Mechanistic relationship between biodegradation and bioaccumulation. Practical outcomes

According to the REACH Regulation, for all substances manufactured or imported in amounts of 10 or more tons per year, that are not exempted from the registration requirement, a Chemical Safety Assessment (CSA) must be conducted. According to CSA criteria, for these substances persistent, bioaccumulative and toxic (PBT), and very persistent and very bioaccumulative (vPvB) assessment is requested. In order to reduce the number of applications of the expensive bioaccumulation test it seems useful to search thresholds for other related parameters above which no bioaccumulation is observed. Given the known relationship between ready biodegradability and bioaccumulation, one such parameter is biodegradation. This article addresses this relationship in searching for BOD threshold above which no vB and B chemicals could be observed. It was found that the regulatory criteria for persistency could be used for identification of not vB and B chemicals. In addition, fish liver metabolism is determined as the most significant factor in reducing of maximum bioaccumulation potential of the chemicals. It was found that parameters associated with the models simulating fish metabolism could be also used for identification of not vB and B chemicals.

Spectroscopic Investigation of the Effect of Microstructure and Energetic Offset on the Nature of Interfacial Charge Transfer States in Polymer: Fullerene Blends

Despite performance improvements of organic photovoltaics, the mechanism of photoinduced electron–hole separation at organic donor–acceptor interfaces remains poorly understood. Inconclusive experimental and theoretical results have produced contradictory models for electron–hole separation in which the role of interfacial charge-transfer (CT) states is unclear, with one model identifying them as limiting separation and another as readily dissociating. Here, polymer–fullerene blends with contrasting photocurrent properties and enthalpic offsets driving separation were studied. By modifying composition, film structures were varied from consisting of molecularly mixed polymer–fullerene domains to consisting of both molecularly mixed and fullerene domains. Transient absorption spectroscopy revealed that CT state dissociation generating separated electron–hole pairs is only efficient in the high energy offset blend with fullerene domains. In all other blends (with low offset or predominantly molecularly mixed domains), nanosecond geminate electron–hole recombination is observed revealing the importance of spatially localized electron–hole pairs (bound CT states) in the electron–hole dynamics. A two-dimensional lattice exciton model was used to simulate the excited state spectrum of a model system as a function of microstructure and energy offset. The results could reproduce the main features of experimental electroluminescence spectra indicating that electron–hole pairs become less bound and more spatially separated upon increasing energy offset and fullerene domain density. Differences between electroluminescence and photoluminescence spectra could be explained by CT photoluminescence being dominated by more-bound states, reflecting geminate recombination processes, while CT electroluminescence preferentially probes less-bound CT states that escape geminate recombination. These results suggest that apparently contradictory studies on electron–hole separation can be explained by the presence of both bound and unbound CT states in the same film, as a result of a range of interface structures.

UVCB substances II: Development of an endpoint-nonspecific procedure for selection of computationally generated representative constituents

Substances of unknown or variable composition, complex reaction products, and biological materials (UVCBs) comprise approximately 40% of all registered substances submitted to the European Chemicals Agency. One of the main characteristics of UVCBs is that they have no unique representation. Industry scientists who are part of the scientific community have been working with academics and consultants to address the problem of a lack of a defined structural description. It has been acknowledged that one of the obstacles is the large number of possible structural isomers. We have recently proposed and published a methodology, based on the generic substance identifiers, to address this issue. The methodology allows for the coding of constituents, their generation, calculation of important characteristics of UVCB constituents, and selection of representative constituents. In the present study we introduce a statistical selection of the minimum number of generated constituents representing a UVCB. This representative sample was selected in such a way that the structural variability and the properties of concern of the UVCB were approximated within a predefined tolerable error. The aim of the statistical selection was to enable the assessment of UVCB substances by decreasing the number of constituents that need to be evaluated. The procedure, which was shown to be endpoint-independent, was validated theoretically and on real case studies. Environ Toxicol Chem 2019;38:682-694. © 2019 SETAC.

CATALOGIC 301C model - validation and improvement

In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL. CATALOGIC 301C model meets all REACH requirements to be used for biodegradability assessment. The model formalism built on scientific understanding for the microbial degradation of chemicals has a well-defined and transparent applicability domain. The model predictions are adequate for the evaluation of the ready degradability of chemicals.

