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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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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: 21] [Impact Index Per Article: 10.5] [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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Phytochemicals as potential inhibitors for COVID-19 revealed by molecular docking, molecular dynamic simulation and DFT studies. Struct Chem 2022; 33:1423-1443. [PMID: 35729939 PMCID: PMC9189813 DOI: 10.1007/s11224-022-01982-4] [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: 03/23/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022]
Abstract
The COVID-19 pandemic outbreak demands the designing of potential drugs as there is no specific treatment available. Thanks to their safety and effectiveness, phytochemicals have been used to treat various diseases, including antiviral therapeutics. Molecular docking is a simple, quick, and effective way to screen a variety of molecules for structure-based drug design. Here, we investigate molecular docking experiments on compounds present in plant species, Cocculus hirsutus and Rhodiola rosea and show their potential for the treatment of COVID-19. Almost all the components showed higher binding affinity than the built-in ligand, and those with significantly higher binding affinity were explored further. Molecular mechanics-based generalized born surface area calculations were used to re-rank the top candidates, rhodionidin and cocsoline, and their stability in association with viral protease was confirmed. Density functional theory was used for detailed investigations of the geometries, and electrical properties of rhodionidin and cocsoline. Using the frontier molecular orbitals method, the charge transfer within the molecule was calculated. Chemical reactivity and intermolecular interactions were studied using molecular electrostatic potential maps. These in silico discoveries will simulate the identification of powerful COVID-19 inhibitors, and similar research is likely to make a significant contribution to antiviral drug discovery. Supplementary information The online version contains supplementary material available at 10.1007/s11224-022-01982-4.
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The Role of AhR in the Hallmarks of Brain Aging: Friend and Foe. Cells 2021; 10:cells10102729. [PMID: 34685709 PMCID: PMC8534784 DOI: 10.3390/cells10102729] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/05/2021] [Accepted: 10/10/2021] [Indexed: 12/24/2022] Open
Abstract
In recent years, aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, has been considered to be involved in aging phenotypes across several species. This receptor is a highly conserved biosensor that is activated by numerous exogenous and endogenous molecules, including microbiota metabolites, to mediate several physiological and toxicological functions. Brain aging hallmarks, which include glial cell activation and inflammation, increased oxidative stress, mitochondrial dysfunction, and cellular senescence, increase the vulnerability of humans to various neurodegenerative diseases. Interestingly, many studies have implicated AhR signaling pathways in the aging process and longevity across several species. This review provides an overview of the impact of AhR pathways on various aging hallmarks in the brain and the implications for AhR signaling as a mechanism in regulating aging-related diseases of the brain. We also explore how the nature of AhR ligands determines the outcomes of several signaling pathways in brain aging processes.
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Rath SN, Jena L, Bhuyan R, Mahanandia NC, Patri M. In silico discovery and evaluation of phytochemicals binding mechanism against human catechol-O-methyltransferase as a putative bioenhancer of L-DOPA therapy in Parkinson disease. Genomics Inform 2021; 19:e7. [PMID: 33840171 PMCID: PMC8042297 DOI: 10.5808/gi.20061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/05/2020] [Indexed: 11/20/2022] Open
Abstract
Levodopa (L-DOPA) therapy is normally practised to treat motor pattern associated with Parkinson disease (PD). Additionally, several inhibitory drugs such as Entacapone and Opicapone are also cosupplemented to protect peripheral inactivation of exogenous L-DOPA (~80%) that occurs due to metabolic activity of the enzyme catechol-O-methyltransferase (COMT). Although, both Entacapone and Opicapone have U.S. Food and Drug Administration approval but regular use of these drugs is associated with high risk of side effects. Thus, authors have focused on in silico discovery of phytochemicals and evaluation of their effectiveness against human soluble COMT using virtual screening, molecular docking, drug-like property prediction, generation of pharmacophoric property, and molecular dynamics simulation. Overall, study proposed, nine phytochemicals (withaphysalin D, withaphysalin N, withaferin A, withacnistin, withaphysalin C, withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant Withania somnifera have strong binding efficiency against human COMT in comparison to both of the drugs i.e., Opicapone and Entacapone, thus may be used as putative bioenhancer in L-DOPA therapy. The present study needs further experimental validation to be used as an adjuvant in PD treatment.
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Affiliation(s)
- Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar 751003, India.,Neurobiology Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack 753003, India
| | - Lingaraja Jena
- Centers for Advanced Research & Excellence, Department of Laboratory Oncology, All India Institute of Medical Science, New Delhi 110023, India
| | - Rajabrata Bhuyan
- Department of Bio-Science and Biotechnology, Banasthali Vidyapeeth (Deemed) University, Banasthali 304022, India
| | | | - Manorama Patri
- Neurobiology Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack 753003, India
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Aftabi Y, Rafei S, Zarredar H, Amiri-Sadeghan A, Akbari-Shahpar M, Khoshkam Z, Seyedrezazadeh E, Khalili M, Mehrnejad F, Fereidouni S, Lawrence BP. Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker: An integrative-SNP ranking web-tool. Comput Biol Chem 2020; 90:107416. [PMID: 33264727 DOI: 10.1016/j.compbiolchem.2020.107416] [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: 04/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
Different bioinformatic methods apply various approaches to predict how much the effect of a SNP could be deleterious and therefore their results may differ significantly. However, variation studies often need to consider an integrated prediction result to analyze the effect of SNPs. To address this problem, we used an algorithm to map ordinal predictions to a numeral space and averaging them, and based on it we developed the ISNPranker web-tool (http://isnpranker.semilab.ir/). It takes heterogonous outputs of different predictors and generates integrated numerical predictions and ranks SNPs based on them. Afterward, we used ISNPranker to identify the most deleterious coding SNPs (cSNPs) of the human aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that governs many molecular and cellular mechanisms and cSNPs may affect its structure, interactions, and function. Forty validated cSNPs of AHR were initially analyzed using 16 publicly available SNP analyzers and the results were introduced to the ISNPranker and integrated predictions were obtained. The cSNPs were ranked in 34 levels of danger and rs200257782 in the ARNT dimerization domain (ADD121-289) of AHR was identified as the most deleterious cSNP. The rs148360742, which affect ADD40-79 and Hsp90 binding domain (HBD27-79) was in the second rank and the third and fourth ranks were occupied by ADD121-289-located variations rs571123681 and rs141667112 respectively. In conclusion, we introduced ISNPranker, which is a web-tool for integrative ranking of SNPs, and we showed that AHR structure and function may be highly sensitive to the cSNPs in the ARNT dimerization domain.
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Affiliation(s)
- Younes Aftabi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
| | - Saleh Rafei
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Amir Amiri-Sadeghan
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Mohsen Akbari-Shahpar
- Department of Computer Engineering, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Zahra Khoshkam
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran; Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Tehran, Tehran, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Majid Khalili
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Sasan Fereidouni
- Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - B Paige Lawrence
- Departments of Environmental Medicine and Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
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Sandhya J, Veeralakshmi S, Kalaiselvam S. Tripolyphosphate crosslinked Triticum aestivum (wheatgrass) functionalized antimicrobial chitosan: Ameliorating effect on physicochemical, mechanical, invitro cytocompatibility and cell migration properties. J Biomol Struct Dyn 2020; 39:1635-1644. [PMID: 32107986 DOI: 10.1080/07391102.2020.1736160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polymeric films for various biomedical applications require to be biocompatible and non- toxic. Chemical route of modifications for functionalization of the films for improved properties lead to undesirable effects for biological applications. Hence a natural way to enhancing their properties is by functionalizing them using plant extracts. This report investigates the synthesis of bioactive phytochemical loaded polymer using Triticum aestivum (wheatgrass) extract incorporated in tripolyphosphate crosslinked chitosan. Physical and mechanical properties of the extract functionalized crosslinked chitosan were analyzed and this showed significant changes in thickness, tensile strength and % elongation of the blend. The extract functionalized chitosan was characterized using Fourier transform infrared spectroscopy (FT-IR), Scanning electron microscopy (SEM) and Energy dispersive spectroscopy (EDAX) confirming the interaction between the functional moieties of the extract and polymer. Antimicrobial analysis showed improved activity against Escherichia coli and Staphylococus aureus and Candida albicans. Presence of the extract in crosslinked chitosan enhanced the cytocompatibility in 3T3 cells carried out by MTT assay and showed improved cell migration properties determined by scratch assay.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J Sandhya
- Department of Applied Science and Technology, Anna University, Chennai, India
| | - S Veeralakshmi
- Department of Applied Science and Technology, Anna University, Chennai, India
| | - S Kalaiselvam
- Department of Applied Science and Technology, Anna University, Chennai, India
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