1
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Imamura K, Akagi KI, Miyanoiri Y, Tsujimoto H, Hirokawa T, Ashida H, Murakami K, Inoue A, Suno R, Ikegami T, Sekiyama N, Iwata S, Kobayashi T, Tochio H. Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy. Structure 2024; 32:352-361.e5. [PMID: 38194963 DOI: 10.1016/j.str.2023.12.008] [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: 02/24/2023] [Revised: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Orexin neuropeptides have many physiological roles in the sleep-wake cycle, feeding behavior, reward demands, and stress responses by activating cognitive receptors, the orexin receptors (OX1R and OX2R), distributed in the brain. There are only subtle differences between OX1R and OX2R in the orthosteric site, which has hindered the rational development of subtype-selective antagonists. In this study, we utilized solution-state NMR to capture the structural plasticity of OX2R labeled with 13CH3-ε-methionine in complex with antagonists. Mutations in the orthosteric site allosterically affected the intracellular tip of TM6. Ligand exchange experiments with the subtype-selective EMPA and the nonselective suvorexant identified three methionine residues that were substantially perturbed. The NMR spectra suggested that the suvorexant-bound state exhibited more structural plasticity than the EMPA-bound state, which has not been foreseen from the close similarity of their crystal structures, providing insights into dynamic features to be considered in understanding the ligand recognition mode.
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Affiliation(s)
- Kayo Imamura
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ken-Ichi Akagi
- Section of Laboratory Equipment, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Tsujimoto
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hideo Ashida
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaori Murakami
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryoji Suno
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - So Iwata
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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2
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Sakamoto K, Hirokawa T. Lipid bilayer membrane permeability mechanism of the K-Ras(G12D)-inhibitory bicyclic peptide KS-58 elucidated by molecular dynamics simulations. Bioorg Med Chem Lett 2024; 100:129649. [PMID: 38341162 DOI: 10.1016/j.bmcl.2024.129649] [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: 12/15/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Peptides are mid-size molecules (700-2000 g/mol) and have attracted particular interest as therapeutic modalities as they are superior in controlling protein-protein interactions, a process that is a typical drug target category, compared with small molecules (<500 g/mol). In 2020, we identified KS-58 (1333 g/mol) as a K-Ras(G12D)-inhibitory bicyclic peptide and suggested its cell membrane permeability. However, the membrane permeability mechanism had not been elucidated. In this study, we aim to clarify the mechanism by molecular dynamics (MD) simulations. Initially, we simulated the molecular conformations of KS-58 in water (a polar solvent) and in chloroform (a non-polar solvent). The identified stable conformations were significantly different in each solvent. KS-58 behaves as a chameleon-like molecule as it alters its polar surface area (PSA) depending on the solvent environment. It was also discovered that orientation of Asp's side chain is a critical energy barrier for KS-58 altering its conformation from hydrophilic to lipophilic. Taking these properties into consideration, we simulated its lipid bilayer membrane permeability. KS-58 shifted toward the inside of the lipid bilayer membrane with altering its conformations to lipophilic. When the simulation condition was set in deionized form of that carboxy group of Asp, KS-58 traveled deeper inside the cell membrane. PSA and the depth of the membrane penetration correlated. In vitro data suggested that cell membrane permeability of KS-58 is improved in weakly acidic conditions leading to partial deionization of the carboxy group. Our data provide an example of the molecular properties of mid-size peptides with membrane accessibility and propose an effective metadynamics approach to elucidate such molecular mechanisms by MD simulations.
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Affiliation(s)
- Kotaro Sakamoto
- Research & Development Depertment, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, 501-0475 Gifu, Japan.
| | - Takatsugu Hirokawa
- Research & Development Depertment, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, 501-0475 Gifu, Japan; Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Japan; Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Japan.
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3
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Fujiwara K, Nagasawa S, Maeyama R, Segawa R, Hirasawa N, Hirokawa T, Iwabuchi Y. Biological Evaluation of Isosteric Applicability of 1,3-Substituted Cuneanes as m-Substituted Benzenes Enabled by Selective Isomerization of 1,4-Substituted Cubanes. Chemistry 2024; 30:e202303548. [PMID: 38012076 DOI: 10.1002/chem.202303548] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 11/29/2023]
Abstract
We herein evaluate a biological applicability of 1,3-substituted cuneanes as an isostere of m-substituted benzenes based on its structural similarity. An investigation of a method to obtain 1,3-substituted cuneanes by selective isomerization of 1,4-substituted cubanes enables this attempt by giving a key synthetic step to obtain a cuneane analogs of pharmaceuticals having m-substituted benzene moiety. Biological evaluation of the synthesized analogs and in silico study of the obtained result revealed a potential usage of cuneane skeleton in medicinal chemistry.
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Affiliation(s)
- Kan Fujiwara
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
| | - Shota Nagasawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
| | - Ryusei Maeyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
| | - Ryosuke Segawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
| | - Noriyasu Hirasawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan
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4
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Kudo G, Yanagisawa K, Yoshino R, Hirokawa T. AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. J Chem Inf Model 2023; 63:7768-7777. [PMID: 38085669 PMCID: PMC10751795 DOI: 10.1021/acs.jcim.3c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023]
Abstract
Peptides have attracted much attention recently owing to their well-balanced properties as drugs against protein-protein interaction (PPI) surfaces. Molecular simulation-based predictions of binding sites and amino acid residues with high affinity to PPI surfaces are expected to accelerate the design of peptide drugs. Mixed-solvent molecular dynamics (MSMD), which adds probe molecules or fragments of functional groups as solutes to the hydration model, detects the binding hotspots and cryptic sites induced by small molecules. The detection results vary depending on the type of probe molecule; thus, they provide important information for drug design. For rational peptide drug design using MSMD, we proposed MSMD with amino acid residue probes, named amino acid probe-based MSMD (AAp-MSMD), to detect hotspots and identify favorable amino acid types on protein surfaces to which peptide drugs bind. We assessed our method in terms of hotspot detection at the amino acid probe level and binding free energy prediction with amino acid probes at the PPI site for the complex structure that formed the PPI. In hotspot detection, the max-spatial probability distribution map (max-PMAP) obtained from AAp-MSMD detected the PPI site, to which each type of amino acid can bind favorably. In the binding free energy prediction using amino acid probes, ΔGFE obtained from AAp-MSMD roughly estimated the experimental binding affinities from the structure-activity relationship. AAp-MSMD, with amino acid probes, provides estimated binding sites and favorable amino acid types at the PPI site of a target protein.
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Affiliation(s)
- Genki Kudo
- Physics
Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8571, Ibaraki Japan
| | - Keisuke Yanagisawa
- Department
of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro 152-8550, Tokyo Japan
- Middle
Molecule IT-based Drug Discovery Laboratory, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro 152-8550, Tokyo Japan
| | - Ryunosuke Yoshino
- Faculty
of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Ibaraki Japan
- Transborder
Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki Japan
| | - Takatsugu Hirokawa
- Faculty
of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Ibaraki Japan
- Transborder
Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki Japan
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5
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Kawada Y, Hayashi E, Katsuragi Y, Imamura-Jinda A, Hirokawa T, Mizukami T, Hayashi M. Identification of Chemicals That Abrogate Folate-Dependent Inhibition of Starch Accumulation in Non-Photosynthetic Plastids of Arabidopsis. Plant Cell Physiol 2023; 64:1551-1562. [PMID: 37801291 DOI: 10.1093/pcp/pcad116] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/26/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
Folate, also known as vitamin B9, is an essential cofactor for a variety of enzymes and plays a crucial role in many biological processes. We previously reported that plastidial folate prevents starch biosynthesis triggered by the influx of sugar into non-starch-accumulating plastids, such as etioplasts, and chloroplasts under darkness; hence the loss of plastidial folate induces the accumulation of starch in plastids. To understand the molecular mechanism underlying this phenomenon, we screened our in-house chemical library and searched their derivatives to identify chemicals capable of inducing starch accumulation in etioplasts. The results revealed four chemicals, compounds #120 and #375 and their derivatives, compounds #120d and #375d, respectively. The derivative compounds induced starch accumulation in etioplasts and suppressed hypocotyl elongation in dark-grown Arabidopsis seedlings. They also inhibited the post-germinative growth of seedlings under illumination. All four chemicals contained the sulfonamide group as a consensus structure. The sulfonamide group is also found in sulfa drugs, which exhibit antifolate activity, and in sulfonylurea herbicides. Further analyses revealed that compound #375d induces starch accumulation by inhibiting folate biosynthesis. By contrast, compound #120d neither inhibited folate biosynthesis nor exhibited the herbicide activity. Protein and metabolite analyses suggest that compound #120d abrogates folate-dependent inhibition of starch accumulation in etioplasts by enhancing starch biosynthesis.
