Molecular modeling and docking study on dopamine D2-like and serotonin 5-HT2A receptors

Journal of Molecular Graphics and Modelling

Volumn 57, Issue , 2015, Pages 143-155

  Duan, Xinli ^a   Zhang, Min ^a   Zhang, Xin ^a   Wang, Fang ^a   Lei, Ming ^a  

^a BEIJING UNIVERSITY OF CHEMICAL TECHNOLOGY   (China)

Author keywords

5 Hydroxytryptamine receptor; Docking; Dopamine receptor; Homology modeling; Molecular dynamics

Indexed keywords

AMINES; AROMATIC COMPOUNDS; BINDING ENERGY; DOCKING; MOLECULAR DYNAMICS; NEUROPHYSIOLOGY;

5-HYDROXYTRYPTAMINE RECEPTOR; DOPAMINE RECEPTOR; HIGH RESOLUTION CRYSTAL STRUCTURE; HOMOLOGY MODELING; MOLECULAR DYNAMICS SIMULATIONS; POLYCYCLIC AROMATIC COMPOUNDS; ROOT MEAN SQUARE DEVIATIONS; SITE DIRECTED MUTAGENESIS;

CRYSTAL STRUCTURE;

APOMORPHINE; BROMPERIDOL; BUTYROPHENONE DERIVATIVE; CLOZAPINE; DOPAMINE 2 RECEPTOR; DOPAMINE 3 RECEPTOR; DOPAMINE 4 RECEPTOR; ETICLOPRIDE; HALOPERIDOL; METERGOLINE; PIMOZIDE; PIPERIDINE DERIVATIVE; POLYCYCLIC AROMATIC COMPOUND; PRAMIPEXOLE; RACLOPRIDE; RISPERIDONE; SEROTONIN 2A RECEPTOR; SERTINDOLE; TRAZODONE; XANOMELINE; ZIPRASIDONE; SALICYLAMIDE DERIVATIVE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; DISULFIDE BOND; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; THREE DIMENSIONAL IMAGING; VIRTUAL REALITY; CHEMISTRY; HUMAN; PROTEIN SECONDARY STRUCTURE; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; HUMANS; MOLECULAR DOCKING SIMULATION; PROTEIN STRUCTURE, SECONDARY; RECEPTOR, SEROTONIN, 5-HT2A; RECEPTORS, DOPAMINE D2; SALICYLAMIDES; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84923686681     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2015.01.014     Document Type: Article

References (77)

