230 results on '"Soshilov, A"'
Search Results
2. Modeling the transplacental transfer of small molecules using machine learning: a case study on per- and polyfluorinated substances (PFAS)
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Abrahamsson, Dimitri, Siddharth, Adi, Robinson, Joshua F, Soshilov, Anatoly, Elmore, Sarah, Cogliano, Vincent, Ng, Carla, Khan, Elaine, Ashton, Randolph, Chiu, Weihsueh A, Fung, Jennifer, Zeise, Lauren, and Woodruff, Tracey J
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Epidemiology ,Public Health ,Health Sciences ,Pediatric ,Good Health and Well Being ,Humans ,Machine Learning ,Exposure modeling ,Child exposure ,health ,Empirical ,statistical models ,PFAS ,Child exposure/health ,Empirical/statistical models ,Chemical Sciences ,Environmental Sciences ,Medical and Health Sciences ,Public health - Abstract
BackgroundDespite their large numbers and widespread use, very little is known about the extent to which per- and polyfluoroalkyl substances (PFAS) can cross the placenta and expose the developing fetus.ObjectiveThe aim of our study is to develop a computational approach that can be used to evaluate the of extend to which small molecules, and in particular PFAS, can cross to cross the placenta and partition to cord blood.MethodsWe collected experimental values of the concentration ratio between cord and maternal blood (RCM) for 260 chemical compounds and calculated their physicochemical descriptors using the cheminformatics package Mordred. We used the compiled database to, train and test an artificial neural network (ANN). And then applied the best performing model to predict RCM for a large dataset of PFAS chemicals (n = 7982). We, finally, examined the calculated physicochemical descriptors of the chemicals to identify which properties correlated significantly with RCM.ResultsWe determined that 7855 compounds were within the applicability domain and 127 compounds are outside the applicability domain of our model. Our predictions of RCM for PFAS suggested that 3623 compounds had a log RCM > 0 indicating preferable partitioning to cord blood. Some examples of these compounds were bisphenol AF, 2,2-bis(4-aminophenyl)hexafluoropropane, and nonafluoro-tert-butyl 3-methylbutyrate.SignificanceThese observations have important public health implications as many PFAS have been shown to interfere with fetal development. In addition, as these compounds are highly persistent and many of them can readily cross the placenta, they are expected to remain in the population for a long time as they are being passed from parent to offspring.ImpactUnderstanding the behavior of chemicals in the human body during pregnancy is critical in preventing harmful exposures during critical periods of development. Many chemicals can cross the placenta and expose the fetus, however, the mechanism by which this transport occurs is not well understood. In our study, we developed a machine learning model that describes the transplacental transfer of chemicals as a function of their physicochemical properties. The model was then used to make predictions for a set of 7982 per- and polyfluorinated alkyl substances that are listed on EPA's CompTox Chemicals Dashboard. The model can be applied to make predictions for other chemical categories of interest, such as plasticizers and pesticides. Accurate predictions of RCM can help scientists and regulators to prioritize chemicals that have the potential to cause harm by exposing the fetus.
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- 2022
3. Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form.
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Soshilov, Anatoly A, Motta, Stefano, Bonati, Laura, and Denison, Michael S
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2 ,3 ,7 ,8-tetrachlorodibenzo-p-dioxin ,ARNT ,AhR ,TCDD ,aryl hydrocarbon receptor ,aryl hydrocarbon receptor nuclear translocator ,heat shock protein 90 ,hsp90 ,molybdate ,2 ,3 ,7 ,8-tetrachlorodibenzo-p-dioxin ,Other Chemical Sciences ,Genetics ,Other Biological Sciences ,Chemical Physics - Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of an AhR lacking the entire PASB structurally diverse chemicals, including halogenated aromatic hydrocarbons. Ligand-dependent transformation of the AhR into its DNA binding form involves a ligand-dependent conformational change, heat shock protein 90 (hsp90), dissociation from the AhR complex and AhR dimerization with the AhR nuclear translocator (ARNT) protein. The mechanism of AhR transformation was examined using mutational approaches and stabilization of the AhR:hsp90 complex with sodium molybdate. Insertion of a single mutation (F281A) in the hsp90-binding region of the AhR resulted in its constitutive (ligand-independent) transformation/DNA binding in vitro. Mutations of AhR residues within the Arg-Cys-rich region (R212A, R217A, R219A) and Asp371 (D371A) impaired AhR transformation without a significant effect on ligand binding. Stabilization of AhR:hsp90 binding with sodium molybdate decreased transformation/DNA binding of the wild type AhR but had no effect on constitutively active AhR mutants. Interestingly, transformation of the AhR in the presence of molybdate allowed detection of an intermediate transformation ternary complex containing hsp90, AhR, and ARNT. These results are consistent with a stepwise transformation mechanism in which binding of ARNT to the liganded AhR:hsp90 complex results in a progressive displacement of hsp90 and conversion of the AhR into its high affinity DNA binding form. The available molecular insights into the signaling mechanism of other Per-ARNT-Sim (PAS) domains and structural information on hsp90 association with other client proteins are consistent with the proposed transformation mechanism of the AhR.
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- 2020
4. Sustained activation of the Aryl hydrocarbon Receptor transcription factor promotes resistance to BRAF-inhibitors in melanoma.
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Corre, Sébastien, Tardif, Nina, Mouchet, Nicolas, Leclair, Héloïse M, Boussemart, Lise, Gautron, Arthur, Bachelot, Laura, Perrot, Anthony, Soshilov, Anatoly, Rogiers, Aljosja, Rambow, Florian, Dumontet, Erwan, Tarte, Karin, Bessede, Alban, Guillemin, Gilles J, Marine, Jean-Christophe, Denison, Michael S, Gilot, David, and Galibert, Marie-Dominique
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Cell Line ,Tumor ,Animals ,Humans ,Mice ,Mice ,SCID ,Melanoma ,Skin Neoplasms ,Oximes ,Imidazoles ,Proto-Oncogene Proteins B-raf ,Receptors ,Aryl Hydrocarbon ,Transcription Factors ,Enzyme Inhibitors ,Protein Kinase Inhibitors ,Tumor Burden ,Xenograft Model Antitumor Assays ,Drug Resistance ,Neoplasm ,Mutation ,MCF-7 Cells ,Molecular Docking Simulation ,Resveratrol ,Vemurafenib ,Cancer ,Genetics ,2.1 Biological and endogenous factors ,5.1 Pharmaceuticals ,Cell Line ,Tumor ,SCID ,Receptors ,Aryl Hydrocarbon ,Drug Resistance ,Neoplasm ,MD Multidisciplinary - Abstract
BRAF inhibitors target the BRAF-V600E/K mutated kinase, the driver mutation found in 50% of cutaneous melanoma. They give unprecedented anti-tumor responses but acquisition of resistance ultimately limits their clinical benefit. The master regulators driving the expression of resistance-genes remain poorly understood. Here, we demonstrate that the Aryl hydrocarbon Receptor (AhR) transcription factor is constitutively activated in a subset of melanoma cells, promoting the dedifferentiation of melanoma cells and the expression of BRAFi-resistance genes. Typically, under BRAFi pressure, death of BRAFi-sensitive cells leads to an enrichment of a small subpopulation of AhR-activated and BRAFi-persister cells, responsible for relapse. Also, differentiated and BRAFi-sensitive cells can be redirected towards an AhR-dependent resistant program using AhR agonists. We thus identify Resveratrol, a clinically compatible AhR-antagonist that abrogates deleterious AhR sustained-activation. Combined with BRAFi, Resveratrol reduces the number of BRAFi-resistant cells and delays tumor growth. We thus propose AhR-impairment as a strategy to overcome melanoma resistance.
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- 2018
5. Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist.
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Faber, Samantha C, Soshilov, Anatoly A, Giani Tagliabue, Sara, Bonati, Laura, and Denison, Michael S
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Animals ,Humans ,Mice ,Indoles ,Receptors ,Aryl Hydrocarbon ,Mutagenesis ,Site-Directed ,Species Specificity ,Binding Sites ,Protein Structure ,Secondary ,Protein Binding ,Models ,Molecular ,Computer Simulation ,Basic Helix-Loop-Helix Transcription Factors ,Molecular Docking Simulation ,In Vitro Techniques ,Polychlorinated Dibenzodioxins ,Ah receptor ,AhR ,TCDD ,in silico ,in vitro ,indirubin ,Chemical Physics ,Other Chemical Sciences ,Genetics ,Other Biological Sciences - Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that modulates gene expression following its binding and activation by structurally diverse chemicals. Species differences in AhR functionality have been observed, with the mouse AhR (mAhR) and human AhR (hAhR) exhibiting significant differences in ligand binding, coactivator recruitment, gene expression and response. While the AhR agonist indirubin (IR) is a more potent activator of hAhR-dependent gene expression than the prototypical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), it is a significantly less potent activator of the mAhR. DNA binding analysis confirmed the greater potency/efficacy of IR in stimulating transformation/DNA binding of the hAhR in vitro and domain-swapping experiments demonstrated that the enhanced response to IR was primarily due to the hAhR ligand binding domain (LBD). Site-directed mutagenesis and functional analysis studies revealed that mutation of H326 and A349 in the mAhR LBD to the corresponding residues in the hAhR LBD significantly increased the potency of IR. Since these mutations had no significant effect on ligand binding, these residues likely contribute to an enhanced efficiency of transformation/DNA binding by IR-bound hAhR. Molecular docking to mAhR LBD homology models further elucidated the different roles of the A375V mutation in TCDD and IR binding, as revealed by [³H]TCDD competitive binding results. These results demonstrate the differential binding of structurally diverse ligands within the LBD of a given AhR and confirm that amino acid differences within the LBD of AhRs contribute to significant species differences in ligand response.