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Affiliation(s)
- Yoshihiro Kawada
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Eriko Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Yuya Katsuragi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Aya Imamura-Jinda
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, Tsukuba University, 1-1-1 Tenmondai, Tsukuba, Ibaragi, 305-8577 Japan
| | - Tamio Mizukami
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
- Frontier Pharma, 1281-8 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
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Watanabe R, Tsuji D, Tanaka H, Uno MS, Ohnishi Y, Kitaguchi S, Matsugu T, Nakae R, Teramoto H, Yamamoto K, Shinohara Y, Hirokawa T, Okino N, Ito M, Itoh K. Lysoglycosphingolipids have the ability to induce cell death through direct PI3K inhibition. J Neurochem 2023; 167:753-765. [PMID: 37975558 DOI: 10.1111/jnc.16012] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/04/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Sphingolipidoses are inherited metabolic disorders associated with glycosphingolipids accumulation, neurodegeneration, and neuroinflammation leading to severe neurological symptoms. Lysoglycosphingolipids (lysoGSLs), also known to accumulate in the tissues of sphingolipidosis patients, exhibit cytotoxicity. LysoGSLs are the possible pathogenic cause, but the mechanisms are still unknown in detail. Here, we first show that lysoGSLs are potential inhibitors of phosphoinositide 3-kinase (PI3K) to reduce cell survival signaling. We found that phosphorylated Akt was commonly reduced in fibroblasts from patients with sphingolipidoses, including GM1/GM2 gangliosidoses and Gaucher's disease, suggesting the contribution of lysoGSLs to the pathogenesis. LysoGSLs caused cell death and decreased the level of phosphorylated Akt as in the patient fibroblasts. Extracellularly administered lysoGM1 permeated the cell membrane to diffusely distribute in the cytoplasm. LysoGM1 and lysoGM2 also inhibited the production of phosphatidylinositol-(3,4,5)-triphosphate and the translocation of Akt from the cytoplasm to the plasma membrane. We also predicted that lysoGSLs could directly bind to the catalytic domain of PI3K by in silico docking study, suggesting that lysoGSLs could inhibit PI3K by directly interacting with PI3K in the cytoplasm. Furthermore, we revealed that the increment of lysoGSLs amounts in the brain of sphingolipidosis model mice correlated with the neurodegenerative progression. Our findings suggest that the down-regulation of PI3K/Akt signaling by direct interaction of lysoGSLs with PI3K in the brains is a neurodegenerative mechanism in sphingolipidoses. Moreover, we could propose the intracellular PI3K activation or inhibition of lysoGSLs biosynthesis as novel therapeutic approaches for sphingolipidoses because lysoGSLs should be cell death mediators by directly inhibiting PI3K, especially in neurons.
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Affiliation(s)
- Ryosuke Watanabe
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Daisuke Tsuji
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Hiroki Tanaka
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Michael Shintaro Uno
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Yukiya Ohnishi
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Shindai Kitaguchi
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Tsuyoshi Matsugu
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Ryuto Nakae
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Hiromi Teramoto
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | - Kei Yamamoto
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Yasuo Shinohara
- Institute for Genome Research, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Nozomu Okino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Makoto Ito
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kohji Itoh
- Department of Medicinal Biotechnology, Graduate school of Pharmaceutical Science, Tokushima University, Tokushima, Japan
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7
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Nakagita T, Matsuya T, Narukawa M, Kobayashi T, Hirokawa T, Misaka T. Modeling the structure of the transmembrane domain of T1R3, a subunit of the sweet taste receptor, with neohesperidin dihydrochalcone using molecular dynamics simulation. Biosci Biotechnol Biochem 2023; 87:1470-1477. [PMID: 37715303 DOI: 10.1093/bbb/zbad133] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Neohesperidin dihydrochalcone (NHDC) is a sweetener, which interacts with the transmembrane domain (TMD) of the T1R3 subunit of the human sweet taste receptor. Although NHDC and a sweet taste inhibitor lactisole share similar structural motifs, they have opposite effects on the receptor. This study involved the creation of an NHDC-docked model of T1R3 TMD through mutational analyses followed by in silico simulations. When certain NHDC derivatives were docked to the model, His7345.44 was demonstrated to play a crucial role in activating T1R3 TMD. The NHDC-docked model was then compared with a lactisole-docked inactive form, several residues were characterized as important for the recognition of NHDC; however, most of them were distinct from those of lactisole. Residues such as His6413.33 and Gln7947.38 were found to be oriented differently. This study provides useful information that will facilitate the design of sweeteners and inhibitors that interact with T1R3 TMD.
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Affiliation(s)
- Tomoya Nakagita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Takumi Matsuya
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masataka Narukawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Food and Nutrition, Kyoto Women's University, Kyoto, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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8
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Igarashi M, Hirokawa T, Takada A. Structural and Energetic Basis for Differential Binding of Ebola and Marburg Virus Glycoproteins to a Bat-Derived Niemann-Pick C1 Protein. J Infect Dis 2023; 228:S479-S487. [PMID: 37119290 DOI: 10.1093/infdis/jiad120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/14/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Our previous study demonstrated that the fruit bat (Yaeyama flying fox)-derived cell line FBKT1 showed preferential susceptibility to Ebola virus (EBOV), whereas the human cell line HEK293T was similarly susceptible to EBOV and Marburg virus (MARV). This was due to 3 amino acid differences of the endosomal receptor Niemann-Pick C1 (NPC1) between FBKT1 and HEK293T (ie, TET and SGA, respectively, at positions 425-427), as well as 2 amino acid differences at positions 87 and 142 of the viral glycoprotein (GP) between EBOV and MARV. METHODS/RESULTS To understand the contribution of these amino acid differences to interactions between NPC1 and GP, we performed molecular dynamics simulations and binding free energy calculations. The average binding free energies of human NPC1 (hNPC1) and its mutant having TET at positions 425-427 (hNPC1/TET) were similar for the interaction with EBOV GP. In contrast, hNPC1/TET had a weaker interaction with MARV GP than wild-type hNPC1. As expected, substitutions of amino acid residues at 87 or 142 in EBOV and MARV GPs converted the binding affinity to hNPC1/TET. CONCLUSIONS Our data provide structural and energetic insights for understanding potential differences in the GP-NPC1 interaction, which could influence the host tropism of EBOV and MARV.
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Affiliation(s)
- Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Division of Biomedical Science, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
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9
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Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb) 2023. [PMID: 37377065 DOI: 10.1039/d3cc02308g] [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] [Indexed: 06/29/2023]
Abstract
Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yue Ma
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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Mizumoto Y, Sakamoto R, Iijima K, Nakaya N, Odagi M, Tera M, Hirokawa T, Sakaki T, Yasuda K, Nagasawa K. Differential Metabolic Stability of 4α,25- and 4β,25-Dihydroxyvitamin D 3 and Identification of Their Metabolites. Biomolecules 2023; 13:1036. [PMID: 37509072 PMCID: PMC10377336 DOI: 10.3390/biom13071036] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
Vitamin D3 (1) is metabolized by various cytochrome P450 (CYP) enzymes, resulting in the formation of diverse metabolites. Among them, 4α,25-dihydroxyvitamin D3 (6a) and 4β,25-dihydroxyvitamin D3 (6b) are both produced from 25-hydroxyvitamin D3 (2) by CYP3A4. However, 6b is detectable in serum, whereas 6a is not. We hypothesized that the reason for this is a difference in the susceptibility of 6a and 6b to CYP24A1-mediated metabolism. Here, we synthesized 6a and 6b, and confirmed that 6b has greater metabolic stability than 6a. We also identified 4α,24R,25- and 4β,24R,25-trihydroxyvitamin D3 (16a and 16b) as metabolites of 6a and 6b, respectively, by HPLC comparison with synthesized authentic samples. Docking studies suggest that the β-hydroxy group at C4 contributes to the greater metabolic stability of 6b by blocking a crucial hydrogen-bonding interaction between the C25 hydroxy group and Leu325 of CYP24A1.
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Affiliation(s)
- Yuka Mizumoto
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
| | - Ryota Sakamoto
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
| | - Kazuto Iijima
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
| | - Naoto Nakaya
- Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Japan
| | - Minami Odagi
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Toshiyuki Sakaki
- Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Japan
| | - Kaori Yasuda
- Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei 184-8588, Japan
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11
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Uezono E, Mizobuchi Y, Miyano K, Ohbuchi K, Murata H, Komatsu A, Manabe S, Nonaka M, Hirokawa T, Yamaguchi K, Iseki M, Uezono Y, Hayashida M, Kawagoe I. Distinct Profiles of Desensitization of µ-Opioid Receptors Caused by Remifentanil or Fentanyl: In Vitro Assay with Cells and Three-Dimensional Structural Analyses. Int J Mol Sci 2023; 24:ijms24098369. [PMID: 37176075 PMCID: PMC10179353 DOI: 10.3390/ijms24098369] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Remifentanil (REM) and fentanyl (FEN) are commonly used analgesics that act by activating a µ-opioid receptor (MOR). Although optimal concentrations of REM can be easily maintained during surgery, it is sometimes switched to FEN for optimal pain regulation. However, standards for this switching protocol remain unclear. Opioid anesthetic efficacy is decided in part by MOR desensitization; thus, in this study, we investigated the desensitization profiles of REM and FEN to MOR. The efficacy and potency during the 1st administration of REM or FEN in activating the MOR were almost equal. Similarly, in β arrestin recruitment, which determines desensitization processes, they showed no significant differences. In contrast, the 2nd administration of FEN resulted in a stronger MOR desensitization potency than that of REM, whereas REM showed a higher internalization potency than FEN. These results suggest that different β arrestin-mediated signaling caused by FEN or REM led to their distinct desensitization and internalization processes. Our three-dimensional analysis, with in silico binding of REM and FEN to MOR models, highlighted that REM and FEN bound to similar but distinct sites of MOR and led to distinct β arrestin-mediated profiles, suggesting that distinct binding profiles to MOR may alter β arrestin activity, which accounts for MOR desensitization and internalization.