Skin Sensitization: Modeling Based on Skin Metabolism Simulation and Formation of Protein Conjugates

A quantitative structure-activity relationship (QSAR) system for estimating skin sensitization potency has been developed that incorporates skin metabolism and considers the potential of parent chemicals and/or their activated metabolites to react with skin proteins. A training set of diverse chemicals was compiled and their skin sensitization potency assigned to one of three classes. These three classes were, significant, weak, or nonsensitizing. Because skin sensitization potential depends upon the ability of chemicals to react with skin proteins either directly or after appropriate metabolism, a metabolic simulator was constructed to mimic the enzyme activation of chemicals in the skin. This simulator contains 203 hierarchically ordered spontaneous and enzyme controlled reactions. Phase I and phase II metabolism were simulated by using 102 and 9 principal transformations, respectively. The covalent interactions of chemicals and their metabolites with skin proteins were described by 83 reactions that fall within 39 alerting groups. The SAR/QSAR system developed was able to correctly classify about 80% of the chemicals with significant sensitizing effect and 72% of nonsensitizing chemicals. For some alerting groups, three-dimensional (3D)-QSARs were developed to describe the multiplicity of physicochemical, steric, and electronic parameters. These 3D-QSARs, so-called pattern recognition-type models, were applied each time a latent alerting group was identified in a parent chemical or its generated metabolite(s). The concept of the mutual influence amongst atoms in a molecule was used to define the structural domain of the skin sensitization model. The utility of the structural model domain and the predictability of the model were evaluated using sensitization potency data for 96 chemicals not used in the model building. The TIssue MEtabolism Simulator (TIMES) software was used to integrate a skin metabolism simulator and 3D-QSARs to evaluate the reactivity of chemicals thus predicting their likely skin sensitization potency.

QSAR Toolbox - workflow and major functionalities

The OECD QSAR Toolbox is a software application intended to be used by governments, the chemical industry and other stakeholders in filling gaps in (eco)toxicity data needed for assessing the hazards of chemicals. The development and release of the Toolbox is a cornerstone in the computerization of hazard assessment, providing an 'all inclusive' tool for the application of category approaches, such as read-across and trend analysis, in a single software application, free of charge. The Toolbox incorporates theoretical knowledge, experimental data and computational tools from various sources into a logical workflow. The main steps of this workflow are substance identification, identification of relevant structural characteristics and potential toxic mechanisms of interaction (i.e. profiling), identification of other chemicals that have the same structural characteristics and/or mechanism (i.e. building a category), data collection for the chemicals in the category and use of the existing experimental data to fill the data gap(s). The description of the Toolbox workflow and its main functionalities is the scope of the present article.

UVCB substances: methodology for structural description and application to fate and hazard assessment

Substances of unknown or variable composition, complex reaction products, or biological materials (UVCBs) have been conventionally described in generic terms. Commonly used substance identifiers are generic names of chemical classes, generic structural formulas, reaction steps, physical-chemical properties, or spectral data. Lack of well-defined structural information has significantly restricted in silico fate and hazard assessment of UVCB substances. A methodology for the structural description of UVCB substances has been developed that allows use of known identifiers for coding, generation, and selection of representative constituents. The developed formats, Generic Simplified Molecular-Input Line-Entry System (G SMILES) and Generic Graph (G Graph), address the need to code, generate, and select representative UVCB constituents; G SMILES is a SMILES-based single line notation coding fixed and variable structural features of UVCBs, whereas G Graph is based on a workflow paradigm that allows generation of constituents coded in G SMILES and end point-specific or nonspecific selection of representative constituents. Structural description of UVCB substances as afforded by the developed methodology is essential for in silico fate and hazard assessment. Data gap filling approaches such as read-across, trend analysis, or quantitative structure-activity relationship modeling can be applied to the generated constituents, and the results can be used to assess the substance as a whole. The methodology also advances the application of category-based data gap filling approaches to UVCB substances.

What determines skin sensitization potency-myths, maybes and realities. Part 1. The 500 molecular weight cut-off

BACKGROUND

It is widely accepted that there is a molecular weight (MW) cut-off of 500, such that single chemicals with MWs higher than 500 cannot be skin sensitizers. If true, this could serve as a useful principle for designing non-sensitizing chemicals.

