Ann Richard - Academia.edu (original) (raw)

Papers by Ann Richard

Current Computer Aided-Drug Design, 2006

... of Structures Tools to perform unsupervised structure-based clustering are available from bot... more ... of Structures Tools to perform unsupervised structure-based clustering are available from both commercial as well as open sources including ... Current Computer-Aided Drug Design, 2006, Vol ... 5). Strategies to data mine structure-integrated toxicity database for linking chemistry to ...

Journal of chemical information and modeling, Jan 23, 2015

Chemotypes are a new approach for representing molecules, chemical substructures and patterns, re... more Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory, and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order to enable che...

Chemical research in toxicology, 2006

A chemistry approach to predictive toxicology relies on structure-activity relationship (SAR) mod... more A chemistry approach to predictive toxicology relies on structure-activity relationship (SAR) modeling to predict biological activity from chemical structure. Such approaches have proven capabilities when applied to well-defined toxicity end points or regions of chemical space. These approaches are less well-suited, however, to the challenges of global toxicity prediction, i.e., to predicting the potential toxicity of structurally diverse chemicals across a wide range of end points of regulatory and pharmaceutical concern. New approaches that have the potential to significantly improve capabilities in predictive toxicology are elaborating the "activity" portion of the SAR paradigm. Recent advances in two areas of endeavor are particularly promising. Toxicity data informatics relies on standardized data schema, developed for particular areas of toxicological study, to facilitate data integration and enable relational exploration and mining of data across both historical and...

Mutation research, Jan 25, 1998

There is a great deal of current interest in the use of commercial, automated programs for the pr... more There is a great deal of current interest in the use of commercial, automated programs for the prediction of mutagenicity and carcinogenicity based on chemical structure. However, the goal of accurate and reliable toxicity prediction for any chemical, based solely on structural information remains elusive. The toxicity prediction challenge is global in its objective, but limited in its solution, to within local domains of chemicals acting according to similar mechanisms of action in the biological system; to predict, we must be able to generalize based on chemical structure, but the biology fundamentally limits our ability to do so. Available commercial systems for mutagenicity and/or carcinogenicity prediction differ in their specifics, yet most fall in two major categories: (1) automated approaches that rely on the use of statistics for extracting correlations between structure and activity; and (2) knowledge-based expert systems that rely on a set of programmed rules distilled fr...

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2000

We determined the mutation spectra in Salmonella of four chlorinated butenoic acid analogues (BA-... more We determined the mutation spectra in Salmonella of four chlorinated butenoic acid analogues (BA-1 through BA-4) of the drinking water mutagen 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) and compared the results with those generated previously by us for MX and a related compound, MCF. We then considered relationships between the properties of mutagenic potency and mutational specificity for these six chlorinated butenoic acid analogues. In TA98, the three most potent mutagens, BA-3, BA-4, MX, and the organic extract, all induced large percentages of complex frameshifts (33-67%), which distinguish these agents from any other class of compound studied previously. In TA100, which has only GC sites for mutation recovery, >71% of the mutations induced by all of the agents were GC-->TA transversions. The availability of both GC and TA sites for mutation in TA104 resulted in greater distinctions in mutational specificity than in TA100. MX targeted GC sites almost exclusively (98%); the structurally similar BA-4 and BA-2 produced mutations at similar frequencies at both GC and AT sites; and the structurally similar BA-3 and BA-1 induced most mutations at AT sites (69%). Thus, large variations in structural properties influencing relative mutagenic potency appeared to be distinct from the more localized similar structural features influencing mutagenic specificity in TA104. Among a set of physicochemical properties examined for the six butenoic acids, a significant correlation was found between pK(a) and mutagenic potency in TA100, even when the unionized fraction of the activity dose was considered. In addition, a correlation in CLOGP for BA-1 to BA-4 suggested a role for bioavailability in determining mutagenic potency. These results illustrate the potential value of structural analyses for exploring the relationship between chemical structure and mutational mechanisms. To our knowledge, this is the first study in which such analyses have been applied to structural analogues for which both mutagenic potency and mutation spectra date were available.

