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Kyei-Barffour I, Margetts M, Vash-Margita A, Pelosi E. The Embryological Landscape of Mayer-Rokitansky-Kuster-Hauser Syndrome: Genetics and Environmental Factors. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:657-672. [PMID: 34970104 PMCID: PMC8686787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a disorder caused by Müllerian ducts dysgenesis affecting 1 in 5000 women with a typical 46,XX karyotype. The etiology of MRKH syndrome is complex and largely unexplained. Familial clustering suggests a genetic component and the spectrum of clinical presentations seems consistent with an inheritance pattern characterized by incomplete penetrance and variable expressivity. Mutations of several candidate genes have been proposed as possible causes based on genetic analyses of human patients and animal models. In addition, studies of monozygotic twins with discordant phenotypes suggest a role for epigenetic changes following potential exposure to environmental compounds. The spectrum of clinical presentations is consistent with intricate disruptions of shared developmental pathways or signals during early organogenesis. However, the lack of functional validation and translational studies have limited our understanding of the molecular mechanisms involved in this condition. The clinical management of affected women, including early diagnosis, genetic testing of MRKH syndrome, and the implementation of counseling strategies, is significantly impeded by these knowledge gaps. Here, we illustrate the embryonic development of tissues and organs affected by MRKH syndrome, highlighting key pathways that could be involved in its pathogenesis. In addition, we will explore the genetics of this condition, as well as the potential role of environmental factors, and discuss their implications to clinical practice.
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Affiliation(s)
- Isaac Kyei-Barffour
- Department of Biomedical Sciences, University of Cape
Coast, Cape Coast, Ghana
| | - Miranda Margetts
- Center for American Indian and Rural Health Equity,
Montana State University, Bozeman, MT, USA
| | - Alla Vash-Margita
- Department of Obstetrics, Gynecology and Reproductive
Sciences, Division of Pediatric and Adolescent Gynecology, Yale University
School of Medicine, New Haven, CT, USA
| | - Emanuele Pelosi
- Centre for Clinical Research, The University of
Queensland, Brisbane, QLD, Australia
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2
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Rattan S, Flaws JA. The epigenetic impacts of endocrine disruptors on female reproduction across generations†. Biol Reprod 2020; 101:635-644. [PMID: 31077281 DOI: 10.1093/biolre/ioz081] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/18/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Humans and animals are repeatedly exposed to endocrine disruptors, many of which are ubiquitous in the environment. Endocrine disruptors interfere with hormone action; thus, causing non-monotonic dose responses that are atypical of standard toxicant exposures. The female reproductive system is particularly susceptible to the effects of endocrine disruptors. Likewise, exposures to endocrine disruptors during developmental periods are particularly concerning because programming during development can be adversely impacted by hormone level changes. Subsequently, developing reproductive tissues can be predisposed to diseases in adulthood and these diseases can be passed down to future generations. The mechanisms of action by which endocrine disruptors cause disease transmission to future generations are thought to include epigenetic modifications. This review highlights the effects of endocrine disruptors on the female reproductive system, with an emphasis on the multi- and transgenerational epigenetic effects of these exposures.
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Affiliation(s)
- Saniya Rattan
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jodi A Flaws
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Illinois, USA
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3
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Cherian P, Zhu J, Bergfeld WF, Belsito DV, Hill RA, Klaassen CD, Liebler DC, Marks JG, Shank RC, Slaga TJ, Snyder PW, Heldreth B. Amended Safety Assessment of Parabens as Used in Cosmetics. Int J Toxicol 2020; 39:5S-97S. [DOI: 10.1177/1091581820925001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Expert Panel for Cosmetic Ingredient Safety (Panel) assessed the safety of 21 parabens as preservatives in cosmetic products. All of these ingredients are reported to function in cosmetics as preservatives; however, 5 are reported to also function as fragrance ingredients. The Panel reviewed relevant data relating to the safety of these ingredients under the reported conditions of use in cosmetic formulations. The Panel concluded that 20 of the 21 parabens included in this report are safe in cosmetics in the present practices of use and concentration described in this safety assessment when the sum of the total parabens in any given formulation does not exceed 0.8%. However, the available data are insufficient to support a conclusion of safety for benzylparaben in cosmetics.
