Structural-functional adaptations of porcine CYP1A1 to metabolize polychlorinated dibenzo-p-dioxins.

Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity. They accumulate in tissues of animals and humans, exerting numerous adverse effects on different systems. In living organisms, dioxins are metabolized by enzymes of the cytochrome P450 family, including CYP1A1. Particular dioxin congeners differ in their toxicity level and ability to undergo biodegradation. Since the molecular mechanisms underlying dioxin susceptibility or resistance to biodegradation are unknown, in the present study the molecular interactions between five selected dioxins and porcine CYP1A1 protein were investigated. It was found that the ability of a dioxin to undergo CYP1A1-mediated degradation is associated mainly with the number and position of chlorine atoms in the dioxin molecule. Among all examined congeners, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) demonstrated the highest affinity to CYP1A1 and, at the same time, the greatest distance to the active site of the enzyme. Interestingly, in contrast to other dioxins, the binding of the TCDD molecule to the porcine CYP1A1 active site resulted in a rapid and continuous closure of substrate channels. All the information may help to explain the extended half-life of TCDD in living organisms as well as its high toxicity.

[1]  Jouni T. Tuomisto,et al.  Synopsis on dioxins and PCBs , 1999 .

[2]  K. Inouye,et al.  Metabolic pathways of dioxin by CYP1A1: species difference between rat and human CYP1A subfamily in the metabolism of dioxins. , 2003, Archives of biochemistry and biophysics.

[3]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[4]  R. Ferriani,et al.  Increased expression of CYP1A1 and CYP1B1 in ovarian/peritoneal endometriotic lesions. , 2016, Reproduction.

[5]  Wei Zhang,et al.  A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..

[6]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[7]  A. Baccarelli,et al.  TCDD-mediated alterations in the AhR-dependent pathway in Seveso, Italy, 20 years after the accident. , 2003, Carcinogenesis.

[8]  Sason Shaik,et al.  Molecular Dynamics and QM/MM Calculations Predict the Substrate-Induced Gating of Cytochrome P450 BM3 and the Regio- and Stereoselectivity of Fatty Acid Hydroxylation. , 2016, Journal of the American Chemical Society.

[9]  M. Häggblom,et al.  Anaerobic reductive dechlorination of 1,2,3,4-tetrachlorodibenzofuran in polychlorinated dibenzo-p-dioxin- and dibenzofuran-contaminated sediments of the Kymijoki River, Finland. , 2014, Chemosphere.

[10]  T. Shimada,et al.  Docking and QSAR comparative studies of polycyclic aromatic hydrocarbons and other procarcinogen interactions with cytochromes P450 1A1 and 1B1 , 2012, SAR and QSAR in environmental research.

[11]  Sandor Vajda,et al.  Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs. , 2007, Biochemistry.

[12]  Thomas E. Cheatham,et al.  Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle , 2012, J. Comput. Chem..

[13]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[14]  Bin Zhao,et al.  Exactly the same but different: promiscuity and diversity in the molecular mechanisms of action of the aryl hydrocarbon (dioxin) receptor. , 2011, Toxicological sciences : an official journal of the Society of Toxicology.

[15]  G. Szklarz,et al.  Human Cytochrome P450 1A1 Structure and Utility in Understanding Drug and Xenobiotic Metabolism* , 2013, The Journal of Biological Chemistry.

[16]  Paolo Brambilla,et al.  Dioxin Exposure, from Infancy through Puberty, Produces Endocrine Disruption and Affects Human Semen Quality , 2007, Environmental health perspectives.

[17]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[18]  Wim F Vranken,et al.  ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.

[19]  N. Bunce,et al.  Metabolism of polychlorinated dibenzo‐p‐dioxins by rat liver microsomes , 1999, Journal of biochemical and molecular toxicology.

[20]  V. Vijaya Padma,et al.  Protective effect of ellagic acid against TCDD-induced renal oxidative stress: Modulation of CYP1A1 activity and antioxidant defense mechanisms , 2014, Molecular Biology Reports.

[21]  D. J. Price,et al.  A modified TIP3P water potential for simulation with Ewald summation. , 2004, The Journal of chemical physics.

[22]  D. Pompon,et al.  Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes. , 2015, Biochimica et biophysica acta.

[23]  G. Perdew,et al.  Aryl hydrocarbon receptor ligands in cancer: friend and foe , 2014, Nature Reviews Cancer.

[24]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[25]  P. Gervasi,et al.  Expression and inducibility of CYP1A1, 1A2, 1B1 by β-naphthoflavone and CYP2B22, CYP3As by rifampicin in heart regions and coronary arteries of pig. , 2013, Research in veterinary science.

[26]  Jaime Pascual,et al.  Conformational adaptation of human cytochrome P450 2B6 and rabbit cytochrome P450 2B4 revealed upon binding multiple amlodipine molecules. , 2012, Biochemistry.

[27]  Y. Fujii‐Kuriyama,et al.  Functional role of AhR in the expression of toxic effects by TCDD. , 2003, Biochimica et biophysica acta.

[28]  M. DeVito,et al.  Inhibition of human and rat CYP1A2 by TCDD and dioxin-like chemicals. , 2005, Toxicological sciences : an official journal of the Society of Toxicology.

[29]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[30]  Rebecca C Wade,et al.  Conformational diversity and ligand tunnels of mammalian cytochrome P450s , 2013, Biotechnology and applied biochemistry.

[31]  Feixiong Cheng,et al.  Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations , 2012, PloS one.

[32]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[33]  Weihua Li,et al.  Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations , 2011, Proteins.

