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Mosa FES, Alqahtani MA, El-Ghiaty MA, Dyck JRB, Barakat K, El-Kadi AOS. Identification of aryl hydrocarbon receptor allosteric antagonists from clinically approved drugs. Drug Dev Res 2024; 85:e22232. [PMID: 38992915 DOI: 10.1002/ddr.22232] [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: 04/20/2024] [Revised: 06/14/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
The human aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor, plays a pivotal role in a diverse array of pathways in biological and pathophysiological events. This position AhR as a promising target for both carcinogenesis and antitumor strategies. In this study we utilized computational modeling to screen and identify FDA-approved drugs binding to the allosteric site between α2 of bHLH and PAS-A domains of AhR, with the aim of inhibiting its canonical pathway activity. Our findings indicated that nilotinib effectively fits into the allosteric pocket and forms interactions with crucial residues F82, Y76, and Y137. Binding free energy value of nilotinib is the lowest among top hits and maintains stable within its pocket throughout entire (MD) simulations time. Nilotinib has also substantial interactions with F295 and Q383 when it binds to orthosteric site and activate AhR. Surprisingly, it does not influence AhR nuclear translocation in the presence of AhR agonists; instead, it hinders the formation of the functional AhR-ARNT-DNA heterodimer assembly, preventing the upregulation of regulated enzymes like CYP1A1. Importantly, nilotinib exhibits a dual impact on AhR, modulating AhR activity via the PAS-B domain and working as a noncompetitive allosteric antagonist capable of blocking the canonical AhR signaling pathway in the presence of potent AhR agonists. These findings open a new avenue for the repositioning of nilotinib beyond its current application in diverse diseases mediated via AhR.
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Affiliation(s)
- Farag E S Mosa
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mohammed A Alqahtani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mahmoud A El-Ghiaty
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jason R B Dyck
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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2
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Smirnov VM, Lasseaux E, Michaud V, Courdier C, Meunier I, Arveiler B, Defoort-Dhellemmes S. Crossed VEP asymmetry in a patient with AHR-linked infantile nystagmus and foveal hypoplasia. Doc Ophthalmol 2024; 149:47-52. [PMID: 38922562 DOI: 10.1007/s10633-024-09979-6] [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: 12/13/2023] [Accepted: 06/05/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Infantile nystagmus and foveal hypoplasia associated with AHR gene defects is a newly recognized and rare disorder. Our aim was to present a patient with a novel biallelic AHR pathogenic variant with electrophysiological evidence of chiasmal misrouting. MATERIALS AND METHODS Complete ocular examination, fundus imaging, visual evoked potentials (VEP) and full-field electroretinography were performed at initial presentation. Genetic testing was performed by whole exome sequencing. RESULTS Female patient of 6 years old presented a reduced best corrected visual acuity, an infantile nystagmus and a grade III typical foveal hypoplasia without ocular hypopigmentation. A crossed asymmetry was discovered on pattern onset/offset VEP. Genetic testing put in evidence a novel homozygous variant in AHR: c.2242del, p. (Gln748Lysfs*5). During 11-years follow-up period, BCVA gradually improved. There was no evidence of retinal degeneration. CONCLUSION AHR gene defects could be associated with infantile nystagmus, foveal hypoplasia and chiasmal misrouting.
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Affiliation(s)
- Vasily M Smirnov
- Service d'Exploration de la Vision et de Neuro-Ophtalmologie, Hôpital Roger Salengro, CHU de Lille, 59000, Lille, France.
- Inserm, U1172-LilNCog-Lille Neuroscience & Cognition, CHU Lille, Univ. Lille, 59045, Lille, France.
| | - Eulalie Lasseaux
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
- Inserm U1211, Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | - Cécile Courdier
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, Sensgene Care Network, ERN-EYE Network, Montpellier University Hospital, University of Montpellier, 34295, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, 34295, Montpellier, France
| | - Benoit Arveiler
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
- Inserm U1211, Maladies Rares, Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | - Sabine Defoort-Dhellemmes
- Service d'Exploration de la Vision et de Neuro-Ophtalmologie, Hôpital Roger Salengro, CHU de Lille, 59000, Lille, France
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Jindra M, Tumova S, Bittova L, Tuma R, Sedlak D. Agonist-dependent action of the juvenile hormone receptor. CURRENT OPINION IN INSECT SCIENCE 2024; 65:101234. [PMID: 39025365 DOI: 10.1016/j.cois.2024.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Juvenile hormone (JH) signaling is realized at the gene regulatory level by receptors of the bHLH-PAS transcription factor family. The sesquiterpenoid hormones and their synthetic mimics are agonist ligands of a unique JH receptor (JHR) protein, methoprene-tolerant (MET). Upon binding an agonist to its PAS-B cavity, MET dissociates from a cytoplasmic chaperone complex including HSP83 and concomitantly switches to a bHLH-PAS partner taiman, forming a nuclear, transcriptionally active JHR heterodimer. This course of events resembles the vertebrate aryl hydrocarbon receptor (AHR), activated by a plethora of endogenous and synthetic compounds. Like in AHR, the pliable PAS-B cavity of MET adjusts to diverse ligands and binds them through similar mechanisms. Despite recent progress, we only begin to discern agonist-induced conformational shifts within the PAS-B domain, with the ultimate goal of understanding how these localized changes stimulate the assembly of the active JHR complex and, thus, fully grasp the mechanism of JHR signaling.
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Affiliation(s)
- Marek Jindra
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic.
| | - Sarka Tumova
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
| | - Lenka Bittova
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
| | - Roman Tuma
- Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - David Sedlak
- Institute of Entomology, Biology Center of the Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic
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Kisor KP, Ruiz DG, Jacobson MP, Barber DL. A role for pH dynamics regulating transcription factor DNA binding selectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595212. [PMID: 38826444 PMCID: PMC11142074 DOI: 10.1101/2024.05.21.595212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.
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Vyavahare S, Ahluwalia P, Gupta SK, Kolhe R, Hill WD, Hamrick M, Isales CM, Fulzele S. The Role of Aryl Hydrocarbon Receptor in Bone Biology. Int J Tryptophan Res 2024; 17:11786469241246674. [PMID: 38757095 PMCID: PMC11097734 DOI: 10.1177/11786469241246674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, is crucial in maintaining the skeletal system. Our study focuses on encapsulating the role of AhR in bone biology and identifying novel signaling pathways in musculoskeletal pathologies using the GEO dataset. The GEO2R analysis identified 8 genes (CYP1C1, SULT6B1, CYB5A, EDN1, CXCR4B, CTGFA, TIPARP, and CXXC5A) involved in the AhR pathway, which play a pivotal role in bone remodeling. The AhR knockout in hematopoietic stem cells showed alteration in several novel bone-related transcriptomes (eg, Defb14, ZNF 51, and Chrm5). Gene Ontology Enrichment Analysis demonstrated 54 different biological processes associated with bone homeostasis. Mainly, these processes include bone morphogenesis, bone development, bone trabeculae formation, bone resorption, bone maturation, bone mineralization, and bone marrow development. Employing Functional Annotation and Clustering through DAVID, we further uncovered the involvement of the xenobiotic metabolic process, p450 pathway, oxidation-reduction, and nitric oxide biosynthesis process in the AhR signaling pathway. The conflicting evidence of current research of AhR signaling on bone (positive and negative effects) homeostasis may be due to variations in ligand binding affinity, binding sites, half-life, chemical structure, and other unknown factors. In summary, our study provides a comprehensive understanding of the underlying mechanisms of the AhR pathway in bone biology.
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Affiliation(s)
- Sagar Vyavahare
- Department of Medicine, Augusta University, Augusta, GA, USA
| | | | | | - Ravindra Kolhe
- Department of Pathology, Augusta University, Augusta, GA, USA
| | - William D Hill
- Department of Pathology, Medical University of South Carolina, Charleston, SC, USA
| | - Mark Hamrick
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Carlos M Isales
- Department of Medicine, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Sadanand Fulzele
- Department of Medicine, Augusta University, Augusta, GA, USA
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
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6
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Mosa FES, Alqahtani MA, El-Ghiaty MA, Barakat K, El-Kadi AOS. Identifying novel aryl hydrocarbon receptor (AhR) modulators from clinically approved drugs: In silico screening and In vitro validation. Arch Biochem Biophys 2024; 754:109958. [PMID: 38499054 DOI: 10.1016/j.abb.2024.109958] [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: 02/22/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024]
Abstract
The aryl hydrocarbon receptor (AhR) functions as a vital ligand-activated transcription factor, governing both physiological and pathophysiological processes. Notably, it responds to xenobiotics, leading to a diverse array of outcomes. In the context of drug repurposing, we present here a combined approach of utilizing structure-based virtual screening and molecular dynamics simulations. This approach aims to identify potential AhR modulators from Drugbank repository of clinically approved drugs. By focusing on the AhR PAS-B binding pocket, our screening protocol included binding affinities calculations, complex stability, and interactions within the binding site as a filtering method. Comprehensive evaluations of all DrugBank small molecule database revealed ten promising hits. This included flibanserin, butoconazole, luliconazole, naftifine, triclabendazole, rosiglitazone, empagliflozin, benperidol, nebivolol, and zucapsaicin. Each exhibiting diverse binding behaviors and remarkably very low binding free energy. Experimental studies further illuminated their modulation of AhR signaling, and showing that they are consistently reducing AhR activity, except for luliconazole, which intriguingly enhances the AhR activity. This work demonstrates the possibility of using computational modelling as a quick screening tool to predict new AhR modulators from extensive drug libraries. Importantly, these findings hold immense therapeutic potential for addressing AhR-associated disorders. Consequently, it offers compelling prospects for innovative interventions through drug repurposing.