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Affiliation(s)
- Priya Cherian
- Cosmetic Ingredient Review Scientific Analyst/Writer, Washington, DC, USA
| | - Jinqiu Zhu
- Cosmetic Ingredient Review Toxicologist, Washington, DC, USA
| | - Wilma F. Bergfeld
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - Donald V. Belsito
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - Ronald A. Hill
- Former Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | | | - Daniel C. Liebler
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - James G. Marks
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - Ronald C. Shank
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - Thomas J. Slaga
- Expert Panel for Cosmetic Ingredient Safety Member, Washington, DC, USA
| | - Paul W. Snyder
- Cosmetic Ingredient Review Toxicologist, Washington, DC, USA
| | - Bart Heldreth
- Cosmetic Ingredient Review Executive Director, Washington, DC, USA
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Zaccaroni M, Massolo A, Beani L, Seta DD, Farabollini F, Giannelli G, Fusani L, Dessì-Fulgheri F. Developmental exposure to low levels of ethinylestradiol affects social play in juvenile male rats. Toxicol Res 2020; 36:301-310. [PMID: 33005589 DOI: 10.1007/s43188-019-00035-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022] Open
Abstract
Juvenile social play contributes to the development of adult social and emotional skills in humans and non-human animals and is therefore a useful endpoint to study the effects of endocrine disrupters on behavior in animal models. Ethinylestradiol (EE2), a widely produced, powerful synthetic estrogen is widespread in the environment mainly because it is a component of the contraceptive pill. To understand whether clinical or environmental exposure to EE2 during critical perinatal periods can affect male social play, we exposed 72 male Sprague-Dawley rats to EE2 or vehicle either during gestation (from gestation day (GD) 5 through 20) or during lactation (from postnatal day (PND) 1 through 21). Two doses of EE2 were used to treat the dams: a lower dose in the range of possible environmental exposure (4 ng/kg/day) and a higher dose similar to that received during contraceptive treatment (400 ng/kg/day). Social play was observed between PND 40 and 45. A principal component analysis (PCA) of frequencies of behavioral items observed during play sessions allowed to allocate behaviors to the two main components that we named aggressive-like play and defensive-like play. Aggressive-like play was increased by gestational and decreased by lactational exposure. Defensive-like play was decreased by treatment. For both types of play the lower dose (4 ng/kg/day) was as effective as the higher one. Total social activity was increased by gestational and decreased by lactational exposure. These findings provide further evidence that exposure to low and to very low doses of EE2 during critical periods of development can affect essential aspects of social behavior, and that the timing of exposure is critical to understand its developmental action.
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Affiliation(s)
- Marco Zaccaroni
- Department di Biology, University of Firenze, Florence, Italy
| | - Alessandro Massolo
- Ethology Unit, Department of Biology, University of Pisa, Pisa, Italy and Laboratoire Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France
| | - Laura Beani
- Department di Biology, University of Firenze, Florence, Italy
| | - Daniele Della Seta
- Department of Medicine, Surgery and Neuroscience University of Siena, Siena, Italy
| | | | | | - Leonida Fusani
- Department of Cognitive Biology, University of Vienna, and Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
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Moldogazieva NT, Ostroverkhova DS, Kuzmich NN, Kadochnikov VV, Terentiev AA, Porozov YB. Elucidating Binding Sites and Affinities of ERα Agonists and Antagonists to Human Alpha-Fetoprotein by In Silico Modeling and Point Mutagenesis. Int J Mol Sci 2020; 21:ijms21030893. [PMID: 32019136 PMCID: PMC7036865 DOI: 10.3390/ijms21030893] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
Alpha-fetoprotein (AFP) is a major embryo- and tumor-associated protein capable of binding and transporting a variety of hydrophobic ligands, including estrogens. AFP has been shown to inhibit estrogen receptor (ER)-positive tumor growth, which can be attributed to its estrogen-binding ability. Despite AFP having long been investigated, its three-dimensional (3D) structure has not been experimentally resolved and molecular mechanisms underlying AFP–ligand interaction remains obscure. In our study, we constructed a homology-based 3D model of human AFP (HAFP) with the purpose of molecular docking of ERα ligands, three agonists (17β-estradiol, estrone and diethylstilbestrol), and three antagonists (tamoxifen, afimoxifene and endoxifen) into the obtained structure. Based on the ligand-docked scoring functions, we identified three putative estrogen- and antiestrogen-binding sites with different ligand binding affinities. Two high-affinity binding sites were located (i) in a tunnel formed within HAFP subdomains IB and IIA and (ii) on the opposite side of the molecule in a groove originating from a cavity formed between domains I and III, while (iii) the third low-affinity binding site was found at the bottom of the cavity. Here, 100 ns molecular dynamics (MD) simulation allowed us to study their geometries and showed that HAFP–estrogen interactions were caused by van der Waals forces, while both hydrophobic and electrostatic interactions were almost equally involved in HAFP–antiestrogen binding. Molecular mechanics/Generalized Born surface area (MM/GBSA) rescoring method exploited for estimation of binding free energies (ΔGbind) showed that antiestrogens have higher affinities to HAFP as compared to estrogens. We performed in silico point substitutions of amino acid residues to confirm their roles in HAFP–ligand interactions and showed that Thr132, Leu138, His170, Phe172, Ser217, Gln221, His266, His316, Lys453, and Asp478 residues, along with two disulfide bonds (Cys224–Cys270 and Cys269–Cys277), have key roles in both HAFP–estrogen and HAFP–antiestrogen binding. Data obtained in our study contribute to understanding mechanisms underlying protein–ligand interactions and anticancer therapy strategies based on ERα-binding ligands.
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Affiliation(s)
- Nurbubu T. Moldogazieva
- Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.O.); (N.N.K.); (Y.B.P.)
- Correspondence:
| | - Daria S. Ostroverkhova
- Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.O.); (N.N.K.); (Y.B.P.)