Nature biotechnology, 2014

Addressing the safety aspects of drugs and environmental chemicals has historically been undertak... more Addressing the safety aspects of drugs and environmental chemicals has historically been undertaken through animal testing. However, the quantity of chemicals in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important chemical libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for chemicals that disrupt physiologically important pathways. Chemical-response signatures for 87 endpoints covering molecular functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental chemicals and 135 reference pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polyph...

Journal of Toxicology and Environmental Health, 1988

A group of 36 aryl azo dyes were examined for their ability to be reduced by rat liver microsomal... more A group of 36 aryl azo dyes were examined for their ability to be reduced by rat liver microsomal azoreductase. This group of azo dyes featured a variety of substituents, including sulfonic acid, phenol, nitro, amide, and methyl functionalities on phenyl, alpha-naphthyl, and beta-naphthyl rings. Reduction rates for each dye were obtained using a spectrophotometric method and anaerobic incubation conditions. These rates ranged from 0 to 7.35 nmol dye reduced/min.mg protein. The reduction rates and dye structures provided the data for a CASE-SAR (computer automated structure evaluation-structure-activity relationship) fragment analysis, and three major structure fragments associated with the ability of this group of azo dyes to be reduced were identified. The three CASE fragments correctly label 92% of the azo dye structures as active or inactive and may be useful in future predictions of the ability of azo dyes to undergo reduction by rat liver azoreductase.

The U.S. Environmental Protection Agency (EPA) is developing methods for utilizing computational ... more The U.S. Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS), and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources toward chemicals that likely represent the greatest hazard to human health and the environment. This chemical prioritization research program, entitled ''ToxCast,'' is being initiated with the purpose of developing the ability to forecast toxicity based on bioactivity profiling. The proof-of-concept phase of ToxCast will focus upon chemicals with an existing, rich toxicological database in order to provide an interpretive context for the ToxCast data. This set of several hundred reference chemicals will represent numerous structural classes and phenotypic outcomes, including tumorigens, developmental and reproductive toxicants, neurotoxicants, and immunotoxicants. The ToxCast program will evaluate chemical properties and bioactivity profiles across a broad spectrum of data domains: physical-chemical, predicted biological activities based on existing structure-activity models, biochemical properties based on HTS assays, cell-based phenotypic assays, and genomic and metabolomic analyses of cells. These data will be generated through a series of external contracts, along with collaborations across EPA, with the National Toxicology Program, and with the National Institutes of Health Chemical Genomics Center. The resulting multidimensional data set provides an informatics challenge requiring appropriate computational methods for integrating various chemical, biological, and toxicological data into profiles and models predicting toxicity.

ACToR (Aggregated Computational Toxicology Resource) is a database and set of software applicatio... more ACToR (Aggregated Computational Toxicology Resource) is a database and set of software applications that bring into one central location many types and sources of data on environmental chemicals. Currently, the ACToR chemical database contains information on chemical structure, in vitro bioassays and in vivo toxicology assays derived from more than 150 sources including the U.S. Environmental Protection Agency (EPA), Centers for Disease Control (CDC), U.S. Food and Drug Administration (FDA), National Institutes of Health (NIH), state agencies, corresponding government agencies in Canada, Europe and Japan, universities, the World Health Organization (WHO) and non-governmental organizations (NGOs). At the EPA National Center for Computational Toxicology, ACToR helps manage large data sets being used in a high-throughput environmental chemical screening and prioritization program called ToxCast.

