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Review

Structure-based discovery and binding site analysis of histamine receptor ligands

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Pages 1165-1185 | Received 30 Jul 2016, Accepted 03 Oct 2016, Published online: 16 Oct 2016

References

  • Fourneau E, Bovet D. Recherches sur l’action sympathicolytique d’un nouveau dérivé du dioxane. Arch Int Pharmacodyn Ther. 1933;46:178–191.
  • Molinder HK. The development of cimetidine: 1964-1976. A human story. J Clin Gastroenterol. 1994;19:248–254.
  • Nauta WT, Harms AF Proceedings of the international pharmacol. meeting, 3rd edn. vol 7. Oxford: Pergamon Press. p 305; 1968.
  • Henderson R, Unwin PN. Three-dimensional model of purple membrane obtained by electron microscopy. Nature. 1975;257:28–32.
  • Henderson R, Baldwin JM, Ceska TA, et al. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol. 1990;213:899–929. DOI:10.1016/S0022-2836(05)80271-2
  • Grigorieff N, Ceska TA, Downing KH, et al. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol. 1996;259:393–421. DOI:10.1006/jmbi.1996.0328
  • Ter Laak AM, Timmerman H, Leurs R, et al. Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation. J Comput Aided Mol Des. 1995;9:319–330.
  • Wieland K, Ter Laak AM, Smit MJ, et al. Mutational analysis of the antagonist-binding site of the histamine H(1) receptor. J Biol Chem. 1999;274:29994–30000.
  • Palczewski K, Kumasaka T, Hori T, et al. Crystal structure of rhodopsin: A G protein-coupled receptor. Science. 2000;289:739–745.
  • Kiss R, Kovári Z, Keseru GM. Homology modelling and binding site mapping of the human histamine H1 receptor. Eur J Med Chem. 2004;39:959–967. DOI:10.1016/j.ejmech.2004.07.009
  • Axe FU, Bembenek SD, Szalma S. Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore. J Mol Graph Model. 2006;24:456–464. DOI:10.1016/j.jmgm.2005.10.005
  • Shin N, Coates E, Murgolo NJ, et al. Molecular modeling and site-specific mutagenesis of the histamine-binding site of the histamine H4 receptor. Mol Pharmacol. 2002;62:38–47.
  • Schnell D, Strasser A, Seifert R. Comparison of the pharmacological properties of human and rat histamine H(3)-receptors. Biochem Pharmacol. 2010;80:1437–1449. DOI:10.1016/j.bcp.2010.07.027
  • Lim HD, Jongejan A, Bakker RA, et al. Phenylalanine 169 in the second extracellular loop of the human histamine H4 receptor is responsible for the difference in agonist binding between human and mouse H4 receptors. J Pharmacol Exp Ther. 2008;327:88–96. DOI:10.1124/jpet.108.140343
  • Shimamura T, Shiroishi M, Weyand S, et al. Structure of the human histamine H1 receptor complex with doxepin. Nature. 2011;475:65–70. DOI:10.1038/nature10236
  • de Graaf C, Kooistra AJ, Vischer. HF, et al. Crystal structure-based virtual screening for fragment-like ligands of the human histamine H1 receptor. J Med Chem. 2011;54:8195–8206. DOI:10.1021/jm2011589
  • Prasad Ratnala VR, Hulsbbergen FB, de Groot HJ, et al. Analysis of histamine and modeling of ligand-receptor interactions in the histamine H(1) receptor for magic angle spinning NMR studies. Inflamm Res. 2003;52:417–423. DOI:10.1007/s00011-003-1195-3
  • Cordova-Sintjago TC, Fang L, Bruysters M, et al. Molecular determinants of ligand binding at the human histamine H1 receptor: site-directed mutagenesis results analyzed with ligand docking and molecular dynamics studies at H1 homology and crystal structure models. J Chem Pharm Res. 2012;4:2937–2951.
  • Shah JR, Mosier PD, Roth BL, et al. Synthesis, structure-affinity relationships, and modeling of AMDA analogs at 5-HT2A and H1 receptors: structural factors contributing to selectivity. Bioorg Med Chem. 2009;17:6496–6504. DOI:10.1016/j.bmc.2009.08.016
  • Bruysters M, Jongejan A, Gillard M, et al. Pharmacological differences between human and guinea pig histamine H1 receptors: Asn84 (2.61) as key residue within an additional binding pocket in the H1 receptor. Mol Pharmacol. 2005;67:1045–1052. DOI:10.1124/mol.104.008847