- Department of Bioengineering, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Nikolai N. Kuzmich
- Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.O.); (N.N.K.); (Y.B.P.)
- Department of Drug Safety, I.M. Smorodintsev Research Institute of Influenza, WHO National Influenza Centre of Russia, 197376 Saint Petersburg, Russia
| | - Vladimir V. Kadochnikov
- Department of Food Biotechnology and Engineering, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 Saint-Petersburg, Russia;
| | - Alexander A. Terentiev
- Deparment of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Yuri B. Porozov
- Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (D.S.O.); (N.N.K.); (Y.B.P.)
- Department of Food Biotechnology and Engineering, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 Saint-Petersburg, Russia;
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7
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Sakkiah S, Guo W, Pan B, Kusko R, Tong W, Hong H. Computational prediction models for assessing endocrine disrupting potential of chemicals. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 36:192-218. [PMID: 30633647 DOI: 10.1080/10590501.2018.1537132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Endocrine disrupting chemicals (EDCs) mimic natural hormones and disrupt endocrine function. Humans and wildlife are exposed to EDCs might alter endocrine functions through various mechanisms and lead to an adverse effects. Hence, EDCs identification is important to protect the ecosystem and to promote the public health. Leveraging in-vitro and in-vivo experiments to identify potential EDCs is time consuming and expensive. Hence, quantitative structure-activity relationship is applied to screen the potential EDCs. Here, we summarize the predictive models developed using various algorithms to forecast the binding activity of chemicals to the estrogen and androgen receptors, alpha-fetoprotein, and sex hormone binding globulin.
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Affiliation(s)
- Sugunadevi Sakkiah
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Wenjing Guo
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Bohu Pan
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Rebecca Kusko
- b Immuneering Corporation , Cambridge , Massachusetts , USA
| | - Weida Tong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Huixiao Hong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , Arkansas , USA
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Sakkiah S, Kusko R, Pan B, Guo W, Ge W, Tong W, Hong H. Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations. Front Pharmacol 2018; 9:492. [PMID: 29867496 PMCID: PMC5962723 DOI: 10.3389/fphar.2018.00492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023] Open
Abstract
When a small molecule binds to the androgen receptor (AR), a conformational change can occur which impacts subsequent binding of co-regulator proteins and DNA. In order to accurately study this mechanism, the scientific community needs a crystal structure of the Wild type AR (WT-AR) ligand binding domain, bound with antagonist. To address this open need, we leveraged molecular docking and molecular dynamics (MD) simulations to construct a structure of the WT-AR ligand binding domain bound with antagonist bicalutamide. The structure of mutant AR (Mut-AR) bound with this same antagonist informed this study. After molecular docking analysis pinpointed the suitable binding orientation of a ligand in AR, the model was further optimized through 1 μs of MD simulations. Using this approach, three molecular systems were studied: (1) WT-AR bound with agonist R1881, (2) WT-AR bound with antagonist bicalutamide, and (3) Mut-AR bound with bicalutamide. Our structures were very similar to the experimentally determined structures of both WT-AR with R1881 and Mut-AR with bicalutamide, demonstrating the trustworthiness of this approach. In our model, when WT-AR is bound with bicalutamide, Val716/Lys720/Gln733, or Met734/Gln738/Glu897 move and thus disturb the positive and negative charge clumps of the AF2 site. This disruption of the AF2 site is key for understanding the impact of antagonist binding on subsequent co-regulator binding. In conclusion, the antagonist induced structural changes in WT-AR detailed in this study will enable further AR research and will facilitate AR targeting drug discovery.
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Affiliation(s)
- Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Rebecca Kusko
- Immuneering Corporation, Cambridge, MA, United States
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Wenjing Guo
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
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Sakkiah S, Wang T, Zou W, Wang Y, Pan B, Tong W, Hong H. Endocrine Disrupting Chemicals Mediated through Binding Androgen Receptor Are Associated with Diabetes Mellitus. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 15:ijerph15010025. [PMID: 29295509 PMCID: PMC5800125 DOI: 10.3390/ijerph15010025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023]
Abstract
Endocrine disrupting chemicals (EDCs) can mimic natural hormone to interact with receptors in the endocrine system and thus disrupt the functions of the endocrine system, raising concerns on the public health. In addition to disruption of the endocrine system, some EDCs have been found associated with many diseases such as breast cancer, prostate cancer, infertility, asthma, stroke, Alzheimer’s disease, obesity, and diabetes mellitus. EDCs that binding androgen receptor have been reported associated with diabetes mellitus in in vitro, animal, and clinical studies. In this review, we summarize the structural basis and interactions between androgen receptor and EDCs as well as the associations of various types of diabetes mellitus with the EDCs mediated through androgen receptor binding. We also discuss the perspective research for further understanding the impact and mechanisms of EDCs on the risk of diabetes mellitus.
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Affiliation(s)
- Sugunadevi Sakkiah
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Tony Wang
- Department of Biology, Arkansas University, Fayetteville, AR 72701, USA.
| | - Wen Zou
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Yuping Wang
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Bohu Pan
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.