Regulatory Toxicology and Pharmacology, 2009

Three high-throughput screening (HTS) genotoxicity assays-GreenScreen HC GADD45a-GFP (Gentronix L... more Three high-throughput screening (HTS) genotoxicity assays-GreenScreen HC GADD45a-GFP (Gentronix Ltd.), CellCiphr p53 (Cellumen Inc.) and CellSensor p53RE-bla (Invitrogen Corp.)-were used to analyze the collection of 320 predominantly pesticide active compounds being tested in Phase I of US. Environmental Protection Agency's ToxCast research project. Between 9% and 12% of compounds were positive for genotoxicity in the assays. However, results of the varied tests only partially overlapped, suggesting a strategy of combining data from a battery of assays. The HTS results were compared to mutagenicity (Ames) and animal tumorigenicity data. Overall, the HTS assays demonstrated low sensitivity for rodent tumorigens, likely due to: screening at a low concentration, coverage of selected genotoxic mechanisms, lack of metabolic activation and difficulty detecting non-genotoxic carcinogens. Conversely, HTS results demonstrated high specificity, >88%. Overall concordance of the HTS assays with tumorigenicity data was low, around 50% for all tumorigens, but increased to 74-78% (vs. 60% for Ames) for those compounds producing tumors in rodents at multiple sites and, thus, more likely genotoxic carcinogens. The aim of the present study was to evaluate the utility of HTS assays to identify potential genotoxicity hazard in the larger context of the ToxCast project, to aid prioritization of environmentally relevant chemicals for further testing and assessment of carcinogenicity risk to humans.

ALTEX, 2013

In vitro high-throughput screening (HTS) assays are seeing increasing use in toxicity testing. HT... more In vitro high-throughput screening (HTS) assays are seeing increasing use in toxicity testing. HTS assays can simultaneously test many chemicals but have seen limited use in the regulatory arena, in part because of the need to undergo rigorous, time-consuming formal validation. Here we discuss streamlining the validation process, specifically for prioritization applications. By prioritization, we mean a process in which less complex, less expensive, and faster assays are used to prioritize which chemicals are subjected first to more complex, expensive, and slower guideline assays. Data from the HTS prioritization assays is intended to provide a priori evidence that certain chemicals have the potential to lead to the types of adverse effects that the guideline tests are assessing. The need for such prioritization approaches is driven by the fact that there are tens of thousands of chemicals to which people are exposed, but the yearly throughput of most guideline assays is small in co...

Toxicology, Jan 28, 2011

Understanding the potential health risks posed by environmental chemicals is a significant challe... more Understanding the potential health risks posed by environmental chemicals is a significant challenge elevated by the large number of diverse chemicals with generally uncharacterized exposures, mechanisms, and toxicities. The present study is a performance evaluation and critical analysis of assay results for an array of 292 high-throughput cell-free assays aimed at preliminary toxicity evaluation of 320 environmental chemicals in EPA's ToxCast™ project (Phase I). The chemicals (309 unique, 11 replicates) were mainly precursors or the active agent of commercial pesticides, for which a wealth of in vivo toxicity data is available. Biochemical HTS (high-throughput screening) profiled cell and tissue extracts using semi-automated biochemical and pharmacological methodologies to evaluate a subset of G-protein coupled receptors (GPCRs), CYP450 enzymes (CYPs), kinases, phosphatases, proteases, HDACs, nuclear receptors, ion channels, and transporters. The primary screen tested all chemi...

