Specific interactions between aryl hydrocarbon receptor and dioxin congeners: Ab initio fragment molecular orbital calculations

In silico epitope prediction and immunogenic analysis for penton base epitope-focused vaccine against hydropericardium syndrome in chicken

Certain strains of fowl adenovirus serotype 4 (FAdV-4) of the family Adenoviridae are recognized to be the causative agents of Hydropericardium Syndrome (HPS) in broiler chicken. Despite the significantly spiking mortality in broilers due to HPS, not much effort has been made to design an effective vaccine against FAdV-4. The combination of immuno- and bioinformatics tools for immunogenic epitope prediction is the most recent concept of vaccine design. It reduces the time and effort required for hunting a potent vaccine candidate and is economical. Previously, we have reported the penton base protein of FAdV-4 to be a candidate for subunit vaccine against HPS. In the present study, we have computationally pre-screened promising B- and T-cell epitopes of the penton base. Multiple methods were employed for linear B-cell epitope identification; BepiPred and five other methods based on physicochemical properties of the amino acids. The penton base was homology modeled by means of Modeller 9.17 and after refinement of the model (by GalaxyRefine web server) ElliPro web tool was used to predict the discontinuous epitopes. NetMHCcons 1.1 and NetMHCIIpan 3.1 servers were used for the likelihood of peptide binding to Major Histocompatibility Complex (MHC) class I & II molecules respectively for T-cell epitope forecast. As a result, we identified the peptide stretch of 1-225  as the most promiscuous B- and T-cell epitope region in penton base Full Length (FL) protein sequence. Escherichia coli based expression vectors were generated containing cloned peptide stretch 1-225 (penton base^1-225) and penton base FL gene sequence. The recombinant penton base^1-225 and penton base FL proteins were expressed and purified using Escherichia coli-based expression system. Purification yield of penton base^1-225 was 3-fold higher compared to penton base FL. These proteins were injected in chickens to determine their competence in protection against HPS. The results showed equal protection level of the two proteins and the commercial inactivated vaccine against FAdV-4 infection. The results suggest the peptide stretch 1-225 of penton base as a valuable candidate for developing an epitope-driven vaccine to combat HPS.

Curcumin and its derivatives inhibit 2,3,7,8,-tetrachloro-dibenzo-p-dioxin-induced expression of drug metabolizing enzymes through aryl hydrocarbon receptor-mediated pathway

Certain dioxins, including 2,3,7,8,-tetrachloro-dibenzo-p-dioxin (TCDD), are exogenous ligands for an aryl hydrocarbon receptor (AhR) and induces various drug-metabolizing enzymes. In this study, we examined the effect of curcumin on expression of drug-metabolizing enzymes through the AhR and NF-E2 related factor 2 (Nrf2) pathways. Curcumin dose-dependently inhibited TCDD-induced expression of phase I enzyme cytochrome P450 1A1 (CYP1A1) and phase II enzymes NAD(P)H:quinone oxidoreductase-1 (NQO1) and heme oxygenase 1 (HO-1) but not tert-butyl hydroquinone-induced NQO1 and HO-1, suggesting that curcumin inhibited only AhR pathway, but not Nrf2 one directly. Furthermore, we used 14 curcumin derivatives and obtained the correlation between hydrophobicity of the compounds and suppressive effect against AhR transformation. Results from the quantitative structure active correlative analysis indicated that methoxy groups and β-diketone structure possessing keto-enol tautomerism in curcumin were necessary to inhibit AhR transformation, and the addition of methyl and methoxy group(s) to the curcumin increased the inhibition effect.

Amino acid sequence of the ligand-binding domain of the aryl hydrocarbon receptor 1 predicts sensitivity of wild birds to effects of dioxin-like compounds

The sensitivity of avian species to the toxic effects of dioxin-like compounds (DLCs) varies up to 1000-fold among species, and this variability has been associated with interspecies differences in aryl hydrocarbon receptor 1 ligand-binding domain (AHR1 LBD) sequence. We previously showed that LD(50) values, based on in ovo exposures to DLCs, were significantly correlated with in vitro EC(50) values obtained with a luciferase reporter gene (LRG) assay that measures AHR1-mediated induction of cytochrome P4501A in COS-7 cells transfected with avian AHR1 constructs. Those findings suggest that the AHR1 LBD sequence and the LRG assay can be used to predict avian species sensitivity to DLCs. In the present study, the AHR1 LBD sequences of 86 avian species were studied, and differences at amino acid sites 256, 257, 297, 324, 337, and 380 were identified. Site-directed mutagenesis, the LRG assay, and homology modeling highlighted the importance of each amino acid site in AHR1 sensitivity to 2,3,7,8-tetrachlorodibenzo-p-dioxin and other DLCs. The results of the study revealed that (1) only amino acids at sites 324 and 380 affect the sensitivity of AHR1 expression constructs of the 86 avian species to DLCs and (2) in vitro luciferase activity of AHR1 constructs containing only the LBD of the species of interest is significantly correlated (r (2) = 0.93, p < 0.0001) with in ovo toxicity data for those species. These results indicate promise for the use of AHR1 LBD amino acid sequences independently, or combined with the LRG assay, to predict avian species sensitivity to DLCs.

New aryl hydrocarbon receptor homology model targeted to improve docking reliability

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-ARNT-Sim (PAS) containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). As no experimentally determined structures of the AhR ligand binding domain (LBD) are available and previous homology models were only derived from apo template structures, we developed a new model based on holo X-ray structures of the hypoxia-inducible factor 2α (HIF-2α) PAS B domain, targeted to improve the accuracy of the binding site for molecular docking applications. We experimentally confirmed the ability of two HIF-2α crystallographic ligands to bind to the mAhR with relatively high affinity and demonstrated that they are AhR agonists, thus justifying the use of the holo HIF-2α structures as templates. A specific modeling/docking approach was proposed to predict the binding modes of AhR ligands in the modeled LBD. It was validated by comparison of the calculated and the experimental binding affinities of active THS ligands and TCDD for the mAhR and by functional activity analysis using several mAhR mutants generated on the basis of the modeling results. Finally the ability of the proposed approach to reproduce the different affinities of TCDD for AhRs of different species was confirmed, and a first test of its reliability in virtual screening is carried out by analyzing the correlation between the calculated and experimental binding affinities of a set of 14 PCDDs.