Current status and future directions for a neurotoxicity hazard assessment framework that integrates in silico approaches

Neurotoxicology is the study of adverse effects on the structure or function of the developing or mature adult nervous system following exposure to chemical, biological, or physical agents. The development of more informative alternative methods to assess developmental (DNT) and adult (NT) neurotoxicity induced by xenobiotics is critically needed. The use of such alternative methods including in silico approaches that predict DNT or NT from chemical structure (e.g., statistical-based and expert rule-based systems) is ideally based on a comprehensive understanding of the relevant biological mechanisms. This paper discusses known mechanisms alongside the current state of the art in DNT/NT testing. In silico approaches available today that support the assessment of neurotoxicity based on knowledge of chemical structure are reviewed, and a conceptual framework for the integration of in silico methods with experimental information is presented. Establishing this framework is essential for the development of protocols, namely standardized approaches, to ensure that assessments of NT and DNT based on chemical structures are generated in a transparent, consistent, and defendable manner.

Adverse outcome pathways for chemical toxicity and their applications to workers' health: a literature review

OBJECTIVE AND METHODS

Various papers related to the application of adverse outcome pathways (AOPs) for the prevention of occupational disease were reviewed. The Internet was used as the primary tool to search for the necessary research data and information, using such online resources as Google Scholar, ScienceDirect, Scopus, NDSL, and PubMed. The key search terms were "adverse outcome pathway," "toxicology," "risk assessment," "human," "worker," "occupational safety and health," and so on.

RESULTS AND CONCLUSION

The aim of this paper is to explain the use of AOP for the understanding of chemical toxicity as a conceptual means and to predict the toxic mechanism. The tools of AOP have emerged as a forward-looking alternative to the existing chemical risk assessment paradigm. AOP is being applied to the assessment of acute toxicity and to chronic toxic chemicals in the workplace. Not only can it lead to breakthroughs in occupational and environmental cancer prevention, it is also widely used in chemical risk assessment and has led to breakthroughs in the prevention of occupational disease in the workplace.

The differential expression of Chironomus spp genes as useful tools in the search for pollution biomarkers in freshwater ecosystems

Insects of the Chironomidae family are characterized by a wide ecological diversity in freshwater ecosystems. The larvae have the physiological potential to tolerate environmental stress even when there is a low concentration of oxygen, the presence of toxic substances or when there are changes in temperature and salinity. On the other hand, it is important to consider that at a cellular level, when individual insects are exposed to environmental changes, it induces responses of groups of genes that govern the molecular mechanisms related to such tolerance. In this review, using fourth instar larvae of Chironomus spp. in natural conditions and of Chironomus columbiensis under controlled conditions, we will discuss the genetic expression of a group of genes that respond to detoxification and also the biological functions involved and impacted on by mining stressors. The study of macroinvertebrate bioindicator species and their gene expression as a result of mining activity opens a window on the search for genetic biomarkers that could be used in environmental pollution assessments in freshwater ecosystems.

Adverse Outcome Pathway (AOP) Informed Modeling of Aquatic Toxicology: QSARs, Read-Across, and Interspecies Verification of Modes of Action

Alternative approaches have been promoted to reduce the number of vertebrate and invertebrate animals required for the assessment of the potential of compounds to cause harm to the aquatic environment. A key philosophy in the development of alternatives is a greater understanding of the relevant adverse outcome pathway (AOP). One alternative method is the fish embryo toxicity (FET) assay. Although the trends in potency have been shown to be equivalent in embryo and adult assays, a detailed mechanistic analysis of the toxicity data has yet to be performed; such analysis is vital for a full understanding of the AOP. The research presented herein used an updated implementation of the Verhaar scheme to categorize compounds into AOP-informed categories. These were then used in mechanistic (quantitative) structure-activity relationship ((Q)SAR) analysis to show that the descriptors governing the distinct mechanisms of acute fish toxicity are capable of modeling data from the FET assay. The results show that compounds do appear to exhibit the same mechanisms of toxicity across life stages. Thus, this mechanistic analysis supports the argument that the FET assay is a suitable alternative testing strategy for the specified mechanisms and that understanding the AOPs is useful for toxicity prediction across test systems.

Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife

There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called 'adverse outcome pathway' (AOP) constructs. The AOP approach provides a framework for organizing information at the chemical and biological level, allowing evidence from both in silico and in vitro studies to be rationally combined to fill gaps in knowledge concerning toxicological events. Fundamental to this new paradigm is a greater understanding of the mechanisms of toxicity and, in particular, where these mechanisms may be conserved across taxa, such as between model animals and related wild species. This presents an opportunity to make predictions across diverse species, where empirical data are unlikely to become available as is the case for most species of wildlife.

Development of an in silico profiler for respiratory sensitisation

In this article, we outline work that led the QSAR and Molecular Modelling Group at Liverpool John Moores University to be jointly awarded the 2013 Lush Science Prize. Our research focuses around the development of in silico profilers for category formation within the Adverse Outcome Pathway paradigm. The development of a well-defined chemical category allows toxicity to be predicted via read-across. This is the central approach used by the OECD QSAR Toolbox. The specific work for which we were awarded the Lush Prize was for the development of such an in silico profiler for respiratory sensitisation. The profiler was developed by an analysis of the mechanistic chemistry associated with covalent bond formation in the lung. The data analysed were collated from clinical reports of occupational asthma in humans. The impact of the development of in silico profilers on the Three Rs is also discussed.

Experimental verification of structural alerts for the protein binding of cyclic compounds acting as Michael acceptors

This study outlines how a combination of and in vitro data can be used to define the applicability domain of selected structural alerts within the protein binding profilers of the Organisation for Economic Co-operation (OECD) Quantitative Structure-Activity Relationship (QSAR) Toolbox. Thirty chemicals containing a cyclic moiety were profiled for reactivity using the OECD and Optimised Approach based on Structural Indices Set (OASIS) protein binding profilers. The profiling results identified 22 of the chemicals as being reactive towards proteins. Analysis of the experimentally data showed 19 of these chemicals to be reactive. Subsequent analysis allowed refinements to be suggested to improve the applicability domain of the structural alerts investigated. The accurate definition of the applicability domain for structural alerts within in silico profilers is important due to their use in chemical category in predictive and regulatory toxicology.

Experimental verification, and domain definition, of structural alerts for protein binding: epoxides, lactones, nitroso, nitros, aldehydes and ketones

This study outlines how a combination of in chemico and Tetrahymena pyriformis data can be used to define the applicability domain of selected structural alerts within the profilers of the OECD QSAR Toolbox. Thirty-three chemicals were profiled using the OECD and OASIS profilers, enabling the applicability domain of six structural alerts to be defined, the alerts being: epoxides, lactones, nitrosos, nitros, aldehydes and ketones. Analysis of the experimental data showed the applicability domains for the epoxide, nitroso, aldehyde and ketone structural alerts to be well defined. In contrast, the data showed the applicability domains for the lactone and nitro structural alerts needed modifying. The accurate definition of the applicability domain for structural alerts within in silico profilers is important due to their use in the chemical category in predictive and regulatory toxicology. This study highlights the importance of utilizing multiple profilers in category formation.

The definition of the toxicologically relevant applicability domain for the SNAr reaction for substituted pyridines and pyrimidines

This study outlines how results from a glutathione reactivity assay (so-called in chemico data) can be used to define the applicability domain for the nucleophilic aromatic substitution (SNAr) reaction for nitrogen-containing aromatic compounds. SNAr is one of the six mechanistic domains that have been shown to be important in toxicological endpoints in which the ability to bind covalently to a protein is a key molecular initiating event. This study has analysed experimental data (2 h RC50 values), allowing a clear and interpretable structure-activity relationship to be developed for pyridines and pyrimidines which reside within the SNAr domain. The in-ring nitrogen(s) act as activating groups in the SNAr reaction. The position(s) of the in-ring nitrogen(s) as well as other activating groups, especially in relationship to the leaving group, affect reactive potency. The experimentally defined applicability domain has resulted in a series of structural alerts. These results build on early work on the benzene derivatives residing in the SNAr domain. The definition of the applicability domain for the SNAr reaction and the resulting structural alerts are likely to be beneficial in the development of computational tools for category formation and read-across in hazard identification, and the development of adverse outcome pathways.

