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Souza TL, da Luz JZ, Barreto LDS, de Oliveira Ribeiro CA, Neto FF. Structure-based modeling to assess binding and endocrine disrupting potential of polycyclic aromatic hydrocarbons in Daniorerio. Chem Biol Interact 2024; 398:111109. [PMID: 38871163 DOI: 10.1016/j.cbi.2024.111109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
Environmental contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have raised concerns regarding their potential endocrine-disrupting effects on aquatic organisms, including fish. In this study, molecular docking and molecular dynamics techniques were employed to evaluate the endocrine-disrupting potential of PAHs in zebrafish, as a model organism. A virtual screening with 72 PAHs revealed a correlation between the number of PAH aromatic rings and their binding affinity to proteins involved in endocrine regulation. Furthermore, PAHs with the highest binding affinities for each protein were identified: cyclopenta[cd]pyrene for AR (-9.7 kcal/mol), benzo(g)chrysene for ERα (-11.5 kcal/mol), dibenzo(a,e)pyrene for SHBG (-8.7 kcal/mol), dibenz(a,h)anthracene for StAR (-11.2 kcal/mol), and 2,3-benzofluorene for TRα (-9.8 kcal/mol). Molecular dynamics simulations confirmed the stability of the protein-ligand complexes formed by the PAHs with the highest binding affinities throughout the simulations. Additionally, the effectiveness of the protocol used in this study was demonstrated by the receiver operating characteristic curve (ROC) analysis, which effectively distinguished decoys from true ligands. Therefore, this research provides valuable insights into the endocrine-disrupting potential of PAHs in fish, highlighting the importance of assessing their impact on aquatic ecosystems.
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Affiliation(s)
- Tugstênio L Souza
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil.
| | - Jessica Zablocki da Luz
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Luiza Dos Santos Barreto
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Ciro Alberto de Oliveira Ribeiro
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Francisco Filipak Neto
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil.
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2
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Mathpal D, Almeleebia TM, Alshahrani KM, Alshahrani MY, Ahmad I, Asiri M, Kamal M, Jawaid T, Srivastava SP, Saeed M, Balaramnavar VM. Identification of 3-((1-(Benzyl(2-hydroxy-2-phenylethyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamoyl)pyrazine-2-carboxylic Acid as a Potential Inhibitor of Non-Nucleosidase Reverse Transcriptase Inhibitors through InSilico Ligand- and Structure-Based Approaches. Molecules 2021; 26:molecules26175262. [PMID: 34500699 PMCID: PMC8433663 DOI: 10.3390/molecules26175262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 12/03/2022] Open
Abstract
Non-nucleosidase reverse transcriptase inhibitors (NNRTIs) are highly promising agents for use in highly effective antiretroviral therapy. We implemented a rational approach for the identification of promising NNRTIs based on the validated ligand- and structure-based approaches. In view of our state-of-the-art techniques in drug design and discovery utilizing multiple modeling approaches, we report here, for the first time, quantitative pharmacophore modeling (HypoGen), docking, and in-house database screening approaches in the identification of potential NNRTIs. The validated pharmacophore model with three hydrophobic groups, one aromatic ring group, and a hydrogen-bond acceptor explains the interactions at the active site by the inhibitors. The model was implemented in pharmacophore-based virtual screening (in-house and commercially available databases) and molecular docking for prioritizing the potential compounds as NNRTI. The identified leads are in good corroboration with binding affinities and interactions as compared to standard ligands. The model can be utilized for designing and identifying the potential leads in the area of NNRTIs.
