Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Beck-Sickinger, A.G., Structural characterization and binding sites of G protein-coupled receptors, Drug Discov. Today, 1 (1996) 502–513.
Findlay, J.B.C. and Pappin, D.J.C., The opsin family of proteins, Biochem. J., 238 (1986) 625–642.
Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E. and Downing, K.H., Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy, J. Mol. Biol., 213 (1990) 899–929.
Hoflack, J., Trumpp-Kallmeyer, S. and Hibert, M., Molecular modeling of G protein-coupled receptors, In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory, methods and applications, ESCOM, Leiden, The Netherlands, 1993, pp. 355–372.
Strader, C.D., Fong, T.M., Tota, M.R., Underwood, D. and Dixon, R.A.F., Structure and function of G protein-coupled receptors, Annu. Rev. Biochem., 63 (1994) 101–132.
Probst, W.C., Snyder, L.A., Schuster, D.I., Brosius, J. and Sealfon, S.C., Sequence alignment of the G protein-coupled receptor superfamily, DNA Cell Biol.. 11 (1992) 1–20.
Lefkowitz, R., Cotecchia, S., Samama, P. and Costa, T., Constitutive activity of receptors coupled to guanine nucleotide regulatory proteins, Trends Pharmacol. Sci., 14 (1993) 303–307.
Strader, C.D., Fong, T.M., Graziano, M.P. and Tota, M.R., The family of G protein-coupled receptors, FASEB J., 9 (1995) 745–754.
Gether, U., Johansen, T.E., Snider, R.M., Lowe III, J.A., Nakanishi, S. and Schwartz, T.W., Different binding epitopes on the NK1 receptor for substance P and a non-peptide antagonist. Nature, 362 (1993) 345–348.
Rosenkilde, M.M., Cahir, M., Gether, U., Hjorth, S.A. and Schwartz, T.W., Mutations along transmembrane segment II of the NK-1 receptor affect substance P competition with non-peptide antagonists but not substance P binding, J. Biol. Chem., 269 (1994) 28160–28164.
Sautel, M., Rudolf, K., Wittneben, H., Herzog, H., Martinez, R., Munoz, M., Eberlein, W., Engle, W., Walker, P. and Beck-Sickinger, A.G., Neuropeptide Y and the non-peptide antagonist BIBP 3226 share an overlapping binding site at the human Y1 receptor, Mol. Pharmacol., 50 (1996) 285–292.
Schwartz., T.W. and Wells, T.N.C., Is there a ‘lock’ for all agonist ‘keys’ in 7TM receptors?, Trends Pharmacol. Sci., 17 (1996) 213–216.
Samuna, P., Cotecchia, S., Costa, T. and Lefkowitz, R.J., A Mutation-induced activated state of the b2-adrenergic receptor, J. Biol. Chem., 268 (1993) 4625–4636.
Kuipers, W., van Wijngaaden, I. and Ijzerman, A.P., A model of the serotonin 5-HTIA receptor: Agonist and antagonist binding sites. Drug Des. Discuss., 11 (1994) 231–249.
Schertler, G.F.X., Villa, C. and Henderson, R., Projection structure of rhodopsin, Nature, 362 (1993) 770–772.
Soppa, J., Two hypotheses—one answer: Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacleriorhodopsin and eukaryotic G protin-coupled receptors, FEBS Lett., 342 (1994) 7–11.
Donnelly, D., Findlay, J.B.C. and Blundell, T.L., The evolution and structure of aminergic G protein-coupled receptors, Receptors Channels, 2 (1994) 61–78.
Baldwin, J.M., The probable arrangement of the helices in G protein-coupled receptors, EMBO J., 12 (1993) 1693–1703.
Hoflack, J., Trumpp-Kallmeyer, S. and Hibert, M., Re-evaluation of bacteriorhodopsin as a model for G protein-coupled receptors, Trends Pharmacol. Sci., 15 (1994) 7–9.