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Affiliation(s)
- Eiko Uezono
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Yusuke Mizobuchi
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
- Department of Anesthesiology and Resuscitology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-0194, Japan
| | - Kanako Miyano
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Dentistry, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Katsuya Ohbuchi
- Tsumura Research Laboratories, Tsumura and Co., Ibaraki 300-1192, Japan
| | - Hiroaki Murata
- Department of Anesthesiology and Intensive Care Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8501, Japan
| | - Akane Komatsu
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Sei Manabe
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
- Department of Anesthesiology and Resuscitology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-0194, Japan
| | - Miki Nonaka
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takatsugu Hirokawa
- Chemical Biology and In Silico Drug Design, Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Keisuke Yamaguchi
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Anesthesiology and Pain Medicine, Juntendo Tokyo Koto Geriatric Medical Center, Tokyo 136-0075, Japan
| | - Masako Iseki
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Yasuhito Uezono
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Control Research, The Jikei University School of Medicine, Tokyo 105-8461, Japan
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Supportive and Palliative Care Research Support Office, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Masakazu Hayashida
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Izumi Kawagoe
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Pain Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
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12
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Kudo G, Hirao T, Yoshino R, Shigeta Y, Hirokawa T. Pocket to Concavity: A Tool for the Refinement of Protein-Ligand Binding Site Shape from Alpha Spheres. Bioinformatics 2023; 39:7136640. [PMID: 37086438 PMCID: PMC10148677 DOI: 10.1093/bioinformatics/btad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/24/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
SUMMARY Understanding the binding site of the target protein is essential for rational drug design. Pocket detection software predicts the ligand binding site of the target protein; however, the predicted protein pockets are often excessively estimated in comparison with the actual volume of the bound ligands. This study proposes a refinement tool for the pockets predicted by an alpha sphere-based approach, Pocket to Concavity (P2C). P2C is divided into two modes: Ligand-Free (LF) and Ligand-Bound (LB) modes. The LF mode provides the shape of the deep and druggable concavity where the core scaffold can bind. The LB mode searches the deep concavity around the bound ligand. Thus, P2C is useful for identifying and designing desirable compounds in Structure-Based Drug Design (SBDD). AVAILABILITY AND IMPLEMENTATION Pocket to Concavity is freely available at https://github.com/genki-kudo/Pocket-to-Concavity. This tool is implemented in Python3 and Fpocket2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Genki Kudo
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Takumi Hirao
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Ryunosuke Yoshino
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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13
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Tsukamoto Y, Hiono T, Yamada S, Matsuno K, Faist A, Claff T, Hou J, Namasivayam V, Vom Hemdt A, Sugimoto S, Ng JY, Christensen MH, Tesfamariam YM, Wolter S, Juranek S, Zillinger T, Bauer S, Hirokawa T, Schmidt FI, Kochs G, Shimojima M, Huang YS, Pichlmair A, Kümmerer BM, Sakoda Y, Schlee M, Brunotte L, Müller CE, Igarashi M, Kato H. Inhibition of cellular RNA methyltransferase abrogates influenza virus capping and replication. Science 2023; 379:586-591. [PMID: 36758070 DOI: 10.1126/science.add0875] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Orthomyxo- and bunyaviruses steal the 5' cap portion of host RNAs to prime their own transcription in a process called "cap snatching." We report that RNA modification of the cap portion by host 2'-O-ribose methyltransferase 1 (MTr1) is essential for the initiation of influenza A and B virus replication, but not for other cap-snatching viruses. We identified with in silico compound screening and functional analysis a derivative of a natural product from Streptomyces, called trifluoromethyl-tubercidin (TFMT), that inhibits MTr1 through interaction at its S-adenosyl-l-methionine binding pocket to restrict influenza virus replication. Mechanistically, TFMT impairs the association of host cap RNAs with the viral polymerase basic protein 2 subunit in human lung explants and in vivo in mice. TFMT acts synergistically with approved anti-influenza drugs.
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Affiliation(s)
- Yuta Tsukamoto
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Takahiro Hiono
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shintaro Yamada
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Keita Matsuno
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Aileen Faist
- Institute of Virology Muenster, Westfaelische Wilhelms-University, Muenster, Germany.,CiM-IMPRS, Westfaelische Wilhelms-University Muenster, International Max Planck Research School - Molecular Biomedicine, Muenster, Germany
| | - Tobias Claff
- PharmaCenter Bonn and Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Jianyu Hou
- PharmaCenter Bonn and Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn and Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Anja Vom Hemdt
- Institute of Virology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Satoko Sugimoto
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jin Ying Ng
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Maria H Christensen
- Institute of Innate Immunity, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Yonas M Tesfamariam
- Institute of Innate Immunity, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Steven Wolter
- Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Stefan Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, Bonn, Germany.,Institute of Immunology, Philipps-University Marburg, Marburg, Germany.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Stefan Bauer
- Institute of Immunology, Philipps-University Marburg, Marburg, Germany
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,Division of Biomedical Science, University of Tsukuba, Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Florian I Schmidt
- Institute of Innate Immunity, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany.,Core Facility Nanobodies, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Masayuki Shimojima
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Yoshihiro Sakoda
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Linda Brunotte
- Institute of Virology Muenster, Westfaelische Wilhelms-University, Muenster, Germany.,Interdisciplinary Center for Medical Research, Medical Faculty Muenster, Germany
| | - Christa E Müller
- PharmaCenter Bonn and Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Manabu Igarashi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
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14
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Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D. Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches. Front Mol Biosci 2023; 10:1110567. [PMID: 36814641 PMCID: PMC9939524 DOI: 10.3389/fmolb.2023.1110567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer.
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Affiliation(s)
- Woong-Hee Shin
- Department of Chemistry Education, Sunchon National University, Suncheon, South Korea,Department of Advanced Components and Materials Engineering, Sunchon National University, Suncheon, South Korea
| | - Keiko Kumazawa
- Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States,Department of Computer Science, Purdue University, West Lafayette, IN, United States,Center for Cancer Research, Purdue University, West Lafayette, IN, United States,*Correspondence: Daisuke Kihara,
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15
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Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz LS, Becker T, Kikkawa M, Pfanner N, Wiedemann N, Endo T. A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat Struct Mol Biol 2023; 30:176-187. [PMID: 36604501 DOI: 10.1038/s41594-022-00897-2] [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: 05/06/2022] [Accepted: 11/11/2022] [Indexed: 01/07/2023]
Abstract
Mitochondrial β-barrel proteins are essential for the transport of metabolites, ions and proteins. The sorting and assembly machinery (SAM) mediates their folding and membrane insertion. We report the cryo-electron microscopy structure of the yeast SAM complex carrying an early eukaryotic β-barrel folding intermediate. The lateral gate of Sam50 is wide open and pairs with the last β-strand (β-signal) of the substrate-the 19-β-stranded Tom40 precursor-to form a hybrid barrel in the membrane plane. The Tom40 barrel grows and curves, guided by an extended bridge with Sam50. Tom40's first β-segment (β1) penetrates into the nascent barrel, interacting with its inner wall. The Tom40 amino-terminal segment then displaces β1 to promote its pairing with Tom40's last β-strand to complete barrel formation with the assistance of Sam37's dynamic α-protrusion. Our study thus reveals a multipoint guidance mechanism for mitochondrial β-barrel folding.
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Affiliation(s)
- Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Nara Institute of Science and Technology, Ikoma, Japan
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST, Waseda University, Tokyo, Japan
| | - Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
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16
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Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz LS, Becker T, Kikkawa M, Pfanner N, Wiedemann N, Endo T. Author Correction: A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat Struct Mol Biol 2023; 30:233. [PMID: 36697808 DOI: 10.1038/s41594-023-00926-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Nara Institute of Science and Technology, Ikoma, Japan
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST, Waseda University, Tokyo, Japan
| | - Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
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17
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Sakamoto K, Asano S, Ago Y, Hirokawa T. AlphaFold version 2.0 elucidates the binding mechanism between VIPR2 and KS-133, and reveals an S–S bond (Cys25−Cys192) formation of functional significance for VIPR2. Biochem Biophys Res Commun 2022; 636:10-16. [DOI: 10.1016/j.bbrc.2022.10.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 11/02/2022]
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18
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Asamitsu K, Hirokawa T, Okamoto T. Identification of a novel CDK9 inhibitor targeting the intramolecular hidden cavity of CDK9 induced by Tat binding. PLoS One 2022; 17:e0277024. [PMCID: PMC9665388 DOI: 10.1371/journal.pone.0277024] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 transcription is specifically augmented by a transcriptional activator complex composed of Tat, an HIV-1-encoded activator, and the host transcription elongation factor P-TEFb, which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. Several observations suggest that P-TEFb is an attractive anti-HIV-1 drug target. However, the long-term cytotoxicity of CDK9 inhibitors hinders their widespread use in HIV-1 therapy. Thus, novel and safe inhibitors are sorely needed. By performing molecular dynamics simulations of the 3D structure of Tat/P-TEFb, we previously identified a unique cavity structure of CDK9, the CDK9 hidden cavity, that is specifically induced by Tat binding. Here, we attempted to identify compounds that fit this cavity and inhibit CDK9 activity by in silico screening. We identified compounds that could inhibit CDK9 activity. One of such compound, 127, showed the strongest inhibitory activity against CDK9. Interestingly, it also inhibited CDK6 to a similar extent. We inspected the amino acid sequence and structural properties of the CDK9 hidden cavity to determine whether it is conserved in other CDKs, such as CDK6. The Ile61, comprising the center of the CDK9 hidden cavity, appears to be crucial for its kinase activity, thus indicating that the identification of the CDK9 hidden cavity may provide vital information for the development of novel CDK9 inhibitors.
