메뉴 건너뛰기




Volumn 51, Issue 10, 2008, Pages 2907-2914

On the applicability of GPCR homology models to computer-aided drug discovery: A comparison between in silico and crystal structures of the β2-adrenergic receptor

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; CARAZOLOL; G PROTEIN COUPLED RECEPTOR; RHODOPSIN;

EID: 43949095157     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm800044k     Document Type: Article
Times cited : (131)

References (63)
  • 2
    • 0027190359 scopus 로고
    • Projection structure of rhodopsin
    • Schertler, G. F.; Villa, C.; Henderson, R. Projection structure of rhodopsin. Nature 1993, 362, 770-772.
    • (1993) Nature , vol.362 , pp. 770-772
    • Schertler, G.F.1    Villa, C.2    Henderson, R.3
  • 3
    • 5044235587 scopus 로고    scopus 로고
    • Electron crystallography reveals the structure of metarhodopsin I
    • Ruprecht, J. J.; Mielke, T.; Vogel, R.; Villa, C.; Schertler, G. F. Electron crystallography reveals the structure of metarhodopsin I. EMBO J. 2004, 23, 3609-3620.
    • (2004) EMBO J , vol.23 , pp. 3609-3620
    • Ruprecht, J.J.1    Mielke, T.2    Vogel, R.3    Villa, C.4    Schertler, G.F.5
  • 7
    • 0035117505 scopus 로고    scopus 로고
    • Minireview: Insights into G protein-coupled receptor function using molecular models
    • Gershengorn, M. C.; Osman, R. Minireview: Insights into G protein-coupled receptor function using molecular models. Endocrinology 2001, 142, 2-10.
    • (2001) Endocrinology , vol.142 , pp. 2-10
    • Gershengorn, M.C.1    Osman, R.2
  • 8
    • 6044234752 scopus 로고    scopus 로고
    • Architecture of P2Y nucleotide receptors: Structural comparison based on sequence analysis, mutagenesis, and homology modeling
    • Costanzi, S.; Mamedova, L.; Gao, Z. G.; Jacobson, K. A. Architecture of P2Y nucleotide receptors: structural comparison based on sequence analysis, mutagenesis, and homology modeling. J. Med. Chem. 2004, 47, 5393-5404.
    • (2004) J. Med. Chem , vol.47 , pp. 5393-5404
    • Costanzi, S.1    Mamedova, L.2    Gao, Z.G.3    Jacobson, K.A.4
  • 9
    • 6944221315 scopus 로고    scopus 로고
    • A model of inverse agonist action at thyrotropin-releasing hormone receptor type 1: Role of a conserved tryptophan in helix 6
    • Lu, X. P.; Huang, W.; Worthington, S.; Drabik, P.; Osman, R.; Gershengorn, M. C. A model of inverse agonist action at thyrotropin-releasing hormone receptor type 1: Role of a conserved tryptophan in helix 6. Mol. Pharmacol. 2004, 66, 1192-1200.
    • (2004) Mol. Pharmacol , vol.66 , pp. 1192-1200
    • Lu, X.P.1    Huang, W.2    Worthington, S.3    Drabik, P.4    Osman, R.5    Gershengorn, M.C.6
  • 11
    • 2942722780 scopus 로고    scopus 로고
    • High-throughput modeling of human G-protein coupled receptors: Amino acid sequence alignment, three-dimensional model building, and receptor library screening
    • Bissantz, C.; Logean, A.; Rognan, D. High-throughput modeling of human G-protein coupled receptors: Amino acid sequence alignment, three-dimensional model building, and receptor library screening. J. Chem. Inf. Comput. Sci. 2004, 44, 1162-1176.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1162-1176
    • Bissantz, C.1    Logean, A.2    Rognan, D.3
  • 13
    • 14044251558 scopus 로고    scopus 로고
    • Agonist-induced corformational changes in thyrotropin-releasing hormone receptor type I: Disulfide cross-linking and molecular modeling approaches
    • Huang, W.; Osman, R.; Gershengorn, M. C. Agonist-induced corformational changes in thyrotropin-releasing hormone receptor type I: Disulfide cross-linking and molecular modeling approaches. Biochemistry 2005, 44, 2419-2431.
    • (2005) Biochemistry , vol.44 , pp. 2419-2431
    • Huang, W.1    Osman, R.2    Gershengorn, M.C.3
  • 14
    • 34250792472 scopus 로고    scopus 로고
    • Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
    • Ivanov, A. A.; Costanzi, S.; Jacobson, K. A. Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling. J. Comput.-Aided Mol. Des. 2006, 20, 417-426.