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Affiliation(s)
- Deepti Mathpal
- School of Pharmacy and Research, Sanskriti University, 28 K. M. Stone, Mathura Delhi Highway, Chhata, Mathura 281401, Uttar Pradesh, India;
| | - Tahani M. Almeleebia
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia;
| | - Kholoud M. Alshahrani
- College of Medicine, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia;
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Mohammed Asiri
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, P.O. Box 173, Al Kharj 11942, Saudi Arabia;
| | - Talha Jawaid
- Department of Pharmacology, College of Medicine, Al Imam Mohammad ibn Saud Islamic University (IMSIU), Othman ibn Affan Street, Riyadh 13317, Saudi Arabia;
| | - Swayam Prakash Srivastava
- Department of Pediatrics, Yale University School of Medicine CT, New Haven, CT 06520, USA;
- Vascular Biology and Therapeutic Program, Yale University School of Medicine CT, New Haven, CT 06511, USA
| | - Mohd Saeed
- Department of Biology College of Sciences, University of Hail, P.O. Box 2440, Hail 55425, Saudi Arabia
- Correspondence: (M.S.); (V.M.B.)
| | - Vishal M. Balaramnavar
- School of Pharmacy and Research, Sanskriti University, 28 K. M. Stone, Mathura Delhi Highway, Chhata, Mathura 281401, Uttar Pradesh, India;
- Correspondence: (M.S.); (V.M.B.)
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3
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Hazarika J, Ganguly M, Mahanta R. Molecular interactions of chlorpyrifos and its environmental degradation products with human sex hormone-binding globulin: an in silico study. J Appl Toxicol 2019; 39:1002-1011. [DOI: 10.1002/jat.3789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Mausumi Ganguly
- Department of Chemistry; Cotton University; Guwahati 781001 Assam India
| | - Rita Mahanta
- Department of Zoology; Cotton University; Guwahati 781001 Assam India
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Lipiński PFJ, Szurmak P. SCRAMBLE'N'GAMBLE: a tool for fast and facile generation of random data for statistical evaluation of QSAR models. CHEMICAL PAPERS 2017; 71:2217-2232. [PMID: 29104352 PMCID: PMC5655615 DOI: 10.1007/s11696-017-0215-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/26/2017] [Indexed: 01/20/2023]
Abstract
A common practice in modern QSAR modelling is to derive models by variable selection methods working on large descriptor pools. As pointed out previously, this is intrinsically burdened with the risk of finding random correlations. Therefore it is desirable to perform tests showing the performance of models built on random data. In this contribution, we introduce a simple and freely available software tool SCRAMBLE’N’GAMBLE that is aimed at facilitating data preparation for y-randomization and pseudo-descriptors tests. Then, four close-to-real-world modelling situations are analysed. The tests indicate what the quality of obtained QSAR models is like in comparison to chance models derived from random data. The non-randomness is not the only requirement for a good QSAR model, however, it is a good practice to consider it together with internal statistical parameters and possible physical interpretations of a model.
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Affiliation(s)
- Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland
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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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Sheikh IA, Tayubi IA, Ahmad E, Ganaie MA, Bajouh OS, AlBasri SF, Abdulkarim IMJ, Beg MA. Computational insights into the molecular interactions of environmental xenoestrogens 4-tert-octylphenol, 4-nonylphenol, bisphenol A (BPA), and BPA metabolite, 4-methyl-2, 4-bis (4-hydroxyphenyl) pent-1-ene (MBP) with human sex hormone-binding globulin. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 135:284-291. [PMID: 27750096 DOI: 10.1016/j.ecoenv.2016.10.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/13/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Environmental contamination has been one of the major drawbacks of the industrial revolution. Several man-made chemicals are constantly released into the environment during the manufacturing process and by leaching from the industrial products. As a result, human and animal populations are exposed to these synthetic chemicals on a regular basis. Many of these chemicals have adverse effects on the physiological functions, particularly on the hormone systems in human and animals and are called endocrine disrupting chemicals (EDCs). Bisphenol A (BPA), 4-tert-octylphenol (OP), and 4-nonylphenol (NP) are three high volume production EDCs that are widely used for industrial purposes and are present ubiquitously in the environment. Bisphenol A is metabolized in the human body to a more potent compound (MBP: 4-Methyl-2, 4-bis (4-hydroxyphenyl) pent-1-ene). Epidemiological and experimental studies have shown the three EDCs to be associated with adverse effects on reproductive system in human and animals. Sex hormone-binding globulin (SHBG) is a circulatory protein that binds sex steroids and is a potential target for endocrine disruptors in the human body. The current study was done in order to understand the binding mechanism of OP, BPA, NP, and MBP with human SHBG using in silico approaches. All four compounds showed high binding affinity with SHBG, however, the binding affinity values were higher (more negative) for MBP and NP than for OP and BPA. The four ligands interacted with 19-23 residues of SHBG and a consistent overlapping of the interacting residues for the four ligands with the residues for the natural ligand, dihydrotestosterone (DHT; 82-91% commonality) was shown. The overlapping SHBG interacting residues among DHT and the four endocrine disruptors suggested that these compounds have potential for interference and disruption in the steroid binding function.