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Affiliation(s)
- Kaori Asamitsu
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
- * E-mail: (KA); (TH)
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaragi, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaragi, Japan
- * E-mail: (KA); (TH)
| | - Takashi Okamoto
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
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19
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Bergant V, Yamada S, Grass V, Tsukamoto Y, Lavacca T, Krey K, Mühlhofer MT, Wittmann S, Ensser A, Herrmann A, Vom Hemdt A, Tomita Y, Matsuyama S, Hirokawa T, Huang Y, Piras A, Jakwerth CA, Oelsner M, Thieme S, Graf A, Krebs S, Blum H, Kümmerer BM, Stukalov A, Schmidt-Weber CB, Igarashi M, Gramberg T, Pichlmair A, Kato H. Attenuation of SARS-CoV-2 replication and associated inflammation by concomitant targeting of viral and host cap 2'-O-ribose methyltransferases. EMBO J 2022; 41:e111608. [PMID: 35833542 PMCID: PMC9350232 DOI: 10.15252/embj.2022111608] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 05/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
The SARS‐CoV‐2 infection cycle is a multistage process that relies on functional interactions between the host and the pathogen. Here, we repurposed antiviral drugs against both viral and host enzymes to pharmaceutically block methylation of the viral RNA 2'‐O‐ribose cap needed for viral immune escape. We find that the host cap 2'‐O‐ribose methyltransferase MTr1 can compensate for loss of viral NSP16 methyltransferase in facilitating virus replication. Concomitant inhibition of MTr1 and NSP16 efficiently suppresses SARS‐CoV‐2 replication. Using in silico target‐based drug screening, we identify a bispecific MTr1/NSP16 inhibitor with anti‐SARS‐CoV‐2 activity in vitro and in vivo but with unfavorable side effects. We further show antiviral activity of inhibitors that target independent stages of the host SAM cycle providing the methyltransferase co‐substrate. In particular, the adenosylhomocysteinase (AHCY) inhibitor DZNep is antiviral in in vitro, in ex vivo, and in a mouse infection model and synergizes with existing COVID‐19 treatments. Moreover, DZNep exhibits a strong immunomodulatory effect curbing infection‐induced hyperinflammation and reduces lung fibrosis markers ex vivo. Thus, multispecific and metabolic MTase inhibitors constitute yet unexplored treatment options against COVID‐19.
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Affiliation(s)
- Valter Bergant
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Shintaro Yamada
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Yuta Tsukamoto
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Teresa Lavacca
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Maria-Teresa Mühlhofer
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Anja Vom Hemdt
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yuriko Tomita
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Shutoku Matsuyama
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,Division of Biomedical Science, University of Tsukuba, Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Yiqi Huang
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Antonio Piras
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Constanze A Jakwerth
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Madlen Oelsner
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Susanne Thieme
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Alexander Graf
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Stefan Krebs
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Helmut Blum
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany.,German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Alexey Stukalov
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Carsten B Schmidt-Weber
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Manabu Igarashi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
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20
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Hirokawa T. [In-Silico Drug Discovery Support-Current Situation and Challenges]. Gan To Kagaku Ryoho 2022; 49:359-364. [PMID: 35444115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In the drug discovery field, the current problems are sluggish drug development due to the depletion of target molecules and other factors, and rising development costs. In silico drug discovery is expected to be a drug discovery support technology that will lead to the discovery of novel drug target molecules, active sites, lead compounds to more efficient development processes. In silico drug discovery can be broadly classified into methods directed by ligand information(ligand-based drug design: LBDD)and methods based on the 3-dimensional structure of target proteins(structure-based drug design: SBDD). LBDD method is based on similar structural and physicochemical properties in overall structure, or substructures and pharmacophore, using known ligands information, and has the advantage that it can be applied even when the 3-dimensional structure of the target protein is unknown. On the other hand, SBDD is a method to discovery and design compounds directed to the 3-dimensional structure of the target protein based on the'lock and key'theory, in which the target protein selects and binds to specific ligands, and has the advantage of leading to the discovery of diversity compounds. This paper outlines the basics of LBDD and SBDD, and the latest topics using AI and large-scale simulations. Furthermore, as an example of in-silico drug discovery support, in-silico drug discovery support research for the discovery of protein-protein interaction inhibitors targeting early-stage lung adenocarcinoma is also introduced.
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Affiliation(s)
- Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba
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21
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Hijikata A, Shionyu-Mitsuyama C, Nakae S, Shionyu M, Ota M, Kanaya S, Hirokawa T, Nakajima S, Watashi K, Shirai T. Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2. FEBS Open Bio 2021; 12:285-294. [PMID: 34850606 PMCID: PMC8727928 DOI: 10.1002/2211-5463.13337] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 10/04/2021] [Revised: 11/01/2021] [Accepted: 11/27/2021] [Indexed: 12/12/2022] Open
Abstract
Cepharanthine (CEP) is a natural biscoclaurine alkaloid of plant origin and was recently demonstrated to have anti‐severe acute respiratory syndrome coronavirus 2 (anti‐SARS‐CoV‐2) activity. In this study, we evaluated whether natural analogues of CEP may act as potential anti‐coronavirus disease 2019 drugs. A total of 24 compounds resembling CEP were extracted from the KNApSAcK database, and their binding affinities to target proteins, including the spike protein and main protease of SARS‐CoV‐2, NPC1 and TPC2 in humans, were predicted via molecular docking simulations. Selected analogues were further evaluated by a cell‐based SARS‐CoV‐2 infection assay. In addition, the efficacies of CEP and its analogue tetrandrine were assessed. A comparison of the docking conformations of these compounds suggested that the diphenyl ester moiety of the molecules was a putative pharmacophore of the CEP analogues.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | | | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Japan
| | - Shigehiko Kanaya
- Computational Biology Laboratory Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Japan.,Transborder Medical Research Center, University of Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shogo Nakajima
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Japan.,Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Japan.,Department of Applied Biological Sciences, Tokyo University of Science, Noda, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
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22
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Queliconi BB, Kojima W, Kimura M, Imai K, Udagawa C, Motono C, Hirokawa T, Tashiro S, Caaveiro JMM, Tsumoto K, Yamano K, Tanaka K, Matsuda N. Unfolding is the driving force for mitochondrial import and degradation of the Parkinson's disease-related protein DJ-1. J Cell Sci 2021; 134:273535. [PMID: 34676411 PMCID: PMC8645234 DOI: 10.1242/jcs.258653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Diverse genes associated with familial Parkinson's disease (familial Parkinsonism) have been implicated in mitochondrial quality control. One such gene, PARK7 encodes the protein DJ-1, pathogenic mutations of which trigger its translocation from the cytosol to the mitochondrial matrix. The translocation of steady-state cytosolic proteins like DJ-1 to the mitochondrial matrix upon missense mutations is rare, and the underlying mechanism remains to be elucidated. Here, we show that the protein unfolding associated with various DJ-1 mutations drives its import into the mitochondrial matrix. Increasing the structural stability of these DJ-1 mutants restores cytosolic localization. Mechanistically, we show that a reduction in the structural stability of DJ-1 exposes a cryptic N-terminal mitochondrial-targeting signal (MTS), including Leu10, which promotes DJ-1 import into the mitochondrial matrix for subsequent degradation. Our work describes a novel cellular mechanism for targeting a destabilized cytosolic protein to the mitochondria for degradation. Summary: Several mutations in Parkinson's disease-related protein DJ-1 cause its mitochondrial import and degradation. We reveal that protein unfolding is the driving force for the import and degradation of DJ-1.
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Affiliation(s)
- Bruno Barros Queliconi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Mayumi Kimura
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Chisato Udagawa
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shinya Tashiro
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Jose M M Caaveiro
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
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23
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Sekiya M, Kainoh K, Sugasawa T, Yoshino R, Hirokawa T, Tokiwa H, Nakano S, Nagatoishi S, Tsumoto K, Takeuchi Y, Miyamoto T, Matsuzaka T, Shimano H. The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis. Nat Commun 2021; 12:6315. [PMID: 34728642 PMCID: PMC8563733 DOI: 10.1038/s41467-021-26638-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/15/2021] [Indexed: 01/19/2023] Open
Abstract
Biological systems to sense and respond to metabolic perturbations are critical for the maintenance of cellular homeostasis. Here we describe a hepatic system in this context orchestrated by the transcriptional corepressor C-terminal binding protein 2 (CtBP2) that harbors metabolite-sensing capabilities. The repressor activity of CtBP2 is reciprocally regulated by NADH and acyl-CoAs. CtBP2 represses Forkhead box O1 (FoxO1)-mediated hepatic gluconeogenesis directly as well as Sterol Regulatory Element-Binding Protein 1 (SREBP1)-mediated lipogenesis indirectly. The activity of CtBP2 is markedly defective in obese liver reflecting the metabolic perturbations. Thus, liver-specific CtBP2 deletion promotes hepatic gluconeogenesis and accelerates the progression of steatohepatitis. Conversely, activation of CtBP2 ameliorates diabetes and hepatic steatosis in obesity. The structure-function relationships revealed in this study identify a critical structural domain called Rossmann fold, a metabolite-sensing pocket, that is susceptible to metabolic liabilities and potentially targetable for developing therapeutic approaches.
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Affiliation(s)
- Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Kenta Kainoh
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takehito Sugasawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryunosuke Yoshino
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo, 171-8501, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshinori Takeuchi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
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24
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Nomura K, Kitagawa Y, Aihara M, Ohki Y, Furuyama K, Hirokawa T. Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX. FEBS Lett 2021; 595:3019-3029. [PMID: 34704252 DOI: 10.1002/1873-3468.14214] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022]
Abstract
The caseinolytic mitochondrial matrix peptidase chaperone subunit (ClpX) plays an important role in the heme-dependent regulation of 5-aminolevulinate synthase (ALAS1), a key enzyme in heme biosynthesis. However, the mechanisms underlying the role of ClpX in this process remain unclear. In this in vitro study, we confirmed the direct binding between ALAS1 and ClpX in a heme-dependent manner. The substitution of C108 P109 [CP motif 3 (CP3)] with A108 A109 in ALAS1 resulted in a loss of ability to bind ClpX. Computational disorder analyses revealed that CP3 was located in a potential intrinsically disordered protein region (IDPR). Thus, we propose that conditional disorder-to-order transitions in the IDPRs of ALAS1 may represent key mechanisms underlying the heme-dependent recognition of ALAS1 by ClpX.
