QSAR trout toxicity models on aromatic pesticides

The pesticides originally designed to kill target organisms are dangerous for many other wild species. Since they are applied directly to the environment, they can easily reach the water basins and the topsoil. A dataset of 125 aromatic pesticides with well-expressed aquatic toxicity towards trout was subjected to quantitative structure activity relationships (QSAR) analysis aimed to establish the relationship between their molecular structure and biological activity. A literature data for LC₅₀ concentration killing 50% of fish was used. In addition to the standard 2D-QSAR analysis, a comparative molecular field analysis (CoMFA) analysis considering the electrostatic and steric properties of the molecules was also performed. The CoMFA analysis helped the recognition of the steric interactions as playing an important role for aquatic toxicity. In addition, the transport properties and the stability of the compounds studied were also identified as important for their biological activity.     

Three-dimensional quantitative structure-activity relationship study for phenylsulfonyl carboxylates using CoMFA and CoMSIA

From both the comparative molecular field analysis (CoMFA) and the comparative molecular similarity indices analysis (CoMSIA), the paper describes two three-dimensional quantitative structure-activity relationship (3D-QSAR) models for the acute toxicity logEC50 (15 min-EC50 in micromoll(-1)) of 56 phenylsulfonyl carboxylates on Photobacterium phosphoreum. Two models yield the leave-one-out cross-validated correlation coefficient q2 values of 0.823 and 0.713, and the conventional correlation coefficient r2 values of 0.958 and 0.933, respectively. The achievement of higher q2 and r2 values of CoMFA model indicates the significance of correlation of steric and electrostatic fields with biological activities. The key features in the CoMFA contour maps are critical to trace the important properties and gain insight into the toxic mechanism of tested compounds. The quality of CoMSIA model is slightly lower than that of CoMFA in terms of q2 and r2 values. Not requiring molecular superposition, CoMSIA is faster than CoMFA in data processing.     

Three-dimensional quantitative structure activity relationship (3D-QSAR) analysis for in vitro toxicity of chlorophenols to HepG2 cells

In the present paper, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to investigate two 3D-QSAR models for the cytotoxicity of chlorophenols. These models have evaluated the intensity of chlorophenols' toxicity on HepG2 cells in vitro. The CoMFA model has both high consistency and predictability. The contribution of the electrostatic field to biological activity is greater than that of the steric field. The CoMSIA model used in this study includes two fields, one is hydrophobic field, and the other is electrostatic field. The relative contribution of them is 0.789:0.211. Consisted with the CoMFA model, the CoMSIA electrostatic filed also plays a dominant role. The CoMFA and CoMSIA contour maps significantly elucidated that the electrostatic field is more important than the other fields and might be one of the reasons resulting in potential reactive mechanism involved in cell proliferation inhibition.     

Three-dimensional quantitative structure activity relationships of quorum-sensing and biofilm inhibitors in gram-negative bacteria

Thirty N-acyl homoserine lactone (AHL) analogs with variable antibacterial activity and displaying inhibition of biofilm formation were selected to develop models for establishing three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) were carried out to determine the optimum structural requirements for selectivity and potency of quorum-sensing and bacterial biofilm inhibition. The best CoMFA model predicted a q2 value of 0.519 and an r2 value of 0.984 and revealed that electrostatic and steric properties play a significant role in potency and selectivity. The CoMSIA model predicted a q2 value of 0.411 and an r2 value of 0.938 based on a combination of steric, electrostatic, and hydrophobic effects. The analysis of the contour maps from each model provide insight into the structural requirements for increasing the activity of a compound. Consequently, manipulating the chemical and physical properties of substituted acyl groups on the homoserine lactone moiety can provide important information toward enhancing the antibacterial properties of the target chemical compound.     

Insights into the structure of urea-like compounds as inhibitors of the juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta: analysis of the binding modes and structure-activity relationships of the inhibitors by docking and CoMFA calculations

Substituted urea compounds are well-known as potent inhibitors of juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta. Docking simulations of 47 derivatives inside JHEH were performed to gain insight into the structural characteristics of these complexes. The obtained orientations show a strong similitude with the observed in the known X-ray crystal structures of human soluble epoxide hydrolase (sEH) complexed with dialkylurea inhibitors. In addition, the predicted inhibitor concentration (IC₅₀) of the above-mentioned compounds as JHEH inhibitors were obtained by a quantitative structure-activity relationship (QSAR) method by using comparative molecular field analysis (CoMFA) applied to aligned dataset. The best models included steric and electrostatic fields and had adequate predictive abilities. In addition, these models were used to predict the activity of an external test set of compounds that was not used for building the model. Furthermore, plots of the CoMFA fields allowed conclusions to be drawn for the choice of suitable inhibitors.     