Rost, B., Casadio, R., Fariselli, P. and Sander, C., Transmembrane helices predicted at 95% accuracy, Protein Sci., 4 (1995) 521–533.
Nordvall, G. and Hacksell, U., Binding-site modeling of the muscarinic m1 receptor: A combination of homology-based and indirect approaches, J. Med. Chem., 36 (1993) 967–976.
Hutchins, C., Three-dimensional models of the D 1 and D 2 dopamine receptors, Endocrine J., 2 (1994) 7–23.
Batlle, M., Campillo, M., Giraldo, J. and Pardo, L., Computer-aided drug designof selective 5-hydroxytryptamine 1A receptor ligands using a three-dimensional model. In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 541–544.
Bourdon, H., Trumpp-Kallmeyer, S., Hoflack, J., Hibert, M. and Wermuth, C.G., Modeling of muscarinic M1 agonists: Study of their interaction with the M1 receptor, In Sanz, F., Giraldo, J., and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 514–518.
Burbach, J.P.H. and Meijer, O.C., The structure of neuropeptide receptors, Eur. J. Pharmacol.-Mol. Pharmacol., 227 (1992) 1–18.
Chou, K.-C., Carlacci, L., Maggiora, G.M., Parodi, L.A. and Schulz, M.W., An energy-based approach to packing the 7-helix bundle of bacterirhodopsin, Protein Sci., 1 (1992) 810–827.
Cronet, P., Sander, C. and Vriend, G., Modeling of transmembrane seven helix bundles, Protein Eng., 6 (1993) 59–64.
Dahl, S.G., Edvardsen, I. and Sylte, I., Molecular dynamics of dopamine at the D 2 receptor, Proc. Natl. Acad. Sci. U.S.A., 88 (1991) 8111–8115.
De Benedetti, P.G., Menziani, M.C., Fanelli, F. and Cocchi, M., The heuristic-direct approach to QSAR analysis of ligand-G-protein coupled receptor complex, In Sanz, F., Giraldo, J., and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 526–527.
Dijkstra, G.D.H., Tulp, M.T.M., Hermkens, P.H.H., van Maarseveen, J.H., Scheeren, H.W. and Kruse, C.G., Synthesis and receptor-affinity profile of N-hydroxytryptamine derivatives for serotonin and tryptamine receptors: A molecular-modeling study, Recl. Trav. Chim. Pays-Bas., 112 (1993) 131–136.
Edvardsen, O., Sylte, I. and Dahl, S.G., Molecular dynamics of serotonin and ritanserin interacting with the 5-HT2, Mol. Brain Res., 14 (1992) 166–178.
Egner, U., Gerbling, K.P., Hoyer, G.-A., Kruger, G. and Wegner, P., Design of inhibitors of photosystem II using a model of the D1 protein, Pestic. Sci., 47 (1996) 145–158.
Fanelli, F., Menziani, M.C., Cocchi, M. and De Benedetti, P.G., Comparative molecular dynamics study of the seven-helix bundle arrangement of G protein-coupled receptors, J. Mol. Struct. (Theochem), 333 (1995) 49–69.
Findlay, J.B.C. and Donnelly, D. (Ed.), The superfamily: molecular modeling, Springer-Verlag, Berlin, Germany, 1993, pp. 17–31.
Grotzinger, J., Engels, M., Jacoby, E., Wollmer, A. and Strassburger, W., A model for the C5a receptor and for its interaction with the ligand, Protein Eng., 4 (1991) 767–771.
Hibert, M., Hoflack, J., Trumpp-Kallmeyer, S., Paquet, J.-L., Leppik, R., Mouillac, B., Chini, B., Barberis, C. and Jard, S. (Ed.), Three-dimensional structure of G protein-coupled receptors: from speculations to facts, Elsevier Science, Amsterdam, The Netherlands, 1996.