[34]  A. Mulholland,et al.  Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2. , 2016, Chemical research in toxicology.

[35]  G J Kleywegt,et al.  Detection, delineation, measurement and display of cavities in macromolecular structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[36]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[37]  N. Walker,et al.  TCDD and omeprazole prime platelets through the aryl hydrocarbon receptor (AhR) non-genomic pathway. , 2015, Toxicology letters.

[38]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[39]  Manfred J. Sippl,et al.  Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..

[40]  W. Yeung,et al.  2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) suppresses spheroids attachment on endometrial epithelial cells through the down-regulation of the Wnt-signaling pathway. , 2012, Reproductive toxicology.

[41]  C. Hadad,et al.  Oxidative dehalogenation of perhalogenated benzenes by cytochrome P450 compound I. , 2007, Biochemistry.

[42]  J. Damborský,et al.  Gates of Enzymes , 2013, Chemical reviews.

[43]  T. Klonisch,et al.  Dioxin exerts anti-estrogenic actions in a novel dioxin-responsive telomerase-immortalized epithelial cell line of the porcine oviduct (TERT-OPEC). , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[44]  Weiliang Zhu,et al.  Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development , 2014, J. Chem. Inf. Model..

[45]  C. Tohyama,et al.  The 2005 World Health Organization reevaluation of human and Mammalian toxic equivalency factors for dioxins and dioxin-like compounds. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[46]  A. Weston,et al.  Correlation between CYP1A1 transcript, protein level, enzyme activity and DNA adduct formation in normal human mammary epithelial cell strains exposed to benzo[a]pyrene. , 2014, Mutagenesis.

[47]  D. Nebert,et al.  Role of the aromatic hydrocarbon receptor and [Ah] gene battery in the oxidative stress response, cell cycle control, and apoptosis. , 2000, Biochemical pharmacology.

[48]  Sequential metabolism of 2,3,7-trichlorodibenzo-p-dioxin (2,3,7-triCDD) by cytochrome P450 and UDP-glucuronosyltransferase in human liver microsomes. , 2004, Drug metabolism and disposition: the biological fate of chemicals.

[49]  B. Wąsowska,et al.  2,3,7,8-Tetrachlorodibenzo-p-dioxin alters steroid secretion but does not affect cell viability and the incidence of apoptosis in porcine luteinised granulosa cells. , 2014, Acta veterinaria Hungarica.

[50]  Eric F. Johnson,et al.  Structural Characterization of the Complex between α-Naphthoflavone and Human Cytochrome P450 1B1* , 2010, The Journal of Biological Chemistry.

[51]  Rajendra Kumar,et al.  g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations , 2014, J. Chem. Inf. Model..

[52]  O. Pelkonen,et al.  Significant interspecies differences in induction profiles of hepatic CYP enzymes by TCDD in bank and field voles , 2012, Environmental toxicology and chemistry.

[53]  Jürgen Pleiss,et al.  Multiple molecular dynamics simulations of human p450 monooxygenase CYP2C9: The molecular basis of substrate binding and regioselectivity toward warfarin , 2006, Proteins.

[54]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[55]  W. Choi,et al.  Understanding the congener-specific toxicity in polychlorinated dibenzo-p-dioxins: chlorination pattern and molecular quadrupole moment. , 2002, Journal of the American Chemical Society.

[56]  F. Casey,et al.  Fate and transport of 1278-TCDD, 1378-TCDD, and 1478-TCDD in soil-water systems. , 2006, The Science of the total environment.

[57]  K. Inouye,et al.  Biodegradation of polychlorinated dibenzo-p-dioxins by recombinant yeast expressing rat CYP1A subfamily. , 2002, Archives of biochemistry and biophysics.

[58]  J. Sridhar,et al.  In silico studies of polyaromatic hydrocarbon inhibitors of cytochrome P450 enzymes 1A1, 1A2, 2A6, and 2B1. , 2010, Chemical research in toxicology.

[59]  Karel Berka,et al.  Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site , 2011, The journal of physical chemistry. A.

[60]  Antonín Pavelka,et al.  CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures , 2012, PLoS Comput. Biol..

[61]  Ryan G. Coleman,et al.  ZINC: A Free Tool to Discover Chemistry for Biology , 2012, J. Chem. Inf. Model..

[62]  R. Rice,et al.  Common Commercial and Consumer Products Contain Activators of the Aryl Hydrocarbon (Dioxin) Receptor , 2013, PloS one.

[63]  F. Song,et al.  A new method for identification of in vitro metabolites of 2,3,7,8-TCDD with rat liver microsomes by using liquid chromatography-mass spectrometry , 2013 .

[64]  K. Inouye,et al.  Metabolism of polychlorinated dibenzo-p-dioxins (PCDDs) by human cytochrome P450-dependent monooxygenase systems. , 2002, Journal of agricultural and food chemistry.

[65]  C David Stout,et al.  Adaptations for the Oxidation of Polycyclic Aromatic Hydrocarbons Exhibited by the Structure of Human P450 1A2*♦ , 2007, Journal of Biological Chemistry.

[66]  Rebecca C Wade,et al.  The ins and outs of cytochrome P450s. , 2007, Biochimica et biophysica acta.

[67]  M. Sippl Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[68]  M. van den Berg,et al.  In vitro neuroendocrine effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in the AhR-expressing hypothalamic rat GnV-3 cell line. , 2013, Toxicology.

[69]  Annalisa Bordogna,et al.  New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability , 2011, J. Chem. Inf. Model..