Homology models of human all-trans retinoic acid metabolizing enzymes CYP26B1 and CYP26B1 spliced variant

Journal of Chemical Information and Modeling

Volumn 52, Issue 10, 2012, Pages 2631-2637

  Saenz Méndez, Patricia ^a   Elmabsout, Ali Ateia ^b   Sävenstrand, Helena ^b   Awadalla, Mohamed Khalid Alhaj ^b   Strid, Åke ^b   Sirsjö, Allan ^b   Eriksson, Leif A ^c  

^a UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

^b ÖREBRO UNIVERSITY   (Sweden)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES;

ALL-TRANS RETINOIC ACIDS; BLOCKING AGENTS; CYTOCHROME P450; FULL-LENGTH ENZYMES; HOMOLOGY MODELING; HOMOLOGY MODELS; NATURAL SUBSTRATES; POTENT INHIBITOR;

CRYSTAL STRUCTURE;

BACTERIAL PROTEIN; BENZOTHIAZOLE DERIVATIVE; CYP120A1 PROTEIN, SYNECHOCYSTIS; CYTOCHROME P450; ENZYME INHIBITOR; ISOENZYME; RETINOIC ACID; RETINOIC ACID 4 HYDROXYLASE; RETINOIC ACID 4-HYDROXYLASE; TALAROZOLE; TETRALIN DERIVATIVE; TRIAZOLE DERIVATIVE;

ALTERNATIVE RNA SPLICING; ARTICLE; CHEMISTRY; ENZYMOLOGY; HUMAN; MOLECULAR DOCKING; STRUCTURAL HOMOLOGY; SYNECHOCYSTIS; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ALTERNATIVE SPLICING; BACTERIAL PROTEINS; BENZOTHIAZOLES; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME P-450 ENZYME SYSTEM; ENZYME INHIBITORS; HUMANS; ISOENZYMES; MOLECULAR DOCKING SIMULATION; STRUCTURAL HOMOLOGY, PROTEIN; SYNECHOCYSTIS; TETRALONES; THERMODYNAMICS; TRETINOIN; TRIAZOLES;

EID: 84867825861     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300264u     Document Type: Article

References (43)

