1
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Rojas BL, Vazquez-Rivera E, Partch CL, Bradfield CA. Dimerization Rules of Mammalian PAS Proteins. J Mol Biol 2024; 436:168406. [PMID: 38109992 PMCID: PMC10922841 DOI: 10.1016/j.jmb.2023.168406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
The PAS (PER, ARNT, SIM) protein family plays a vital role in mammalian biology and human disease. This analysis arose from an interest in the signaling mechanics by the Ah receptor (AHR) and the Ah receptor nuclear translocator (ARNT). After more than fifty years by studying this and related mammalian sensor systems, describing the role of PAS domains in signal transduction is still challenging. In this perspective, we attempt to interpret recent studies of mammalian PAS protein structure and consider how this new insight might explain how these domains are employed in human signal transduction with an eye towards developing strategies to target and engineer these molecules for a new generation of therapeutics. Our approach is to integrate our understanding of PAS protein history, cell biology, and molecular biology with recent structural discoveries to help explain the mechanics of mammalian PAS protein signaling. As a learning set, we focus on sequences and crystal structures of mammalian PAS protein dimers that can be visualized using readily available software.
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Affiliation(s)
- Brenda L Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA
| | | | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, USA
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA; McArdle Laboratory for Cancer Research. University of Wisconsin, School of Medicine and Public Health, Madison, WI, USA.
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2
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Nishina A, Ukiya M, Motegi K, Kiryu R, Sato D, Sada M, Hori Y, Satsu H, Uemura K, Koketsu M, Ninomiya M, Myint LMM, Kimura H. Promotion of ABCG2 gene expression by neolignans from Piper longum L. Biosci Biotechnol Biochem 2023; 87:1523-1531. [PMID: 37709570 DOI: 10.1093/bbb/zbad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
We focused on Piper longum L., a herbal drug produced in Myanmar, which has a renoprotective effect. Thus, we attempted to isolate and identify compounds that enhance the expression of the ABCG2 gene from the aerial parts of the plant except for the fruit. Among the various P. longum extracts, we isolated and identified the components. Using Caco-2 cells, the hABCG2 mRNA expression-enhancing effects of the isolated compounds were compared with the positive reference compound (3-methylcholanthrene [3MC]) using real-time polymerase chain reaction. Six compounds were isolated and identified from the methanol extract of P. longum. Among the isolated compounds, licarin A and neopomatene had lower toxicity and higher hABCG2 mRNA expression-enhancing effects in Caco-2 cells. Suppression of hAhR expression by siRNA reduced the activity of licarin A and neopomatene, as well as the hAhR agonist 3MC, suggesting that these 2 compounds may act as hAhR agonists to promote hABCG2 expression.
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Affiliation(s)
- Atsuyoshi Nishina
- School of Health and Nutrition, Tokai Gakuen University, Nagoya, Aichi, Japan
| | - Motohiko Ukiya
- College of Science and Technology, Nihon University, Chiyoda, Tokyo, Japan
| | - Kazuki Motegi
- College of Science and Technology, Nihon University, Chiyoda, Tokyo, Japan
| | - Risa Kiryu
- College of Science and Technology, Nihon University, Chiyoda, Tokyo, Japan
| | - Daisuke Sato
- Department of Biomedical Information Engineering, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Mitsuru Sada
- Department of Health Science, Gunma Paz University Graduate School, Takasaki, Gunma, Japan
| | - Yuki Hori
- Department of Biotechnology, Maebashi Institute of Technology, Maebashi, Gunma, Japan
| | - Hideo Satsu
- Department of Biotechnology, Maebashi Institute of Technology, Maebashi, Gunma, Japan
| | - Kazuhiro Uemura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Mamoru Koketsu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Masayuki Ninomiya
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
- Division of Instrumental Analysis, Life Science Research Center, Gifu University, Gifu, Japan
| | - Lwin Mon Mon Myint
- Division of Research and Development, FAME Pharmaceuticals Industry Co., Ltd, Yangon, Myanmar
| | - Hirokazu Kimura
- College of Science and Technology, Nihon University, Chiyoda, Tokyo, Japan
- Department of Health Science, Gunma Paz University Graduate School, Takasaki, Gunma, Japan
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3
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Rosales-Hernández MC, Bello M, Toledano JV, Feregrino BCE, Correa Basurto J, Fragoso Morales LG, Torres-Ramos MA. Molecular dynamics simulations depict structural motions of the whole human aryl hydrocarbon receptor influencing its binding of ligands and HSP90. J Biomol Struct Dyn 2023; 41:13138-13153. [PMID: 36705144 DOI: 10.1080/07391102.2023.2171132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/15/2023] [Indexed: 01/28/2023]
Abstract