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Affiliation(s)
- Ishfaq A Sheikh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Iftikhar A Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Ejaz Ahmad
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Majid A Ganaie
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Kingdom of Saudi Arabia
| | - Osama S Bajouh
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Samera F AlBasri
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ibtihal M J Abdulkarim
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohd A Beg
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
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Sheikh IA, Yasir M, Abu-Elmagd M, Dar TA, Abuzenadah AM, Damanhouri GA, Al-Qahtani M, Beg MA. Human sex hormone-binding globulin as a potential target of alternate plasticizers: an in silico study. BMC STRUCTURAL BIOLOGY 2016; 16:15. [PMID: 27719672 PMCID: PMC5056528 DOI: 10.1186/s12900-016-0067-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Currently, alternate plasticizers are used to replace phthalate plasticizers in children's toys, medical equipments and food packaging, due to the adverse effects of phthalate compounds on human health and laws prohibiting their use. Current information regarding the safety and potential adverse effects of alternate plasticizers is limited and recent studies have found alternate plasticizers to display similar characteristics to those observed in phthalate plasticizers. This study was undertaken to evaluate and predict the potential endocrine disrupting activity of the three most commonly used alternate plasticizers: di(2-ethylhexyl)terephthalate (DEHT), tris(2-ethylhexyl)trimellitate (TOTM), and diisononyl hexahydrophthalate (DINCH) against human sex hormone-binding globulin (SHBG) using in silico approaches. MATERIALS AND METHODS The crystal structure of human SHBG (Id: 1D2S) was retrieved from Protein Data Bank. PubChem database was searched for the structures of alternate plasticizers, DEHT, TOTM, and DINCH. Docking was performed using Glide (Schrodinger) Induced Fit Docking module. RESULTS Induced Fit Docking of three alternate plasticizer compounds indicated that each of the three compounds fitted well into the steroid binding pocket of SHBG. Docking displays showed interactions of alternate plasticizers with 25-30 amino-acid residues of SHBG; 18-20 amino residues overlapped between the natural ligand, DHT, and the three compounds (commonality of 82-91 %). The hydrogen-bonding interaction of the amino-acid residue, Asn-82, of SHBG was also present in displays of DHT and all the three alternate phthalates. The binding affinity of all the three alternate phthalates was higher than DHT; maximum in DINCH followed by TOTM and DEHT. CONCLUSION Our results suggested that the three alternate plasticizers have potential to engage the important interacting residues of SHBG and thus interfere in its steroid homeostatic function.
