Homology modelling and molecular dynamics study of human fatty acid amide hydrolase

Molecular Simulation

Volumn 35, Issue 14, 2009, Pages 1201-1208

  Zhao, Yong Shan ^a   Zheng, Qing Chuan ^a   Zhang, Hong Xing ^a   Chu, Hui Ying ^a   Sun, Chia Chung ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

Docking; Fatty acid amide hydrolase; Homology modelling

Indexed keywords

ACTIVE SITE; FATTY ACID AMIDE HYDROLASE; HOMOLOGY MODELLING; MOLECULAR DYNAMICS METHODS; PROPOFOL; REFINED MODEL; STRUCTURAL ANALOGUE; THREE-DIMENSIONAL (3D) MODEL; VAN DER WAAL INTERACTIONS;

ACIDS; AMIDES; CRYSTAL STRUCTURE; DOCKING; FATTY ACIDS; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PHENOLS; SUBSTRATES;

THREE DIMENSIONAL;

EID: 70449091934     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020903033133     Document Type: Article

References (53)

1. B.F. Cravatt, D.K. Giang, S.P. Mayfield, D.L. Boger, R.A. Lerner, and N.B. Gilula, Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides, Nature 384 (1996), pp. 83-87.
2. D.K. Giang and B.F. Cravatt, Molecular characterization of human and mouse fatty acid amide hydrolases, Proc. Natl Acad. Sci. USA 4 (1997), pp. 2238-2242.
3. H. Chebrou, F. Bigey, A. Arnaud, and P. Galzy, Study of the amidase signature group, Biochim. Biophys. Acta 1298 (1996), pp. 285-293.
4. W.A. Devane, L. Hanus, A. Breuer, R.G. Pertwee, L.A. Stevenson, G. Griffin, D. Gibson, A. Mandelbaum, A. Etinger, and R. Mechoulam, Isolation and structure of a brain constituent that binds to the cannabinoid receptor, Science 258 (1992), pp. 1946- 1949.
5. B.R. Martin, R. Mechoulam, and R.K. Razdan, Discovery and characterization of endogenous cannabinoids, Life Sci. 65 (1999), pp. 573-595.
6. V. Di Marzo, T. Bisogno, L. De Petrocellis, D. Melck, and B.R. Martin, Cannabimimetic fatty acid derivatives: the anandamide family and other 'Endocannabinoids', Curr. Med. Chem. 6 (1999), pp. 721-744.
7. H.H. Schmid, P.C. Schmid, and V. Natarajan, N-acylated glycerophospholipids and their derivatives, Prog. Lipid. Res. 29 (1990), pp. 41-43.
8. D.L. Boger, S.J. Henriksen, and B.F. Cravatt, Oleamide: an endogenoussleep-inducing lipid and prototypical member of a new class of lipid signaling molecules, Curr. Pharm. Des. 4 (1998), pp. 303-314.
9. B.F. Cravatt, R.A. Lerner, and D.L. Boger, Structure determination of an endogenous sleep-inducing lipid cis-9-octadecenamide (Oleamide): a synthetic approach to the chemical analysis of trace quantities of a natural product, J. Am. Chem. Soc. 118 (1996), pp. 580-590.
10. B.F. Cravatt, O. Prospero-Garcia, G. Suizdak, N.B. Gilula, S.J. Henriksen, D.L. Boger, and R.A. Lerner, Chemical characterization of a family of brain lipids that induce sleep, Science 268 (1995), pp. 1506-1509.
11. D.M. Lambert, S. Vandevoorde, K.O. Jonsson, and C.J. Fowler, The palmitoylethanolamide family: a new class of antiinflammatory agents? Curr. Med. Chem. 9 (2002), pp. 663-674.
12. F. Rodríguez de Fonseca, M. Navarro, R. Gómez, L. Escuredo, F. Nava, J. Fu, E. Murillo-Rodríguez, A. Giuffrida, J. LoVerme, S. Gaetani, S. Kathuria, C. Gall, and D. Piomelli, An anorexic lipid mediator regulated by feeding, Nature 414 (2001), pp. 209-212.
13. B.F. Cravatt, K. Demarest, M.P. Patricelli, M.H. Bracey, D.K. Giang, B.R. Martin, and A.H. Lichtman, Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase, Proc. Natl Acad. Sci. USA 98 (2001), pp. 9371-9376.
14. A.H. Lichtman, C.C. Shelton, T. Advani, and B.F. Cravatt, Mice lacking fatty acid amide hydrolase exhibit a cannabinoid receptormediated phenotypic hypoalgesia, Pain 109 (2004), pp. 319-327.
15. B.F. Cravatt, A. Saghatelian, E.G. Hawkins, A.B. Clement, M.H. Bracey, and A.H. Lichtman, Functional disassociation of the central and peripheral fatty acid amide signaling systems, Proc. Natl Acad. Sci. USA 101 (2004), pp. 10821-10826.