The aryl hydrocarbon receptor (AhR) has broad biological functions when its ligands activate it; the non-binding interactions with AhR have not been fully elucidated due to the absence of a complete tridimensional (3D) structure. Therefore, utilization of the whole 3D structure from Homo sapiens AhR by in silico studies will allow us to better study and analyze the binding mode of its full and partial agonists, and antagonists, as well as its interaction with the HSP90 chaperone. The 3D AhR structure was obtained from I-TASSER and subjected to molecular dynamics (MD) simulations to obtain different structural conformations and determine the most populated AhR conformer by clustering analyses. The AhR-3D structures selected from MD simulations and those from clustering analyses were used to achieve docking studies with some of its ligands and protein-protein docking with HSP90. Once the AhR-3D structure was built, its Ramachandran maps and energy showed a well-qualified 3D model. MD simulations showed that the per-Arnt-Sim homology (PAS) PAS A, PAS B, and Q domains underwent conformational changes, identifying the conformation when agonists were binding also, and HSP90 was binding near the PAS A, PAS B, and Q domains. However, when antagonists are binding, HSP90 does not bind near the PAS A, PAS B, and Q domains. These studies show that the complex agonist-AhR-HSP90 can be formed, but this complex is not formed when an antagonist is binding. Knowing the conformations when the ligands bind to AHR and the behavior of HSP90 allows for an understanding of its activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Jazziel Velazquez Toledano
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Barbara Citlali Escudero Feregrino
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Mexico City, México
| | - José Correa Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Leticia Guadalupe Fragoso Morales
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
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4
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In-depth analysis of the interactions of various aryl hydrocarbon receptor ligands from a computational perspective. J Mol Graph Model 2023; 118:108339. [PMID: 36183684 DOI: 10.1016/j.jmgm.2022.108339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/01/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that acts as a machinery that controls the expression of many genes, including cytochrome P450 CYP1A1, CYP1A2 and CYP1B1. It plays a principal role in numerous biological and toxicological functions, making it a promising target for developing therapeutic agents. Several novel small molecules targeting the AhR signaling pathway are currently under investigation as antitumor agents. Some have already advanced into clinical trials in patients with various tumors. Activation of AhR by diverse chemicals either endogenous or exogenous is initiated by the binding of these ligands to the PAS-B domain, which modulates AhR functions. There is, however, limited information about how various ligands interact with the PAS-B domain for activating or inhibiting the AhR. To better understand the mode of action of AhR agonists/antagonists. The current work proposes a combination of several computational tools to build dynamical models for the PAS-B domain bound to different ligands in mouse and human. Our findings reveal the essential roles of specific PAS-B residues (e.g., S365, V381& Q383), which mediate the AhR ligand-binding process. Our results also explain how these residues regulate the promiscuity of AhR in accommodating various chemicals in its binding PAS-B ligand-binding pocket.
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5
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Flegel J, Shaaban S, Jia ZJ, Schulte B, Lian Y, Krzyzanowski A, Metz M, Schneidewind T, Wesseler F, Flegel A, Reich A, Brause A, Xue G, Zhang M, Dötsch L, Stender ID, Hoffmann JE, Scheel R, Janning P, Rastinejad F, Schade D, Strohmann C, Antonchick AP, Sievers S, Moura-Alves P, Ziegler S, Waldmann H. The Highly Potent AhR Agonist Picoberin Modulates Hh-Dependent Osteoblast Differentiation. J Med Chem 2022; 65:16268-16289. [PMID: 36459434 PMCID: PMC9791665 DOI: 10.1021/acs.jmedchem.2c00956] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Identification and analysis of small molecule bioactivity in target-agnostic cellular assays and monitoring changes in phenotype followed by identification of the biological target are a powerful approach for the identification of novel bioactive chemical matter in particular when the monitored phenotype is disease-related and physiologically relevant. Profiling methods that enable the unbiased analysis of compound-perturbed states can suggest mechanisms of action or even targets for bioactive small molecules and may yield novel insights into biology. Here we report the enantioselective synthesis of natural-product-inspired 8-oxotetrahydroprotoberberines and the identification of Picoberin, a low picomolar inhibitor of Hedgehog (Hh)-induced osteoblast differentiation. Global transcriptome and proteome profiling revealed the aryl hydrocarbon receptor (AhR) as the molecular target of this compound and identified a cross talk between Hh and AhR signaling during osteoblast differentiation.
