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Jin Zhang, Afshan Begum, Kristoffer Brännström, Christin Grundström, Irina Iakovleva, Anders Olofsson, A Elisabeth Sauer-Eriksson, Patrik L Andersson
Thyroid disruption by xenobiotics is associated with a broad spectrum of severe adverse outcomes. One possible molecular target of thyroid hormone disrupting chemicals (THDCs) is transthyretin (TTR), a thyroid hormone transporter in vertebrates. To better understand the interactions between TTR and THDCs, we determined the crystallographic structures of human TTR in complex with perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and 2,2',4,4'-tetrahydroxybenzophenone (BP2). The molecular interactions between the ligands and TTR were further characterized using molecular dynamics simulations...
October 10, 2016: Environmental Science & Technology
Kathryn Ribay, Marlene T Kim, Wenyi Wang, Daniel Pinolini, Hao Zhu
Estrogen receptors (ERα) are a critical target for drug design as well as a potential source of toxicity when activated unintentionally. Thus, evaluating potential ERα binding agents is critical in both drug discovery and chemical toxicity areas. Using computational tools, e.g., Quantitative Structure-Activity Relationship (QSAR) models, can predict potential ERα binding agents before chemical synthesis. The purpose of this project was to develop enhanced predictive models of ERα binding agents by utilizing advanced cheminformatics tools that can integrate publicly available bioassay data...
March 2016: Front Environ Sci
Jui-Hua Hsieh
Compound activity identification is the primary goal in high-throughput screening (HTS) assays. However, assay artifacts including both systematic (e.g., compound auto-fluorescence) and nonsystematic (e.g., noise) complicate activity interpretation. In addition, other than the traditional potency parameter, half-maximal effect concentration (EC50), additional activity parameters (e.g., point-of-departure, POD) could be derived from HTS data for activity profiling. A data analysis pipeline has been developed to handle the artifacts and to provide compound activity characterization with either binary or continuous metrics...
2016: Methods in Molecular Biology
Ruili Huang
The US Tox21 program has developed in vitro assays to test large collections of environmental chemicals in a quantitative high-throughput screening (qHTS) format, using triplicate 15-dose titrations to generate over 50 million data points to date. Counter screens are also employed to minimize interferences from non-target-specific assay artifacts, such as compound auto fluorescence and cytotoxicity. New data analysis approaches are needed to integrate these data and characterize the activities observed from these assays...
2016: Methods in Molecular Biology
Chia-Wen Amy Hsu, Jinghua Zhao, Menghang Xia
The farnesoid X receptor (FXR) is a nuclear receptor responsible for homeostasis of bile acids, lipids, and glucose. Compounds that alter endogenous FXR signaling can be used as therapeutic candidates or identified as potentially hazardous compounds depending on exposure doses and health states. Therefore, there is an increasing need for high-throughput screening assays of FXR activity to profile large numbers of environmental chemicals and drugs. This chapter describes a workflow of FXR modulator identification and characterization...
2016: Methods in Molecular Biology
Caroline L Pinto, Kamel Mansouri, Richard Judson, Patience Browne
The US Environmental Protection Agency's (EPA) Endocrine Disruptor Screening Program (EDSP) is using in vitro data generated from ToxCast/Tox21 high-throughput screening assays to assess the endocrine activity of environmental chemicals. Considering that in vitro assays may have limited metabolic capacity, inactive chemicals that are biotransformed into metabolites with endocrine bioactivity may be missed for further screening and testing. Therefore, there is a value in developing novel approaches to account for metabolism and endocrine activity of both parent chemicals and their associated metabolites...
