Reduced specificity for the local lymph node assay for lipophilic chemicals: Implications for the validation of new approach methods for skin sensitization.

Meaningful and accurate reference data are crucial for the validation of New Approach Methodologies (NAMs) in toxicology. For skin sensitization, multiple reference datasets are available including human patch test data, guinea pig data and data from the mouse local lymph node assay (LLNA). When assessed against the LLNA, a reduced sensitivity has been reported for in vitro and in chemico assays for lipophilic chemicals with a LogP ≥3.5, resulting in reliability restrictions within the h-CLAT OECD test guideline. Here we address the question of whether LLNA data are an appropriate reference for chemicals in this physicochemical range. Analysis of LLNA vs human reference data indicates that the false-discovery rate of the LLNA is significantly higher for chemicals with LogP ≥3.5. We present a mechanistic hypothesis whereby irritation caused by testing lipophilic chemicals at high test doses leads to unspecific cell proliferation. The accompanying analysis indicates that for lipophilic chemicals with negative calls in in vitro and in chemico assays, resorting to the LLNA is not necessarily a better option. These results indicate that the validation of NAMs in this particular LogP range should be based on a more holistic evaluation of the reference data and not solely upon LLNA data.

Standardisation and international adoption of defined approaches for skin sensitisation.

In the absence of stand-alone one-to-one replacements for existing animal tests, efforts were made to integrate data from in silico, in chemico and in vitro methods to ensure sufficient mechanistic coverage of the skin sensitisation Adverse Outcome Pathway (AOP) and generate predictions suitable for hazard identification and potency sub-categorisation. A number of defined approaches (DAs), using fixed data interpretation procedures (DIP) to integrate data from multiple non-animal information sources, were proposed and documented using a standard reporting template developed by the Organisation for Economic Co-operation and Development (OECD). Subsequent international activities focused on the extensive characterisation of three of these DAs with respect to the reference in vivo data, applicability domains, limitations, predictive performances and characterisations of the level of confidence associated with the predictions. The ultimate product of this project was an OECD Guideline that provides information equivalent to that provided by the animal studies and that can be used to satisfy countries' regulatory data requirements for skin sensitisation. This Defined Approach Guideline was the first of its kind for the OECD, and provides an important precedent for regulatory adoption of human biology-relevant new approach methodologies with performances equivalent to, or better than, traditional animal tests. This mini review summarizes the principal features of the defined approaches described in OECD guideline 497.

Towards a qAOP framework for predictive toxicology - Linking data to decisions.

The adverse outcome pathway (AOP) is a conceptual construct that facilitates organisation and interpretation of mechanistic data representing multiple biological levels and deriving from a range of methodological approaches including in silico, in vitro and in vivo assays. AOPs are playing an increasingly important role in the chemical safety assessment paradigm and quantification of AOPs is an important step towards a more reliable prediction of chemically induced adverse effects. Modelling methodologies require the identification, extraction and use of reliable data and information to support the inclusion of quantitative considerations in AOP development. An extensive and growing range of digital resources are available to support the modelling of quantitative AOPs, providing a wide range of information, but also requiring guidance for their practical application. A framework for qAOP development is proposed based on feedback from a group of experts and three qAOP case studies. The proposed framework provides a harmonised approach for both regulators and scientists working in this area.

SpheraCosmolife: a new tool for the risk assessment of cosmetic products.

A new, freely available software for cosmetic products has been designed that considers the regulatory framework for cosmetics. The software allows an overall toxicological evaluation of cosmetic ingredients without the need for additional testing and, depending on the product type, it applies defined exposure scenarios to derive risk for consumers. It takes regulatory thresholds into account and uses either experimental values, if available, or predictions. Based on the exper­imental or predicted no observed adverse effect level (NOAEL), the software can define a point of departure (POD), which is used to calculate the margin of safety (MoS) of the query chemicals. The software also provides other toxico­logical properties, such as mutagenicity, skin sensitization, and the threshold of toxicological concern (TTC) to provide an overall evaluation of the potential chemical hazard. Predictions are calculated using in silico models implemented within the VEGA software. The full list of ingredients of a cosmetic product can be processed at the same time, at the effective concentrations in the product as given by the user. SpheraCosmolife is designed as a support tool for safety assessors of cosmetic products and can be used to prioritize the cosmetic ingredients or formulations according to their potential risk to consumers. The major novelty of the tool is that it wraps a series of models (some of them new) into a single, user-friendly software system.

EURL ECVAM Genotoxicity and Carcinogenicity Database of Substances Eliciting Negative Results in the Ames Test: Construction of the Database.