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2005

Toxicology Mechanisms and Methods, 2008

ABSTRACT Chemical toxicity data at all levels of description, from treatment-level dose response ... more ABSTRACT Chemical toxicity data at all levels of description, from treatment-level dose response data to a high-level summarized toxicity "endpoint," effectively circumscribe, enable, and limit predictive toxicology approaches and capabilities. Several new and evolving public data initiatives focused on the world of chemical toxicity information-as represented here by ToxML (Toxicology XML standard), DSSTox (Distributed Structure-Searchable Toxicity Database Network), and ACToR (Aggregated Computational Toxicology Resource)-are contributing to the creation of a more unified, mineable, and modelable landscape of public toxicity data. These projects address different layers in the spectrum of toxicological data representation and detail and, additionally, span diverse domains of toxicology and chemistry in relation to industry and environmental regulatory concerns. For each of the three projects, data standards are the key to enabling "read-across" in relation to toxicity data and chemical-indexed information. In turn, "read-across" capability enables flexible data mining, as well as meaningful aggregation of lower levels of toxicity information to summarized, modelable endpoints spanning sufficient areas of chemical space for building predictive models. By means of shared data standards and transparent and flexible rules for data aggregation, these and related public data initiatives are effectively spanning the divides among experimental toxicologists, computational modelers, and the world of chemically indexed, publicly available toxicity information.

Toxicology Mechanisms and Methods, 2008

ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed da... more ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed database using the ToxML schema. The public database sources include the U.S. Food and Drug Administration (FDA) submission data from approved new drug applications, food contact notifications, generally recognized as safe food ingredients, and chemicals from the NTP and CCRIS databases. The data from public sources were then combined with data from private industry according to ToxML criteria. The resulting "integrated" database, enriched in pharmaceuticals, was used for data mining analysis. Structural features describing the database were used to differentiate the chemical spaces of drugs/candidates, food ingredients, and industrial chemicals. In general, structures for drugs/candidates and food ingredients are associated with lower frequencies of mutagenicity and clastogenicity, whereas industrial chemicals as a group contain a much higher proportion of positives. Structural features were selected to analyze endpoint outcomes of the genetic toxicity studies. Although most of the well-known genotoxic carcinogenic alerts were identified, some discrepancies from the classic Ashby-Tennant alerts were observed. Using these influential features as the independent variables, the results of four types of genotoxicity studies were correlated. High Pearson correlations were found between the results of Salmonella mutagenicity and mouse lymphoma assay testing as well as those from in vitro chromosome aberration studies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.

Toxicological Sciences, 2013

Endocrine-active chemicals can potentially have adverse effects on both humans and wildlife. They... more 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.

Toxicological Sciences, 2012

The massive undertaking reported in represents an important step forward as we integrate innovati... more The massive undertaking reported in represents an important step forward as we integrate innovative in vitro chemical screening efforts such as ToxCast into risk assessment approaches. However, the authors overstate the degree to which their exposure estimates represent the "highest estimated U.S. population exposures" and consequently underestimate the number of chemicals for which current exposures exceed levels associated with biological activity.

Riassunto (Un approccio innovativo: i database chimico relazionali e il ruolo del database ISSCAN... more Riassunto (Un approccio innovativo: i database chimico relazionali e il ruolo del database ISSCAN per la valutazione della cancerogenesi chimica). Basi di dati di cancerogenesi e mutagenesi sono essenziali per la stima del rischio chimico. Finora queste si presentavano essenzialmente come tavole statiche, ma i progressi nel campo delle relazioni struttura-attività hanno permesso di creare nuove tipologie dove l'unione del

Toxicological Sciences, 2000

Both qualitative and quantitative modeling methods relating chemical structure to biological acti... more Both qualitative and quantitative modeling methods relating chemical structure to biological activity, called structure-activity relationship analyses or SAR, are applied to the prediction and characterization of chemical toxicity. This minireview will discuss some generic issues and modeling approaches that are tailored to problems in toxicology. Different approaches to, and some facets and limitations of the practice and science of, SAR as they pertain to current toxicology analyses, and the basic elements of SAR and SAR-model development and prediction systems are discussed. Other topics include application of 3-D SAR to understanding of the propensity of chemicals to cause endocrine disruption, and the use of models to analyze biological activity of metal ions in toxicology. An example of integration of knowledge pertaining to mechanisms into an expert system for prediction of skin sensitization to chemicals is also discussed. This minireview will consider the utility of modeling approaches as one component for better integration of physicochemical and biological properties into risk assessment, and also consider the potential for both environmental and human health effects of chemicals and their interactions.