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- 2018
6. Editor’s Highlight: Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure–Activity Relationships and Receptor Modeling
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Cheng, Yating, Jin, Un-Ho, Davidson, Laurie A, Chapkin, Robert S, Jayaraman, Arul, Tamamis, Phanourios, Orr, Asuka, Allred, Clint, Denison, Michael S, Soshilov, Anatoly, Weaver, Evelyn, and Safe, Stephen
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Digestive Diseases ,5.1 Pharmaceuticals ,Development of treatments and therapeutic interventions ,Cancer ,Animals ,Caco-2 Cells ,Cell Line ,Cytochrome P-450 CYP1A1 ,Cytochrome P-450 CYP1B1 ,Guinea Pigs ,Humans ,Mice ,Models ,Theoretical ,Naphthalenes ,Naphthols ,Polychlorinated Dibenzodioxins ,Receptors ,Aryl Hydrocarbon ,Structure-Activity Relationship ,1 ,4-DHNA ,structure-activity ,Ah receptor ,agonists ,antagonists ,antagonists. ,Toxicology ,Pharmacology and pharmaceutical sciences - Abstract
1,4-Dihydroxy-2-naphthoic acid (1,4-DHNA) is a bacterial-derived metabolite that binds the aryl hydrocarbon receptor (AhR) and exhibits anti-inflammatory activity in the gut. The structure-dependent AhR activity of hydroxyl/carboxy-substituted naphthoic acids (NAs) was determined in young adult mouse colonic (YAMC) cells and human Caco2 colon cancer cells using CYP1A1/CYP1B1 mRNAs as Ah-responsive genes. Compounds used in this study include 1,4-, 3,5-, and 3,7-DHNA, 1,4-dimethoxy-2-naphthoic acid (1,4-DMNA), 1- and 4-hydroxy-2-naphthoic acid (1-HNA, 4-HNA), 1- and 2-naphthoic acid (1-NA, 2-NA), and 1- and 2-naphthol (1-NOH, 2-NOH). 1,4-DHNA was the most potent compound among hydroxyl/carboxy naphthalene derivatives, and the fold induction response for CYP1A1 and CYP1B1 was similar to that observed for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in YAMC and Caco2 cells. 1- and 4-HNA were less potent than 1,4-DHNA but induced maximal (TCDD-like) response for CYP1B1 (both cell lines) and CYP1A1 (Caco2 cells). With the exception of 1- and 2-NA, all compounds significantly induced Cyp1b1 in YAMC cells and these responses were not observed in AhR-deficient YAMC cells generated using CRISPR/Cas9 technology. In addition, we also observed that 1- and 2-NOH (and 1,4-DHNA) were weak AhR agonists, and 1- and 2-NOH also exhibited partial AhR antagonist activity. Structure-activity relationship studies for CYP1A1 but not CYP1B1 were similar in both cell lines, and CYP1A1 induction required one or both 1,4-dihydroxy substituents and activity was significantly enhanced by the 2-carboxyl group. We also used computational analysis to show that 1,4-DHNA and TCDD share similar interactions within the AhR binding pocket and differ primarily due to the negatively charged group of 1,4-DHNA.
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- 2017
7. Auto-induction mechanism of aryl hydrocarbon receptor 2 (AHR2) gene by TCDD-activated AHR1 and AHR2 in the red seabream (Pagrus major)
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Bak, Su-Min, Iida, Midori, Soshilov, Anatoly A, Denison, Michael S, Iwata, Hisato, and Kim, Eun-Young
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Agent Orange & Dioxin ,Biotechnology ,Genetics ,Prevention ,5' Flanking Region ,Animals ,COS Cells ,Chlorocebus aethiops ,Clone Cells ,Electrophoretic Mobility Shift Assay ,Fish Proteins ,Guinea Pigs ,Ligands ,Mutation ,Polychlorinated Dibenzodioxins ,Promoter Regions ,Genetic ,Protein Isoforms ,RNA ,Messenger ,Receptors ,Aryl Hydrocarbon ,Recombinant Proteins ,Response Elements ,Sea Bream ,Sequence Analysis ,DNA ,Transcriptional Activation ,Up-Regulation ,Water Pollutants ,Aryl hydrocarbon receptor ,Auto-induction ,Xenobiotic-responsive elements ,2 ,3 ,7 ,8-Tetrachlorodibenzo-p-dioxin ,Red seabream ,Toxicology ,Biochemistry and cell biology ,Pharmacology and pharmaceutical sciences - Abstract
The toxic effects of dioxins and related compounds (DRCs) are mediated by the aryl hydrocarbon receptor (AHR). Our previous study identified AHR1 and AHR2 genes from the red seabream (Pagrus major). Moreover, we found that AHR2 mRNA levels were notably elevated by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure in the early life stage of red seabream embryos, while AHR1 mRNA level was not altered. In this study, to investigate the regulatory mechanism of these AHR transcripts, we cloned and characterized 5'-flanking regions of AHR1 and AHR2 genes. Both of the 5'-flanking regions in these AHR genes contained three potential xenobiotic-responsive elements (XREs). To assess whether the 5'-flanking region is transactivated by rsAHR1 and rsAHR2 proteins, we measured the transactivation potency of the luciferase reporter plasmids containing the 5'-flanking regions by AHR1 and AHR2 proteins that were transiently co-expressed in COS-7. Only reporter plasmid (pGL4-rsAHR2-3XREs) that contained three putative XRE sites in the 5'-flanking region of AHR2 gene showed a clear TCDD dose-dependent transactivation by AHR1 and AHR2 proteins. TCDD-EC50 values for the rsAHR2-derived XRE transactivation were 1.3 and 1.4 nM for AHR1 and AHR2, respectively. These results suggest that the putative XREs of AHR2 gene have a function for AHR1- and AHR2-mediated transactivation, supporting our in ovo observation of an induction of AHR2 mRNA levels by TCDD exposure. Mutations in XREs of AHR2 gene led to a decrease in luciferase induction. Electrophoretic mobility shift assay showed that XRE1, the closest XRE from the start codon in AHR2 gene, is mainly responsible for the binding with TCDD-activated AHR. This suggests that TCDD-activated AHR1 and AHR2 up-regulate the AHR2 mRNA levels and this auto-induced AHR2 may amplify the signal transduction of its downstream targets including CYP1A in the red seabream.
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- 2017
8. Structure-based virtual screening of perfluoroalkyl and polyfluoroalkyl substances (PFASs) as endocrine disruptors of androgen receptor activity using molecular docking and machine learning
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Azhagiya Singam, Ettayapuram Ramaprasad, Tachachartvanich, Phum, Fourches, Denis, Soshilov, Anatoly, Hsieh, Jennifer C.Y., La Merrill, Michele A., Smith, Martyn T., and Durkin, Kathleen A.
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- 2020
- Full Text
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9. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.
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Corrada, Dario, Soshilov, Anatoly A, Denison, Michael S, and Bonati, Laura
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Humans ,Receptors ,Aryl Hydrocarbon ,Computational Biology ,Mutation ,Models ,Molecular ,Aryl Hydrocarbon Receptor Nuclear Translocator ,Protein Domains ,Bioinformatics ,Biological Sciences ,Information and Computing Sciences ,Mathematical Sciences - Abstract
The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the functional activity of the AhR.