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Affiliation(s)
- Kazumi Nomura
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yu Kitagawa
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Marina Aihara
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yusuke Ohki
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | | | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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25
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Ma Y, Wakabayashi Y, Watatani N, Saito R, Hirokawa T, Tera M, Nagasawa K. Vinylnaphthalene-bearing hexaoxazole as a fluorescence turn-on type G-quadruplex ligand. Org Biomol Chem 2021; 19:8035-8040. [PMID: 34492672 DOI: 10.1039/d1ob01500a] [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: 11/21/2022]
Abstract
Oxazole-type fluorophores show an increase of fluorescence intensity upon interaction with nucleic acids, and therefore can be used as tools for nucleic acid-sensing and fluorescence imaging. Here, we developed a novel stilbene-type fluorophore, MO-VN (1), consisting of a mono oxazole bearing a vinyl naphthalene moiety. This compound (1) was embedded in a trioxazole 2 and a cyclic hexaoxazole 3a. The fluorescence properties of 1, 2, and 3a were evaluated in the presence of various nucleic acid sequences. Compound 3 showed significant fluorescent enhancement upon interacting with G-quadruplex (G4) structure, which plays critical roles in various biological phenomena. Further structural development focusing on the vinyl naphthalene moiety of 3a afforded a turn-on type G4 ligand 3e that shows G4-specific fluorescence. Measurement of the fluorescence of 3e during titration of a telomeric DNA, telo24, with its C-rich complementary sequence, which unwinds the G4 structure, allowed us to monitor the dynamics of G4.
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Affiliation(s)
- Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, To-kyo 184-8588, Japan.
| | - Yuki Wakabayashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Ko-ganei, Tokyo 184-8588, Japan.
| | - Naruyuki Watatani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Ko-ganei, Tokyo 184-8588, Japan.
| | - Ryota Saito
- Department of Chemistry Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo 135-0064, Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Ko-ganei, Tokyo 184-8588, Japan.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Ko-ganei, Tokyo 184-8588, Japan.
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26
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Motono C, Yanagida S, Sato M, Hirokawa T. MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. Bioinformatics 2021; 38:273-274. [PMID: 34289011 PMCID: PMC8696114 DOI: 10.1093/bioinformatics/btab538] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Comparing results from multiple MD simulations performed under different conditions is essential during the initial stages of analysis. We propose a tool called MD Contact Comparison (MDContactCom) that compares residue-residue contact fluctuations of two MD trajectories, quantifies the differences, identifies sites that exhibit large differences and visualizes those sites on the protein structure. Using this method, it is possible to identify sites affected by varying simulation conditions and reveal the path of propagation of the effect even when differences between the 3D structure of the molecule and the fluctuation RMSF of each residue is unclear. MDContactCom can monitor differences in complex protein dynamics between two MD trajectories and identify candidate sites to be analyzed in more detail. As such, MDContactCom is a versatile software package for analyzing most MD simulations. AVAILABILITY AND IMPLEMENTATION MDContactCom is freely available for download on GitLab. The software is implemented in Python3. https://gitlab.com/chiemotono/mdcontactcom. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chie Motono
- To whom correspondence should be addressed. or
| | - Shunsuke Yanagida
- Bioscience & Healthcare Engineering Division, DX Infrastructure Engineering Unit 1, Mitsui Knowledge Industry Co., Ltd, Tokyo 164-0003, Japan
| | - Miwa Sato
- Bioscience & Healthcare Engineering Division, DX Infrastructure Engineering Unit 1, Mitsui Knowledge Industry Co., Ltd, Tokyo 164-0003, Japan
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27
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Nishimura T, Kawahara T, Kagaya N, Ogura Y, Takikawa H, Suenaga H, Adachi M, Hirokawa T, Doi T, Shin-Ya K. JBIR-155, a Specific Class D β-Lactamase Inhibitor of Microbial Origin. Org Lett 2021; 23:4415-4419. [PMID: 34029112 DOI: 10.1021/acs.orglett.1c01352] [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: 11/29/2022]
Abstract
We discovered JBIR-155 as a novel specific class D β-lactamase inhibitor from Streptomyces polymachus SoB100815Hv02. JBIR-155 consists of a 6-oxabicyclo[3.2.0]heptan-7-one skeleton and a long unsaturated alkyl chain moiety of which absolute configuration was determined by spectroscopic data, modified Mosher's method, and analyses of the relative configuration of chemically modified derivative. JBIR-155 specifically exhibited inhibitory activity against the class D β-lactamase, with an IC50 value of 0.36 μM.
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Affiliation(s)
- Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064 Japan
| | - Noritaka Kagaya
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yusuke Ogura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masaatsu Adachi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takatsugu Hirokawa
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kazuo Shin-Ya
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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28
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Nakagita T, Taketani C, Narukawa M, Hirokawa T, Kobayashi T, Misaka T. Ibuprofen, a Nonsteroidal Anti-Inflammatory Drug, is a Potent Inhibitor of the Human Sweet Taste Receptor. Chem Senses 2021; 45:667-673. [PMID: 32832995 DOI: 10.1093/chemse/bjaa057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A sweet taste receptor is composed of heterodimeric G-protein-coupled receptors T1R2 and T1R3. Although there are many sweet tastants, only a few compounds have been reported as negative allosteric modulators (NAMs), such as lactisole, its structural derivative 2,4-DP, and gymnemic acid. In this study, candidates for NAMs of the sweet taste receptor were explored, focusing on the structural motif of lactisole. Ibuprofen, a nonsteroidal anti-inflammatory drug (NSAID), has an α-methylacetic acid moiety, and this structure is also shared by lactisole and 2,4-DP. When ibuprofen was applied together with 1 mM aspartame to the cells that stably expressed the sweet taste receptor, it inhibited the receptor activity in a dose-dependent manner. The IC50 value of ibuprofen against the human sweet taste receptor was calculated as approximately 12 μM, and it was almost equal to that of 2,4-DP, which is known as the most potent NAM for the receptor to date. On the other hand, when the inhibitory activities of other profens were examined, naproxen also showed relatively potent NAM activity against the receptor. The results from both mutant analysis for the transmembrane domain (TMD) of T1R3 and docking simulation strongly suggest that ibuprofen and naproxen interact with T1R3-TMD, similar to lactisole and 2,4-DP. However, although 2,4-DP and ibuprofen had almost the same inhibitory activities, these activities were acquired by filling different spaces of the ligand pocket of T1R3-TMD; this knowledge could lead to the rational design of a novel NAM against the sweet taste receptor.
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Affiliation(s)
- Tomoya Nakagita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,Proteo-Science Center, Ehime University, Bunkyo-cho, Matsuyama, Ehime, Japan
| | - Chiaki Taketani
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Masataka Narukawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institutes of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, Japan.,Department of Chemical Biology, Faculty of Medicine, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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29
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Ohbuchi K, Hirokawa T. Protein druggability assessment for natural products using in silico simulation: A case study with estrogen receptor and the flavonoid genistein. Gene 2021; 791:145726. [PMID: 34010704 DOI: 10.1016/j.gene.2021.145726] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 05/13/2021] [Indexed: 11/26/2022]
Abstract
Traditional herbal medicine (THM) comprises a vast number of natural compounds. Most of them are metabolized into different structures after administration, which makes the clarification of THM's mode of action more complicated. To evaluate the biological activities of those components and metabolites, in silico simulation technology is helpful. We focused on mixed-solvent molecular dynamics (MD) simulation for druggability assessment of natural products. Mixed-solvent MD is an in silico simulation method for the exploration of ligand-binding sites on target proteins, which uses water and an organic molecule mixture. The selection of organic small molecules is an important factor for predicting the characteristics of natural products. In this study, we used the known crystal structure of estrogen receptors with genistein as a test case and explored fragments reflecting the characteristics of natural products. We found that structures with a 4-pyrone structure are more often included in the natural products database compared with the DrugBank database, and we selectively detected the known-binding sites of estrogen receptor α and β. The results indicate that the 4-pyrone structure might be promising for predicting the protein druggability of flavonoids. Additionally, mixed-solvent MD simulation discriminates the selectivity of genistein between estrogen receptor β and α, indicating that the simulation can be evaluated using indices that differ from those of traditional ligand docking. Although this approach is still in its early stages, it has the potential to provide valuable information for understanding the diverse biological activities of natural products.
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Affiliation(s)
- Katsuya Ohbuchi
- Tsumura Kampo Research Laboratories, Tsumura & CO., 3586 Yoshiwara, Ami, Inashiki, Ibaraki 300-1192, Japan.
| | - Takatsugu Hirokawa
- 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; Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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30
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Misawa K, Sugai Y, Fujimori T, Hirokawa T. Structural insights from an in silico molecular docking simulation of complement component 3a receptor 1 with an antagonist. J Mol Graph Model 2021; 106:107914. [PMID: 33932736 DOI: 10.1016/j.jmgm.2021.107914] [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: 11/20/2020] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/18/2022]
Abstract
Complement component 3a receptor 1 (C3aR) is an anaphylatoxin receptor that mediates inflammatory processes. Although considerable effort has gone into discovering the antagonists and agonists of C3aR, structural insights are required to search for effective ligands and to elucidate their binding modes and the mechanism of activation and inactivation. No experimental structural data of C3aR have yet been reported. We investigated the binding mode of an antagonist of C3aR using a combination of homology modeling, ligand docking, molecular dynamics simulations, and binding free energy calculations. We produced a plausible binding model consistent with the reported experimental data. We believe that this model is appropriate for the identification of new C3aR antagonists, as it can distinguish between antagonists and decoy compounds.