Current Computer Aided-Drug Design, 2006

... of Structures Tools to perform unsupervised structure-based clustering are available from bot... more ... of Structures Tools to perform unsupervised structure-based clustering are available from both commercial as well as open sources including ... Current Computer-Aided Drug Design, 2006, Vol ... 5). Strategies to data mine structure-integrated toxicity database for linking chemistry to ...

Journal of chemical information and modeling, Jan 23, 2015

Chemotypes are a new approach for representing molecules, chemical substructures and patterns, re... more Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory, and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order to enable che...

Chemical research in toxicology, 2006

A chemistry approach to predictive toxicology relies on structure-activity relationship (SAR) mod... more A chemistry approach to predictive toxicology relies on structure-activity relationship (SAR) modeling to predict biological activity from chemical structure. Such approaches have proven capabilities when applied to well-defined toxicity end points or regions of chemical space. These approaches are less well-suited, however, to the challenges of global toxicity prediction, i.e., to predicting the potential toxicity of structurally diverse chemicals across a wide range of end points of regulatory and pharmaceutical concern. New approaches that have the potential to significantly improve capabilities in predictive toxicology are elaborating the "activity" portion of the SAR paradigm. Recent advances in two areas of endeavor are particularly promising. Toxicity data informatics relies on standardized data schema, developed for particular areas of toxicological study, to facilitate data integration and enable relational exploration and mining of data across both historical and...

Mutation research, Jan 25, 1998

There is a great deal of current interest in the use of commercial, automated programs for the pr... more There is a great deal of current interest in the use of commercial, automated programs for the prediction of mutagenicity and carcinogenicity based on chemical structure. However, the goal of accurate and reliable toxicity prediction for any chemical, based solely on structural information remains elusive. The toxicity prediction challenge is global in its objective, but limited in its solution, to within local domains of chemicals acting according to similar mechanisms of action in the biological system; to predict, we must be able to generalize based on chemical structure, but the biology fundamentally limits our ability to do so. Available commercial systems for mutagenicity and/or carcinogenicity prediction differ in their specifics, yet most fall in two major categories: (1) automated approaches that rely on the use of statistics for extracting correlations between structure and activity; and (2) knowledge-based expert systems that rely on a set of programmed rules distilled fr...

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2000

We determined the mutation spectra in Salmonella of four chlorinated butenoic acid analogues (BA-... more We determined the mutation spectra in Salmonella of four chlorinated butenoic acid analogues (BA-1 through BA-4) of the drinking water mutagen 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) and compared the results with those generated previously by us for MX and a related compound, MCF. We then considered relationships between the properties of mutagenic potency and mutational specificity for these six chlorinated butenoic acid analogues. In TA98, the three most potent mutagens, BA-3, BA-4, MX, and the organic extract, all induced large percentages of complex frameshifts (33-67%), which distinguish these agents from any other class of compound studied previously. In TA100, which has only GC sites for mutation recovery, >71% of the mutations induced by all of the agents were GC-->TA transversions. The availability of both GC and TA sites for mutation in TA104 resulted in greater distinctions in mutational specificity than in TA100. MX targeted GC sites almost exclusively (98%); the structurally similar BA-4 and BA-2 produced mutations at similar frequencies at both GC and AT sites; and the structurally similar BA-3 and BA-1 induced most mutations at AT sites (69%). Thus, large variations in structural properties influencing relative mutagenic potency appeared to be distinct from the more localized similar structural features influencing mutagenic specificity in TA104. Among a set of physicochemical properties examined for the six butenoic acids, a significant correlation was found between pK(a) and mutagenic potency in TA100, even when the unionized fraction of the activity dose was considered. In addition, a correlation in CLOGP for BA-1 to BA-4 suggested a role for bioavailability in determining mutagenic potency. These results illustrate the potential value of structural analyses for exploring the relationship between chemical structure and mutational mechanisms. To our knowledge, this is the first study in which such analyses have been applied to structural analogues for which both mutagenic potency and mutation spectra date were available.