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- 2016
10. Activation of the aryl hydrocarbon receptor by the widely used Src family kinase inhibitor 4-amino-5-(4-chlorophenyl)-7-(dimethylethyl)pyrazolo[3,4-d]pyrimidine (PP2)
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Frauenstein, Katrin, Tigges, Julia, Soshilov, Anatoly A, Kado, Sarah, Raab, Nadeshda, Fritsche, Ellen, Haendeler, Judith, Denison, Michael S, Vogel, Christoph FA, and Haarmann-Stemmann, Thomas
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Biochemistry and Cell Biology ,Biological Sciences ,Biotechnology ,Cytochrome P-450 CYP1A1 ,Dose-Response Relationship ,Drug ,Electrophoretic Mobility Shift Assay ,Gene Expression ,Genes ,Reporter ,Hep G2 Cells ,Humans ,Keratinocytes ,Ligands ,Protein Binding ,Pyrimidines ,RNA Interference ,RNA ,Messenger ,Receptors ,Aryl Hydrocarbon ,src-Family Kinases ,Aryl hydrocarbon receptor ,CYP1A1 ,PP2 ,Off-target effect ,Src family kinase ,Pharmacology and Pharmaceutical Sciences ,Toxicology ,Biochemistry and cell biology ,Pharmacology and pharmaceutical sciences - Abstract
Small molecular weight protein kinase inhibitors are frequently used tools to unravel the complex network of cellular signal transduction under certain physiological and pathophysiological conditions. 4-amino-5-(4-chlorophenyl)-7-(dimethylethyl)pyrazolo[3,4-d]pyrimidine (PP2) is a widely used compound to block the activity of Src family kinases, the major group of non-receptor tyrosine kinases, which trigger multiple cellular signaling pathways. Here, we show that PP2 induces cytochrome P450 1A1 mRNA expression and enzyme activity in a dose-dependent manner in human HepG2 hepatoma cells and NCTC 2544 keratinocytes. By means of reporter gene assays, RNA interference, electrophoretic mobility shift assay, and competitive ligand-binding assay, we further demonstrate that PP2 is a ligand for the aryl hydrocarbon receptor (AHR), an intracellular chemosensor that regulates xenobiotic metabolism, environmental stress responses, and immune functions. Upon ligand-dependent activation, the AHR translocates into the nucleus and dimerizes with the AHR nuclear translocator (ARNT) to modulate the expression of its target genes. In addition, AHR activation is frequently accompanied by an activation of the tyrosine kinase c-Src, resulting in stimulation of cell-surface receptors and downstream signal transduction. As PP2 activates the AHR/ARNT pathway by simultaneously blocking c-Src-mediated alternative signaling routes, this compound may be a suitable tool to study the contribution of the different AHR-dependent signaling pathways to biological processes and adverse outcomes. On the other hand, the unexpected property of PP2 to stimulate AHR/ARNT signaling should be carefully taken into account in future investigations in order to avoid a false interpretation of experimental results and molecular interrelations.
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- 2015
11. Pityriazepin and other potent AhR ligands isolated from Malassezia furfur yeast
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Mexia, Nikitia, Gaitanis, Georgios, Velegraki, Aristea, Soshilov, Anatoly, Denison, Michael S, and Magiatis, Prokopios
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Microbiology ,Biological Sciences ,Genetics ,Animals ,Azepines ,Binding ,Competitive ,Cell Line ,Tumor ,Genes ,Reporter ,Humans ,Indole Alkaloids ,Ligands ,Malassezia ,Mice ,Rabbits ,Receptors ,Aryl Hydrocarbon ,Signal Transduction ,Species Specificity ,Malassezia furfur ,Aryl-hydrocarbon receptor ,Indole metabolites ,Pityriacitrin ,Pityriazepin ,Biochemistry and Cell Biology ,Biochemistry & Molecular Biology ,Biochemistry and cell biology - Abstract
Malassezia furfur yeast strains isolated from diseased human skin preferentially biosynthesize indole alkaloids which can be detected in the human skin and are highly potent activators of the aryl hydrocarbon receptor (AhR) and AhR-dependent gene expression. Chemical analysis of an EtOAc extract of a M. furfur strain obtained from diseased human skin and grown on l-tryptophan agar revealed several known AhR active tryptophan metabolites along with a previously unidentified compound, pityriazepin. While its structure resembled that of the known alkaloid pityriacitrin, the comprised pyridine ring had been transformed into an azepinone. The indoloazepinone scaffold of pityriazepin is extremely rare in nature and has only been reported once previously. Pityriazepin, like the other isolated compounds, was found to be a potent activator of the AhR-dependent reporter gene assay in recombinant cell lines derived from four different species, although significant species differences in relative potency were observed. The ability of pityriazepin to competitively bind to the AhR and directly stimulate AhR DNA binding classified it as a new naturally-occurring potent AhR agonist. M. furfur produces an expanded collection of extremely potent naturally occurring AhR agonists, which produce their biological effects in a species-specific manner.
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- 2015
12. Ligand Promiscuity of Aryl Hydrocarbon Receptor Agonists and Antagonists Revealed by Site-Directed Mutagenesis
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Soshilov, Anatoly A and Denison, Michael S
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Biological Sciences ,Biomedical and Clinical Sciences ,Health Sciences ,Genetics ,Biotechnology ,Aetiology ,2.1 Biological and endogenous factors ,Cancer ,Animals ,Basic Helix-Loop-Helix Transcription Factors ,Binding Sites ,Cell Line ,HSP90 Heat-Shock Proteins ,Ligands ,Mice ,Models ,Molecular ,Mutagenesis ,Site-Directed ,Protein Binding ,Receptors ,Aryl Hydrocarbon ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse chemicals. To examine the mechanisms responsible for the promiscuity in AhR ligand binding, we determined the effects of mutations within the AhR ligand-binding domain (LBD) on the activity of diverse AhR ligands. Site-directed mutagenesis identified Ile319 of the mouse AhR and, to a lesser extent, Phe318 as residues involved in ligand-selective modulation of AhR transformation using a panel of 12 AhR ligands. These ligands could be categorized into four distinct structurally related groups based on their ability to activate AhR mutants at position 319 in vitro. The mutation I319K was selectively activated by FICZ and not by other examined ligands in vitro and in cell culture. F318L and F318A mutations resulted in the conversion of AhR agonists β-naphthoflavone and 3-methylcholanthrene, respectively, into partial agonists/antagonists. Hsp90 binding to the AhR was decreased with several mutations and was inversely correlated with AhR ligand-binding promiscuity. Together, these data define overlapping amino acid residues within the AhR LBD involved in the selectivity of ligand binding, the agonist or antagonist mode of ligand binding, and hsp90 binding and provide insights into the ligand diversity of AhR activators.
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- 2014
13. Enantiospecific Effects of Ketoconazole on Aryl Hydrocarbon Receptor
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Novotna, Aneta, Korhonova, Martina, Bartonkova, Iveta, Soshilov, Anatoly A, Denison, Michael S, Bogdanova, Katerina, Kolar, Milan, Bednar, Petr, and Dvorak, Zdenek
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Biochemistry and Cell Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Genetics ,Aetiology ,2.1 Biological and endogenous factors ,Aged ,Animals ,Antifungal Agents ,Candida ,Cytochrome P-450 CYP1A1 ,Cytochrome P-450 CYP1A2 ,Female ,Guinea Pigs ,Hep G2 Cells ,Hepatocytes ,Humans ,Ketoconazole ,Male ,Mice ,Middle Aged ,RNA ,Messenger ,Receptors ,Aryl Hydrocarbon ,Signal Transduction ,Stereoisomerism ,Structure-Activity Relationship ,Transcription ,Genetic ,General Science & Technology - Abstract
Azole antifungal ketoconazole (KET) was demonstrated to activate aryl hydrocarbon receptor (AhR). Since clinically used KET is a racemic mixture of two cis-enantiomers (2R,4S)-(+)-KET and (2S,4R)-(-)-KET, we examined the effects of KET enantiomers on AhR signaling pathway. (+)-KET dose-dependently activated AhR in human gene reporter cell line AZ-AHR, and displayed 5-20× higher agonist activity (efficacy), as compared to (-)-KET; both enantiomers were AhR antagonists with equal potency (IC50). Consistently, (+)-KET strongly induced CYP1A1 mRNA and protein in human HepG2 cells, while (-)-KET exerted less than 10% of (+)-KET activity. In primary human hepatocytes, both enantiomers preferentially induced CYP1A2 over CYP1A1 mRNA and protein, and the potency of (+)-KET was slightly higher as compared to (-)-KET. Ligand binding assay with guinea pig liver cytosols revealed that both (+)-KET and (-)-KET are weak ligands of AhR that displaced [3H]-TCDD with comparable potency. Similarly, both enantiomers weakly transformed AhR to DNA-binding form with similar potency, as showed by EMSA, in guinea pig liver cytosolic extracts and nuclear extracts from mouse Hepa-1 cells. We also examined effects of KET on glucocorticoid receptor (GR), a regulator of AhR activity. Both KET enantiomers antagonized GR with similar potency, as revealed by gene reporter assay in AZ-GR cell line and down-regulation of tyrosine aminotransferase mRNA in human hepatocytes. Finally, we demonstrate enantiospecific antifungal activities of KET enantiomers in six Candida spp. strains. In conclusion, the significance of current study is providing the first evidence of enatiospecific effects of cis-enantiomers of ketoconazole on AhR-CYP1A pathway.