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Affiliation(s)
- Jana Flegel
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Saad Shaaban
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Institute of Organic Chemistry, University of Vienna Währinger Str. 38, Vienna 1090, Austria
| | - Zhi Jun Jia
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Britta Schulte
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Yilong Lian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Adrian Krzyzanowski
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Malte Metz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Tabea Schneidewind
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Fabian Wesseler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Anke Flegel
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Alisa Reich
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Alexandra Brause
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Minghao Zhang
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Rebecca Scheel
- Faculty of Chemistry, Inorganic Chemistry, Technical University Dortmund, Dortmund 44227, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Fraydoon Rastinejad
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Dennis Schade
- Dept. of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
| | - Carsten Strohmann
- Faculty of Chemistry, Inorganic Chemistry, Technical University Dortmund, Dortmund 44227, Germany
| | - Andrey P Antonchick
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany.,Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, United Kingdom
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Compound Management and Screening Center, Dortmund 44227, Germany
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.,Faculty of Chemistry, Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
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6
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Yamashiro T, Shiraishi A, Nakayama K, Satake H. Key Amino Acids for Transferase Activity of GDSL Lipases. Int J Mol Sci 2022; 23:ijms232315141. [PMID: 36499468 PMCID: PMC9736205 DOI: 10.3390/ijms232315141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The Gly-Asp-Ser-Leu (GDSL) motif of esterase/lipase family proteins (GELPs) generally exhibit esterase activity, whereas transferase activity is markedly preferred in several GELPs, including the Tanacetum cinerariifolium GDSL lipase TciGLIP, which is responsible for the biosynthesis of the natural insecticide, pyrethrin I. This transferase activity is due to the substrate affinity regulated by the protein structure and these features are expected to be conserved in transferase activity-exhibiting GELPs (tr-GELPs). In this study, we identified two amino acid residues, [N/R]208 and D484, in GELP sequence alignments as candidate key residues for the transferase activity of tr-GELPs by two-entropy analysis. Molecular phylogenetic analysis demonstrated that each tr-GELP is located in the clusters for non-tr-GELPs, and most GELPs conserve at least one of the two residues. These results suggest that the two conserved residues are required for the acquisition of transferase activity in the GELP family. Furthermore, substrate docking analyses using ColabFold-generated structure models of both natives and each of the two amino acids-mutated TciGLIPs also revealed numerous docking models for the proper access of substrates to the active site, indicating crucial roles of these residues of TciGLIP in its transferase activity. This is the first report on essential residues in tr-GELPs for the transferase activity.
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Affiliation(s)
- Takanori Yamashiro
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka 561-0827, Osaka, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Hyogo, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Souraku 619-0284, Kyoto, Japan
| | - Koji Nakayama
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka 561-0827, Osaka, Japan
| | - Honoo Satake
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Hyogo, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Souraku 619-0284, Kyoto, Japan
- Correspondence: ; Tel.: +81-5031820704
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7
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Structure and dynamics of hydrophobic deep eutectic solvents composed from terpene-fatty acids investigated by molecular dynamics simulation. J Mol Graph Model 2022; 114:108180. [DOI: 10.1016/j.jmgm.2022.108180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/09/2021] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
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8
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Molecular and structural basis of interactions of vitamin D3 hydroxyderivatives with aryl hydrocarbon receptor (AhR): An integrated experimental and computational study. Int J Biol Macromol 2022; 209:1111-1123. [PMID: 35421413 DOI: 10.1016/j.ijbiomac.2022.04.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/10/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022]
Abstract
To better understand the molecular and structural basis underlying the interaction of vitamin D3 hydroxyderivatives with AhR, molecular simulation was used to probe the binding of 1,20(OH)2D3, 1,25(OH)2D3, 20,23(OH)2D3 and 20(OH)D3 to AhR. qPCR showed that vitamin D3 derivatives stimulate expression of cyp1A1 and cyp1B1 genes that are downstream targets of AhR signaling. These secosteroids stimulated the translocation of the AhR to the nucleus, as measured by flow cytometry and western blotting. Molecular dynamics simulations were used to model the binding of vitamin D3 derivatives to AhR to examine their influence on the structure, conformation and dynamics of the AhR ligand binding domain (LBD). Binding thermodynamics, conformation, secondary structure, dynamical motion and electrostatic potential of AhR were analyzed. The molecular docking scores and binding free energy were all favorable for the binding of D3 derivatives to the AhR. These established ligands and the D3 derivatives are predicted to have different patterns of hydrogen bond formation with the AhR, and varied residue conformational fluctuations and dynamical motion for the LBD. These changes could alter the shape, size and electrostatic potential distribution of the ligand binding pocket, contributing to the different binding affinities of AhR for the natural ligands and D3 derivatives.
