Computational investigation of interactions between human H2 receptor and its agonists

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 5, 2011, Pages 693-701

  Sun, Xianqiang ^a   Li, Yaozong ^a   Li, Weihua ^a   Xu, Zhejun ^a   Tang, Yun ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

H2R agonists; Histamine receptors; Homology modeling; Molecular docking; Pharmacophore modeling

Indexed keywords

H2R AGONISTS; HISTAMINE RECEPTORS; HOMOLOGY MODELING; MOLECULAR DOCKING; PHARMACOPHORE MODELING;

COMPUTER SIMULATION; HYDROCHLORIC ACID; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; MOLECULAR MODELING; PHARMACODYNAMICS; SEARCH ENGINES;

COMPUTATIONAL CHEMISTRY;

BETA 1 ADRENERGIC RECEPTOR; HISTAMINE H2 RECEPTOR; HISTAMINE H2 RECEPTOR AGONIST;

ARTICLE; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DATA BASE; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PHARMACOPHORE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SCREENING; SIMULATION; STRUCTURAL HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; DATABASES, FACTUAL; HISTAMINE AGONISTS; HISTAMINE H2 ANTAGONISTS; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTORS, HISTAMINE H2; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 79751533089     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.12.001     Document Type: Article

References (57)

1. M. Jutel, M. Akdis, and C.A. Akdis Histamine, histamine receptors and their role in immune pathology Clinical and Experimental Allergy 39 2009 1786 1800
2. S.J. Hill, C.R. Ganellin, H. Timmerman, J.C. Schwartz, N.P. Shankley, J.M. Young, W. Schunack, R. Levi, and H.L. Haas International Union of Pharmacology. XIII. Classification of histamine receptors Pharmacol. Rev. 49 1997 253 278 (Pubitemid 27414915)
3. M.E. Parsons, and C.R. Ganellin Histamine and its receptors Br. J. Pharmacol. 147 Suppl. 1 2006 S127 135
4. J. Kim, A. Gai, S. Nakatani, K. Hashimura, H. Kanzaki, K. Komamura, M. Asakura, H. Asanuma, S. Kitamura, H. Tomoike, and M. Kitakaze Impact of blockade of histamine H-2 receptors on chronic heart failure revealed by retrospective and prospective randomized studies J. Am. Coll. Cardiol. 48 2006 1378 1384 (Pubitemid 44436824)
5. R. Seifert, A. Hoer, I. Schwaner, and A. Buschauer Histamine increases cytosolic Ca2+ in HL-60 promyelocytes predominantly via H2 receptors with an unique agonist/antagonist profile and induces functional differentiation Mol. Pharmacol. 42 1992 235 241 (Pubitemid 23026154)
6. R. Burde, A. Buschauer, and R. Seifert Characterization of histamine H2-receptors in human neutrophils with a series of guanidine analogues of impromidine. Are cell type-specific H2-receptors involved in the regulation of NADPH oxidase? Naunyn Schmiedebergs Arch. Pharmacol. 341 1990 455 461 (Pubitemid 20154559)
7. G.J. Durant, W.A. Duncan, C.R. Ganellin, M.E. Parsons, R.C. Blakemore, and A.C. Rasmussen Impromidine (SK&F 92676) is a very potent and specific agonist for histamine H2 receptors Nature 276 1978 403 405 (Pubitemid 9096472)
8. A. Buschauer Synthesis and in vitro pharmacology of arpromidine and related phenyl(pyridylalkyl)guanidines, a potential new class of positive inotropic drugs J. Med. Chem. 32 1989 1963 1970 (Pubitemid 19204387)
9. A. Kraus, P. Ghorai, T. Birnkammer, D. Schnell, S. Elz, R. Seifert, S. Dove, G. Bernhardt, and A. Buschauer N(G)-acylated aminothiazolylpropylguanidines as potent and selective histamine H(2) receptor agonists ChemMedChem. 4 2009 232 240
10. P. Ghorai, A. Kraus, M. Keller, C. Gotte, P. Igel, E. Schneider, D. Schnell, G. Bernhardt, S. Dove, M. Zabel, S. Elz, R. Seifert, and A. Buschauer Acylguanidines as bioisosteres of guanidines: NG-acylated imidazolylpropylguanidines, a new class of histamine H2 receptor agonists J. Med. Chem. 51 2008 7193 7204
11. S.X. Xie, A. Kraus, P. Ghorai, Q.Z. Ye, S. Elz, A. Buschauer, and R. Seifert N1-(3-cyclohexylbutanoyl)-N2-[3-(1H-imidazol-4-yl)propyl]guanidine (UR-AK57), a potent partial agonist for the human histamine H1- and H2-receptors J. Pharmacol. Exp. Ther. 317 2006 1262 1268 (Pubitemid 43764132)