- Published
- 2014
14. Rosmarinus officinalis L. Leaf Extracts and Their Metabolites Inhibit the Aryl Hydrocarbon Receptor (AhR) Activation In Vitro and in Human Keratinocytes: Potential Impact on Inflammatory Skin Diseases and Skin Cancer
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Panagiotis Kallimanis, Ioanna Chinou, Angeliki Panagiotopoulou, Anatoly A. Soshilov, Guochun He, Michael S. Denison, and Prokopios Magiatis
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Rosmarinus officinalis L. ,AhR ,TCDD ,FICZ ,pityriazepin ,indirubin ,Organic chemistry ,QD241-441 - Abstract
Aryl hydrocarbon receptor (AhR) activation by environmental agents and microbial metabolites is potentially implicated in a series of skin diseases. Hence, it would be very important to identify natural compounds that could inhibit the AhR activation by ligands of microbial origin as 6-formylindolo[3,2-b]carbazole (FICZ), indirubin (IND) and pityriazepin (PZ) or the prototype ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Five different dry Rosmarinus officinalis L. extracts (ROEs) were assayed for their activities as antagonists of AhR ligand binding with guinea pig cytosol in the presence of [3H]TCDD. The methanolic ROE was further assayed towards CYP1A1 mRNA induction using RT-PCR in human keratinocytes against TCDD, FICZ, PZ, and IND. The isolated metabolites, carnosic acid, carnosol, 7-O-methyl-epi-rosmanol, 4′,7-O-dimethylapigenin, and betulinic acid, were assayed for their agonist and antagonist activity in the presence and absence of TCDD using the gel retardation assay (GRA). All assayed ROE extracts showed similar dose-dependent activities with almost complete inhibition of AhR activation by TCDD at 100 ppm. The methanol ROE at 10 ppm showed 99%, 50%, 90%, and 85% inhibition against TCDD, FICZ, IND, and PZ, respectively, in human keratinocytes. Most assayed metabolites exhibited dose-dependent antagonist activity. ROEs inhibit AhR activation by TCDD and by the Malassezia metabolites FICZ, PZ, and IND. Hence, ROE could be useful for the prevention or treatment of skin diseases mediated by activation of AhR.
- Published
- 2022
- Full Text
- View/download PDF
15. 2,3-cis-2R,3R-(¿)-epiafzelechin-3-O-p-coumarate, a novel flavan-3-ol isolated from Fallopia convolvulus seed, is an estrogen receptor agonist in human cell lines
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Brennan, Jennifer C, Denison, Michael S, Holstege, Dirk M, Magiatis, Prokopios, Dallas, Jerry L, Gutierrez, Elisa G, Soshilov, Anatoly A, and Millam, James R
- Abstract
Abstract Background The plant genus Fallopia is well-known in Chinese traditional medicine and includes many species that contain bioactive compounds, namely phytoestrogens. Consumption of phytoestrogens may be linked to decreased incidence of breast and prostate cancers therefore discovery of novel phytoestrogens and novel sources of phytoestrogens is of interest. Although phytoestrogen content has been analyzed in the rhizomes of various Fallopia sp., seeds of a Fallopia sp. have never been examined for phytoestrogen presence. Methods Analytical chemistry techniques were used with guidance from an in vitro estrogen receptor bioassay (a stably transfected human ovarian carcinoma cell line) to isolate and identify estrogenic components from seeds of Fallopia convolvulus. A transiently transfected human breast carcinoma cell line was used to characterize the biological activity of the isolated compounds on estrogen receptors (ER) α and β. Results Two compounds, emodin and the novel flavan-3-ol, (−)-epiafzelechin-3-O-p-coumarate (rhodoeosein), were identified to be responsible for estrogenic activity of F. convolvulus seed extract. Absolute stereochemistry of rhodoeosein was determined by 1 and 2D NMR, optical rotation and circular dichroism. Emodin was identified by HPLC/DAD, LC/MS/MS, and FT/ICR-MS. When characterizing the ER specificity in biological activity of rhodoeosein and emodin, rhodoeosein was able to exhibit a four-fold greater relative estrogenic potency (REP) in breast cells transiently-transfected with ERβ as compared to those transfected with ERα, and emodin exhibited a six-fold greater REP in ERβ-transfected breast cells. Cell type-specific differences were observed with rhodoeosein but not emodin; rhodoeosein produced superinduction of reporter gene activity in the human ovarian cell line (> 400% of maximum estradiol [E2] induction) but not in the breast cell line. Conclusion This study is the first to characterize the novel flavan-3-ol compound, rhodoeosein, and its ability to induce estrogenic activity in human cell lines. Rhodoeosein and emodin may have potential therapeutic applications as natural products activating ERβ, and further characterization of rhodoeosein is necessary to evaluate its selectivity as a cell type-specific ER agonist.
- Published
- 2013
16. Ginsenosides are novel naturally-occurring aryl hydrocarbon receptor ligands.
- Author
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Hu, Qin, He, Guochun, Zhao, Jing, Soshilov, Anatoly, Denison, Michael S, Zhang, Aiqian, Yin, Huijun, Fraccalvieri, Domenico, Bonati, Laura, Xie, Qunhui, and Zhao, Bin
- Subjects
Cell Line ,Tumor ,Animals ,Humans ,Guinea Pigs ,Mice ,Rats ,Ginsenosides ,Receptors ,Aryl Hydrocarbon ,Polychlorinated Dibenzodioxins ,Cell Line ,Tumor ,Receptors ,Aryl Hydrocarbon ,General Science & Technology - Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates many of the biological and toxicological actions of structurally diverse chemicals. In this study, we examined the ability of a series of ginsenosides extracted from ginseng, a traditional Chinese medicine, to bind to and activate/inhibit the AHR and AHR signal transduction. Utilizing a combination of ligand and DNA binding assays, molecular docking and reporter gene analysis, we demonstrated the ability of selected ginsenosides to directly bind to and activate the guinea pig cytosolic AHR, and to stimulate/inhibit AHR-dependent luciferase gene expression in a recombinant guinea pig cell line. Comparative studies revealed significant species differences in the ability of ginsenosides to stimulate AHR-dependent gene expression in guinea pig, rat, mouse and human cell lines. Not only did selected ginsenosides preferentially activate the AHR from one species and not others, mouse cell line was also significantly less responsive to these chemicals than rat and guinea pig cell lines, but the endogenous gene CYP1A1 could still be inducted in mouse cell line. Overall, the ability of these compounds to stimulate AHR signal transduction demonstrated that these ginsenosides are a new class of naturally occurring AHR agonists.
- Published
- 2013
17. Sustained activation of the Aryl hydrocarbon Receptor transcription factor promotes resistance to BRAF-inhibitors in melanoma
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Sébastien Corre, Nina Tardif, Nicolas Mouchet, Héloïse M. Leclair, Lise Boussemart, Arthur Gautron, Laura Bachelot, Anthony Perrot, Anatoly Soshilov, Aljosja Rogiers, Florian Rambow, Erwan Dumontet, Karin Tarte, Alban Bessede, Gilles J. Guillemin, Jean-Christophe Marine, Michael S. Denison, David Gilot, and Marie-Dominique Galibert
- Subjects
Science - Abstract
Resistance to BRAF inhibitors limits their clinical benefit in melanoma patients. Here, the authors show that the Aryl hydrocarbon Receptor (AhR) is a key mediator of resistant genes and use resveratrol, an AhR antagonist, to revert resistance in melanoma bearing mice.
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- 2018
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18. Metformin inhibits 7,12-dimethylbenz[a]anthracene-induced breast carcinogenesis and adduct formation in human breast cells by inhibiting the cytochrome P4501A1/aryl hydrocarbon receptor signaling pathway
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Maayah, Zaid H., Ghebeh, Hazem, Alhaider, Abdulqader A., El-Kadi, Ayman O.S., Soshilov, Anatoly A., Denison, Michael S., Ansari, Mushtaq Ahmad, and Korashy, Hesham M.
- Published
- 2015
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19. Modeling the transplacental transfer of small molecules using machine learning: a case study on per- and polyfluorinated substances (PFAS)
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Dimitri Abrahamsson, Adi Siddharth, Joshua F. Robinson, Anatoly Soshilov, Sarah Elmore, Vincent Cogliano, Carla Ng, Elaine Khan, Randolph Ashton, Weihsueh A. Chiu, Jennifer Fung, Lauren Zeise, and Tracey J. Woodruff
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Pediatric ,Epidemiology ,PFAS ,Public Health, Environmental and Occupational Health ,health ,statistical models ,Toxicology ,Pollution ,Medical and Health Sciences ,Exposure modeling ,Empirical ,Machine Learning ,Good Health and Well Being ,Child exposure ,Chemical Sciences ,Humans ,Empirical/statistical models ,Child exposure/health ,Environmental Sciences - Abstract
BackgroundDespite their large numbers and widespread use, very little is known about the extent to which per- and polyfluoroalkyl substances (PFAS) can cross the placenta and expose the developing fetus.ObjectiveThe aim of our study is to develop a computational approach that can be used to evaluate the of extend to which small molecules, and in particular PFAS, can cross to cross the placenta and partition to cord blood.MethodsWe collected experimental values of the concentration ratio between cord and maternal blood (RCM) for 260 chemical compounds and calculated their physicochemical descriptors using the cheminformatics package Mordred. Weused the compiled database to, train and test an artificial neural network (ANN). And then applied the best performing model to predict RCM for a large dataset of PFAS chemicals (n = 7982). We, finally, examined the calculatedphysicochemical descriptors of the chemicals to identify which properties correlated significantly with RCM.ResultsWe determined that 7855 compounds were within the applicability domain and 127 compounds are outside the applicability domain of our model. Our predictions of RCM for PFAS suggested that 3623 compounds had a log RCM > 0 indicating preferable partitioning to cord blood. Some examples of these compounds were bisphenol AF, 2,2-bis(4-aminophenyl)hexafluoropropane, and nonafluoro-tert-butyl 3-methylbutyrate.SignificanceThese observations have important public health implications as many PFAS have been shown to interfere with fetal development.In addition, asthese compounds are highly persistent and many of them can readilycross the placenta,they are expected to remain in the population for a long time as they are being passed from parent to offspring.ImpactUnderstanding the behavior of chemicals in the human body during pregnancy is critical in preventing harmful exposures during critical periods of development. Many chemicals can cross the placenta and expose the fetus, however, the mechanism by which this transport occurs is not well understood. In our study, we developed a machine learning model that describes the transplacental transfer of chemicals as a function of their physicochemical properties. The model was then used to make predictions for a set of 7982 per-and polyfluorinated alkyl substances that are listed on EPA's CompTox Chemicals Dashboard.The model can be applied to make predictions for other chemical categories of interest, such as plasticizers and pesticides. Accurate predictions of RCMcan help scientists and regulators to prioritize chemicals that have the potential to cause harm by exposing the fetus.
