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.     

Structure-activity relationships and response-surface analysis of nitroaromatics toxicity to the yeast (Saccharomyces cerevisiae)

Inhibition of growth of the yeast Saccharomyces cerevisiae (Cmiz, the minimum concentration that produced a clear inhibition zone within 12 h) for 24 nitroaromatic compounds was investigated and a quantitative structure-activity relationship (QSAR) developed based on hydrophobicity expressed as the l-octanol/water partition coefficient in logarithm form, log K(ow), electrophilicity based on the energy of the lowest unoccupied orbital (E(lumo)). All nitrobenzene derivatives exhibited enhanced reactive toxicity than baseline. The toxicities of mono-nitrobenzenes and di-nitrobenzenes were elicited by different mechanisms of toxic action. For mono-nitro-derivatives, both significant log K(ow) based and strong E(lumo)-dependent relationships were observed indicating that their toxicities were affected both by the penetration process and the interaction with target sites of interaction. The toxicities of di-nitrobenzenes were greater than mono-nitrobenzenes and no log K(ow)-dependent but highly significant E(lumo)-based relationship was obtained. This suggests that toxicity of di-nitrobenzenes was highly electrophilic and involved mainly their in vivo electrophilic interaction with biomacromolecules. In an effort to model the elevated toxicity of all nitrobenzenes, a response-surface analysis was performed and this resulted in a highly predictive two-variable QSAR without reference to their exact mechanisms (Cmiz = 0.41 log K(ow) - 0.89 E(lumo) - 0.46, r2 = 0.87, Q2 = 0.86, n = 24).     

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.     

Acute toxicity of substituted phenols to Rana japonica tadpoles and mechanism-based quantitative structure-activity relationship (QSAR) study.

Acute 12 h and 24 h lethal toxicity (12 h-LC50 and 24 h-LC50) of 31 substituted phenols to Rana japonica tadpoles was determined. Results indicate that toxicity of phenols to tadpoles varied only slightly with length of exposure and the 12-h test could serve as surrogate of the 24-h test. A mechanism-based quantitative structure-activity relationship (QSAR) method was employed and 1-octanol/water partition coefficient (log K(ow))-dependent models were developed to study different modes of toxic action. Most phenols elicited their response via a polar narcotic mechanism and an excellent logK(ow)-dependent model was obtained. Soft electrophilicity and pro-electrophilicity were observed for some phenols and a good log K(ow)-dependent model was also achieved. Additionally, the significant dissociation of carboxyl on benzoic acid derivatives sharply reduced their toxicity. A statistically robust QSAR model was developed for all studied compounds with the combined application of log K(ow), energy of lowest unoccupied orbital (E(lumo)), heat of formation (HOF) and the first-order path molecular connectivity dices (1chi(p)).     

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 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.     

Acute toxicity of chlorophenols to earthworms using a simple paper contact method and comparison with toxicities to fresh water organisms

An acute toxicity test of chlorophenols on earthworms (Eisenia fetida) was performed using a simple paper contact method proposed by OECD testing guideline no. 207, that were applied as an earthworm toxicity test. The median lethal concentration, EC50, had significant correlation with logP(ow) (1-octanol/water partition coefficient) of the chemicals. The toxicity of chlorophenols on E. fetida was compared with toxicities for other species: an algae (Selenostrum capricornutum), a crustacean (Daphnia magna), and a fish (Oryzias latipes). It was found that the toxicity of chlorophenols was almost same for E. fetida and for fresh water organisms. These results suggest the possibility of drawing correlations between the effects of pollutants on living things in different environments, fresh water and soil.     

Quantitative structure-toxicity relationships of organophosphorous pesticides to fish (Cyprinus carpio)

This study was conducted to determine the relationships between 1381 chemical and structural parameters of 43 organophosphorus pesticides (OPs) and their toxicity to fish, Cyprinus carpio, using ChemOffice 8.03 and Dragon 2.1. By multivariate linear regression and intervariable regression analyses, various equations have been derived to calculate the lethal toxicity value, LC(50), for 43 OPs found in fish with different levels of toxicity. Results show that for all selected OPs, especially those of low toxic OPs (LC(50)< 2.5 mM), the equation, LC(50) = 56.259 - 13.071 lg K(ow)+17.510 MATS8P-17.455 Mor24u - 0.085 MW + 1.706 (lg K(ow))(2) + 2.306 (Mor14e)(2) + 6.849 Mor20 m (n = 43, F = 36.815, r = 0.942, r(adj)(2) = 0.862, SE = 2.899, p < 10(-6)), could account for 86.2% of the variability of the toxic effect. The steric and electronic characteristics and the hydrophobicity of OPs, in particular, are among the most important parameters determining the toxicity of OPs to fish. For the OPs with high toxicity, different structural parameters were introduced into the following two equations: LC(50)=3.795-1.195 (H1p)(2)-0.037 U-2.225 MATS3v-19.593 Tcon (n = 16, F = 56.820, r = 0.977, r(adj)(2) = 0.937, SE = 0.143, p < 10(-6)), where LC(50) is less than 2.5 mM, and LC(50) = 0.341-0.561 (HOMA)(2) + 0.231 HOMA (n = 3,r(adj)(2) = 1), where LC(50) is less than 0.3 mM. These results suggest that chemical and structural parameters could be useful in modeling chemical reactivity within homologous series of OP compounds and elucidating possible mechanisms associated with different levels of toxicity to fish.     

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.     

QSAR study on the toxicity of substituted benzenes to the algae (Scenedesmus obliquus).

50% effective inhibition concentration 48h-EC50 of 40 substituted benzenes to the algae (Scenedesmus obliquus) was determined. The energy of the lowest unoccupied molecular orbital (E(LUMO)) was calculated by the quantum chemical method MOPAC6.0-AM1. By using E(LUMO) and the hydrophobicity parameter log K(OW) the quantitative structure-activity relationship model (QSAR) was developed: log1/EC50=0.272 logK(OW) - 0.659E(LUMO) + 2.54, R2 = 0.793, S.E. = 0.316, F = 71.07, n = 40. A series of equations were obtained about the measured EC50 values of different subclasses of compounds. For those compounds containing double -NO2, their toxicity may be related chiefly to the intracellular reduction of -NO2 obtaining electron, while for anilines and phenols, K(OW) contributes most to the QSAR and E(LUMO) very little.     

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.     

Does lipophilicity of toxic compounds determine effects on drought tolerance of the soil collembolan Folsomia candida?

The ability of Collembola to survive drought stress is crucial for their distribution in the terrestrial environment. Previous studies have suggested that several toxic compounds affect the drought tolerance of Folsomia candida in a synergistic manner and that these compounds have the feature in common that they elicit their toxicity by causing membrane damage. We hypothesised that the detrimental effect of toxic chemicals on drought tolerance in F. candida depends on the lipophilicity (log K(ow)) of the compound because a higher log K(ow) would mean a closer interaction with membranes. In this study the three chemicals 4-nonylphenol, pyrene and p,p'-DDE were tested. Surprisingly, 4-nonylphenol, with the lowest log K(ow), was the most potent with respect to reducing drought tolerance followed by pyrene, suggesting that interactions between drought tolerance and chemical stress do not depend on lipophilicity alone.     

Comparison of in vitro and in vivo acute fish toxicity in relation to toxicant mode of action

Acute toxicity to fish hepatoma cell line PLHC-1 and to juvenile rainbow trout was examined for 18 plant protection products. The main objective was to explore whether hepatoma cells could be used to predict acute toxicity in fish taking into account the mode of toxic action and compound properties. Acute fish toxicity was determined using the OECD guideline test 203 and compared to predicted baseline LC50 of acute fish toxicity calculated with a quantitative structure-activity relationship (QSAR) derived for guppy fish. Cytotoxicity was determined through the inhibition of neutral red uptake (NR(50)) into lysosomes and compared to predicted baseline cytotoxicity derived for goldfish GFS cells. In general, NR50 values were higher by a factor ranging from 3 to 3000 than the corresponding acute LC50. A weak correlation between NR50 and LC50 values was found (log/log: r2=0.62). Also the lipophilicity (log K(ow)) was not a good predictor for cytotoxicity (r2=0.43) and lethality (r2=0.57) of these pesticides. The neutral red assay is detecting general baseline toxicity only. Comparing LC50 data to QSAR results, the compounds can be classified to act as narcotics or reactive compounds with a specific mode of toxic action in fish. The results indicate that limitation of the neutral red assay in predicting acute fish toxicity. A promising alternative might be the assessment of toxicity in a set of in vitro systems addressing also cell-specific functions which are related to the mode of toxic action of the compound.     

Correlation relationships between physico-chemical properties and gas chromatographic retention index of polychlorinated-dibenzofurans

Correlation relationships between physico-chemical properties including vapor pressures (P), water solubilities (S), Henry's law constants (H(c)), n-octanol-water partition coefficients (K(ow)), sediment-water partition coefficient (K(pw)) and biotic lipid-water partition coefficient (K(bw), bioconcentration factor) of polychlorinated-dibenzofurans (PCDFs) and their gas chromatographic retention indices (GC-RIs) were established. A model equation between GC-RIs (= RI) and these physico-chemical properties (K) of PCDFs was in a form of log K = aRI2 + bRI + c with correlation coefficients (R2) greater than 0.94, except H(c). These equations were derived from six experimental data (five experimental data for log K(bw)) in each physico-chemical properties of PCDFs reported previously. The values of log P, log S, log H(c), log K(ow), log K(pw) and log K(bw) of PCDFs predicted by these equations based on their GC-RIs in the present study derviated from those calculated by the solubility parameters for fate analysis method in a previous study by 0.49, 0.32, 0.11, 0.34, 0.14 and 0.22 log units, respectively.     

Vapour pressures, aqueous solubilities, Henry's Law constants, and octanol/water partition coefficients of a series of mixed halogenated dimethyl bipyrroles

Basic physical-chemical properties of five bromine and chlorine containing mixed halogenated dimethyl bipyrroles (HDBPs) were determined using established methods. Subcooled liquid vapour pressures (P(o)(L,25)), aqueous solubilities (S(w,25)), and octanol/water partition coefficients (K(ow)) were determined using the gas chromatography-retention time, generator column, and slow-stirring methods, respectively. Henry's Law constants (H25) were estimated using experimentally-derived P(o)(L) and S(w,25) data. Values of all four properties were generally similar to those reported for other polyhalogenated aromatic compounds [P(o)(L,25) = (7.55-191) x 10(-6) Pa; S(w,25) = (1.0-1.9) x 10(-5) g/l; log K(ow) = 6.4-6.7; H25 = 0.0020-0.14 Pa m3/mol]. The effect of replacing a chlorine with a bromine atom significantly decreased P(o)(L,25) (log P(o)(L,25) = -0.4197 (# bromine atoms) - 2.643, p<0.01) and H25 (log H25 = -0.508 (# bromine atoms) + 0.394, p<0.02). There were no significant effects of bromine/chlorine substitution on S(w,25) or K(ow). A simple Level I equilibrium partitioning model predicted the environmental behaviour of HDBPs to be similar to a tetrabrominated diphenyl ether. Only slight differences in behaviour amongst HDBP congeners were predicted since substitution of a bromine for a chlorine (Cl/Br substitution) atom had less effect than H/Cl or H/Br substitution on P(o)(L,25), S(w,25), H25, and K(ow).