Toxicology 327 (2015) 87–94 Contents lists available at ScienceDirect Toxicology journal homepage: www.elsevier.com/locate/toxicol EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals Diana Montes-Grajales, Jesus Olivero-Verbel * Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Campus of Zaragocilla, Cartagena, Bolivar 130015, Colombia A R T I C L E I N F O A B S T R A C T Article history: Received 8 August 2014 Received in revised form 31 October 2014 Accepted 23 November 2014 Available online 25 November 2014 Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. ã 2014 Elsevier Ireland Ltd. All rights reserved. Keywords: Xenobiotic Endocrine disruptor Database Virtual screening Computational toxicology 1. Introduction Endocrine disrupting chemicals (EDCs) are environmental toxicants proposed to cause adverse effects in the body through disruption of the endocrine system (Stoji c et al., 2010). These have been defined by the US Environmental Protection Agency as exogenous agents that interfere with the synthesis, secretion, transportation, binding, action, or elimination of natural hormones Abbreviations: CCRIS, chemical carcinogenesis research information system; EADB, estrogenic activity database; EDCs, endocrine disrupting chemicals; CID, PubChem compound identifier; CTD, comparative toxicogenomics database; EDID, endocrine disrupting chemicals–diet interaction database; EDKB, established knowledge base for endocrine disrupting chemicals; EDPSD, endocrine disruptor priority settings database; GENE-TOX, genetic toxicology data bank; HSDB, hazardous substances data bank; HTML, hypertext markup language; IRIS, integrated risk information system; ITER, international toxicity estimates for risk; PCA, principal component analysis; PHP, PHP hypertext preprocessor; POPs, persistent organic pollutant; log P, octanol–water partition; RBD, development of the receptor database; SMILES, simplified molecular input line entry specification; TOXNET, toxicology data network. * Corresponding author. Tel.: +57 5 6698179/80; fax: +57 5 6698323. E-mail addresses: dmontesg@unicartagena.edu.co (D. Montes-Grajales), joliverov@unicartagena.edu.co (J. Olivero-Verbel). http://dx.doi.org/10.1016/j.tox.2014.11.006 0300-483X/ ã 2014 Elsevier Ireland Ltd. All rights reserved. in the body that are responsible for the maintenance of homeostasis, reproduction, development, and/or behavior. EDCs include a wide range of compounds such as insecticides, plasticizers and monomers, flame retardants, natural products, fragrances, industrial chemicals, organic pollutants and food contact materials, among others (Markey et al., 2002; Mezcua et al., 2012; Muncke, 2011). Nowadays, these compounds give reason for growing international concern (Rousselle et al., 2013), due to their widespread exposure to the general population (Meeker, 2010). Increasing evidence from both experimental animal and epidemiology studies suggest that there is a link between exposure to EDCs and many diseases (Gore et al., 2014). Some of the potential health problems that have been related to certain EDCs include reproductive disorders, dysplasia and the development or progression of cancers, such as breast, ovarian, testicular and prostate cancer (Xi et al., 2013), obesity, diabetes, heart disease, neurodevelopmental and neurodegenerative disorders (Mezcua et al., 2012). In addition, these chemicals may affect biota, producing adverse ecological and human health effects (Kumar and Xagoraraki, 2010). EDCs are widely found in various everyday products and have been detected in waste water treatment plants (Stasinakis et al., 88 D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 2008). However, the identification of compounds with estrogenic activity remains a challenge. Although hundreds of these molecules have been identified – including persistent organic pollutants (POPs) – the information known about them is just the tip of the iceberg. Therefore, EDCs are of special interest because of the large production volumes linked to some of these substances (Birnbaum, 2013). Exposure to the EDCs is spread in urban areas through consumer products. In the environment, they are mainly deposited in sediments and biosolids due to their large octanol– water partition coefficient (log P) (Stasinakis et al., 2008). The report from the World Health Organization and UNEP (http://www.who.int/ceh/publications/endocrine/en/) indicates that EDCs are a global problem requiring global solutions. These compounds pollute the planet through the air and water flows. Hundreds of them have been detected in humans and wildlife, including even those from remote parts of the world such as the Arctic. Therefore, it is almost impossible to find a population that is not exposed to EDCs (Birnbaum, 2013). EDCs belong to diverse groups of chemicals with very dissimilar structures, biochemical properties and mechanisms of action (Stoji c et al., 2010). The majority of these are still unknown (Vuorinen et al., 2013). Furthermore, computer-based predictions of the toxicity of EDCs are increasingly used, due to the growing need to screen a large number of chemicals in order to determine their adverse biological activity (Stoji c et al., 2010). Despite the efforts that have been made to identify these compounds and provide experimental data, there was not a repository with threedimensional structures for performing toxicology computational studies. Therefore, the main purpose of this work was to develop a database that would provide structural information of these compounds, open to both the general public and academia. 