Computational Toxicology最新文献

There is international interest in using alternatives to animal testing, including (Q)SARs, in chemical hazard assessments. The regulatory acceptance of alternative methods requires principles for considering the scientific rigour of methods and their results. The OECD (Q)SAR assessment Framework (QAF) was developed as guidance for regulators when considering (Q)SAR models and predictions in chemical evaluation. The QAF builds on existing principles for evaluating models and, learning from the longstanding regulatory experience in assessing (Q)SAR predictions, establishes new principles for evaluating predictions and results from multiple predictions. Assessment elements, identified for all principles lay out criteria for assessing the confidence and uncertainties in (Q)SAR models and predictions, while maintaining the flexibility necessary to adapt to different regulatory contexts and purposes. Using the QAF, assessors can consistently and transparently evaluate and decide on the validity of (Q)SARs, and model developers and users have clear requirements to meet. The publication of the QAF is expected to increase the regulatory use and acceptance of (Q)SARs and may become an example to build similar prescriptive frameworks for other new approach methodologies (NAMs). This article provides an overview of the main scientific aspects of the QAF guidance and provides context for how this guidance can promote the use of alternative methods in chemical assessments.

Developmental and reproductive toxicity (DART) are key regulatory endpoints for the protection of human health. DART assessments require large numbers of animals, are expensive and often run at late stages of drug development. Therefore, new approach methodologies (NAMs) are being developed to transition away from animal testing. These NAMs (including in silico models) can be used to screen for DART hazards at the early stages of compound development and may in the future be used for regulatory DART assessments. Due to the implications of a mischaracterised developmental toxicant, both high confidence and understanding of the assessments made using NAMs will be required; it is likely that multiple NAMs will be needed in order to replace the current animal-based assessments. Adverse outcome pathways (AOPs) serve as a pragmatic tool for documenting mechanisms of toxicity. NAMs can be associated to key events (KEs) along an AOP, providing context to their outputs, and therefore increasing confidence in their use. It is likely that networks of pathways will be required for a specific toxicity endpoint in order to confidently apply an AOP-based approach to safety assessments. An insufficient number of DART AOPs are currently described within the public domain; therefore, using a literature-based approach, a network consisting of 340 KEs (including 68 MIEs) was developed. This foundation of pathways was made chemically aware through the association of relevant assays, data and expert rule-based structural alerts to appropriate KEs. The use of the network as a hazard screening tool was assessed, and the application of this to aid an ICH S5 workflow investigated. The knowledge captured within this AOP network can also guide the further development and use of DART-relevant NAMs and integrated approaches to testing and assessments (IATAs).

We describe the development of the GSK vEXP (virtual enhanced cross screen panel) for off-target pharmacology alerts. The derivation of a panel of machine learning classification models or QSAR models (Quantitative Structure-Activity Relationship) for off-target safety assessment allows early alerting to risk factors in candidate drugs. The models are matched to an internal in-vitro biochemical screening panel described previously with some updates reported here. The extreme imbalance of some internal GSK datasets and most of the related external ChEMBL datasets is shown when considering potency thresholds relevant to in-vitro screening. The small size and bias to the active class make many ChEMBL datasets un-modellable using such thresholds. Although larger, many GSK datasets remain too imbalanced to give a performant model. The value of merging internal and external data to help rebalance datasets and improve the domain of applicability is demonstrated with improvements in model performance frequently seen on merged data. Efforts to collate public datasets with a far better balance of the missing in-actives would likely do more to improve opensource models than simply increasing dataset size. We investigate the use of moving the probability threshold and applying imbalanced learners to help overcome the imbalance problem. Both methods can produce models with improved performance when applied to imbalanced datasets. Datasets with class imbalance 95:5 % or with <100 compounds were un-modellable. Where datasets had a class imbalance of 90:10 % the imbalanced learn methods were often more performant than standard tree-based classifiers. No one classification algorithm consistently out-performed all others and our approach emphasises a standardised, automated build and evaluate approach across all classifiers to identify the best model. The application of vEXP includes ranking of hit compounds for fast prioritisation, flagging of hit series that contain systematic scaffold or functional group related risks and the confirmation that late-stage optimisation is not introducing new off-target activities in established chemical series.

