Molecular Polarization Potential as a Molecular Descriptor to Predict Biological Activity of Dioxins and Dibenzofurans

Molecular interaction potential (MIP) maps are a powerful tool to develop structure-activity relationships of a series of compounds. In the present study we have studied the effect of molecular polarization on the description of the toxicity of a series of dioxins and benzofurans using their MIPs. Specifically, we have used principal component analysis in an exploratory way to understand the common structural features that describe the toxicity of these molecules through the analysis of their MIPs and each of their components, i.e.; molecular electrostatic and polarization potentials. Moreover, we have developed a predictive model using PLS that permits to evaluate the toxicity of compounds belonging to any of the families of compounds studied in the present work on the basis of their molecular electrostatic and interaction potentials.

Predictive insight into the relationship between AhR binding property and toxicity of polybrominated diphenyl ethers by PLS-derived QSAR

Polybrominated diphenyl ethers (PBDEs) are experimentally indicated to be capable of binding to the cytosolic aryl hydrocarbon receptor (AhR) and show a weak or moderate toxicity. However, little is yet known about the AhR-mediated toxicology. To fully evaluate the structural effects of PBDE ligand on AhR binding affinity and toxicity, quantitative structure-activity relationships (QSARs) were developed by PLS analysis. In this study, a simple but potent QSAR that was qualified with much better or comparable performance of prediction was optimally established for PBDE toxicity. With QSAR analysis, the AhR binding property was carefully described to reflect the origin of AhR binding affinity. Besides the effects from topological characters, the dispersion and electrostatic interactions were of indispensability for AhR binding affinity whereas the dispersion was further suggested to be dominant. The structural requirement for AhR binding affinity and toxicity was also investigated. As was similarly observed for polychlorinated biphenyls (PCBs), the preferential bromination at para- and meta (particularly 3,3'-)-sites was confirmed as a key determinant to improve the AhR binding affinity and the toxicity of PBDEs.

Mechanism-based common reactivity pattern (COREPA) modelling of aryl hydrocarbon receptor binding affinity

The aryl hydrocarbon receptor is a ligand-activated transcription factor responsive to both natural and synthetic environmental compounds, with the most potent agonist being 2,3,7,8-tetrachlotrodibenzo-p-dioxin. The aim of this work was to develop a categorical COmmon REactivity PAttern (COREPA)-based structure-activity relationship model for predicting aryl hydrocarbon receptor ligands within different binding ranges. The COREPA analysis suggested two different binding mechanisms called dioxin- and biphenyl-like, respectively. The dioxin-like model predicts a mechanism that requires a favourable interaction with a receptor nucleophilic site in the central part of the ligand and with electrophilic sites at both sides of the principal molecular axis, whereas the biphenyl-like model predicted a stacking-type interaction with the aryl hydrocarbon receptor allowing electron charge transfer from the receptor to the ligand. The current model was also adjusted to predict agonistic/antagonistic properties of chemicals. The mechanism of antagonistic properties was related to the possibility that these chemicals have a localized negative charge at the molecule's axis and ultimately bind with the receptor surface through the electron-donating properties of electron-rich groups. The categorization of chemicals as agonists/antagonists was found to correlate with their gene expression. The highest increase in gene expression was elicited by strong agonists, followed by weak agonists producing lower increases in gene expression, whereas all antagonists (and non-aryl hydrocarbon receptor binders) were found to have no effect on gene expression. However, this relationship was found to be quantitative for the chemicals populating the areas with extreme gene expression values only, leaving a wide fuzzy area where the quantitative relationship was unclear. The total concordance of the derived aryl hydrocarbon receptor binding categorical structure-activity relationship model was 82% whereas the Pearson's coefficient was 0.88.