2. Materials and methods 2.1. Data sources 2.1.1. Molecular structures In the context of this database, EDCs are those molecules with the potential to affect the endocrine system with reported data in the scientific literature. Therefore, the names and CAS numbers of the EDCs were obtained from the EU list of potential endocrine disruptors (http://www.mst.dk/English/Chemicals/endocrine_disruptors/the_EU_list_of_potential_endocrine_disruptors/) and the TEDX list (http://endocrinedisruption.org/endocrine-disruption/ tedx-list-of-potential-endocrine-disruptors/overview). Molecules stored in these repositories have been cited at least once as endocrine disruptors in scientific articles. The molecular structures of the EDCs with three-dimensional structures available in PubChem (Bolton et al., 2008) were downloaded in 2D- and 3Dsdf formats. These last, were used for building an internal chemical library in Instant JChem (http://www.chemaxon.com), which was then saved as a single sdf file containing all the three-dimensional structures of the EDCs, as well as basic information of each one. The 3D-sdf files were also translated to mol2, pdb and pdbqt format files employing Sybyl X-2.0 program package (Tripos, St. Louis, MO), Open Babel (O’Boyle et al., 2011) and AutoDock tools (http:// autodock.scripps.edu/resources/adt), respectively. health, poisoning, risk assessment and regulations, and toxicology; ACToR (Judson et al., 2007), a database with structural, toxicological and bioactivity information of environmental chemicals derived from more than 150 sources of information including ToxCast (Dix et al., 2007) – a database of activity data for numerous compounds obtained by high-throughput screening assays; Fable (http://fable.chop.edu), a fast, automated tool for finding human genes associated with a keyword and biomedical literature extraction; and PubMed (http://www.ncbi.nlm.nih.gov/pubmed). This database has two links to PubMed, the first one is for a general search of articles containing the name of the compound, and the second one further includes 40 keywords related with endocrine disruption in the PubMed query as a filter to present only the articles associated with endocrine disruption. Those terms were previously selected using the text mining tool PubMed PubReMiner (http://hgserver2.amc.nl/cgi-bin/miner/miner2.cgi). An example of a query search using this link for 3,5-dichlorobiphenyl is presented below: “3,5-dichlorobiphenyl” and (“androgen” or “androgenic” or “adrenergic” or “antiadrenergic” or “antiandrogen” or “antiandrogenic” or “antiestrogenic” or “antithyroid” or “aromatase” or “catecholamines” or “EDCs” or “endocrine” or “ERalpha” or “estradiol” or “estrogen” or “estrogenic” or “estrogenicity” or “fertility” or “glucocorticoid” or “hormone” or “proestrogenic” or “progesterone” or “progesteronic” or “reproductive” or “semen” or “sperm” or “spermatogenesis” or “steoroids” or “thyroid” or “urogenital” or “xenoestrogen” or “xenoestrogenic” or “xenoestrogens” or “imposex” or “cancer” or “ovary” or “pregnancy” or “testosterone” or “uterus” or “tumor”). 2.1.3. Graphics High quality images of the 2D- and 3D-structures of each compound were prepared in Marvin Sketch (http://www.chemaxon.com) and PyMol (http://www.pymol.org/), using as input the obtained 2D- and 3D-sdf files, setting colors by atom type in order to facilitate their reading. These images are useful for obtaining a general overview of the geometry of the molecules and possible sites of interactions. In addition, icons of the different sources of EDCs were generated as a user-friendly tool that enables a quick identification of the potential places for greatest risk of exposure, helping to remember them for educational purposes. 2.2. Data schemes and database implementation In order to offer a structure for the EDCs DataSheet (page containing the information for each EDC) in the web development and database management, all data were organized in the following sections: name, synonyms, source, identifiers, structural properties, pharmacophore features, downloads, similarity search, toxicological information, external links and keywords, as shown in Table 1. The EDCs DataBank website was developed from scratch using HTML (hypertext markup language), CSS, JQuery, JavaScript and PHP languages (PHP hypertext preprocessor) in a NotePad++ editor. The database was built on MySQL, the most popular open source database. The architecture of EDCs DataBank is shown in Fig. 1. 2.3. Quality assurance, validation, completeness and curation 2.1.2. External links, physico-chemical and toxicological information A wide variety of information for each compound was obtained from different databases and search engines, such as PubChem (Bolton et al., 2008), a database of chemical molecules and their activities against biological assays; TOXNET (toxicology data network; http://toxnet.nlm.nih.gov/) (Wexler, 2001), a group of databases covering chemicals and drugs, diseases and the environment, environmental health, occupational safety and All the information has been hand cured in order to reduce, as much as possible, the errors, and the fields of this database have been completed based on all available information. Most of the structural information contained in EDCs DataBank was obtained directly from PubChem (Bolton