title: Homo-timeric structural model of human microsomal prostaglandin E synthase-1 and characterization of its substrate/inhibitor binding interactions.
abstract: Inducible, microsomal prostaglandin E synthase 1 (mPGES-1), the terminal enzyme in the prostaglandin (PG) biosynthetic pathway, constitutes a promising therapeutic target for the development of new anti-inflammatory drugs. To elucidate structure-function relationships and to enable structure-based design, an mPGES-1 homology model was developed using the three-dimensional structure of the closest homologue of the MAPEG family (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism), mGST-1. The ensuing model of mPGES-1 is a homo-trimer, with each monomer consisting of four membrane-spanning segments. Extensive structure refinement revealed an inter-monomer salt bridge (K26-E77) as well as inter-helical interactions within each monomer, including polar hydrogen bonds (e.g. T78-R110-T129) and hydrophobic pi-stacking (F82-F103-F106), all contributing to the overall stability of the homo-trimer of mPGES-1. Catalytic co-factor glutathione (GSH) was docked into the mPGES-1 model by flexible optimization of both the ligand and the protein conformations, starting from the initial location ascertained from the mGST-1 structure. Possible binding site for the substrate, prostaglandin H(2) (PGH(2)), was identified by systematically probing the refined molecular structure of mPGES-1. A binding model was generated by induced fit docking of PGH(2) in the presence of GSH. The homology model prescribes three potential inhibitor binding sites per mPGES-1 trimer. This was further confirmed experimentally by equilibrium dialysis study which generated a binding stoichiometric ratio of approximately three inhibitor molecules to three mPGES-1 monomers. The structural model that we have derived could serve as a useful tool for structure-guided design of inhibitors for this emergently important therapeutic target.
authors.affiliation: Department of Structural and Computational Chemistry, St. Louis Laboratories, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. li.xing@pfizer.com
authors.forename: Li
authors.initials: L
authors.lastname: Xing
authors.forename: Ravi G
authors.initials: RG
authors.lastname: Kurumbail
authors.forename: Ronald B
authors.initials: RB
authors.lastname: Frazier
authors.forename: Michael S
authors.initials: MS
authors.lastname: Davies
authors.forename: Hideji
authors.initials: H
authors.lastname: Fujiwara
authors.forename: Robin A
authors.initials: RA
authors.lastname: Weinberg
authors.forename: James K
authors.initials: JK
authors.lastname: Gierse
authors.forename: Nicole
authors.initials: N
authors.lastname: Caspers
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Carter
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: McDonald
authors.forename: William M
authors.initials: WM
authors.lastname: Moore
authors.forename: Michael L
authors.initials: ML
authors.lastname: Vazquez
mesh_terms: D000595:Amino Acid Sequence; D001704:Biopolymers; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006801:Humans; D019746:Intramolecular Oxidoreductases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D008861:Microsomes / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D000071876:Prostaglandin-E Synthases; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D001704:Biopolymers; D004791:Enzyme Inhibitors; D019746:Intramolecular Oxidoreductases; C000605862:PTGES protein, human; D000071876:Prostaglandin-E Synthases
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11790-5
references.pmid: 16864802
references.citation: J Biol Chem. 2003 Jun 20;278(25):22199-209
references.pmid: 12672824
references.citation: J Immunol. 2006 Aug 1;177(3):1879-85
references.pmid: 16849500
references.citation: J Clin Invest. 2006 May;116(5):1391-9
references.pmid: 16614756
references.citation: J Biol Chem. 2000 Oct 20;275(42):32775-82
references.pmid: 10922363
references.citation: Bioorg Med Chem. 2006 May 15;14(10):3553-62
references.pmid: 16439136
references.citation: J Biochem Mol Biol. 2005 Nov 30;38(6):633-8
references.pmid: 16336776
references.citation: Prog Lipid Res. 2004 Jan;43(1):3-35
references.pmid: 14636669
references.citation: J Chem Inf Model. 2008 Jan;48(1):179-85
references.pmid: 18052142
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: J Neurochem. 2005 Sep;94(6):1546-58
references.pmid: 16000148
references.citation: J Biol Chem. 2000 Jul 28;275(30):23045-52
references.pmid: 10811660
references.citation: Science. 2007 Jul 27;317(5837):510-2
references.pmid: 17600184
references.citation: Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7220-5
references.pmid: 10377395
references.citation: Biochem Biophys Res Commun. 1997 Jun 9;235(1):148-52
references.pmid: 9196052
references.citation: J Biol Chem. 2003 Sep 26;278(39):37937-47
references.pmid: 12835322
references.citation: J Immunol. 2002 Jun 1;168(11):5811-6
references.pmid: 12023384
references.citation: FEBS J. 2005 Apr;272(7):1688-703
references.pmid: 15794756
references.citation: Arthritis Res Ther. 2004;6(4):R355-65
references.pmid: 15225371
references.citation: J Immunol. 1998 Mar 15;160(6):2974-82
references.pmid: 9510202
references.citation: Nature. 1998 Sep 17;395(6699):281-4
references.pmid: 9751056
references.citation: Protein Sci. 1999 Mar;8(3):689-92
references.pmid: 10091672
references.citation: Nature. 2007 Aug 2;448(7153):609-12
references.pmid: 17632548
references.citation: J Biol Chem. 2000 Oct 20;275(42):32783-92
references.pmid: 10869354
references.citation: J Phys Chem B. 2008 Jun 19;112(24):7320-9
references.pmid: 18476739
references.citation: Biochem Biophys Res Commun. 2002 Mar 8;291(4):884-9
references.pmid: 11866447
references.citation: Nature. 2007 Aug 2;448(7153):613-6
references.pmid: 17632546
references.citation: J Mol Biol. 2005 May 20;348(5):1163-76
references.pmid: 15854652
references.citation: Curr Opin Rheumatol. 2004 Sep;16(5):623-7
references.pmid: 15314505
references.citation: Science. 2002 Apr 19;296(5567):539-41
references.pmid: 11964481
references.citation: J Exp Med. 1996 Sep 1;184(3):883-91
references.pmid: 9064348
references.citation: Curr Opin Investig Drugs. 2007 May;8(5):411-5
references.pmid: 17520870
references.citation: Bioorg Med Chem Lett. 2007 Dec 15;17(24):6816-20
references.pmid: 18029174
references.citation: Neuroreport. 2004 Jun 28;15(9):1395-8
references.pmid: 15194860
references.citation: J Biol Chem. 2004 Aug 6;279(32):33684-95
references.pmid: 15140897
references.citation: J Immunol. 1995 Nov 1;155(9):4437-44
references.pmid: 7594605
references.citation: Biochemistry. 2007 Jul 17;46(28):8414-24
references.pmid: 17585783
references.citation: Curr Pharm Des. 2006;12(8):943-54
references.pmid: 16533161
references.citation: Bioorg Med Chem Lett. 2005 Jul 15;15(14):3352-5
references.pmid: 15953724
references.citation: J Mol Biol. 2006 Jul 28;360(5):934-45
references.pmid: 16806268
references.citation: Methods Enzymol. 2005;401:147-61
references.pmid: 16399384
references.citation: Pharmacol Rev. 2007 Sep;59(3):207-24
references.pmid: 17878511
references.citation: J Biol Chem. 2001 Feb 9;276(6):4469-75
references.pmid: 11067848