  • Strasser A, Wittmann HJ. LigPath: a module for predictive calculation of a ligand’s pathway into a receptor-application to the gpH1-receptor. J Mol Model. 2007;13:209–218. DOI:10.1007/s00894-006-0152-9
  • Strasser A, Wittmann HJ. Analysis of the activation mechanism of the guinea-pig Histamine H1-receptor. J Comput Aided Mol Des. 2007;21:499–509. DOI:10.1007/s10822-007-9131-1
  • Sato M, Hirokawa T. Extended template-based modeling and evaluation method using consensus of binding mode of GPCRs for virtual screening. J Chem Inf Model. 2014;54:3153–3161. DOI:10.1021/ci500499j
  • Yang Y, Li Y, Pan Y, et al. Computational analysis of structure-based interactions for novel H₁-Antihistamines. Int J Mol Sci. 2016;17:pii:E129. DOI:10.3390/ijms17010129
  • Kooistra AJ, Vischer HF, McNaught-Flores D, et al. Function-specific virtual screening for GPCR ligands using a combined scoring method. Sci Rep. 2016;6:28288. DOI:10.1038/srep28288
  • Sun X, Li Y, Li W, et al. Computational investigation of interactions between human H2 receptor and its agonists. J Mol Graph Model. 2011;29:693–701. DOI:10.1016/j.jmgm.2010.12.001
  • Kelley MT, Bürckstümmer T, Wenzel-Seifert K, et al. Distinct interaction of human and guinea pig histamine H2-receptor with guanidine-type agonists. Mol Pharmacol. 2001;60:1210–1225.
  • Yao BB, Hutchins CW, Carr TL, et al. Molecular modeling and pharmacological analysis of species-related histamine H(3) receptor heterogeneity. Neuropharmacology. 2003;44:773–786.
  • Kuder K, Łażewska D, Latacz G, et al. Chlorophenoxy aminoalkyl derivatives as histamine H(3)R ligands and antiseizure agents. Bioorg Med Chem. 2016;24:53–72. DOI:10.1016/j.bmc.2015.11.021
  • Rai BK, Tawa GJ, Katz AH, et al. Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists. Proteins. 2010;78:457–473. DOI:10.1002/prot.22571
  • Lorenzi S, Mor M, Bordi F, et al. Validation of a histamine H3 receptor model through structure-activity relationships for classical H3 antagonists. Bioorg Med Chem. 2005;13:5647–5657. DOI:10.1016/j.bmc.2005.05.072
  • Kim SK, Fristrup P, Abrol R, et al. Structure-based prediction of subtype selectivity of histamine H3 receptor selective antagonists in clinical trials. J Chem Inf Model. 2011;51:3262–3274. DOI:10.1021/ci200435b
  • Feng Z, Hou T, Li Y. Docking and MD study of histamine H4R based on the crystal structure of H1R. J Mol Graph Model. 2013;39:1–12. DOI:10.1016/j.jmgm.2012.10.003
  • Bajda M, Kuder KJ, Lażewska D, et al. Dual-acting diether derivatives of piperidine and homopiperidine with histamine H(3) receptor antagonistic and anticholinesterase activity. Arch Pharm (Weinheim). 2012;345:591–597. DOI:10.1002/ardp.201200018
  • Schlegel B, Laggner C, Meier R, et al. Generation of a homology model of the human histamine H(3) receptor for ligand docking and pharmacophore-based screening. J Comput Aided Mol Des. 2007;21:437–453. DOI:10.1007/s10822-007-9127-x
  • Dastmalchi S, Hamzeh-Mivehroud M, Ghafourian T, et al. Molecular modeling of histamine H3 receptor and QSAR studies on arylbenzofuran derived H3 antagonists. J Mol Graph Model. 2008;26:834–844. DOI:10.1016/j.jmgm.2007.05.002
  • Uveges AJ, Kowal D, Zhang Y, et al. The role of transmembrane helix 5 in agonist binding to the human H3 receptor. J Pharmacol Exp Ther. 2002;301:451–458
  • Levoin N, Calmels T, Poupardin-Olivier O, et al. Refined docking as a valuable tool for lead optimization: application to histamine H3 receptor antagonists. Arch Pharm (Weinheim). 2008;341:610–623. DOI:10.1002/ardp.200800042
  • Jacobsen ML, Rimvall K, Hastrup S, et al. XXXII annual meeting of the European histamine research society. Noordwijkerhout: Netherlands; 2003.
  • Abrol R, Bray JK, Goddard WA. Bihelix: towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins. 2012;80:505–518. DOI:10.1002/prot.23216
  • Sirci F, Istyastono EP, Vischer HF, et al. Virtual fragment screening: discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints. J Chem Inf Model. 2012;52:3308–3324. DOI:10.1021/ci3004094
