Density functional theory-based reactivity descriptors for dioxins

Studying the chemical reactivity properties of the target tumor-environment tripeptides NGR (asparagine-glycine-arginine) and RGD (arginine-glycine-aspartic acid) in their interactions with tamoxifen through conceptual density functional theory

Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and cross-reactivities were analyzed. The interactions of the tripeptides with the nanodiamond-tamoxifen (ND-TAM) complex where the nanodiamond acts as a nanocarrier were also examined theoretically. In addition, their intestinal absorption was predicted based on the polar surface area. The results showed that tamoxifen interacts with RGD, and this interaction remained after the addition of the nanodiamond. An analysis of the chemical hardnesses of the tripeptides was carried out to explore their possible use as synthetic vectors when joined to the nanodiamond. Results indicated that NGR is the most stable of the tripeptides and could be used for active targeting. All calculations were implemented using the conceptual framework of density functional theory.

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.

Decabromobiphenyl (PBB-209) activates the aryl hydrocarbon receptor while decachlorobiphenyl (PCB-209) is inactive: experimental evidence and computational rationalization of the different behavior of some halogenated biphenyls

In rat H4IIE cells permanently transfected with a luciferase gene under the control of AhR, incubation with PBB-209 led to a statistically significant increase of luminescence. In this system, PCB-209 only caused a small induction of luciferase activity. In a fish cell line, only PBB-209 was able to provoke an induction of ethoxyresorufin- O-deethylase activity. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR is very unlikely to occur without ligand binding. None of the biphenyls studied provoked any activation of AhR in this system. To rationalize the results and to get insight into the molecular mechanism of activation of AhR by PBB-209 as compared with PCB-209, a comprehensive computational study was carried out on these congeners as well as on PCB-126 and PCB-169, two potent AhR activators through ligand binding. The calculations include (i) conformational analysis and dipole moments of each conformer, (ii) aromaticity indices, (iii) molecular electrostatic potentials, (iv) quadrupole moments, (v) electronic and reactivity descriptors, and (vi) dissociation energies of C-Cl and C-Br bonds in model aromatic compounds. It was found that some molecular features of PBB-209, such as the electrostatic potential (EP) and EP-derived descriptors (Politzer's parameters), indicate that PBB-209 is more similar to PCB-126 and PCB-169 than to PCB-209, which share quite similar geometries based on the substitution pattern. The similarity between PBB-209, PCB-126, and PCB-169 seems to hint that these three compounds can share, at least partially, similar mechanisms of activation of AhR. It is unquestionable that PCB-126 and PCB-169 directly bind AhR and PBB-209 does not. We hypothesize that there are several simultaneous mechanisms for activation of AhR, and the most active compounds act for more than one mechanism.

Aryl Hydrocarbon Receptor-Mediated Effects of Chlorinated Polycyclic Aromatic Hydrocarbons

Chlorinated polycyclic aromatic hydrocarbons (ClPAHs) with 3-5 rings are ubiquitous environmental contaminants. However, toxicities of ClPAHs remain unclear. In this study, aryl hydrocarbon receptor (AhR)-mediated activities of ClPAHs were investigated by using a yeast assay system. All environmentally relevant 18 ClPAHs showed the AhR activities in the test; the activities were elevated with the number of chlorine atoms on the lower molecular weight PAH ( approximately three-ring and fluoranthene derivatives) but not for higher molecular weight ClPAHs (>four-ring). The similar trends were also observed in certain ClPAHs-induced cytochrome P450 1A1 expression in MCF-7 cells. The structure-activity relationship between the AhR activity and the corresponding solvent accessible surface area of ClPAHs revealed a parabolic relationship, with approximately 350 A (2)/molecule as the optimal dimensions as the ligand for binding to AhR. These findings indicate that the spatial dimensions of ClPAHs apparently influence their ability to activate the AhR. Finally, we discussed the toxicity of exposure to ClPAHs based on the AhR activities, estimated that it would be approximately 30-50 times higher than that of dioxins.

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.

Density functional theory fragment descriptors to quantify the reactivity of a molecular family: Application to amino acids

By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology.

Electrophilicity index as a possible descriptor of biological activity

The purpose of this study is to probe the suitability of DFT based chemical reactivity parameter, electrophilicity index as a possible biological activity descriptor in the development of QSAR. Testosterone derivatives with activity described in terms of various biological activity parameters and the estrogen derivatives by relative binding affinity (RBA) values have been selected as model systems. The implications for the ability of electrophilicity to describe the biological activities are discussed. From the results it is possible to observe that electrophilicity index may be suitable to effectively describe the biological activity.