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Affiliation(s)
- Kensuke Misawa
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi, 321-3497, Japan.
| | - Yoshiya Sugai
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi, 321-3497, Japan
| | - Taketoshi Fujimori
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi, 321-3497, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan; Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan; Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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31
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Ohashi H, Watashi K, Saso W, Shionoya K, Iwanami S, Hirokawa T, Shirai T, Kanaya S, Ito Y, Kim KS, Nomura T, Suzuki T, Nishioka K, Ando S, Ejima K, Koizumi Y, Tanaka T, Aoki S, Kuramochi K, Suzuki T, Hashiguchi T, Maenaka K, Matano T, Muramatsu M, Saijo M, Aihara K, Iwami S, Takeda M, McKeating JA, Wakita T. Potential anti-COVID-19 agents, cepharanthine and nelfinavir, and their usage for combination treatment. iScience 2021; 24:102367. [PMID: 33817567 DOI: 10.1101/2020.04.14.039925] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/02/2020] [Accepted: 03/24/2021] [Indexed: 05/22/2023] Open
Abstract
Antiviral treatments targeting the coronavirus disease 2019 are urgently required. We screened a panel of already approved drugs in a cell culture model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and identified two new agents having higher antiviral potentials than the drug candidates such as remdesivir and chroloquine in VeroE6/TMPRSS2 cells: the anti-inflammatory drug cepharanthine and human immunodeficiency virus protease inhibitor nelfinavir. Cepharanthine inhibited SARS-CoV-2 entry through the blocking of viral binding to target cells, while nelfinavir suppressed viral replication partly by protease inhibition. Consistent with their different modes of action, synergistic effect of this combined treatment to limit SARS-CoV-2 proliferation was highlighted. Mathematical modeling in vitro antiviral activity coupled with the calculated total drug concentrations in the lung predicts that nelfinavir will shorten the period until viral clearance by 4.9 days and the combining cepharanthine/nelfinavir enhanced their predicted efficacy. These results warrant further evaluation of the potential anti-SARS-CoV-2 activity of cepharanthine and nelfinavir.
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Affiliation(s)
- Hirofumi Ohashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- MIRAI, JST, Saitama 332-0012, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Wakana Saso
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kaho Shionoya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan
| | - Shigehiko Kanaya
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yusuke Ito
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Takao Nomura
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tateki Suzuki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazane Nishioka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Shuji Ando
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Yoshiki Koizumi
- National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Tomohiro Tanaka
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
| | - Kouji Kuramochi
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Katsumi Maenaka
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Center for Life Innovation, Hokkaido University, Sapporo 060-0812, Japan
| | - Tetsuro Matano
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo 113-8654, Japan
| | - Shingo Iwami
- MIRAI, JST, Saitama 332-0012, Japan
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo 135-8550, Japan
- Science Groove Inc., Fukuoka 810-0041, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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32
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Ohashi H, Watashi K, Saso W, Shionoya K, Iwanami S, Hirokawa T, Shirai T, Kanaya S, Ito Y, Kim KS, Nomura T, Suzuki T, Nishioka K, Ando S, Ejima K, Koizumi Y, Tanaka T, Aoki S, Kuramochi K, Suzuki T, Hashiguchi T, Maenaka K, Matano T, Muramatsu M, Saijo M, Aihara K, Iwami S, Takeda M, McKeating JA, Wakita T. Potential anti-COVID-19 agents, cepharanthine and nelfinavir, and their usage for combination treatment. iScience 2021; 24:102367. [PMID: 33817567 PMCID: PMC7997640 DOI: 10.1016/j.isci.2021.102367] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/02/2020] [Accepted: 03/24/2021] [Indexed: 12/16/2022] Open
Abstract
Antiviral treatments targeting the coronavirus disease 2019 are urgently required. We screened a panel of already approved drugs in a cell culture model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and identified two new agents having higher antiviral potentials than the drug candidates such as remdesivir and chroloquine in VeroE6/TMPRSS2 cells: the anti-inflammatory drug cepharanthine and human immunodeficiency virus protease inhibitor nelfinavir. Cepharanthine inhibited SARS-CoV-2 entry through the blocking of viral binding to target cells, while nelfinavir suppressed viral replication partly by protease inhibition. Consistent with their different modes of action, synergistic effect of this combined treatment to limit SARS-CoV-2 proliferation was highlighted. Mathematical modeling in vitro antiviral activity coupled with the calculated total drug concentrations in the lung predicts that nelfinavir will shorten the period until viral clearance by 4.9 days and the combining cepharanthine/nelfinavir enhanced their predicted efficacy. These results warrant further evaluation of the potential anti-SARS-CoV-2 activity of cepharanthine and nelfinavir.
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Affiliation(s)
- Hirofumi Ohashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- MIRAI, JST, Saitama 332-0012, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Wakana Saso
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kaho Shionoya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan
| | - Shigehiko Kanaya
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yusuke Ito
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Takao Nomura
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tateki Suzuki
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazane Nishioka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Shuji Ando
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN 47405, USA
| | - Yoshiki Koizumi
- National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Tomohiro Tanaka
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
| | - Kouji Kuramochi
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Katsumi Maenaka
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Center for Life Innovation, Hokkaido University, Sapporo 060-0812, Japan
| | - Tetsuro Matano
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo 113-8654, Japan
| | - Shingo Iwami
- MIRAI, JST, Saitama 332-0012, Japan
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo 135-8550, Japan
- Science Groove Inc., Fukuoka 810-0041, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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33
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Koiwai K, Morohashi K, Inaba K, Ebihara K, Kojima H, Okabe T, Yoshino R, Hirokawa T, Nampo T, Fujikawa Y, Inoue H, Yumoto F, Senda T, Niwa R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S-transferase Noppera-bo. J Pestic Sci 2021; 46:75-87. [PMID: 33746549 PMCID: PMC7953034 DOI: 10.1584/jpestics.d20-072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Insect growth regulators (IGRs) can be developed by elucidating the molecular mechanisms of insect-specific biological events. Because insect molting, and metamorphosis are controlled by ecdysteroids, their biosynthetic pathways can serve as targets for IGR development. The glutathione S-transferase Noppera-bo (Nobo), which is conserved in dipteran and lepidopteran species, plays an essential role in ecdysteroid biosynthesis. Our previous study using 17β-estradiol as a molecular probe revealed that Asp113 of Drosophila melanogaster Nobo (DmNobo) is essential for its biological function. However, to develop IGRs with a greater Nobo inhibitory activity than 17β-estradiol, further structural information is warranted. Here, we report five novel non-steroidal DmNobo inhibitors. Analysis of crystal structures of complexes revealed that DmNobo binds these inhibitors in an Asp113-independent manner. Among amino acid residues at the substrate-recognition site, conformation of conserved Phe39 was dynamically altered upon inhibitor binding. Therefore, these inhibitors can serve as seed compounds for IGR development.
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Affiliation(s)
- Kotaro Koiwai
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
| | - Kana Morohashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8572, Japan
| | - Kazue Inaba
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8572, Japan
| | - Kana Ebihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8572, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, The University of Tokyo, 7–3–1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7–3–1 Hongo, Bunkyo-ku, Tokyo 113–0033, Japan
| | - Ryunosuke Yoshino
- Graduate School of Comprehensive Human Sciences Majors of Medical Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8575, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8575, Japan
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2–4–7 Aomi, Koto-ku, Tokyo 135–0064, Japan
| | - Taiki Nampo
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo 192–0392, Japan
| | - Yuuta Fujikawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo 192–0392, Japan
| | - Hideshi Inoue
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo 192–0392, Japan
| | - Fumiaki Yumoto
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
- School of High Energy Accelerator Science, SOKENDAI University, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1–1–1 Tennodai, Ibaraki 305–8571, Japan
| | - Ryusuke Niwa
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1–1 Oho, Tsukuba, Ibaraki 305–0801, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8572, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
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Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K. Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Adv 2020; 10:43319-43323. [PMID: 35519695 PMCID: PMC9058415 DOI: 10.1039/d0ra09413g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
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Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D. Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs. Adv Appl Bioinform Chem 2020; 13:11-25. [PMID: 33209039 PMCID: PMC7669531 DOI: 10.2147/aabc.s235542] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
It has been noticed that the efficiency of drug development has been decreasing in the past few decades. To overcome the situation, protein-protein interactions (PPIs) have been identified as new drug targets as early as 2000. PPIs are more abundant in human cells than single proteins and play numerous important roles in cellular processes including diseases. However, PPIs have very different physicochemical features from the conventional drug targets, which make targeting PPIs challenging. Therefore, as of now, only a small number of PPI inhibitors have been approved or progressed to a stage of clinical trial. In this article, we first overview previous works that analyzed differences between PPIs with PPI targeting ligands and conventional drugs with their binding pockets. Then, we constructed an up-to-date list of PPI targeting drugs that have been approved or are currently under clinical trial and have bound drug-target structures available. Using the dataset, we analyzed the PPIs and their ligands using several scores of druggability. Druggability scores showed that PPI sites and their drugs targeting PPIs are less druggable than conventional binding pockets and drugs, which also indicates that PPI drugs do not follow the conventional rules for drug design, such as Lipinski's rule of five. Our analyses suggest that developing a new rule would be beneficial for guiding PPI-drug discovery.