The bacterial reverse mutation test (Ames test) is the most commonly used genotoxicity test; it is a primary component of the chemical safety assessment data required by regulatory agencies worldwide. Within the current accepted in vitro genotoxicity test battery, it is considered capable of revealing DNA reactivity, and identifying substances that can produce gene mutations via different mechanisms. The previously published consolidated EURL ECVAM Genotoxicity and Carcinogenicity Database, which includes substances that elicited a positive response in the Ames test, constitutes a collection of data that serves as a reference for a number of regulatory activities in the area of genotoxicity testing. Consequently, we considered it important to expand the database to include substances that fail to elicit a positive response in the Ames test, i.e., Ames negative substances. Here, we describe a curated collection of 211 Ames negative substances, with a summary of complementary data available for other genotoxicity endpoints in vitro and in vivo, plus available carcinogenicity data. A descriptive analysis of the data is presented. This includes a representation of the chemical space formed by the Ames-negative database with respect to other substances (e.g. REACH registered substances, approved drugs, pesticides, etc.) and a description of the organic functional groups found in the database. We also provide some suggestions on further analyses that could be made.

Validation of in vitro methods for human cytochrome P450 enzyme induction: Outcome of a multi-laboratory study.

CYP enzyme induction is a sensitive biomarker for phenotypic metabolic competence of in vitro test systems; it is a key event associated with thyroid disruption, and a biomarker for toxicologically relevant nuclear receptor-mediated pathways. This paper summarises the results of a multi-laboratory validation study of two in vitro methods that assess the potential of chemicals to induce cytochrome P450 (CYP) enzyme activity, in particular CYP1A2, CYP2B6, and CYP3A4. The methods are based on the use of cryopreserved primary human hepatocytes (PHH) and human HepaRG cells. The validation study was coordinated by the European Union Reference Laboratory for Alternatives to Animal Testing of the European Commission's Joint Research Centre and involved a ring trial among six laboratories. The reproducibility was assessed within and between laboratories using a validation set of 13 selected chemicals (known human inducers and non-inducers) tested under blind conditions. The ability of the two methods to predict human CYP induction potential was assessed. Chemical space analysis confirmed that the selected chemicals are broadly representative of a diverse range of chemicals. The two methods were found to be reliable and relevant in vitro tools for the assessment of human CYP induction, with the HepaRG method being better suited for routine testing. Recommendations for the practical application of the two methods are proposed.

Role of Physiologically Based Kinetic modelling in addressing environmental chemical mixtures - A review.

The role of Physiologically Based Kinetic (PBK) modelling in assessing mixture toxicology has been growing for the last three decades. It has been widely used to investigate and address interactions in mixtures. This review describes the current state-of-the-art of PBK models for chemical mixtures and to evaluate the applications of PBK modelling for mixtures with emphasis on their role in chemical risk assessment. A total of 35 mixture PBK models were included after searching web resources (Scopus, PubMed, Web of Science, and Google Scholar), screening for duplicates, and excluding articles based on eligibility criteria. Binary mixtures and volatile organic compounds accounted for two-thirds of the chemical mixtures identified. The most common exposure route and modelled system were found to be inhalation and rats respectively. Twenty two (22) models were for binary mixtures, 5 for ternary mixtures, 3 for quaternary mixtures, and 5 for complex mixtures. Both bottom-up and top-down PBK modelling approaches are described. Whereas bottom-up approaches are based on a series of binary interactions, top-down approaches are based on the lumping of mixture components. Competitive inhibition is the most common type of interaction among the various types of mixtures, and usually becomes a concern at concentrations higher than environmental exposure levels. It leads to reduced biotransformation that either means a decrease in the amount of toxic metabolite formation or an increase in toxic parent chemical accumulation. The consequence is either lower or higher toxicity compared to that estimated for the mixture based on the additivity principle. Therefore, PBK modelling can play a central role in predicting interactions in chemical mixture risk assessment.

Silver Nanoparticles and Metallic Silver Interfere with the Griess Reaction: Reduction of Azo Dye Formation via a Competing Sandmeyer-Like Reaction.

