Predictions of binding for dopamine D2 receptor antagonists by the SIE method

Journal of Chemical Information and Modeling

Volumn 49, Issue 10, 2009, Pages 2369-2375

  Wang, Yeng Tseng ^a,b   Su, Zhi Yuan ^c   Hsieh, Chang Huain ^a   Chen, Cheng Lung ^b  

^a NATIONAL CENTER FOR HIGH PERFORMANCE COMPUTING   (Taiwan)

^b NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^c CHIA NAN UNIVERSITY OF PHARMACY AND SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; CRYSTALS; MOLECULAR DYNAMICS; NEUROPHYSIOLOGY;

BINDING AFFINITIES; BINDING MODES; BINDING POCKETS; HOMOLOGY MODELS; INTERACTION ENERGIES; MOLECULAR DYNAMICS SIMULATIONS; POTENTIAL TARGETS; RECEPTOR ANTAGONISTS;

BINDING ENERGY;

DOPAMINE 2 RECEPTOR; HETEROCYCLIC COMPOUND; SOLVENT;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CONFORMATION; DRUG ANTAGONISM; HUMAN; IC 50; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN BINDING; SEQUENCE HOMOLOGY; THERMODYNAMICS;

AMINO ACID SEQUENCE; HETEROCYCLIC COMPOUNDS; HUMANS; INHIBITORY CONCENTRATION 50; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; RECEPTORS, DOPAMINE D2; SEQUENCE HOMOLOGY, AMINO ACID; SOLVENTS; THERMODYNAMICS;

EID: 70350501157     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9002238     Document Type: Article

References (53)