1. R. Tandon, M.S. Keshavan, and H.A. Nasrallah Schizophrenia, "just the facts" what we know in 2008. 2. Epidemiology and etiology Schizophr. Res. 102 2008 1 18
2. H.M. Ibrahim, and C.A. Tamminga Schizophrenia: treatment targets beyond monoamine systems Annu. Rev. Pharmacol. Toxicol. 51 2011 189 209
3. J. van Os, and S. Kapur Schizophrenia Lancet 374 2009 635 645
4. S. Saha, D. Chant, and J. McGrath A systematic review of mortality in schizophrenia: is the differential mortality gap worsening over time? Arch. Gen. Psychiatry 64 2007 1123
5. R. Tandon, H.A. Nasrallah, and M.S. Keshavan Schizophrenia, "just the facts" 4. Clinical features and conceptualization Schizophr. Res. 110 2009 1 23
6. S. Miyamoto, G. Duncan, C. Marx, and J. Lieberman Treatments for schizophrenia: a critical review of pharmacology and mechanisms of action of antipsychotic drugs Mol. Psychiatry 10 2004 79 104
7. D. Mamo, S. Kapur, C. Shammi, G. Papatheodorou, S. Mann, F. Therrien, and G. Remington A PET study of dopamine D2 and serotonin 5-HT2 receptor occupancy in patients with schizophrenia treated with therapeutic doses of ziprasidone Am. J. Psychiatry 161 2004 818 825
8. A.B. Minns, and R.F. Clark Toxicology and overdose of atypical antipsychotics J. Emerg. Med. 43 2012 906 913
9. H.Y. Meltzer, and S.M. Stahl The dopamine hypothesis of schizophrenia Schizophr. Bull. 2 1976 19 76
10. H.Y. Meltzer Update on typical and atypical antipsychotic drugs Annu. Rev. Med. 64 2013 393 406
11. H.Y. Meltzer An atypical compound by any other name is still a Psychopharmacology (Berl.) 148 2000 16 19
12. C. Toro, and J. Deakin Adult neurogenesis and schizophrenia: a window on abnormal early brain development? Schizophr. Res. 90 2007 1 14
13. A. Abi-Dargham, and M. Laruelle Mechanisms of action of second generation antipsychotic drugs in schizophrenia: insights from brain imaging studies Eur. Psychiatry 20 2005 15 27
14. D.E. Casey Clozapine: neuroleptic-induced EPS and tardive dyskinesia Psychopharmacology (Berl.) 99 Suppl. 1989 S47 S53
15. M.W. Jann Clozapine Pharmacotherapy 11 1991 179 195
16. 2 receptor occupancy profile of loxapine determined using PET Neuropsychopharmacology 15 1996 562 566
17. G. Seminara, V. Trassari, N. Prestifilippo, R. Chiavetta, and C. Calandra Atypical tricyclic neuroleptics for treatment of schizophrenia. Clothiapine and clozapine Minerva Psychiatry 34 1993 95 99
18. I. Creese, D.R. Burt, and S.H. Snyder Dopamine receptor binding predicts clinical and pharmacological potencies of antischizophrenic drugs Science 192 1976 481 483
19. S. Kapur, and P. Seeman Antipsychotic agents differ in how fast they come off the dopamine D2 receptors. Implications for atypical antipsychotic action J. Psychiatry Neurosci. 25 2000 161
20. 2A receptor antagonism potentiates haloperidol-induced dopamine release in rat medial prefrontal cortex and inhibits that in the nucleus accumbens in a dose-dependent manner Brain Res. 947 2002 157 165
21. S. Bhattacharyya, I. Raote, A. Bhattacharya, R. Miledi, and M.M. Panicker Activation, internalization, and recycling of the serotonin 2A receptor by dopamine Proc. Natl. Acad. Sci. U. S. A. 103 2006 15248 15253
22. H.Y. Meltzer, Z. Li, Y. Kaneda, and J. Ichikawa Serotonin receptors: their key role in drugs to treat schizophrenia Prog. Neuropsychopharmacol. Biol. Psychiatry 27 2003 1159 1172
23. G. Gross, K. Wicke, and K.U. Drescher Dopamine D3 receptor antagonism - still a therapeutic option for the treatment of schizophrenia Naunyn. Schmiedebergs Arch. Pharmacol. 386 2013 155 166
24. F. Lejeune, and M.J. Millan Activation of dopamine D3 autoreceptors inhibits firing of ventral tegmental dopaminergic neurones in vivo Eur. J. Pharmacol. 275 1995 R7 R9
25. M.A. Ungless, and A.A. Grace Are you or aren't you? Challenges associated with physiologically identifying dopamine neurons Trends Neurosci. 35 2012 422 430
26. L. Redden, B. Rendenbach-Mueller, W.M. Abi-Saab, D.A. Katz, A. Goenjian, W.Z. Robieson, Y. Wang, S.L. Goss, N. Greco IV, and M.D. Saltarelli A double-blind, randomized, placebo-controlled study of the dopamine D3 receptor antagonist ABT-925 in patients with acute schizophrenia J. Clin. Psychopharmacol. 31 2011 221 225
27. S. Fujisawa, and G. Buzsaki A 4 Hz oscillation adaptively synchronizes prefrontal, VTA, and hippocampal activities Neuron 72 2011 153 165
28. N. Ginovart, and S. Kapur Role of dopamine D2 receptors for antipsychotic activity Current Antipsychotics 2012 Springer 27 52