Training needs for toxicity testing in the 21st century: a survey-informed analysis

Current training needs on the use of alternative methods in predictive toxicology, including new approaches based on mode-of-action (MoA) and adverse outcome pathway (AOP) concepts, are expected to evolve rapidly. In order to gain insight into stakeholder preferences for training, the European Commission's Joint Research Centre (JRC) conducted a single-question survey with twelve experts in regulatory agencies, industry, national research organisations, NGOs and consultancies. Stakeholder responses were evaluated by means of theory-based qualitative data analysis. Overall, a set of training topics were identified that relate both to general background information and to guidance for applying alternative testing methods. In particular, for the use of in silico methods, stakeholders emphasised the need for training on data integration and evaluation, in order to increase confidence in applying these methods for regulatory purposes. Although the survey does not claim to offer an exhaustive overview of the training requirements, its findings support the conclusion that the development of well-targeted and tailor-made training opportunities that inform about the usefulness of alternative methods, in particular those that offer practical experience in the application of in silico methods, deserves more attention. This should be complemented by transparent information and guidance on the interpretation of the results generated by these methods and software tools.

Categorization of nitrobenzenes for repeated dose toxicity based on adverse outcome pathways

Adoption of the data-gap filling method for complex endpoints such as repeated dose toxicity (RDT) and reproductive/developmental toxicity is one of the most important issues affecting international chemical management at present. A categorization method based on adverse outcome pathways (AOPs) has recently been investigated for such complex endpoints. In this paper, we report results of the categorization of nitrobenzenes for RDT based on the AOPs obtained by analysing the detailed RDT test reports for 24 different nitrobenzenes already evaluated. In most RDT testing of nitrobenzenes without hydroxyl groups or acid groups, findings related to haemolytic anaemia and liver effects were observed at low dosages. It was, therefore, possible to assume common AOPs for haemolytic anaemia and liver effects induced by these nitrobenzenes. As a result, a group of nitrobenzenes was defined as a single category for both haemolytic anaemia and liver effects, respectively, based on these AOPs.

The definition of the applicability domain relevant to skin sensitization for the aromatic nucleophilic substitution mechanism

This study outlines how a glutathione reactivity assay (so-called in chemico data) can be used to define the applicability domain for the nucleophilic aromatic substitution (S(N)Ar) reaction for benzenes. This reaction is one of the six mechanistic domains that have been shown to be important in toxicological endpoints in which the ability to bind covalently to a protein is a key molecular initiating event. This study has analysed the experimental data, allowing a clear and interpretable structure-activity relationship to be developed for the S(N)Ar domain. The applicability domain has resulted in a series of structural alerts. The definition of the applicability domain for the S(N)Ar reaction and the resulting structural alerts are likely to be beneficial in the development of computational tools for category formation and read-across. The study concludes with how this information can be used in the development of adverse outcome pathways.

In silico models for drug-induced liver injury--current status

INTRODUCTION

Drug-induced liver injury (DILI) is one of the most important reasons for drug attrition at both pre-approval and post-approval stages. Therefore, it is crucial to develop methods that will detect potential hepatotoxicity among drug candidates as early and quickly as possible. However, the complexity of hepatotoxicity endpoint makes it very difficult to predict. In addition, there is still a lack of sensitive and specific biomarkers for DILI that consequently leads to a scarcity of reliable hepatotoxic data, which are the key to any modelling approach.

AREAS COVERED

This review explores the current status of existing in silico models predicting hepatotoxicity. Over the past decade, attempts have been made to compile hepatotoxicity data and develop in silico models, which can be used as a first-line screening of drug candidates for further testing.

EXPERT OPINION

Most of the predictive methods discussed in this review are based on the structural properties of chemicals and do not take into account genetic and environmental factors; therefore, their predictions are still uncertain. To improve the predictability of in silico models for DILI, it is essential to better understand its mechanisms as well as to develop sensitive toxicogenomics biomarkers, which show relatively good differentiation between hepatotoxins and non-hepatotoxins.

The Use of a Chemistry-based Profiler for Covalent DNA Binding in the Development of Chemical Categories for Read-across for Genotoxicity

An important molecular initiating event for genotoxicity is the ability of a compound to bind covalently with DNA. However, not all compounds that can undergo covalent binding mechanisms will result in genotoxicity. One approach to solving this problem, when in silico prediction techniques are being used, is to develop tools that allow chemicals to be grouped into categories based on their ability to bind covalently to DNA. For this analysis to take place, compounds need to be placed within categories where the trend in toxicity can be explained by simple descriptors, such as hydrophobicity. However, this can occur only when the compounds within a category are structurally and mechanistically similar. Chemistry-based profilers have the ability to screen compounds and highlight those with similar structures to a target compound, and are thus likely to act via a similar mechanism of action. Here, examples are reported to highlight how structure-based profilers can be used to form categories and hence fill data gaps. The importance of developing a well-defined and robust category is discussed in terms of both mechanisms of action and structural similarity.