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Affiliation(s)
- Ishfaq A. Sheikh
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, 21589 Jeddah, Kingdom of Saudi Arabia
| | - Muhammad Yasir
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, 21589 Jeddah, Kingdom of Saudi Arabia
| | - Muhammad Abu-Elmagd
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Tanveer A. Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, India
| | - Adel M. Abuzenadah
- KACST Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ghazi A. Damanhouri
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, 21589 Jeddah, Kingdom of Saudi Arabia
| | - Mohammed Al-Qahtani
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohd A. Beg
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, 21589 Jeddah, Kingdom of Saudi Arabia
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Rutkowska AZ, Diamanti-Kandarakis E. Polycystic ovary syndrome and environmental toxins. Fertil Steril 2016; 106:948-58. [PMID: 27559705 DOI: 10.1016/j.fertnstert.2016.08.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/15/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022]
Abstract
Polycystic ovary syndrome (PCOS) is the most common, heterogeneous, and multifactorial endocrine disorder in premenopausal women. The pathophysiology of this endocrinopathy is still unclear; however, the heterogeneity of its features within ethnic races, geographic location, and families suggests that environment and lifestyle are of prime importance. This work is mainly focused on the possible role of the most common and studied environmental toxins for this syndrome in the pathogenesis of PCOS. Plasticizers, such as bisphenol A (BPA) or phthalates, which belong to the categories of endocrine disrupting chemicals (EDCs) and advanced glycation end products (AGEs), affect humans' health in everyday, industrialized life; therefore special attention should be paid to such exposure. Timing of exposure to EDCs is crucial for the intensity of adverse health effects. It is now evident that fetuses, infants, and/or young children are the most susceptible groups, especially in the early development periods. Prenatal exposure to EDCs that mimic endogenous hormones may contribute to the altered fetal programming and in consequence lead to PCOS and other adverse health effects, potentially transgenerationally. Acute or prolonged exposure to EDCs and AGEs through different life cycle stages may result in destabilization of the hormonal homeostasis and lead to disruption of reproductive functions. They may also interfere with metabolic alterations such as obesity, insulin resistance, and compensatory hyperinsulinemia that can exacerbate the PCOS phenotype and contribute to PCOS consequences such as type 2 diabetes and cardiovascular disease. Since wide exposure to environmental toxins and their role in the pathophysiology of PCOS are supported by extensive data derived from diverse scientific models, protective strategies and strong recommendations should be considered to reduce human exposure to protect present and future generations from their adverse health effects.
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Affiliation(s)
| | - Evanthia Diamanti-Kandarakis
- Department of Endocrinology and Diabetes Center of Excellence, Medical School University of Athens, EUROCLINIC, Athens, Greece.
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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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Endocrine Disruption: Computational Perspectives on Human Sex Hormone-Binding Globulin and Phthalate Plasticizers. PLoS One 2016; 11:e0151444. [PMID: 26963243 PMCID: PMC4786149 DOI: 10.1371/journal.pone.0151444] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/29/2016] [Indexed: 11/23/2022] Open
Abstract
Phthalates are a class of high volume production chemicals used as plasticizers for household and industrial use. Several members of this chemical family have endocrine disrupting activity. Owing to ubiquitous environmental distribution and exposure of human population at all stages of life, phthalate contamination is a continuous global public health problem. Clinical and experimental studies have indicated that several phthalates are associated with adverse effects on development and function of human and animal systems especially the reproductive system and exposures during pregnancy and early childhood are by far of utmost concern. Sex hormone-binding globulin (SHBG) is a plasma carrier protein that binds androgens and estrogens and represents a potential target for phthalate endocrine disruptor function in the body. In the present study, the binding mechanism of the nine phthalates i.e. DMP, DBP, DIBP, BBP, DNHP, DEHP, DNOP, DINP, DIDP with human SHBG was delineated by molecular docking simulation. Docking complexes of the nine phthalates displayed interactions with 15–31 amino acid residues of SHBG and a commonality of 55–95% interacting residues between natural ligand of SHBG, dihydrotestosterone, and the nine phthalate compounds was observed. The binding affinity values were more negative for long chain phthalates DEHP, DNOP, DINP, and DIDP compared to short chain phthalates such as DMP and DBP. The Dock score and Glide score values were also higher for long chain phthalates compared to short chain phthalates. Hence, overlapping of interacting amino acid residues between phthalate compounds and natural ligand, dihydrotestosterone, suggested potential disrupting activity of phthalates in the endocrine homeostasis function of SHBG, with long chain phthalates expected to be more potent than the short chain phthalates.
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11
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Mandalapu D, Singh DK, Gupta S, Balaramnavar VM, Shafiq M, Banerjee D, Sharma VL. Discovery of monocarbonyl curcumin hybrids as a novel class of human DNA ligase I inhibitors: in silico design, synthesis and biology. RSC Adv 2016. [DOI: 10.1039/c5ra25853g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A pharmacophore model identified a novel class of hLigI inhibitors to treat cancer. 36 compounds were synthesized and the identified inhibitor, compound 23 shown antiligase activity at IC50 24.9 μM by abolishing the interaction between hLigI and DNA.