- Published
- 2022
20. Methylated pentavalent arsenic metabolites are bifunctional inducers, as they induce cytochrome P450 1A1 and NAD(P)H:quinone oxidoreductase through AhR- and Nrf2-dependent mechanisms
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Anwar-Mohamed, Anwar, Elshenawy, Osama H., Soshilov, Anatoly A., Denison, Michael S., Chris Le, X., Klotz, Lars-Oliver, and El-Kadi, Ayman O.S.
- Published
- 2014
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21. Augmented data routing algorithms for satellite delay-tolerant networks. Development and validation
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Fedorov, Andrei A., primary, Soshilov, Igor V., additional, and Loginov, Valery N., additional
- Published
- 2022
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22. Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form
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Soshilov, A, Motta, S, Bonati, L, Denison, M, Soshilov, Anatoly A., Motta, Stefano, Bonati, Laura, Denison, Michael S., Soshilov, A, Motta, S, Bonati, L, Denison, M, Soshilov, Anatoly A., Motta, Stefano, Bonati, Laura, and Denison, Michael S.
- Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of an AhR lacking the entire PASB structurally diverse chemicals, including halogenated aromatic hydrocarbons. Ligand-dependent transformation of the AhR into its DNA binding form involves a ligand-dependent conformational change, heat shock protein 90 (hsp90), dissociation from the AhR complex and AhR dimerization with the AhR nuclear translocator (ARNT) protein. The mechanism of AhR transformation was examined using mutational approaches and stabilization of the AhR:hsp90 complex with sodium molybdate. Insertion of a single mutation (F281A) in the hsp90-binding region of the AhR resulted in its constitutive (ligand-independent) transformation/DNA binding in vitro. Mutations of AhR residues within the Arg-Cys-rich region (R212A, R217A, R219A) and Asp371 (D371A) impaired AhR transformation without a significant effect on ligand binding. Stabilization of AhR:hsp90 binding with sodium molybdate decreased transformation/DNA binding of the wild type AhR but had no effect on constitutively active AhR mutants. Interestingly, transformation of the AhR in the presence of molybdate allowed detection of an intermediate transformation ternary complex containing hsp90, AhR, and ARNT. These results are consistent with a stepwise transformation mechanism in which binding of ARNT to the liganded AhR:hsp90 complex results in a progressive displacement of hsp90 and conversion of the AhR into its high affinity DNA binding form. The available molecular insights into the signaling mechanism of other Per-ARNT-Sim (PAS) domains and structural information on hsp90 association with other client proteins are consistent with the proposed transformation mechanism of the AhR.
- Published
- 2020
23. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR: ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.
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Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, and Laura Bonati
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- 2016
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24. New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability.
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Ilaria Motto, Annalisa Bordogna, Anatoly A. Soshilov, Michael S. Denison, and Laura Bonati
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- 2011
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25. Harmaline and harmalol inhibit the carcinogen-activating enzyme CYP1A1 via transcriptional and posttranslational mechanisms
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El Gendy, Mohamed A.M., Soshilov, Anatoly A., Denison, Michael S., and El-Kadi, Ayman O.S.
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- 2012
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26. Rosmarinus officinalis L. Leaf Extracts and Their Metabolites Inhibit the Aryl Hydrocarbon Receptor (AhR) Activation In Vitro and in Human Keratinocytes: Potential Impact on Inflammatory Skin Diseases and Skin Cancer
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Kallimanis, Panagiotis, primary, Chinou, Ioanna, additional, Panagiotopoulou, Angeliki, additional, Soshilov, Anatoly A., additional, He, Guochun, additional, Denison, Michael S., additional, and Magiatis, Prokopios, additional
- Published
- 2022
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27. Heuristic algorithms for finding routes for data transmission in satellite systems and their validation
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A.A. Fedorov, V.N. Loginov, and S.V. Soshilov
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Heuristic ,Computer science ,Satellite ,Algorithm ,Data transmission - Published
- 2020
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- View/download PDF
28. Modeling the transplacental transfer of small molecules: A case study on poly/perfluorinated substances (PFAS)
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Abrahamsson, Dimitri, Siddharth, Adi, Robinson, Joshua F., Soshilov, Anatoly, Elmore, Sarah, Cogliano, Vincent, Ng, Carla, Khan, Elaine, Ashton, Randolph, Chiu, Weihsueh A., Zeise, Lauren, and Woodruff, Tracey J.
- Subjects
placenta, transfer, environmental contaminants, PFAS, machine learning - Abstract
Background: Despite their large numbers and widespread use, very little is known about the extent to which per- and polyfluoroalkyl substances (PFAS) are transferred to the fetus during pregnancy. Objective: The aim of our study is to develop computational approaches that can be used to evaluate theextent towhich PFAS can cross to cross the placenta and partition to cord blood. Methods: We collected experimental values of the central tendency of concentration ratio between cord and maternal blood (RCM) for 264 chemical compounds and calculated their physicochemical descriptors. We developed and tested three machine learning models, an artificial neural network (ANN), a random forest (RF), and a support vector machine (SVM), and used the compiled database to train the models. We then applied our best-performing models to make predictions of RCM for a large dataset of PFAS chemicals (n=4,292). We, finally, used the calculated descriptors of the chemicals to identify which properties correlated significantly with RCM. Results: ANN showed the best performance in terms of accuracy and predictive power. Our predictions of RCM for PFAS suggest that 2,030 compounds are expected to partition favorably to cord blood. Significance: This observation has public important implications as many PFAS have been shown to interfere with fetal development.
- Published
- 2022
- Full Text
- View/download PDF
29. Ligand Displaces Heat Shock Protein 90 from Overlapping Binding Sites within the Aryl Hydrocarbon Receptor Ligand-binding Domain
- Author
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Soshilov, Anatoly and Denison, Michael S.
- Published
- 2011
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30. Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form
- Author
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Anatoly A. Soshilov, Michael S. Denison, Stefano Motta, Laura Bonati, Soshilov, A, Motta, S, Bonati, L, and Denison, M
- Subjects
Models, Molecular ,TCDD ,Cell Transformation ,Ligands ,8-tetrachlorodibenzo-p-dioxin ,lcsh:Chemistry ,chemistry.chemical_compound ,Models ,Receptors ,Basic Helix-Loop-Helix Transcription Factors ,Ternary complex ,lcsh:QH301-705.5 ,Spectroscopy ,Cancer ,biology ,Chemistry ,aryl hydrocarbon receptor ,aryl hydrocarbon receptor nuclear translocator ,General Medicine ,respiratory system ,Ligand (biochemistry) ,Hsp90 ,Computer Science Applications ,Cell biology ,DNA-Binding Proteins ,ARNT ,molybdate ,Cell Transformation, Neoplastic ,Aryl Hydrocarbon ,Protein Binding ,Aryl hydrocarbon receptor nuclear translocator ,1.1 Normal biological development and functioning ,Catalysis ,Article ,Inorganic Chemistry ,Structure-Activity Relationship ,Underpinning research ,Genetics ,Humans ,2,3,7,8-tetrachlorodibenzo-p-dioxin ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,HSP90 Heat-Shock Proteins ,Physical and Theoretical Chemistry ,heat shock protein 90 ,Molecular Biology ,Transcription factor ,Molybdenum ,Neoplastic ,Chemical Physics ,Organic Chemistry ,AhR ,Wild type ,Molecular ,DNA ,Aryl hydrocarbon receptor ,hsp90 ,respiratory tract diseases ,CHIM/02 - CHIMICA FISICA ,Receptors, Aryl Hydrocarbon ,lcsh:Biology (General) ,lcsh:QD1-999 ,Mutation ,biology.protein ,Generic health relevance ,Other Biological Sciences ,Other Chemical Sciences - Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of an AhR lacking the entire PASB structurally diverse chemicals, including halogenated aromatic hydrocarbons. Ligand-dependent transformation of the AhR into its DNA binding form involves a ligand-dependent conformational change, heat shock protein 90 (hsp90), dissociation from the AhR complex and AhR dimerization with the AhR nuclear translocator (ARNT) protein. The mechanism of AhR transformation was examined using mutational approaches and stabilization of the AhR:hsp90 complex with sodium molybdate. Insertion of a single mutation (F281A) in the hsp90-binding region of the AhR resulted in its constitutive (ligand-independent) transformation/DNA binding in vitro. Mutations of AhR residues within the Arg-Cys-rich region (R212A, R217A, R219A) and Asp371 (D371A) impaired AhR transformation without a significant effect on ligand binding. Stabilization of AhR:hsp90 binding with sodium molybdate decreased transformation/DNA binding of the wild type AhR but had no effect on constitutively active AhR mutants. Interestingly, transformation of the AhR in the presence of molybdate allowed detection of an intermediate transformation ternary complex containing hsp90, AhR, and ARNT. These results are consistent with a stepwise transformation mechanism in which binding of ARNT to the liganded AhR:hsp90 complex results in a progressive displacement of hsp90 and conversion of the AhR into its high affinity DNA binding form. The available molecular insights into the signaling mechanism of other Per-ARNT-Sim (PAS) domains and structural information on hsp90 association with other client proteins are consistent with the proposed transformation mechanism of the AhR.