12. M.T. Kelley, T. Burckstummer, K. Wenzel-Seifert, S. Dove, A. Buschauer, and R. Seifert Distinct interaction of human and guinea pig histamine H2-receptor with guanidine-type agonists Mol. Pharmacol. 60 2001 1210 1225 (Pubitemid 33144892)
13. J. Christiaans, H.v.d. Goot, W. Menge, and H. Timmerman Synthesis and in vitro pharmacology of dimaprit analogues with histamine Hz-agonistic and HI-antagonistic activities Eur. J. Med. Chem. 30 1995 673 678
14. J.C. Eriks, H. van der Goot, G.J. Sterk, and H. Timmerman Histamine H2-receptor agonists. Synthesis, in vitro pharmacology, and qualitative structure-activity relationships of substituted 4- and 5-(2-aminoethyl)thiazoles J. Med. Chem. 35 1992 3239 3246
15. S. Dove, and A. Buschauer Imidazolylpropylguanidines as histamine H2 receptor agonists: 3D-QSAR of a large series Pharm. Acta Helv. 73 1998 145 155 (Pubitemid 28347362)
16. S. Dove, and A. Buschauer Improved alignment by weighted field fit in CoMFA of histamine H-2 receptor agonists imidazolylpropylguanidines Quant. Struct.-Act. Rel. 18 1999 329 341 (Pubitemid 29504988)
17. J. Zou, H.Z. Xie, S.Y. Yang, J.J. Chen, J.X. Ren, and Y.Q. Wei Towards more accurate pharmacophore modeling: multicomplex-based comprehensive pharmacophore map and most-frequent-feature pharmacophore model of CDK2 J. Mol. Graph. Model. 27 2008 430 438
18. F. Cheng, Z. Xu, G. Liu, and Y. Tang Insights into binding modes of adenosine A2B antagonists with ligand-based and receptor-based methods Eur. J. Med. Chem. 45 2010 3459 3471
19. S.Y. Yang Pharmacophore modeling and applications in drug discovery: challenges and recent advances Drug Discov. Today. 15 2010 444 450
20. Z. Xu, F. Cheng, C. Da, G. Liu, and Y. Tang Pharmacophore modeling of human adenosine receptor A2A antagonists J. Mol. Model. 16 2010 1867 1876
21. X. Zhao, M. Yuan, B. Huang, H. Ji, and L. Zhu Ligand-based pharmacophore model of N-aryl and N-heteroaryl piperazine alpha 1A-adrenoceptors antagonists using GALAHAD J. Mol. Graph. Model. 29 2010 126 136
22. I. Gantz, J. DelValle, L.D. Wang, T. Tashiro, G. Munzert, Y.J. Guo, Y. Konda, and T. Yamada Molecular basis for the interaction of histamine with the histamine H2 receptor J. Biol. Chem. 267 1992 20840 20843
23. H. Preuss, P. Ghorai, A. Kraus, S. Dove, A. Buschauer, and R. Seifert Point mutations in the second extracellular loop of the histamine H2 receptor do not affect the species-selective activity of guanidine-type agonists Naunyn Schmiedebergs Arch. Pharmacol. 376 2007 253 264 (Pubitemid 50002453)
24. H. Weinstein, D. Chou, C.L. Johnson, S. Kang, and J.P. Green Tautomerism and the receptor action of histamine: a mechanistic model Mol. Pharmacol. 12 1976 738 745
25. S.G. Rasmussen, H.J. Choi, D.M. Rosenbaum, T.S. Kobilka, F.S. Thian, P.C. Edwards, M. Burghammer, V.R. Ratnala, R. Sanishvili, R.F. Fischetti, G.F. Schertler, W.I. Weis, and B.K. Kobilka Crystal structure of the human beta2 adrenergic G-protein-coupled receptor Nature 450 2007 383 387 (Pubitemid 350126755)
26. T. Warne, M.J. Serrano-Vega, J.G. Baker, R. Moukhametzianov, P.C. Edwards, R. Henderson, A.G. Leslie, C.G. Tate, and G.F. Schertler Structure of a beta1-adrenergic G-protein-coupled receptor Nature 454 2008 486 491
27. P. Scheerer, J.H. Park, P.W. Hildebrand, Y.J. Kim, N. Krauss, H.W. Choe, K.P. Hofmann, and O.P. Ernst Crystal structure of opsin in its G-protein-interacting conformation Nature 455 2008 497 502
28. S.L. Dixon, A.M. Smondyrev, E.H. Knoll, S.N. Rao, D.E. Shaw, and R.A. Friesner PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results J. Comput. Aided. Mol. Des. 20 2006 647 671 (Pubitemid 46023928)
29. H. Preuss, P. Ghorai, A. Kraus, S. Dove, A. Buschauer, and R. Seifert Mutations of Cys-17 and Ala-271 in the human histamine H2 receptor determine the species selectivity of guanidine-type agonists and increase constitutive activity J. Pharmacol. Exp. Ther. 321 2007 975 982 (Pubitemid 46762690)
30. S.X. Xie, P. Ghorai, Q.Z. Ye, A. Buschauer, and R. Seifert Probing ligand-specific histamine H1- and H2-receptor conformations with NG-acylated Imidazolylpropylguanidines J. Pharmacol. Exp. Ther. 317 2006 139 146
31. Ligprep. Schordinger, LLC, New York, NY. (2008).