Humblet, C., Lunney, E.A. and Mirzadegan, T. (Ed.), Docking ligands in the receptor cavity: What have we learned?, ESCOM, Leiden, The Netherlands, 1993, pp. 35–43.
Kenakin, T., Receptor conformational induction versus selection: All part of the same energy landscape, Trends Pharmacol. Sci., 17(1996) 190–191.
Krause, G., Kuhne, R. and Hubel, S. (Ed.), G protein-coupled receptors, glucagon type: How to overcome the alignment/fit dilemma to the bacteriorhodopsin template, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 531–533.
Kuipers, W., Kruse, C.G., van Wijngaarden, I., Standaar, P.J., Tulp, M.T.M., Veldman, N., Spek, A.L. and Ijzerman, A.P., 5-HT 1A -versus D 2 -receptor selectivity of flesinoxan and analogous N4-substituted N1-arylpiperazines, J. Med. Chem., 40 (1997) 300–312.
Livingstone, C.D., Strange, P.G. and Naylor, L.H., Molecular modeling of D 2 -like dopamine receptors, Biochem. J., 287 (1992) 277–282.
Luo, X., Zhang, D. and Weinstein. H., Ligand-induced domain motion in the activation mechanism of a G protein-coupled receptor, Protein Engng., 7 (1994) 1441–1448.
Maloney Huss, K. and Lybrand, T.P., Three-dimensional structure for the β 2 adrenergic receptor protein based on computer modeling studies, J. Mol. Biol., 225 (1992) 859–871.
Menziani, M.C., Cocchi, M., Fanelli, F. and De Benedetti, P.G., Theoretical QSAR analysis on three dimensional models of the complexes between peptide and non-peptide antagonists with the FT 1 and FT 6 receptors, In Sanz, F., Giraldo, J., and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain. 1995, pp. 519–525.
Moereels, H. and Leysen, J.E., Novel computational model for the interaction of dopamine with the D 2 receptor, Recept. Channels, 1 (1993) 89–97.
Nederkoorn, P.H.J., va Lenthe, J.H., van der Goot, H., den Kelder, G.M.D.-O. and Timmerman, H., The agonistic binding site at the histamine H2 receptor: 1. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane α-helix, J. Comput.-Aid. Mol. Design, 10 (1996) 461–478.
Nero, T.L., lakovidis, D. and Louis, W.J., Molecular modeling of the human β 1 -adrenoceptor. In Sanz, F., Giraldo, J., and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 528–530.
Pardo, L., Ballesteros, J.A., Osman, R. and Weinstein, H., On the use of the transmembrane domain of the bacteriorhodopsin as a template for modeling the three-dimensional structure of guanine nucleotide-binding regulatory protein-coupled receptors, Proc. Natl. Acad. Sci. U.S.A., 89 (1992) 4009–4012.
Sagara, T., Egashira, H., Okamura, M., Fujii, I., Shimohigashi, Y. and Kanematsu, K., Ligand recognition in mu opioid receptor: Experimentally based modeling of mu opioid receptor binding sites and their testing by ligand docking, Bioorg. Med. Chem., 4 (1996) 2151–2166.
Sankararamakrishnan, R. and Vishveshwara, S., Characterization of proline-containing α-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies, Proteins: Struct. Fund. Genet., 15 (1993) 26–41.
Sugden, D., Chong, N.W.S. and Lewis, D.F.V., Structural requirements at the melatonin receptor, Br. J. Pharmacol., 114 (1995) 618–623.
Sylte, I., Edvardsen, O. and Dahl, S.G., Molecular modeling of UH-301 and 5-HT 1a receptor interactions. Protein Eng., 9 (1996) 149–160.
Teeter, M.M., Froimowitz, M., Stec, B. and DuRand, C.J., Homology modeling of the dopamine D 2 receptor and its testing by docking of agonists and tricyclic antagonists, J. Med. Chem., 37 (1994) 2874–2888.
Trumpp-Kallmeyer, S., Chini, B., Mouillac, B., Barberis, C., Hoflack, J. and Hilbert, M., Towards understanding the role of the first extracellular loop for the binding of peptide harmones to G protein-coupled receptors. Pharm. Acta Helv., 70 (1995) 255–262.
Weinstein, H. and Zhang, D., Receptor models and ligand-induced responses: New insights for structure-activity relations. In Sanz, F., Giraldo, J., and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, J.R. Prous Science Publishers, Barcelona, Spain, 1995, pp. 497–507.
Yamamoto, Y., Kamiya, K. and Terao, S., Modeling of human thromboxane A2 receptor and analysis of the receptor-ligand interaction, J. Med. Chem., 36 (1993) 820–825.
Zhang, S. and Weinstein, H., Signal transduction by a 5-HT 2 receptor: A mechanistic hypothesis from molecular dynamics simulations of the three-dimensional model of the receptor complexed to ligands, J. Med. Chem., 36 (1993) 934–938.
Baxevanis, A.D., Makalowski, W., Ouellette, B.F.F. and Recipon, H., Web alert protein engineering, Curr. Opinion Biotech., 7 (1996) 462.
Peitsch, M.C., Herzyk, P., Wells, T.N.C. and Hubbard, R.E., Automated modeling of the transmembrane region of G protein-coupled receptor by Swiss-Model, Receptors Channels, 4 (1996) 161–164.
Hibert, M.F., Trumpp-Kallmeyer, S., Hoflack, J. and Bruinvels, A., This is not a G protein-coupled receptor, Trends Pharmacol. Sci., 14 (1993) 7–12.
Rost, B. and Valencia, A., Pitfalls of protein sequence analysis, Curr. Opinion Biotech., 7 (1996) 457–461.
Navajas, C., Kokkola, T., Poso, A., Honka, N., Gynther, J. and Laitinen, J.T., A rhodopsin-based model for melatonin recognition at its G protein-coupled receptor, Eur. J. Pharmacol., 304 (1996) 173–183.
Gaillard, P., Carrupt, P.-A., Testa, B. and Schambel, P., Binding of arylpiperazines, (aryloxy) propanolamines, and tetrahydropyridlindoles to the 5-HT 1A receptor: Contribution of the molecular lipophilicity potential to three-dimensional quantitative structure-affinity relationship models, J.Med. Chem., 39(1996) 126–134.
Dove, S., Kuhne, R. and Schunack, W., H 1 agonistic 2-heteroaryl and 2-phenylhistamines: CoMFA and possible receptor binding sites. In Sanz, F., Giraldo, J., Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, Proceedings of the 10th European Symposium on Structure-Activity Relationships: QSAR and Molecular Modeling, Barcelona, Spain, September 4–9, 1994, J.R. Prous Science Publishers, Barcelona, 1995, pp. 427–432.
Trumpp-Kallmeyer, S., Hoflack, J., Bruinvels, A. and Hibert, M., Modeling of G-protein-coupled receptors: Application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors, J. Med. Chem., 35 (1992) 3448–3462.
Yamashita, M., Fukui, H., Sugama, K., Yoshiyuki, H., Ito, S., Mizuguchi, H. and Wada, H., Expression cloning of a cDNA encoding the bovine histamine H 1 receptor, Proc. Natl. Acad. Sci. U.S.A., 88 (1991) 11515–11519.
Carriere, A., Altomare, C., Barreca, M.L., Contento, A., Carotti, A. and Hansch, C., Papain catalyzed hydrolysis of aryl esters: A comparison of the Hansch, docking and CoMFA methods, Farmaco, 49 (1994)573–585.
Smith, R.N., Hansch, C., Kim, K.H., Omiya, B., Fukumura, G., Selassie, C.D., Jow, P.Y.C., Blaney, J.M. and Langridge, R., The use of crystallography, graphics, and quantitative structure-activity relationships in the analysis of the papain hydrolysis of X-phenyl hippurates, Arch. Biochem. Biophys., 215 (1982)319–328.