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9
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Goya-Jorge E, Doan TQ, Scippo ML, Muller M, Giner RM, Barigye SJ, Gozalbes R. Elucidating the aryl hydrocarbon receptor antagonism from a chemical-structural perspective. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:209-226. [PMID: 31916862 DOI: 10.1080/1062936x.2019.1708460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
The aryl hydrocarbon receptor (AhR) plays an important role in several biological processes such as reproduction, immunity and homoeostasis. However, little is known on the chemical-structural and physicochemical features that influence the activity of AhR antagonistic modulators. In the present report, in vitro AhR antagonistic activity evaluations, based on a chemical-activated luciferase gene expression (AhR-CALUX) bioassay, and an extensive literature review were performed with the aim of constructing a structurally diverse database of contaminants and potentially toxic chemicals. Subsequently, QSAR models based on Linear Discriminant Analysis and Logistic Regression, as well as two toxicophoric hypotheses were proposed to model the AhR antagonistic activity of the built dataset. The QSAR models were rigorously validated yielding satisfactory performance for all classification parameters. Likewise, the toxicophoric hypotheses were validated using a diverse set of 350 decoys, demonstrating adequate robustness and predictive power. Chemical interpretations of both the QSAR and toxicophoric models suggested that hydrophobic constraints, the presence of aromatic rings and electron-acceptor moieties are critical for the AhR antagonism. Therefore, it is hoped that the deductions obtained in the present study will contribute to elucidate further on the structural and physicochemical factors influencing the AhR antagonistic activity of chemical compounds.
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Affiliation(s)
- E Goya-Jorge
- CEEI (Centro Europeo de Empresas Innovadoras), ProtoQSAR SL, Parque Tecnológico de Valencia, Valencia, Spain
- Departament de Farmacologia, Facultat de Farmàcia, Universitat de València, Valencia, Spain
| | - T Q Doan
- Laboratory of Food Analysis, FARAH-Veterinary Public Health, ULiège, Liège, Belgium
| | - M L Scippo
- Laboratory of Food Analysis, FARAH-Veterinary Public Health, ULiège, Liège, Belgium
| | - M Muller
- Laboratory for Organogenesis and Regeneration, GIGA-Research, ULiège, Liège, Belgium
| | - R M Giner
- Departament de Farmacologia, Facultat de Farmàcia, Universitat de València, Valencia, Spain
| | - S J Barigye
- CEEI (Centro Europeo de Empresas Innovadoras), ProtoQSAR SL, Parque Tecnológico de Valencia, Valencia, Spain
| | - R Gozalbes
- CEEI (Centro Europeo de Empresas Innovadoras), ProtoQSAR SL, Parque Tecnológico de Valencia, Valencia, Spain
- R&D Department, MolDrug AI Systems SL, Valencia, Spain
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10
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Kato H. Computational prediction of cytochrome P450 inhibition and induction. Drug Metab Pharmacokinet 2019; 35:30-44. [PMID: 31902468 DOI: 10.1016/j.dmpk.2019.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/27/2019] [Accepted: 11/17/2019] [Indexed: 12/14/2022]
Abstract
Cytochrome P450 (CYP) enzymes play an important role in the phase I metabolism of many xenobiotics. Most drug-drug interactions (DDIs) associated with CYP are caused by either CYP inhibition or induction. The early detection of potential DDIs is highly desirable in the pharmaceutical industry because DDIs can cause serious adverse events, which can lead to poor patient health and drug development failures. Recently, many computational studies predicting CYP inhibition and induction have been reported. The current computational modeling approaches for CYP metabolism are classified as ligand- and structure-based; various techniques, such as quantitative structure-activity relationships, machine learning, docking, and molecular dynamic simulation, are involved in both the approaches. Recently, combining these two approaches have resulted in improvements in the prediction accuracy of DDIs. In this review, we present important, recent developments in the computational prediction of the inhibition of four clinically crucial CYP isoforms (CYP1A2, 2C9, 2D6, and 3A4) and three nuclear receptors (aryl hydrocarbon receptor, constitutive androstane receptor, and pregnane X receptor) involved in the induction of CYP1A2, 2B6, and 3A4, respectively.