Anticancer activity and quantitative-structure activity relationship (QSAR) studies of a series of antioxidant/anti-inflammatory aryl-acetic and hydroxamic acids

A series of aryl-acetic acids and hydroxamic acids possessing antioxidant/anti-inflammatory activities were tested for anticancer activity using different cancer cell lines. The compounds have low antitumor activity considering the 1/IC(50) values attained for the cell lines. Compound 5iv presents the best anticancer activity. Moreover, they depict the same activity pattern, suggesting similar mechanisms of action correlated to their antioxidant activities. The obtained results subjected in a QSAR analysis. It seems reasonable to conclude that the same molecular structural features are responsible for the compounds biological activity, these being the electron accepting/donating ability and the molar volume. For all cellular lines (HT-29, A-549 and OAW-42) log 1/IC(50) exhibits a reasonable correlation with a two parameters relationship in which the Esp-min and D term are present. Apart from Esp-min the other descriptor found important for anticancer activity is the molar volume (MgVol). The QSAR analyses did not indicate any role for lipophilicity Electrostatic potential, dipole moment and the bulk, primarily affect the biological response.

QSARs for congener-specific toxicity of polyhalogenated dibenzo-p-dioxins with DFT and WHIM theory

Polyhalogenated dibenzo-p-dioxins (PHDDs) have become the most notorious pollutants in the environment. However, the origin of their congener-specific toxicity is not well understood. For explaining the difference in toxicity between PHDDs as well as their potencies of aryl hydrocarbon hydroxylase (AHH) and 7-ethoxyresorufin O-deethylase (EROD) induction, quantitative structure-activity relationships (QSARs) were constructed through the combined application of DFT (density functional theory) and WHIM (weighted holistic invariant molecular) theory. Results from the QSAR analyses suggest that dispersion interaction along the lateral sites of PHDDs should interpret the vast majority of variance of binding affinities as well as the consequent toxicity. Although electrostatic interaction is comparatively less influential, it should not be negligible. Long-range dispersion interaction is also described in QSARs with minute influence. Quadrupole moment tensor perpendicular to the ring plane, i.e., Q(zz) and its implicated electrostatic interaction plays an important role in the contribution to induction potencies.

Receptor interactions by polybrominated diphenyl ethers versus polychlorinated biphenyls: a theoretical Structure-activity assessment

The extensive body of literature regarding the interaction of polychlorinated biphenyls (PCBs) with transcription factors (receptors) has great value to understand similarities and distinctions and in formulating hypotheses regarding the activity of polybrominated diphenyl ethers (PBDEs) toward those same receptors. Our goal is to present the most comprehensive overview of PBDE effects on AhR, CAR, PXR, ER, AR, PR, DHT, TH, T3, T4 and IGF, as well as hypothetical biological activities of PPAR, RyR, GR and GABA. Aside the influence of the conformation of the ligand, we discuss its constitution influencing the binding affinity: size and polarizability, hydrophilicity, Gibbs free energy of solvation, inductive and mesomeric effects. We evaluate the techniques to determine the biologically relevant conformation of these halogenated hydrocarbons, including computation methods, X-ray and microwave spectroscopy. A novel fluoro-tagged ligand approach holds promise as tools for illuminating the steric and electronic effects in ligand-receptor interaction. Based on our assessment, we predict that PBDEs do not exhibit AhR activity themselves, but impurities are responsible for these effects.

DFT study on the structure-toxicity relationship of dioxin compounds using PLS analysis

Density functional theory (DFT) at B3LYP/6-311G** level was employed to optimise the dioxin compounds, i.e., 25 polychlorinated or brominated dibenzo-p-dioxins (PCDDs or PBDDs) and 34 polychlorinated dibenzofurans (PCDFs) involved in this investigation. Three groups of descriptors mainly related to chemical reactivity, molecular overall charge distribution and thermochemical property were calculated. With partial least squares (PLS) analysis and variable importance in the projection (VIP), the least significant descriptors were removed from the quantitative structure-activity relationship (QSAR), which was focused on exploring the influential factors responsible for the variance of binding affinities of dioxins to aryl hydrocarbon receptor (AhR). With better-improved and predictive QSAR (Q(2)(cum) = 0.827), further understanding of the nature of toxicity was available. Both dispersion interaction and electrostatic interaction were considered to be important and together capable of accounting for the most part of the total binding affinities, though the former could make more contribution than the latter. Comparatively, the long-range dispersion interaction should be very small.