OBJECTIVES

To assess whether the 500 MW cut-off is a myth or a reality.

METHODS

A database of 699 chemicals tested for skin sensitization in guinea pigs or mice was analysed to establish the number of tested chemicals with MW > 500, and to establish whether any of these were sensitizers.

RESULTS

Only 13 (2%) of the 699 chemicals in the database have MW > 500. Of the 13 tested compounds with MW > 500 in the database, five are sensitizers and eight are non-sensitizers.

CONCLUSIONS

The 500 MW cut-off for skin sensitization is a myth, probably derived from the widespread misconception that ability to efficiently penetrate the stratum corneum is a key determinant of sensitization potency. The scarcity of sensitizers with MW > 500 simply reflects the general scarcity of chemicals with MW > 500.

Ghrelin signaling in human mesenteric arteries

The hypothesis is that the ghrelin signal pathway consists of new participants including a local second mediator in human mesenteric arteries. The contractile force of isometric artery preparations was measured using a wire-myograph. Whole-cell patch clamp experiments were performed on freshly isolated single smooth muscle cells from the same tissue. After the addition of ghrelin (100 nmol) the outward potassium currents conducted through iberiotoxin-sensitive calcium-activated potassium channels with a large conductance were almost entirely abolished. The effect of ghrelin on potassium currents was insensitive to selective inhibitors of cAMP-dependent protein kinase and soluble guanylate cyclase, but was eliminated in the presence of des-octanoyl ghrelin and O-(octahydro-4,7-methano-1H-inden-5-yl) carbonopotassium dithioate (D-609). Ghrelin dose-dependently increased the force of contraction of native, endothelium-denuded and mostly of endothelium-denuded and treated with tetrodotoxin human mesenteric arteries preconstricted with 1 nmol endothelin-1. This effect of ghrelin was blocked when the bath solution contained 1,4-diamino-2,3-dicyano-1,4-bis(2-aminophenylthio)butadiene (U0126), 4-amino-5-(4-methylphenyl)-7-(t-butyl) pyrazolo[3,4-d] pyrimidine (PP2), D-609, 2-[1-(3-dimethylaminopropyl)indol-3-yl]-3-(indol-3-yl) maleimide (GF109203x), pertussis toxin, 2-aminoethyl diphenylborinate (2-APB), indomethacin, (5Z,13E)-(9S,11S,15R)-9,15,Dihydroxy-11-fluoro-15-(2-indanyl)-16,17,18,19,20,pentanor-5,13-prostadienoic acid (AL-8810) - a non-selective prostanoid receptor antagonist, 5-(4-Chlorophenyl)-1-(4-methoxyphenyl)-3-trifluoromethyl pyrazolo (SC-560) - a selective cyclooxygenase 1 inhibitor, ozagrel - a selective thromboxane A(2) synthase inhibitor or T prostanoid receptor antagonist GR32191B. It is concluded that ghrelin increases the force of contraction of human mesenteric arteries by a novel mechanism that involves Src kinase, mitogen-activated protein kinase kinase (MEK), cyclooxygenase 1 and T prostanoid receptor agonist, most probably thromboxane A(2).

Bioaccumulation assessment using predictive approaches

Mandated efforts to assess chemicals for their potential to bioaccumulate within the environment are increasingly moving into the realm of data inadequacy. Consequently, there is an increasing reliance on predictive tools to complete regulatory requirements in a timely and cost-effective manner. The kinetic processes of absorption, distribution, metabolism, and elimination (ADME) determine the extent to which chemicals accumulate in fish and other biota. Current mathematical models of bioaccumulation implicitly or explicitly consider these ADME processes, but there is a lack of data needed to specify critical model input parameters. This is particularly true for compounds that are metabolized, exhibit restricted diffusion across biological membranes, or do not partition simply to tissue lipid. Here we discuss the potential of in vitro test systems to provide needed data for bioaccumulation modeling efforts. Recent studies demonstrate the utility of these systems and provide a "proof of concept" for the prediction models. Computational methods that predict ADME processes from an evaluation of chemical structure are also described. Most regulatory agencies perform bioaccumulation assessments using a weight-of-evidence approach. A strategy is presented for incorporating predictive methods into this approach. To implement this strategy it is important to understand the "domain of applicability" of both in vitro and structure-based approaches, and the context in which they are applied.