16. M. Karsak, E. Gaffal, R. Date, L. Wang-Eckhardt, J. Rehnelt, S. Petrosino, K. Starowicz, R. Steuder, E. Schlicker, B.F. Cravatt, R. Mechoulam, R. Buettner, S. Werner, V. Di Marzo, T. Tüting, and A. Zimmer, Attenuation of allergic contact dermatitis through the endocannabinoid system, Science 316 (2007), pp. 1494-1497.
17. S. Huitroń-Reseńdiz, L. Gombart, B.F. Cravatt, and S.J. Henriksen, Effect of oleamide on sleep and its relationship to blood pressure, body temperature, and locomotor activity in rats, Exp. Neurol. 172 (2001), pp. 235-243.
18. S. Huitroń-Reseńdiz, M. Sanchez-Alavez, D.N. Wills, B.F. Cravatt, S.J. Henriksen, Characterization of the sleep-wake patterns in mice lacking fatty acid amide hydrolase, Sleep 27 (2004), pp. 857-865.
19. D. Leung, C. Hardouin, D.L. Boger, and B.F. Cravatt, Discovering potent and selective reversible inhibitors of enzymes in complex proteomes, Nat. Biotechnol. 21 (2003), pp. 687-691.
20. D.L. Boger, S. Haruhiko, E.L. Aaron, P.H. Michael, A.F. Robert, M. Hiroshi, D.W. Gordon, J.A. Bryce, P.P. Matthew, and F.C. Benjamin, Exceptionally potent inhibitors of fatty acid amide hydrolase: the enzyme responsible for degradation of endogenous oleamide and anandamide, Proc. Natl Acad. Sci. USA 97 (2000), pp. 5044-5049.
21. K. Ahn, D.S. Johnson, L.R. Fitzgerald, M. Liimatta, A. Arendsen, T. Stevenson, E.T. Lund, R.A. Nugent, T.K. Nomanbhoy, J.P. Alexander, and B.F. Cravatt, Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity, Biochemistry 46 (2007), pp. 13019-13030.
22. M. Mileni, D.S. Johnson, Z. Wang, D.S. Everdeen, M. Liimatta, B. Pabst, K. Bhattacharya, R.A. Nugent, S. Kamtekar, B.F. Cravatt, K. Ahn, and R.C. Stevens, Structrue-guided inhibitor design for human FAAH by interspecies active site conversion, Proc. Natl Acad. Sci. USA 105 (2008), pp. 12820-12824.
23. Q.C. Zheng, Z.S. Li, M. Sun, Y. Zhang, and C.C. Sun, Homology modeling and substrate binding study of nudix hydrolase Ndx1 from thermos thermophilus HB8, Biochem. Biophys. Res. Commun. 333 (2005), pp. 881-887.
24. W. Xu, P. Cai, M. Yan, L. Xu, and P.K. Ouyang, Molecular docking of xylitol and xylose isomerase from thermus thermophilus and model analysis, Chem. J. Chinese Universities 28 (2007), pp. 971-973.
25. Y.P. He, H.R. Hu, and L.S. Xu, Structure-activity relationship studies on 6-naphthylmethyl substituted HEPT derivatives as nonnucleoside reverse transcriptase inhibitors based on molecular docking, Chem. J. Chinese Universities 26 (2005), pp. 254-258.
26. M.H. Bracey, M.A. Hanson, K.R. Masuda, R.C. Stevens, and B.F. Cravatt, Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling, Science 298 (2002), pp. 1793-1796.
27. A. Bairoch and R. Apweiler, The SWISS-PORT protein sequence data bank and its supplement TrEMBL, Nucl. Acids Res. 25 (1997), pp. 31-36.
28. S.F. Altschul, T.L. Madden, A.A. Schfer, J.Z. Zhang, W. Miller, and D.J. Lipman, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucl. Acid. Res. 25 (1997), pp. 3389-3402.
29. A. Sali and J.P. Overington, Derivation of rules for comparative protein modeling from a database of protein structure alignments, Protein Sci. 3 (1994), pp. 1582-1596.
30. A. Sali and T.L. Blundell, Comparative protein modeling by satisfaction of spatial restraints, J. Mol. Biol. 234 (1993), pp. 779-815.
31. A. Sali, L. Potterton, F. Yuan, H. Vlijmen, and M. Karplus, Evaluation of comparative protein modeling by modeller, Proteins 23 (1995), pp. 318-326.
32. A. Sali and T.L. Blundell, Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming, Curr. Opin. Biotechnol. 6 (1995), pp. 437-451.
33. D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriew, Jr, C. Simmerling, B. Wang, and R.J. Woods, The Amber bimolecular simulation programs, J. Comp. Chem. 26 (2005), pp. 1668-1688.
