1
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Bekker GJ, Fukunishi Y, Higo J, Kamiya N. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS Omega 2024; 9:3412-3422. [PMID: 38284074 PMCID: PMC10809319 DOI: 10.1021/acsomega.3c06826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
Flavin mononucleotide riboswitches are common among many pathogenic bacteria and are therefore considered to be an attractive target for antibiotics development. The riboswitch binds riboflavin (RBF, also known as vitamin B2), and although an experimental structure of their complex has been solved with the ligand bound deep inside the RNA molecule in a seemingly unreachable state, the binding mechanism between these molecules is not yet known. We have therefore used our Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol to analyze their binding mechanism by simulating the binding process between the riboswitch aptamer domain and the RBF, starting from the apo state of the riboswitch. Here, the refinement stage was crucial to identify the native binding configuration, as several other binding configurations were also found by McMD-based docking simulations. RBF initially binds the interface between P4 and P6 including U61 and G62, which forms a gateway where the ligand lingers until this gateway opens sufficiently to allow the ligand to pass through and slip into the hidden binding site including A48, A49, and A85.
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Affiliation(s)
- Gert-Jan Bekker
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - 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
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Narutoshi Kamiya
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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2
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Fukuda I, Moritsugu K, Higo J, Fukunishi Y. A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems. J Chem Phys 2023; 159:234116. [PMID: 38112509 DOI: 10.1063/5.0172270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
We introduce a simple cutoff-based method for precise electrostatic energy calculations in the molecular dynamics (MD) simulations of point-particle systems. Our method employs a theoretically derived smooth pair potential function to define electrostatic energy, offering stability and computational efficiency in MD simulations. Instead of imposing specific physical conditions, such as dielectric environments or charge neutrality, we focus on the relationship represented by a single summation formula of charge-weighted pair potentials. This approach allows an accurate energy approximation for each particle, enabling a straightforward error analysis. The resulting particle-dependent pair potential captures the charge distribution information, making it suitable for heterogeneous systems and ensuring an enhanced accuracy through distant information inclusion. Numerical investigations of the Madelung constants of crystalline systems validate the method's accuracy.
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Affiliation(s)
- Ikuo Fukuda
- Graduate School of Science, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8231, Japan
- Japan Biological Informatics Consortium, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Kei Moritsugu
- Graduate School of Science, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8231, Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo650-0047, Japan
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - 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
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lintuluoto M, Abe M, Horioka Y, Fukunishi Y, Tamura H, Lintuluoto JM. Investigation on substrate specificity and catalytic activity of serine protease neuropsin. Biophys Physicobiol 2022; 19:e190040. [DOI: 10.2142/biophysico.bppb-v19.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/21/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Mitsumasa Abe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Yota Horioka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hideki Tamura
- Laboratory of Biofunctional Science, Hoshi University School of Pharmacy and Pharmaceutical Sciences
| | - Juha M. Lintuluoto
- Graduate School of Engineering, Department of Synthetic and Biological Chemistry, Kyoto University
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5
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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6
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Moritsugu K, Takeuchi K, Kamiya N, Higo J, Yasumatsu I, Fukunishi Y, Fukuda I. Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. J Chem Inf Model 2021; 61:1921-1930. [PMID: 33835817 DOI: 10.1021/acs.jcim.0c01427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantifying the cell permeability of cyclic peptides is crucial for their rational drug design. However, the reasons remain unclear why a minor chemical modification, such as the difference between Ras inhibitors cyclorasin 9A5 and 9A54, can substantially change a peptide's permeability. To address this question, we performed enhanced sampling simulations of these two 11-mer peptides using the coupled Nosé-Hoover equation (cNH) we recently developed. The present cNH simulations realized temperature fluctuations over a wide range (240-600 K) in a dynamic manner, allowing structural samplings that were well validated by nuclear Overhauser effect measurements. The derived structural ensembles were comprehensively analyzed by all-atom structural clustering, mapping the derived clusters onto principal components (PCs) that characterize the cyclic structure, and calculating cluster-dependent geometric and chemical properties. The planar-open conformation was dominant in aqueous solvent, owing to inclusion of the Trp side chain in the main-chain ring, while the compact-closed conformation, which favors cell permeation due to its compactness and high polarity, was also accessible. Conformation-dependent cell permeability was observed in one of the derived PCs, demonstrating that decreased cell permeability in 9A54 is due to the high free energy barrier separating the two conformations. The origin of the change in free energy surface was determined to be loss of flexibility in the modified residues 2-3, resulting from the increased bulkiness of their side chains. The derived molecular mechanism of cell permeability highlights the significance of complete structural dynamics surveys for accelerating drug development with cyclic peptides.
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Affiliation(s)
- Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Isao Yasumatsu
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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7
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Lintuluoto M, Horioka Y, Hongo S, Lintuluoto JM, Fukunishi Y. Molecular Dynamics Simulation Study on Allosteric Regulation of CD44-Hyaluronan Binding as a Force Sensing Mechanism. ACS Omega 2021; 6:8045-8055. [PMID: 33817464 PMCID: PMC8014924 DOI: 10.1021/acsomega.0c05502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/05/2021] [Indexed: 06/01/2023]
Abstract
CD44 protein exists on surfaces of a variety of human cells, acts as a receptor for the hyaluronan (HA) molecule, and mediates cell adhesion via the HA binding in leukocyte trafficking, cell rolling, and so on. The molecular structures of both CD44 and HA are well known, and the previous work shows that the external-mechanical force induces the partially disordered (PD) conformation from the ordered (O) conformation of CD44. The PD conformation has the higher HA affinity compared to the O conformation. However, the details of force-sensing mechanics have remained unclear. This study provides new insights into allosteric regulation of HA binding by conformational shift from the O to the PD conformation of the CD44 HA binding domain by using the classical molecular dynamics simulations. The O conformation was more favorable than the PD conformation under the equilibrium state, and the O conformation showed weak HA-binding affinity. Our simulation suggests that the PD conformation induced by the external force can refold to a compact structure similar to the O conformation keeping the bound HA. This new conformation showed a higher affinity than the O and PD conformations. Our results show that the unfolding of a remote disordered region from the ligand binding site by the external force allosterically regulates the HA affinity. This study promotes understanding not only the mechanism of CD44-mediated cell rolling but also the allosteric regulation induced by the external mechanical force.