TIMES-SS—A Mechanistic Evaluation of an External Validation Study Using Reaction Chemistry Principles

The TImes MEtabolism Simulator platform used for predicting skin sensitization (TIMES-SS) is a hybrid expert system that was developed at Bourgas University using funding and data from a consortium comprised of industry and regulators. TIMES-SS encodes structure-toxicity and structure-skin metabolism relationships through a number of transformations, some of which are underpinned by mechanistic three-dimensional quantitative structure-activity relationships. Here, we describe an external validation exercise that was recently carried out. As part of this exercise, data were generated for 40 new chemicals in the murine local lymph node assay (LLNA) and then compared with predictions made by TIMES-SS. The results were promising with an overall good concordance (83%) between experimental and predicted values. The LLNA results were evaluated with respect to reaction chemistry principles for sensitization. Additional testing on a further four chemicals was carried out to explore some of the specific reaction chemistry findings in more detail. Improvements for TIMES-SS, where appropriate, were put forward together with proposals for further research work. TIMES-SS is a promising tool to aid in the evaluation of skin sensitization potential under legislative programs such as REACH.

TIMES-SS—A promising tool for the assessment of skin sensitization hazard. A characterization with respect to the OECD validation principles for (Q)SARs and an external evaluation for predictivity

The TImes MEtabolism Simulator platform used for predicting Skin Sensitization (TIMES-SS) is a hybrid expert system that was developed at Bourgas University using funding and data from a Consortium comprising industry and regulators. The model was developed with the aim of minimizing animal testing and to be scientifically valid in accordance with the OECD principles for (Q)SAR validation. TIMES-SS encodes structure-toxicity and structure-skin metabolism relationships through a number of transformations, some of which are underpinned by mechanistic 3D QSARs. Here, we describe the extent to which the five OECD principles are met and in particular the results from an external evaluation exercise that was recently carried out. As part of this exercise, data were generated for 40 new chemicals in the murine local lymph node assay (LLNA) and then compared with predictions made by TIMES-SS. The results were promising with an overall good concordance (83%) between experimental and predicted values. Further evaluation of these results highlighted certain inconsistencies which were rationalized by a consideration of reaction chemistry principles for sensitization. Improvements for TIMES-SS were proposed where appropriate. TIMES-SS is a promising tool to aid in the evaluation of skin sensitization hazard under legislative programs such as REACH.

POPs: a QSAR system for developing categories for persistent, bioaccumulative and toxic chemicals and their metabolites

This paper presents the framework of a QSAR-based decision support system which provides a rapid screening of potential hazards, classification of chemicals with respect to risk management thresholds, and estimation of missing data for the early stages of risk assessment. At the simplest level, the framework is designed to rank hundreds of chemicals according to their profile of persistence, bioaccumulation potential and toxicity often called the persistent organic pollutant (POP) profile or the PBT (persistent bioaccumulative toxicant) profile. The only input data are the chemical structure. The POPs framework enables decision makers to introduce the risk management thresholds used in the classification of chemicals under various authorities. Finally, the POPs framework advances hazard identification by integrating a metabolic simulator that generates metabolic map for each parent chemical. Both the parent chemicals and plausible metabolites are systematically evaluated for metabolic activation and POPs profile.

A Systematic Approach to Simulating Metabolism in Computational Toxicology. I. The TIMES Heuristic Modelling Framework

Designing biologically active chemicals and managing their risks requires a holistic perspective on the chemical-biological interactions that form the basis of selective toxicity. The balance of therapeutic and adverse outcomes for new drugs and pesticides is managed by shaping the probabilities for transport, metabolism, and molecular initiating events. For chemicals activated as well as detoxified by metabolism, selective toxicity may be considered in terms of relative probabilities, which shift dramatically across species as well as within a population, depending on many factors. The complexity in toxicology that results from metabolism has been troublesome in QSAR research because the parent structure is less relevant to predicting ultimate effects and finding reference species/conditions for metabolic rates seems hopeless. Even the complexity of comparative xenobiotic metabolism itself seems paradoxical in light of the evidence of highly conserved catabolic processes across species. Clearly, predicting the role of metabolism in selective toxicity and adverse health outcomes requires a probabilistic framework for deterministic models as well as the many factors shaping the metabolic probability distributions under specific conditions. This paper presents a tissue metabolism simulator (TIMES), which uses a heuristic algorithm to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions and estimates for system-specific transformation probabilities. The transformation probabilities can be calibrated to specific reference conditions using transformation rate information from systematic testing. In the absence of rate data, a combinatorial algorithm is used to translate known metabolic maps taken from reference systems into best-fit transformation probabilities. Finally, toxicity test data itself can be used to shape the transformation probabilities for toxicity pathways in which the metabolic activation is the rate-limiting process leading to a toxic effect. The conceptual approach for metabolic simulation will be presented along with practical uses in forecasting plausible activated metabolites.

Non-linear modeling of bioconcentration using partition coefficients for narcotic chemicals

Bioconcentration factors (BCFs) have traditionally been used to describe the tendency of chemicals to concentrate in aquatic organisms. A reexamination of the log-log QSAR between the BCF and Kow for non-congener narcotic chemicals is presented on the basis of recommended data for fish. The model is extended to give a simple correlation between BCF and the toxicity of highly, moderately and weakly hydrophilic chemicals. For the first time, in this study an equation for calculating BCF was applied in a QSAR model for predicting the acute toxicity of chemicals to aquatic organisms.

Expression of BRCA1, NBR1 and NBR2 genes in human breast cancer cells

BRCA1 is a tumour suppressor gene with a caretaker function in the DNA-damage repair and the maintenance of genome integrity. The human BRCA1 and NBR2 genes and the homologous Brcal and Nbr1 mouse genes are situated head-to-head on human chromosome 17q21 and on mouse chromosome 11, respectively. Their transcription start sites, located on opposite DNA strands, are separated by 218 bp in humans, and by 289 bp in mice. Because of this intimate contact and because of our previous observation of a quasi-reciprocal expression pattern of Brca1 and Nbr1 in mouse spermatogenesis, we estimated here the relative mRNA expression of BRCA1, NBR1 (next-to-BRCA1) and NBR2 genes in a panel of permanent cell lines and primary cell cultures derived from human breast cancer or normal mammary tissue. The analysis revealed highly significant downregulation of BRCA1 in 11 out of 12 examined tumour cell lines and primary cell cultures as compared to non-malignant mammary cells. Two isoforms of NBR1(1A) and the classical NBR1(1B) transcripts were found in cells from malignant mammary tissues, all of them downregulated in respect to normal cells. The expression of NBR2 differed, being increased in three permanent tumour cell lines and slightly decreased in all primary breast cancer cell cultures. The in silico analysis revealed two new putative domains of the predicted NBR1 protein, suggesting its role in the ubiquitin pathway. The recent identification of the ubiquitin protein ligase activity of BRCA1 implies a possible functional connection between both genes.

Main components of voltage-sensitive K+ currents of the human colonic smooth muscle cells

The aim of the present study is to characterize voltage-sensitive macroscopic K+ current (IK) components in freshly isolated human colonic smooth muscle cells. IK components were studied by the conventional whole-cell voltage clamp method. We found two main components of IK. A transient IK component with fast kinetics, IK(fi), activated upon a holding potential of Vh = -80 mV and inactivated completely following a 4-second-long prepulse to 0 mV. IK(fi) was abolished by Vh = -50 mV, as well as by a pipette solution containing 11 mM EGTA. The second, non-inactivating IK component, IK(ni), had comparable amplitudes at Vh = -80 mV and Vh = -50 mV and could not be inactivated completely, even by positive conditioning stimuli. The amplitudes of IK(ni) depended strongly on the Ca2+ entry, while the amplitudes and the time course of IK(fi) were modulated mainly by the intracellular Ca2+ concentration. About 80% of IK(ni) was selectively inhibited by 0.5 microM apamin. IK(fi) was insensitive to apamin and was totally abolished by 20 mM tetraethyl ammonium extracellularly. According to their voltage dependencies, inactivation properties and pharmacological sensitivity to various K+ channels antagonists, these IK components differ from those described in colonic smooth muscle cells of laboratory animals.