    • (2006) J. Comput.-Aided Mol. Des , vol.20 , pp. 417-426
    • Ivanov, A.A.1    Costanzi, S.2    Jacobson, K.A.3
  • 15
    • 33745178449 scopus 로고    scopus 로고
    • Ligand-based homology modeling as attractive tool to inspect GPCR structural plasticity
    • Moro, S.; Deflorian, F.; Bacilieri, M.; Spalluto, G. Ligand-based homology modeling as attractive tool to inspect GPCR structural plasticity. Curr. Pharm. Des 2006, 12, 2175-2185.
    • (2006) Curr. Pharm. Des , vol.12 , pp. 2175-2185
    • Moro, S.1    Deflorian, F.2    Bacilieri, M.3    Spalluto, G.4
  • 16
    • 33744761830 scopus 로고    scopus 로고
    • Homology modeling of G-protein-coupled receptors and implications in drug design
    • Patny, A.; Desai, P. V.; Avery, M. A. Homology modeling of G-protein-coupled receptors and implications in drug design. Curr. Med. Chem. 2006, 13, 1667-1691.
    • (2006) Curr. Med. Chem , vol.13 , pp. 1667-1691
    • Patny, A.1    Desai, P.V.2    Avery, M.A.3
  • 17
    • 61849104465 scopus 로고    scopus 로고
    • Implications for understanding molecular function and dysfunction of glycoprotein hormone receptors by a new sequence-structure- function analysis resource
    • Kleinau, G.; Krause, G. Implications for understanding molecular function and dysfunction of glycoprotein hormone receptors by a new sequence-structure- function analysis resource. Exp. Clin. Endocrinol. Diabetes 2007, 115, S34.
    • (2007) Exp. Clin. Endocrinol. Diabetes , vol.115
    • Kleinau, G.1    Krause, G.2
  • 18
    • 34347220548 scopus 로고    scopus 로고
    • Bidirectional, iterative approach to the structural delineation of the functional "Chemoprint" in GPR40 for agonist recognition
    • Tikhonova, I. G.; Sum, C. S.; Neumann, S.; Thomas, C. J.; Raaka, B. M.; Costanzi, S.; Gershengorn, M. C. Bidirectional, iterative approach to the structural delineation of the functional "Chemoprint" in GPR40 for agonist recognition. J. Med. Chem. 2007, 50, 2981-2989.
    • (2007) J. Med. Chem , vol.50 , pp. 2981-2989
    • Tikhonova, I.G.1    Sum, C.S.2    Neumann, S.3    Thomas, C.J.4    Raaka, B.M.5    Costanzi, S.6    Gershengorn, M.C.7
  • 19
    • 34447258678 scopus 로고    scopus 로고
    • Structural models of class A G protein-coupled receptors as a tool for drug design: Insights on transmembrane bundle plasticity
    • Deupi, X.; Dolker, N.; Lopez-Rodriguez, M. L.; Campillo, M.; Ballesteros, J. A.; Pardo, L. Structural models of class A G protein-coupled receptors as a tool for drug design: Insights on transmembrane bundle plasticity. Curr. Top. Med. Chem. 2007, 7, 991-998.
    • (2007) Curr. Top. Med. Chem , vol.7 , pp. 991-998
    • Deupi, X.1    Dolker, N.2    Lopez-Rodriguez, M.L.3    Campillo, M.4    Ballesteros, J.A.5    Pardo, L.6
  • 20
    • 34250902691 scopus 로고    scopus 로고
    • Costanzi, S.; Ivanov, A. A.; Tikhonova, I. G.; Jacobson, K. A. Structure and function of G protein-coupled receptors studied using sequence analysis, molecular modeling, and receptor engineering: Adenosine receptors. In Frontiers in Drug Design and Discovery; Caldwell, G. W., Rahman, A. U., Player, M. R., Chouday, M. I., Eds.; Bentham: The Netherlands, 2007; pp 63-79.
    • Costanzi, S.; Ivanov, A. A.; Tikhonova, I. G.; Jacobson, K. A. Structure and function of G protein-coupled receptors studied using sequence analysis, molecular modeling, and receptor engineering: Adenosine receptors. In Frontiers in Drug Design and Discovery; Caldwell, G. W., Rahman, A. U., Player, M. R., Chouday, M. I., Eds.; Bentham: The Netherlands, 2007; pp 63-79.
  • 21
    • 33747877141 scopus 로고    scopus 로고
    • Human cytidine deaminase: A three-dimensional homology model of a tetrameric metallo-enzyme inferred from the crystal structure of a distantly related dimeric homologue
    • Costanzi, S.; Vincenzetti, S.; Cristalli, G.; Vita, A. Human cytidine deaminase: A three-dimensional homology model of a tetrameric metallo-enzyme inferred from the crystal structure of a distantly related dimeric homologue. J. Mol. Graphics Modell. 2006, 25, 10-16.