September 19, 2016: Chemical Research in Toxicology
Michelle M Miller, Rebecca A Alyea, Caroline LeSommer, Daniel L Doheny, Sean M Rowley, Kristin M Childs, Pergentino Balbuena, Susan M Ross, Jian Dong, Bin Sun, Melvin A Andersen, Rebecca A Clewell
A toxicity pathway approach was taken to develop an in vitro assay using human uterine epithelial adenocarcinoma (Ishikawa) cells as a replacement for measuring an in vivo uterotrophic response to estrogens. The Ishikawa cell was determined to be fit for the purpose of recapitulating in vivo uterine response by verifying fidelity of the biological pathway components and the dose-response predictions to women of child-bearing age. Expression of the suite of estrogen receptors that control uterine proliferation (ERα66, ERα46, ERα36, ERβ, G-protein coupled estrogen receptor (GPER)) were confirmed across passages and treatment conditions...
August 7, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
Ming Hao, Stephen H Bryant, Yanli Wang
BACKGROUND: As one of the largest publicly accessible databases for hosting chemical structures and biological activities, PubChem has been processing bioassay submissions from the community since 2004. With the increase in volume for the deposited data in PubChem, the diversity and wealth of information content also grows. Recently, the Tox21 program, has deposited a series of pairwise data in PubChem regarding to different mechanism of actions (MOA), such as androgen receptor (AR) agonist and antagonist datasets, to study cell toxicity...
2016: Journal of Cheminformatics
Salomon Sand, Fred Parham, Christopher J Portier, Raymond R Tice, Daniel Krewski
BACKGROUND: The National Research Council's vision for toxicity testing in the 21(st) century anticipates that points of departure (PODs) for establishing human exposure guidelines in future risk assessments will increasingly be based on in vitro high-throughput screening (HTS) data. OBJECTIVES: The aim of this study was to compare different PODs for HTS data. Specifically, benchmarks doses (BMDs) were compared to the signal-to-noise crossover dose (SNCD) introduced by Sand et al...
July 6, 2016: Environmental Health Perspectives
Ann M Richard, Richard S Judson, Keith A Houck, Christopher M Grulke, Patra Volarath, Inthirany Thillainadarajah, Chihae Yang, James Rathman, Matthew T Martin, John F Wambaugh, Thomas B Knudsen, Jayaram Kancherla, Kamel Mansouri, Grace Patlewicz, Antony J Williams, Stephen B Little, Kevin M Crofton, Russell S Thomas
The U.S. Environmental Protection Agency's (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches to support the development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay end points. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in the public release of screening data at the end of 2013. Subsequent expansion in Phase III has resulted in more than 3800 chemicals actively undergoing ToxCast screening, 96% of which are also being screened in the multi-Agency Tox21 project...
August 15, 2016: Chemical Research in Toxicology
Ulf Norinder, Scott Boyer
Quantitative structure-activity relationships (QSAR) are critical to exploitation of the chemical information in toxicology databases. Exploitation can be extraction of chemical knowledge from the data but also making predictions of new chemicals based on quantitative analysis of past findings. In this study, we analyzed the ToxCast and Tox21 estrogen receptor data sets using Conformal Prediction to enhance the full exploitation of the information in these data sets. We applied aggregated conformal prediction (ACP) to the ToxCast and Tox21 estrogen receptor data sets using support vector machine classifiers to compare overall performance of the models but, more importantly, to explore the performance of ACP on data sets that are significantly enriched in one class without employing sampling strategies of the training set...
June 20, 2016: Chemical Research in Toxicology
Warren M Casey
The National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM) provides validation support for US Federal agencies and the US Tox21 interagency consortium, an interagency collaboration that is using high throughput screening (HTS) and other advanced approaches to better understand and predict chemical hazards to humans and the environment. The use of HTS data from assays relevant to the estrogen receptor signaling data pathway is used as an example of how HTS data can be combined with computational modeling to meet the needs of US agencies...
January 2016: Toxicological Research
Anthony L Schroeder, Gerald T Ankley, Keith A Houck, Daniel L Villeneuve
High-throughput toxicity testing technologies along with the World Wide Web are revolutionizing both generation of and access to data regarding the biological activities that chemicals can elicit when they interact with specific proteins, genes, or other targets in the body of an organism. To date, however, most of the focus has been on the application of such data to assessment of individual chemicals. The authors suggest that environmental surveillance and monitoring represent the next frontiers for high-throughput toxicity testing...