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Affiliation(s)
- Farag E S Mosa
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mohammed A Alqahtani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mahmoud A El-Ghiaty
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada.
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7
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Mosa FES, AlRawashdeh S, El-Kadi AOS, Barakat K. Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. J Chem Inf Model 2024; 64:2021-2034. [PMID: 38457778 DOI: 10.1021/acs.jcim.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates biological signals to control various complicated cellular functions. It plays a crucial role in environmental sensing and xenobiotic metabolism. Dysregulation of AhR is associated with health concerns, including cancer and immune system disorders. Upon binding to AhR ligands, AhR, along with heat shock protein 90 and other partner proteins undergoes a transformation in the nucleus, heterodimerizes with the aryl hydrocarbon receptor nuclear translocator (ARNT), and mediates numerous biological functions by inducing the transcription of various AhR-responsive genes. In this manuscript, the 3-dimensional structure of the entire human AhR is obtained using an artificial intelligence tool, and molecular dynamics (MD) simulations are performed to study different structural conformations. These conformations provide insights into the protein's function and movement in response to ligand binding. Understanding the dynamic behavior of AhR will contribute to the development of targeted therapies for associated health conditions. Therefore, we employ well-tempered metadynamics (WTE-metaD) simulations to explore the conformational landscape of AhR and obtain a better understanding of its functional behavior. Our computational results are in excellent agreement with previous experimental findings, revealing the closed and open states of helix α1 in the basic helix-loop-helix (bHLH domain) in the cytoplasm at the atomic level. We also predict the inactive form of AhR and identify Arginine 42 as a key residue that regulates switching between closed and open conformations in existing AhR modulators.
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Affiliation(s)
- Farag E S Mosa
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Sara AlRawashdeh
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
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8
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Kim Y, Bereketoglu C, Sercinoglu O, Pradhan A. In Vitro, In Vivo, and In Silico Analysis of Pyraclostrobin and Cyprodinil and Their Mixture Reveal New Targets and Signaling Mechanisms. Chem Res Toxicol 2024; 37:497-512. [PMID: 38419406 DOI: 10.1021/acs.chemrestox.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Pyraclostrobin and cyprodinil are broad-spectrum fungicides that are used in crops to control diseases. However, they are excessively used and, as a result, end up in the environment and threaten human health and ecosystems. Hence, knowledge of their mechanisms of action is critical to revealing their environmental fate and negative effects and regulating their use. In the present study, we conducted a comprehensive study to show the adverse effects of pyraclostrobin, cyprodinil, and their mixture using zebrafish larvae and different cell lines. Several end points were investigated, including mortality, development, gene expression, reporter assays, and molecular docking simulations. We found that both compounds and their mixture caused developmental delays and mortality in zebrafish, with a higher effect displayed by pyraclostrobin. Both compounds altered the expression of genes involved in several signaling pathways, including oxidative stress and mitochondrial function, lipid and drug metabolisms, the cell cycle, DNA damage, apoptosis, and inflammation. A noteworthy result of this study is that cyprodinil and the mixture group acted as NFκB activators, while pyraclostrobin demonstrated antagonist activity. The AHR activity was also upregulated by cyprodinil and the mixture group; however, pyraclostrobin did not show any effect. For the first time, we also demonstrated that pyraclostrobin had androgen receptor antagonist activity.
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Affiliation(s)
- Yeju Kim
- Biology, the Life Science Center, School of Science and Technology, Örebro University, Örebro SE-70182, Sweden
| | - Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul 34722, Turkey
| | - Onur Sercinoglu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli 41400, Turkey
| | - Ajay Pradhan
- Biology, the Life Science Center, School of Science and Technology, Örebro University, Örebro SE-70182, Sweden
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9
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Xie H, Yang N, Yu C, Lu L. Uremic toxins mediate kidney diseases: the role of aryl hydrocarbon receptor. Cell Mol Biol Lett 2024; 29:38. [PMID: 38491448 PMCID: PMC10943832 DOI: 10.1186/s11658-024-00550-4] [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: 10/18/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
Aryl hydrocarbon receptor (AhR) was originally identified as an environmental sensor that responds to pollutants. Subsequent research has revealed that AhR recognizes multiple exogenous and endogenous molecules, including uremic toxins retained in the body due to the decline in renal function. Therefore, AhR is also considered to be a uremic toxin receptor. As a ligand-activated transcriptional factor, the activation of AhR is involved in cell differentiation and senescence, lipid metabolism and fibrogenesis. The accumulation of uremic toxins in the body is hazardous to all tissues and organs. The identification of the endogenous uremic toxin receptor opens the door to investigating the precise role and molecular mechanism of tissue and organ damage induced by uremic toxins. This review focuses on summarizing recent findings on the role of AhR activation induced by uremic toxins in chronic kidney disease, diabetic nephropathy and acute kidney injury. Furthermore, potential clinical approaches to mitigate the effects of uremic toxins are explored herein, such as enhancing uremic toxin clearance through dialysis, reducing uremic toxin production through dietary interventions or microbial manipulation, and manipulating metabolic pathways induced by uremic toxins through controlling AhR signaling. This information may also shed light on the mechanism of uremic toxin-induced injury to other organs, and provide insights into clinical approaches to manipulate the accumulated uremic toxins.
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Affiliation(s)
- Hongyan Xie
- Department of Nephrology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Ninghao Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Chen Yu
- Department of Nephrology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China.
| | - Limin Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China.
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10
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Tian H, Wang L, Hardy R, Kozhaya L, Placek L, Fleming E, Oh J, Unutmaz D, Yao X. Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:518-526. [PMID: 38308645 DOI: 10.1021/jasms.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Aryl hydrocarbon receptor (AhR) is a transcription factor that regulates gene expression upon ligand activation, enabling microbiota-dependent induction, training, and function of the host immune system. A spectrum of metabolites, encompassing indole and tryptophan derivatives, have been recognized as activators. This work introduces an integrated, mass spectrometry-centric workflow that employs a bioassay-guided, fractionation-based methodology for the identification of AhR activators derived from human bacterial isolates. By leveraging the workflow efficiency, the complexities inherent in metabolomics profiling are significantly reduced, paving the way for an in-depth and focused mass spectrometry analysis of bioactive fractions isolated from bacterial culture supernatants. Validation of AhR activator candidates used multiple criteria─MS/MS of the synthetic reference compound, bioassay of AhR activity, and elution time confirmation using a C-13 isotopic reference─and was demonstrated for N-formylkynurenine (NFK). The workflow reported provides a roadmap update for improved efficiency of identifying bioactive metabolites using mass spectrometry-based metabolomics. Mass spectrometry datasets are accessible at the National Metabolomics Data Repository (PR001479, Project DOI: 10.21228/M8JM7Q).
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Affiliation(s)
- Huidi Tian
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Rachel Hardy
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Lina Kozhaya
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Lindsey Placek
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Elizabeth Fleming
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Julia Oh
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Derya Unutmaz
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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11
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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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12
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Bonati L, Motta S, Callea L. The AhR Signaling Mechanism: A Structural Point of View. J Mol Biol 2024; 436:168296. [PMID: 37797832 DOI: 10.1016/j.jmb.2023.168296] [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: 07/28/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
The Aryl hydrocarbon Receptor (AhR) is a well-known sensor of xenobiotics; moreover, it is considered a promising drug target as it is involved in the regulation of many patho-physiological processes. For these reasons the study of its ligand-activated transcription mechanism has stimulated several studies for over twenty years. In this review we highlight the key role of molecular structural information in understanding the different steps of the signaling mechanism. The architecture of the AhR cytosolic complex, encompassing the hsp90 chaperone protein and the XAP2 and p23 co-chaperones, has become available in the last year thanks to Cryo-EM experiments. The structure of the AhR ligand-binding (PAS-B) domain has remained elusive for a long time; it has been predicted by homology modelling, based on known PAS systems, and its ligand-bound forms were modelled through ligand molecular docking. Although very recently some structural information on this domain has become available, considerable efforts are still needed to determine the binding geometries of the AhR key ligands by experimental high-resolution studies. On the other hand, the dimeric structure of AhR with the ARNT protein, bound to the specific DNA responsive element, was partially determined by X-ray crystallography and it was completed by homology modelling. On the whole the current structural knowledge of the main protein complexes that form over the AhR mechanism opens the way to confirm and further investigate the main steps of the proposed ligand-activated transcription mechanism of the AhR.
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Affiliation(s)
- Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Lara Callea
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
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Haidar R, Shabo R, Moeser M, Luch A, Kugler J. The nuclear entry of the aryl hydrocarbon receptor (AHR) relies on the first nuclear localization signal and can be negatively regulated through IMPα/β specific inhibitors. Sci Rep 2023; 13:19668. [PMID: 37951956 PMCID: PMC10640566 DOI: 10.1038/s41598-023-47066-z] [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: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Abstract
The human aryl hydrocarbon receptor (AHR) undergoes continuous shuttling between nucleus and cytoplasm. Binding to exogenous or endogenous ligands promotes its rapid nuclear import. The proposed mechanism for the ligand-dependent import is based on exposing the bipartite nuclear localisation signal (NLS) to members of the importin (IMP) superfamily. Among this, the molecular interactions involved in the basal import still need to be clarified. Utilizing fluorescently fused AHR variants, we recapitulated and characterized AHR localization and nucleo-cytoplasmic shuttling in living cells. Analysis of AHR variants carrying NLS point mutations demonstrated a mandatory role of first (13RKRRK17) and second (37KR-R40) NLS segments on the basal import of AHR. Further experiments indicated that ligand-induced import is mainly regulated through the first NLS, while the second NLS is supportive but not essential. Additionally, applying IMPα/β specific inhibitors, ivermectin (IVM) and importazole (IPZ), slowed down the ligand-induced import and, correspondingly, decreased the basal nuclear accumulation of the receptor. In conclusion, our data show that ligand-induced and basal nuclear entry of AHR rely on the same mechanism but are controlled uniquely by the two NLS components.