Silver (Ag) is the most common nanomaterial (NM) in consumer products. Much research has been focused on elucidating the potential impact of Ag-containing NMs on human health, e.g., cytotoxicity, genotoxicity, or proinflammatory responses. In the case of proinflammatory responses, a frequently used end point is the induction of nitric oxide (NO), which is indirectly quantified as nitrite (NO2-) with the Griess reaction. After preliminary studies in a macrophage-like cell culture system showed anomalous false negative results in the presence of silver nanoparticles (Ag NPs), we studied the influence of Ag on the detection of NO2- in a cell-free environment. Solutions containing a known concentration of NaNO2 were prepared in H2O, PBS, or complete cell culture medium (CCM) and analyzed using the Griess reaction in the presence of Ag in its metallic or ionic state. In Milli-Q H2O, the impact of salts on the detection was investigated using NaCl and KBr. After completion of the Griess reaction, the samples were analyzed spectrophotometrically or chromatographically. It was found that the presence of metallic but not ionic Ag interfered with the quantification of NO2-. The effect was more pronounced in PBS and H2O containing NaCl or KBr. The chromatographical analysis provided evidence of a competing reaction consuming the intermediate diazonium salt, which is critical to the Griess reaction. These findings demonstrate yet another substantial interference of NMs with a frequently used in vitro assay. If gone unnoticed, this interference might cause false negative results and an impaired hazard assessment of Ag NMs.

The virtual cell based assay: Current status and future perspectives.

In order to replace the use of animals in toxicity testing, there is a need to predict in vivo toxic doses from concentrations that cause toxicological effects in relevant in vitro systems. The Virtual Cell Based Assay (VCBA) estimates time-dependent concentration of a test chemical in the cell and cell culture for a given in vitro system. The concentrations in the different compartments of the cell and test system are derived from ordinary differential equations, physicochemical parameters of the test chemical and properties of the cell line. The VCBA has been developed for a range of cell lines including BALB/c 3T3 cells, HepG2, HepaRG, lung A459 cells, and cardiomyocytes. The model can be used to design and refine in vitro experiments and extrapolate in vitro effective concentrations to in vivo doses that can be applied in risk assessment. In this paper, we first discuss potential applications of the VCBA: i) design of in vitro High Throughput Screening (HTS) experiments; ii) hazard identification (based on acute systemic toxicity); and iii) risk assessment. Further extension of the VCBA is discussed in the second part, exploring potential application to i) manufactured nanomaterials, ii) additional cell lines and endpoints, and considering iii) other opportunities.

Exploring waiving opportunities for mammalian acute systemic toxicity tests.

A survey was carried out to explore opportunities for waiving mammalian acute systemic toxicity tests. We were interested in finding out whether data from a sub-acute toxicity test could be used to predict the outcome of an acute systemic toxicity test. The survey was directed at experts in the field of toxicity testing, and was carried out in the context of the upcoming 2018 final registration deadline for chemicals under the EU REACH Regulation. In addition to the survey, a retrospective data analysis of chemicals that had already been registered with the European Chemicals Agency, and for which both acute and sub-acute toxicity data were available, was carried out. This data analysis was focused on chemicals that were administered via the oral route. The answers to the questionnaire showed a willingness to adopt waiving opportunities. In addition, the responses showed that data from a sub-acute toxicity test or dose-range finding study might be useful for predicting chemicals that do not require classification for acute oral toxicity (LD50 > 2000mg/kg body weight). However, with the exception of substances that fall into the non-classified category, it is difficult to predict current acute oral toxicity categories.

Can currently available non-animal methods detect pre and pro-haptens relevant for skin sensitization?

Predictive testing to characterize substances for their skin sensitization potential has historically been based on animal tests such as the Local Lymph Node Assay (LLNA). In recent years, regulations in the cosmetics and chemicals sectors have provided strong impetus to develop non-animal alternatives. Three test methods have undergone OECD validation: the direct peptide reactivity assay (DPRA), the KeratinoSens™ and the human Cell Line Activation Test (h-CLAT). Whilst these methods perform relatively well in predicting LLNA results, a concern raised is their ability to predict chemicals that need activation to be sensitizing (pre- or pro-haptens). This current study reviewed an EURL ECVAM dataset of 127 substances for which information was available in the LLNA and three non-animal test methods. Twenty eight of the sensitizers needed to be activated, with the majority being pre-haptens. These were correctly identified by 1 or more of the test methods. Six substances were categorized exclusively as pro-haptens, but were correctly identified by at least one of the cell-based assays. The analysis here showed that skin metabolism was not likely to be a major consideration for assessing sensitization potential and that sensitizers requiring activation could be identified correctly using one or more of the current non-animal methods.

Electronic states of porphycene-O2 complex and photoinduced singlet O2 production.

Porphycene (PC), a structural isomer of porphine, is a promising photosensitizer for photodynamic therapy. Its excited states can be quenched by molecular oxygen, generating singlet O2. The electronic structures of PC and of the PC⋯O2 complex were investigated using complete active space perturbation theory. It is shown that singlet oxygen generation involves 12 electronic states of the complex, with singlet, triplet, and quintet multiplicities. Two scenarios for singlet-O2 yield are analyzed: (I) quenching of triplet states of PC and (II) quenching of singlet states of PC. In the first scenario, which is favored under low O2 concentration, singlet-O2 yield is limited by the relatively low triplet quantum yield of PC. We discuss how the singlet-O2 yield would be busted if conditions for occurrence of the second scenario could be achieved.