Nature biotechnology, 2014

Addressing the safety aspects of drugs and environmental chemicals has historically been undertak... more Addressing the safety aspects of drugs and environmental chemicals has historically been undertaken through animal testing. However, the quantity of chemicals in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important chemical libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for chemicals that disrupt physiologically important pathways. Chemical-response signatures for 87 endpoints covering molecular functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental chemicals and 135 reference pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polyph...

Journal of Toxicology and Environmental Health, 1988

A group of 36 aryl azo dyes were examined for their ability to be reduced by rat liver microsomal... more A group of 36 aryl azo dyes were examined for their ability to be reduced by rat liver microsomal azoreductase. This group of azo dyes featured a variety of substituents, including sulfonic acid, phenol, nitro, amide, and methyl functionalities on phenyl, alpha-naphthyl, and beta-naphthyl rings. Reduction rates for each dye were obtained using a spectrophotometric method and anaerobic incubation conditions. These rates ranged from 0 to 7.35 nmol dye reduced/min.mg protein. The reduction rates and dye structures provided the data for a CASE-SAR (computer automated structure evaluation-structure-activity relationship) fragment analysis, and three major structure fragments associated with the ability of this group of azo dyes to be reduced were identified. The three CASE fragments correctly label 92% of the azo dye structures as active or inactive and may be useful in future predictions of the ability of azo dyes to undergo reduction by rat liver azoreductase.

The U.S. Environmental Protection Agency (EPA) is developing methods for utilizing computational ... more The U.S. Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS), and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources toward chemicals that likely represent the greatest hazard to human health and the environment. This chemical prioritization research program, entitled ''ToxCast,'' is being initiated with the purpose of developing the ability to forecast toxicity based on bioactivity profiling. The proof-of-concept phase of ToxCast will focus upon chemicals with an existing, rich toxicological database in order to provide an interpretive context for the ToxCast data. This set of several hundred reference chemicals will represent numerous structural classes and phenotypic outcomes, including tumorigens, developmental and reproductive toxicants, neurotoxicants, and immunotoxicants. The ToxCast program will evaluate chemical properties and bioactivity profiles across a broad spectrum of data domains: physical-chemical, predicted biological activities based on existing structure-activity models, biochemical properties based on HTS assays, cell-based phenotypic assays, and genomic and metabolomic analyses of cells. These data will be generated through a series of external contracts, along with collaborations across EPA, with the National Toxicology Program, and with the National Institutes of Health Chemical Genomics Center. The resulting multidimensional data set provides an informatics challenge requiring appropriate computational methods for integrating various chemical, biological, and toxicological data into profiles and models predicting toxicity.

ACToR (Aggregated Computational Toxicology Resource) is a database and set of software applicatio... more ACToR (Aggregated Computational Toxicology Resource) is a database and set of software applications that bring into one central location many types and sources of data on environmental chemicals. Currently, the ACToR chemical database contains information on chemical structure, in vitro bioassays and in vivo toxicology assays derived from more than 150 sources including the U.S. Environmental Protection Agency (EPA), Centers for Disease Control (CDC), U.S. Food and Drug Administration (FDA), National Institutes of Health (NIH), state agencies, corresponding government agencies in Canada, Europe and Japan, universities, the World Health Organization (WHO) and non-governmental organizations (NGOs). At the EPA National Center for Computational Toxicology, ACToR helps manage large data sets being used in a high-throughput environmental chemical screening and prioritization program called ToxCast.