Drenth, J., Kalk, K.H. and Swen, H.M., Binding of chloromethyl ketone substrate analogues to crystalline papain, Biochem., 15 (1976) 3731–3738.
Watson, K., Mitchell, E.P., Johnson, L.N., Cruciani, G., Son, J.C., Bichard, C.J.F., Fleet, G.W.J., Oikonomakos, N.G., Kontou, M. and Zographos, S.E., Glucose analogue inhibitors of glycogen phosphorylase: From crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection, Acta Cryst., D51 (1995) 458–472.
Cruciani, G. and Watson, K.A., Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b, J. Med. Chem., 37 (1994)2589–2601.
Recanatini, M., Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole, J. Comput.-Aid. Mol. Design, 10 (1996) 74–82.
Laughton, C.A., Zvelebil, M.J.J.M. and Neidle, S., A detailed molecular model for human aromatase, J. Steroid Biochem. Mol. Biol., 44 (1993) 399–407.
Zhou, D., L., C.L., Laughton, C.A., Korzekwa, K.R. and Chen, S., Mutagenesis study at a postulated hydrophobic region near the active site of aromatase cytochrome P450, J. Biol. Chem., 269 (1994) 19501–19508.
Diana, G.D., Nitz., T.J., Mallamo, J.P. and Treasurywala, A.M., Antipicornavirus compounds: Use of rational drug design and molecular modeling, Antivir. Chem. Chemother., 4 (1993) 1–10.
Artico, M., Botta, M., Corelli, F., Mai, A., Massa, S. and Ragno, R., Investigation on QSAR and binding mode of a new class of human rhinovirus-14 inhibitors by CoMFA and docking experiments, Bioorg. Med. Chem., 4 (1996) 1715–1724.
Cho, S.J., Garsia, M.L.S., Bier, J. and Tropsha, A., Structure-based alignment and comparative molecular field analysis of acetylcholinesterase inhibitors, J. Med. Chem., 39 (1996) 5064–5071.
Tong, W., Collantes, E.R., Chen, Y. and Welsh, W.J., A comparative molecular field analysis study of N-benzylpiperidines as acelylcholinesterase inhibitors, J. Med. Chem., 39 (1996) 380–387.
Oprea, T.I., Waller, C.L. and Marshall, G.R., 3D QSAR of human immunodeficiency virus (I) protease inhibitors: 3. Interpretation of CoMFA results, Drug Des. Discovery, 12(1994) 29–51.
Greco, G., Novellino, E., Pellecchia, M., Silipo, C. and Vittoria, A., Effects of variable section on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR, J. Comput.-Aided Mol. Design, 8(1994)97–112.
Kroemer, R.T. and Hecht, P., A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors, J. Compul.-Aid. Mol. Design, 9 (1995) 396–406.
Kroemer, R.T. and Hecht, P., Replacement of steric 6–12 potential-derived interaction energies by atombased indicator variables in CoMFA leads to models of higher consistency, J. Comput.-Aid. Mol. Design, 9(1995)205–212.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1998 Kluwer Academic Publishers
About this chapter
Cite this chapter
Kim, K.H. (1998). Building a Bridge between G-Protein-Coupled Receptor Modelling, Protein Crystallography and 3D QSAR Studies for Ligand Design. In: Kubinyi, H., Folkers, G., Martin, Y.C. (eds) 3D QSAR in Drug Design. Three-Dimensional Quantitative Structure Activity Relationships, vol 3. Springer, Dordrecht. https://doi.org/10.1007/0-306-46858-1_15
Download citation
DOI: https://doi.org/10.1007/0-306-46858-1_15
Publisher Name: Springer, Dordrecht
Print ISBN: 978-0-7923-4791-0
Online ISBN: 978-0-306-46858-2
eBook Packages: Springer Book Archive