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Affiliation(s)
- Rashad Haidar
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Reneh Shabo
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Marie Moeser
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Josephine Kugler
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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14
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Liu S, Yan W, Lv Q, Yang L, Miao Y, Hu Y, Wei Z. 3, 3'-diindolylmethane, a natural aryl hydrocarbon receptor agonist, alleviates ulcerative colitis by enhancing "glycolysis-lactate-STAT3″ and TIP60 signals-mediated Treg differentiation. Mol Immunol 2023; 163:147-162. [PMID: 37793204 DOI: 10.1016/j.molimm.2023.09.009] [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: 03/29/2023] [Revised: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Aryl hydrocarbon receptor (AhR) plays an important role in the occurrence and development of ulcerative colitis (UC). In this study, the effect and mechanism of 3, 3'-diindolylmethane (DIM), the classical AhR agonist, on UC was investigated from the angle of recovering the balance of Th17/Treg. METHODS The in vivo colitis model was established in mice by using dextran sulfate sodium, and CD4+ T cells were used to simulate the in vitro differentiation of Treg and Th17 cells. The proportions and related factors of Th17 and Treg cells were measured using flow cytometry, Q-PCR and western blotting. The glycolysis was evaluated by examining the glucose uptake, glucose consumption and lactate production using kits or immunofluorescence. The activation of AhR was detected by western blotting and the XRE-luciferase reporter gene. The co-immunoprecipitation, transfection or other methods were selected to investigate and identify the signaling molecular pathway. RESULTS DIM significantly attenuated symptoms of colitis mice by rebuilding the balance of Th17/Treg in anoxic colons. In hypoxia, a more potent promotion of Treg differentiation was showed by DIM relative to normoxia, and siFoxp3 prevented DIM-suppressed Th17 differentiation. DIM repressed the excessive glycolysis in hypoxia evidenced by down-regulated glucose uptake, lactate production, Glut1 and HK2 levels. Interestingly, IL-10, the function-related factor of Treg cells, showed the feedback effect of DIM-suppressed glycolysis. Besides, 2-deoxy-D-glucose, HK2 plasmid and IL-10 antibody prevented increase of DIM on the expression of Foxp3 at the transcriptional level and subsequent Treg differentiation through the lactate-STAT3 pathway, and reasons for the direct improvement of DIM on Foxp3 protein was attributed to promoting the formation of HIF-1α/TIP60 complexes as well as subsequent acetylation and protein stability. Finally, AhR dependence and mechanisms for DIM-improved Treg differentiation in vitro and in vivo were well confirmed by using plasmids or inhibitors. CONCLUSIONS DIM enhances activation of AhR and subsequent "glycolysis-lactate-STAT3″ and TIP60 signals-mediated Treg differentiation.
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Affiliation(s)
- Shukun Liu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Wenxin Yan
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Qi Lv
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Ling Yang
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Yumeng Miao
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Yuxiao Hu
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China
| | - Zhifeng Wei
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China.
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15
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Li K, Li K, He Y, Liang S, Shui X, Lei W. Aryl hydrocarbon receptor: A bridge linking immuno-inflammation and metabolism in atherosclerosis. Biochem Pharmacol 2023; 216:115744. [PMID: 37579858 DOI: 10.1016/j.bcp.2023.115744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Cardiovascular disease is the leading cause of death worldwide, and atherosclerosis is a major contributor to this etiology. The ligand-activated transcription factor, known as the aryl hydrocarbon receptor (AhR), plays an essential role in the interactions between genes and the environment. In a number of human diseases, including atherosclerosis, the AhR signaling pathway has recently been shown to be aberrantly expressed and activated. It's reported that AhR can regulate the immuno-inflammatory response and metabolism pathways in atherosclerosis, potentially serving as a bridge that links these processes. In this review, we highlight the involvement of AhR in atherosclerosis. From the literature, we conclude that AhR is a potential target for controlling atherosclerosis through precise interventions.
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Affiliation(s)
- Kongwei Li
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Cardiovascular Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Kaiyue Li
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yuan He
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Laboratory of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Shan Liang
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Cardiovascular Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Xiaorong Shui
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Laboratory of Vascular Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.
| | - Wei Lei
- Guangdong Provincial Engineering Technology Research Center for Molecular Diagnosis and Innovative Drugs Translation of Cardiopulmonary Vascular Diseases, University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Department of Precision Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.
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16
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Walter Bock K. Aryl hydrocarbon receptor (AHR): towards understanding intestinal microbial ligands including vitamin B12 and folic acid as natural antagonists. Biochem Pharmacol 2023:115658. [PMID: 37336251 DOI: 10.1016/j.bcp.2023.115658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
AHR has been identified as ligand-modulated transcription factor and environmental sensor. However, explanation of its multiple agonistic and antagonistic ligands is far from complete. Studies of AHR's role in host-microbiome interaction are currently a fruitful area of research. Microbial products and virulence factors have been identified as AHR agonists. In steady state they are involved in safeguarding intestinal barrier integrity. When virulence factors from pathogenic bacteria are identified by AHR of intestinal immune cells, anti-microbial defense mechanisms are activated by generating reactive oxygen species (ROS) in intestinal epithelial cells and recruited immune cells. ROS production has to be strictly controlled, and anti-inflammatory responses have to be initiated timely in the resolution phase of inflammation to avoid tissue damage and chronic inflammatory responses. Surprisingly, bacteria-generated vitamin B12/cobalamin and vitamin B9/folic acid have been identified as natural AHR antagonists, stimulating the interest of biochemists. Hints for AHR-cobalamin antagonism are pointing to cobalamin-dependent enzymes leading to alterations of TCA cycle intermediates, and TCDD-mediated loss of serum cobalamin. Although we are still at the beginning to understand mechanisms, it is likely that scientific efforts are on a rewarding path to understand novel AHR functions.
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Affiliation(s)
- Karl Walter Bock
- Institute of Experimental and Clinical Pharmacology, Wilhelmstrasse 56, D-72074 Tübingen, Germany.
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17
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Ondrová K, Zůvalová I, Vyhlídalová B, Krasulová K, Miková E, Vrzal R, Nádvorník P, Nepal B, Kortagere S, Kopečná M, Kopečný D, Šebela M, Rastinejad F, Pu H, Soural M, Rolfes KM, Haarmann-Stemmann T, Li H, Mani S, Dvořák Z. Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female mice. Nat Commun 2023; 14:2728. [PMID: 37169746 PMCID: PMC10174618 DOI: 10.1038/s41467-023-38478-6] [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: 11/27/2020] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
The human aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that is a pivotal regulator of human physiology and pathophysiology. Allosteric inhibition of AhR was previously thought to be untenable. Here, we identify carvones as noncompetitive, insurmountable antagonists of AhR and characterize the structural and functional consequences of their binding. Carvones do not displace radiolabeled ligands from binding to AhR but instead bind allosterically within the bHLH/PAS-A region of AhR. Carvones do not influence the translocation of ligand-activated AhR into the nucleus but inhibit the heterodimerization of AhR with its canonical partner ARNT and subsequent binding of AhR to the promoter of CYP1A1. As a proof of concept, we demonstrate physiologically relevant Ahr-antagonism by carvones in vivo in female mice. These substances establish the molecular basis for selective targeting of AhR regardless of the type of ligand(s) present and provide opportunities for the treatment of disease processes modified by AhR.
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Affiliation(s)
- Karolína Ondrová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Iveta Zůvalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Barbora Vyhlídalová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kristýna Krasulová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Eva Miková
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Radim Vrzal
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petr Nádvorník
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Binod Nepal
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sandhya Kortagere
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Biochemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Fraydoon Rastinejad
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Hua Pu
- Target Discovery Institute Nuffield Department of Medicine Research Building Brasenose College University of Oxford, Oxford, UK
| | - Miroslav Soural
- Department of Organic Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | | | - Hao Li
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sridhar Mani
- Department of Medicine, Oncology, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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18
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Giordano D, Facchiano A, Moccia S, Meola AMI, Russo GL, Spagnuolo C. Molecular Docking of Natural Compounds for Potential Inhibition of AhR. Foods 2023; 12:foods12101953. [PMID: 37238771 DOI: 10.3390/foods12101953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a highly conserved environmental sensor, historically known for mediating the toxicity of xenobiotics. It is involved in numerous cellular processes such as differentiation, proliferation, immunity, inflammation, homeostasis, and metabolism. It exerts a central role in several conditions such as cancer, inflammation, and aging, acting as a transcription factor belonging to the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) protein family. A key step in the canonical AhR activation is AhR-ARNT heterodimerization followed by the binding to the xenobiotic-responsive elements (XREs). The present work aims to investigate the potential AhR inhibitory activity of selected natural compounds. Due to the absence of a complete structure of human AhRs, a model consisting of the bHLH, the PAS A, and the PAS B domains was constructed. Blind and focused docking simulations revealed the presence of further binding pockets, different from the canonical one presented in the PAS B domain, which could be important for AhR inhibition due to the possibility to impede AhR:ARNT heterodimerization, either preventing conformational changes or masking crucial sites necessary for protein-protein interaction. Two of the compounds retrieved from the docking simulations, i.e., β-carotene and ellagic acid, confirmed their capacity of inhibiting benzo[a]pyrene (BaP)-induced AhR activation in in vitro tests on the human hepatoma cell line HepG2, validating the efficacy of the computational approach.