QSARs for the toxicity of polychlorinated dibenzofurans through DFT-calculated descriptors of polarizabilities, hyperpolarizabilities and hyper-order electric moments

DFT-B3LYP method with 6-31G(**) basis set was employed to fully optimize the electronic structures of 135 polychlorinated dibenzofurans and parent compound, namely dibenzofuran. It was demonstrated that polarizability anisotropy and mean polarizability could change sensitively and systematically with chlorine number and substitution pattern. And new quantitative structure-activity relationships (QSARs) focused on the binding affinities of aryl hydrocarbon receptor (AhR), aryl hydrocarbon hydroxylase (AHH) and 7-ethoxyresorufin O-deethylase (EROD) induction potencies of PCDFs were developed. It was concluded that polarizability anisotropy in conjunction with hyperpolarizabilties and hyper-order electric moments, e.g. octupole moments could well interpret the variation of toxicity of different congeners and dispersion interaction should be the leading form among various interactions. Although the terms of hyperpolarizabilities and hyper-order electric moments were not the same significant ones as polarizability anisotropy, the long-range interactions characterized by them should not be ignored in explaining the toxicity.

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.

SAR and QSAR modeling of endocrine disruptors

A number of xenobiotics by mimicking natural hormones can disrupt crucial functions in wildlife and humans. These chemicals termed endocrine disruptors are able to exert adverse effects through a variety of mechanisms. Fortunately, there is a growing interest in the study of these structurally diverse chemicals mainly through research programs based on in vitro and in vivo experimentations but also by means of SAR and QSAR models. The goal of our study was to retrieve from the literature all the papers dealing with structure-activity models on endocrine disruptor xenobiotics. A critical analysis of these models was made focusing our attention on the quality of the biological data, the significance of the molecular descriptors and the validity of the statistical tools used for deriving the models. The predictive power and domain of application of these models were also discussed.

Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1

Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2', 6 and 6'). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic non-ortho-chlorinated PCBs, 3,4,3',4'-tetrachlorobiphenyl and 3,4,3',4',5'-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between V(L) and V(H), with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a pi-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1.

Synthesis and QSAR study of the anticancer activity of some novel indane carbocyclic nucleosides

A set of 14 indane carbocyclic nucleosides were synthesized and experimentally assayed for their inhibitory effects in the proliferation of murine leukemia (L1210/0) and human T-lymphocyte (Molt4/C8, CEM/0) cells. The compounds have promising inhibitory activity judging from the IC(50) values obtained for all these cellular lines. Multiple linear regression analysis was then applied to build up consistent QSAR models based on quantum mechanics-derived molecular descriptors. The derived models reproduce well the experimental data of both three cells (r(2) >/=0.90), display a good predictive power and are, above all, easily interpretable. They show that frontier-orbital energies and hydrophobicity are mainly responsible for the activity of the synthesized compounds and also, suggest similar mechanisms of action. The final QSAR-models involve only two descriptors: the lowest unoccupied molecular orbital energy and the solvent accessible-hydrophobic surface area, but describe a sound correlation between predicted and experimental activity data (r(2)=0.931, r(2)=0.936 and r(2)=0.931 for the cells L1210/0, Molt4/C8 and CEM/0, respectively).

Electronic elasticity-toxicity relationships for polychlorinated dibenzo-p-dioxin congeners

SCF-MO computations have been performed on tetra- to octa-chlorinated dibenzo-p-dioxin congeners (PCDD) using an MNDO-PM3 Hamiltonian. Qualitative relationships were developed between empirical, international-toxic equivalence factors for PCDD congeners and their relative (specific) polarizabilities and mean values of second hyperpolarizabilities estimated using finite-field theory.

Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 2. Application of the novel 3D molecular descriptors to QSAR/QSPR studies

In a previous paper the theory of the new molecular descriptors called GETAWAY (GEometry, Topology, and Atom-Weights AssemblY) was explained. These descriptors have been proposed with the aim of matching 3D-molecular geometry, atom relatedness, and chemical information. In this paper prediction ability in structure-property correlations of GETAWAY descriptors has been tested extensively by analyzing the regressions of these descriptors for selected properties of some reference compound classes. Moreover, the general performance of the new descriptors in QSAR/QSPR has been evaluated with respect to other well-known sets of molecular descriptors.