et al., 2008) and managed through Instant JChem (http://www.chemaxon.com), for its inclusion directly in the MySQL database of EDCs DataBank. The D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 89 Table 1 Structure of the information contained in the EDCs DataSheets. Field Description Name The most common name for the molecule. Synonyms Source Identifiers Sructural properties Pharmacophore features Downloads Similarity search Toxicological information External links Keywords Source TEDX list (http://www.endocrinedisruption.com/endocrine.TEDXList. overview.php) and EU list of potential endocrine disruptors (http://www. mst.dk/English/Chemicals/endocrine_disruptors/ the_EU_list_of_potential_endocrine_disruptors/). Alternative names given to the compound. PubChem (Bolton et al., 2008). Exposure sources for each EDC. Internet. IUPAC name, CAS number, PubChem ID, InChiKey and canonical SMILES. TEDX list (http://www.endocrinedisruption.com/endocrine.TEDXList. overview.php) and PubChem (Bolton et al., 2008) It includes molecular formula and molecular weight. PubChem (Bolton et al., 2008). Number of bond donors, bond acceptors and atoms different from hydrogen (heavy atoms). 2D structure (2D-sdf file) and 3D structures (3D-sdf file, mol2, pdb and pdbqt) It searches for similar molecules into the database. PubChem (Bolton et al., 2008). PubChem (Bolton et al., 2008); the formats mol2, pdb and pdbqt were obtaining by translation of the original sdf files. The matrix was generated using the PubChem Score Matrix Service (http://pubchem.ncbi.nlm.nih.gov//score_matrix/score_matrix.cgi). This is a resource that presents the available toxicological information in ACToR (Judson et al., 2007), TEDX list (http://www.endocrinedisruption. the databases ACToR, hazardous substances data bank (HSDB), chemical com/endocrine.TEDXList.overview.php) and TOXNET (Wexler, 2001). carcinogenesis research information system (CCRIS), GENE-TOX, comparative toxicogenomics database (CTD), integrated risk information system (IRIS), international toxicity estimates for risk (ITER) and TEDX list. These are links to other databases and search engines. PubChem (Bolton et al., 2008), PubMed (http://www.ncbi.nlm.nih.gov/ pubmed), PhysProp (http://esc.syrres.com/fatepointer/search.asp) and Fable (http://fable.chop.edu). Words related to each EDC. The words with the largest letters represent a LigerCat (Sarkar et al., 2009). major association. theoretical models of the three-dimensional structures were also obtained directly from PubChem (Bolton et al., 2008; https:// pubchem.ncbi.nlm.nih.gov/release3d.html), leading the file names as default, and translated to several formats using standardized protocols in order to avoid typing errors. All the information contained in each EDC DataSheet was carefully revised. The whole texts of each datasheet were revised three times by a Ph.D. student and an undergraduate student, the correct functioning of the external links and toxicological information iframes was also checked. The concordance between the name, 2D structure, 3D structure and Jmol interactive molecular viewer (http://jmol.sourceforge.net/index.en.html/) was examined; and each 2D and 3D structure was downloaded and the geometry was checked using pymol in order to be sure that the 3D-structures contain three-dimensional features, expected connectivity and normal bond lengths. These revisions will be performed systematically and regularly in order to keep the database updated and curated. Users are also encouraged to suggest improvements to the database through the “questions and comments” form, located in the Contact us option of the main menu. The website of EDCs DataBanks is hosted as a subdomain of the University of Cartagena website (http://edcs.unicartagena.edu.co/), which contributes to its permanency and continuous development Fig. 1. EDCs DataBank arquitecture. 90 D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 by the students of the Ph.D. Program in Environmental Toxicology of this University, working in the research line of the endocrine disruptors and environmental pollutants. Additional information and new molecules will be included in the database, in accordance with the information available and the new discoveries in this field. 3. Results 3.1. Data sources 3.1.1. Molecular structures EDCs DataBank currently contains 615 molecules. This database allows the download of the whole 2D and 3D structures stored on it, in several formats (mol2, pdb, pdbqt, sdf). This can be executed from the download section of each EDC DataSheet or from the download option of the main menu. This possibility contributes to an easy use of these compounds in docking, QSAR and virtual screening studies. 