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Affiliation(s)
- Deborah Giordano
- National Research Council, Institute of Food Sciences, 83100 Avellino, Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Sciences, 83100 Avellino, Italy
| | - Stefania Moccia
- National Research Council, Institute of Food Sciences, 83100 Avellino, Italy
| | | | - Gian Luigi Russo
- National Research Council, Institute of Food Sciences, 83100 Avellino, Italy
| | - Carmela Spagnuolo
- National Research Council, Institute of Food Sciences, 83100 Avellino, Italy
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19
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Lin L, Liu Y, Chen L, Dai Y, Xia Y. Discovery of Norisoboldine Analogue III 11 as a Novel and Potent Aryl Hydrocarbon Receptor Agonist for the Treatment of Ulcerative Colitis. J Med Chem 2023; 66:6869-6888. [PMID: 37154394 DOI: 10.1021/acs.jmedchem.3c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a transcript factor, belonging to the basic helix-loop-helix-Per-ARNT-SIM family, is closely associated with health and diseases. Targeting AhR is an emerging therapeutic strategy for various diseases. Norisoboldine (NOR), which is the main alkaloid of Linderae Radix, has been known to activate AhR. Unfortunately, the oral bioavailability (F) of NOR is only 2.49%. To improve the chemical efficacy and bioavailability, we designed and synthesized NOR analogues. Using various in vitro assays, 2-methoxy-5,6,6a,7-tetrahydro-4H-dibenzo[de,g]quinoline-9-ol (III11) was discovered as a potent AhR agonist. Compound III11 enhanced the expression of AhR downstream target genes, triggered AhR nuclear translocation, and promoted differentiation of regulatory T cells. More importantly, III11 exhibited good bioavailability (F = 87.40%) and remarkable therapeutic effects in a mouse model of ulcerative colitis at a dosage of 10 mg/kg. These findings may serve as a reference for the design of novel AhR agonists against immune and inflammatory diseases.
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Affiliation(s)
- Li Lin
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yongmin Liu
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Li Chen
- Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yue Dai
- Department of Pharmacology of Chinese Materia Medica, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yufeng Xia
- Department of Pharmacognosy, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
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20
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Nguyen BD, Stevens BL, Elson DJ, Finlay D, Gamble J, Kopparapu P, Tanguay RL, Buermeyer AB, Kerkvliet NI, Kolluri SK. 11-Cl-BBQ, a select modulator of AhR-regulated transcription, suppresses lung cancer cell growth via activation of p53 and p27 Kip1. FEBS J 2023; 290:2064-2084. [PMID: 36401795 PMCID: PMC10807707 DOI: 10.1111/febs.16683] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/01/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor and functions as a tumour suppressor in different cancer models. In the present study, we report detailed characterization of 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ) as a select modulator of AhR-regulated transcription (SMAhRT) with anti-cancer actions. Treatment of lung cancer cells with 11-Cl-BBQ induced potent and sustained AhR-dependent anti-proliferative effects by promoting G1 phase cell cycle arrest. Investigation of 11-Cl-BBQ-induced transcription in H460 cells with or without the AhR expression by RNA-sequencing revealed activation of p53 signalling. In addition, 11-Cl-BBQ suppressed multiple pathways involved in DNA replication and increased expression of cyclin-dependent kinase inhibitors, including p27Kip1 , in an AhR-dependent manner. CRISPR/Cas9 knockout of individual genes revealed the requirement for both p53 and p27Kip1 for the AhR-mediated anti-proliferative effects. Our results identify 11-Cl-BBQ as a potential lung cancer therapeutic, highlight the feasibility of targeting AhR and provide important mechanistic insights into AhR-mediated-anticancer actions.
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Affiliation(s)
- Bach D. Nguyen
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Brenna L. Stevens
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Daniel J. Elson
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John Gamble
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Prasad Kopparapu
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robyn L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
| | - Andrew B. Buermeyer
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Nancy I. Kerkvliet
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Siva K. Kolluri
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
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21
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Elson DJ, Kolluri SK. Tumor-Suppressive Functions of the Aryl Hydrocarbon Receptor (AhR) and AhR as a Therapeutic Target in Cancer. BIOLOGY 2023; 12:biology12040526. [PMID: 37106727 PMCID: PMC10135996 DOI: 10.3390/biology12040526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor involved in regulating a wide range of biological responses. A diverse array of xenobiotics and endogenous small molecules bind to the receptor and drive unique phenotypic responses. Due in part to its role in mediating toxic responses to environmental pollutants, AhR activation has not been traditionally viewed as a viable therapeutic approach. Nonetheless, the expression and activation of AhR can inhibit the proliferation, migration, and survival of cancer cells, and many clinically approved drugs transcriptionally activate AhR. Identification of novel select modulators of AhR-regulated transcription that promote tumor suppression is an active area of investigation. The development of AhR-targeted anticancer agents requires a thorough understanding of the molecular mechanisms driving tumor suppression. Here, we summarized the tumor-suppressive mechanisms regulated by AhR with an emphasis on the endogenous functions of the receptor in opposing carcinogenesis. In multiple different cancer models, the deletion of AhR promotes increased tumorigenesis, but a precise understanding of the molecular cues and the genetic targets of AhR involved in this process is lacking. The intent of this review was to synthesize the evidence supporting AhR-dependent tumor suppression and distill insights for development of AhR-targeted cancer therapeutics.
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Affiliation(s)
- Daniel J. Elson
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Siva K. Kolluri
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
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22
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Wen Z, Zhang Y, Zhang B, Hang Y, Xu L, Chen Y, Xie Q, Zhao Q, Zhang L, Li G, Zhao B, Sun F, Zhai Y, Zhu Y. Cryo-EM structure of the cytosolic AhR complex. Structure 2023; 31:295-308.e4. [PMID: 36649707 DOI: 10.1016/j.str.2022.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/24/2022] [Accepted: 12/21/2022] [Indexed: 01/17/2023]
Abstract
Aryl hydrocarbon receptor (AhR) is an important ligand-activated transcription factor involved in the regulation of various important physiological functions. Here, we report the cryo-EM structures of the Hsp90-AhR-p23 complex with or without bound XAP2, where the structure of the mouse AhR PAS-B domain is resolved. A highly conserved bridge motif of AhR is responsible for the interaction with the Hsp90 dimeric lumen. The ligand-free AhR PAS-B domain is attached to the Hsp90 dimer and is stabilized in the complex with bound XAP2. In addition, the DE-loop and a group of conserved pocket inner residues in the AhR PAS-B domain are found to be important for ligand binding. These results reveal the structural basis of the biological functions of AhR. Moreover, the protein purification method presented here allows the isolation of stable mouse AhR protein, which could be used to develop high-sensitivity biosensors for environmental pollutant detection.
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Affiliation(s)
- Zuoling Wen
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Beirong Zhang
- University of Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yumo Hang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yangsheng Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China.
| | - Yujia Zhai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Patil NY, Friedman JE, Joshi AD. Role of Hepatic Aryl Hydrocarbon Receptor in Non-Alcoholic Fatty Liver Disease. RECEPTORS (BASEL, SWITZERLAND) 2023; 2:1-15. [PMID: 37284280 PMCID: PMC10240927 DOI: 10.3390/receptors2010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Numerous nuclear receptors including farnesoid X receptor, liver X receptor, peroxisome proliferator-activated receptors, pregnane X receptor, hepatic nuclear factors have been extensively studied within the context of non-alcoholic fatty liver disease (NAFLD). Following the first description of the Aryl hydrocarbon Receptor (AhR) in the 1970s and decades of research which unveiled its role in toxicity and pathophysiological processes, the functional significance of AhR in NAFLD has not been completely decoded. Recently, multiple research groups have utilized a plethora of in vitro and in vivo models that mimic NAFLD pathology to investigate the functional significance of AhR in fatty liver disease. This review provides a comprehensive account of studies describing both the beneficial and possible detrimental role of AhR in NAFLD. A plausible reconciliation for the paradox indicating AhR as a 'double-edged sword' in NAFLD is discussed. Finally, understanding AhR ligands and their signaling in NAFLD will facilitate us to probe AhR as a potential drug target to design innovative therapeutics against NAFLD in the near future.