Cytochrome P450 induction by nitrated polycyclic aromatic hydrocarbons, azaarenes, and binary mixtures in fish hepatoma cell line PLHC-1

Nitrated polycyclic aromatic hydrocarbons (NPAHs) and N-heterocyclic aromatic hydrocarbons (azaarenes) are as ubiquitous in the environment as their parent PAH compounds, although occurring at lower concentrations. The toxicological importance of NPAHs and azaarenes is based on their mutagenic and carcinogenic potential. Azaarenes possess a higher solubility and mobility in the environment than PAHs. However, very little is known about the toxicity and cytochrome P450 (CYP)1A induction potencies of NPAHs and azaarenes in fish. Here we report on the cytotoxicities and relative CYP1A induction potencies of 12 NPAHs, 12 azaarenes, and 11 PAHs, determined as neutral red uptake and ethoxyresorufin-O-deethylase (EROD) activity, respectively, in fish hepatoma PLHC-1 cells. Additionally, CYP1A enzyme protein was determined by ELISA for two NPAHs, azaarenes, PAHs, and binary mixtures. Compared with the structurally analogous PAHs, 2-nitronaphthalene, 3-nitrofluoranthene, 2-aza- and 7-azafluoranthene, 1,6-dinitropyrene, benzo[a]acridine and benzo[h]quinoline revealed higher induction potencies, whereas the other compounds showed similar or less activity. The induction potency was highly dependent on the compounds structural properties, reflected by significant correlations between the half-maximal EROD induction (-log EC50) and the molecular descriptors lipophilicity (log Kow) and maximal molecular length (Lmax). Binary mixtures of 6-nitrochrysene + benzo[a]anthracene, 6-nitrochrysene + benzo[a]acridine, and benzo[a]acridine + benzo[a]anthracene showed an additive interaction. The CYP1A induction potencies of NPAHs and azaarenes, demonstrated here for the first time in fish hepatoma cells, suggest that their contribution to the overall CYP1A induction potencies in PAH-contaminated environmental samples have to be taken into account.

Electronic eigenvalue (EEVA): a new QSAR/QSPR descriptor for electronic substituent effects based on molecular orbital energies. A QSAR approach to the Ah receptor binding affinity of polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs)

A new descriptor of molecular structure for use in the derivation of predictive QSAR and QSPR models, electronic eigenvalue (EEVA), is described. This is a modification of the recently proposed EVA approach, but is based on computationally-derived molecular orbital energies instead of vibrational frequencies. Like EVA, it is also invariant as to the alignment of the structures concerned. Its performance has been tested with respect to the Ah receptor binding of PCBs, PCDDs and PCDFs, and its predictive ability has been clearly demonstrated. In particular, it seems to be suitable for 'pure' electronic substituent effects. i.e., for cases in which both hydrophobic and steric factors are of minor importance.

Synthesis and biological evaluation of new imidazole, pyrimidine, and purine derivatives and analogs as inhibitors of xanthine oxidase

Several derivatives of 4,5-disubstituted imidazole, 2,4,5-trisubstituted pyrimidine, 2-substituted purine, thiazolo[3,2-alpha]purine, [1,3]thiazino[3,2-alpha]purine, thiazolo[2,3-i]purine, [1,3]thiazino-[2,3-i]purine, and 6-substituted pyrazolo[3,4-d]pyrimidine were synthesized and tested as inhibitors of the xanthine oxidase enzyme. Of those, some 4-(acylamino)-5-carbamoylimidazoles and 2-thioalkyl-substituted purines exhibited very good inhibitory activity, being at least 500 times more effective than allopurinol. The ineffectiveness of 6-n-alkylpyrazolo[3,4-d]pyrimidines is imputable to the alkyl chain which could hinder the coordination with molybdenum according to the known mechanism for the binding of the inhibitor allopurinol; the effectiveness of imidazole derivatives, by contrast with the ineffectiveness of 4,5-diamino-2-(thioalkyl)-6-hydroxypyrimidines, indicates the relative importance of the five-membered ring in the interaction with the enzyme. Moreover, the marked effectiveness of the angularly-cyclized [1,3]thiazino[2,3-i]purinones, which constitute an interesting new class of inhibitors, together with the weak activity of linearly-cyclized derivatives, allowed us to characterize more precisely the lipophilic region of the enzyme facing the N(1)-C(2) positions of the substrate hypoxanthine.