- Published
- 2020
31. Vemurafenib acts as an aryl hydrocarbon receptor antagonist: Implications for inflammatory cutaneous adverse events
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Peter Arne Gerber, Jean Krutmann, Péter Oláh, Heike C Hawerkamp, Afaque Ahmad Imtiyaz Momin, Michael S. Denison, Katharina M. Rolfes, Stefan T. Arold, Stephan Meller, Angeliki Datsi, Stephan Alexander Braun, Anatoly A. Soshilov, Andreas Kislat, Mario E. Lacouture, Marius Pollet, Bernhard Homey, and Thomas Haarmann-Stemmann
- Subjects
Models, Molecular ,0301 basic medicine ,Chemokine ,Protein Conformation ,Biopsy ,Guinea Pigs ,Immunology ,Antineoplastic Agents ,Dermatitis ,Inflammation ,Article ,Proinflammatory cytokine ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,T-Lymphocyte Subsets ,Basic Helix-Loop-Helix Transcription Factors ,Cytochrome P-450 CYP1A1 ,medicine ,Animals ,Humans ,Immunology and Allergy ,Vemurafenib ,Protein Kinase Inhibitors ,Aged ,biology ,business.industry ,Melanoma ,Th1 Cells ,Aryl hydrocarbon receptor ,medicine.disease ,Disease Models, Animal ,030104 developmental biology ,Receptors, Aryl Hydrocarbon ,030228 respiratory system ,Case-Control Studies ,biology.protein ,Cancer research ,Tumor necrosis factor alpha ,medicine.symptom ,business ,Biomarkers ,medicine.drug - Abstract
Background In recent years, the BRAF inhibitor vemurafenib has been successfully established in the therapy of advanced melanoma. Despite its superior efficacy, the use of vemurafenib is limited by frequent inflammatory cutaneous adverse events that affect patients' quality of life and may lead to dose reduction or even cessation of anti-tumor therapy. To date, the molecular and cellular mechanisms of vemurafenib-induced rashes have remained largely elusive. Methods In this study, we deployed immunohistochemistry, RT-qPCR, flow cytometry, lymphocyte activation tests, and different cell-free protein-interaction assays. Results We here demonstrate that vemurafenib inhibits the downstream signaling of the canonical pathway of aryl hydrocarbon receptor (AhR) in vitro, thereby inducing the expression of proinflammatory cytokines (eg, TNF) and chemokines (eg, CCL5). In line with these results, we observed an impaired expression of AhR-regulated genes (eg, CYP1A1) and an upregulation of the corresponding proinflammatory genes in vivo. Moreover, results of lymphocyte activation tests showed the absence of drug-specific T cells in respective patients. Conclusion Taken together, we obtained no hint of an underlying sensitization against vemurafenib but found evidence suggesting that vemurafenib enhances proinflammatory responses by inhibition of canonical AhR signaling. Our findings contribute to our understanding of the central role of the AhR in skin inflammation and may point toward a potential role for topical AhR agonists in supportive cancer care.
- Published
- 2019
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32. Enantiospecific effects of ketoconazole on aryl hydrocarbon receptor.
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Aneta Novotna, Martina Korhonova, Iveta Bartonkova, Anatoly A Soshilov, Michael S Denison, Katerina Bogdanova, Milan Kolar, Petr Bednar, and Zdenek Dvorak
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Medicine ,Science - Abstract
Azole antifungal ketoconazole (KET) was demonstrated to activate aryl hydrocarbon receptor (AhR). Since clinically used KET is a racemic mixture of two cis-enantiomers (2R,4S)-(+)-KET and (2S,4R)-(-)-KET, we examined the effects of KET enantiomers on AhR signaling pathway. (+)-KET dose-dependently activated AhR in human gene reporter cell line AZ-AHR, and displayed 5-20× higher agonist activity (efficacy), as compared to (-)-KET; both enantiomers were AhR antagonists with equal potency (IC50). Consistently, (+)-KET strongly induced CYP1A1 mRNA and protein in human HepG2 cells, while (-)-KET exerted less than 10% of (+)-KET activity. In primary human hepatocytes, both enantiomers preferentially induced CYP1A2 over CYP1A1 mRNA and protein, and the potency of (+)-KET was slightly higher as compared to (-)-KET. Ligand binding assay with guinea pig liver cytosols revealed that both (+)-KET and (-)-KET are weak ligands of AhR that displaced [3H]-TCDD with comparable potency. Similarly, both enantiomers weakly transformed AhR to DNA-binding form with similar potency, as showed by EMSA, in guinea pig liver cytosolic extracts and nuclear extracts from mouse Hepa-1 cells. We also examined effects of KET on glucocorticoid receptor (GR), a regulator of AhR activity. Both KET enantiomers antagonized GR with similar potency, as revealed by gene reporter assay in AZ-GR cell line and down-regulation of tyrosine aminotransferase mRNA in human hepatocytes. Finally, we demonstrate enantiospecific antifungal activities of KET enantiomers in six Candida spp. strains. In conclusion, the significance of current study is providing the first evidence of enatiospecific effects of cis-enantiomers of ketoconazole on AhR-CYP1A pathway.
- Published
- 2014
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33. Role of the Per/Arnt/Sim Domains in Ligand-dependent Transformation of the Aryl Hydrocarbon Receptor
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Soshilov, Anatoly and Denison, Michael S.
- Published
- 2008
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- View/download PDF
34. Ginsenosides are novel naturally-occurring aryl hydrocarbon receptor ligands.
- Author
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Qin Hu, Guochun He, Jing Zhao, Anatoly Soshilov, Michael S Denison, Aiqian Zhang, Huijun Yin, Domenico Fraccalvieri, Laura Bonati, Qunhui Xie, and Bin Zhao
- Subjects
Medicine ,Science - Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates many of the biological and toxicological actions of structurally diverse chemicals. In this study, we examined the ability of a series of ginsenosides extracted from ginseng, a traditional Chinese medicine, to bind to and activate/inhibit the AHR and AHR signal transduction. Utilizing a combination of ligand and DNA binding assays, molecular docking and reporter gene analysis, we demonstrated the ability of selected ginsenosides to directly bind to and activate the guinea pig cytosolic AHR, and to stimulate/inhibit AHR-dependent luciferase gene expression in a recombinant guinea pig cell line. Comparative studies revealed significant species differences in the ability of ginsenosides to stimulate AHR-dependent gene expression in guinea pig, rat, mouse and human cell lines. Not only did selected ginsenosides preferentially activate the AHR from one species and not others, mouse cell line was also significantly less responsive to these chemicals than rat and guinea pig cell lines, but the endogenous gene CYP1A1 could still be inducted in mouse cell line. Overall, the ability of these compounds to stimulate AHR signal transduction demonstrated that these ginsenosides are a new class of naturally occurring AHR agonists.