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Affiliation(s)
- Nikhil Y. Patil
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
| | - Jacob E. Friedman
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
| | - Aditya D. Joshi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
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24
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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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25
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Alves CC, Arns T, Oliveira ML, Moreau P, Antunes DA, Castelli EC, Mendes-Junior CT, Giuliatti S, Donadi EA. Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene. Hum Immunol 2023:S0198-8859(23)00004-6. [PMID: 36710086 DOI: 10.1016/j.humimm.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/29/2023]
Abstract
We took advantage of the increasingly evolving approaches for in silico studies concerning protein structures, protein molecular dynamics (MD), protein-protein and protein-DNA docking to evaluate: (i) the structure and MD characteristics of the HLA-G well-recognized isoforms, (ii) the impact of missense mutations at HLA-G receptor genes (LILRB1/2), and (iii) the differential binding of the hypoxia-inducible factor 1 (HIF1) to hypoxia-responsive elements (HRE) at the HLA-G gene. Besides reviewing these topics, they were revisited including the following novel results: (i) the HLA-G6 isoforms were unstable docked or not with β2-microglobulin or peptide, (ii) missense mutations at LILRB1/2 genes, exchanging amino acids at the intracellular domain, particularly those located within and around the ITIM motifs, may impact the HLA-G binding strength, and (iii) HREs motifs at the HLA-G promoter or exon 2 regions exhibiting a guanine at their third position present a higher affinity for HIF1 when compared to an adenine at the same position. These data shed some light into the functional aspects of HLA-G, particularly how polymorphisms may influence the role of the molecule. Computational and atomistic studies have provided alternative tools for experimental physical methodologies, which are time-consuming, expensive, demanding large quantities of purified proteins, and exhibit low output.
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Affiliation(s)
- Cinthia C Alves
- Department of Medicine, Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Thaís Arns
- Luxembourg Centre for Systems Biomedicine, Luxembourg
| | - Maria L Oliveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Philippe Moreau
- CEA, DRF-Institut François Jacob, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France; U976 HIPI Unit, IRSL, Université Paris-Cité, Paris, France
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, USA
| | - Erick C Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Silvana Giuliatti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil
| | - Eduardo A Donadi
- Department of Medicine, Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, SP, Brazil.
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26
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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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27
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Cheng Z, Xiong X, Wu F, Zhao Y, Dong R, Jiang S, Fang K, Huang P, Chen G. Network Pharmacology Research Indicates that Wu-Mei-Wan Treats Obesity by Inhibiting Th17 Cell Differentiation and Alleviating Metabolic Inflammation. Comb Chem High Throughput Screen 2023; 26:30-48. [PMID: 35189797 DOI: 10.2174/1386207325666220221121919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Wu-Mei-Wan (WMW), a traditional Chinese medicine (TCM) formula, has a good effect on the treatment of obesity and has been proven helpful to promote the metabolism of adipose tissue. However, its underlying mechanism remains to be studied. This study aims to explore the potential pharmacological mechanism of WMW in the treatment of obesity. METHODS Network pharmacology was used to sort out the relationship between WMW putative targets and obesity-related drug targets or disease targets, which indicated the mechanism of WMW in treating obesity from two aspects of clinical drugs approved by the Food and Drug Administration (FDA) and obesity-related diseases. Databases such as Traditional Chinese Medicine Systems Pharmacology (TCMSP), PubChem, DrugBank, DisGeNET, and Genecards were used to collect information about targets. String platform was used to convert the data into gene symbol of "homo sapiens", and perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. With the Human Protein Reference Database (HPRD) as background data, Cytoscape 3.6.0 software was used to construct a new protein-protein interaction (PPI) network. Mechanism diagrams of key pathways were obtained from the KEGG database. AutoDock Vina software was used to conduct molecular docking verification. RESULTS The number of targets in the overlap between WMW putative targets and obesity-related drug targets accounted for more than 50% of the latter, and HTR3A, SLC6A4, and CYP3A4 were core targets. In obesity-related disease targets-WMW putative targets PPI network, the Th17 cell differentiation pathway, and the IL-17 signaling pathway were key pathways, and the 1st module and the 7th module were central function modules that were highly associated with immunity and inflammation. Molecular docking verified that STAT3, TGFB1, MMP9, AHR, IL1B, and CCL2 were core targets in the treatment of WMW on obesity. CONCLUSION WMW has similar effects on lipid and drug metabolism as the current obesity-related drugs, and is likely to treat obesity by inhibiting Th17 cell differentiation and alleviating metabolic inflammation.
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Affiliation(s)
- Zhe Cheng
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xinyu Xiong
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fan Wu
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Zhao
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ruolan Dong
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shujun Jiang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Fang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Panpan Huang
- Key Laboratory of Chinese Medicine Compound and Chinese Medicine Resources Ministry of Education, Hubei University of Chinese Medicine, Wuhan 430065, China
- Basic Medical Sciences College, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Guang Chen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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28
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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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29
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An overview of aryl hydrocarbon receptor ligands in the Last two decades (2002–2022): A medicinal chemistry perspective. Eur J Med Chem 2022; 244:114845. [DOI: 10.1016/j.ejmech.2022.114845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/21/2022]
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30
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Gruszczyk J, Grandvuillemin L, Lai-Kee-Him J, Paloni M, Savva CG, Germain P, Grimaldi M, Boulahtouf A, Kwong HS, Bous J, Ancelin A, Bechara C, Barducci A, Balaguer P, Bourguet W. Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex. Nat Commun 2022; 13:7010. [PMID: 36385050 PMCID: PMC9668932 DOI: 10.1038/s41467-022-34773-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites. However, the scarcity of structural data precludes understanding of how AHR is activated by such diverse compounds. Our 2.85 Å structure of the human indirubin-bound AHR complex with the chaperone Hsp90 and the co-chaperone XAP2, reported herein, reveals a closed conformation Hsp90 dimer with AHR threaded through its lumen and XAP2 serving as a brace. Importantly, we disclose the long-awaited structure of the AHR PAS-B domain revealing a unique organisation of the ligand-binding pocket and the structural determinants of ligand-binding specificity and promiscuity of the receptor. By providing structural details of the molecular initiating event leading to AHR activation, our study rationalises almost forty years of biochemical data and provides a framework for future mechanistic studies and structure-guided drug design.
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Affiliation(s)
- Jakub Gruszczyk
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
| | - Loïc Grandvuillemin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Josephine Lai-Kee-Him
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Christos G Savva
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester, UK
| | - Pierre Germain
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Marina Grimaldi
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Abdelhay Boulahtouf
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Hok-Sau Kwong
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Aurélie Ancelin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Cherine Bechara
- IGF, University of Montpellier, CNRS, Inserm, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Patrick Balaguer
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - William Bourguet
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
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31
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Dai S, Qu L, Li J, Zhang Y, Jiang L, Wei H, Guo M, Chen X, Chen Y. Structural insight into the ligand binding mechanism of aryl hydrocarbon receptor. Nat Commun 2022; 13:6234. [PMID: 36266304 PMCID: PMC9585082 DOI: 10.1038/s41467-022-33858-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/04/2022] [Indexed: 12/25/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR), a member of the basic helix-loop-helix (bHLH) Per-Arnt-Sim (PAS) family of transcription factors, plays important roles in regulating xenobiotic metabolism, cellular differentiation, stem cell maintenance, as well as immunity. More recently, AHR has gained significant interest as a drug target for the development of novel cancer immunotherapy drugs. Detailed understanding of AHR-ligand binding has been hampered for decades by the lack of a three-dimensional structure of the AHR PAS-B domain. Here, we present multiple crystal structures of the Drosophila AHR PAS-B domain, including its apo, ligand-bound, and AHR nuclear translocator (ARNT) PAS-B-bound forms. Together with biochemical and cellular assays, our data reveal structural features of the AHR PAS-B domain, provide insights into the mechanism of AHR ligand binding, and provide the structural basis for the future development of AHR-targeted therapeutics.
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Affiliation(s)
- Shuyan Dai
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Lingzhi Qu
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Jun Li
- grid.461579.8Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421001 China
| | - Ye Zhang
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Longying Jiang
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Hudie Wei
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Ming Guo
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Xiaojuan Chen
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Yongheng Chen
- grid.216417.70000 0001 0379 7164Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
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Mixture Effects of Tryptophan Intestinal Microbial Metabolites on Aryl Hydrocarbon Receptor Activity. Int J Mol Sci 2022; 23:ijms231810825. [PMID: 36142735 PMCID: PMC9505659 DOI: 10.3390/ijms231810825] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Aryl hydrocarbon receptor (AHR) plays pivotal roles in intestinal physiology and pathophysiology. Intestinal AHR is activated by numerous dietary, endogenous, and microbial ligands. Whereas the effects of individual compounds on AHR are mostly known, the effects of real physiological mixtures occurring in the intestine have not been studied. Using reporter gene assays and RT-PCR, we evaluated the combinatorial effects (3520 combinations) of 11 microbial catabolites of tryptophan (MICTs) on AHR. We robustly (n = 30) determined the potencies and relative efficacies of single MICTs. Synergistic effects of MICT binary mixtures were observed between low- or medium-efficacy agonists, in particular for combinations of indole-3-propionate and indole-3-lactate. Combinations comprising highly efficacious agonists such as indole-3-pyruvate displayed rather antagonist effects, caused by saturation of the assay response. These synergistic effects were confirmed by RT-PCR as CYP1A1 mRNA expression. We also tested mimic multicomponent and binary mixtures of MICTs, prepared based on the metabolomic analyses of human feces and colonoscopy aspirates, respectively. In this case, AHR responsiveness did not correlate with type of diet or health status, and the indole concentrations in the mixtures were determinative of gross AHR activity. Future systematic research on the synergistic activation of AHR by microbial metabolites and other ligands is needed.