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Affiliation(s)
- Harutoshi Kato
- DMPK Research Laboratories, Mitsubishi Tanabe Pharma Corporation, Aoba-ku, Yokohama-shi, 227-0033, Japan.
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11
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de Souza JV, Reznikov S, Zhu R, Bronowska AK. Druggability assessment of mammalian Per-Arnt-Sim [PAS] domains using computational approaches. MEDCHEMCOMM 2019; 10:1126-1137. [PMID: 31391885 PMCID: PMC6640724 DOI: 10.1039/c9md00148d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/01/2019] [Indexed: 01/10/2023]
Abstract
Per-Arnt-Sim (PAS) domains are key regions that occur in different regulatory proteins from all kingdoms of life. PAS domains show a remarkably conserved structural scaffold, despite a highly variable primary sequence. In this study we have attempted to address some of the gaps in knowledge regarding the druggability of PAS-A domains, differences in structure and dynamics within the PAS domain family and how this affects the druggability potential, as well as give insight into the druggability of steroid receptor coactivators and putative binding modes of the NCOA1. Investigations were performed through a range of computational methods including molecular docking studies, atomistic molecular dynamics simulations, and hotspot mapping. Atomistic molecular dynamics simulations show that the function of the AhR PAS-B domain is regulated by the dynamics of the highly conserved tyrosine Y322 residue, which acts as a "gatekeeper" controlling the access to the binding cavity and finely tuning the binding affinity. Furthermore, the transition between the partially unfolded and helical conformation of the loop1 segment within PAS-B domains was shown to be essential for the generation of "druggable" sites, especially for the NCOA1 PAS-B domain. Finally, our simulations indicated the undruggability of PAS-A domains, caused by the inherent characteristics of their putative binding sites. In conclusion, this work emphasises the role of intrinsic dynamics in tuning the druggability of PAS-B domains and shows that PAS-B domains of steroid receptor coactivators, such as NCOA1, can be targeted by small molecule ligands, which highlights the potential of developing new therapeutics designed to target these coactivators using structure-based approaches.
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Affiliation(s)
- João V de Souza
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Sylvia Reznikov
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Ruidi Zhu
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Agnieszka K Bronowska
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
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12
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Zhou Y, Shen C, Du H, Bao Y, He C, Wang C, Zuo Z. Bioassay system for the detection of aryl hydrocarbon receptor agonists in waterborne pesticides using zebrafish cyp1a1 promoter-luciferase recombinant hepatic cells. CHEMOSPHERE 2019; 220:61-68. [PMID: 30579175 DOI: 10.1016/j.chemosphere.2018.12.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Currently used pesticides are widely distributed in surface water. Most of them are harmful to aquatic animals. In the present study, a novel recombinant hepatic cell line was developed for detecting the activity of aryl hydrocarbon receptor (AhR) agonists, and their potential bio-toxicity to aquatic animals was evaluated. First, HepG2 cells were stably transfected with a luciferase reporter plasmid containing a zebrafish (Danio rerio) cyp1a1 promoter with twelve copies of dioxin-responsive elements. The minimal detection limit was a 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) concentration of 0.3 ng/L (equivalent to 0.93 pM). The AhR agonist activity of thirty-seven pesticides was screened by measuring luciferase expression in the recombinant cells. Four pesticides (ipconazole, mepanipyrim, quinoxyfen and pencycuron) significantly induced luciferase expression. Additionally, cells treated with these four pesticides increased the cyp1a1 mRNA expression level, which further confirmed that they are AhR agonists. In conclusion, for the first time, we developed recombinant hepatic cells with a luciferase reporter plasmid containing a modified zebrafish cyp1a1 promoter. The cyp1a1 promoter luciferase reporter cells can be used as a sensitive and specific model to screen AhR agonists among currently used pesticides in water, which could be beneficial for risk assessment in aquatic environments.