Three-dimensional, quantitative-structure-property-relationship study of aqueous solubility for phenylsulfonyl carboxylates using comparative-molecular-field analysis and comparative-molecular-similarity-indices analysis.

With both the comparative-molecular-field analysis (CoMFA) and the comparative-molecular-similarity-indices analysis (CoMSIA), the paper describes two five-component, three-dimensional, quantitative-structure-property-relationship (3D-QSPR) models for the aqueous solubility logSw (Sw, mol x L(-1)) of 52 phenylsulfonyl carboxylates. Two models yield the leave-one-out cross-validated correlation coefficient q2 values 0.851 and 0.821, and the conventional correlation coefficient r2 values 0.963 and 0.929, respectively. The achievement of high q2 and r2 values of the CoMFA model indicates the significance of correlation of steric and electrostatic fields with the aqueous solubility. The key features in the CoMFA contour maps are critical to trace the important properties and gain insight to the solvation mechanism of tested compounds. The quality of CoMSIA model is slightly lower than that of CoMFA in terms of q2 and r2 values. Not requiring molecular superposition, CoMSIA may be faster than CoMFA in data processing.     

Three-dimensional quantitative structure activity relationships of quorum-sensing and biofilm inhibitors in gram-negative bacteria

Thirty N-acyl homoserine lactone (AHL) analogs with variable antibacterial activity and displaying inhibition of biofilm formation were selected to develop models for establishing three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) were carried out to determine the optimum structural requirements for selectivity and potency of quorum-sensing and bacterial biofilm inhibition. The best CoMFA model predicted a q² value of 0.519 and an r² value of 0.984 and revealed that electrostatic and steric properties play a significant role in potency and selectivity. The CoMSIA model predicted a q² value of 0.411 and an r² value of 0.938 based on a combination of steric, electrostatic, and hydrophobic effects. The analysis of the contour maps from each model provide insight into the structural requirements for increasing the activity of a compound. Consequently, manipulating the chemical and physical properties of substituted acyl groups on the homoserine lactone moiety can provide important information toward enhancing the antibacterial properties of the target chemical compound.     

3D QSAR studies of dioxins and dioxin-like compounds using CoMFA and CoMSIA

In the present study we have performed comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) on structurally diverse ligands of Ah (dioxin) receptor to explore the physico-chemical requirements for binding. All CoMFA and CoMSIA models have given q(2) value of more than 0.5 and r(2) value of more than 0.84. The predictive ability of the models was validated by an external test set, which gave satisfactory predictive r(2) values. Best predictions were obtained with CoMFA model of combined modified training set (q(2) = 0.631, r(2) = 0.900), giving predictive residual value = 0.02 log unit for the test compound. Addition of CoMSIA study has elucidated the role of hydrophobicity and hydrogen bonding along with the effect of steric and electrostatic properties revealed by CoMFA. We have suggested a model comprises of four structurally different compounds, which offers a good predictability for various ligands. Our QSAR model is consistent with all previously established QSAR models with less structurally diverse ligands.     

Ecological risk of pesticide residues in the British Columbia environment: 1973–2012

An updated ecological risk assessment was conducted to re-evaluate and review the overall risk of pesticide residues to certain aquatic life. The focus was the impact on offsite non-target, freshwater organisms of pesticide operational sprays in British Columbia from 1973 until 2012. The values of risk quotients for pesticides of selected indicator organisms were determined to measure the effect. When compared with organophosphorus, carbamate, and other miscellaneous pesticides, this risk assessment analysis suggests that the historical use of persistent and highly toxic organochlorine pesticides posed, and continue to pose, a deleterious ecological risk. The risk is both short-term acute and long-term sub-acute, chronic toxicity to offsite, non-target aquatic invertebrates and juvenile salmonid fish. Data indicated that these organisms were, and remain, subjected to harmful effects of pesticide residues to varying degrees. Most vulnerable were, and also are, benthic organisms inhabiting bottom sediments. This substrate is the natural sink for persistent pesticide residues, predominantly organochlorine pesticides from historical use, as well as dioxins, furans, and polycyclic aromatic hydrocarbons from wood preservatives, and other sources. Environment Canada's main aquatic protection strategy was a 10 metre no-treatment buffer zone, augmented with an additional appropriate setback along shorelines of fishery and wildlife resource-sensitive water bodies. This study discusses why this guideline was necessary, useful and effective, but was only partially successful. The physical-chemical properties of pesticide residues, from either an individual compound or different compounds in combination, also influence the nature of biological impacts on non-target, aquatic organisms. Few studies have been conducted in British Columbia aquatic environments to investigate the significance of this aspect.     

