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Volumn 2, Issue 4, 2011, Pages 293-297

Homology model versus X-ray structure in receptor-based drug design: A retrospective analysis with the dopamine D3 receptor

Author keywords

docking; Dopamine D3 receptor; G protein coupled receptors; homology model; lead optimization

Indexed keywords

DOPAMINE 3 RECEPTOR; G PROTEIN COUPLED RECEPTOR;

EID: 79954578394     PISSN: None     EISSN: 19485875     Source Type: Journal    
DOI: 10.1021/ml100288q     Document Type: Article
Times cited : (19)

References (34)
  • 1
    • 71749086377 scopus 로고    scopus 로고
    • G Protein-Coupled Receptors: Target-based in silico screening
    • Senderowitz, H.; Marantz, Y. G Protein-Coupled Receptors: Target-based in silico screening Curr. Pharm. Des. 2009, 15, 4049-4068
    • (2009) Curr. Pharm. Des. , vol.15 , pp. 4049-4068
    • Senderowitz, H.1    Marantz, Y.2
  • 2
    • 71749112086 scopus 로고    scopus 로고
    • Customizing G Protein-coupled receptor models for structure-based virtual screening
    • de Graaf, C.; Rognan, D. Customizing G Protein-coupled receptor models for structure-based virtual screening Curr. Pharm. Des. 2009, 15, 4026-4048
    • (2009) Curr. Pharm. Des. , vol.15 , pp. 4026-4048
    • De Graaf, C.1    Rognan, D.2
  • 4
    • 33749521608 scopus 로고    scopus 로고
    • Latest development in drug discovery on G protein-coupled receptors
    • DOI 10.2174/138920306778559403
    • Lundstrom, K. Latest development in drug discovery on G protein-coupled receptors Curr. Protein Pept. Sci. 2006, 7, 465-470 (Pubitemid 44524494)
    • (2006) Current Protein and Peptide Science , vol.7 , Issue.5 , pp. 465-470
    • Lundstrom, K.1
  • 14
    • 33745714411 scopus 로고    scopus 로고
    • On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins
    • Forrest, L. R.; Tang, C. L.; Honig, B. On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins Biophys. J. 2006, 91, 508-517
    • (2006) Biophys. J. , vol.91 , pp. 508-517
    • Forrest, L.R.1    Tang, C.L.2    Honig, B.3
  • 15
    • 79958097972 scopus 로고    scopus 로고
    • Exploring the structure of opioid receptors with homology modeling based on single and multiple templates and subsequent docking: A comparative study
    • Bera, I.; Laskar, A.; Ghoshal, N. Exploring the structure of opioid receptors with homology modeling based on single and multiple templates and subsequent docking: A comparative study J. Mol. Model. 2010, 1-15
    • (2010) J. Mol. Model. , pp. 1-15
    • Bera, I.1    Laskar, A.2    Ghoshal, N.3
  • 16
    • 0025179967 scopus 로고
    • Molecular cloning and characterization of a novel dopamine receptor (D3) as a target for neuroleptics
    • Sokoloff, P.; Giros, B.; Martres, M.-P.; Bouthenet, M.-L.; Schwartz, J.-C. Molecular cloning and characterization of a novel dopamine receptor (D3) as a target for neuroleptics Nature 1990, 347, 146-151
    • (1990) Nature , vol.347 , pp. 146-151
    • Sokoloff, P.1    Giros, B.2    Martres, M.-P.3    Bouthenet, M.-L.4    Schwartz, J.-C.5
  • 17
    • 0037235663 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    • DOI 10.1002/prot.10237
    • Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets? Proteins 2003, 50, 5-25 (Pubitemid 36090604)
    • (2003) Proteins: Structure, Function and Genetics , vol.50 , Issue.1 , pp. 5-25
    • Bissantz, C.1    Bernard, P.2    Hibert, M.3    Rognan, D.4
  • 18
    • 43949095157 scopus 로고    scopus 로고
    • 2-adrenergic receptor