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Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Yota Horioka
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Saki Hongo
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Juha Mikael Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
| | - 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
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8
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Bekker GJ, Fukuda I, Higo J, Fukunishi Y, Kamiya N. Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations. Sci Rep 2021; 11:5046. [PMID: 33658550 PMCID: PMC7930018 DOI: 10.1038/s41598-021-84488-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/17/2021] [Indexed: 01/11/2023] Open
Abstract
We have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - 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
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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9
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Higo J, Kusaka A, Kasahara K, Kamiya N, Hayato I, Qilin X, Takahashi T, Fukuda I, Mori K, Hata Y, Fukunishi Y. GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics. Biophys Physicobiol 2021; 17:161-176. [PMID: 33585149 DOI: 10.2142/biophysico.bsj-2020008] [Citation(s) in RCA: 7] [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: 04/16/2020] [Accepted: 12/22/2020] [Indexed: 12/01/2022] Open
Abstract
We introduced a conformational sampling method in an earlier report: The multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD) enhances conformational sampling of a biomolecular system by computer simulations. Herein, new sampling method, a subzone-based mD-VcMD, is presented as an extension of mD-VcMD. Then, the subzone-based method is extended further using a genetic algorithm (GA) named the GA-guided mD-VcMD. In these methods, iterative simulation runs are performed to increase the sampled region gradually. The new methods have the following benefits: (1) They are free from a production run: i.e., all snapshots from all iterations are useful for analyses. (2) They are free from fine tuning of a weight function (probability distribution function or potential of mean force). (3) A canonical ensemble (i.e., a thermally equilibrated ensemble) is generated from a simple procedure. A thermodynamic weight is assigned to each snapshot. (4) Selective sampling can be performed for particularly addressing a poorly sampled region without breaking the proportion of the canonical ensemble if the poorly sampled conformational region emerges in sampling. By applying the methods to a simple system that involves an energy barrier between potential-energy minima, we demonstrated that the new methods have considerably higher sampling efficiency than the original mD-VcMD does.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Itaya Hayato
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Xie Qilin
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan.,National Institute of Technology, Maizuru College, Maizuru, Kyoto 625-8511, Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, 135-0064, Japan
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10
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Iida S, Fukunishi Y. Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water. BBA Adv 2021; 1:100016. [PMID: 34235495 PMCID: PMC8214910 DOI: 10.1016/j.bbadva.2021.100016] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world. It is necessary to examine the viral proteins that play a notorious role in the invasion of our body. The main protease (3CLpro) facilitates the maturation of the coronavirus. It is thought that the dimerization of 3CLpro leads to its catalytic activity; the detailed mechanism has, however, not been suggested. Furthermore, the structural differences between the predecessor SARS-CoV 3CLpro and SARS-CoV-2 3CLpro have not been fully understood. Here, we show the structural and dynamical differences between the two main proteases, and demonstrate the relationship between the dimerization and the activity via atomistic molecular dynamics simulations. Simulating monomeric and dimeric 3CLpro systems for each protease, we show that (i) global dynamics between the two different proteases are not conserved, (ii) the dimerization stabilizes the catalytic dyad and hydration water molecules behind the dyad, and (iii) the substrate-binding site (active site) and hydration water molecules in each protomer fluctuate asymmetrically. We then speculate the roles of hydration water molecules in their catalytic activity.
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Affiliation(s)
- Shinji Iida
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo, Japan 135-0064
- Corresponding author.
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo, Japan 135-0064
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11
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Iida S, Nakamura HK, Mashimo T, Fukunishi Y. Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design. J Phys Chem B 2020; 124:9977-9986. [PMID: 33140952 DOI: 10.1021/acs.jpcb.0c04963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryptic sites are binding pockets that are transiently formed in an apo form or that are induced by ligand binding. The investigation of cryptic sites is crucial for drug discovery, since these sites are ubiquitous in disease-related human proteins, and targeting them expands the number of drug targets greatly. However, although many computational studies have attempted to identify cryptic sites, the detection remains challenging. Here, we aimed to characterize and detect cryptic sites in terms of structural fluctuations in an apo form, investigating proteins each of which possesses a cryptic site. From their X-ray structures, we saw that aromatic residues tended to be found in cryptic sites. To examine structural fluctuations of the apo forms, we performed molecular dynamics (MD) simulations, producing probability distributions of the solvent-accessible surface area per aromatic residue. To detect aromatic residues in cryptic sites, we have proposed a "cryptic-site index" based on the distribution, demonstrating the performance via several measures, such as recall and specificity. Besides, we found that high-ranking aromatic residues were likely to probe concaves in a cryptic site. This implies that such fluctuations provide a profile of scaffolds of compounds with the potential to bind to a particular cryptic site.
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Affiliation(s)
- Shinji Iida
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hironori K Nakamura
- Biomodeling Research Co., Ltd., 1-704-2, Uedanishi, Tenpaku-ku, Nagoya, Aichi 468-0058, Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.,IMSBIO Co., Ltd., 4-21-1, Higashiikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, AIST Tokyo Waterfront, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
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12
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Higo J, Kawabata T, Kusaka A, Kasahara K, Kamiya N, Fukuda I, Mori K, Hata Y, Fukunishi Y, Nakamura H. Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J Chem Inf Model 2020; 60:4867-4880. [PMID: 32910853 DOI: 10.1021/acs.jcim.0c00551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enhanced conformational sampling, a genetic-algorithm-guided multidimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semistable complex structures and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spot are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding constant changes resulting from the alanine mutation experiment for the residues. We also performed a simulation of nonphosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Maizuru College, 234 Shiroya, Maizuru, Kyoto 625-8511 Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - 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
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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13
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Asano T, Noda Y, Tanaka KI, Yamakawa N, Wada M, Mashimo T, Fukunishi Y, Mizushima T, Takenaga M. A 2B adenosine receptor inhibition by the dihydropyridine calcium channel blocker nifedipine involves colonic fluid secretion. Sci Rep 2020; 10:3555. [PMID: 32103051 PMCID: PMC7044278 DOI: 10.1038/s41598-020-60147-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 01/28/2020] [Indexed: 11/26/2022] Open
Abstract
The adenosine A2B receptor is a critical protein in intestinal water secretion. In the present study, we screened compound libraries to identify inhibitors of the A2B receptor and evaluated their effect on adenosine-induced intestinal fluid secretion. The screening identified the dihydropyridine calcium antagonists nifedipine and nisoldipine. Their respective affinities for the A2B receptor (Ki value) were 886 and 1,399 nM. Nifedipine and nisoldipine, but not amlodipine or nitrendipine, inhibited both calcium mobilization and adenosine-induced cAMP accumulation in cell lines. Moreover, adenosine injection into the lumen significantly increased fluid volume in the colonic loop of wild-type mice but not A2B receptor-deficient mice. PSB-1115, a selective A2B receptor antagonist, and nifedipine prevented elevated adenosine-stimulated fluid secretion in mice. Our results may provide useful insights into the structure–activity relationship of dihydropyridines for A2B receptor. As colonic fluid secretion by adenosine seems to rely predominantly on the A2B receptor, nifedipine could be a therapeutic candidate for diarrhoea-related diseases.