Reactivity and aquatic toxicity of aromatic compounds transformable to quinone-type Michael acceptors

Reactive toxicity encompasses important endpoints such as skin and respiratory sensitization, hepatotoxicity and elevated acute aquatic toxicity. These adverse effects are initiated by, among others, electrophilic chemicals and those transformed into electrophiles; i.e. non-reactive chemicals activated into reactive electrophilic species by either a biotransformation (pro-electrophiles) or abiotic mechanism (pre-electrophiles). The presence of pro- and pre-electrophiles is important when developing quantitative structure-activity relationships (QSARs). In this study, the reactivity of potential pre-electrophile polyphenolics was investigated using an in chemico assay based on glutathione (GSH) depletion; in addition, the toxicity to Tetrahymena pyriformis was determined. For pre-electrophiles, no direct relationship between toxic potency and reactivity to GSH was obtained. The structural determinants for the pre-electrophile domain were characterized qualitatively by assessing structure-activity relationships (SARs). From this analysis, structural alerts for the pre-Michael acceptor domain (i.e. non-reactive chemicals activated into Michael acceptors) were extracted from the in chemico GSH data. A series of 10 structural alerts corresponding to 1,2- and 1,4-hydroxy and amino-substituted aromatics was developed. The relevance of the alerts was assessed by investigating the aquatic toxicity of these compounds. The structural alerts should help to identify and group pre-Michael acceptors and thus potent reactive toxicants.

A review of the electrophilic reaction chemistry involved in covalent DNA binding

The need to assess the ability of a chemical to act as a mutagen or a genotoxic carcinogen (collectively termed genotoxicity) is one of the primary requirements in regulatory toxicology. Several pieces of legislation have led to an increased interest in the use of in silico methods, specifically the formation of chemical categories for the assessment of toxicological endpoints. A key step in the development of chemical categories for genotoxicity is defining the organic chemistry associated with the formation of a covalent bond between DNA and an exogenous chemical. This organic chemistry is typically defined as structural alerts. To this end, this article has reviewed the literature defining the structural alerts associated with covalent DNA binding. Importantly, this review article also details the mechanistic organic chemistry associated with each of the structural alerts. This information is extremely important in terms of meeting regulatory requirements for the acceptance of the chemical category approach. The structural alerts and associated mechanistic chemistry have been incorporated into the Organisation for Economic Co-operation and Development (OECD) (Q)SAR Application Toolbox.

Reactivity-based toxicity modelling of five-membered heterocyclic compounds: application to Tetrahymena pyriformis

A diverse set of 57 heterocyclic organic chemicals, consisting of a five-membered unsaturated ring of four carbon atoms and one oxygen (furans), or sulfur (thiophenes), or nitrogen (pyrroles) were evaluated for reactivity with thiol and acute aquatic toxicity assays using glutathione (GSH) as a model nucleophile and the ciliate Tetrahymena pyriformis, respectively. Reactivity was quantified by the RC₅₀ value, the concentration of test compound that produced 50% reaction of the GSH thiol groups in 2 hours. Under standard conditions, RC₅₀ values are mathematically proportional to reciprocal rate constants. Toxicity was quantified by the IGC₅₀, the concentration of the test compound that produces 50% inhibition of population growth in 40 hours. Pyrroles with polarized α,β-unsaturated substructures were found to be non-reactive with GSH and did not exhibit excess toxicity in the Tetrahymena assay. In contrast, those furans and thiophenes with polarized α,β-unsaturated substructures were reactive with GSH via the Michael addition mechanism and did exhibit excess acute aquatic toxicity in Tetrahymena. For furans and thiophenes, reactivity and toxicity varied with the number, type, and location on the ring of the π-bond-containing polarized moieties. Comparisons of reactivity and toxicity potency between furan and thiophene derivatives revealed furans to be twice as potent as thiophenes. QSAR analysis revealed that aquatic toxicity IGC₅₀ to Tetrahymena is correlated with RC₅₀ values: log (IGC₅₀(-1)) = 1.13 log (RC₅₀(-1)) + 1.43; n = 23, r²= 0.815, r²(adj) = 0.806, s = 0.41, F = 92.