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Affiliation(s)
- Woong-Hee Shin
- Department of Chemical Science Education, Sunchon National University, Suncheon57922, Republic of Korea
| | - Keiko Kumazawa
- Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Tokyo191-8512, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo135-0064, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo135-0064, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN47906, USA
- Department of Computer Science, Purdue University, West Lafayette, IN47906, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN47906, USA
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Care, University of Cincinnati, Cincinnati, OH45229, USA
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36
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Inaba K, Koiwai K, Ebihara K, Yoshino R, Hirokawa T, Imamura R, Kojima H, Okabe T, Nagano T, Inoue H, Fujikawa Y, Sakuma C, Kanuka H, Yumoto F, Senda T, Niwa R. Structure–activity relationship analysis of mosquito glutathione S-transferase Noppera-bo and its inhibitors for insecticide development. Acta Crystallogr A Found Adv 2020. [DOI: 10.1107/s010876732009827x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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37
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Koiwai K, Inaba K, Morohashi K, Enya S, Arai R, Kojima H, Okabe T, Fujikawa Y, Inoue H, Yoshino R, Hirokawa T, Kato K, Fukuzawa K, Shimada-Niwa Y, Nakamura A, Yumoto F, Senda T, Niwa R. An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo. J Biol Chem 2020; 295:7154-7167. [PMID: 32241910 PMCID: PMC7242711 DOI: 10.1074/jbc.ra119.011463] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/23/2020] [Indexed: 12/16/2022] Open
Abstract
Ecdysteroids are the principal steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis encoded by Halloween genes were identified and genetically and biochemically characterized. However, the tertiary structures of these proteins have not yet been characterized. Here, we report the results of an integrated series of in silico, in vitro, and in vivo analyses of the Halloween GST protein Noppera-bo (Nobo). We determined crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with GSH and 17β-estradiol, a DmNobo inhibitor. 17β-Estradiol almost fully occupied the putative ligand-binding pocket and a prominent hydrogen bond formed between 17β-estradiol and Asp-113 of DmNobo. We found that Asp-113 is essential for 17β-estradiol–mediated inhibition of DmNobo enzymatic activity, as 17β-estradiol did not inhibit and physically interacted less with the D113A DmNobo variant. Asp-113 is highly conserved among Nobo proteins, but not among other GSTs, implying that this residue is important for endogenous Nobo function. Indeed, a homozygous nobo allele with the D113A substitution exhibited embryonic lethality and an undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue that appears to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. To the best of our knowledge, ours is the first study describing the structural characteristics of insect steroidogenic Halloween proteins. Our findings provide insights relevant for applied entomology to develop insecticides that specifically inhibit ecdysteroid biosynthesis.
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Affiliation(s)
- Kotaro Koiwai
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kazue Inaba
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kana Morohashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Sora Enya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Reina Arai
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuuta Fujikawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hideshi Inoue
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ryunosuke Yoshino
- Graduate School of Comprehensive Human Sciences Majors of Medical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koichiro Kato
- Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akira Nakamura
- Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Fumiaki Yumoto
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,School of High Energy Accelerator Science, Sokendai University, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Ryusuke Niwa
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan .,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Adachi K, Yamada T, Ishizuka H, Oki M, Tsunogae S, Shimada N, Chiba O, Orihara T, Hidaka M, Hirokawa T, Odagi M, Konoki K, Yotsu‐Yamashita M, Nagasawa K. Synthesis of C12‐Keto Saxitoxin Derivatives with Unusual Inhibitory Activity Against Voltage‐Gated Sodium Channels. Chemistry 2020; 26:2025-2033. [DOI: 10.1002/chem.201904184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/04/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Kanna Adachi
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Tomoshi Yamada
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Hayate Ishizuka
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Mana Oki
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Shunsuke Tsunogae
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Noriko Shimada
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Osamu Chiba
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Tatsuya Orihara
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Masafumi Hidaka
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8575 Japan
- Division of Biomedical Science University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8575 Japan
- Molecular Profiling Research Center for Drug Discovery National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Minami Odagi
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Keiichi Konoki
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Mari Yotsu‐Yamashita
- Graduate School of Agriculture Science Tohoku University 468-1 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8572 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
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39
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Abe H, Nhung Nguyen H, Suzuki K, Kimura Y, Hirokawa T, Murakami-Tonami Y. Synthesis and Biological Evaluation of NMDI14 Derivatives as Anti-Mesothelioma Agents. HETEROCYCLES 2020. [DOI: 10.3987/com-19-14191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin WH, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin KY, Gupta V, Kitano H, Sakamoto M, Higuchi A, Miura N, Yura K, Mochizuki M, Ramakrishnan C, Thangakani AM, Velmurugan D, Gromiha MM, Nakane I, Uchida N, Hakariya H, Tan M, Nakamura HK, Suzuki SD, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto KZ, Moriwaki Y, Oda K, Kobayashi D, Okuno T, Minami S, Chikenji G, Prathipati P, Nagao C, Mohsen A, Ito M, Mizuguchi K, Honma T, Ishida T, Hirokawa T, Akiyama Y, Sekijima M. A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Sci Rep 2019; 9:19585. [PMID: 31863054 PMCID: PMC6925144 DOI: 10.1038/s41598-019-55069-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
Abstract
Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.
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Affiliation(s)
- Shuntaro Chiba
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan
| | | | - Petro Borysko
- Bienta/Enamine Ltd., 78 Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., 78 Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Nobuaki Yasuo
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Research Fellow of the Japan Society for the Promotion of Science DC1, Tokyo, Japan
| | - Ryunosuke Yoshino
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8575, Japan
| | - Kazuyoshi Ikeda
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Woong-Hee Shin
- Department of Biological Science, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, Indiana, 47907, USA.,Department of Computer Science, Purdue University, Indiana, 47907, USA
| | - Mitsuo Iwadate
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Hideaki Umeyama
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Takaaki Ichikawa
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Reiji Teramoto
- Discovery technology research department, Research division, Chugai Pharmaceutical Co.,Ltd., 200, Kajiwara, Kamakura, Kanagawa, 247-8530, Japan
| | - Kun-Yi Hsin
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan
| | - Vipul Gupta
- The Systems Biology Research Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Hiroaki Kitano
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan.,The Systems Biology Research Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan.,Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Mika Sakamoto
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Akiko Higuchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Nobuaki Miura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.,Center for Simulation Science and Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.,School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masahiro Mochizuki
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,IMSBIO Co., Ltd., Level 6 OWL TOWER, 4-21-1 Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan
| | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - A Mary Thangakani
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - D Velmurugan
- CAS in Crystallography and Biophysics and Bioinformatics Facility, University of Madras, Chennai, 600025, Tamilnadu, India
| | - M Michael Gromiha
- Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - Itsuo Nakane
- Okazaki City Hall, 2-9 Juo-cho Okazaki, Aichi, 444-8601, Japan
| | - Nanako Uchida
- IQVIA Services Japan K.K., 4-10-18 Takanawa Minato-ku, Tokyo, 108-0074, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Training Program of Leaders for Integrated Medical System (LIMS), Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Modong Tan
- Department of Chemistry & Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hironori K Nakamura
- Biomodeling Research Co., Ltd., 1-704-2 Uedanishi, Tenpaku-ku, Nagoya, 468-0058, Japan
| | - Shogo D Suzuki
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tomoki Ito
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Masahiro Kawatani
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Kentaroh Kudoh
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Sakurako Takashina
- Faculty of Medicine, Akita University, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Kazuki Z Yamamoto
- Isotope Science Center, The University of Tokyo, 2-11- 16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Keita Oda
- Google Japan Inc., 6-10-1 Roppongi, Minato-ku, Tokyo, 106-6126, Japan.,Otemachi Bldg. 3F, 1-6-1, Preferred Networks, Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Daisuke Kobayashi
- Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tatsuya Okuno
- Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Shintaro Minami
- Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - George Chikenji
- Department of Computational Science and Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Philip Prathipati
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Chioko Nagao
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Attayeb Mohsen
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Mari Ito
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes for Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Teruki Honma
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takashi Ishida
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, 305-8575, Japan.,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan
| | - Yutaka Akiyama
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan.,Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan
| | - Masakazu Sekijima
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan. .,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, J3-23-4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Japan. .,Initiative for Parallel Bioinformatics, Level 14 Hibiya Central Building, 1-2-9 Nishi-Shimbashi Minato-Ku, Tokyo, 105-0003, Japan.
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41
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Fukushi K, Hirokawa T, Timerbaev AR. Recent developments of capillary electrophoresis in seawater analysis. J Chromatogr A 2019; 1606:360240. [PMID: 31109744 DOI: 10.1016/j.chroma.2019.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/07/2019] [Accepted: 05/12/2019] [Indexed: 12/17/2022]
Abstract
Recent applications of capillary electrophoresis (CE) to the determination of various seawater analytes are critically examined, with the aim to reveal method's state-of-the-art and possible future research trends in the area. Given highly developed separation and detection methodology, emphasis is given to the most advantageous sample preconcentration strategies used to evolve the method's practical utility, particularly to low-level analytes. Analytical performance of CE applied to seawater analysis is illustrated with a selection of real-world applications published from 2006, from which it appears that the primary developmental tendency is presently confined to a transit from inorganic to organic seawater analytes.
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Affiliation(s)
- K Fukushi
- Kobe University, 1-1, Rokkodai-cho, Nada-ku, 657-8501 Kobe, Japan
| | - T Hirokawa
- Professor-in-residence, 1087-3, Kamifukawa-cho, Asakita-ku, 739-1752 Hiroshima, Japan
| | - A R Timerbaev
- Vernadsky Institute of Geochemistry and Analytical Chemistry, Kosygin St. 19, 119991 Moscow, Russian Federation.
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42
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Yamada K, Nakazawa M, Matsumoto K, Tagami U, Hirokawa T, Homma K, Mori S, Matsumoto R, Saikawa W, Kitajima S. Unnatural Tripeptides as Potent Positive Allosteric Modulators of T1R2/T1R3. ACS Med Chem Lett 2019; 10:800-805. [PMID: 31098002 DOI: 10.1021/acsmedchemlett.9b00051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/25/2019] [Indexed: 11/28/2022] Open
Abstract
T1R2/T1R3 belongs to G protein coupled receptors, which recognizes diverse natural and synthetic sweeteners. A novel class of positive allosteric modulators (PAMs) of T1R2/T1R3 was identified through high-throughput screening campaign. Comparing the structure of the potent compound with previously known PAM, we classified the structure of known PAM into three parts, defined as "head", "linker", and "tail". We then investigated the linker-tail structure. It was suggested by molecular docking models of T1R2/T1R3 that an amine that we introduced in the tail was the key for interaction with the receptor binding pocket. We thus synthesized various molecules and found unnatural tripeptide-PAMs, which potently enhance the sweetness of sucrose in sensory evaluation tests.