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Affiliation(s)
- Teita Asano
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1, Sugao, Miyamae-ku, Kawasaki, 216-8512, Japan.
| | - Yuto Noda
- LTT Bio-Pharma Co., Ltd, Shiodome Building 3F, 1-2-20 Kaigan, Minato-ku, Tokyo, 105-0022, Japan
| | - Ken-Ichiro Tanaka
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20, Shin-machi, Nishi-Tokyo, 202-8585, Japan
| | - Naoki Yamakawa
- School of Pharmacy, Shujitsu University, 1-6-1, Nishi-kawahara, Naka-ku, Okayama, 703-8516, Japan
| | - Mitsuhito Wada
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Tadaaki Mashimo
- 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.,IMSBIO Co., Ltd., Owl Tower, 4-21-1, Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan
| | - 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
| | - Tohru Mizushima
- LTT Bio-Pharma Co., Ltd, Shiodome Building 3F, 1-2-20 Kaigan, Minato-ku, Tokyo, 105-0022, Japan.
| | - Mitsuko Takenaga
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1, Sugao, Miyamae-ku, Kawasaki, 216-8512, Japan
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14
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Fukunishi Y, Mashimo T, Kurosawa T, Wakabayashi Y, Nakamura HK, Takeuchi K. Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion. Mol Inform 2020; 39:e1900071. [PMID: 31609549 PMCID: PMC7050510 DOI: 10.1002/minf.201900071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2019] [Indexed: 12/24/2022]
Abstract
Membrane permeability is an important property of drugs in adsorption. Many prediction methods work well for small molecules, but the prediction of middle-molecule permeability is still difficult. In the present study, we modified a classical permeability model based on Fick's law to study passive membrane permeability. The model consisted of the distribution of solute from water to membrane and the diffusion of solute in each solvent. The diffusion coefficient is the inverse of the resistance, and we examined the inertial resistance in addition to the viscous resistance, the latter of which has been widely used in permeability prediction. Also, we examined three models changing the balance between the diffusion of solute in membrane and the conformational change of solute. The inertial resistance improved the prediction results in addition to the viscous resistance. The models worked well not only for small molecules but also for middle molecules, whose structures have more conformational freedom.
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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-kuTokyo135-0064Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
- IMSBIO Co., Ltd.Owl Tower, 4–21-1, Higashi-Ikebukuro, Toshima-kuTokyo170-0013Japan
| | - Takashi Kurosawa
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
- Hitachi Solutions East Japan, 12–1 Ekimaehoncho, Kawasaki-ku, KawasakiKanagawa210-0007Japan
| | | | - Hironori K. Nakamura
- Biomodeling Research Co., Ltd.1-704-2 Uedanishi, Tenpaku-ku, NagoyaAichi468-0058Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (molprof)National Institute of Advanced Industrial Science and Technology (AIST)2-3-26, Aomi, Koto-kuTokyo135-0064Japan
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15
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Higo J, Kasahara K, Wada M, Dasgupta B, Kamiya N, Hayami T, Fukuda I, Fukunishi Y, Nakamura H. Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism. Protein Eng Des Sel 2019; 32:297-308. [PMID: 31608410 PMCID: PMC7052515 DOI: 10.1093/protein/gzz029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 01/05/2023] Open
Abstract
The free-energy landscape of interaction between a medium-sized peptide, endothelin 1 (ET1), and its receptor, human endothelin type B receptor (hETB), was computed using multidimensional virtual-system coupled molecular dynamics, which controls the system's motions by introducing multiple reaction coordinates. The hETB embedded in lipid bilayer was immersed in explicit solvent. All molecules were expressed as all-atom models. The resultant free-energy landscape had five ranges with decreasing ET1-hETB distance: completely dissociative, outside-gate, gate, binding pocket, and genuine-bound ranges. In the completely dissociative range, no ET1-hETB interaction appeared. In the outside-gate range, an ET1-hETB attractive interaction was the fly-casting mechanism. In the gate range, the ET1 orientational variety decreased rapidly. In the binding pocket range, ET1 was in a narrow pathway with a steep free-energy slope. In the genuine-bound range, ET1 was in a stable free-energy basin. A G-protein-coupled receptor (GPCR) might capture its ligand from a distant place.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Osaka, Suita 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Shiga, Kusatsu 525-8577, Japan
| | - Mitsuhito Wada
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26, Aomi, Tokyo, Koto-ku 135-0064, Japan
| | - Bhaskar Dasgupta
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Osaka, Suita 565-0871, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Osaka, Suita 565-0871, Japan
| | - Tomonori Hayami
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Osaka, Suita 565-0871, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Tokyo, Koto-ku 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Osaka, Suita 565-0871, Japan
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16
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Yamashita Y, Tanaka KI, Yamakawa N, Asano T, Kanda Y, Takafuji A, Kawahara M, Takenaga M, Fukunishi Y, Mizushima T. Chemical modification-mediated optimisation of bronchodilatory activity of mepenzolate, a muscarinic receptor antagonist with anti-inflammatory activity. Bioorg Med Chem 2019; 27:3339-3346. [PMID: 31204225 DOI: 10.1016/j.bmc.2019.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/07/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 11/26/2022]
Abstract
The treatment for patients with chronic obstructive pulmonary disease (COPD) usually involves a combination of anti-inflammatory and bronchodilatory drugs. We recently found that mepenzolate bromide (1) and its derivative, 3-(2-hydroxy-2, 2-diphenylacetoxy)-1-(3-phenoxypropyl)-1-azoniabicyclo[2.2.2]octane bromide (5), have both anti-inflammatory and bronchodilatory activities. We chemically modified 5 with a view to obtain derivatives with both anti-inflammatory and longer-lasting bronchodilatory activities. Among the synthesized compounds, (R)-(-)-12 ((R)-3-(2-hydroxy-2,2-diphenylacetoxy)-1-(3-phenylpropyl)-1-azoniabicyclo[2.2.2]octane bromide) showed the highest affinity in vitro for the human muscarinic M3 receptor (hM3R). Compared to 1 and 5, (R)-(-)-12 exhibited longer-lasting bronchodilatory activity and equivalent anti-inflammatory effect in mice. The long-term intratracheal administration of (R)-(-)-12 suppressed porcine pancreatic elastase-induced pulmonary emphysema in mice, whereas the same procedure with a long-acting muscarinic antagonist used clinically (tiotropium bromide) did not. These results suggest that (R)-(-)-12 might be therapeutically beneficial for use with COPD patients given the improved effects seen against both inflammatory pulmonary emphysema and airflow limitation in this animal model.
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Affiliation(s)
- Yasunobu Yamashita
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ken-Ichiro Tanaka
- Department of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishi-Tokyo 202-8585, Japan
| | - Naoki Yamakawa
- Shujitsu University School of Pharmacy, 1-6-1, Nishigawara, Naka-ku, Okayama 703-8516, Japan
| | - Teita Asano
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1, Sugao, Miyamae-ku, Kawasaki 216-8512, Japan
| | - Yuki Kanda
- Department of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishi-Tokyo 202-8585, Japan
| | - Ayaka Takafuji
- Department of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishi-Tokyo 202-8585, Japan
| | - Masahiro Kawahara
- Department of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishi-Tokyo 202-8585, Japan
| | - Mitsuko Takenaga
- Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1, Sugao, Miyamae-ku, Kawasaki 216-8512, Japan
| | - 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
| | - Tohru Mizushima
- LTT Bio-Pharma Co., Ltd, Shiodome Building 3F, 1-2-20 Kaigan, Minato-ku, Tokyo 105-0022, Japan.