    • DOI 10.1021/jm800044k
    • Costanzi, S. 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 J. Med. Chem. 2008, 51, 2907-2914 (Pubitemid 351706019)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.10 , pp. 2907-2914
    • Costanzi, S.1
  • 19
    • 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
    • DOI 10.1021/bi972241y
    • Javitch, J. A.; Ballesteros, J. A.; Weinstein, H.; Chen, J. 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 (Pubitemid 28100601)
    • (1998) Biochemistry , vol.37 , Issue.4 , pp. 998-1006
    • Javitch, J.A.1    Ballesteros, J.A.2    Weinstein, H.3    Chen, J.4
  • 20
    • 0033045716 scopus 로고    scopus 로고
    • 3 dopamine receptors
    • DOI 10.1046/j.1471-4159.1999.0722621.x
    • Sartania, N.; Strange, P. G. Role of Conserved Serine Residues in the Interaction of Agonists with D3 Dopamine Receptors J. Neurochem. 1999, 72, 2621-2624 (Pubitemid 29242216)
    • (1999) Journal of Neurochemistry , vol.72 , Issue.6 , pp. 2621-2624
    • Sartania, N.1    Strange, P.G.2
  • 21
    • 0028971630 scopus 로고
    • Hydrophobic Residues of the D2 Dopamine Receptor Are Important for Binding and Signal Transduction
    • Cho, W.; Taylor, L. P.; Mansour, A.; Akil, H. Hydrophobic Residues of the D2 Dopamine Receptor Are Important for Binding and Signal Transduction J. Neurochem. 1995, 65, 2105-2115
    • (1995) J. Neurochem. , vol.65 , pp. 2105-2115
    • Cho, W.1    Taylor, L.P.2    Mansour, A.3    Akil, H.4
  • 25
    • 0031595788 scopus 로고    scopus 로고
    • 3 receptor binding site by pharmacological characterization of mutants expressed in CHO cells with the Semliki Forest virus system
    • Lundstrom, K.; Turpin, M. P.; Large, C.; Robertson, G.; Thomas, P.; Lewell, X. Q. Mapping of Dopamine D3 Receptor Binding Site by Pharmacological Characterization of Mutants Expressed in Cho Cells with the Semliki Forest Virus System J. Recept. Signal Transduction 1998, 18, 133-150 (Pubitemid 28299116)
    • (1998) Journal of Receptor and Signal Transduction Research , vol.18 , Issue.2-3 , pp. 133-150
    • Lundstrom, K.1    Turpin, M.P.2    Large, C.3    Robertson, G.4    Thomas, P.5    Lewell, X.-Q.6
  • 26
    • 9444228286 scopus 로고    scopus 로고
    • Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain
    • DOI 10.1124/mol.104.001321
    • Kortagere, S.; Gmeiner, P.; Weinstein, H.; Schetz, J. A. Certain 1,4-Disubstituted Aromatic Piperidines and Piperazines with Extreme Selectivity for the Dopamine D4 Receptor Interact with a Common Receptor Microdomain Mol. Pharmacol. 2004, 66, 1491-1499 (Pubitemid 39564775)
    • (2004) Molecular Pharmacology , vol.66 , Issue.6 , pp. 1491-1499
    • Kortagere, S.1    Gmeiner, P.2    Weinstein, H.3    Schetz, J.A.4
  • 27
    • 79954588238 scopus 로고    scopus 로고
    • We developed a dedicated scoring function (D3R-score) by using a consensus of functions DOCK-SCORE, PLP1, and Ludi-1. logD was added to the energy term to account for the cost of ligand desolvation. The principal moment of inertia along Y -axis was also added to penalize folded conformers of ligands: D3R-score = DOCK-SCORE × PLP1 × Ludi-1 × logD × PMI-Y
    • We developed a dedicated scoring function (D3R-score) by using a consensus of functions DOCK-SCORE, PLP1, and Ludi-1. logD was added to the energy term to account for the cost of ligand desolvation. The principal moment of inertia along Y -axis was also added to penalize folded conformers of ligands: D3R-score = DOCK-SCORE × PLP1 × Ludi-1 × logD × PMI-Y