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Affiliation(s)
- Dhanaraju Mandalapu
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Deependra Kumar Singh
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Sonal Gupta
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishal M. Balaramnavar
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Mohammad Shafiq
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Dibyendu Banerjee
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishnu Lal Sharma
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
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12
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Tokarz J, Möller G, Hrabě de Angelis M, Adamski J. Steroids in teleost fishes: A functional point of view. Steroids 2015; 103:123-44. [PMID: 26102270 DOI: 10.1016/j.steroids.2015.06.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/23/2023]
Abstract
Steroid hormones are involved in the regulation of a variety of processes like embryonic development, sex differentiation, metabolism, immune responses, circadian rhythms, stress response, and reproduction in vertebrates. Teleost fishes and humans show a remarkable conservation in many developmental and physiological aspects, including the endocrine system in general and the steroid hormone related processes in particular. This review provides an overview of the current knowledge about steroid hormone biosynthesis and the steroid hormone receptors in teleost fishes and compares the findings to the human system. The impact of the duplicated genome in teleost fishes on steroid hormone biosynthesis and perception is addressed. Additionally, important processes in fish physiology regulated by steroid hormones, which are most dissimilar to humans, are described. We also give a short overview on the influence of anthropogenic endocrine disrupting compounds on steroid hormone signaling and the resulting adverse physiological effects for teleost fishes. By this approach, we show that the steroidogenesis, hormone receptors, and function of the steroid hormones are reasonably well understood when summarizing the available data of all teleost species analyzed to date. However, on the level of a single species or a certain fish-specific aspect of physiology, further research is needed.
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Affiliation(s)
- Janina Tokarz
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Gabriele Möller
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Member of German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Member of German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.
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Saxena M, Bhunia SS, Saxena AK. Molecular modelling studies on 2-substituted octahydropyrazinopyridoindoles for histamine H2 receptor antagonism. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:739-755. [PMID: 26461804 DOI: 10.1080/1062936x.2015.1088572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
The human histamine H2 receptor (hH2HR) is a G-protein coupled receptor protein with seven transmembrane (TM)-spanning helices primarily involved in regulation of gastric acid secretion. Antagonists targeting hH2HR are useful in the treatment of hyperacidic conditions such as peptic ulcers, gastresophageal reflux disease and gastrointestinal bleeding. We have previously reported the antagonism of 2-substituted pyrazinopyridoindoles at the human histamine H1 receptor and mode of binding of these compounds at the hH1HR using in silico methods. Interestingly, some of the compounds in the series also showed promising activity towards hH2HR that prompted us to investigate the mode of binding of these compounds at hH2HR. In the absence of the crystal structure of hH2HR a homology model has been constructed using multiple sequence alignment, using the X-ray crystal structures of Turkey β1-adrenergic receptor (tβ1AR), Human histamine H1 receptor (hH1HR), Human β2-adrenergic receptor (hβ2AR) and Human D3 dopamine receptor (hD3R). The important residues for binding were depicted in TMIII, TMV, TMVI and TMVII by the homology modelled hH2HR for 2-substituted pyrazinopyridoindoles. A comparative study for deducing the selectivity regarding the binding towards hH1HR and hH2HR has been carried out, which may be useful in designing of selective hH1HR/hH2HR antagonists in these classes of compounds.