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Affiliation(s)
- Yixi Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chao Shen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Hong Du
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yuanyuan Bao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chengyong He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chonggang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zhenghong Zuo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China.
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13
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Xue Z, Li D, Yu W, Zhang Q, Hou X, He Y, Kou X. Mechanisms and therapeutic prospects of polyphenols as modulators of the aryl hydrocarbon receptor. Food Funct 2017; 8:1414-1437. [DOI: 10.1039/c6fo01810f] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polyphenolic AhR modulators displayed concentration-, XRE-, gene-, species- and cell-specific agonistic/antagonistic activity.
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Affiliation(s)
- Zhaohui Xue
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Dan Li
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Wancong Yu
- Medical Plant Laboratory
- Tianjin Research Center of Agricultural Biotechnology
- Tianjin 3000381
- China
| | - Qian Zhang
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Xiaonan Hou
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Yulong He
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Xiaohong Kou
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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14
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Cocci P, Mozzicafreddo M, Angeletti M, Mosconi G, Palermo FA. In silico prediction and in vivo analysis of antiestrogenic potential of 2-isopropylthioxanthone (2-ITX) in juvenile goldfish (Carassius auratus). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 133:202-210. [PMID: 27454205 DOI: 10.1016/j.ecoenv.2016.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Previous studies have shown both anti-estrogenic and anti-androgenic activities of 2-isopropylthioxanthone (2-ITX), a well known food contaminant, in in vitro assays. However, no data are available on the anti-estrogenic potentials and risks of 2-ITX in aquatic organisms. This work evaluated the potential endocrine disrupting effects of 2-ITX at the level of estrogen receptor (ER) signaling cascade using juvenile goldfish (Carassius auratus) as model. Firstly, we investigated the ligand binding efficiency of 2-ITX to the ligand binding domains (LBD) of goldfish ER subtypes using a molecular docking approach. Secondly, we assessed the effects of 2-ITX on E2-induced hepatic expression of ERα1, ERβ1, ERβ2, and vitellogenin (VTG) in vivo. Crosstalk between ER-VTG and aryl hydrocarbon receptor 2 (AhR2)-cytochrome P4501A (CYP1A) was also investigated. Fish were injected with increasing doses of 2-ITX ranging from 2 to 10µg/g BW, and results were compared to the effect of tamoxifen, a well-known ER modulator. We observed that compared to ERβ, the interaction potentials of 2-ITX to goldfish ERα1 LBD was more stable in the inactive receptor conformation. The in silico docking simulation analysis also revealed that 2-ITX acted as agonist for the goldfish AhR2 LBDs suggesting the ability of this compound to activate the cross-talk between the ERα- and AhR-signaling pathways. In vivo experiments confirm in silico simulation predictions demonstrating that 2-ITX reduced the estrogenicity of E2 at both transcriptional and post-transcriptional levels, indicating a clear anti-estrogenic effect. Co-exposure of E2 and 2-ITX also resulted in a significant decrease of CYP1A gene expression with respect to 2-ITX alone. Results from these studies collectively revealed that the antiestrogenic property of 2-ITX can be ascribed to a combination of effects on multiple signaling pathways suggesting the potential for this environmental contaminant to affect the hormonal control of reproductive processes in fish.
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Affiliation(s)
- Paolo Cocci
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032 Camerino, MC, Italy.
| | - Matteo Mozzicafreddo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032 Camerino, MC, Italy
| | - Mauro Angeletti
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032 Camerino, MC, Italy
| | - Gilberto Mosconi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032 Camerino, MC, Italy
| | - Francesco Alessandro Palermo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano, I-62032 Camerino, MC, Italy
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