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17
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Fukunishi Y, Yamashita Y, Mashimo T, Nakamura H. Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications. Mol Inform 2018; 37:e1700120. [PMID: 29442436 PMCID: PMC6055825 DOI: 10.1002/minf.201700120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/18/2022]
Abstract
We used protein-compound docking simulations to develop a structure-based quantitative structure-activity relationship (QSAR) model. The prediction model used docking scores as descriptors. The binding free energy was approximated by a weighted average of docking scores for multiple proteins. This approximation was based on a pharmacophore model of receptor pockets and compounds. The weights of the docking scores were restricted to small values to avoid unrealistic weights by a regularization term. Additional outlier elimination improved the results. We applied this method to two groups of targets. The first target was the kinase family. The cross-validation results of 107 kinase proteins showed that the RMSE of predicted binding free energies was 1.1 kcal/mol. The second target was the matrix metalloproteinase (MMP) family, which has been difficult for docking programs. MMPs require metal-binding groups in their inhibitor structures in many cases. A quantum effect contributes to the metal-ligand interaction. Despite this difficulty, the present method worked well for the MMPs. This method showed that the RMSE of predicted binding free energies was 1.1 kcal/mol. In comparison, with the original docking method the RMSE was 1.7 kcal/mol. The results suggest that the present QSAR model should be applied to general target proteins.
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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)2-3-26Aomi, Koto-ku, Tokyo135-0064Japan
| | - Yasunobu Yamashita
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry2-3-26, Aomi, Koto-kuTokyo135-0064Japan
- IMSBIO Co., Ltd.Owl Tower, 4-21-1Higashi-Ikebukuro, Toshima-kuTokyo170-0013Japan
| | - Haruki Nakamura
- Institute for Protein ResearchOsaka University3-2 YamadaokaSuita, Osaka565-0871Japan
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18
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Tanaka KI, Yamakawa N, Yamashita Y, Asano T, Kanda Y, Takafuji A, Kawahara M, Takenaga M, Fukunishi Y, Mizushima T. Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity. Front Pharmacol 2018; 9:344. [PMID: 29692733 PMCID: PMC5902689 DOI: 10.3389/fphar.2018.00344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/26/2018] [Indexed: 11/21/2022] Open
Abstract
The standard treatment for chronic obstructive pulmonary disease is a combination of anti-inflammatory drugs and bronchodilators. We recently found that mepenzolate bromide (MP), an antagonist for human muscarinic M3 receptor (hM3R), has both anti-inflammatory and short-acting bronchodilatory activities. To obtain MP derivatives with longer-lasting bronchodilatory activity, we synthesized hybrid compounds based on MP and two other muscarinic antagonists with long-acting bronchodilatory activity glycopyrronium bromide (GC) and aclidinium bromide (AD). Of these three synthesized hybrid compounds (MP-GC, GC-MP, MP-AD) and MP, MP-AD showed the highest affinity for hM3R and had the longest lasting bronchodilatory activity, which was equivalent to that of GC and AD. Both MP-GC and MP-AD exhibited an anti-inflammatory effect equivalent to that of MP, whereas, in line with GC and AD, GC-MP did not show this effect. We also confirmed that administration of MP-AD suppressed elastase-induced pulmonary emphysema in a mouse model. These findings provide important information about the structure-activity relationship of MP for both bronchodilatory and anti-inflammatory activities.
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Affiliation(s)
- Ken-Ichiro Tanaka
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Nishi-Tokyo, Japan
| | | | - Yasunobu Yamashita
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Teita Asano
- Institute of Medical Science, School of Medicine, St. Marianna University, Kawasaki, Japan
| | - Yuki Kanda
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Nishi-Tokyo, Japan
| | - Ayaka Takafuji
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Nishi-Tokyo, Japan
| | - Masahiro Kawahara
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, Nishi-Tokyo, Japan
| | - Mitsuko Takenaga
- Institute of Medical Science, School of Medicine, St. Marianna University, Kawasaki, Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Iida S, Mashimo T, Kurosawa T, Hojo H, Muta H, Goto Y, Fukunishi Y, Nakamura H, Higo J. Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. J Comput Chem 2016; 37:2687-2700. [PMID: 27735058 PMCID: PMC5242334 DOI: 10.1002/jcc.24494] [Citation(s) in RCA: 22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/26/2016] [Accepted: 08/31/2016] [Indexed: 12/29/2022]
Abstract
The C-terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non-neutralized. Because of the flexibility of the unbound CTD, a free-energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all-atom model and were immersed in an explicit solvent. The acetylation and charge-neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha-helix structures that are more compact than sheet/loop conformations. The charge-neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Shinji Iida
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26 Aomi, Koto-Ku, Tokyo, 135-0064, Japan
- IMSBIO Co, Ltd, Owl Tower 6F, 4-21-1, Higashi-ikebukuro, Toshima-ku, Tokyo, 170-0013, 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, 21-1 Ekimaehoncho, Kawasaki-ku, Kanagawa, 210-0007, Japan
| | - Hironobu Hojo
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroya Muta
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuji Goto
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshifumi Fukunishi
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26 Aomi, Koto-Ku, Tokyo, 135-0064, Japan
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-36, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Junichi Higo
- Institute for Protein Research Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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21
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Yanagihara Y, Sugahara T, Fukunishi Y. Visual Interpretation Compared with Caliper and Computerized Measurements in Experimental Vessel Stenosis. Acta Radiol 2016. [DOI: 10.1177/028418519203300608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To explain visual interpretation errors on angiograms, visual interpretation, caliper measurement, and computerized measurement of cine film were compared using each of 10 graphic models and 10 acrylic models with “stenotic vessels”. Stenosis > 40% was overestimated and stenosis < 40% underestimated by visual interpretation. In caliper measurement, stenosis > 40% at exposure of 90 kV was greatly overestimated by a degree similar to the estimation by visual interpretation, and stenosis > 40% at exposures of 74 kV and 58 kV was slightly overestimated. In computerized measurement, the estimation was consistent with the actual degree of stenosis. Therefore, visual interpretation was not reliable for estimation, and computerized measurement was indispensable for estimation of vessel stenosis. Moreover, we consider the most common cause of error in visual interpretation to be optical illusions.
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Fukunishi Y, Mashimo T, Misoo K, Wakabayashi Y, Miyaki T, Ohta S, Nakamura M, Ikeda K. Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics. Curr Pharm Des 2016; 22:3555-68. [PMID: 27075578 PMCID: PMC5080912 DOI: 10.2174/1381612822666160414142547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/12/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design.