34. W.L. Jorgensen, J. Chandraskhar, J. Madura, and M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983), pp. 926-935.
35. J.P. Rychaert, G. Ciccotti, and H.J.C. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comp. Phys. 23 (1977), pp. 327-341.
36. Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G.M. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comp. Chem. 24 (2003), pp. 1999-2012.
37. Insight II Profile-3D User Guide, Biosym/MSI, San Diego, 2000.
38. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Cryst. 26 (1993), pp. 283-291.
39. M.J. Sippl, Recognition of errors in three-dimensional structures of proteins, Proteins 17 (1993), pp. 355-362.
40. Binding Site Analysis User Guide, Accelrys Inc., San Diego, CA, USA, 2000.
41. Insight II Affinity User Guide, San Diego, Biosym/MSI, 2000.
42. M.J.T. Frisch, G.W. Schlegel, H.B. Scuseria, G.E. Robb, M.A. Cheeseman, J.R. Montgomery, Jr, J.A. Vreven, T. Kudin, K.N. Burant, J.C. Millam, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyenger, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Peterson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, K. Kitato, N. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C.. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al- Laham, C.Y. Peng, A. Nanayakkara, M. Chellacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, and J.A. Pople, Gaussian 03, Gaussian Inc., Wallingford, CT, 2004.
43. Insight II Ludi User Guide, San Diego, Biosym/MSI, 2000.
44. D.G. Deutch, S. Lin, W.A. Hill, K.L. Morse, D. Salehani, G. Arreaza, R.L. Omeir, and A. Makriyannis, Fatty acid sulfonyl fluorides inhibit anandamide metabolism and bind to the cannabinoid receptor, Biochem. Biophys. Res. Commun. 231 (1997), pp. 217-221.
45. Y. Segall, G.B. Quistad, D.K. Nomura, and J.E. Casida, Arachidonylsulfonyl derivatives as cannabinoid CB1 receptor and fatty acid amide hydrolase inhibitors, Bioorg. Med. Chem. Lett. 13 (2003), pp. 3301-3303.
46. D.G. Deutch, R. Omeir, G. Arreaza, D. Salehani, G.D. Prestwich, Z. Huang, and A. Howlett, Methyl arachidonyl fluorophosphonate: a potent irreversible inhibitor of anandamide amidase, Biochem. Pharmacol. 53 (1997), pp. 255-260.
47. B. Koutek, G.D. Prestwich, A.C. Howlett, S.A. Chin, D. Salehani, N. Akhavan, and D.G. Deutch, Inhibitors of arachidonoyl ethanolamide hydrolysis, J. Biol. Chem. 269 (1994), pp. 22937- 22940.
48. L. De Petrocellis, D. Melck, N. Ueda, S. Maurelli, Y. Kurahashi, S. Yamamoto, G. Marino, and V. Di Marzo, Novel inhibitors of brain, neuronal, and basophilic anandamide amidohydrolase, Biochem. Biophys. Res. Commun. 231 (1997), pp. 82-88.
49. A.H. Lichtman, D. Leung, C. Shelton, A. Saghatelian, C. Hardouin, D.L. Boger, and B.F. Cravatt, Reversible inhibitors of fatty acid amide hydrolase that promote analgesia: evidence for an unprecented combination of potency and selectivity, J. Pharmacol. Exp. Ther. 311 (2004), pp. 441-448.
50. M.J. Myllymäki, S.M. Saario, A.O. Kataja, J.A. Castillo-Melendez, T. Nevalainen, R.O. Juvonen, T. Järvinen, and A.M.P. Koskinen, Design, synthesis, and in vitro evaluation of carbamate erivatives of 2-benzoxazolyl- and 2-benzothiazolyl-(3-hydroxyphenyl)-methanones as novel fatty acid amide hydrolase inhibitors, J. Med. Chem. 50 (2007), pp. 4236-4242.
51. S.-Y. Sit and K. Xie, WO Patent 087569, 2002.
52. S. Patel, E.R. Wohlfeil, D.J. Rademacher, E.J. Carrier, L.J. Perry, A. Kundu, J.R. Falck, K. Nithipatikom, W.B. Campbell, and C.J. Hillard, The general anesthetic propofol increases brain N-arachidonylethanolamine (anandamide) content and inhibits fatty acid amide hydrolase, Br. J. Pharmacol. 139 (2003), pp. 1005- 1013.
53. M. Seierstad and J.G. Breitenbucher, Discovery and development of fatty acid amide hydrolase (FAAH) inhibitors, J. Med. Chem. 51 (2008), pp. 7327-7343.