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10
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Zaccaroni M, Massolo A, Della Seta D, Farabollini F, Giannelli G, Fusani L, Dessì-Fulgheri F. Developmental Exposure to Low Levels of Ethinylestradiol Affects Play Behavior in Juvenile Female Rats. Neurotox Res 2017; 33:876-886. [PMID: 29260494 DOI: 10.1007/s12640-017-9852-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Juvenile social play contributes to the development of adult social and emotional skills in humans and non-human animals, and is therefore a useful endpoint to study the effects of endocrine disrupters on behavior in animal models. Ethinylestradiol (EE2) is a widely produced, powerful synthetic estrogen that is widespread in the environment mainly because is a component of the contraceptive pill. In addition, fetuses may be exposed to EE2 when pregnancy is undetected during contraceptive treatment. To understand whether exposure to EE2 during gestation or lactation affects social play, we exposed 72 female Sprague-Dawley rats to EE2 or vehicle either during gestation (gestation day (GD) 5 through GD 20) or during lactation (from postnatal day (PND) 1 through PND 21). Two doses of EE2 were used to treat the dams: a lower dose in the range of possible environmental exposure (4 ng/kg/day) and a higher dose equivalent to that received during contraceptive treatment (400 ng/kg/day). Behavioral testing was carried out between PND 40 and 45. A principal component analysis of frequencies of behavioral items observed during play sessions identified three main components: defensive-like play, aggressive-like play, and exploration. Aggressive-like play was significantly increased by both doses of EE2, and the gestational administration was in general more effective than the lactational one. Defensive-like play and exploration were not significantly affected by treatment. This research showed that low and very low doses of EE2 that mimic clinical or environmental exposure during development can affect important aspects of social behavior even during restricted time windows.
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Affiliation(s)
- Marco Zaccaroni
- Department di Biology, University of Firenze, Florence, Italy.
| | - Alessandro Massolo
- Ethology Unit, Department of Biology, University of Pisa, Pisa, Italy.,Laboratoire Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France
| | - Daniele Della Seta
- Department of Medicine, Surgery and Neuroscience University of Siena, Siena, Italy
| | | | | | - Leonida Fusani
- Department of Cognitive Biology, University of Vienna, and Konrad Lorenz Institute for Ethology, University of Veterinary Medicine, Vienna, Austria
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11
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NTP Research Report on Biological Activity of Bisphenol A (BPA) Structural Analogues and Functional Alternatives. ACTA ACUST UNITED AC 2017. [DOI: 10.22427/ntp-rr-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Sakkiah S, Selvaraj C, Gong P, Zhang C, Tong W, Hong H. Development of estrogen receptor beta binding prediction model using large sets of chemicals. Oncotarget 2017; 8:92989-93000. [PMID: 29190972 PMCID: PMC5696238 DOI: 10.18632/oncotarget.21723] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/27/2017] [Indexed: 12/31/2022] Open
Abstract
We developed an ERβ binding prediction model to facilitate identification of chemicals specifically bind ERβ or ERα together with our previously developed ERα binding model. Decision Forest was used to train ERβ binding prediction model based on a large set of compounds obtained from EADB. Model performance was estimated through 1000 iterations of 5-fold cross validations. Prediction confidence was analyzed using predictions from the cross validations. Informative chemical features for ERβ binding were identified through analysis of the frequency data of chemical descriptors used in the models in the 5-fold cross validations. 1000 permutations were conducted to assess the chance correlation. The average accuracy of 5-fold cross validations was 93.14% with a standard deviation of 0.64%. Prediction confidence analysis indicated that the higher the prediction confidence the more accurate the predictions. Permutation testing results revealed that the prediction model is unlikely generated by chance. Eighteen informative descriptors were identified to be important to ERβ binding prediction. Application of the prediction model to the data from ToxCast project yielded very high sensitivity of 90-92%. Our results demonstrated ERβ binding of chemicals could be accurately predicted using the developed model. Coupling with our previously developed ERα prediction model, this model could be expected to facilitate drug development through identification of chemicals that specifically bind ERβ or ERα.
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Affiliation(s)
- Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Chaoyang Zhang
- School of Computer Science, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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13
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Selvaraj C, Sakkiah S, Tong W, Hong H. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology. Food Chem Toxicol 2017; 112:495-506. [PMID: 28843597 DOI: 10.1016/j.fct.2017.08.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations.