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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.
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Okazaki H, Takeda S, Ikeda E, Fukunishi Y, Ishii H, Taniguchi A, Tokuyasu M, Himeno T, Kakizoe K, Matsumoto K, Shindo M, Aramaki H. Bongkrekic acid as a selective activator of the peroxisome proliferator-activated receptor γ (PPARγ) isoform. J Toxicol Sci 2015; 40:223-33. [PMID: 25786526 DOI: 10.2131/jts.40.223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bongkrekic acid (BKA), an antibiotic isolated from Pseudomonas cocovenans, is an inhibitory molecule of adenine nucleotide translocase. Since this translocase is a core component of the mitochondrial permeability transition pore (MPTP) formed by apoptotic stimuli, BKA has been used as a tool to abrogate apoptosis. However, the other biochemical properties of BKA have not yet been resolved. Although the definition of a fatty acid is a carboxylic acid (-COOH) with a long hydrocarbon chain (tail), when focused on the chemical structure of BKA, the molecule was revealed to be a branched unsaturated tricarboxylic acid that resembled the structure of polyunsaturated fatty acids (PUFAs). Peroxisome proliferator-activated receptors (PPARs) consist of a subfamily of three isoforms: α, β, and γ, the ligands of which include PUFAs. Using completely synthesized BKA together with simplified BKA derivatives (purity: > 98%), we herein demonstrated the utility of BKA as a selective activator of the human PPARγ isoform, which may not be associated with the anti-apoptotic nature of BKA. We also discussed the possible usefulness of BKA.
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Nguyen H, Tran T, Fukunishi Y, Higo J, Nakamura H, Le L. Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J Chem Inf Model 2015; 55:1936-43. [DOI: 10.1021/acs.jcim.5b00319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hung Nguyen
- Life
Science Laboratory, Institute for Computational Science and Technology, Ho Chi
Minh City, Vietnam
| | - Tien Tran
- University of Technology, Ho Chi Minh City, Vietnam
| | - Yoshifumi Fukunishi
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Junichi Higo
- Institute
for Protein Research, Osaka University, Osaka, Japan
| | - Haruki Nakamura
- Institute
for Protein Research, Osaka University, Osaka, Japan
| | - Ly Le
- Life
Science Laboratory, Institute for Computational Science and Technology, Ho Chi
Minh City, Vietnam
- School
of Biotechnology, International University, Vietnam National University, Ho
Chi Minh City, Vietnam
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Moriya J, Takeuchi K, Tai K, Arai K, Kobayashi N, Yoneda N, Fukunishi Y, Inoue A, Kihara M, Murakami T, Chiba K, Shimada I. Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6. J Med Chem 2015; 58:5674-83. [PMID: 26132273 DOI: 10.1021/acs.jmedchem.5b00778] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interactions between tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and TNF superfamily receptors (TNFRSFs) are promising targets for rheumatoid arthritis (RA) treatment. However, due to the challenging nature of protein-protein interactions (PPIs), a potent inhibitor that surpasses the affinity of the TRAF6-TNFRSF interactions has not been developed. We developed a small-molecule PPI inhibitor of TRAF6-TNFRSF interactions using NMR and in silico techniques. The most potent compound, TRI4, exhibited an affinity higher than those of TNFRSFs and competitively inhibited a TRAF6-TNFRSF interaction. Structural characterization of the TRAF6-TRI4 complex revealed that TRI4 supplants key interactions in the TRAF6-TNFRSF interfaces. In addition, some TRAF6-TRI4 interactions extend beyond the TRAF6-TNFRSF interfaces and increase the binding affinity. Our successful development of TRI4 provides a new opportunity for RA treatment and implications for structure-guided development of PPI inhibitors.
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Affiliation(s)
- Jun Moriya
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Koh Takeuchi
- ‡Biological Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Kenji Tai
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Kenzo Arai
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Naoki Kobayashi
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Naoki Yoneda
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Yoshifumi Fukunishi
- ‡Biological Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Atsushi Inoue
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Miho Kihara
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Takumi Murakami
- §Pharmacological Evaluation Unit, Tsukuba Division, Sunplanet Co., Ltd., Tokodai 5-11-1, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Kenichi Chiba
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Ichio Shimada
- ∥Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Higo J, Dasgupta B, Mashimo T, Kasahara K, Fukunishi Y, Nakamura H. Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J Comput Chem 2015; 36:1489-501. [DOI: 10.1002/jcc.23948] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Bhaskar Dasgupta
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next Generation Natural Products Chemistry; 2-3-26 Aomi Koto-Ku Tokyo 135-0064 Japan
- Information, Mathematical Science and Bioinformatics Co., Ltd.; 4-21-1, Higashiikebukuro Toshima-ku Tokyo 170-0013 Japan
| | - Kota Kasahara
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - 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
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
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Fukunishi Y, Kurosawa T, Mikami Y, Nakamura H. Prediction of synthetic accessibility based on commercially available compound databases. J Chem Inf Model 2014; 54:3259-67. [PMID: 25420000 DOI: 10.1021/ci500568d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction databases and the availability of starting materials. We developed a new method of predicting SA using commercially available compound databases and molecular descriptors. SA was estimated from the probability of existence of substructures consisting of the compound in question, the number of symmetry atoms, the graph complexity, and the number of chiral centers of the compound. The probabilities of the existence of given substructures were estimated based on a compound library. The predicted SA results reproduced the expert manual assessments with a Pearson correlation coefficient of 0.56. Since our method required a compound database and not a reaction database, it should be easy to customize the prediction for compound vendors. The correlation between the sales price of approved drugs and the SA values was also examined and found to be weak. The price most likely depends on the total cost of development and other factors.
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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
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Yamashita Y, Tanaka KI, Asano T, Yamakawa N, Kobayashi D, Ishihara T, Hanaya K, Shoji M, Sugai T, Wada M, Mashimo T, Fukunishi Y, Mizushima T. Synthesis and biological comparison of enantiomers of mepenzolate bromide, a muscarinic receptor antagonist with bronchodilatory and anti-inflammatory activities. Bioorg Med Chem 2014; 22:3488-97. [PMID: 24844758 DOI: 10.1016/j.bmc.2014.04.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 03/05/2014] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 01/05/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by abnormal inflammatory responses and airflow limitations. We recently proposed that the muscarinic antagonist mepenzolate bromide (mepenzolate) would be therapeutically effective against COPD due to its muscarinic receptor-dependent bronchodilatory activity as well as anti-inflammatory properties. Mepenzolate has an asymmetric carbon atom, thus providing us with the opportunity to synthesize both of its enantiomers ((R)- and (S)-mepenzolate) and to examine their biochemical and pharmacological activities. (R)- or (S)-mepenzolate was synthesized by condensation of benzilic acid with (R)- or (S)-alcohol, respectively, followed by quaternization of the tertiary amine. As predicted by computational simulation, a filter-binding assay in vitro revealed that (R)-mepenzolate showed a higher affinity for the muscarinic M3 receptor than (S)-mepenzolate. In vivo, the bronchodilatory activity of (R)-mepenzolate was superior to that of (S)-mepenzolate, whereas anti-inflammatory activity was indistinguishable between the two enantiomers. We confirmed that each mepenzolate maintained its original stereochemistry in the lung when administered intratracheally. These results suggest that (R)-mepenzolate may have superior properties to (S)-mepenzolate as a drug to treat COPD patients given that the former has more potent bronchodilatory activity than the latter.