  • Levoin N, Labeeuw O, Krief S, et al. Determination of the binding mode and interacting amino-acids for dibasic H3 receptor antagonists. Bioorg Med Chem. 2013;21:4526–4529. DOI:10.1016/j.bmc.2013.05.035
  • Christopher F, Thangam EB, Suresh MX. A bioinformatics search for selective histamine h4 receptor antagonists through structure-based virtual screening strategies. Chem Biol Drug Des. 2012;79:749–759. DOI:10.1111/j.1747-0285.2012.01336.x
  • Kiss R, Noszál B, Rácz A, et al. Binding mode analysis and enrichment studies on homology models of the human histamine H4 receptor. Eur J Med Chem. 2008;43:1059–1070. DOI:10.1016/j.ejmech.2007.07.014
  • Jójárt B, Kiss R, Viskolcz B, et al. Activation mechanism of the human histamine H4 receptor–an explicit membrane molecular dynamics simulation study. J Chem Inf Model. 2008;48:1199–1210. DOI:10.1021/ci700450w
  • Jongejan A, Lim HD, Smits RA, et al. Delineation of agonist binding to the human histamine H4 receptor using mutational analysis, homology modeling, and ab initio calculations. J Chem Inf Model. 2008;48:1455–1463. DOI:10.1021/ci700474a
  • Schultes A, Nijmeijer S, Engelhardt H, et al. Mapping histamine H4 receptor–ligand binding modes. Med Chem Commun. 2013;4:193–204. DOI:10.1039/C2MD20212C
  • Engelhardt H, Schultes S, De Graaf C, et al. Bispyrimidines as potent histamine H(4) receptor ligands: delineation of structure-activity relationships and detailed H(4) receptor binding mode. J Med Chem. 2013;56:4264–4276. DOI:10.1021/jm301886t
  • Łażewska D, Więcek M, Ner J, et al. Aryl-1,3,5-triazine derivatives as histamine H4 receptor ligands. Eur J Med Chem. 2014;83:534–546. DOI:10.1016/j.ejmech.2014.06.032
  • Kiss R, Kiss B, Könczöl Á, et al. Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening. J Med Chem. 2008;51:3145–3153. DOI:10.1021/jm7014777
  • Istyastono EP, Nijmeijer S, Lim HD, et al. Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies. J Med Chem. 2011;54:8136–8147. DOI:10.1021/jm201042n
  • Deml KF, Beermann S, Neumann D, et al. Interactions of histamine H1-receptor agonists and antagonists with the human histamine H4-receptor. Mol Pharmacol. 2009;76:1019–1030. DOI:10.1124/mol.109.058651
  • Wittmann HJ, Elz S, Seifert R, et al. N (α)-Methylated phenylhistamines exhibit affinity to the hH(4)R-a pharmacological and molecular modelling study. Naunyn Schmiedebergs Arch Pharmacol. 2011;384:287–299. DOI:10.1007/s00210-011-0671-5
  • Igel P, Geyer R, Strasser A, et al. Synthesis and structure-activity relationships of cyanoguanidine-type and structurally related histamine H4 receptor agonists. J Med Chem. 2009;52:6297–6313. DOI:10.1021/jm900526h
  • Pappalardo M, Shachaf N, Basile L, et al. Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism. PLoS One. 2014;9:e109340. DOI:10.1371/journal.pone.0109340
  • Tarcsay A, Paragi G, Vass M, et al. The impact of molecular dynamics sampling on the performance of virtual screening against GPCRs. J Chem Inf Model. 2013;53:2990–2999. DOI:10.1021/ci400087b
  • Vass M, Schmidt É, Horti F, et al. Virtual fragment screening on GPCRs: a case study on dopamine D3 and histamine H4 receptors. Eur J Med Chem. 2014;77:38–46. DOI:10.1016/j.ejmech.2014.02.034
  • Kiss R, Jójárt B, Schmidt É, et al. Identification of novel Histamine H4 ligands by virtual screening on molecular dynamics ensembles. Mol Inform. 2014;33:264–268. DOI:10.1002/minf.201300072
  • Gatica EA, Cavasotto CN. Ligand and decoy sets for docking to G protein-coupled receptors. J Chem Inf Model. 2012;52:1–6. DOI:10.1021/ci200412p
  • Farrens DL, Altenbach C, Yang K, et al. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science. 1996;274:768–770
  • Beuming T, Sherman W. Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines. J Chem Inf Model. 2012;52:3263–3277. DOI:10.1021/ci300411b

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