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Affiliation(s)
- Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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Liu H, Yang X, Yin C, Wei M, He X. Development of predictive models for predicting binding affinity of endocrine disrupting chemicals to fish sex hormone-binding globulin. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 136:46-54. [PMID: 27816713 DOI: 10.1016/j.ecoenv.2016.10.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/23/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
Disturbing the transport process is a crucial pathway for endocrine disrupting chemicals (EDCs) exerting disrupting endocrine function. However, this mechanism has not received enough attention compared with that of hormones receptors and synthetase. Recently, we have explored the interaction between EDCs and sex hormone-binding globulin of human (hSHBG). In this study, interactions between EDCs and sex hormone-binding globulin of eight fish species (fSHBG) were investigated by employing classification methods and quantitative structure-activity relationships (QSAR). In the modeling, the relative binding affinity (RBA) of a chemical with 17β-estradiol binding to fSHBG was selected as the endpoint. Classification models were developed for two fish species, while QSAR models were established for the other six fish species. Statistical results indicated that the models had satisfactory goodness of fit, robustness and predictive ability, and that application domain covered a large number of endogenous and exogenous steroidal and non-steroidal chemicals. Additionally, by comparing the log RBA values, it was found that the same chemical may have different affinities for fSHBG from different fish species, thus species diversity should be taken into account. However, the affinity of fSHBG showed a high correlation for fishes within the same Order (i.e., Salmoniformes, Cypriniformes, Perciformes and Siluriformes), thus the fSHBG binding data for one fish species could be used to extrapolate other fish species in the same Order.
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Affiliation(s)
- Huihui Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China.
| | - Xianhai Yang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Jiang-wang-miao Street, Nanjing 210042, China.
| | - Cen Yin
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China
| | - Mengbi Wei
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China
| | - Xiao He
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China
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sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. Sci Rep 2016; 6:32115. [PMID: 27558848 PMCID: PMC4997263 DOI: 10.1038/srep32115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022] Open
Abstract
Understanding the binding between human leukocyte antigens (HLAs) and peptides is important to understand the functioning of the immune system. Since it is time-consuming and costly to measure the binding between large numbers of HLAs and peptides, computational methods including machine learning models and network approaches have been developed to predict HLA-peptide binding. However, there are several limitations for the existing methods. We developed a network-based algorithm called sNebula to address these limitations. We curated qualitative Class I HLA-peptide binding data and demonstrated the prediction performance of sNebula on this dataset using leave-one-out cross-validation and five-fold cross-validations. This algorithm can predict not only peptides of different lengths and different types of HLAs, but also the peptides or HLAs that have no existing binding data. We believe sNebula is an effective method to predict HLA-peptide binding and thus improve our understanding of the immune system.
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16
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Liu H, Yang X, Lu R. Development of classification model and QSAR model for predicting binding affinity of endocrine disrupting chemicals to human sex hormone-binding globulin. CHEMOSPHERE 2016; 156:1-7. [PMID: 27156209 DOI: 10.1016/j.chemosphere.2016.04.077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 06/05/2023]
Abstract
Disturbing the transport process is a crucial pathway for endocrine disrupting chemicals (EDCs) to disrupt endocrine function. However, this mechanism has not gotten enough attention, compared with that of hormone receptors and synthetase up to now, especially for the sex hormone transport process. In this study, we selected sex hormone-binding globulin (SHBG) and EDCs as a model system and the relative competing potency of a chemical with testosterone binding to SHBG (log RBA) as the endpoints, to develop classification models and quantitative structure-activity relationship (QSAR) models. With the classification model, a satisfactory model with nR09, nR10 and RDF155v as the most relevant variables was screened. Statistic results indicated that the model had the sensitivity, specificity, accuracy of 86.4%, 80.0%, 84.4% and 85.7%, 87.5%, 86.2% for the training set and validation set, respectively, highlighting a high classification performance of the model. With the QSAR model, a satisfactory model with statistical parameters, specifically, an adjusted determination coefficient (Radj(2)) of 0.810, a root mean square error (RMSE) of 0.616, a leave-one-out cross-validation squared correlation coefficient (QLOO(2)) of 0.777, a bootstrap method (QBOOT(2)) of 0.756, an external validation coefficient (Qext(2)) of 0.544 and a RMSEext of 0.859, were obtained, which implied satisfactory goodness of fit, robustness and predictive ability. The applicability domain of the current model covers a large number of structurally diverse chemicals, especially a few classes of nonsteroidal compounds.
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Affiliation(s)
- Huihui Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China.
| | - Xianhai Yang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Jiang-wang-miao Street, Nanjing, 210042, China
| | - Rui Lu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu Province, China
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17
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Zaccaroni M, Seta DD, Farabollini F, Fusani L, Dessì-Fulgheri F. Developmental Exposure to Very Low Levels of Ethynilestradiol Affects Anxiety in a Novelty Place Preference Test of Juvenile Rats. Neurotox Res 2016; 30:553-562. [DOI: 10.1007/s12640-016-9645-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 11/24/2022]
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Sakkiah S, Ng HW, Tong W, Hong H. Structures of androgen receptor bound with ligands: advancing understanding of biological functions and drug discovery. Expert Opin Ther Targets 2016; 20:1267-82. [PMID: 27195510 DOI: 10.1080/14728222.2016.1192131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Androgen receptor (AR) is a ligand-dependent transcription factor and a member of the nuclear receptor superfamily. It plays a vital role in male sexual development and regulates gene expression in various tissues, including prostate. Androgens are compounds that exert their biological effects via interaction with AR. Binding of androgens to AR initiates conformational changes in AR that affect binding of co-regulator proteins and DNA. AR agonists and antagonists are widely used in a variety of clinical applications (i.e. hypogonadism and prostate cancer therapy). AREAS COVERED This review provides a close look at structures of AR-ligand complexes and mutations in the receptor that have been revealed, discusses current challenges in the field, and sheds light on future directions. EXPERT OPINION AR is one of the primary targets for the treatment of prostate cancer, as AR antagonists inhibit prostate cancer growth. However, these drugs are not effective for long-term treatment and lead to castration-resistant prostate cancer. The structures of AR-ligand complexes are an invaluable scientific asset that enhances our understanding of biological functions and mechanisms of androgenic and anti-androgenic chemicals as well as promotes the discovery of superior drug candidates.