Regulatory Toxicology and Pharmacology, 2009

Three high-throughput screening (HTS) genotoxicity assays-GreenScreen HC GADD45a-GFP (Gentronix L... more Three high-throughput screening (HTS) genotoxicity assays-GreenScreen HC GADD45a-GFP (Gentronix Ltd.), CellCiphr p53 (Cellumen Inc.) and CellSensor p53RE-bla (Invitrogen Corp.)-were used to analyze the collection of 320 predominantly pesticide active compounds being tested in Phase I of US. Environmental Protection Agency's ToxCast research project. Between 9% and 12% of compounds were positive for genotoxicity in the assays. However, results of the varied tests only partially overlapped, suggesting a strategy of combining data from a battery of assays. The HTS results were compared to mutagenicity (Ames) and animal tumorigenicity data. Overall, the HTS assays demonstrated low sensitivity for rodent tumorigens, likely due to: screening at a low concentration, coverage of selected genotoxic mechanisms, lack of metabolic activation and difficulty detecting non-genotoxic carcinogens. Conversely, HTS results demonstrated high specificity, >88%. Overall concordance of the HTS assays with tumorigenicity data was low, around 50% for all tumorigens, but increased to 74-78% (vs. 60% for Ames) for those compounds producing tumors in rodents at multiple sites and, thus, more likely genotoxic carcinogens. The aim of the present study was to evaluate the utility of HTS assays to identify potential genotoxicity hazard in the larger context of the ToxCast project, to aid prioritization of environmentally relevant chemicals for further testing and assessment of carcinogenicity risk to humans.

ALTEX, 2013

In vitro high-throughput screening (HTS) assays are seeing increasing use in toxicity testing. HT... more In vitro high-throughput screening (HTS) assays are seeing increasing use in toxicity testing. HTS assays can simultaneously test many chemicals but have seen limited use in the regulatory arena, in part because of the need to undergo rigorous, time-consuming formal validation. Here we discuss streamlining the validation process, specifically for prioritization applications. By prioritization, we mean a process in which less complex, less expensive, and faster assays are used to prioritize which chemicals are subjected first to more complex, expensive, and slower guideline assays. Data from the HTS prioritization assays is intended to provide a priori evidence that certain chemicals have the potential to lead to the types of adverse effects that the guideline tests are assessing. The need for such prioritization approaches is driven by the fact that there are tens of thousands of chemicals to which people are exposed, but the yearly throughput of most guideline assays is small in co...

Toxicology, Jan 28, 2011

Understanding the potential health risks posed by environmental chemicals is a significant challe... more Understanding the potential health risks posed by environmental chemicals is a significant challenge elevated by the large number of diverse chemicals with generally uncharacterized exposures, mechanisms, and toxicities. The present study is a performance evaluation and critical analysis of assay results for an array of 292 high-throughput cell-free assays aimed at preliminary toxicity evaluation of 320 environmental chemicals in EPA's ToxCast™ project (Phase I). The chemicals (309 unique, 11 replicates) were mainly precursors or the active agent of commercial pesticides, for which a wealth of in vivo toxicity data is available. Biochemical HTS (high-throughput screening) profiled cell and tissue extracts using semi-automated biochemical and pharmacological methodologies to evaluate a subset of G-protein coupled receptors (GPCRs), CYP450 enzymes (CYPs), kinases, phosphatases, proteases, HDACs, nuclear receptors, ion channels, and transporters. The primary screen tested all chemi...

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2005

Toxicology Mechanisms and Methods, 2008

ABSTRACT Chemical toxicity data at all levels of description, from treatment-level dose response ... more ABSTRACT Chemical toxicity data at all levels of description, from treatment-level dose response data to a high-level summarized toxicity "endpoint," effectively circumscribe, enable, and limit predictive toxicology approaches and capabilities. Several new and evolving public data initiatives focused on the world of chemical toxicity information-as represented here by ToxML (Toxicology XML standard), DSSTox (Distributed Structure-Searchable Toxicity Database Network), and ACToR (Aggregated Computational Toxicology Resource)-are contributing to the creation of a more unified, mineable, and modelable landscape of public toxicity data. These projects address different layers in the spectrum of toxicological data representation and detail and, additionally, span diverse domains of toxicology and chemistry in relation to industry and environmental regulatory concerns. For each of the three projects, data standards are the key to enabling "read-across" in relation to toxicity data and chemical-indexed information. In turn, "read-across" capability enables flexible data mining, as well as meaningful aggregation of lower levels of toxicity information to summarized, modelable endpoints spanning sufficient areas of chemical space for building predictive models. By means of shared data standards and transparent and flexible rules for data aggregation, these and related public data initiatives are effectively spanning the divides among experimental toxicologists, computational modelers, and the world of chemically indexed, publicly available toxicity information.