Cosmetic ingredients of choice are those appropriate for a specific commercial use and deemed safer than existing alternatives. In the LIFE VERMEER project (https://www.life-vermeer.eu/), the ToxEraser Cosmetics software was developed as a platform under which an ingredient is presented with a list of potential substitutes, from an archive of 2233 items. Key information about the safety of each item concerns: (a) the risk assessment addressed by seven regulatory and other specialized European-US authorities; (b) the safety class emerging from the systematic evaluation and integration of each authority’s assessment. Read-across analysis makes the substitution possible even when the ingredient is not included in the archive. The list of alternatives can be extended or reduced flexibly, since the commercial use of cosmetics is dictated by attributes indicating progressively detailed and hierarchically related categories. Finally, the identification of significant validated structural alerts for endpoints of interest serves in detecting which part of the structure is associated with certain hazardous properties. This tool will be joined with VERMEER Cosmolife, the other tool for cosmetics developed as part of the VERMEER project. ToxEraser offers a systematic, flexible approach to explore safer cosmetic substitutes, acknowledging the sources of evidence produced by VERMEER Cosmolife, offering a forward-looking tool for the cosmetic sector. More in general, the novelty is the shift to in silico models, not only to assess possible concern associated with a substance, but also to move towards safer alternatives.

Electronic nicotine delivery systems (ENDS) heat a liquid solution typically containing propylene glycol, vegetable glycerin, water, nicotine, and flavor chemicals to deliver an aerosol to the user. ENDS aerosols are complex, multi-constituent mixtures of droplets and vapors. Lung dosimetry predictions require mechanistic models that account for the physico-chemical properties of the constituents and thermodynamic processes of the aerosol as it travels through the respiratory tract and deposits in lung airways. In this study, a model formulated to predict ENDS aerosol deposition in the oral cavity and lung airways was linked with a physiologically-based pharmacokinetic (PBPK) model to predict nicotine pharmacokinetics (PK) as a function of product characteristics and puff topography. Predicted plasma nicotine PK compared favorably with available experimental data and captured the rapid increase in plasma levels followed by a clearance phase after ENDS use. E-liquid nicotine concentration and puff duration substantially increased nicotine lung deposition and plasma nicotine levels. Increasing the puff duration from 1 to 5 s while assuming a constant aerosol flow rate resulted in an ∼5-fold increase in nicotine lung deposition (45.0 µg to 243.7 µg) and increased maximum plasma nicotine concentrations from 4.7 ng/mL to 25.0 ng/mL; increasing the e-liquid nicotine concentration from 1 % to 5 % yielded increases in nicotine lung deposition (41.0 µg to 204.5 µg) and maximum plasma nicotine concentration (4.2 ng/mL to 21.1 ng/mL). Model predictions demonstrate the sensitivity of ENDS aerosol lung deposition and plasma nicotine profiles to user behavior and allow for quantification of constituent deposition and nicotine absorption after ENDS use.

Monitoring oral exposure to pesticides in wildlife is crucial for assessing environmental risks and preventing adverse effects on non-target species. Traditionally, this requires invasive tissue sampling, raising ethical, regulatory, and economic concerns. To address this gap, our study aims to develop a method for assessing external oral dose levels in rats using physiologically-based kinetic (PBK) modeling based on blood concentration levels of two pesticides, imidacloprid and carbendazim, and one of their primary metabolites. We utilized in vitro metabolic kinetic data from hepatic microsomal and S9 incubations to inform our models. These models were then evaluated by comparing their predictions with existing in vivo experimental data from the literature. Our results demonstrate that the models provide accurate predictions, presenting a novel in vitro and in silico approach for environmental exposure and risk assessment of pesticides. This methodology has the potential for application in wildlife species, advancing the frontier of knowledge in non-invasive pesticide exposure assessment.

