Ivanka Tsakovska

The Role of the European Chemicals Bureau in Promoting the Regulatory Use of (Q)SAR Methods

Under the proposed REACH (Registration, Evaluation and Authorisation of CHemicals) legislation, (Q)SAR models and grouping methods (chemical categories and read across approaches) are expected to play a significant role in prioritising industrial chemicals for further assessment, and for filling information gaps for the purposes of classification and labelling, risk assessment and the assessment of persistent, bioaccumulative and toxic (PBT) chemicals. The European Chemicals Bureau (ECB), which is part of the European Commissions Joint Research Centre (JRC), has a well-established role in providing independent scientific and technical advice to European policy makers. The ECB also promotes consensus and capacity building on scientific and technical matters among stakeholders in the Member State authorities and industry. To promote the availability and use of (Q)SARs and related estimation methods, the ECB is carrying out a range of activities, including applied research in computational toxicology, the assessment of (Q)SAR models and methods, the development of technical guidance documents and computational tools, and the organisation of training courses. This article provides an overview of ECB activities on computational toxicology, which are intended to promote the development, validation, acceptance and use of (Q)SARs and related estimation methods, both at the European and international levels. †Presented at the 12th International Workshop on Quantitative Structure-Activity Relationships in Environmental Toxicology (QSAR2006), 8–12 May 2006, Lyon, France.

Interactions of Poly(vinylpyrrolidone) with Ibuprofen and Naproxen: Experimental and Modeling Studies

Purpose.To elucidate the differences in the interaction of chiralic ibuprofen (IBP) and naproxen (NAP) with poly(vinylpyrrolidone) (PVP) in a solid state.Methods.Drugs/PVP physical mixtures and solid dispersions were characterized by scanning electron microscope (SEM), Fourier transform infrared spectrometry (FT-IR), solid state 13C NMR spectroscopy, and x-ray diffractometry. Molecular modeling study of the crystal structures and PVP was performed.Results.A spontaneous conversion of IBP/PVP physical mixtures in a stable glasslike form (solid dispersion) was observed after storage. The enantiomer reacted more strongly than the racemate. NAP did not interact with PVP. The crystal structures of drugs showed differences in the hydrogen bonding, aromatic interactions, molecular energies, and distances inside the crystals. The trimer structure of PVP was built and optimized. It was proposed that each PVP monomer could interact with one IBP dimmer in contrast to NAP, where two out of three PVP monomers faced the catemer carboxylic groups.Conclusions.The differences in the interaction of PVP with racemic IBP, enantiomer IBP, and NAP can be related to the differences in their crystal structures. The correlation between the experimental data and the results of the molecular modeling analysis suggest that the IBP dimmer structures are likely to perform HB and aromatic interactions with PVP.

Validation of counter propagation neural network models for predictive toxicology according to the OECD principles: a case study

The OECD has proposed five principles for validation of QSAR models used for regulatory purposes. Here we present a case study investigating how these principles can be applied to models based on Kohonen and counter propagation neural networks. The study is based on a counter propagation network model that has been built using toxicity data in fish fathead minnow for 541 compounds. The study demonstrates that most, if not all, of the OECD criteria may be met when modeling using this neural network approach.

Evaluation of SARs for the prediction of skin irritation/corrosion potential–structural inclusion rules in the BfR decision support system†

The German Federal Institute for Risk Assessment (BfR) has developed a Decision Support System (DSS) to assess certain hazardous properties of pure chemicals, including skin and eye irritation/corrosion. The BfR–DSS is a rule-based system that could be used for the regulatory classification of chemicals in the European Union. The system is based on the combined use of two predictive approaches: exclusion rules based on physicochemical cut-off values to identify chemicals that do not exhibit a certain hazard (e.g., skin irritation/corrosion), and inclusion rules based on structural alerts to identify chemicals that do show a particular toxic potential. The aim of the present study was to evaluate the structural inclusion rules implemented in the BfR–DSS for the prediction of skin irritation and corrosion. The following assessments were performed: (a) a confirmation of the structural rules by rederiving them from the original training set (1358 substances), and (b) an external validation by using a test set of 200 chemicals not used in the derivation of the rules. It was found as a result that the test data set did not match the training set relative to the inclusion of structural alerts associated with skin irritation/corrosion, albeit some skin irritants were in the test set. †Presented at the 12th International Workshop on Quantitative Structure-Activity Relationships in Environmental Toxicology (QSAR2006), 8–12 May 2006, Lyon, France.

Computational Studies of Free Radical-Scavenging Properties of Phenolic Compounds

For more than half a century free radical-induced alterations at cellular and organ levels have been investigated as a probable underlying mechanism of a number of adverse health conditions. Consequently, significant research efforts have been spent for discovering more effective and potent antioxidants / free radical scavengers for treatment of these adverse conditions. Being by far the most used antioxidants among natural and synthetic compounds, mono- and polyphenols have been the focus of both experimental and computational research on mechanisms of free radical scavenging. Quantum chemical studies have provided a significant amount of data on mechanisms of reactions between phenolic compounds and free radicals outlining a number of properties with a key role for the radical scavenging activity and capacity of phenolics. The obtained quantum chemical parameters together with other molecular descriptors have been used in quantitative structure-activity relationship (QSAR) analyses for the design of new more effective phenolic antioxidants and for identification of the most useful natural antioxidant phenolics. This review aims at presenting the state of the art in quantum chemical and QSAR studies of phenolic antioxidants and at analysing the trends observed in the field in the last decade.