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Affiliation(s)
- Kei Yamada
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Masakazu Nakazawa
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Kayo Matsumoto
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Uno Tagami
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center of Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Keisuke Homma
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Suguru Mori
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Ryo Matsumoto
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Wakana Saikawa
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
| | - Seiji Kitajima
- Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan
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43
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Shawki HH, Ishikawa-Yamauchi Y, Kawashima A, Katoh Y, Matsuda M, Al-Soudy AS, Minisy FM, Kuno A, Gulibaikelamu X, Hirokawa T, Takahashi S, Oishi H. EFCAB2 is a novel calcium-binding protein in mouse testis and sperm. PLoS One 2019; 14:e0214687. [PMID: 30933994 PMCID: PMC6443151 DOI: 10.1371/journal.pone.0214687] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/18/2019] [Indexed: 11/18/2022] Open
Abstract
Calcium-binding proteins regulate ion metabolism and the necessary signaling pathways for the maturational events of sperm. Our aim is to identify the novel calcium-binding proteins in testis. The gene EFCAB2 (GenBank NM_026626.3, NP_080902.1) was not previously examined, and its properties and exact mechanisms of action are unknown. In this study, we performed phylogenetic and structure prediction analyses of EFCAB2, which displays definitive structural features. Additionally, the distribution, localization, and calcium binding ability of mouse EFCAB2 were investigated. Results revealed extensive conservation of EFCAB2 among different eukaryotic orthologs. The constructed 3D model predicted that mouse EFCAB2 contains seven α-helices and two EF-hand motifs. The first EF-hand motif is located in N-terminal, while the second is located in C-terminal. By aligning the 3D structure of Ca2+-binding loops from EFCAB2 with calmodulin, we predicted six residues that might be involved in Ca2+ binding. The distribution of the Efcab2 mRNA, as determined by northern blotting, was detected only in the testis among mouse tissues. Native and recombinant EFCAB2 protein were detected by western blotting as one band at 20 kDa. In situ hybridization and immunohistochemical analyses showed its localization specifically in spermatogenic cells from primary spermatocytes to elongate spermatids within the seminiferous epithelium, but neither spermatogonia nor somatic cells were expressed. Moreover, EFCAB2 was specifically localized to the principal piece of cauda epididymal sperm flagellum. Furthermore, the analyses of purified recombinant EFCAB2 by Stains-all, ruthenium red staining, and by applying in vitro autoradiography assay showed that the physiological function of this protein is Ca2+ binding. These results suggested that EFCAB2 might be involved in the control of sperm flagellar movement. Altogether, here we describe about EFCAB2 as a novel calcium-binding protein in mouse testis and sperm.
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Affiliation(s)
- Hossam H. Shawki
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
- Department of Animal Genetic Resources, National Gene Bank, Giza, Egypt
- Department of Comparative and Experimental Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- * E-mail: (HHS); (AK)
| | - Yu Ishikawa-Yamauchi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akihiro Kawashima
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
- Department of Comparative and Experimental Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- * E-mail: (HHS); (AK)
| | - Yuki Katoh
- Institute for Advanced Medical Research, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Manabu Matsuda
- Department of Arts and Sciences, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Al-Sayed Al-Soudy
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
- Department of Animal Genetic Resources, National Gene Bank, Giza, Egypt
| | - Fatma M. Minisy
- Department of Comparative and Experimental Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Pathology Department, Medical Research Division, National Research Centre, Giza, Egypt
| | - Akihiro Kuno
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Xiafukaiti Gulibaikelamu
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Koutou-ku, Tokyo, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Hisashi Oishi
- Department of Comparative and Experimental Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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44
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Nakagita T, Ishida A, Matsuya T, Kobayashi T, Narukawa M, Hirokawa T, Hashimoto M, Misaka T. Structural insights into the differences among lactisole derivatives in inhibitory mechanisms against the human sweet taste receptor. PLoS One 2019; 14:e0213552. [PMID: 30883570 PMCID: PMC6422327 DOI: 10.1371/journal.pone.0213552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/23/2019] [Indexed: 11/22/2022] Open
Abstract
Lactisole, an inhibitor of the human sweet taste receptor, has a 2-phenoxypropionic acid skeleton and has been shown to interact with the transmembrane domain of the T1R3 subunit (T1R3-TMD) of the receptor. Another inhibitor, 2,4-DP, which shares the same molecular skeleton as lactisole, was confirmed to be approximately 10-fold more potent in its inhibitory activity than lactisole; however the structural basis of their inhibitory mechanisms against the receptor remains to be elucidated. Crystal structures of the TMD of metabotropic glutamate receptors, which along with T1Rs are categorized as class C G-protein coupled receptors, have recently been reported and made it possible to create an accurate structural model for T1R3-TMD. In this study, the detailed structural mechanism underlying sweet taste inhibition was characterized by comparing the action of lactisole on T1R3-TMD with that of 2,4-DP. We first performed a series of experiments using cultured cells expressing the sweet taste receptor with mutations and examined the interactions with these inhibitors. Based on the results, we next performed docking simulations and then applied molecular dynamics-based energy minimization. Our analyses clearly revealed that the (S)-isomers of both lactisole and 2,4-DP, interacted with the same seven residues in T1R3-TMD and that the inhibitory potencies of those inhibitors were mainly due to stabilizing interactions mediated via their carboxyl groups in the vertical dimension of the ligand pocket of T1R3-TMD. In addition, 2,4-DP engaged in a hydrophobic interaction mediated by its o-Cl group, and this interaction may be chiefly responsible for the higher inhibitory potency of 2,4-DP.
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Affiliation(s)
- Tomoya Nakagita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko Ishida
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takumi Matsuya
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Narukawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institutes of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Chemical Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Makoto Hashimoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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45
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Sakaue H, Shiota T, Ishizaka N, Kawano S, Tamura Y, Tan KS, Imai K, Motono C, Hirokawa T, Taki K, Miyata N, Kuge O, Lithgow T, Endo T. Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly. Mol Cell 2019; 73:1044-1055.e8. [DOI: 10.1016/j.molcel.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
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46
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Shiba-Ishii A, Hong J, Hirokawa T, Kim Y, Nakagawa T, Sakashita S, Sakamoto N, Kozuma Y, Sato Y, Noguchi M. Stratifin Inhibits SCFFBW7 Formation and Blocks Ubiquitination of Oncoproteins during the Course of Lung Adenocarcinogenesis. Clin Cancer Res 2019; 25:2809-2820. [DOI: 10.1158/1078-0432.ccr-18-3631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 11/16/2022]
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47
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Ma Y, Iida K, Sasaki S, Hirokawa T, Heddi B, Phan AT, Nagasawa K. Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains. Molecules 2019; 24:molecules24020263. [PMID: 30642002 PMCID: PMC6358838 DOI: 10.3390/molecules24020263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 12/13/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 01/02/2023] Open
Abstract
G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore “sequence-dependent” selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4.
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Affiliation(s)
- Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan.
| | - Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Takatsugu Hirokawa
- Transborder Medical Reserch Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo 135-0064, Japan.
| | - Brahim Heddi
- Laboratoire de Biologie et Pharmacologie appliquée, CNRS UMR 8113, ENS paris-saclay 60 avenue du president Wilson, 94230 Cachan, France.
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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48
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Ohsawa K, Yoshida M, Izumikawa M, Takagi M, Shin-ya K, Goshima N, Hirokawa T, Natsume T, Doi T. Synthesis and biological evaluation of thielocin B1 analogues as protein-protein interaction inhibitors of PAC3 homodimer. Bioorg Med Chem 2018; 26:6023-6034. [DOI: 10.1016/j.bmc.2018.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022]
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49
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Kawamura S, Ito Y, Hirokawa T, Hikiyama E, Yamada S, Shuto S. Ligand-Phospholipid Conjugation: A Versatile Strategy for Developing Long-Acting Ligands That Bind to Membrane Proteins by Restricting the Subcellular Localization of the Ligand. J Med Chem 2018; 61:4020-4029. [PMID: 29652494 DOI: 10.1021/acs.jmedchem.8b00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We hypothesized that if drug localization can be restricted to a particular subcellular domain where their target proteins reside, the drugs could bind to their target proteins without being metabolized and/or excreted, which would significantly extend the half-life of the corresponding drug-target complex. Thus, we designed ligand-phospholipid conjugates in which the ligand is conjugated with a phospholipid through a polyethylene glycol linker to restrict the subcellular localization of the ligand in the vicinity of the lipid bilayer. Here, we present the design, synthesis, pharmacological activity, and binding mode analysis of ligand-phospholipid conjugates with muscarinic acetylcholine receptors as the target proteins. These results demonstrate that ligand-phospholipid conjugation can be a versatile strategy for developing long-acting ligands that bind to membrane proteins in drug discovery.
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Affiliation(s)
| | - Yoshihiko Ito
- Center for Pharma-Food Research, Department of Pharmacokinetics and Pharmacodynamics, Graduate School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (MOLPROF) , National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi , Koutou-ku, Tokyo 135-0064 , Japan
| | - Eriko Hikiyama
- Center for Pharma-Food Research, Department of Pharmacokinetics and Pharmacodynamics, Graduate School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Shizuo Yamada
- Center for Pharma-Food Research, Department of Pharmacokinetics and Pharmacodynamics, Graduate School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
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50
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Sakai Y, Kawaguchi A, Nagata K, Hirokawa T. Analysis by metadynamics simulation of binding pathway of influenza virus M2 channel blockers. Microbiol Immunol 2018; 62:34-43. [DOI: 10.1111/1348-0421.12561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yuri Sakai
- PhD Program in Human Biology; School of Integrative and Global Majors; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
| | - Atsushi Kawaguchi
- PhD Program in Human Biology; School of Integrative and Global Majors; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Department of Infection Biology; Faculty of Medicine; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Transborder Medical Research Center; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
| | - Kyosuke Nagata
- Department of Infection Biology; Faculty of Medicine; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science; Faculty of Medicine; University of Tsukuba; 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Molecular Profiling Research Center for Drug Discovery; National Institute of Advanced Industrial Science and Technology; 2-4-7 Aomi, Koto-ku Tokyo, 135-0064 Japan
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