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Lee E, Ahn H, Park S, Kim G, Kim H, Noh MG, Kim Y, Yeon JS, Park H. Staphylococcus epidermidis WF2R11 Suppresses PM 2.5-Mediated Activation of the Aryl Hydrocarbon Receptor in HaCaT Keratinocytes. Probiotics Antimicrob Proteins 2022; 14:915-933. [PMID: 35727505 PMCID: PMC9474527 DOI: 10.1007/s12602-022-09922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
The skin supports a diverse microbiome whose imbalance is related to skin inflammation and diseases. Exposure to fine particulate matter (PM2.5), a major air pollutant, can adversely affect the skin microbiota equilibrium. In this study, the effect and mechanism of PM2.5 exposure in HaCaT keratinocytes were investigated. PM2.5 stimulated the aryl hydrocarbon receptor (AhR) to produce reactive oxygen species (ROS) in HaCaT cells, leading to mitochondrial dysfunction and intrinsic mitochondrial apoptosis. We observed that the culture medium derived from a particular skin microbe, Staphylococcus epidermidis WF2R11, remarkably reduced oxidative stress in HaCaT cells caused by PM2.5-mediated activation of the AhR pathway. Staphylococcus epidermidis WF2R11 also exhibited inhibition of ROS-induced inflammatory cytokine secretion. Herein, we demonstrated that S. epidermidis WF2R11 could act as a suppressor of AhRs, affect cell proliferation, and inhibit apoptosis. Our results highlight the importance of the clinical application of skin microbiome interventions in the treatment of inflammatory skin diseases.
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Affiliation(s)
- Eulgi Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hyeok Ahn
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Shinyoung Park
- Genome and Company, Pangyo-ro 253, Bundang-gu, Seoungnam-si, Gyeonggi-do, 13486, Republic of Korea
| | - Gihyeon Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hyun Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Myung-Giun Noh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Yunjae Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Jae-Sung Yeon
- Genome and Company, Pangyo-ro 253, Bundang-gu, Seoungnam-si, Gyeonggi-do, 13486, Republic of Korea
| | - Hansoo Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea. .,Genome and Company, Pangyo-ro 253, Bundang-gu, Seoungnam-si, Gyeonggi-do, 13486, Republic of Korea.
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Grishanova AY, Perepechaeva ML. Aryl Hydrocarbon Receptor in Oxidative Stress as a Double Agent and Its Biological and Therapeutic Significance. Int J Mol Sci 2022; 23:ijms23126719. [PMID: 35743162 PMCID: PMC9224361 DOI: 10.3390/ijms23126719] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/02/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) has long been implicated in the induction of a battery of genes involved in the metabolism of xenobiotics and endogenous compounds. AhR is a ligand-activated transcription factor necessary for the launch of transcriptional responses important in health and disease. In past decades, evidence has accumulated that AhR is associated with the cellular response to oxidative stress, and this property of AhR must be taken into account during investigations into a mechanism of action of xenobiotics that is able to activate AhR or that is susceptible to metabolic activation by enzymes encoded by the genes that are under the control of AhR. In this review, we examine various mechanisms by which AhR takes part in the oxidative-stress response, including antioxidant and prooxidant enzymes and cytochrome P450. We also show that AhR, as a participant in the redox balance and as a modulator of redox signals, is being increasingly studied as a target for a new class of therapeutic compounds and as an explanation for the pathogenesis of some disorders.
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Yu HX, Feng Z, Lin W, Yang K, Liu RQ, Li JQ, Liu XY, Pei M, Yang HT. Ongoing Clinical Trials in Aging-Related Tissue Fibrosis and New Findings Related to AhR Pathways. Aging Dis 2022; 13:732-752. [PMID: 35656117 PMCID: PMC9116921 DOI: 10.14336/ad.2021.1105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/05/2021] [Indexed: 11/06/2022] Open
Abstract
Fibrosis is a pathological manifestation of wound healing that replaces dead/damaged tissue with collagen-rich scar tissue to maintain homeostasis, and complications from fibrosis contribute to nearly half of all deaths in the industrialized world. Ageing is closely associated with a progressive decline in organ function, and the prevalence of tissue fibrosis dramatically increases with age. Despite the heavy clinical and economic burden of organ fibrosis as the population ages, to date, there is a paucity of therapeutic strategies that are specifically designed to slow fibrosis. Aryl hydrocarbon receptor (AhR) is an environment-sensing transcription factor that exacerbates aging phenotypes in different tissues that has been brought back into the spotlight again with economic development since AhR could interact with persistent organic pollutants derived from incomplete waste combustion. In addition, gut microbiota dysbiosis plays a pivotal role in the pathogenesis of numerous diseases, and microbiota-associated tryptophan metabolites are dedicated contributors to fibrogenesis by acting as AhR ligands. Therefore, a better understanding of the effects of tryptophan metabolites on fibrosis modulation through AhR may facilitate the exploitation of new therapeutic avenues for patients with organ fibrosis. In this review, we primarily focus on how tryptophan-derived metabolites are involved in renal fibrosis, idiopathic pulmonary fibrosis, hepatic fibrosis and cardiac fibrosis. Moreover, a series of ongoing clinical trials are highlighted.
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Affiliation(s)
- Hang-Xing Yu
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Zhe Feng
- 3Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Wei Lin
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Kang Yang
- 4Kidney Disease Treatment Center, The first affiliated hospital of Henan university of CM, Zhengzhou, Henan, China
| | - Rui-Qi Liu
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Jia-Qi Li
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Xin-Yue Liu
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Ming Pei
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Hong-Tao Yang
- 1Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,2National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
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Tan YQ, Wang YN, Feng HY, Guo ZY, Li X, Nie XL, Zhao YY. Host/microbiota interactions-derived tryptophan metabolites modulate oxidative stress and inflammation via aryl hydrocarbon receptor signaling. Free Radic Biol Med 2022; 184:30-41. [PMID: 35367341 DOI: 10.1016/j.freeradbiomed.2022.03.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that induces the expression of a broad range of downstream genes such as cytochromes P450 enzymes and cyclooxygenase-2. Recent research focuses are shifting from AhR activation induced by xenobiotics to its response patterns to physiological ligands that expand our understanding of how endogenous metabolites as ligands to modulate AhR signaling pathway under homeostasis and pathological conditions. With increasing interest in AhR and its endogenous ligands, it would seem advisable to summarize a variety of endogenous ligands especially host/gut microbiota-derived tryptophan metabolites. Mounting evidence has indicated that AhR play a critical role in the regulation of redox homeostasis and immune responses. In this review, we outline the canonical and non-canonical AhR signalling pathway that is mediated by host/gut microbiota-derived tryptophan metabolites. Through several typical endogenous AhR ligands, we investigated the molecular mechanisms of AhR-induced oxidative stress and inflammation in the pathological milieu, including diabetes, diabetic kidney disease and end-stage renal disease. Finally, we summarize and emphasize the limitations and breakthrough of endogenous AhR ligands from host/microbial tryptophan catabolites. This review might provide novel diagnostic and prognostic approach for refractory human diseases and establish new therapeutic strategies for AhR activation.
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Affiliation(s)
- Yue-Qi Tan
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Yan-Ni Wang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Hao-Yu Feng
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Zhi-Yuan Guo
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xia Li
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China; Department of General Practice, Xi'an International Medical Center Hospital, Northwest University, No. 777 Xitai Road, Xi'an, Shaanxi, 710100, China.
| | - Xiao-Li Nie
- Department of Nephrology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, No.13, Shi Liu Gang Road, Haizhu District, Guangzhou, Guangdong, 510315, China.
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
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Van Der Ven LT, Van Ommeren P, Zwart EP, Gremmer ER, Hodemaekers HM, Heusinkveld HJ, van Klaveren JD, Rorije E. Dose Addition in the Induction of Craniofacial Malformations in Zebrafish Embryos Exposed to a Complex Mixture of Food-Relevant Chemicals with Dissimilar Modes of Action. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:47003. [PMID: 35394809 PMCID: PMC8992969 DOI: 10.1289/ehp9888] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 02/08/2022] [Accepted: 03/02/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND Humans are exposed to combinations of chemicals. In cumulative risk assessment (CRA), regulatory bodies such as the European Food Safety Authority consider dose addition as a default and sufficiently conservative approach. The principle of dose addition was confirmed previously for inducing craniofacial malformations in zebrafish embryos in binary mixtures of chemicals with either similar or dissimilar modes of action (MOAs). OBJECTIVES In this study, we explored a workflow to select and experimentally test multiple compounds as a complex mixture with each of the compounds at or below its no observed adverse effect level (NOAEL), in the same zebrafish embryo model. METHODS Selection of candidate compounds that potentially induce craniofacial malformations was done using in silico methods-structural similarity, molecular docking, and quantitative structure-activity relationships-applied to a database of chemicals relevant for oral exposure in humans via food (EuroMix inventory, n=1,598). A final subselection was made manually to represent different regulatory fields (e.g., food additives, industrial chemicals, plant protection products), different chemical families, and different MOAs. RESULTS A final selection of eight compounds was examined in the zebrafish embryo model, and craniofacial malformations were observed in embryos exposed to each of the compounds, thus confirming the developmental toxicity as predicted by the in silico methods. When exposed to a mixture of the eight compounds, each at its NOAEL, substantial craniofacial malformations were observed; according to a dose-response analysis, even embryos exposed to a 7-fold dilution of this mixture still exhibited a slight abnormal phenotype. The cumulative effect of the compounds in the mixture was in accordance with dose addition (added doses of the individual compounds after adjustment for relative potencies), despite different MOAs of the compounds involved. DISCUSSION This case study of a complex mixture inducing craniofacial malformations in zebrafish embryos shows that dose addition can adequately predicted the cumulative effect of a mixture of multiple substances at low doses, irrespective of the (expected) MOA. The applied workflow may be useful as an approach for CRA in general. https://doi.org/10.1289/EHP9888.