Toxicology Mechanisms and Methods, 2008

ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed da... more ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed database using the ToxML schema. The public database sources include the U.S. Food and Drug Administration (FDA) submission data from approved new drug applications, food contact notifications, generally recognized as safe food ingredients, and chemicals from the NTP and CCRIS databases. The data from public sources were then combined with data from private industry according to ToxML criteria. The resulting "integrated" database, enriched in pharmaceuticals, was used for data mining analysis. Structural features describing the database were used to differentiate the chemical spaces of drugs/candidates, food ingredients, and industrial chemicals. In general, structures for drugs/candidates and food ingredients are associated with lower frequencies of mutagenicity and clastogenicity, whereas industrial chemicals as a group contain a much higher proportion of positives. Structural features were selected to analyze endpoint outcomes of the genetic toxicity studies. Although most of the well-known genotoxic carcinogenic alerts were identified, some discrepancies from the classic Ashby-Tennant alerts were observed. Using these influential features as the independent variables, the results of four types of genotoxicity studies were correlated. High Pearson correlations were found between the results of Salmonella mutagenicity and mouse lymphoma assay testing as well as those from in vitro chromosome aberration studies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.

Toxicological Sciences, 2013

Endocrine-active chemicals can potentially have adverse effects on both humans and wildlife. They... more 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.

Toxicological Sciences, 2012

The massive undertaking reported in represents an important step forward as we integrate innovati... more The massive undertaking reported in represents an important step forward as we integrate innovative in vitro chemical screening efforts such as ToxCast into risk assessment approaches. However, the authors overstate the degree to which their exposure estimates represent the "highest estimated U.S. population exposures" and consequently underestimate the number of chemicals for which current exposures exceed levels associated with biological activity.

Riassunto (Un approccio innovativo: i database chimico relazionali e il ruolo del database ISSCAN... more Riassunto (Un approccio innovativo: i database chimico relazionali e il ruolo del database ISSCAN per la valutazione della cancerogenesi chimica). Basi di dati di cancerogenesi e mutagenesi sono essenziali per la stima del rischio chimico. Finora queste si presentavano essenzialmente come tavole statiche, ma i progressi nel campo delle relazioni struttura-attività hanno permesso di creare nuove tipologie dove l'unione del

Toxicological Sciences, 2000

Both qualitative and quantitative modeling methods relating chemical structure to biological acti... more Both qualitative and quantitative modeling methods relating chemical structure to biological activity, called structure-activity relationship analyses or SAR, are applied to the prediction and characterization of chemical toxicity. This minireview will discuss some generic issues and modeling approaches that are tailored to problems in toxicology. Different approaches to, and some facets and limitations of the practice and science of, SAR as they pertain to current toxicology analyses, and the basic elements of SAR and SAR-model development and prediction systems are discussed. Other topics include application of 3-D SAR to understanding of the propensity of chemicals to cause endocrine disruption, and the use of models to analyze biological activity of metal ions in toxicology. An example of integration of knowledge pertaining to mechanisms into an expert system for prediction of skin sensitization to chemicals is also discussed. This minireview will consider the utility of modeling approaches as one component for better integration of physicochemical and biological properties into risk assessment, and also consider the potential for both environmental and human health effects of chemicals and their interactions.