1. Balmer, J. E.; Blomhoff, R. Gene expression regulation by retinoic acid J. Lipid Res. 2002, 43, 1773-1808
2. Ross, A. C.; Zolfaghari, R.; Weisz, J. Vitamin A: recent advances in the biotransformation, transport, and metabolism of retinoids Curr. Opin. Gastroenterol. 2001, 17, 184-192
3. Blomhoff, R.; Blomhoff, H. K. Overview of retinoid metabolism and function J. Neurobiol. 2006, 66, 606-630
4. Zhao, Q.; Dobbs-Mc; E., L. Expression of CYP26B1 during zebrafish early development Gene Expression Patterns 2005, 5, 363-369
5. Reijntjes, S.; Gale, E. Expression of the retinoic acid catabolising enzyme CYP26B1 in the chick embryo and its regulation by retinoic acid Gene Expression Patterns 2003, 3, 621-627
6. Ray, W. J.; Bain, G.; Yao, M.; Gottlieb, D. I. CYP26, a novel mammalian cytochrome P450, is induced by retinoic acid and defines a new family J. Biol. Chem. 1997, 272, 18702-18708
7. McSorley, L. C.; Daly, A. K. Identification of human cytochrome P450 isoforms that contribute to all-trans-retinoic acid 4-hydroxylation Biochem. Pharmacol. 2000, 60, 517-526
8. Marill, J.; Cresteil, T.; Lanotte, M.; Chabot, G. G. Identification of human cytochrome P450s involved in the formation of all-trans-retinoic acid principal metabolites Mol. Pharmacol. 2000, 58, 1341-1348
9. White, J. A.; Beckett-Jones, B.; Guo, Y. D.; Dilworth, F. J.; Bonasoro, J.; Jones, G.; Petkovich, M. cDNA cloning of human retinoic acid-metabolizing enzyme (hP450RAI) identifies a novel family of cytochromes P450 J. Biol. Chem. 1997, 272, 18538-18541
10. Pavez Lorié, E.; Li, H.; Vahlquist, A.; Törmä, H. The involvement of cytochrome P450 (CYP) 26 in the retinoic acid metabolism of human epidermal keratinocytes Biochim. Biophys. Acta 2009, 1791, 220-228
11. Fujii, H.; Sato, T.; Kaneko, S.; Gotoh, O.; Fujii-Kuriyama, Y.; Osawa, K.; Kato, S.; Hamada, H. Metabolic inactivation of retinoic acid by a novel P450 differentially expressed in developing mouse embryos EMBO J. 1997, 16, 4163-4173
12. Zolfaghari, R.; Cifelli, C. J.; Lieu, S. O.; Chen, Q.; Li, N.-q.; Ross, A. C. Lipopolysaccharide opposes the induction of CYP26A1 and CYP26B1 gene expression by retinoic acid in the rat liver in vivo Am. J. Physiol. Gastrointest. Liver Physiol. 2007, 292, G1029-G1036
13. Mac Lean, G.; Abu-Abed Cloning of a novel retinoic-acid metabolizing cytochrome P450, Cyp26B1, and comparative expression analysis with Cyp26A1 during early murine development Mech. Dev. 2001, 107, 195-201
14. Topletz, A. R.; Thatcher, J. E.; Zelter, A.; Lutz, J. D.; Tay, S.; Nelson, W. L.; Isoherranen, N. Comparison of the function and expression of CYP26A1 and CYP26B1, the two retinoic acid hydroxylases Biochem. Pharmacol. 2012, 83, 149-163
15. Taimi, M.; Helvig, C.; Wisniewski, J.; Ramshaw, H.; White, J.; Amad, M.; Korczak, B.; Petkovich, M. A novel human cytochrome P450, CYP26C1, involved in metabolism of 9-cis and all-trans isomers of retinoic acid J. Biol. Chem. 2004, 279, 77-85
16. Gallagher, R. E. Retinoic acid resistance in acute promyelocytic leukemia Leukemia 2002, 16, 1940-1958
17. Vanwauwe, J. P.; Coene, M. C.; Goossens, J.; Cools, W.; Monbaliu, J. Effects of cytochrome P-450 inhibitors on the in vivo metabolism of all-trans-retinoic acid in rats J. Pharmacol. Exp. Ther. 1990, 252, 365-369
18. Kizaki, M.; Ueno, H.; Yamazoe, Y.; Shimada, M.; Takayama, N.; Muto, A.; Matsushita, H.; Nakajima, H.; Morikawa, M.; Koeffler, H. P.; Ikeda, Y. Mechanisms of retinoid resistance in leukemic cells: possible role of cytochrome P450 and P-glycoprotein Blood 1996, 87, 725-733
19. Osanai, M.; Petkovich, M. Expression of the retinoic acid-metabolizing enzyme CYP26A1 limits programmed cell death Mol. Pharmacol. 2005, 67, 1808-1817