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Affiliation(s)
- Leo T.M. Van Der Ven
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | - Paul Van Ommeren
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | - Edwin P. Zwart
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | - Eric R. Gremmer
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | - Hennie M. Hodemaekers
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | - Harm J. Heusinkveld
- Centre for Health Protection, Dutch National Institute of Public Health and Environment (RIVM), Bilthoven, Netherlands
| | | | - Emiel Rorije
- Centre for Safety of Substances and Products, RIVM, Bilthoven, Netherlands
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Nieves KM, Hirota SA, Flannigan KL. Xenobiotic receptors and the regulation of intestinal homeostasis: harnessing the chemical output of the intestinal microbiota. Am J Physiol Gastrointest Liver Physiol 2022; 322:G268-G281. [PMID: 34941453 DOI: 10.1152/ajpgi.00160.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The commensal bacteria that reside in the gastrointestinal tract exist in a symbiotic relationship with the host, driving the development of the immune system and maintaining metabolic and tissue homeostasis in the local environment. The intestinal microbiota has the capacity to generate a wide array of chemical metabolites to which the cells of the intestinal mucosa are exposed. Host cells express xenobiotic receptors, such as the aryl hydrocarbon receptor (AhR) and the pregnane X receptor (PXR), that can sense and respond to chemicals that are generated by nonhost pathways. In this review, we outline the physiological and immunological processes within the intestinal environment that are regulated by microbial metabolites through the activation of the AhR and the PXR, with a focus on ligands generated by the stepwise catabolism of tryptophan.
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Affiliation(s)
- Kristoff M Nieves
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Simon A Hirota
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kyle L Flannigan
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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Comprehensive Statistical and Bioinformatics Analysis in the Deciphering of Putative Mechanisms by Which Lipid-Associated GWAS Loci Contribute to Coronary Artery Disease. Biomedicines 2022; 10:biomedicines10020259. [PMID: 35203469 PMCID: PMC8868589 DOI: 10.3390/biomedicines10020259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
The study was designed to evaluate putative mechanisms by which lipid-associated loci identified by genome-wide association studies (GWAS) are involved in the molecular pathogenesis of coronary artery disease (CAD) using a comprehensive statistical and bioinformatics analysis. A total of 1700 unrelated individuals of Slavic origin from the Central Russia, including 991 CAD patients and 709 healthy controls were examined. Sixteen lipid-associated GWAS loci were selected from European studies and genotyped using the MassArray-4 system. The polymorphisms were associated with plasma lipids such as total cholesterol (rs12328675, rs4846914, rs55730499, and rs838880), LDL-cholesterol (rs3764261, rs55730499, rs1689800, and rs838880), HDL-cholesterol (rs3764261) as well as carotid intima-media thickness/CIMT (rs12328675, rs11220463, and rs1689800). Polymorphisms such as rs4420638 of APOC1 (p = 0.009), rs55730499 of LPA (p = 0.0007), rs3136441 of F2 (p < 0.0001), and rs6065906 of PLTP (p = 0.002) showed significant associations with the risk of CAD, regardless of sex, age, and body mass index. A majority of the observed associations were successfully replicated in large independent cohorts. Bioinformatics analysis allowed establishing (1) phenotype-specific and shared epistatic gene–gene and gene–smoking interactions contributing to all studied cardiovascular phenotypes; (2) lipid-associated GWAS loci might be allele-specific binding sites for transcription factors from gene regulatory networks controlling multifaceted molecular mechanisms of atherosclerosis.
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Cannon AS, Nagarkatti PS, Nagarkatti M. Targeting AhR as a Novel Therapeutic Modality against Inflammatory Diseases. Int J Mol Sci 2021; 23:288. [PMID: 35008717 PMCID: PMC8745713 DOI: 10.3390/ijms23010288] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 12/12/2022] Open
Abstract
For decades, activation of Aryl Hydrocarbon Receptor (AhR) was excluded from consideration as a therapeutic approach due to the potential toxic effects of AhR ligands and the induction of the cytochrome P450 enzyme, Cyp1a1, following AhR activation. However, it is now understood that AhR activation not only serves as an environmental sensor that regulates the effects of environmental toxins, but also as a key immunomodulator where ligands induce a variety of cellular and epigenetic mechanisms to attenuate inflammation. Thus, the emergence of further in-depth research into diverse groups of compounds capable of activating this receptor has prompted reconsideration of its use therapeutically. The aim of this review is to summarize the body of research surrounding AhR and its role in regulating inflammation. Specifically, evidence supporting the potential of targeting this receptor to modulate the immune response in inflammatory and autoimmune diseases will be highlighted. Additionally, the opportunities and challenges of developing AhR-based therapies to suppress inflammation will be discussed.
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Affiliation(s)
| | | | - Mitzi Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (A.S.C.); (P.S.N.)
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Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Microbiol Spectr 2021; 9:e0102621. [PMID: 34937179 PMCID: PMC8694187 DOI: 10.1128/spectrum.01026-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
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Alves CC, Donadi EA, Giuliatti S. Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of the HLA-G Promoter Region. Int J Mol Sci 2021; 22:ijms222313046. [PMID: 34884849 PMCID: PMC8657931 DOI: 10.3390/ijms222313046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Human Antigen Leukocyte-G (HLA-G) gene encodes an immune checkpoint molecule that has restricted tissue expression in physiological conditions; however, the gene may be induced in hypoxic conditions by the interaction with the hypoxia inducible factor-1 (HIF1). Hypoxia regulatory elements (HRE) located at the HLA-G promoter region and at exon 2 are the major HIF1 target sites. Since the G allele of the −964G > A transversion induces higher HLA-G expression when compared to the A allele in hypoxic conditions, here we analyzed HIF1-HRE complex interaction at the pair-atom level considering both −964G > A polymorphism alleles. Mouse HIF2 dimer crystal (Protein Data Bank ID: 4ZPK) was used as template to perform homology modelling of human HIF1 quaternary structure using MODELLER v9.14. Two 3D DNA structures were built from 5′GCRTG’3 HRE sequence containing the −964G/A alleles using x3DNA. Protein-DNA docking was performed using the HADDOCK v2.4 server, and non-covalent bonds were computed by DNAproDB server. Molecular dynamic simulation was carried out per 200 ns, using Gromacs v.2019. HIF1 binding in the HRE containing −964G allele results in more hydrogen bonds and van der Waals contact formation than HRE with −964A allele. Protein-DNA complex trajectory analysis revealed that HIF1-HRE-964G complex is more stable. In conclusion, HIF1 binds in a more stable and specific manner at the HRE with G allele.
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Affiliation(s)
- Cinthia C. Alves
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Eduardo A. Donadi
- Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Silvana Giuliatti
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
- Correspondence:
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Vazquez-Rivera E, Rojas B, Parrott JC, Shen AL, Xing Y, Carney PR, Bradfield CA. The aryl hydrocarbon receptor as a model PAS sensor. Toxicol Rep 2021; 9:1-11. [PMID: 34950569 PMCID: PMC8671103 DOI: 10.1016/j.toxrep.2021.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins containing PER-ARNT-SIM (PAS) domains are commonly associated with environmental adaptation in a variety of organisms. The PAS domain is found in proteins throughout Archaea, Bacteria, and Eukarya and often binds small-molecules, supports protein-protein interactions, and transduces input signals to mediate an adaptive physiological response. Signaling events mediated by PAS sensors can occur through induced phosphorelays or genomic events that are often dependent upon PAS domain interactions. In this perspective, we briefly discuss the diversity of PAS domain containing proteins, with particular emphasis on the prototype member, the aryl hydrocarbon receptor (AHR). This ligand-activated transcription factor acts as a sensor of the chemical environment in humans and many chordates. We conclude with the idea that since mammalian PAS proteins often act through PAS-PAS dimers, undocumented interactions of this type may link biological processes that we currently think of as independent. To support this idea, we present a framework to guide future experiments aimed at fully elucidating the spectrum of PAS-PAS interactions with an eye towards understanding how they might influence environmental sensing in human and wildlife populations.
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Affiliation(s)
- Emmanuel Vazquez-Rivera
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Brenda Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Jessica C. Parrott
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Anna L. Shen
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Yongna Xing
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Patrick R. Carney
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Christopher A. Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
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van Daal MT, Folkerts G, Garssen J, Braber S. Pharmacological Modulation of Immune Responses by Nutritional Components. Pharmacol Rev 2021; 73:198-232. [PMID: 34663688 DOI: 10.1124/pharmrev.120.000063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The incidence of noncommunicable diseases (NCDs) has increased over the last few decades, and one of the major contributors to this is lifestyle, especially diet. High intake of saturated fatty acids and low intake of dietary fiber is linked to an increase in NCDs. Conversely, a low intake of saturated fatty acids and a high intake of dietary fiber seem to have a protective effect on general health. Several mechanisms have been identified that underlie this phenomenon. In this review, we focus on pharmacological receptors, including the aryl hydrocarbon receptor, binding partners of the retinoid X receptor, G-coupled protein receptors, and toll-like receptors, which can be activated by nutritional components and their metabolites. Depending on the nutritional component and the receptors involved, both proinflammatory and anti-inflammatory effects occur, leading to an altered immune response. These insights may provide opportunities for the prevention and treatment of NCDs and their inherent (sub)chronic inflammation. SIGNIFICANCE STATEMENT: This review summarizes the reported effects of nutritional components and their metabolites on the immune system through manipulation of specific (pharmacological) receptors, including the aryl hydrocarbon receptor, binding partners of the retinoid X receptor, G-coupled protein receptors, and toll-like receptors. Nutritional components, such as vitamins, fibers, and unsaturated fatty acids are able to resolve inflammation, whereas saturated fatty acids tend to exhibit proinflammatory effects. This may aid decision makers and scientists in developing strategies to decrease the incidence of noncommunicable diseases.