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Affiliation(s)
| | | | - Teita Asano
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Naoki Yamakawa
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | | | | | - Kengo Hanaya
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Mitsuru Shoji
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Takeshi Sugai
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan
| | - Mitsuhito Wada
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan; Biochemical Information Project, Fujitsu Limited, 1-9-3, Nakase, Mihama-ku, Chiba 261-8588, Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan; Information and Mathematical Science and Bioinformatics Co., Ltd, Owl Tower, 4-21-1, Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tohru Mizushima
- Faculty of Pharmacy, Keio University, Tokyo 105-8512, Japan.
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Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T. Structural insights into the function of a thermostable copper-containing nitrite reductase. ACTA ACUST UNITED AC 2013; 155:123-35. [DOI: 10.1093/jb/mvt107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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30
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Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I, Nakamura H. Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions. J Chem Theory Comput 2013; 9:5599-609. [PMID: 26592294 DOI: 10.1021/ct400342e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecular dynamics (MD) simulation program for biological macromolecules was implemented with a non-Ewald scheme for long-ranged electrostatic interactions and run on a general purpose graphics processing unit (GPU). We recently developed several non-Ewald methods to compute the electrostatic energies with high precision. In particular, the zero-dipole summation (ZD) method, which takes into account the neutralities of charges and dipoles in a truncated subset, enables the calculation of electrostatic interactions with high accuracy and low computational cost, and its algorithm is simple enough to be implemented in a GPU. We developed an MD program with the space decomposition algorithm, myPresto/psygene, and applied it to several biological macromolecular systems with GPUs implementing the ZD method. Rapid computing performance with high accuracy was obtained.
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Affiliation(s)
- Tadaaki Mashimo
- Japan Biological Informatics Consortium (JBIC), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.,Information and Mathematical Science Bio Inc., Owl Tower, 4-21-1, Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - 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
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yu Takano
- Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuo Fukuda
- Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- 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.,Institute for Protein Research, Osaka University , 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H. LigandBox: A database for 3D structures of chemical compounds. Biophysics (Nagoya-shi) 2013; 9:113-21. [PMID: 27493549 PMCID: PMC4629684 DOI: 10.2142/biophysics.9.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 07/11/2013] [Indexed: 12/22/2022] Open
Abstract
A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.
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Affiliation(s)
- Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusuke Sugihara
- Fujitsu Kyushu R&D Center, Life Science Systems Dept., Fujitsu Kyushu Systems Limited, 2-1, Momochihama 2-Chome, Sawara-ku, Fukuoka, 814-8589, Japan
| | - Yoshifumi Fukunishi
- Molecular Profiling Research Center for Drug Discovery (molprof), AIST, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
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Hagiwara Y, Ohno K, Kamohara M, Takasaki J, Watanabe T, Fukunishi Y, Nakamura H, Orita M. Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists. Expert Opin Drug Discov 2013; 8:951-64. [PMID: 23682717 DOI: 10.1517/17460441.2013.799134] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION G protein-coupled receptors (GPCRs) are integral membrane proteins which contain seven-transmembrane-spanning alpha-helices. GPCR-mediated signaling has been associated with various human diseases, positioning GPCRs as attractive targets in the drug discovery field. Recently, through advances in protein engineering and crystallography, the number of resolved GPCR structures has increased dramatically. This growing availability of GPCR structures has greatly accelerated structure-based drug design (SBDD) and in silico screening for GPCR-targeted drug discovery. AREAS COVERED The authors introduce the current status of X-ray crystallography of GPCRs and what has been revealed from the resolved crystal structures. They also review the recent advances in SBDD and in silico screening for GPCR-targeted drug discovery and discuss a docking study, using homology modeling, with the discovery of potent antagonists of the vasopressin 1b receptor. EXPERT OPINION Several innovative protein engineering techniques and crystallographic methods have greatly accelerated SBDD, not only for already-resolved GPCRs but also for those structures which remain unclear. These technological advances are expected to enable the determination of GPCR-fragment complexes, making it practical to perform fragment-based drug discovery. This paves the way for a new era of GPCR-targeted drug discovery.
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Affiliation(s)
- Yohsuke Hagiwara
- Drug Discovery Research, Astellas Pharma, Inc., 21, Miyukigaoka, Ibaraki 305-8585, Japan.
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Fukunishi Y, Nakamura H. Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules. Pharmaceuticals (Basel) 2013; 6:604-22. [PMID: 24276169 PMCID: PMC3817721 DOI: 10.3390/ph6050604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 11/16/2022] Open
Abstract
We previously developed the direct interaction approximation (DIA) method to estimate the protein-ligand binding free energy (DG). The DIA method estimates the DG value based on the direct van der Waals and electrostatic interaction energies between the protein and the ligand. In the current study, the effect of the entropy of the ligand was introduced with protein dynamic properties by molecular dynamics simulations, and the interaction between each residue of the protein and the ligand was also weighted considering the hydration of each residue. The molecular dynamics simulation of the apo target protein gave the hydration effect of each residue, under the assumption that the residues, which strongly bind the water molecules, are important in the protein-ligand binding. These two effects improved the reliability of the DIA method. In fact, the parameters used in the DIA became independent of the target protein. The averaged error of DG estimation was 1.3 kcal/mol and the correlation coefficient between the experimental DG value and the calculated DG value was 0.75.
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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
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
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Fukunishi Y, Nakamura H. Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking. Pharmaceuticals (Basel) 2012; 5:1332-45. [PMID: 24281339 PMCID: PMC3816669 DOI: 10.3390/ph5121332] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 11/24/2012] [Accepted: 11/30/2012] [Indexed: 01/05/2023] Open
Abstract
Ligand-based and structure-based drug screening methods were integrated for in silico drug development by combining the maximum-volume overlap (MVO) method with a protein-compound docking program. The MVO method is used to select reliable docking poses by calculating volume overlaps between the docking pose in question and the known ligand docking pose, if at least a single protein-ligand complex structure is known. In the present study, the compounds in a database were docked onto a target protein that had a known protein-ligand complex structure. The new score is the summation of the docking score and the MVO score, which is the measure of the volume overlap between the docking poses of the compound in question and the known ligand. The compounds were sorted according to the new score. The in silico screening results were improved by comparing the MVO score to the original docking score only. The present method was also applied to some target proteins with known ligands, and the results demonstrated that it worked well.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail: (H.N.)
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35
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Fukunishi Y, Nakamura H. Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation. Pharmaceuticals (Basel) 2012; 5:1064-79. [PMID: 24281257 PMCID: PMC3816655 DOI: 10.3390/ph5101064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 11/28/2022] Open
Abstract
We have developed a method for estimating protein-ligand binding free energy (DG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the DG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated DG values was 0.81, and the average error of DG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mizukoshi Y, Abe A, Takizawa T, Hanzawa H, Fukunishi Y, Shimada I, Takahashi H. An Accurate Pharmacophore Mapping Method by NMR Spectroscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104905] [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: 11/08/2022]
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Mizukoshi Y, Abe A, Takizawa T, Hanzawa H, Fukunishi Y, Shimada I, Takahashi H. An accurate pharmacophore mapping method by NMR spectroscopy. Angew Chem Int Ed Engl 2011; 51:1362-5. [PMID: 22213544 DOI: 10.1002/anie.201104905] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/21/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Yumiko Mizukoshi
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Japan
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Takashima Y, Hatanaka S, Mizohata E, Nagata N, Fukunishi Y, Matsumura H, Urade Y, Inoue T. Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2α synthase, AKR1B3. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1630-2. [PMID: 22139184 PMCID: PMC3232157 DOI: 10.1107/s1744309111036165] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 09/05/2011] [Indexed: 11/11/2022]
Abstract
Aldo-keto reductase 1B3 (AKR1B3) catalyzes the NADPH-dependent reduction of prostaglandin H(2) (PGH(2)), which is a common intermediate of various prostanoids, to form PGF(2α). AKR1B3 also reduces PGH(2) to PGD(2) in the absence of NADPH. AKR1B3 produced in Escherichia coli was crystallized in complex with NADPH by the sitting-drop vapour-diffusion method. The crystal was tetragonal, belonging to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 107.62, c = 120.76 Å. X-ray diffraction data were collected to 2.4 Å resolution at 100 K using a synchrotron-radiation source.
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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
| | - Seika Hatanaka
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nanae Nagata
- Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshifumi Fukunishi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Urade
- Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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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] [What about the content of this article? (0)] [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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Wada M, Kanamori E, Nakamura H, Fukunishi Y. Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes. J Chem Inf Model 2011; 51:2398-407. [PMID: 21848279 DOI: 10.1021/ci200236x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a new protocol for in silico drug screening for G-protein-coupled receptors (GPCRs) using a set of "universal active probes" (UAPs) with an ensemble docking procedure. UAPs are drug-like compounds, which are actual active compounds of a variety of known proteins. The current targets were nine human GPCRs whose three-dimensional (3D) structures are unknown, plus three GPCRs, namely β(2)-adrenergic receptor (ADRB2), A(2A) adenosine receptor (A(2A)), and dopamine D3 receptor (D(3)), whose 3D structures are known. Homology-based models of the GPCRs were constructed based on the crystal structures with careful sequence inspection. After subsequent molecular dynamics (MD) simulation taking into account the explicit lipid membrane molecules with periodic boundary conditions, we obtained multiple model structures of the GPCRs. For each target structure, docking-screening calculations were carried out via the ensemble docking procedure, using both true active compounds of the target proteins and the UAPs with the multiple target screening (MTS) method. Consequently, the multiple model structures showed various screening results with both poor and high hit ratios, the latter of which could be identified as promising for use in in silico screening to find candidate compounds to interact with the proteins. We found that the hit ratio of true active compounds showed a positive correlation to that of the UAPs. Thus, we could retrieve appropriate target structures from the GPCR models by applying the UAPs, even if no active compound is known for the GPCRs. Namely, the screening result that showed a high hit ratio for the UAPs could be used to identify actual hit compounds for the target GPCRs.
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Affiliation(s)
- Mitsuhito Wada
- Japan Biological Informatics Consortium (JBiC), Tokyo, Japan
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Abstract
We have developed a computational method that predicts the positions of active compounds, making it possible to increase activity as a fragment evolution strategy. We refer to the positions of these compounds as the active position. When an active fragment compound is found, the following lead generation process is performed, primarily to increase activity. In the current method, to predict the location of the active position, hydrogen atoms are replaced by small side chains, generating virtual compounds. These virtual compounds are docked to a target protein, and the docking scores (affinities) are examined. The hydrogen atom that gives the virtual compound with good affinity should correspond to the active position and it should be replaced to generate a lead compound. This method was found to work well, with the prediction of the active position being 2 times more efficient than random synthesis. In the current study, 15 examples of lead generation were examined. The probability of finding active positions among all hydrogen atoms was 26%, and the current method accurately predicted 60% of the active positions.
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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; E-Mail: ; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099
- Pharmaceutical Innovation Value Chain, BioGrid Center Kansai/ 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan
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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
- Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Fukunishi Y, Nakamura H. Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library. Protein Sci 2011; 20:95-106. [PMID: 21064162 DOI: 10.1002/pro.540] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new approach to predicting the ligand-binding sites of proteins was developed, using protein-ligand docking computation. In this method, many compounds in a random library are docked onto the whole protein surface. We assumed that the true ligand-binding site would exhibit stronger affinity to the compounds in the random library than the other sites, even if the random library did not include the ligand corresponding to the true binding site. We also assumed that the affinity of the true ligand-binding site would be correlated to the docking scores of the compounds in the random library, if the ligand-binding site was correctly predicted. We call this method the molecular-docking binding-site finding (MolSite) method. The MolSite method was applied to 89 known protein-ligand complex structures extracted from the Protein Data Bank, and it predicted the correct binding sites with about 80-99% accuracy, when only the single top-ranked site was adopted. In addition, the average docking score was weakly correlated to the experimental protein-ligand binding free energy, with a correlation coefficient of 0.44.
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Affiliation(s)
- Yoshifumi Fukunishi
- Protein Structural Information Analysis Team, Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan.