3.1.2. External links, physico-chemical and toxicological information The EDCs belonging to EDCs DataBank include pesticides, flavonoids and medicinal plants; as well as compounds used in cosmetics, plastics and pharmaceutical industry, among others. Many of them also correspond to environmental pollutants, or are components of everyday goods, such as household and personal care products. A broad diversity of data regarding each compound is available in the DataSheet of each compound, organized in the following sections: name, synonyms, source, identifiers, structural properties, pharmacophore features, downloads, similarity search and keywords. In addition, this database is hyperlinked to other important databases in the field of toxicology and literature search such as PubMed, PubChem (Bolton et al., 2008), ACToR (Judson et al., 2007), LigerCat (Sarkar et al., 2009), PhysProp and TOXNET – HSDB (hazardous substances data bank), CCRIS (chemical carcinogenesis research information system), GENE-TOX (genetic toxicology data bank), CTD (comparative toxicogenomics database), IRIS (integrated risk information system) and ITER (international toxicity estimates for risk). These links are present as a section on toxicological information, external links and keywords of the DataSheet for each compound. In the case of the items of the toxicological information and physical properties hyperlink, its availability depends of the existence of the information in the source database. The number of molecules in EDCs DataBank with available data in those fields is presented in Fig. 2. 3.1.3. Graphics Fig. 2. Number of molecules with toxicological and physicochemical data available in EDCs DataBank. Each EDC has images of its 2D- and 3D-structures in high-quality. In addition, a Jmol application (http://jmol.sourceforge.net/index.en.html/) was included to the EDCs DataSheet, which allows the interaction with the three-dimensional structure and simple calculations by right-clicking on the image. In order to use this applet, an updated version of Java is required. The 51 icons regarding the different sources of EDCs are also available as a search tool in the home page, and for information in the EDCs DataSheets. 3.2. Data schemes and database implementation 3.2.1. EDCs DataBank description EDCs DataBank is a unique database with three-dimensional structures of EDCs for virtual screening. It includes compounds utilized in pesticides, cosmetics, gasoline and food, health care and household products, among others. It is suitable for virtual screening because each molecule is presented in several formats (mol2, pdb, pdbqt, sdf), allowing the use of different computer aided tools for their analysis. Consequently, EDCs DataBank is a valuable repository to study the interactions of these compounds with macromolecules involved in several diseases, such as breast cancer, obesity and diabetes. The databank also benefits the community and students, since it contains possible sources of exposure to EDCs, toxicological information and links to different databases in a user-friendly environment. 3.2.2. Website map At the top of the page is the main menu of the EDCs DataBank. The user can find the search bar and access the advanced search. The website of the database possesses a download page in which the user can obtain the 3D structures of all molecules stored in EDCs DataBank in different formats, as well as images regarding statistical information of all compounds. This page also contains a questions and comments form in the contact us button, in which the user can communicate their inquiries and suggestions. The website includes an about and help links with detailed information regarding EDCs DataBank and its use. The map of the website is shown in Fig. 3. 3.2.3. Search and advanced search This database is fully searchable. The general searcher (Fig. 4A), located at the top of the website home page, allows the user to seek expressions found in the category name, synonyms and the IUPAC name. The searcher considers many options to call a molecule, facilitating the searching and identification of the compounds. The advanced search (Fig. 4B) generates a query according to the search parameter selected by the users. Compounds may be searched in a range of molecular weight, number of bond donors, number of heavy atoms (atoms different from hydrogen), number of bond acceptors, and a multiple entry search. The search by source (Fig. 4C), found at the home page below the search box, consists of 51 icons representing the possible sources of exposure to endocrine disruptors. This tool helps to make our database more user-friendly and useful to the general public, by showing the compounds that may be found on certain elements or products to which people could be exposed. 3.2.4. EDCs DataSheet EDCs DataBank is a non-redundant database built on MySQL. The identifier InChIKey has been used as a primary key, in order to make it not redundant. In addition, given the current state of information and the difficulty of handling it, especially in terms of codes of molecules, we decided not to incorporate a new identifier of molecules for our database. Therefore, we use the existing and widely recognized PubChem compound identifier (CID) (Bolton D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 Fig. 3. Map of EDCs DataBank website. Fig. 4. Screenshot of search of (A) search, (B) advanced search and (C) source. 