    • (2006) J. Mol. Graphics Modell , vol.25 , pp. 10-16
    • Costanzi, S.1    Vincenzetti, S.2    Cristalli, G.3    Vita, A.4
  • 22
    • 0027506471 scopus 로고
    • The probable arrangement of the helices in G protein-coupled receptors
    • Baldwin, J. M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 1993, 12, 1693-1703.
    • (1993) EMBO J , vol.12 , pp. 1693-1703
    • Baldwin, J.M.1
  • 25
    • 0023656534 scopus 로고
    • 2- adrenergic receptor - Localization of the sites of binding, glycosylation, and regulatory phosphorylation by limited proteolysis
    • 2- adrenergic receptor - Localization of the sites of binding, glycosylation, and regulatory phosphorylation by limited proteolysis. J. Biol. Chem. 1987, 262, 14282-14288.
    • (1987) J. Biol. Chem , vol.262 , pp. 14282-14288
    • Dohlman, H.G.1    Bouvier, M.2    Benovic, J.L.3    Caron, M.G.4    Lefkowitz, R.J.5
  • 26
    • 0034948696 scopus 로고    scopus 로고
    • Structural mimicry in G protein-coupled receptors: Implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors
    • Ballesteros, J. A.; Shi, L.; Javitch, J. A. Structural mimicry in G protein-coupled receptors: Implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol. Pharmacol. 2001, 60, 1-19.
    • (2001) Mol. Pharmacol , vol.60 , pp. 1-19
    • Ballesteros, J.A.1    Shi, L.2    Javitch, J.A.3
  • 27
    • 0001228323 scopus 로고
    • A common motif in G-protein-coupled 7 transmembrane helix receptors
    • Oliveira, L.; Paiva, A. C. M.; Vriend, G. A common motif in G-protein-coupled 7 transmembrane helix receptors. J. Comput.-Aided Mol. Des. 1993, 7, 649-658.
    • (1993) J. Comput.-Aided Mol. Des , vol.7 , pp. 649-658
    • Oliveira, L.1    Paiva, A.C.M.2    Vriend, G.3
  • 28
    • 77957055780 scopus 로고
    • Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G-protein coupled receptors
    • Ballesteros, J. A.; Weinstein, H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G-protein coupled receptors. Methods Neurosci. 1995, 25, 366-428.
    • (1995) Methods Neurosci , vol.25 , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 29
    • 0029919840 scopus 로고    scopus 로고
    • vanRhee, A. M.; Jacobson, K. A. Molecular architecture of G protein-coupled receptors. Drug Dev. Res. 1996, 37, 1-38.
    • vanRhee, A. M.; Jacobson, K. A. Molecular architecture of G protein-coupled receptors. Drug Dev. Res. 1996, 37, 1-38.
  • 35
    • 0037020329 scopus 로고    scopus 로고
    • Drug design strategies for targeting G-protein-coupled receptors
    • Klabunde, T.; Hessler, G. Drug design strategies for targeting G-protein-coupled receptors. ChemBioChem 2002, 3, 929-944.
    • (2002) ChemBioChem , vol.3 , pp. 929-944
    • Klabunde, T.1    Hessler, G.2
  • 36
    • 0347123444 scopus 로고    scopus 로고
    • Ligand-supported homology modeling of G-protein-coupled receptor sites: Models sufficient for successful virtual screening
    • Evers, A.; Klebe, G. Ligand-supported homology modeling of G-protein-coupled receptor sites: Models sufficient for successful virtual screening. Angew. Chem., Int. Ed. 2004, 43, 248-251.
    • (2004) Angew. Chem., Int. Ed , vol.43 , pp. 248-251
    • Evers, A.1    Klebe, G.2
  • 37
    • 28644447577 scopus 로고    scopus 로고
    • Focused library design in GPCR projects on the example of 5-HT2c agonists: Comparison of structure-based virtual screening with ligand-based search methods
    • Bissantz, C.; Schalon, C.; Guba, W.; Stahl, M. Focused library design in GPCR projects on the example of 5-HT2c agonists: Comparison of structure-based virtual screening with ligand-based search methods. Proteins: Struct., Funct., Bioinf. 2005, 61, 938-952.
    • (2005) Proteins: Struct., Funct., Bioinf , vol.61 , pp. 938-952
    • Bissantz, C.1    Schalon, C.2    Guba, W.3    Stahl, M.4
  • 38
    • 13944255377 scopus 로고    scopus 로고
    • Structure-based drug discovery using GPCR homology modeling: Successful virtual screening for antagonists of the Alpha1A adrenergic receptor
    • Evers, A.; Klabunde, T. Structure-based drug discovery using GPCR homology modeling: Successful virtual screening for antagonists of the Alpha1A adrenergic receptor. J. Med. Chem. 2005, 48, 1088-1097.
    • (2005) J. Med. Chem , vol.48 , pp. 1088-1097
    • Evers, A.1    Klabunde, T.2
  • 48
    • 33846978093 scopus 로고    scopus 로고
    • Contacts between extracellular loop two and transmembrane helix six determine basal activity of the thyroid-stimulating hormone receptor
    • Kleinau, G.; Claus, M.; Jaeschke, H.; Mueller, S.; Neumann, S.; Paschke, R.; Krause, G. Contacts between extracellular loop two and transmembrane helix six determine basal activity of the thyroid-stimulating hormone receptor. J. Biol. Chem. 2007, 282, 518-525.
    • (2007) J. Biol. Chem , vol.282 , pp. 518-525
    • Kleinau, G.1    Claus, M.2    Jaeschke, H.3    Mueller, S.4    Neumann, S.5    Paschke, R.6    Krause, G.7
  • 49
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali, A.; Blundell, T. L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 50
    • 0028051828 scopus 로고
    • Derivation of rules for comparative protein modeling from a database of protein-structure alignments
    • Sali, A.; Overington, J. P. Derivation of rules for comparative protein modeling from a database of protein-structure alignments. Protein Sci. 1994, 3, 1582-1596.
    • (1994) Protein Sci , vol.3 , pp. 1582-1596
    • Sali, A.1    Overington, J.P.2
  • 51
    • 0028318173 scopus 로고
    • 2-adrenergic receptor requires unique interaction between conserved and nonconserved extracellular loop cysteines
    • 2-adrenergic receptor requires unique interaction between conserved and nonconserved extracellular loop cysteines. J. Biol. Chem. 1994, 269, 6743-6752.
    • (1994) J. Biol. Chem , vol.269 , pp. 6743-6752
    • Noda, K.1    Saad, Y.2    Graham, R.M.3    Karnik, S.S.4
  • 52
    • 43949085806 scopus 로고    scopus 로고
    • 4.5, Schrödinger, LLC
    • Glide, [4.5]; Schrödinger, LLC, 2007.
    • (2007) Glide
  • 53
    • 43949126617 scopus 로고    scopus 로고
    • 1.6, Schrödinger, LLC
    • Prime, [1.6]; Schrödinger, LLC, 2007.
    • (2007) Prime
  • 57
    • 33644865912 scopus 로고    scopus 로고
    • Molecular evolution of adrenoceptors and dopamine receptors: Implications for the binding of catecholamines
    • Xhaard, H.; Rantanen, V. V.; Nyronen, T.; Johnson, M. S. Molecular evolution of adrenoceptors and dopamine receptors: Implications for the binding of catecholamines. J. Med. Chem. 2006, 49, 1706-1719.
    • (2006) J. Med. Chem , vol.49 , pp. 1706-1719
    • Xhaard, H.1    Rantanen, V.V.2    Nyronen, T.3    Johnson, M.S.4
  • 58
    • 33746382921 scopus 로고    scopus 로고
    • 2-adrenoceptor. Nature Chem. Biol. 2006, 2, 417-422.
    • 2-adrenoceptor. Nature Chem. Biol. 2006, 2, 417-422.
  • 60
    • 0032570306 scopus 로고    scopus 로고
    • A cluster of aromatic residues in the sixth membrane-spanning segment of the dopamine D2 receptor is accessible in the binding-site crevice
    • Javitch, J. A.; Ballesteros, J. A.; Weinstein, H.; Chen, J. Y. A cluster of aromatic residues in the sixth membrane-spanning segment of the dopamine D2 receptor is accessible in the binding-site crevice. Biochemistry 1998, 37, 998-1006.
    • (1998) Biochemistry , vol.37 , pp. 998-1006
    • Javitch, J.A.1    Ballesteros, J.A.2    Weinstein, H.3    Chen, J.Y.4
  • 61
  • 62
    • 0043162336 scopus 로고
    • An internal coordinate Monte-Carlo method for searching conformational space
    • Chang, G.; Guida, W. C.; Still, W. C. An internal coordinate Monte-Carlo method for searching conformational space. J. Am. Chem. Soc. 1989, 111, 4379-4386.
    • (1989) J. Am. Chem. Soc , vol.111 , pp. 4379-4386
    • Chang, G.1    Guida, W.C.2    Still, W.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.