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Affiliation(s)
- M Saxena
- a Department of Chemistry , Amity University , Lucknow , India
| | - S S Bhunia
- b Global Institute of Pharmaceutical Education and Research , Kashipur , Uttarakhand , India
| | - A K Saxena
- c Division of Medicinal and Process Chemistry , CSIR Central Drug Research Institute , Lucknow , India
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Sashidhara KV, Avula SR, Doharey PK, Singh LR, Balaramnavar VM, Gupta J, Misra-Bhattacharya S, Rathaur S, Saxena AK, Saxena JK. Designing, synthesis of selective and high-affinity chalcone-benzothiazole hybrids as Brugia malayi thymidylate kinase inhibitors: In vitro validation and docking studies. Eur J Med Chem 2015; 103:418-28. [DOI: 10.1016/j.ejmech.2015.09.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 11/29/2022]
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15
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Bro E, Millot F, Decors A, Devillers J. Quantification of potential exposure of gray partridge (Perdix perdix) to pesticide active substances in farmlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 521-522:315-25. [PMID: 25847175 DOI: 10.1016/j.scitotenv.2015.03.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 05/15/2023]
Abstract
Estimating exposure of wild birds to plant protection products is of key importance in the risk assessment process evaluating their harmful potential. In this paper, we propose an ecologically-relevant methodology to estimate potential exposure to active substances (ASs) of a farmland focal bird, the gray partridge Perdix perdix. It is based on bird habitat use of fields at the time of pesticide applications. It accounts for spatio-temporal heterogeneity at population and landscape scales. We identify and quantify the potential exposure to 179 ASs of 140 clutches during pre-laying, laying, and incubation phases, and of 75 coveys. The data come from a large scale field study combining radiotelemetry and a farmer survey. They were collected in 12 different representative sites. The proportion of clutches potentially exposed to a given chemical was ≥5% for 32 ASs; prothioconazole and epoxiconazole ranking first. 71% of clutches were potentially exposed to ≥1 AS and 67% to ≥2 ASs. Mixtures involved 2 to 22 ASs. They emerged from commercial formulations, tank mixtures, bird habitat use, and combinations. ASs were fungicides (53%), herbicides (25%), and insecticides (16%) used on a variety of crops in April-June, when ground-nesting birds are breeding. The European Food Safety Authority conclusions report a long-term first-tier toxicity-to-exposure ratio (TERlt) <5 for 11 out of 19 documented ASs, and higher-tier TERlt <5 for 5 out of 10 ASs. This suggests a potential risk for bird reproduction in farmlands. Globally 13% of coveys were potentially exposed to 18 ASs during the first month (1-4 coveys per AS). The use of our field data in future research and risk assessment is discussed.
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Affiliation(s)
- Elisabeth Bro
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - Florian Millot
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - Anouk Decors
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - James Devillers
- Centre de Traitement de l'Information Scientifique (CTIS), 3 chemin de la Gravière, 69140 Rillieux La Pape, France.
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Saxena A, Devillers J, Bhunia S, Bro E. Modelling inhibition of avian aromatase by azole pesticides. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:757-82. [PMID: 26535448 PMCID: PMC4673582 DOI: 10.1080/1062936x.2015.1090749] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/26/2015] [Indexed: 05/26/2023]
Abstract
The potential effects of pesticides and their metabolites on the endocrine system are of major concern to wildlife and human health. In this context, the azole pesticides have earned special attention due to their cytochrome P450 aromatase inhibition potential. Cytochrome P450 aromatase (CYP19) catalyses the conversion of androstenedione and testosterone into oestrone and oestradiol, respectively. Thus, aromatase modulates the oestrogenic balance essential not only for females, but also for male physiology, including gonadal function. Its inhibition affects reproductive organs, fertility and sexual behaviour in humans and wildlife species. Several studies have shown that azole pesticides are able to inhibit human and fish aromatases but the information on birds is lacking. Consequently, it appeared to be of interest to estimate the aromatase inhibition of azoles in three different avian species, namely Gallus gallus, Coturnix coturnix japonica and Taeniopygia guttata. In the absence of the crystal structure of the aromatase enzyme in these bird species, homology models for the individual avian species were constructed using the crystal structure of human aromatase (hAr) (pdb: 3EQM) that showed high sequence similarity for G. gallus (82.0%), T. guttata (81.9%) and C. japonica (81.2%). A homology model with Oncorhynchus mykiss (81.9%) was also designed for comparison purpose. The homology-modelled aromatase for each avian and fish species and crystal structure of human aromatase were selected for docking 46 structurally diverse azoles and related compounds. We showed that the docking behaviour of the chemicals on the different aromatases was broadly the same. We also demonstrated that there was an acceptable level of correlation between the binding score values and the available aromatase inhibition data. This means that the homology models derived on bird and fish species can be used to approximate the potential inhibitory effects of azoles on their aromatase.
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Affiliation(s)
| | | | - S.S. Bhunia
- Global Institute of Pharmaceutical Education and Research, Kashipur, India
| | - E. Bro
- Research Department, National Game and Wildlife Institute (ONCFS), Le Perray en Yvelines, France
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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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