Molecular Modelling Study of the PPARγ Receptor in Relation to the Mode of Action/Adverse Outcome Pathway Framework for Liver Steatosis

The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.

QSAR and 3D-QSAR of phenothiazine type multidrug resistance modulators in P388/ADR cells

A series of 25 phenothiazines and structurally related compounds was investigated by QSAR (quantitative structure activity relationship) and 3D-QSAR methods with respect to their MDR (multidrug resistance) reversing activity in P388/ADR- murine leukemia cell line resistant to ADR (adriamycin). The objective was to outline structural properties important for the investigated activity. Different measures for MDR reversal were used and compared. Two 3D-QSAR approaches were applied-CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis). Both, neutral and protonated forms of the compounds were investigated. Molecular models with good predictive power were derived using a hydrophobic field alone and a combination of steric, hydrophobic, and hydrogen bond acceptor fields of the compounds. In the combined models highest contribution of the hydrogen bond acceptor field was noticed. Thus, the dominant role of the hydrophobic and hydrogen bond acceptor fields for MDR reversing activity of the investigated compounds was demonstrated. The structural regions responsible for the differences in anti-MDR activity were analyzed in respect to their hydrophobic, hydrogen bond acceptor and steric nature. The results may direct design of new phenothiazines and related compounds as MDR modulators.

Modes-of-Action Related to Repeated Dose Toxicity: Tissue-Specific Biological Roles of PPAR γ Ligand-Dependent Dysregulation in Nonalcoholic Fatty Liver Disease.

Comprehensive understanding of the precise mode of action/adverse outcome pathway (MoA/AOP) of chemicals becomes a key step towards superseding the current repeated dose toxicity testing methodology with new generation predictive toxicology tools. The description and characterization of the toxicological MoA leading to non-alcoholic fatty liver disease (NAFLD) are of specific interest, due to its increasing incidence in the modern society. Growing evidence stresses on the PPARγ ligand-dependent dysregulation as a key molecular initiating event (MIE) for this adverse effect. The aim of this work was to analyze and systematize the numerous scientific data about the steatogenic role of PPARγ. Over 300 papers were ranked according to preliminary defined criteria and used as reliable and significant sources of data about the PPARγ-dependent prosteatotic MoA. A detailed analysis was performed regarding proteins which PPARγ-mediated expression changes had been confirmed to be prosteatotic by most experimental evidence. Two probable toxicological MoAs from PPARγ ligand binding to NAFLD were described according to the Organisation for Economic Cooperation and Development (OECD) concepts: (i) PPARγ activation in hepatocytes and (ii) PPARγ inhibition in adipocytes. The possible events at different levels of biological organization starting from the MIE to the organ response and the connections between them were described in details.

Recent advances in the molecular modeling of estrogen receptor-mediated toxicity.

In the past two decades, there has been increasing concern about the potentially adverse effects of exogenous endocrine active substances (EAS) that alter the function of the endocrine system by interfering with hormone regulation. The mechanistic pathways by which EAS may elicit adverse effects, such as developmental and reproductive toxicity, often involve direct binding to nuclear hormone receptors. Certainly, the best studied nuclear receptor is the estrogen receptor (ER). Large-scale in vitro and in vivo methods have been developed to assess the estrogenic toxicity of chemicals. However, there are financial and animal welfare concerns related to their application. Quantitative structure-activity relationship (QSAR) approaches have proven their utility as a priority setting tool in the risk assessment of EAS. In addition, the models help to clarify the binding mode of the interacting substances. As estrogen-mediated effects are usually related to ligand-receptor interactions, and as there have been comprehensive structural studies on the ER, molecular modeling together with other in silico approaches provide a suitable means of studying these estrogenic effects. This chapter provides an overview of the molecular modeling approaches applied to ligand-ER interactions. The progress in the field is outlined, and some critical issues are analyzed based on recently published models where these approaches are applied.

Phenothiazines and Structurally Related Compounds as Modulators of Cancer Multidrug Resistance

Phenothiazines and structurally related compounds alongside their other biological activities are able to modulate multidrug resistance (MDR) in tumor cells. The extensive investigations on their MDR modulation effects consist part of the efforts to overcome MDR - the major obstacle in cancer chemotherapy. In this article we try to systematize the results collected in the last two decades in two main aspects. The first one comprises the mechanism of modulation by phenothiazine-type MDR modulators. Two main possible mechanisms of MDR reversal are reviewed: (i) direct interaction with Pgp; (ii) interactions with membrane phospholipids. The second aspect relates to the structural properties of phenothiazines and related compounds responsible for their MDR reversing effect. The structural alerts and physicochemical properties influencing anti-MDR activity are considered as identified by structure--activity (SAR) or quantitative structure--activity relationship (QSAR) studies. Results discussed in the article point to MDR modulation by phenothiazines and related compounds as a complex process in which more than one mechanism are certainly involved. Further investigations in this direction should contribute to elucidation of the possible mechanisms of MDR modulation by these compounds. On the basis of the studies discussed the potential use of phenothiazine-type MDR modulators as a model system in the further investigations of the MDR phenomenon is outlined.