Dioxins, furans and AHH-active PCB congeners in eggs of two gull species from the western Mediterranean

Polychlorinated biphenyls, dibenzodioxins and dibenzofurans were analysed in eggs of a protected gull species, the Audouin's Gull (Larus audouinii) and compared to those of the Yellow-legged Gull (Larus cachinnans), both breeding in the Western Mediterranean (Ebro Delta and Medes Islands, respectively). Differences in concentrations as well as in congener profiles reflected differences in both habitat and diet of the two species. Levels of AHH-active PCB congeners were lower in Yellow-legged Gull (0.4-1.6 micrograms/g d.w) than in Audouin's Gull eggs (1.2-33.9 micrograms/g d.w.). These concentrations, expressed in international toxic equivalence factors (i-TEQ/g d.w.), were on average 24 times higher in the Audouin's gull. I-TEQ levels due to dioxins were also higher in this species by a factor of ca. 7. I-TEQ levels related to PCBs resulted 90-230 times higher than those of dioxins and furans. Thus, AHH-inducing PCBs might represent even higher toxicological hazards than dioxins and furans to some populations of seabirds. The necessity of assessing the impact of these compounds in rare and protected species is pointed out.

Benz[a]anthracene diols: predicted carcinogenicity and structure-estrogen receptor binding affinity relationships

Benz[a]anthracenes are ubiquitous environmental carcinogens that exert estrogenic and antiestrogenic effects directly or via hydroxylated metabolites. In this paper, the structure-estrogen receptor binding relationships of four 3,9-benz[a]anthracene diols are described: unsubstituted, 7-methyl, 12-methyl, and 7,12-dimethyl. Compounds unsubstituted at the 12-position have flat molecular topology, whereas methyl substitution at the 12-position in the bay region induces twisting of the molecular framework. The oxygen-oxygen distances (11.94-11.98 A) are similar to diethylstilbestrol (12.1 A). The binding affinities range from 0.43% to 26% that of estradiol. Methyl substitution at the 7-position enhances affinity; 12-methyl substitution decreases it. These results are contrary to many estrogen receptor (ER) ligand systems, in which the compounds with the flatter molecular geometries typically have lower binding affinity. Molecular graphics were used to analyze the fit of the four compounds with a receptor excluded volume model for the ER. These studies suggest that these compounds bind to the ER in a manner in which the anthracene fragment acts as the steroid AB-ring mimic (i.e, the benz[a]anthracene 9-position corresponds to the estradiol 3-position). Molecular orbital (AM1) calculations were used to calculate the charges of selected atoms. The 7-methyl compound was found to have greater charge similarity to estradiol than the other three compounds. The high affinity of the 7-methyl compound is ascribed to its charge similarity to estradiol, hydrophobic interactions in the receptor region that would accommodate a substituent in the planar 6-position of a delta 6,7-steroid, and favorable dispersive interactions with the receptor secondary to its extended planar system. Molecular orbital calculations also suggest that some of the benz[a]anthracene monophenols and diphenols have sufficiently low ionization potentials to act as carcinogens by a radical cation process.

Do residue levels of polychlorinated biphenyls (PCBs) in human blood produce mild hypothyroidism?

PCBs are nearly ubiquitous environmental contaminants, occurring in most human adipose tissue and blood samples. It has recently been recognized that PCBs and related compounds share important structural properties with thyroid hormones and can bind thyroid hormone binding proteins. It is reasonable that such specific binding interactions can modulate the distribution of these compounds in the body and alter hormone-protein interactions that are responsible for the maintenance of normal thyroid status. Most of the available evidence indicates that the levels of free thyroid hormones in plasma are a reflection of the maintenance of normal thyroid status in any individual. A theoretical model for the transport of thyroid hormones in blood has been extended to estimate the modulating effects of PCBs on free thyroid hormones. Using conservative assumptions based on experimental data, our calculations indicate that PCB concentrations normally found in humans can effect significant increases in free thyroxine levels in serum by competing with serum thyroid hormone binding proteins. Experimental data are discussed which support the proposal that antagonist binding of PCBs to thyroid hormone binding proteins in serum could produce varying degrees of hypothyroidism. The biological result is compatible with the "equilibrium hypothesis" in which thyroid hormone redistributes between specific and nonspecific binding proteins rather than emphasizing the importance of free hormone as the active moiety.