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Affiliation(s)
- Sugunadevi Sakkiah
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Hui Wen Ng
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Weida Tong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Huixiao Hong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
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Hong H, Shen J, Ng HW, Sakkiah S, Ye H, Ge W, Gong P, Xiao W, Tong W. A Rat α-Fetoprotein Binding Activity Prediction Model to Facilitate Assessment of the Endocrine Disruption Potential of Environmental Chemicals. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:372. [PMID: 27023588 PMCID: PMC4847034 DOI: 10.3390/ijerph13040372] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/10/2016] [Accepted: 03/22/2016] [Indexed: 11/21/2022]
Abstract
Endocrine disruptors such as polychlorinated biphenyls (PCBs), diethylstilbestrol (DES) and dichlorodiphenyltrichloroethane (DDT) are agents that interfere with the endocrine system and cause adverse health effects. Huge public health concern about endocrine disruptors has arisen. One of the mechanisms of endocrine disruption is through binding of endocrine disruptors with the hormone receptors in the target cells. Entrance of endocrine disruptors into target cells is the precondition of endocrine disruption. The binding capability of a chemical with proteins in the blood affects its entrance into the target cells and, thus, is very informative for the assessment of potential endocrine disruption of chemicals. α-fetoprotein is one of the major serum proteins that binds to a variety of chemicals such as estrogens. To better facilitate assessment of endocrine disruption of environmental chemicals, we developed a model for α-fetoprotein binding activity prediction using the novel pattern recognition method (Decision Forest) and the molecular descriptors calculated from two-dimensional structures by Mold² software. The predictive capability of the model has been evaluated through internal validation using 125 training chemicals (average balanced accuracy of 69%) and external validations using 22 chemicals (balanced accuracy of 71%). Prediction confidence analysis revealed the model performed much better at high prediction confidence. Our results indicate that the model is useful (when predictions are in high confidence) in endocrine disruption risk assessment of environmental chemicals though improvement by increasing number of training chemicals is needed.
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Affiliation(s)
- Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Jie Shen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Hui Wen Ng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Hao Ye
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA.
| | - Wenming Xiao
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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20
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Ng HW, Doughty SW, Luo H, Ye H, Ge W, Tong W, Hong H. Development and Validation of Decision Forest Model for Estrogen Receptor Binding Prediction of Chemicals Using Large Data Sets. Chem Res Toxicol 2015; 28:2343-51. [PMID: 26524122 DOI: 10.1021/acs.chemrestox.5b00358] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Some chemicals in the environment possess the potential to interact with the endocrine system in the human body. Multiple receptors are involved in the endocrine system; estrogen receptor α (ERα) plays very important roles in endocrine activity and is the most studied receptor. Understanding and predicting estrogenic activity of chemicals facilitates the evaluation of their endocrine activity. Hence, we have developed a decision forest classification model to predict chemical binding to ERα using a large training data set of 3308 chemicals obtained from the U.S. Food and Drug Administration's Estrogenic Activity Database. We tested the model using cross validations and external data sets of 1641 chemicals obtained from the U.S. Environmental Protection Agency's ToxCast project. The model showed good performance in both internal (92% accuracy) and external validations (∼ 70-89% relative balanced accuracies), where the latter involved the validations of the model across different ER pathway-related assays in ToxCast. The important features that contribute to the prediction ability of the model were identified through informative descriptor analysis and were related to current knowledge of ER binding. Prediction confidence analysis revealed that the model had both high prediction confidence and accuracy for most predicted chemicals. The results demonstrated that the model constructed based on the large training data set is more accurate and robust for predicting ER binding of chemicals than the published models that have been developed using much smaller data sets. The model could be useful for the evaluation of ERα-mediated endocrine activity potential of environmental chemicals.
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Affiliation(s)
- Hui Wen Ng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Stephen W Doughty
- School of Pharmacy, University of Nottingham Malaysia Campus , Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Heng Luo
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Hao Ye
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
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21
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Zhang C, Hong H, Mendrick DL, Tang Y, Cheng F. Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science. Biomark Med 2015; 9:1241-52. [PMID: 26506997 DOI: 10.2217/bmm.15.81] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Improved biomarker-based assessment of drug safety is needed in drug discovery and development as well as regulatory evaluation. However, identifying drug safety-related biomarkers such as genes, proteins, miRNA and single-nucleotide polymorphisms remains a big challenge. The advances of 'omics' and computational technologies such as genomics, transcriptomics, metabolomics, proteomics, systems biology, network biology and systems pharmacology enable us to explore drug actions at the organ and organismal levels. Computational and experimental systems pharmacology approaches could be utilized to facilitate biomarker-based drug safety assessment for drug discovery and development and to inform better regulatory decisions. In this article, we review the current status and advances of systems pharmacology approaches for the development of predictive models to identify biomarkers for drug safety assessment.