32. G. Chang, W.C. Guida, and W.C. Still An internal coordinate monte carlo method for searching conformational space J. Am. Chem. Soc. 111 1989 4379 4386
33. J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182 (Pubitemid 40736970)
34. M. Jacobsson, P. Liden, E. Stjernschantz, H. Bostrom, and U. Norinder Improving structure-based virtual screening by multivariate analysis of scoring data J. Med. Chem. 46 2003 5781 5789 (Pubitemid 37543328)
35. Prime. Schrodinger, LLC, New York, NY. (2008).
36. C.H. Wu, L.S. Yeh, H. Huang, L. Arminski, J. Castro-Alvear, Y. Chen, Z. Hu, P. Kourtesis, R.S. Ledley, B.E. Suzek, C.R. Vinayaka, J. Zhang, and W.C. Barker The protein information resource Nucl. Acids Res. 31 2003 345 347 (Pubitemid 36150400)
37. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucl. Acids Res. 22 1994 4673 4680 (Pubitemid 24354800)
38. Maestro. Schordinger, LLC, New York, NY. (2008).
39. Desmond. D.E. Shaw Research, Desmond Molecular Dynamics System, New York, NY. (2008).
40. K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.E. Shaw Scalable algorithms for molecular dynamics simulations on commodity clusters Proc. ACM/IEEE Conf. Supercomput. 2006
41. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236 (Pubitemid 26399746)
42. H. Heller, M. Schaefer, and K. Schulten Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase J. Phys. Chem. 97 1993 8343 8360
43. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
44. M.A. Lomize, A.L. Lomize, I.D. Pogozheva, and H.I. Mosberg OPM: orientations of proteins in membranes database Bioinformatics 22 2006 623 625 (Pubitemid 43372827)
45. A.L. Lomize, I.D. Pogozheva, M.A. Lomize, and H.I. Mosberg The role of hydrophobic interactions in positioning of peripheral proteins in membranes BMC Struct. Biol. 7 2007 44
46. A.L. Lomize, I.D. Pogozheva, M.A. Lomize, and H.I. Mosberg Positioning of proteins in membranes: a computational approach Protein Sci. 15 2006 1318 1333 (Pubitemid 43800004)
47. V. Kräutler, W.F.v. Gunsteren, and P.H. Hünenberger A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations J. Computat. Chem. 22 2001 501 508 (Pubitemid 32291686)
48. P. Ghorai, A. Kraus, T. Birnkammer, R. Geyer, G. Bernhardt, S. Dove, R. Seifert, S. Elz, and A. Buschauer Chiral NG-acylated hetarylpropylguanidine-type histamine H2 receptor agonists do not show significant stereoselectivity Bioorg. Med. Chem. Lett. 20 2010 3173 3176
49. F.U. Axe, S.D. Bembenek, and S. Szalma Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore J. Mol. Graph. Model. 24 2006 456 464
50. MacroModel. Schordinger, LLC, New York, NY. (2008).
51. A.L. Morris, M.W. MacArthur, E.G. Hutchinson, and J.M. Thornton Stereochemical quality of protein structure coordinates Proteins 12 1992 345 364
52. J.C. Eriks, H. van der Goot, and H. Timmerman New activation model for the histamine H2 receptor, explaining the activity of the different classes of histamine H2 receptor agonists Mol. Pharmacol. 44 1993 886 894 (Pubitemid 23317305)
53. P.H. Nederkoorn, J.H. van Lenthe, H. van der Goot, G.M. Donne-Op den Kelder, and H. Timmerman The agonistic binding site at the histamine H2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane alpha-helix J. Comput. Aided. Mol. Des. 10 1996 461 478 (Pubitemid 126712441)
54. P.H. Nederkoorn, E.M. van Gelder, G.M. Donne-Op den Kelder, and H. Timmerman The agonistic binding site at the histamine H2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven alpha-helical transmembrane domain J. Comput. Aided. Mol. Des 10 1996 479 489 (Pubitemid 126712442)
55. S. Dove, S. Elz, R. Seifert, and A. Buschauer Structure-activity relationships of histamine H2 receptor ligands Mini. Rev. Med. Chem. 4 2004 941 954 (Pubitemid 39406254)
56. Y. Tang, W. Zhu, K. Chen, and H. Jiang New technologies in computer-aided drug design: toward target identification and new chemical entity discovery Drug Discov. Today: Technol. 3 2006 307 313 (Pubitemid 44734724)
57. P. Prathipati, A. Dixit, and A.K. Saxena Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design Curr. Comput.-Aided Drug Des. 3 2007 133 148 (Pubitemid 46916266)