Exploring the sloped-to-peaked S2/S1 seam of intersection of thymine with electronic structure and direct quantum dynamics calculations.

The role of the seam of intersection between the lowest (pi,pi*) and (n,pi*) excited states in the decay of electronically excited singlet thymine has been investigated with ab initio complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics on the full-dimensional CASSCF surface, with 39 degrees of freedom. The seam has a sloped-to-peaked topography, and the dynamics at the different segments of the seam have been studied by varying the initial conditions of the propagation. When the wave packet is directed to the peaked segments, part of it traverses the seam, stays on the (pi,pi*) state and heads towards decay to the ground state. In contrast to this, when the wave packet is driven to sloped seam segments it bounces back to the minimum of the (pi,pi*) state. Significant population transfer to the (n,pi*) state is observed in both cases. The results suggest that a sloped-to-peaked topography can be used to control photochemical reactivity, by driving the wave packet to different regions of the seam where a different outcome of the propagation can be expected.

Photophysics of the pi,pi* and n,pi* states of thymine: MS-CASPT2 minimum-energy paths and CASSCF on-the-fly dynamics.

The photodynamics along the main decay paths of thymine after excitation to the lowest pi,pi* state have been studied with MS-CASPT2 calculations and semiclassical CASSCF dynamics calculations including a surface hopping algorithm. The static calculations show that there are two decay paths from the Franck-Condon structure that lead to a conical intersection with the ground state. The first path goes directly to the intersection, while the second one is indirect and involves a minimum of the pi,pi* state, a small barrier, and a crossing between the pi,pi* and n,pi* states. From the static calculations, both paths have similar slopes. The dynamics calculations along the indirect path show that, after the barrier, part of the trajectories are funneled to the intersection with the ground state, where they are efficiently quenched to the ground state. The remaining trajectories populate the n,pi* state. They are also quenched to the ground state in less than 1 ps, but the static calculations show that the decay rate of the n,pi* state is largely overestimated at the CASSCF level used for the dynamics. Overall, these results suggest that both direct and indirect paths contribute to the subpicosecond decay components found experimentally. The indirect path also provides a way for fast population of the n,pi* state, which will account for the experimental picosecond decay component.

Benign decay vs. photolysis in the photophysics and photochemistry of 5-bromouracil. A computational study.

The excited state potential energy surface of 5-bromouracil has been studied with ab initio CASPT2//CASSCF calculations to rationalize the competition between the benign decay and the photolysis found experimentally. The surface is characterized by an extended region of degeneracy between S(1) and S(0). The access to this region has been studied with minimum energy path calculations from the FC structure, the seam of intersection has been mapped in detail, and the decay paths from different regions of the seam have been characterized. There are two decay paths with low barriers that are limiting cases for the actual decay dynamics. The first path involves the bromine elimination and leads to a region of near degeneracy between the ground and excited states, and the second one leads back to the reactant through a conical intersection between the two states. The conical intersection for benign decay is part of a seam that lies along the C(5)-Br stretching coordinate, and decay at the region of the seam with a stretched C(5)-Br bond leads to photolysis. Thus, the reactivity depends on the point of the seam at which decay to the ground state takes place. The low experimental photolysis quantum yield suggests that the energetically favored decay is the one that regenerates the reactant, while the low barriers computed to access the region of decay are in agreement with the measured picosecond excited state lifetime.

Intramolecular Basis Set Superposition Error Effects on the Planarity of DNA and RNA Nucleobases.

Molecules of utmost importance like DNA and RNA nucleobases are predicted to be nonplanar by a typical ab initio method, such as second order Møller-Plesset perturbation theory (MP2) combined with standard Pople's basis sets. Similarly to the case of other planar aromatic systems, these pitfalls can be explained in terms of intramolecular basis set superposition error (BSSE) effects, induced by local basis set deficiencies. We demonstrate that conventional BSSE correction techniques such as the Counterpoise method can account for this wrong behavior and provide proper correction whenever spurious results occur, mainly in case of thymine, uracil and guanine but also to lower extent for adenine and cytosine. We also show that special care must be taken when assessing the BSSE by means of ghost-orbital calculations for strongly overlapping fragments. Often molecular orbitals in the isolated fragment calculation have a different orientation as in the ghost-orbital calculation. This can lead to bogus derivatives of the CP-correction term, essential to account for geometry and vibrational BSSE effects.

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: a solution to the problem.

Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople's basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C-H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree-Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed.