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Shimmin BA, Haines LG, Shaw IC. In silico studies on the molecular interactions of steroid hormones and steroid hormone mimicking drugs in the androgen receptor binding cleft - Implications for prostate cancer treatment. Steroids 2024; 208:109456. [PMID: 38889811 DOI: 10.1016/j.steroids.2024.109456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/20/2024]
Abstract
Occupancy of prostate cancer (PCa) cell androgen receptors (AR) signals proliferation, therefore testosterone biosynthesis inhibitors and AR antagonists are important PCa treatments. Conversely, androgen mimics (e.g., prednisone) used in management of PCa might cause proliferation. The balance between PCa proliferation and inhibition predicts treatment success. We used in silico molecular modelling to explore interactions between ARs, androgens (testosterone, dihydrotestosterone (DHT)) and drugs used to treat (bicalutamide) and manage (dexamethasone, prednisone, hydrocortisone) PCa. We found that hydrogen (H-) bonds between testosterone, DHT and Arg752, Asn705 and Thr877 followed by ligand binding cleft hydrophobic interactions signal proliferation, whereas bicalutamide antagonism is via Phe764 interactions. Hydrocortisone, dexamethasone and prednisone H-bond Asn705 and Thr877, but not Arg752 in the absence of a water molecule. Studies with a bicalutamide agonist AR mutation showed different amino acid interactions, indicating testosterone and DHT would not promote proliferation as effectively as via the native receptor. However, hydrocortisone and bicalutamide form Arg752 and Asn705 H-bonds indicating agonism. Our results suggest that as PCa progresses the resulting mutations will change the proliferative response to androgens and their drug mimics, which have implications for the treatment of prostate cancer.
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Affiliation(s)
- Bridget A Shimmin
- Human Toxicology Research Group, School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand.
| | - Lydell G Haines
- Human Toxicology Research Group, School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Ian C Shaw
- Human Toxicology Research Group, School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
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2
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Cossaboon JM, Teh SJ, Sant KE. Reproductive toxicity of DDT in the Japanese medaka fish model: Revisiting the impacts of DDT+ on female reproductive health. CHEMOSPHERE 2024; 357:141967. [PMID: 38615950 PMCID: PMC11160350 DOI: 10.1016/j.chemosphere.2024.141967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
The organochlorine pesticide dichlorodiphenyltrichloroethane (DDT) is an endocrine-disrupting compound (EDC) that has been banned by most countries for decades. However, it continues to be detected in nearly all humans and wildlife due to its biological and environmental persistence. The ovarian dysgenesis syndrome hypothesis speculates that exposure to EDCs during sensitive developmental windows such as early gonadal differentiation lead to reproductive disorders later in life. Yet, mechanisms by which DDT affects developing gonads remain unclear due to the inherent challenge of getting developmental exposure data from adults presenting with reproductive disease. The Japanese medaka (Oryzias latipes) is a valuable fish model for sex-specific toxicological studies due to its chromosomal sex determination, external embryonic development, short generation time, and extensively mapped genome. It is well documented that medaka exposed to DDT and its metabolites and byproducts (herein referred to as DDT+) at different developmental time points experience permanent alterations in gonadal morphology, reproductive success, and molecular and hormonal signaling. However, the overwhelming majority of studies focus primarily on functional and morphological outcomes in males and females and have rarely investigated long-term transcriptional or molecular effects. This review summarizes previous experimental findings and the state of our knowledge concerning toxic effects DDT + on reproductive development, fertility, and health in the valuable medaka model. It also identifies gaps in knowledge, emphasizing a need for more focus on molecular mechanisms of ovarian endocrine disruption using enhanced molecular tools that have become increasingly available over the past few decades. Furthermore, DDT forms a myriad of over 45 metabolites and transformation products in biota and the environment, very few of which have been evaluated for environmental abundance or health effects. This reinforces the demand for high throughput and economical in vivo models for predictive toxicology screening, and the Japanese medaka is uniquely positioned to meet this need.
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Affiliation(s)
| | - Swee J Teh
- School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Karilyn E Sant
- School of Public Health, San Diego State University, San Diego, CA, 92182, USA.
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Long XB, Yao CR, Li SY, Zhang JG, Lu ZJ, Ma DD, Chen CE, Ying GG, Shi WJ. Screening androgen receptor agonists of fish species using machine learning and molecular model in NORMAN water-relevant list. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133844. [PMID: 38394900 DOI: 10.1016/j.jhazmat.2024.133844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Androgen receptor (AR) agonists have strong endocrine disrupting effects in fish. Most studies mainly investigate AR binding capacity using human AR in vitro. However, there is still few methods to rapidly predict AR agonists in aquatic organisms. This study aimed to screen AR agonists of fish species using machine learning and molecular models in water-relevant list from NORMAN, a network of reference laboratories for monitoring contaminants of emerging concern in the environment. In this study, machine learning approaches (e.g., Deep Forest (DF)), Random Forests and artificial neural networks) were applied to predict AR agonists. Zebrafish, fathead minnow, mosquitofish, medaka fish and grass carp are all important aquatic model organisms widely used to evaluate the toxicity of new pollutants, and the molecular models of ARs from these five fish species were constructed to further screen AR agonists using AlphaFold2. The DF method showed the best performances with 0.99 accuracy, 0.97 sensitivity and 1 precision. The Asn705, Gln711, Arg752, and Thr877 residues in human AR and the corresponding sites in ARs from the five fish species were responsible for agonist binding. Overall, 245 substances were predicted as suspect AR agonists in the five fish species, including, certain glucocorticoids, cholesterol metabolites, and cardiovascular drugs in the NORMAN list. Using machine learning and molecular modeling hybrid methods rapidly and accurately screened AR agonists in fish species, and helping evaluate their ecological risk in fish populations.
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Affiliation(s)
- Xiao-Bing Long
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Chong-Rui Yao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Si-Ying Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jin-Ge Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Zhi-Jie Lu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dong-Dong Ma
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Chang-Er Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Wen-Jun Shi
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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4
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Asnake S, Modig C, Olsson PE. Species differences in ligand interaction and activation of estrogen receptors in fish and human. J Steroid Biochem Mol Biol 2019; 195:105450. [PMID: 31437548 DOI: 10.1016/j.jsbmb.2019.105450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/22/2022]
Abstract
Estrogen receptor (ER) sequences vary between species and this suggests that there are differences in the ligand-specificity, leading to species-specific effects. This would indicate that it is not possible to generalize effects across species. In this study, we investigated the differences in activation potencies and binding affinities of ER´s alpha (α) and beta (β) in human, zebrafish and sea bream to elucidate species differences in response to estradiol, estrone, estriol and methyltestosterone. In vitro analysis showed that estradiol had the highest activity for all the ER´s except for human ERβ and seabream ERβ2. Alignment of the ligand binding domain and ligand binding pocket (LBP) residues of the three species showed that different residues were involved in the LBPs which led to differences in pocket volume, affected binding affinity and orientation of the ligands. By combining in silico and in vitro results, it was possible to identify the ligand specificities of ER´s. The results demonstrated that the human ER´s show lower resolution in ligand-dependent activation, suggesting higher promiscuity, than the zebrafish and seabream ER´s. These results show species-specificity of ER´s and suggest that species-specific differences must be taken into consideration when studying different exposure scenarios.
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Affiliation(s)
- Solomon Asnake
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden.
| | - Carina Modig
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Per-Erik Olsson
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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Zhou F, Zhao W, Zuo Z, Sheng Y, Zhou X, Hou Y, Cheng H, Zhou R. Characterization of androgen receptor structure and nucleocytoplasmic shuttling of the rice field eel. J Biol Chem 2010; 285:37030-40. [PMID: 20841357 PMCID: PMC2978631 DOI: 10.1074/jbc.m110.161968] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 09/07/2010] [Indexed: 11/06/2022] Open
Abstract
Androgen receptor (AR) plays a critical role in prostate cancer and male sexual differentiation. We have identified AR from a primitive vertebrate with a sex reversal characteristic, the rice field eel. AR of this species (eAR) is distinct from human AR, especially in the ligand binding domain (LBD), and its expression in gonads shows an increasing tendency during gonadal transformation from ovary via ovotestis to testis. eAR has a restricted androgen-dependent transactivation function after a nuclear translocation upon dihydrotestosterone exposure. A functional nuclear localization signal was further identified in the DNA binding domain and hinge region. Although nuclear export is CRM1-independent, eAR has a novel nuclear export signal, which is negatively charged, indicating that a nuclear export pathway may be mediated by electrostatic interaction. Further, our studies have identified critical sequences for ligand binding in the C terminus. A structure of three α-helices in the LBD has been conserved from eels to humans during vertebrate evolution, despite a distinct amino acid sequence. Mutation analysis confirmed that the LBD is essential for dihydrotestosterone-induced nuclear import of eAR and following transactivation function in the nucleus. In addition, eAR interacts with both Sox9a1 and Sox9a2, and their interaction regulates transactivation of eAR. Our data suggest that the primitive species conserves and especially acquires key novel domains, the nuclear export signal and LBD, for the eAR function in spite of a rapid sequence evolution.
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MESH Headings
- Active Transport, Cell Nucleus
- Amino Acid Sequence
- Androgens/pharmacology
- Animals
- Blotting, Northern
- COS Cells
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Chlorocebus aethiops
- Dihydrotestosterone/pharmacology
- Eels/genetics
- In Situ Hybridization
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nuclear Localization Signals
- Phylogeny
- Protein Conformation
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- SOX9 Transcription Factor/genetics
- SOX9 Transcription Factor/metabolism
- Sequence Homology, Amino Acid
- Subcellular Fractions
- Transcriptional Activation
- Exportin 1 Protein
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Affiliation(s)
- Fang Zhou
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Wei Zhao
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Zhixiang Zuo
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Yue Sheng
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Yu Hou
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hanhua Cheng
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Rongjia Zhou
- From the Department of Genetics and Center for Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China
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Verhaegen Y, Parmentier K, Swevers L, Rougé P, Soin T, De Coen W, Cooreman K, Smagghe G. The brown shrimp (Crangon crangon L.) ecdysteroid receptor complex: cloning, structural modeling of the ligand-binding domain and functional expression in an EcR-deficient Drosophila cell line. Gen Comp Endocrinol 2010; 168:415-23. [PMID: 20515691 DOI: 10.1016/j.ygcen.2010.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 04/23/2010] [Accepted: 05/24/2010] [Indexed: 01/10/2023]
Abstract
cDNAs encoding ecdysteroid receptor (EcR) and retinoid X receptor (RXR) were cloned and sequenced from brown shrimp Crangon crangon (Crustacea: Decapoda), a common faunal species and commercially important in the North-West European coastal waters. A 3D model of the ligand-binding domain (LBD) of EcR was created and docking of ponasterone A (PonA) was simulated in silico. Finally, we report the transfection of expression plasmids for these receptors in the mutant Drosophila L57-3-11 cell line. Through an ecdysteroid responsive reporter assay we clearly prove the functionality of shrimp ecdysteroid receptor in the transfected L57-3-11 cell line. Our results indicate that the Drosophila L57-3-11 cell line and in silico LBD modeling can be used to study the function of crustacean ecdysteroid receptors and be applied to assess endocrine disrupting effects on non-target crustacean species.
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Affiliation(s)
- Yves Verhaegen
- Laboratory of Agrozoology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Wu B, Ford T, Gu JD, Zhang XX, Li AM, Cheng SP. Computational studies of interactions between endocrine disrupting chemicals and androgen receptor of different vertebrate species. CHEMOSPHERE 2010; 80:535-541. [PMID: 20546840 DOI: 10.1016/j.chemosphere.2010.04.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 04/13/2010] [Accepted: 04/18/2010] [Indexed: 05/29/2023]
Abstract
Homology modeling and molecular docking were used to in silico analyze the interactions between six endocrine disrupting chemicals (EDCs) and 11 androgen receptors (ARs) of different vertebrate species. The MODELLER 9V7 program was employed to construct the homology models of AR ligand binding domains (LBDs) from birds, amphibians, bony fishes and cartilaginous fishes. The Surflex-Dock program was applied to calculate and analyze the binding affinities between the six EDCs and AR LBDs. The docking experiment showed that AR LBDs had high affinities with nonyl phenol (NP) and butyl benzyl phthalate (BBP), but low affinities with the 2,2',4,4',5,5'-hexabromodiphenyl ether (BDE153). The results of cluster analysis suggested that predicted binding affinities were species-specific, which was consistent with the phylogenetic analysis of AR LBDs. The difference of binding affinities could be mainly due to the different hydrogen bonds and the orientation of ligands in the binding pockets. Our results suggest that integrated methods of phylogenetic analysis, homology modeling and molecular docking might be a potential tool to predict the different interactions between contaminants and associated receptors in different trophic levels.
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Exploration of endocrine-disrupting chemicals on estrogen receptor alpha by the agonist/antagonist differential-docking screening (AADS) method: 4-(1-adamantyl)phenol as a potent endocrine disruptor candidate. Toxicol Lett 2009; 191:33-9. [PMID: 19666091 DOI: 10.1016/j.toxlet.2009.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Revised: 07/31/2009] [Accepted: 08/04/2009] [Indexed: 11/22/2022]
Abstract
We established a novel screening method to survey endocrine-disrupting chemicals by means of in silico docking calculations. Endocrine disruptors target the human nuclear receptor, which bind a chemical in a pocket presenting in the ligand-binding domain (LBD). The LBD alters its conformation, depending upon the binding of either agonist or antagonist. We discovered that the chemicals can be differentiated into either agonist or antagonist by the docking calculations of the chemical for the LBD. We used the crystal structures of both agonist-bound LBDs and antagonist-bond LBDs as templates in the docking calculations, and estimated binding energies to discriminate between agonist and antagonist bindings. This agonist/antagonist differential-docking screening (AADS) method predicted, for example, 4-(1-adamantyl)phenol as an agonist of the human estrogen receptor alpha (hERalpha). Indeed, this compound, one of the essential raw materials for nanoporous organosilicate thin films, was confirmed to exhibit strong agonist activity in the reporter-gene assay for hERalpha with a high binding affinity. The AADS method is an approach that appears to foresee both the binding ability and the agonist/antagonist function of chemicals for the target nuclear receptors.
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