91 92 D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 Fig. 5. EDCs DataSheet screenshot for methyl-paraben. D. Montes-Grajales, J. Olivero-Verbel / Toxicology 327 (2015) 87–94 et al., 2008), which is shown in identifiers and utilized to name the 2D- and 3D-structure files and images in the different formats offered by this database. All the information stored in the MySQL database is presented in a user-friendly web environment in the EDCs DataSheets (Fig. 5). The website has been developed utilizing HTML, PHP, CSS, JQuery and JavaScript languages using an appropriately graphic design in order to simplify the process of finding and reading data. EDCs DataSheets show the information for each single compound selected by the user. The data is presented in 10 main categories: name, synonyms, source, identifiers, structural properties, pharmacophore features, downloads, search similar structures, toxicological information, external links and keywords, which are accompanied by source icons, 2D- and 3D-structure figures and an interactive three-dimensional view of each compound by Jmol (http://jmol. sourceforge.net/index.en.html/), allowing to perform simple calculations such as van der Waal surface, distances, angles, dihedral angles, among other. Another interesting tool in the EDCs DataSheet is its capability of searching for similar molecules. The tool was created by employing a similarity matrix calculated in the PubChem Score Matrix Service (https://pubchem.ncbi.nlm.nih.gov/score_matrix/score_matrix-help.html). The 2D similarity (substructure keys) between molecules was used as a scoring method, so that the client only has to include the range of similitude percentage for the search. Currently, EDCs DataBank is the unique database of endocrine disruptors with three dimensional structures available for virtual screening, with a complete repository of information regarding EDCs and their molecular structures. Therefore, it will have an impact in the study of these compounds through bioinformatics and computational toxicology strategies. 3.3. Quality assurance, validation, completeness and curation The data contained in EDCs DataBank has been revised and hand curated, diminishing the possible errors. All the fields of this database are fully complete with exception of external links and toxicological information that depend on the availability of the data in the source databases. In addition, this database uses PubChem as primary source for the three-dimensional structures, which is one of the most recognized and used databases for getting chemical structures of low molecular weight compounds (Bolton et al., 2008). 93 the receptor database), which can assist with the problem of endocrine disruptors, presenting information about steroid hormone receptors to which endocrine disruptors could join (Nakata et al., 1999); EDID (endocrine disrupting chemicals–diet interaction database) has information about the possible interactions between diet and endocrine disruptors, allowing the search for scientific papers, showing this information by entering words found in the article title, keywords, and/or publication year (Baldi and Mantovani, 2008); EDPSD (endocrine disruptor priority settings database), a useful database which ranks priority chemical parameters for screening and testing endocrine disruptors (http:// www.epa.gov/endo/pubs/prioritysetting/finalarch.htm); and EADB (estrogenic activity database), contains information of estrogenic activity for 8212 chemicals in in vitro and in vivo assays of different species (Shen et al., 2013). However, there was not a database of EDCs with threedimensional structures available for virtual screening. This database is a valuable repository to study the interactions of these compounds with macromolecules involved in several diseases, such as breast cancer, obesity and diabetes, among others. In addition, it was created in a very user-friendly environment that makes it helpful for community information regarding EDCs exposure in everyday products and their eventual toxicity impact in environmental and human health. 5. Conclusions EDCs DataBank is the unique database with three-dimensional structures of EDCs for virtual screening, freely available on http://edcs.unicartagena.edu.co. It is also suitable for its use with other computational approaches as all molecular structures stored in it can be downloaded in several formats. Therefore, it is a valuable repository to study the molecular basis of the interaction between these molecules and macromolecules involved in diverse pathologies. In addition, EDCs DataBank has been developed in a user-friendly environment and provides a vast amount of structural and toxicological information of each compound that can be used for research, academia and general population. Conflict of interest The authors declare that there are no conflicts of interest. 4. Discussion Historically, the public, scientific and regulatory concerns regarding the potential adverse health effects of exposure to EDCs were initiated in the early 1990s (Safe, 2000). Since then, numerous efforts have been made to compile information related to these compounds. In 1988, before the term was coined “endocrine disruptor”, Dr. Theo Colborn began the search for compounds with potential to interfere with the endocrine system. These compounds were consolidated in the TEDX list of potential endocrine disruptors (http://endocrinedisruption.org/endocrinedisruption/tedx-list-of-potential-endocrine-disruptors/overview). Another interesting project started in mid-1990s, was EDKB (established knowledge base for endocrine disrupting chemicals), which consists of a database with information on the chemical structure, name, testing and supply of the experiment, containing more than 3257 records and about 1800 EDCs (Ding et al., 2010). In 2010, Nashev et al. created an internal database of endocrine disruptors which was used to perform virtual screening studies with protein 17b dehydrogenase type 3 (Nashev et al., 2010). Later, in 2012, the database was employed for the identification of xenobiotics as potential disruptors of corticosteroid action (Nashev et al., 2012). 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