Characterisation of cholinesterases and evaluation of the inhibitory potential of chlorpyrifos and dichlorvos to Artemia salina and Artemia parthenogenetica

In this study, the acute toxicity of the organophosphorous pesticides dichlorvos and chlorpyrifos to two different species of Artemia (A. salina and A. parthenogenetica) was evaluated. In addition, the in vivo effect of these two pesticides on cholinesterase (ChE) activity of both A. salina and A. parthenogenetica was also determined. The characterisation of the ChE, using different substrates and specific inhibitors, and the normal range of activity in non-exposed individuals were previously investigated for both species. The results obtained indicate that the ChE of A. salina is different from that of A. parthenogenetica and that both enzymes cannot be classified neither as acetylcholinesterase nor as butyrylcholinesterase since they show intermediary characteristics between the two vertebrate forms. The range of normal ChE activity was 2.65+/-0.15 U/mg protein for A. salina, and 3.69+/-0.17 U/mg protein for A. parthenogenetica. Significant in vivo effects of both pesticides on Artemia ChE activity were found, at concentrations between 5.38 and 9.30 mg/l for dichlorvos and between 1.85 and 3.19 mg/l for chlorpyrifos. Both Artemia species are resistant to these pesticides and they are able to survive with more than 80% ChE inhibition. However, A. parthenogenetica is more resistant than A. salina, with about a 95% reduction in its ChE activity respect to the control for nauplii exposed to the median lethal concentrations (LC50), without lethal effects after 24 h of exposure.     

Effects of bensulfuron-methyl and cinosulfuron on growth of four freshwater species of phytoplankton

The acute toxicity of sulfonylurea herbicides bensulfuron-methyl and cinosulfuron was tested on the five species of freshwater phytoplankton: Scenedesmus acutus, Scenedesmus subspicatus, Chlorella vulgaris and Chlorella saccharophila. Herbicide concentrations eliciting a 50% growth reduction over 96 h (EC50) ranged from 8 to 104 mg/l for cinosulfuron and from 0.015 to 6.2 mg/l for bensulfuron-methyl. The pesticides bensulfuron-methyl, atrazine and benthiocarb were more toxic than cinosulfuron, chlorsulfuron, molinate, fenitrothion and pyridaphenthion in a toxicity study with the same algal species. The transformation of effective concentrations of bensulfuron-methyl and cinosulfuron and other pesticides, obtained from toxicity measurements, into percent of the saturation level in water is used as a first evaluation of potential hazard to aquatic systems. The herbicides cinosulfuron, methyl-bensulfuron, atrazine and chlorsulfuron were more dangerous than the herbicides benthiocarb and molinate and than the insecticides fenitrothion and pyridaphenthion, in a study of hazard evaluation. The two species of Chlorella were more tolerant to both herbicides than the two species of Scenedesmus. A potential environmental hazard of sulfonylurea herbicides to aquatic systems has to be expected even at low environmental concentrations.     

Studies of 3D-quantitative structure-activity relationships on a set of nitroaromatic compounds: CoMFA,advanced CoMFA and CoMSIA

By using comparative molecular field analysis (CoMFA), advanced CoMFA and comparative molecular similarity index analysis (CoMSIA) methods, the 3D relationships between the structures of 35 nitroaromatic compounds and their toxicities have been investigated to yield statistically reliable models of considerable predictive power. In contrast to CoMFA, CoMSIA produces better results for the correlation. Moreover, the obtained CoMSIA contour maps that interpret the correlations in terms of field contributions allow physicochemical properties relevant for binding to be easily mapped back onto molecular structures, and thus elucidate structural features among ligands that are responsible for toxicities. Besides, most of the highlighted regions in CoMSIA and CoMFA contour maps are mirrored by features in the surrounding environment. Thereby, CoMFA and CoMSIA both help to give explanations of the toxic mechanism of tested compounds.     

The antiviral activity and cytotoxicity of 15 natural phenolic compounds with previously demonstrated antifungal activity

The present study attempted to evaluate the carcinogenicity of natural phenolic compounds with previously demonstrated antifungal activity, using a computational structure–cytotoxicity approach, namely the quantum structure cytotoxicity relationship model. The cytotoxicity of 15 phenolic compounds with antiviral activity 96?h after treatment was studied using the AdmetSAR computational program. Per the EPA classification, four of the investigated compounds would be included in the second cytotoxicity category, four in the third category, and six showed no toxicity, rendering the studied natural phenolic compounds much less toxic to aquatic life than synthetic pesticides, the organophosphorus compounds, which mostly fall into the first and second categories of toxicity.     

Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach

Effluents are a main source of direct and continuous input of pollutants to the aquatic environment, and can cause ecotoxicological effects at different levels of biological organization. Since gene expression responses represent the primary interaction site between environmental contaminants and biota, they provide essential clues to understand how chemical exposure can affect organismal health. The aim of the present study was to investigate the applicability of a microarray approach for unraveling modes of action of whole effluent toxicity and impact assessment. A chronic toxicity test with common carp (Cyprinus carpio) was conducted where fish were exposed to a control and 100% effluent for 21 days under flow-through conditions. Microarray analysis revealed that effluent treatment mainly affected molecular pathways associated with the energy balance of the fish, including changes in carbohydrate and lipid metabolism, as well as digestive enzyme activity. These gene expression responses were in clear agreement with, and provided additional mechanistic information on various cellular and higher level effects observed for the same effluent. Our results demonstrate the benefit of toxicogenomic tools in a “systems toxicology” approach, involving the integration of adverse effects of chemicals and stressors across multiple levels of biological complexity.     

Application of a computational model for Michael addition reactivity in the prediction of toxicity to Tetrahymena pyriformis

A computational model to predict acute aquatic toxicity to the ciliate Tetrahymena pyriformis has been developed. A general prediction of toxicity can be based on three consecutive steps: 1. Identification of a potential reactive mechanism via structural alerts; 2. Confirmation and quantification of (bio)chemical reactivity; 3. Establishing a relationship between calculated reactivity and toxicity. The method described herein uses a combination of a reactive toxicity (RT) model, including computed kinetic rate constants for adduct formation (log k) via a Michael acceptor mechanism of action, and baseline toxicity (BT), modelled by hydrophobicity (octanol-water partition coefficient). The maximum of the RT and BT values defines acute toxicity for a particular compound. The reactive toxicity model is based on site-specific steric and quantum chemical ground state electronic properties. The performance of the model was examined in terms of predicting the toxicity of 106 potential Michael acceptor compounds covering several classes of compounds (aldehydes, ketones, esters, heterocycles). The advantages of the computational method are described. The method allows for a closer and more transparent mechanistic insight into the molecular initiating events of toxicological endpoints.     

Biological and chemical analysis of the toxic potency of pesticides in rainwater.

A newly developed method for measuring the integrated esterase inhibiting potency of rainwater samples was applied in practice, and the results are compared to the toxic potency calculated from concentrations of 31 organophosphate (OP) and carbamate pesticides, out of a total of 66 chemically analyzed pesticides. In addition, the general toxic potency of the rainwater samples was evaluated in a microtiter luminescence assay with Vibrio fischeri bacteria. Rainwater samples were collected over four consecutive 14-day periods in both open and wet-only samplers. The esterase inhibiting potency of the open rainwater samples (expressed as ng dichlorvos-equivalents/l) corresponded well with the chemical analyses of the rainwater samples collected by both types of samplers (r = 0.83-0.86). By far, the highest esterase inhibiting potency was found in a sample collected in an area with intense horticultural activities in June, and was attributed to high concentrations of dichlorvos, mevinphos, pirimiphos-methyl and methiocarb. The esterase inhibiting potency of this sample was equivalent to a dichlorvos concentration of 1380 ng/l in the rainwater, which is almost 2000 times higher than the maximum permissible concentration (MPC) of dichlorvos set for surface water in Netherlands. Maximum individual concentrations of dichlorvos and pirimiphos-methyl even exceeded the EC50 for Daphnia, suggesting that pesticides in rainwater pose a risk for aquatic organisms. Not all responses of the luminescence-assay for general toxicity could be explained by the analyzed pesticide concentrations. The bio-assays enable a direct assessment the toxic potency of all individual compounds present in the complex mixture of rainwater pollutants, even if they are unknown or present at concentrations below the detection limit. Therefore, they are valuable tools for prescreening and hazard characterization purposes.     

Mechanistic insights into the specificity of human cytosolic sulfotransferase 2A1 (hSULT2A1) for hydroxylated polychlorinated biphenyls through the use of fluoro-tagged probes

Determining the relationships between the structures of substrates and inhibitors and their interactions with drug-metabolizing enzymes is of prime importance in predicting the toxic potential of new and legacy xenobiotics. Traditionally, quantitative structure activity relationship (QSAR) studies are performed with many distinct compounds. Based on the chemical properties of the tested compounds, complex relationships can be established so that models can be developed to predict toxicity of novel compounds. In this study, the use of fluorinated analogues as supplemental QSAR compounds was investigated. Substituting fluorine induces changes in electronic and steric properties of the substrate without substantially changing the chemical backbone of the substrate. In vitro assays were performed using purified human cytosolic sulfotransferase hSULT2A1 as a model enzyme. A mono-hydroxylated polychlorinated biphenyl (4-OH PCB 14) and its four possible mono-fluoro analogues were used as test compounds. Remarkable similarities were found between this approach and previously published QSAR studies for hSULT2A1. Both studies implicate the importance of dipole moment and dihedral angle as being important to PCB structure in respect to being substrates for hSULT2A1. We conclude that mono-fluorinated analogues of a target substrate can be a useful tool to study the structure activity relationships for enzyme specificity.