  • 28
    • 17144385534 scopus 로고    scopus 로고
    • Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
    • DOI 10.1021/jm049092j
    • Triballeau, N.; Acher, F.; Brabet, I.; Pin, J.-P.; Bertrand, H.-O. Virtual Screening Workflow Development Guided by the Receiver Operating Characteristic Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4 J. Med. Chem. 2005, 48, 2534-2547 (Pubitemid 40520517)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.-P.4    Bertrand, H.-O.5
  • 29
    • 77957820654 scopus 로고    scopus 로고
    • Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
    • Chang, M. W.; Ayeni, C.; Breuer, S.; Torbett, B. E. Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina PLoS ONE 2010, 5, e11955
    • (2010) PLoS ONE , vol.5 , pp. 11955
    • Chang, M.W.1    Ayeni, C.2    Breuer, S.3    Torbett, B.E.4
  • 30
    • 65249117481 scopus 로고    scopus 로고
    • Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase
    • Hevener, K. E.; Zhao, W.; Ball, D. M.; Babaoglu, K.; Qi, J.; White, S. W.; Lee, R. E. Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase J. Chem. Inf. Model. 2009, 49, 444-460
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 444-460
    • Hevener, K.E.1    Zhao, W.2    Ball, D.M.3    Babaoglu, K.4    Qi, J.5    White, S.W.6    Lee, R.E.7
  • 31
    • 67650097331 scopus 로고    scopus 로고
    • Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
    • Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy J. Chem. Inf. Model. 2009, 49, 1455-1474
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1455-1474
    • Cross, J.B.1    Thompson, D.C.2    Rai, B.K.3    Baber, J.C.4    Fan, K.Y.5    Hu, Y.6    Humblet, C.7
  • 32
    • 65049089399 scopus 로고    scopus 로고
    • Identifying conformational changes of the β-2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators
    • Reynolds, K.; Katritch, V.; Abagyan, R. Identifying conformational changes of the β-2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators J. Comput.-Aided Mol. Des. 2009, 23, 273-288
    • (2009) J. Comput.-Aided Mol. Des. , vol.23 , pp. 273-288
    • Reynolds, K.1    Katritch, V.2    Abagyan, R.3
  • 33
    • 79954586733 scopus 로고    scopus 로고
    • note
    • i threshold of 3.5 nM, it is divided in two equal subpopulations (775 active and 804 inactive ligands). Sensitivity Se = TP/(TP + FN) and specificity Sp = TN/(TN + FP) were calculated at this threshold. Here, TP stands for true positives, FN for false negatives, TN for true negatives, and FP for false positives. The protonation of ligands was supposed to be the majority state at pH 7. Conformers were generated with the Catalyst module implemented in Discovery Studio (around 250 conformers obtained with the "best" method, with an energy threshold of 20 kcal/mol).
  • 34
    • 33846905526 scopus 로고    scopus 로고
    • Recent progress in development of dopamine receptor subtype-selective agents: Potential therapeutics for neurological and psychiatric disorders
    • DOI 10.1021/cr050263h
    • Zhang, A.; Neumeyer, J. L.; Baldessarini, R. J. Recent Progress in Development of Dopamine Receptor Subtype-Selective Agents: Potential Therapeutics for Neurological and Psychiatric Disorders Chem. Rev. 2006, 107, 274-302 (Pubitemid 46237370)
    • (2007) Chemical Reviews , vol.107 , Issue.1 , pp. 274-302
    • Zhang, A.1    Neumeyer, J.L.2    Baldessarini, R.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.