- Published
- 2013
- Full Text
- View/download PDF
35. Comparative in vitro and in silico analysis of the selectivity of indirubin as a human ah receptor agonist
- Author
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Faber, S, Soshilov, A, Giani Tagliabue, S, Bonati, L, Denison, M, Faber, SC, Soshilov, AA, Denison, MS, Faber, S, Soshilov, A, Giani Tagliabue, S, Bonati, L, Denison, M, Faber, SC, Soshilov, AA, and Denison, MS
- Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that modulates gene expression following its binding and activation by structurally diverse chemicals. Species differences in AhR functionality have been observed, with the mouse AhR (mAhR) and human AhR (hAhR) exhibiting significant differences in ligand binding, coactivator recruitment, gene expression and response. While the AhR agonist indirubin (IR) is a more potent activator of hAhR-dependent gene expression than the prototypical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), it is a significantly less potent activator of the mAhR. DNA binding analysis confirmed the greater potency/efficacy of IR in stimulating transformation/DNA binding of the hAhR in vitro and domain-swapping experiments demonstrated that the enhanced response to IR was primarily due to the hAhR ligand binding domain (LBD). Site-directed mutagenesis and functional analysis studies revealed that mutation of H326 and A349 in the mAhR LBD to the corresponding residues in the hAhR LBD significantly increased the potency of IR. Since these mutations had no significant effect on ligand binding, these residues likely contribute to an enhanced efficiency of transformation/DNA binding by IR-bound hAhR. Molecular docking to mAhR LBD homology models further elucidated the different roles of the A375V mutation in TCDD and IR binding, as revealed by [3H]TCDD competitive binding results. These results demonstrate the differential binding of structurally diverse ligands within the LBD of a given AhR and confirm that amino acid differences within the LBD of AhRs contribute to significant species differences in ligand response.
- Published
- 2018
36. Effective Resonators for THz Quantum Waves of Electron States (QWES)
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S. V. Koshevaya, Oksana Bilous, Denis Soshilov, V. V. Grimalsky, Felix Yanovsky, and Y. G. Rapoport
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Resonator ,Materials science ,Condensed matter physics ,Graphene ,law ,Electron optics ,Physics::Optics ,Metamaterial ,Electron ,Quantum ,Diffraction grating ,law.invention ,Magnetic field - Abstract
We present here a farther development of the ideas of 2D solid-state graphene metamaterial electron optics (GMEO) and a general method to graphene-based metamaterials that includes three levels of a consideration. This method includes a metamaterial approach to the QWES, or the electron probability waves, in 2D electron gas where a finite effective electron mass is allowed; a good example of this can be the electron graphene resonators and diffraction gratings. The characteristics of the transport of QWES are determined accounting for proper boundary conditions for the system like "Graphene with Zero Electron Mass-Finite Electron Mass Material-Graphene with Zero Electron Mass" (GZEM-FEMM-GZEM). Effects on electron transport from electric and magnetic fields, exchange and spin-orbit interactions are accounted for. Possibility of formation of the controllable high-Q 2D magnetoelectric resonators and diffraction gratings for the QWES on the structure GZEM-FEMM-GZEM is shown.
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- 2020
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37. Structure-Based Virtual Screening of Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) as Endocrine Disruptors of Androgen Receptor Activity Using Molecular Docking and Machine Learning
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Phum Tachachartvanich, Anatoly Soshilov, Jennifer C.Y. Hsieh, Azhagiya Singam Ettayapuram Ramaprasad, Denis Fourches, Michele A. La Merrill, Martyn T. Smith, and Kathleen A. Durkin
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Endocrine Disruptors ,010501 environmental sciences ,Machine learning ,computer.software_genre ,01 natural sciences ,Biochemistry ,Machine Learning ,03 medical and health sciences ,0302 clinical medicine ,Mass Screening ,Endocrine system ,030212 general & internal medicine ,0105 earth and related environmental sciences ,General Environmental Science ,Fluorocarbons ,Virtual screening ,business.industry ,Chemistry ,Molecular Docking Simulation ,Androgen receptor ,Receptors, Androgen ,Docking (molecular) ,Structure based ,Artificial intelligence ,business ,Androgen receptor activity ,computer - Abstract
Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) pose a substantial threat as endocrine disruptors, and thus early identification of those that may interact with steroid hormone receptors, such as the androgen receptor (AR), is critical. In this study we screened 5,206 PFASs from the CompTox database against the different binding sites on the AR using both molecular docking and machine learning techniques. We developed support vector machine models trained on Tox21 data to classify the active and inactive PFASs for AR using different chemical fingerprints as features. The maximum accuracy was 95.01% and Matthew’s correlation coefficient (MCC) was 0.76 respectively, based on MACCS fingerprints (MACCSFP). The combination of docking-based screening and machine learning models identified 29 PFASs that have strong potential for activity against the AR and should be considered priority chemicals for biological toxicity testing.
- Published
- 2020
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38. DNA Binding (Gel Retardation Assay) Analysis for Identification of Aryl Hydrocarbon (Ah) Receptor Agonists and Antagonists
- Author
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Soshilov, Anatoly A., primary and Denison, Michael S., additional
- Published
- 2013
- Full Text
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39. A novel prenylflavone restricts breast cancer cell growth through AhR-mediated destabilization of ERα protein
- Author
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Tiong, Chi Tze, Chen, Chen, Zhang, Shi Jun, Li, Jun, Soshilov, Anatoly, Denison, Michael S., Lee, Lawrence Soon-U, Tam, Vincent H., Wong, Shih Peng, Xu, H.Eric, and Yong, Eu-Leong
- Published
- 2012
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40. Exactly the Same but Different: Promiscuity and Diversity in the Molecular Mechanisms of Action of the Aryl Hydrocarbon (Dioxin) Receptor
- Author
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Denison, Michael S., Soshilov, Anatoly A., He, Guochun, DeGroot, Danica E., and Zhao, Bin
- Published
- 2011
- Full Text
- View/download PDF
41. Effective Resonators for THz Quantum Waves of Electron States (QWES)
- Author
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Rapoport, Yuriy, primary, Grimalsky, Vladimir, additional, Koshevaya, Svetlana, additional, Soshilov, Denis, additional, Yanovsky, Felix, additional, and Bilous, Oksana, additional
- Published
- 2020
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42. Structure-Based Virtual Screening of Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) as Endocrine Disruptors of Androgen Receptor Activity Using Molecular Docking and Machine Learning
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Ettayapuram Ramaprasad, Azhagiya Singam, primary, Tachachartvanich, Phum, primary, Fourches, Denis, primary, Soshilov, Anatoly, primary, Hsieh, Jennifer C.Y., primary, La merrill, Michele, primary, Smith, Martyn T., primary, and Durkin, Kathleen A., primary
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- 2020
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43. Heuristic algorithms for finding routes for data transmission in satellite systems and their validation
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Fedorov, A.A., primary, Soshilov, S.V., additional, and Loginov, V.N., additional
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- 2020
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44. Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist
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Laura Bonati, Anatoly A. Soshilov, Samantha C Faber, Michael S. Denison, Sara Giani Tagliabue, Faber, S, Soshilov, A, Giani Tagliabue, S, Bonati, L, and Denison, M
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Models, Molecular ,0301 basic medicine ,Secondary ,TCDD ,Indoles ,Polychlorinated Dibenzodioxins ,Protein Structure, Secondary ,lcsh:Chemistry ,Mice ,Models ,Gene expression ,Receptors ,Basic Helix-Loop-Helix Transcription Factors ,Site-Directed ,lcsh:QH301-705.5 ,Spectroscopy ,Cancer ,biology ,Chemistry ,in vitro ,General Medicine ,Ligand (biochemistry) ,3. Good health ,Computer Science Applications ,Molecular Docking Simulation ,Biochemistry ,Aryl Hydrocarbon ,in silico ,Protein Binding ,Agonist ,Protein Structure ,medicine.drug_class ,In silico ,In Vitro Techniques ,Article ,Catalysis ,indirubin ,Inorganic Chemistry ,03 medical and health sciences ,Species Specificity ,Coactivator ,medicine ,Genetics ,Animals ,Humans ,Computer Simulation ,Physical and Theoretical Chemistry ,Molecular Biology ,Transcription factor ,Binding Sites ,Chemical Physics ,030102 biochemistry & molecular biology ,Activator (genetics) ,Organic Chemistry ,AhR ,Molecular ,Aryl hydrocarbon receptor ,030104 developmental biology ,Receptors, Aryl Hydrocarbon ,lcsh:Biology (General) ,lcsh:QD1-999 ,Mutagenesis ,Agent Orange & Dioxin ,Ah receptor ,Mutagenesis, Site-Directed ,biology.protein ,Other Biological Sciences ,Other Chemical Sciences - Abstract
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that modulates gene expression following its binding and activation by structurally diverse chemicals. Species differences in AhR functionality have been observed, with the mouse AhR (mAhR) and human AhR (hAhR) exhibiting significant differences in ligand binding, coactivator recruitment, gene expression and response. While the AhR agonist indirubin (IR) is a more potent activator of hAhR-dependent gene expression than the prototypical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), it is a significantly less potent activator of the mAhR. DNA binding analysis confirmed the greater potency/efficacy of IR in stimulating transformation/DNA binding of the hAhR in vitro and domain-swapping experiments demonstrated that the enhanced response to IR was primarily due to the hAhR ligand binding domain (LBD). Site-directed mutagenesis and functional analysis studies revealed that mutation of H326 and A349 in the mAhR LBD to the corresponding residues in the hAhR LBD significantly increased the potency of IR. Since these mutations had no significant effect on ligand binding, these residues likely contribute to an enhanced efficiency of transformation/DNA binding by IR-bound hAhR. Molecular docking to mAhR LBD homology models further elucidated the different roles of the A375V mutation in TCDD and IR binding, as revealed by [3H]TCDD competitive binding results. These results demonstrate the differential binding of structurally diverse ligands within the LBD of a given AhR and confirm that amino acid differences within the LBD of AhRs contribute to significant species differences in ligand response.