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Affiliation(s)
- Chen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Huixiao Hong
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Feixiong Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China.,State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan, China
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22
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Ng HW, Shu M, Luo H, Ye H, Ge W, Perkins R, Tong W, Hong H. Estrogenic activity data extraction and in silico prediction show the endocrine disruption potential of bisphenol A replacement compounds. Chem Res Toxicol 2015; 28:1784-95. [PMID: 26308263 DOI: 10.1021/acs.chemrestox.5b00243] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bisphenol A (BPA) replacement compounds are released to the environment and cause widespread human exposure. However, a lack of thorough safety evaluations on the BPA replacement compounds has raised public concerns. We assessed the endocrine disruption potential of BPA replacement compounds in the market to assist their safety evaluations. A literature search was conducted to ascertain the BPA replacement compounds in use. Available experimental estrogenic activity data of these compounds were extracted from the Estrogenic Activity Database (EADB) to assess their estrogenic potential. An in silico model was developed to predict the estrogenic activity of compounds lacking experimental data. Molecular dynamics (MD) simulations were performed to understand the mechanisms by which the estrogenic compounds bind to and activate the estrogen receptor (ER). Forty-five BPA replacement compounds were identified in the literature. Seven were more estrogenic and five less estrogenic than BPA, while six were nonestrogenic in EADB. A two-tier in silico model was developed based on molecular docking to predict the estrogenic activity of the 27 compounds lacking data. Eleven were predicted as ER binders and 16 as nonbinders. MD simulations revealed hydrophobic contacts and hydrogen bonds as the main interactions between ER and the estrogenic compounds.
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Affiliation(s)
- Hui Wen Ng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Mao Shu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Heng Luo
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Hao Ye
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Roger Perkins
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration , 3900 NCTR Road, Jefferson, Arkansas 72079, United States
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23
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Shirota M, Kawashima J, Nakamura T, Kamiie J, Shirota K, Yoshida M. Dose-dependent acceleration in the delayed effects of neonatal oral exposure to low-dose 17α-ethynylestradiol on reproductive functions in female Sprague-Dawley rats. J Toxicol Sci 2015; 40:727-38. [DOI: 10.2131/jts.40.727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Mariko Shirota
- Laboratory of Comparative Toxicology, School of Veterinary Medicine
| | - Jun Kawashima
- Laboratory of Comparative Toxicology, School of Veterinary Medicine
| | | | | | - Kinji Shirota
- Laboratory of Veterinary Pathology, Azabu University
- Research Institute of Biosciences, Azabu University
| | - Midori Yoshida
- Division of Pathology, National Institute of Health Sciences
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24
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Hong H, Branham WS, Ng HW, Moland CL, Dial SL, Fang H, Perkins R, Sheehan D, Tong W. Human sex hormone-binding globulin binding affinities of 125 structurally diverse chemicals and comparison with their binding to androgen receptor, estrogen receptor, and α-fetoprotein. Toxicol Sci 2014; 143:333-48. [PMID: 25349334 DOI: 10.1093/toxsci/kfu231] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One endocrine disruption mechanism is through binding to nuclear receptors such as the androgen receptor (AR) and estrogen receptor (ER) in target cells. The concentration of a chemical in serum is important for its entry into the target cells to bind the receptors, which is regulated by the serum proteins. Human sex hormone-binding globulin (SHBG) is the major transport protein in serum that can bind androgens and estrogens and thus change a chemical's availability to enter the target cells. Sequestration of an androgen or estrogen in the serum can alter the chemical elicited AR- and ER-mediated responses. To better understand the chemical-induced endocrine activity, we developed a competitive binding assay using human pregnancy plasma and measured the binding to the human SHBG for 125 structurally diverse chemicals, most of which were known to bind AR and ER. Eighty seven chemicals were able to bind the human SHBG in the assay, whereas 38 chemicals were nonbinders. Binding data for human SHBG are compared with that for rat α-fetoprotein, ER and AR. Knowing the binding profiles between serum and nuclear receptors will improve assessment of a chemical's potential for endocrine disruption. The SHBG binding data reported here represent the largest data set of structurally diverse chemicals tested for human SHBG binding. Utilization of the SHBG binding data with AR and ER binding data could enable better evaluation of endocrine disrupting potential of chemicals through AR- and ER-mediated responses since sequestration in serum could be considered.