March 2016: Environmental Toxicology and Chemistry
Thomas Luechtefeld, Alexandra Maertens, Daniel P Russo, Costanza Rovida, Hao Zhu, Thomas Hartung
The European Chemicals Agency (ECHA) warehouses the largest public dataset of in vivo and in vitro toxicity tests. In December 2014 this data was converted into a structured, machine readable and searchable database using linguistic search engines. It contains data for 9,801 unique substances, 3,609 unique study descriptions and 816,048 study documents.This allows exploring toxicological data on a scale far larger than previously available. Substance similarity analysis was used to determine clustering of substances for hazards by mapping to PubChem...
2016: ALTEX
Julia E Rager, Mark J Strynar, Shuang Liang, Rebecca L McMahen, Ann M Richard, Christopher M Grulke, John F Wambaugh, Kristin K Isaacs, Richard Judson, Antony J Williams, Jon R Sobus
There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U...
March 2016: Environment International
Ruili Huang, Menghang Xia, Srilatha Sakamuru, Jinghua Zhao, Sampada A Shahane, Matias Attene-Ramos, Tongan Zhao, Christopher P Austin, Anton Simeonov
Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼ 10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure-activity relationships that are useful for the generation of mechanistic hypotheses...
2016: Nature Communications
Cindy Zhang, Jonathan Ball, Julie Panzica-Kelly, Karen Augustine-Rauch
There has been increasing focus on generation and assessment of in vitro developmental toxicology models for assessing teratogenic liability of chemicals. The driver for this focus has been to find reliable in vitro assays that will reduce or replace the use of in vivo tests for assessing teratogenicity. Such efforts may be eventually applied in testing pharmaceutical agents where a developmental toxicology assay or battery of assays may be incorporated into regulatory testing to replace one of the two species currently used in teratogenic assessment...
April 18, 2016: Chemical Research in Toxicology
Mikyung Lee, Ruili Huang, Weida Tong
Nuclear receptors (NRs) are ligand-activated transcriptional regulators that play vital roles in key biological processes such as growth, differentiation, metabolism, reproduction, and morphogenesis. Disruption of NRs can result in adverse health effects such as NR-mediated endocrine disruption. A comprehensive understanding of core transcriptional targets regulated by NRs helps to elucidate their key biological processes in both toxicological and therapeutic aspects. In this study, we applied a probabilistic graphical model to identify the transcriptional targets of NRs and the biological processes they govern...
March 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
Terry McCann
The Lush Prize supports animal-free testing by rewarding the most effective projects and individuals who have been working toward the goal of replacing animals in product or ingredient safety testing. A Background Paper is prepared each year, prior to the judging process, to provide the panel with a brief overview of current developments in the field of Replacement alternatives, particularly those relevant to the concept of toxicity pathways. This Background Paper includes information on recent work by the relevant scientific institutions and projects in this area, including AXLR8, OECD, CAAT, The Hamner Institutes, the Human Toxome Project, EURL ECVAM, ICCVAM, the US Tox21 Programme, the ToxCast programme, and the Human Toxicology Project Consortium...
November 2015: Alternatives to Laboratory Animals: ATLA
Marlene Thai Kim, Ruili Huang, Alexander Sedykh, Wenyi Wang, Menghang Xia, Hao Zhu
BACKGROUND: Hepatotoxicity accounts for a substantial number of drugs being withdrawn from the market. Using traditional animal models to detect hepatotoxicity is expensive and time-consuming. Alternative in vitro methods, in particular cell-based high-throughput screening (HTS) studies, have provided the research community with a large amount of data from toxicity assays. Among the various assays used to screen potential toxicants is the antioxidant response element beta lactamase reporter gene assay (ARE-bla), which identifies chemicals that have the potential to induce oxidative stress and was used to test > 10,000 compounds from the Tox21 program...
May 2016: Environmental Health Perspectives
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