There is widespread acceptance that non-animal studies can be used to assess chemical safety in humans. These New Approach Methodologies (NAMs) typically integrate data from multiple sources including in silico and in vitro models. Regulatory guidelines are being updated to recognise that these scientific advances are allowing animal studies to be replaced without compromising human safety. One such regulation, ICH S1B(R1), was updated in 2022 to include the provision for a weight-of-evidence assessment for carcinogenicity, using six factors to determine if there was sufficient evidence to waive the need to run a rat carcinogenicity assay. The volume of data and evidence, however, can be hard to organise and interpret into a cohesive evaluation. To aid such assessments, software has been developed that combines adverse outcome pathways (AOPs) and reasoning, to organise and contextualise knowledge, and provide an outcome based on the data available. Using this framework, a workflow has been developed to assess the initial outcome and structure expert review to investigate the factors, and potential biological mechanisms which could contribute to a compound’s carcinogenic potential (or lack thereof). The framework was used to structure expert review of three examples of differing activity and levels of supporting evidence. This highlighted where AOPs supported expert review by showing 1) the value in using AOPs to analyse data, 2) the importance of expert review to strengthen confidence in outcomes, and 3) how this approach can accurately predict experimental results. Therefore, using this approach to assess evidence for ICH S1B(R1) will give transparent, scientifically robust, and reproducible calls, and thus reduce the need for rat carcinogenicity studies.

The advancement of protein structural prediction tools, exemplified by AlphaFold and Iterative Threading ASSEmbly Refinement, has enabled the prediction of protein structures across species based on available protein sequence and structural data. In this study, we introduce an innovative molecular docking method that capitalizes on this wealth of structural data to enhance predictions of chemical susceptibility across species. We demonstrated this method using the androgen receptor as a pertinent modulator of endocrine function. By using protein structures, this method contextualizes species susceptibility within a functional framework and helps to integrate molecular docking into the repertoire of New Approach Methodologies (NAMs) that support the Next-Generation Risk Assessment (NGRA) paradigm through the novel integration of various open-source tools.

Genotoxicity assessment is a key component of regulatory decision-making in pesticide authorization and biocide approval. Conventionally, these genotoxicity requirements are addressed with OECD test guideline-compliant in vitro tests. In recent years, in silico approaches, such as (Q)SAR, have matured sufficiently so that they may be suitable to support, complement or even replace in vitro testing as a first tier of genotoxicity assessment. Among the different endpoints for genotoxicity, a high reliability is expected for in silico predictions of the endpoint bacterial mutagenicity. For other endpoints predictive performance is either unclarified or seems to be comparably lower. Herein, we describe the evaluation of several commercial and freely available (Q)SAR models and complementary combinations thereof with respect to the endpoints bacterial mutagenicity and chromosome damage in vitro. We used curated in-house test sets derived from OECD test guideline-compliant studies, gathered from submissions for the regulatory approval of biocides and plant protection products. The data set comprises active substances, metabolites and impurities. In line with previous publications we show that (Q)SAR models for bacterial mutagenicity generally performed well for compounds of the pesticide domain. Model combinations significantly increased the respective sensitivity. Models for chromosome damage still need to improve prior to their stand-alone use in regulatory decision-making, either strongly leaning towards sensitivity, at the expense of specificity or vice versa. Similar to the endpoint bacterial mutagenicity, combinations of models for chromosome damage increase sensitivity when compared to the individual models alone.

Adverse outcome pathway AOPs are conceptual frameworks that organize scientific knowledge about how stressors disrupt specific biological targets, pathways. AOP network consists of two or more AOPs that share common key events (KEs), including crucial events like molecular initiating events (MIEs) and adverse outcomes (AOs), which offer the opportunity to link toxicological pathways. Thus, to better understand the sequential series of KEs involved in the AOP 492 (https://aopwiki.org/aops/492), which is triggered by atrazine (ATZ), we first generated a Reproductive Toxicity via Oxidative Stress (RTOS) AOP network from individual AOPs published in the AOP-Wiki database, using this AOP as a seed. The KEs “Increased, Reactive oxygen species” and “Apoptosis” were considered the most common/highly connected KE within this network and an important point of divergence. Furthermore, “Increased, DNA damage and mutations” is a critical KE within the network, as it is highly connected and central, and represents a point of divergence. This suggests that these three KEs have a high predictive value and could, for example, serve as a basis for the development/selection of in vitro assays to assess reproductive toxicity. The in silico analyses revealed that the pivotal target proteins for ATZ-induced infertility via oxidative stress in humans are Tp53, Bcl2, Esr1, and Nos3, which interact indirectly with ATZ via intermediary factors such as Mapk3, Mapk1, and Cyp19a1. Further, the gene enrichment analyses indicate that these entities are involved in several biological processes and pathways directly associated with oxidative stress, DNA damage and apoptosis, further reinforcing the developed network.