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Affiliation(s)
- Huixiao Hong
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - William S Branham
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Hui Wen Ng
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Carrie L Moland
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Stacey L Dial
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Hong Fang
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Roger Perkins
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Daniel Sheehan
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
| | - Weida Tong
- *Division of Bioinformatics and Biostatistics, Division of Systems Biology, Division of Genetic and Molecular Toxicology and Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
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25
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Shang G, Xue J, Li M, Hu HY, Lu Y. Estrogen receptor affinity chromatography: a new method for characterization of novel estrogenic disinfection by-products. CHEMOSPHERE 2014; 104:251-257. [PMID: 24548648 DOI: 10.1016/j.chemosphere.2014.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/11/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
To identify the unknown estrogenic disinfection by-products (DBPs) from the chlorination extract, an effective method based on affinity chromatography with immobilized human recombinant estrogen receptor α (ERα) was developed, which has an advantage in targeting different potential estrogenic compounds from mixed sample simultaneously by comparing their relative binding activities to ER. The new method worked well for six known environmental estrogens. To further test the validity of this method for unknown chemicals, six DBPs of diethylstilbestrol (DES) with relatively strong ER binding affinity after chlorination were isolated and identified. It was found that except for 2-chloro-DES which showed 1.36 times stronger binding affinity than DES, most of the by-products bound to ER much more weakly than DES. All these seven by-products induced a dose-dependent transcriptional activation in two-hybrid-yeast assays. Z,Z-dienestrol (DE) and 2-chloro-DES, which exhibiting the weakest and the strongest binding affinity, were further tested for their transcriptional potential as 0.00243 and 0.014 compared to DES, respectively. However, they were still potential harmful environmental estrogenic disruptors as their estrogenic activities were much stronger than that of bisphenol A (BPA). These results demonstrated that the new method can help to screen unknown estrogenic compounds from mixture more efficiently.
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Affiliation(s)
- Guodong Shang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jinling Xue
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Man Li
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hong-Ying Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Yun Lu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
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26
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Shen J, Zhang W, Fang H, Perkins R, Tong W, Hong H. Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC Bioinformatics 2013; 14 Suppl 14:S6. [PMID: 24266910 PMCID: PMC3851483 DOI: 10.1186/1471-2105-14-s14-s6] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind and sequester estrogens, thus preventing entry to the target cell and where they could otherwise induce ER-mediated endocrine activity. Recently, we reported rat AFP binding affinities for a large set of structurally diverse chemicals, including 53 binders and 72 non-binders. However, the lack of three-dimensional (3D) structures of rat AFP hinders further understanding of the structural dependence for binding. Therefore, a 3D structure of rat AFP was built using homology modeling in order to elucidate rat AFP-ligand binding modes through docking analyses and molecular dynamics (MD) simulations. Methods Homology modeling was first applied to build a 3D structure of rat AFP. Molecular docking and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) scoring were then used to examine potential rat AFP ligand binding modes. MD simulations and free energy calculations were performed to refine models of binding modes. Results A rat AFP tertiary structure was first obtained using homology modeling and MD simulations. The rat AFP-ligand binding modes of 13 structurally diverse, representative binders were calculated using molecular docking, (MM-GBSA) ranking and MD simulations. The key residues for rat AFP-ligand binding were postulated through analyzing the binding modes. Conclusion The optimized 3D rat AFP structure and associated ligand binding modes shed light on rat AFP-ligand binding interactions that, in turn, provide a means to estimate binding affinity of unknown chemicals. Our results will assist in the evaluation of the endocrine disruption potential of chemicals.
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Shen J, Xu L, Fang H, Richard AM, Bray JD, Judson RS, Zhou G, Colatsky TJ, Aungst JL, Teng C, Harris SC, Ge W, Dai SY, Su Z, Jacobs AC, Harrouk W, Perkins R, Tong W, Hong H. EADB: an estrogenic activity database for assessing potential endocrine activity. Toxicol Sci 2013; 135:277-91. [PMID: 23897986 DOI: 10.1093/toxsci/kft164] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Endocrine-active chemicals can potentially have adverse effects on both humans and wildlife. They can interfere with the body's endocrine system through direct or indirect interactions with many protein targets. Estrogen receptors (ERs) are one of the major targets, and many endocrine disruptors are estrogenic and affect the normal estrogen signaling pathways. However, ERs can also serve as therapeutic targets for various medical conditions, such as menopausal symptoms, osteoporosis, and ER-positive breast cancer. Because of the decades-long interest in the safety and therapeutic utility of estrogenic chemicals, a large number of chemicals have been assayed for estrogenic activity, but these data exist in various sources and different formats that restrict the ability of regulatory and industry scientists to utilize them fully for assessing risk-benefit. To address this issue, we have developed an Estrogenic Activity Database (EADB; http://www.fda.gov/ScienceResearch/BioinformaticsTools/EstrogenicActivityDatabaseEADB/default.htm) and made it freely available to the public. EADB contains 18,114 estrogenic activity data points collected for 8212 chemicals tested in 1284 binding, reporter gene, cell proliferation, and in vivo assays in 11 different species. The chemicals cover a broad chemical structure space and the data span a wide range of activities. A set of tools allow users to access EADB and evaluate potential endocrine activity of chemicals. As a case study, a classification model was developed using EADB for predicting ER binding of chemicals.
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Affiliation(s)
- Jie Shen
- * Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079
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