Nishijima K. Crystal structure of MCoA-ACPT from Thermus thermophilusHB8. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305079729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Kittaka A, Saito N, Masuda M, Saito H, Takenouchi K, Ishizuka S, Namekawa JI, Takimoto-Kamimura M. Synthesis of 24,24-Ethanovitamin D3 Lactones Using Ruthenium-Catalyzed Intermolecular Enyne Metathesis: Potent Vitamin D Receptor Antagonists. SYNTHESIS-STUTTGART 2005. [DOI: 10.1055/s-2005-872075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Saito N, Masuda M, Matsunaga T, Saito H, Anzai M, Takenouchi K, Miura D, Ishizuka S, Takimoto-Kamimura M, Kittaka A. 24,24-Dimethylvitamin D3-26,23-lactones and their 2α-functionalized analogues as highly potent VDR antagonists. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.05.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Koizumi M, Muratani E, Fujii K, Takimoto-Kamimura M. Crystal structure of the complex of porcine pancreatic elastase with TEI-8362. J Synchrotron Radiat 2004; 11:101-104. [PMID: 14646146 DOI: 10.1107/s0909049503023550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2003] [Accepted: 10/15/2003] [Indexed: 05/24/2023]
Abstract
The crystal structure of porcine pancreatic elastase (PPE) complexed with a new benzoxazinone inhibitor, TEI-8362, of human neutrophil elastase (HNE) was determined at 1.8 A resolution. The hydroxyl oxygen of Ser195 opened the benzoxazinone by nucleophilic attack and formed a covalent bond with the carbonyl carbon. Hydrophobic interaction between the terminal benzene of TEI-8362 and the S4 pocket is reinforced by the side chain of Arg217 and has an impact on the ligand binding conformation. Two additional interactions with the oxyanion hole and His57 are introduced to the benzoxazinone structure of TEI-8362. These combinatorial interactions will also exist in HNE and cause high preference of TEI-8362 for HNE.
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Affiliation(s)
- Masahiro Koizumi
- Teijin Institute for Bio-Medical Research, Asahigaoka, Hino, Tokyo 191-8512, Japan.
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Koyano K, Saitoh Y, Oshida J, Takimoto-Kamimura M. Dimer and superstructure of the active form of a vitamin D3; 1 alpha,24(R)dihydroxy-vitamin D3 monohydrate, C27O3H44.H2O. Chem Pharm Bull (Tokyo) 2001; 49:305-11. [PMID: 11253921 DOI: 10.1248/cpb.49.305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystals of 1alpha24(R)dihydroxy-vitamin D3 monohydrate, C27O3H44.H2O are orthorhombic in the space group P2(1)2(1)2(1) with cell dimensions a=25.719, b=42.572, c=9.851A and Z=16. The asymmetric unit consists of two subunits with b/8, and each subunit contains a dimer in which two molecules are hydrogen-bonded through water molecules into non-crystallographical symmetry of C2. The two-fold axes are the straight lines, x=1/2, z=0.256 and x=1/2, z=0.623. The two dimers are the same in the rigid ring part, but differ in the conformation of the flexible chains. The dimers further make C2 symmetry between the rigid ring parts to form a superstructure, and the two-fold axis of the straight line, y=1/8, z=0.435 goes through a point that is a little apart from the hypercenter (1/2, 1/8, 1/2). The structure was solved by integrated Patterson and direct methods and refined on Fo2 under restraints. The final R1 is 0.228 on Fo for 1623 reflections with Fo>3sigma, resolutions 1.0-3.0 A, 313 restraints, 490 parameters and average Ueq=0.120. Not all the atoms of the chains appeared nor the hydrogen atoms. The missing atoms of the dimer were modeled from another pair molecule by C2 symmetry and hydrogen atoms were added. The structure of the dimer was optimized by ab initio molecular orbital of HF/6-31G.
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Affiliation(s)
- K Koyano
- Biomedical Research Institute, Teijin Ltd., Hino, Tokyo, Japan.
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Abstract
BACKGROUND Recent structural results have shown that antibodies use an induced fit mechanism to recognize and bind their antigens. Here we present the crystallographically determined structure of an Fab directed against an HIV-1 peptide (Fab 50.1) in the unliganded state and compare it with the peptide-bound structure. We perform a detailed analysis of the components that contribute to enhanced antigen binding and recognition. RESULTS Induced fit of Fab 50.1 to its peptide antigen involves a substantial rearrangement of the third complementarity determining region loop of the heavy chain (H3), as well as a large rotation of the variable heavy (VH) chain relative to the variable light (VL) chain. Analysis of other Fab structures suggests that the extent of the surface area buried at the VL-VH interface correlates with the ability to alter antibody quaternary structure by reorientation of the VL-VH domains. CONCLUSION Fab 50.1 exhibits the largest conformational changes yet observed in a single antibody. These can be attributed to the flexibility of the variable region. Comparisons of new data with previous examples lend to the general conclusion that a small VL-VH interface, due in part to a short H3 loop, permits substantial alterations to the antigen-binding pocket. This has major implications for the prediction, engineering and design of antibody-combining sites.
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Affiliation(s)
- R L Stanfield
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
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40
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Takimoto-Kamimura M, Stanfield RL, Stura EA, Profy AT, Wilson IA. The structure of HIV-1 neutralizing antibody 50.1. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378097998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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41
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Abstract
C10H18N2O5S.H2O, Mr = 296.39, monoclinic, P2(1), a = 19.600 (1), b = 7.480 (1), c = 5.061 (1) A, beta = 94.74 (1) degree, V = 739.445 (1) A3, Z = 2, Dm = 1.31, Dx = 1.331 g cm-3, Cu K alpha, lambda = 1.54178 A, mu = 21.4 cm-1, F(000) = 316, room temperature, R = 0.057 for 1263 reflections. The molecule adopts an extended form. The molecules are arranged so as to form double molecular sheets parallel to the bc plane through some hydrogen bonds.
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Takimoto-Kamimura M, Takenaka A, Sasada Y, Ohki M. Structure of 9-{2-[(4-imidazolyl)methylthio]ethyl}adenine. Acta Crystallogr C 1986. [DOI: 10.1107/s0108270186095239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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