20. Soppie, P.; Borgers, M.; Borghgraef, P.; Dillen, L.; Goossens, J.; Sanz, J.; Szel, H.; van Hove, C.; van Nyen, G.; Nobels, G.; Vanden Bossche, H.; Venet, M.; Willemsens, G.; Van Wauwe, J. P. R115866 inhibits all-trans-retinoic acid metabolism and exerts retinoidal effects in rodents J. Pharmacol. Exp. Ther. 2000, 293, 304-312
21. Yamamoto, Y.; Zolfaghari, R.; Ross, A. C. Regulation of CYP26 (cytochrome P450RAI) mRNA expression and retinoic acid metabolism by retinoids and dietary vitamin A in liver of mice and rats FASEB J. 2000, 14, 2119-2127
22. Nelson, D. R. A Second CYP26 P450 in Humans and Zebrafish: CYP26B1 Arch. Biochem. Biophys. 1999, 371, 345-347
23. Ateia Elmabsout, A.; Kumawat, A.; Saenz-Méndez, P.; Krivospitskaya, O.; Sävenstrand, H.; Olofsson, P. S.; Eriksson, L. A.; Strid, Å.; Valen, G.; Törmä, H.; Sirsjö, A. Cloning and Functional Studies of a Splice Variant of CYP26B1 Expressed in Vascular Cells PLoS ONE 2012, 7, e36839
24. Krieger, E.; Nabuurs, S. B.; Vriend, G. Homology Modeling. In Structural Bioinformatics; Bourne, P. E.; Weissig, H., Eds.; Wiley-Liss, Inc.: Hoboken, NJ, 2003; Vol. 44, pp 507-521.
25. Gomaa, M. S.; Yee, S. W.; Milbourne, C. E.; Barbera, M. C.; Simons, C.; Brancale, A. Homology model of human retinoic acid metabolising enzyme cytochrome P450 26A1 (CYP26A1): Active site architecture and ligand binding J. Enzyme Inhib. Med. Chem. 2006, 21, 361-369
26. Karlsson, M.; Strid, Å.; Sirsjö, A.; Eriksson, L. A. Homology Models and Molecular Modeling of Human Retinoic Acid Metabolizing Enzymes Cytochrome P450 26A1 (CYP26A1) and P450 26B1 (CYP26B1) J. Chem. Theory Comput. 2008, 4, 1021-1027
27. Krieger, E. Yet Another Scientific Artificial Reality Application (YASARA), 2004.
28. Krieger, E.; Joo, K.; Lee, J.; Lee, J.; Raman, S.; Thompson, J.; Tyka, M.; Baker, D.; Karplus, K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 Proteins 2009, 77, 114-122
29. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
30. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103, 8577-8593
31. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997, 25, 3389-3402
32. Kühnel, K.; Ke, N.; Cryle, M. J.; Sligar, S. G.; Schuler, M. A.; Schlichting, I. Crystal Structures of Substrate-Free and Retinoic Acid-Bound Cyanobacterial Cytochrome P450 CYP120A1 Biochemistry 2008, 47, 6552-6559
33. Surendhar Reddy, C.; Vijayasarathy, K.; Srinivas, E.; Madhavi Sastry, G.; Narahari Sastry, G. Homology modeling of membrane proteins: A critical assessment Comput. Biol. Chem. 2006, 30, 120-126
34. Xiang, Z. Advances in Homology Protein Structure Modeling Curr. Protein Pept. Sci. 2006, 7, 217-227
35. Kirton, S. B.; Baxter, C. A.; Sutcliffe, M. J. Comparative modeling of cytochromes P450 Adv. Drug Delivery Rev. 2002, 54, 385-406
36. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK-a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 1993, 26, 283-291
37. Bowie, J. U.; Lüthy, R.; Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure Science 1991, 253, 164-170
38. RAMPAGE server: http://mordred.bioc.cam.ac.uk/∼rapper/rampage.php.
39. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
40. Pontius, J.; Richelle, J.; Wodak, S. J. Deviations from Standard Atomic Volumes as a Quality Measure for Protein Crystal Structures J. Mol. Biol. 1996, 264, 121-136
41. Bujnicki, J.; Rychlewski, L.; Fischer, D. Fold-recognition detects an error in the Protein Data Bank Bioinf. Discovery 2002, 18, 1391-1395
42. Yee, S. W.; Jarno, L.; Gomaa, M. S.; Elford, C.; Ooi, L. L.; Coogan, M. P.; McClelland, R.; Nicholson, R. I.; Evans, B. A. J.; Brancale, A.; Simons, C. Novel tetralone-derived retinoic acid metabolism blocking agents: Synthesis and in vitro evaluation with liver microsomal and MCF-7 CYP26A1 cell assays J. Med. Chem. 2005, 48, 7123-7131
43. White, J. A.; Ramshaw, H.; Taimi, M.; Stangle, W.; Zhang, A.; Everingham, S.; Creighton, S.; Tam, S.-P.; Jones, G.; Petkovich, M. Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6403-6408