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Nagata N, Kusakari Y, Fukunishi Y, Inoue T, Urade Y. Catalytic mechanism of the primary human prostaglandin F2α synthase, aldo-keto reductase 1B1--prostaglandin D2 synthase activity in the absence of NADP(H). FEBS J 2011; 278:1288-98. [PMID: 21306562 DOI: 10.1111/j.1742-4658.2011.08049.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aldo-keto reductase 1B1 and 1B3 (AKR1B1 and AKR1B3) are the primary human and mouse prostaglandin F(2α) (PGF(2α)) synthases, respectively, which catalyze the NADPH-dependent reduction of PGH(2), a common intermediate of various prostanoids, to form PGF(2α). In this study, we found that AKR1B1 and AKR1B3, but not AKR1B7 and AKR1C3, also catalyzed the isomerization of PGH(2) to PGD(2) in the absence of NADPH or NADP(+). Both PGD(2) and PGF(2α) synthase activities of AKR1B1 and AKR1B3 completely disappeared in the presence of NADP(+) or after heat treatment of these enzymes at 100 °C for 5 min. The K(m), V(max), pK and optimum pH values of the PGD(2) synthase activities of AKR1B1 and AKR1B3 were 23 and 18 μM, 151 and 57 nmol·min(-1)·(mg protein)(-1), 7.9 and 7.6, and pH 8.5 for both AKRs, respectively, and those of PGF(2α) synthase activity were 29 and 33 μM, 169 and 240 nmol·min(-1)·(mg protein)(-1), 6.2 and 5.4, and pH 5.5 and pH 5.0, respectively, in the presence of 0.5 mm NADPH. Site-directed mutagenesis of the catalytic tetrad of AKR1B1, composed of Tyr, Lys, His and Asp, revealed that the triad of Asp43, Lys77 and His110, but not Tyr48, acts as a proton donor in most AKR activities, and is crucial for PGD(2) and PGF(2α) synthase activities. These results, together with molecular docking simulation of PGH(2) to the crystallographic structure of AKR1B1, indicate that His110 acts as a base in concert with Asp43 and Lys77 and as an acid to generate PGD(2) and PGF(2α) in the absence of NADPH or NADP(+) and in the presence of NADPH, respectively.
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Affiliation(s)
- Nanae Nagata
- Department of Molecular Behavioral Biology, Osaka Bioscience Institute, Suita, Osaka, Japan
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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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Takeda S, Hirayama A, Urata S, Mano N, Fukagawa K, Imamura M, Irii A, Kitajima S, Masuyama T, Nomiyama M, Tatei S, Tomita S, Kudo T, Noguchi M, Yamaguchi Y, Okamoto Y, Amamoto T, Fukunishi Y, Watanabe K, Omiecinski CJ, Aramaki H. Cannabidiol-2',6'-dimethyl ether as an effective protector of 15-lipoxygenase-mediated low-density lipoprotein oxidation in vitro. Biol Pharm Bull 2011; 34:1252-1256. [PMID: 21804214 PMCID: PMC4012644 DOI: 10.1248/bpb.34.1252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2023]
Abstract
15-Lipoxygenase (15-LOX) is one of the key enzymes responsible for the formation of oxidized low-density lipoprotein (ox-LDL), a major causal factor for atherosclerosis. Both enzymatic (15-LOX) and non-enzymatic (Cu(2+)) mechanisms have been proposed for the production of ox-LDL. We have recently reported that cannabidiol-2',6'-dimethyl ether (CBDD) is a selective and potent inhibitor of 15-LOX-catalyzed linoleic acid oxygenation (Takeda et al., Drug Metab. Dispos., 37, 1733-1737 (2009)). In the LDL, linoleic acid is present as cholesteryl linoleate, the major fatty acid esterified to cholesterol, and is susceptible to oxidative modification by 15-LOX or Cu(2+). In this investigation, we examined the efficacy of CBDD on i) 15-LOX-catalyzed oxygenation of cholesteryl linoleate, and ii) ox-LDL formation catalyzed by 15-LOX versus Cu(2+)-mediated non-enzymatic generation of this important mediator. The results obtained demonstrate that CBDD is a potent and selective inhibitor of ox-LDL formation generated by the 15-LOX pathway. These studies establish CBDD as both an important experimental tool for characterizing 15-LOX-mediated ox-LDL formation, and as a potentially useful therapeutic agent for treatment of atherosclerosis.
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Affiliation(s)
- Shuso Takeda
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Akari Hirayama
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Shino Urata
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Nobutaka Mano
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Keiko Fukagawa
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Midori Imamura
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Ayumi Irii
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Satomi Kitajima
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Tomoko Masuyama
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Mai Nomiyama
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Sachiko Tatei
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Saari Tomita
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Taichi Kudo
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Momoko Noguchi
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Yasuhiro Yamaguchi
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Yoshiko Okamoto
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
| | - Toshiaki Amamoto
- NEUES Corporation; Yaesu Center Building 3F, 1-6-6 Yaesu, Chuo-ku, Tokyo 103-0028, Japan
| | - 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
| | - Kazuhito Watanabe
- Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Hokuriku University; Ho-3 Kanagawa-machi, Kanazawa 920-1181, Japan
| | - Curtis John Omiecinski
- Center for Molecular Toxicology and Carcinogenesis; 101 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, United States
| | - Hironori Aramaki
- Department of Molecular Biology, Daiichi University of Pharmacy; 22-1 Tamagawa-cho, Minami-ku, Fukuoka 815-8511, Japan
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Kanamori E, Igarashi S, Osawa M, Fukunishi Y, Shimada I, Nakamura H. Structure determination of a protein assembly by amino acid selective cross-saturation. Proteins 2010; 79:179-90. [PMID: 20954264 DOI: 10.1002/prot.22871] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 08/25/2010] [Accepted: 08/27/2010] [Indexed: 11/10/2022]
Abstract
Amino acid selective cross-saturation (ASCS) method not only provides information about the interface of a protein assembly by the spin relaxation experiment, but also identifies the amino acid residues in the acceptor protein, which are located close to the selectively labeled amino acid residues in the donor protein. Here, a new method was developed to build a precise structural model of a protein assembly, which satisfies the experimental ASCS values, using simulated annealing computation. This method was applied to the ubiquitin-yeast ubiquitin hydrolase 1 (Ub-YUH1) complex to build a precise complex structure compatible with that determined by X-ray crystallography.
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Affiliation(s)
- Eiji Kanamori
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo 135-0064, Japan.
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Fukunishi Y, Ohno K, Orita M, Nakamura H. Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). J Chem Inf Model 2010; 50:1233-40. [DOI: 10.1021/ci100108p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, Japan Biological Informatics Consortium (JBIC), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Chemistry Research Laboratories, Drug Discovery Research, Astellas Pharma Incorporated, 21 Miyukigaoka, Tsukuba, Ibaraki
| | - Kazuki Ohno
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, Japan Biological Informatics Consortium (JBIC), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Chemistry Research Laboratories, Drug Discovery Research, Astellas Pharma Incorporated, 21 Miyukigaoka, Tsukuba, Ibaraki
| | - Masaya Orita
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, Japan Biological Informatics Consortium (JBIC), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Chemistry Research Laboratories, Drug Discovery Research, Astellas Pharma Incorporated, 21 Miyukigaoka, Tsukuba, Ibaraki
| | - Haruki Nakamura
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan, Pharmaceutical Innovation Value Chain, BioGrid Center Kansai, 1-4-2 Shinsenri-Higashimachi, Toyonaka, Osaka 560-0082, Japan, Japan Biological Informatics Consortium (JBIC), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan, Chemistry Research Laboratories, Drug Discovery Research, Astellas Pharma Incorporated, 21 Miyukigaoka, Tsukuba, Ibaraki
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50
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