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- 2018
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45. Auto-induction mechanism of aryl hydrocarbon receptor 2 (AHR2) gene by TCDD-activated AHR1 and AHR2 in the red seabream (Pagrus major)
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Midori Iida, Su Min Bak, Michael S. Denison, Anatoly A. Soshilov, Eun-Young Kim, and Hisato Iwata
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0301 basic medicine ,Polychlorinated Dibenzodioxins ,5' Flanking Region ,Health, Toxicology and Mutagenesis ,Messenger ,8-Tetrachlorodibenzo-p-dioxin ,Electrophoretic Mobility Shift Assay ,Ligands ,Toxicology ,medicine.disease_cause ,Xenobiotic-responsive elements ,Transactivation ,0302 clinical medicine ,Pharmacology And Pharmaceutical Sciences ,Receptors ,Chlorocebus aethiops ,Protein Isoforms ,Water Pollutants ,Promoter Regions, Genetic ,Aryl hydrocarbon receptor ,Mutation ,biology ,Red seabream ,General Medicine ,Auto-induction ,Recombinant Proteins ,Up-Regulation ,Aryl Hydrocarbon ,030220 oncology & carcinogenesis ,COS Cells ,Signal transduction ,Sequence Analysis ,Fish Proteins ,Transcriptional Activation ,Guinea Pigs ,5' flanking region ,Response Elements ,Article ,Cercopithecus aethiops ,Promoter Regions ,03 medical and health sciences ,Genetic ,medicine ,Animals ,Electrophoretic mobility shift assay ,Luciferase ,RNA, Messenger ,2,3,7,8-Tetrachlorodibenzo-p-dioxin ,Gene ,Sequence Analysis, DNA ,DNA ,Molecular biology ,Sea Bream ,Clone Cells ,030104 developmental biology ,Receptors, Aryl Hydrocarbon ,biology.protein ,RNA - Abstract
© 2016, Springer-Verlag Berlin Heidelberg. The toxic effects of dioxins and related compounds (DRCs) are mediated by the aryl hydrocarbon receptor (AHR). Our previous study identified AHR1 and AHR2 genes from the red seabream (Pagrus major). Moreover, we found that AHR2 mRNA levels were notably elevated by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure in the early life stage of red seabream embryos, while AHR1 mRNA level was not altered. In this study, to investigate the regulatory mechanism of these AHR transcripts, we cloned and characterized 5′-flanking regions of AHR1 and AHR2 genes. Both of the 5′-flanking regions in these AHR genes contained three potential xenobiotic-responsive elements (XREs). To assess whether the 5′-flanking region is transactivated by rsAHR1 and rsAHR2 proteins, we measured the transactivation potency of the luciferase reporter plasmids containing the 5′-flanking regions by AHR1 and AHR2 proteins that were transiently co-expressed in COS-7. Only reporter plasmid (pGL4-rsAHR2-3XREs) that contained three putative XRE sites in the 5′-flanking region of AHR2 gene showed a clear TCDD dose-dependent transactivation by AHR1 and AHR2 proteins. TCDD-EC50 values for the rsAHR2-derived XRE transactivation were 1.3 and 1.4 nM for AHR1 and AHR2, respectively. These results suggest that the putative XREs of AHR2 gene have a function for AHR1- and AHR2-mediated transactivation, supporting our in ovo observation of an induction of AHR2 mRNA levels by TCDD exposure. Mutations in XREs of AHR2 gene led to a decrease in luciferase induction. Electrophoretic mobility shift assay showed that XRE1, the closest XRE from the start codon in AHR2 gene, is mainly responsible for the binding with TCDD-activated AHR. This suggests that TCDD-activated AHR1 and AHR2 up-regulate the AHR2 mRNA levels and this auto-induced AHR2 may amplify the signal transduction of its downstream targets including CYP1A in the red seabream.
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- 2016
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46. Deciphering the ahr:arnt dimerization process: how to assembly the functional puzzle of interacting interfaces
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Corrada, D, Soshilov, A, Denison, M, Bonati, L, CORRADA, DARIO, BONATI, LAURA, Soshilov, AA, Denison, MS, Corrada, D, Soshilov, A, Denison, M, Bonati, L, CORRADA, DARIO, BONATI, LAURA, Soshilov, AA, and Denison, MS
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- 2016
47. Binding specificity of diverse AhR ligands interpreted by Molecular Modeling
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GIANI TAGLIABUE, S, Soshilov, A, Denison, M, Bonati, L, GIANI TAGLIABUE, SARA, BONATI, LAURA, Soshilov, AA, Denison, MS, GIANI TAGLIABUE, S, Soshilov, A, Denison, M, Bonati, L, GIANI TAGLIABUE, SARA, BONATI, LAURA, Soshilov, AA, and Denison, MS
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- 2016
48. Vemurafenib acts as an aryl hydrocarbon receptor antagonist: Implications for inflammatory cutaneous adverse events
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Hawerkamp, Heike C., primary, Kislat, Andreas, additional, Gerber, Peter A., additional, Pollet, Marius, additional, Rolfes, Katharina M., additional, Soshilov, Anatoly A., additional, Denison, Michael S., additional, Momin, Afaque A., additional, Arold, Stefan T., additional, Datsi, Angeliki, additional, Braun, Stephan A., additional, Oláh, Péter, additional, Lacouture, Mario E., additional, Krutmann, Jean, additional, Haarmann‐Stemmann, Thomas, additional, Homey, Bernhard, additional, and Meller, Stephan, additional
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- 2019
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49. Induction of the CYP2B genes by triphenyldioxane treatment in the rat liver
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Grigorieva, E, Soshilov, A, Surovtseva, Y, Schwartz, E.L, Duzhak, T.G, Gulyaeva, L.F, and Lyakhovich, V.V
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- 2002
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50. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
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Anatoly A. Soshilov, Dario Corrada, Michael S. Denison, Laura Bonati, Corrada, D, Soshilov, A, Denison, M, Bonati, L, and Keskin, Ozlem
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Models, Molecular ,0301 basic medicine ,homology modeling ,Physical Chemistry ,Biochemistry ,Mathematical Sciences ,Binding Analysis ,Protein structure ,Electricity ,Models ,PAS domain ,Receptors ,Macromolecular Structure Analysis ,lcsh:QH301-705.5 ,Free Energy ,Cancer ,Genetics ,Ecology ,biology ,Chemistry ,Physics ,Biological Sciences ,respiratory system ,Cell biology ,ARNT ,Computational Theory and Mathematics ,Aryl Hydrocarbon ,Modeling and Simulation ,Physical Sciences ,Thermodynamics ,Dimerization ,mutagenesis ,Research Article ,Biotechnology ,Protein Structure ,Aryl hydrocarbon receptor nuclear translocator ,Bioinformatics ,Chemical physics ,1.1 Normal biological development and functioning ,Protein domain ,Research and Analysis Methods ,DNA-binding protein ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Rare Diseases ,Protein Domains ,Electrostatics ,Underpinning research ,Information and Computing Sciences ,Aryl hydrocarbon Receptor ,DNA-binding proteins ,Humans ,Homology modeling ,protein dimer ,Molecular Biology ,Transcription factor ,Chemical Characterization ,Ecology, Evolution, Behavior and Systematics ,MM-GBSA ,Energy Decomposition ,Biology and life sciences ,030102 biochemistry & molecular biology ,Aryl Hydrocarbon Receptor Nuclear Translocator ,AhR ,Proteins ,Computational Biology ,Molecular ,Dimers (Chemical physics) ,Aryl hydrocarbon receptor ,030104 developmental biology ,Receptors, Aryl Hydrocarbon ,Chemical Properties ,lcsh:Biology (General) ,Mutation ,biology.protein ,Generic health relevance - Abstract
The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the functional activity of the AhR., Author Summary Computational modeling combined with experimental validation may give insight into structural and functional properties of protein systems. The basic Helix-Loop-Helix PER-ARNT-SIM (bHLH-PAS) proteins show conserved functional domains despite the broad range of functions exerted by the different systems. Within this protein family, the Aryl hydrocarbon Receptor (AhR) is known to mediate the toxic effects of a number of environmental contaminants, including dioxins and dioxin-like chemicals, and it also exerts other biochemical and physiological effects. Despite the absence of experimentally determined structures, theoretical models of the AhR PAS domains developed on the basis of homologous systems have allowed understanding of some aspects of the molecular mechanisms underlying its function. In this work we present alternative structural models of the transcriptionally active complex of AhR with the AhR Nuclear Translocator (ARNT) protein. Computational characterization of the modeled protein-protein interaction interfaces guided the design of mutagenesis experiments, and evaluation of the DNA binding ability of the resulting AhR:ARNT dimer mutants allowed validation of the models and selection of the most reliable one. These findings open new research directions for understanding the molecular mechanisms underlying the functional activity of the AhR.
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- 2016
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