29. H. Tost, T. Alam, and A. Meyer-Lindenberg Dopamine and psychosis: theory, pathomechanisms and intermediate phenotypes Neurosci. Biobehav. Rev. 34 2010 689 700
30. S. Linz, J. Müller, H. Hübner, P. Gmeiner, and R. Troschütz Design, synthesis and dopamine D4 receptor binding activities of new N-heteroaromatic 5/6-ring Mannich bases Bioorg. Med. Chem. 17 2009 4448 4458
31. M.A. Sanner, T.A. Chappie, A.R. Dunaiskis, A.F. Fliri, K.A. Desai, S.H. Zorn, E.R. Jackson, C.G. Johnson, J.M. Morrone, and P.A. Seymour Synthesis, SAR and pharmacology of CP-293, 019: a potent, selective dopamine D4 receptor antagonist Bioorg. Med. Chem. Lett. 8 1998 725 730
32. 6 receptors in learning and memory Trends Pharmacol. Sci. 29 2008 482 492
33. 1A receptors in learning and memory Behav. Brain Res. 195 2008 54 77
34. S. Butini, S. Gemma, G. Campiani, S. Franceschini, F. Trotta, M. Borriello, N. Ceres, S. Ros, S.S. Coccone, and M. Bernetti Discovery of a new class of potential multifunctional atypical antipsychotic agents targeting dopamine D3 and serotonin 5-HT1A and 5-HT2A receptors: design, synthesis, and effects on behavior J. Med. Chem. 52 2008 151 169
35. D.H. Kim, and S.M. Stahl Antipsychotic Drug Development, Behavioral Neurobiology of Schizophrenia and its Treatment 2010 Springer 123 139
36. M. Angoa-Perez, M.J. Kane, D.I. Briggs, N. Herrera-Mundo, C.E. Sykes, D.M. Francescutti, and D.M. Kuhn Mice genetically depleted of brain serotonin do not display a depression-like behavioral phenotype ACS Chem. Neurosci. 5 2014 908 919
37. D.R. Sibley, and F.J. Monsma Jr. Molecular biology of dopamine receptors Trends Pharmacol. Sci. 13 1992 61 69
38. R.J. Romanelli, J.T. Williams, and K.A. Neve Dopamine receptor signaling: intracellular pathways to behavior The Dopamine Receptors 2010 Springer 137 173
39. P. Sokoloff, and J.-C. Schwartz Novel dopamine receptors half a decade later Trends Pharmacol. Sci. 16 1995 270 275
40. L. Zhao, L. Zhang, and M. Lei 3D-QSAR and docking studies on 2-arylbenzoxazole and linker-Y transthyretin amyloidogenesis inhibitors Sci. China Chem. 56 2013 1550 1563
41. Z. Lijun, and L. Ming Computational chemical studies on transthyretin Prog. Chem. 29 2014 193 202
42. T. Yuan, X. Zhang, Z. Hu, F. Wang, and M. Lei Molecular dynamics studies of the antimicrobial peptides piscidin 1 and its mutants with a DOPC lipid bilayer Biopolymers 97 2012 998 1009
43. K. Ehrlich, A. Gotz, S. Bollinger, N. Tschammer, L. Bettinetti, S. Harterich, H. Hübner, H. Lanig, and P. Gmeiner Dopamine D2, D3, and D4 selective phenylpiperazines as molecular probes to explore the origins of subtype specific receptor binding J. Med. Chem. 52 2009 4923 4935
44. E.Y. Chien, W. Liu, Q. Zhao, V. Katritch, G.W. Han, M.A. Hanson, L. Shi, A.H. Newman, J.A. Javitch, and V. Cherezov Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist Science 330 2010 1091 1095
45. C. Wang, Y. Jiang, J. Ma, H. Wu, D. Wacker, V. Katritch, G.W. Han, W. Liu, X.-P. Huang, and E. Vardy Structural basis for molecular recognition at serotonin receptors Science 340 2013 610 614
46. D. Wacker, C. Wang, V. Katritch, G.W. Han, X.-P. Huang, E. Vardy, J.D. McCorvy, Y. Jiang, M. Chu, and F.Y. Siu Structural features for functional selectivity at serotonin receptors Science 340 2013 615 619
47. L. Shi, and J.A. Javitch The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice Proc. Natl. Acad. Sci. U. S. A. 101 2004 440 445
48. F.M. McRobb, B. Capuano, I.T. Crosby, D.K. Chalmers, and E. Yuriev Homology modeling and docking evaluation of aminergic G protein-coupled receptors J. Chem. Inf. Model. 50 2010 626 637
49. Y.-T. Wang, Z.-Y. Su, C.-H. Hsieh, and C.-L. Chen Predictions of binding for dopamine D2 receptor antagonists by the SIE method J. Chem. Inf. Model. 49 2009 2369 2375
50. Q. Wang, R.H. Mach, R.R. Luedtke, and D.E. Reichert Subtype selectivity of dopamine receptor ligands: insights from structure and ligand-based methods J. Chem. Inf. Model. 50 2010 1970 1985
51. C.B.M. Platania, S. Salomone, G.M. Leggio, F. Drago, and C. Bucolo Homology modeling of dopamine D2 and D3 receptors: molecular dynamics refinement and docking evaluation PLoS ONE 7 2012 e44316
52. S. Costanzi 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. 51 2008 2907 2914
53. M. St. Louis SYBYL-X 1.3, Molecular Modeling Software 2011 Tripos Associates http://www.tripos.com
54. V. Cherezov, D.M. Rosenbaum, M.A. Hanson, S.R.G. Rasmussen, F.S. Thian, T.S. Kobilka, H.-J. Choi, P. Kuhn, W.I. Weis, and B.K. Kobilka High-resolution crystal structure of an engineered human B2-adrenergic G protein-coupled receptor Science 318 2007 1258 1265
55. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
56. Z.-Y. Zhu, A. Ali, and T.L. Blundell A variable gap penalty function and feature weights for protein 3-D structure comparisons Protein Eng. 5 1992 43 51
57. T.A.D.D.A. Case, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R.R.C.W. Luo, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, A.W.G.J. Swails, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, S.R.B.X. Wu, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G.D.R.R. Cui, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T.S.G. Luchko, A. Kovalenko, and P.A. Kollman AMBER 12 2012 University of California San Francisco
58. W.L. Jorgensen Revised TIPS for simulations of liquid water and aqueous solutions J. Chem. Phys. 77 1982 4156 4163
59. J.A.D. Izaguirre, P.J. Catarello, M.R. Wozniak, and D. Skeel Langevin stabilization of molecular dynamics J. Chem. Phys. 114 2001 2090 2098
60. H.J. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684
61. T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N [center-dot] log(N) method for Ewald sums in large systems J. Med. Chem. 98 1993 10089 10092
62. J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
63. B.T.E.W. Sayers, D.A. Benson, E. Bolton, and S.H. Bryant Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 40 2012 D13 D25
64. S.-H. Lee, H.T.M. Van, S.H. Yang, K.-T. Lee, Y. Kwon, and W.-J. Cho Molecular design, synthesis and docking study of benz[b]oxepines and 12-oxobenzo[c]phenanthridinones as topoisomerase 1 inhibitors Bioorg. Med. Chem. Lett. 19 2009 2444 2447
65. J. Sun, S. Cai, N. Yan, and H. Mei Docking and 3D-QSAR studies of influenza neuraminidase inhibitors using three-dimensional holographic vector of atomic interaction field analysis Eur. J. Med. Chem. 45 2010 1008 1014
66. J. Ruppert, W. Welch, and A.N. Jain Automatic identification and representation of protein binding sites for molecular docking Protein Sci. 6 1997 524 533
67. M. Shen, H. Yu, Y. Li, P. Li, P. Pan, S. Zhou, L. Zhang, S. Li, S.M.-Y. Lee, and T. Hou Discovery of Rho-kinase inhibitors by docking-based virtual screening Mol. Biosyst. 9 2013 1511 1521
68. S. Tian, H. Sun, Y. Li, P. Pan, D. Li, and T. Hou Development and evaluation of an integrated virtual screening strategy by combining molecular docking and pharmacophore searching based on multiple protein structures J. Chem. Inf. Model. 53 2013 2743 2756
69. A.A. Ivanov, D. Barak, and K.A. Jacobson Evaluation of homology modeling of G-protein-coupled receptors in light of the A2A adenosine receptor crystallographic structure J. Med. Chem. 52 2009 3284 3292
70. L. Shi, M.M. Simpson, J.A. Ballesteros, and J.A. Javitch The first transmembrane segment of the dopamine D2 receptor: accessibility in the binding-site crevice and position in the transmembrane bundle Biochemistry 40 2001 12339 12348
71. J.A. Javitch, L. Shi, M.M. Simpson, J. Chen, V. Chiappa, I. Visiers, H. Weinstein, and J.A. Ballesteros The fourth transmembrane segment of the dopamine D2 receptor: accessibility in the binding-site crevice and position in the transmembrane bundle Biochemistry 39 2000 12190 12199
72. J.A. Javitch, J.A. Ballesteros, J. Chen, V. Chiappa, and M.M. Simpson Electrostatic and aromatic microdomains within the binding-site crevice of the D2 receptor: contributions of the second membrane-spanning segment Biochemistry 38 1999 7961 7968
73. J.A. Javitch, X. Li, J. Kaback, and A. Karlin A cysteine residue in the third membrane-spanning segment of the human D2 dopamine receptor is exposed in the binding-site crevice Proc. Natl. Acad. Sci. U. S. A. 91 1994 10355 10359
74. J.A. Javitch, D. Fu, and J. Chen Differentiating dopamine D2 ligands by their sensitivities to modification of the cysteine exposed in the binding-site crevice Mol. Pharmacol. 49 1996 692 698
75. J.A. Javitch, D. Fu, J. Chen, and A. Karlin Mapping the binding-site crevice of the dopamine D2 receptor by the substituted-cysteine accessibility method Neuron 14 1995 825 831
76. L. Shi, and J.A. Javitch The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop Annu. Rev. Pharmacol. Toxicol. 42 2002 437 467
77. C.D. Wang, T.K. Gallaher, and J.C. Shih Site-directed mutagenesis of the serotonin 5-hydroxytrypamine2 receptor: identification of amino acids necessary for ligand binding and receptor activation Mol. Pharmacol. 43 1993 931 940