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Affiliation(s)
- Marthe T van Daal
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG, Utrecht, The Netherlands (M.T.v.D., G.F., J.G., S.B.); and Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands (J.G.)
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG, Utrecht, The Netherlands (M.T.v.D., G.F., J.G., S.B.); and Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands (J.G.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG, Utrecht, The Netherlands (M.T.v.D., G.F., J.G., S.B.); and Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands (J.G.)
| | - Saskia Braber
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG, Utrecht, The Netherlands (M.T.v.D., G.F., J.G., S.B.); and Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands (J.G.)
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45
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Lim TX, Ahamed M, Reutens DC. The aryl hydrocarbon receptor: A diagnostic and therapeutic target in glioma. Drug Discov Today 2021; 27:422-435. [PMID: 34624509 DOI: 10.1016/j.drudis.2021.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/29/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022]
Abstract
Glioblastoma multiforme (GBM) is a deadly disease; 5-year survival rates have shown little improvement over the past 30 years. In vivo positron emission tomography (PET) imaging is an important method of identifying potential diagnostic and therapeutic molecular targets non-invasively. The aryl hydrocarbon receptor (AhR) is a transcription factor that regulates multiple genes involved in immune response modulation and tumorigenesis. The AhR is an attractive potential drug target and studies have shown that its activation by small molecules can modulate innate and adaptive immunity beneficially and prevent AhR-mediated tumour promotion in several cancer types. In this review, we provide an overview of the role of the AhR in glioma tumorigenesis and highlight its potential as an emerging biomarker for glioma therapies targeting the tumour immune response and PET diagnostics.
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Affiliation(s)
- Ting Xiang Lim
- ARC Centre for Innovation in Biomedical Imaging Technology, Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Muneer Ahamed
- ARC Centre for Innovation in Biomedical Imaging Technology, Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - David C Reutens
- ARC Centre for Innovation in Biomedical Imaging Technology, Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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47
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The role of DNA-binding and ARNT dimerization on the nucleo-cytoplasmic translocation of the aryl hydrocarbon receptor. Sci Rep 2021; 11:18194. [PMID: 34521881 PMCID: PMC8440571 DOI: 10.1038/s41598-021-97507-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 01/19/2023] Open
Abstract
The human aryl hydrocarbon receptor (AHR) is predominantly located in the cytoplasm, while activation depends on its nuclear translocation. Binding to endogenous or xenobiotic ligands terminates the basal nucleo-cytoplasmic shuttling and stabilizes an exclusive nuclear population. The precise mechanisms that facilitate such stable nuclear accumulation remain to be clarified as essential step in the activation cascade. In this study, we have tested whether the sustained nuclear compartmentalization of ligand-bound or basal AHR might further require heterodimerization with the AHR-nuclear translocator (ARNT) and binding to the cognate XRE-motif. Mutagenesis of the DNA-binding motif or of selected individual residues in the ARNT-binding motif did not lead to any variation in AHR’s nucleo-cytoplasmic distribution. In response to ligands, all mutants were retained in the nucleus demonstrating that the stable compartmentalization of activated AHR in the nucleus is neither dependent on interactions with DNA, nor ARNT. Knocking down the ARNT gene using small interfering RNA confirmed that ARNT does not play any role in the intracellular trafficking of AHR.
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48
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Bai Y, Zhu P, Zhou K, Zhang SG. Effect of the acid suppressor omeprazole on the proliferation, migration, invasion and cell cycle of esophageal squamous cell carcinoma cells via the aryl hydrocarbon receptor pathway. Exp Ther Med 2021; 22:1187. [PMID: 34475977 PMCID: PMC8406681 DOI: 10.3892/etm.2021.10621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Esophageal cancer is a malignant tumor type with one of the highest mortality rates worldwide. The aryl hydrocarbon receptor (AHR), which has been investigated in recent years, has been confirmed to be associated with the occurrence and development of esophageal cancer. AHR has a variety of different ligands, which regulate its activity following binding. The widely known acid inhibitor omeprazole (OME) also affects AHR and its downstream proteins (such as the cytochrome P450 family) by non-ligand binding; however, the mechanisms have remained to be fully elucidated. Therefore, the aim of the present study was to investigate the role of OME in esophageal squamous cell carcinoma (ESCC), whether the mechanism proceeds via the AHR pathway and how OME regulates AHR to affect the occurrence and development of esophageal carcinoma. The AHR-selective regulator OME was used to treat the ESCC cell lines TE1 and KYSE150. Western blot analysis was used to verify the effect of OME on AHR and proliferating cell nuclear antigen (PCNA) protein expression levels, while Cell Counting Kit (CCK)-8, wound-healing and Transwell assays were used to determine the proliferation, migration and invasion of the ESCCs, respectively, following treatment with OME. In addition, flow cytometry was used to investigate the cell cycle distribution of the ESCCs following incubation with OME. AHR was highly expressed in the ESCCs and following treatment with OME, the protein expression levels of AHR and PCNA were downregulated. The CCK-8 assay indicated that the proliferation of the ESCCs was also reduced following treatment with OME. Furthermore, flow cytometry revealed a notable block of the cells in G1/G0 phase, while the results of the wound-healing and Transwell assays respectively suggested that cell migration and invasion were reduced. In conclusion, OME inhibited the proliferation, migration and invasion of ESCC cells and blocked the cell cycle via the AHR pathway, which may provide a therapeutic effect on esophageal squamous cell cancer.
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Affiliation(s)
- Yu Bai
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Peiyao Zhu
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Kun Zhou
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Shu-Guang Zhang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Zhou Y, Zhao WJ, Quan W, Qiao CM, Cui C, Hong H, Shi Y, Niu GY, Zhao LP, Shen YQ. Dynamic changes of activated AHR in microglia and astrocytes in the substantia nigra-striatum system in an MPTP-induced Parkinson's disease mouse model. Brain Res Bull 2021; 176:174-183. [PMID: 34478811 DOI: 10.1016/j.brainresbull.2021.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/10/2021] [Accepted: 08/29/2021] [Indexed: 01/19/2023]
Abstract
Aryl Hydrocarbon Receptor (AHR) is a ligand-activated transcription factor expressed in various brain regions. However, little is known about the role of AHR during neuroinflammation in the 1-methyl-4-phenyl-1,2,3,6-tetrathydropyridine (MPTP)-induced Parkinson's disease (PD) mouse model. Here, mice were sacrificed at day 4, day 6 and day 8 respectively after MPTP or saline treatment. Behavioral tests, Tyrosine hydroxylase (TH) expression, glial reaction, and AHR expression and activation were then assayed. As expected, mice treated with MPTP showed apparent behavioral dysfunctions and significantly reduced TH content. Immunofluorescence (IF) labeling showed an increased trend of phosphorylated AHR activation in the Substantia Nigra pars compacta (SNpc) and striatum after MPTP treatment. Western blot analysis demonstrated that MPTP treatment induced a significantly increased level of AHR at each time point tested, with the highest level observed at day 6 in the striatum. To determine exactly the AHR activation in relation to changes of glial cell reactivity, double IF labeling was performed for either IBA1 (microglia marker) and p-AHR, or GFAP (astrocyte marker) and p-AHR. The results demonstrated that MPTP treatment not only increases the number of p-AHR-positive IBA1-expressing cells in the striatum and the SNpc, but also increases that of p-AHR-positive GFAP-expressing cells in the striatum. Intriguingly, the increase of the number of cells co-expressing both p-AHR and IBA1 was highest at day 4 in response to MPTP in the striatum and at day 8 in the SNpc. The number of cells co-expressing both p-AHR and GFAP was increased at days 4, 6 and 8 in the striatum. In conclusion, our study suggests that AHR activation may facilitate PD diagnosis and serve as a target for the treatment of PD.
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Affiliation(s)
- Yu Zhou
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei-Jiang Zhao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
| | - Wei Quan
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Chen-Meng Qiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Chun Cui
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Hong
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yun Shi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Gu-Yu Niu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Li-Ping Zhao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Qin Shen
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Neurodegeneration and Injury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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50
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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. ACTA ACUST UNITED AC 2021; 2:723-740. [DOI: 10.1038/s43018-021-00201-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022]
Abstract
AbstractThe dynamics and phenotypes of intratumoral myeloid cells during tumor progression are poorly understood. Here we define myeloid cellular states in gliomas by longitudinal single-cell profiling and demonstrate their strict control by the tumor genotype: in isocitrate dehydrogenase (IDH)-mutant tumors, differentiation of infiltrating myeloid cells is blocked, resulting in an immature phenotype. In late-stage gliomas, monocyte-derived macrophages drive tolerogenic alignment of the microenvironment, thus preventing T cell response. We define the IDH-dependent tumor education of infiltrating macrophages to be causally related to a complex re-orchestration of tryptophan metabolism, resulting in activation of the aryl hydrocarbon receptor. We further show that the altered metabolism of IDH-mutant gliomas maintains this axis in bystander cells and that pharmacological inhibition of tryptophan metabolism can reverse immunosuppression. In conclusion, we provide evidence of a glioma genotype-dependent intratumoral network of resident and recruited myeloid cells and identify tryptophan metabolism as a target for immunotherapy of IDH-mutant tumors.
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