1. Missale, C.; Nash, S. R.; Robinson, S. W.; Jaber, M.; Caron, M. G. Dopamine receptors: from structure to function. Phvsiol. Rev. 1998, 78, 189-225.
2. Lotharius, J.; Brundin, P. Pathogenesis of parkinson's disease: dopamine, vesicles and alpha-synuclein. Nature Rev. Neurosci. 2002, 3, 932-942.
3. Kapur, S.; Mamo, D. Half a century of antipsychotics and still a central role for dopamine D2 receptors. Proe. Neuropsychopharm. Bio. Psych. 2003, 27, 1081-1090.
4. Jin, G. Z.; Zhu, A. T.; Fu, Y. Stepholidine: a potential novel antipsychotic drug with dual Dl receptor agonist and D2 receptor antagonist actions. Trends Pharmacol, Sci. 2002, 23, A-I.
5. Neville, M. J.; Johnstone, E. C.; Walton, R. T. Identification and characterization of ANKKl: a novel kinase gene closely linked to DRD2 on chromosome band llq23.1. Hum. Mutat. 2004, 23, 540545.
6. (6) Payne, S. L.; Johansson, A. M.; Strange, P. G. Mechanisms of ligand binding and efficacy at the human D2(short) dopamine receptor. J. Neurochem. 2002, 82, 1106-1117. (Pubitemid 34966623)
7. Javitch, J. A.; Fu, D.; Chen, J.; Karlin, A. Mapping the binding-site crevice of the dopamine D2 receptor by the substitutedcysteine accessibility method. J. Neuron 1995, 14, 825-831.
8. Grandt, P.; Husband, S. L. J.; Luedtke, R. R.; Taylor, M.; Newman, A. H. Analogues of the dopamine D2 receptor antagonist L741.626: binding, function, and SAR. Bioorg. Med Chem. Lett. 2007,17, 745749.
9. Imhof, R.; Godel, T.; Burkard, W. P.; Keller, H. H.; Da, P. M.; Scherschilicht, R. New insight into structural and stereochemical requirements for selective, high affinity ligands at the dopamine D2 receptor. Neurochem. Int. 1992, 20, 75S-80S.
10. Naijue, Z.; Li, L.; Stevens, C. L. K. A CoMFA study of Dopamine D2 Receptor Agonists and X-Ray Crystal Structure of Quinelorane Dihydrochloride Dihydrate, R(-)-Apomorphine Hydrochloride and R(-)-N-n-Propylnorapomorphine Hydrochloride. Struct. Chem. 2004, 6, 553-565.
11. Chidester, C. G.; Lin, C. H.; Lahti, R. A.; Haadsma-Svensson, S. R.; Smith, M. W. Comparison of 5-H.TlA and dopamine D2 pharmacophores. X-ray structures and affinities of conformationally constrained ligands. J. Med. Chem. 1993, 36, 1301-1315.
12. Johansson, A. M..; Karlen, A.; Grol, C. J.; Sundell, S.; Kenne, L.; Hacksell, U. J. Dopaminergic 2-aminotetralins: affinities for dopamine D2-receptors, molecular structures, and conformational preferences. Mal, Pharmacol. 1986, 30, 258-269.
13. Grözinger, M.¡ Dragicevic, A.; Hiemke, C.; Shams, M.; Müller, M. J.; Härtter, S. Melperone is an inhibitor of the CYP2.D6 catalyzed O-demethylation of venlafaxine. Pharmacopsychiatry 2003, 36, 3-6.
14. (14) Szarfman, A.; Tonning, J. M.; Levine, J. G.; Doraiswamy, P. M. Atypical antipsychotics and pituitary tumors: a pharmacovigilance study. Pharmacotherapy 2006, 26, 748-758 (Pubitemid 43807626)
15. Seeman, P.; Watanabe, M.; Grigoriadis, D.; Tedesco, J. L.; George, S. R.; Svensson, U.; Nissan, J. L. G.; Neumeyer, J. L. Dopamine D2 receptor binding sites for agonists. Mal- Pharmacol 1985, 28, 391-399.
16. Mewshaw, R. E.; Verwijs, A.; Shi, X.; McGaughey, G. B.; Nelson, J. A.; Mazandarani, H.; Brennan, J. A.; Marquis, K. L.; Coupet, J.; Andree, T. H. New generation dopaminergic agents. 5. heterocyclic bioisosteres that exploit the 3-O.H-N.l-phenylpiperazine dopaminergic template. Bioorg. Med. Chem. Lett. 1998, 5, 2675-2680.
17. Martin, Y. C.; Bures, M. G.; Dabaher, E. A.; Delazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. .7. ComputAided Mol. Des. 1993, 7, 83-102.
18. Newman, A. H.; Grandt, P.; Cyriac, G.; Deschamps, J. R.; Taylor, M.; Kumar, R.; Ho, D.; Luedtke, R. R. N-(4-(4-(2,3-Dichloro-or2methoxyphe.nyl) piperazin-l-yl)butyl)heterobiarylcarboxamides with functionalized linking chains as high affinity and enantioselective D3 receptor antagonists. J. Med. Chem. 2009, 52, 2559-2570.
19. Fu, W.; Shen, J.; Luo, X.; Zhu, W.; Cheng, J.; Yu, K.; Briggs, J. M.; Jin, G.; Chen, K.; Jiang, H. Dopamine Dl Receptor Agonist and D2 Receptor Antagonist Effects of the Natural Product (2)-Stepholidine: Molecular Modeling and Dynamics Simulations, Biophys J. 2007, 93, 1431-1441.
20. (20) Nervall, M.; Hanspers, P.; Carlsson, J.; Boukharta, L.; Ãqvist, J. Predicting binding modes from free energy calculations. J. Med. Chem. 2008, 51, 2657-2667. (Pubitemid 351620787)
21. Bertolino, A.; Fazio, L.; Giorgio, A.; Blasi, G.; Romano, R.; Taurisano, P.; Caforio, G.; Sinibaldi, L.; Ursini, G.; Popolizio, T.; Tirotta, E.; Papp, A.; Dallapiccola, B.; Borrelli, E.; Sadee, W. Genetically Determined Interaction between the Dopamine Transporter and the D2 Receptor on Prefronto-Striatal Activity and Volume in Humans. J. Neurosci. 2009, 29, 1224-1234.
22. Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J. H.; Zhang, Z.; Miller, W.; Lipman, J. T. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402.
23. Hanson, M. A.; Cherezov, V.; Griffith, M. T.; Roth, C. B.; Jaakola, V. P.; Chien, E. Y.; Velasquez, J.; Kuhn, P.; Stevens, R. C. A specific cholesterol binding site is established by the 2.8 A structure of the human beta2-adrenergic receptor. Structure 2008, 16, 897-905.
24. Rosenbaum, D. M.; Cherezov, V.; Hanson, M. A.; Rasmussen, S. G.; Thian, F. S.; Kobilka, T. S.; Choi, H. J.; Yao, X. Y.; Weis, W. I.; Stevens, R. C.; Kobilka, B. K. GPCR engineering yields highresolution structural insights into beta2-adrenergic receptor function. Science 2007, 318, 1266-1273.
25. Jaakola, V. P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y.; Lane, J. R.; Ijzerman, A. P.; Stevens, R. C. The 2.6 a crystal structure of a human a2a adenosine receptor bound to zm241385. Science 2008, 522, 1211-1217.
26. Rasmussen, S. G.; Choi, H. T.; Rosenbaum, D. M.; Kobilka, T. S.; Thian, F. S.; Edwards, P. C.; Burghammer, M.; Ratnala, V. R.; anishvili, R.; Fischetti, R. F.; Schertler, G. F.; Weis, W. L.; Kobilka, B. K. Crystal structure of the human beta2 adrenergic G-proteincoupled receptor. Nature 2007, 450, 383-387.
27. Thompson, J. D.; Gibson, T. J.; Plewniak, F.; Jeanmougin, F.; Higgins, D. G. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876-14782
28. (28) Marti-Renom, M., A.; Stuart, A.; Fiser, A.; Sánchez, R.; Melo, F.; Sali, A. Comparative protein, structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol, Struct. 2000, 29, 291-325. (Pubitemid 30599596)
29. (29) Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815. (Pubitemid 24007801)
30. Fiser, A.; Do, R. K.; Sali, A. Modeling of loops in protein structures. Protein Sci. 2000, 9, 1753-1773.
31. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 16681688.
32. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl, Crystallogr. 1993, 26, 283-291.
33. SYBYL, version 8.1; Tripos International: St. Louis, MO, 2008.
34. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol, Biol. 1997, 267, 727-748.
35. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general Amber force field. J. Comput. Chem. 2004,25, 1157-1174.
36. Bren, U.; Hodoscek, M.; Koller, J. Development and validation of empirical force field parameters for netropsin. J. Chem. Inf. Model. 2005, 45, 1546-1552.
37. Vailikhita, V.; Treesuwana, W.; Hannongbua, S. A combined MD-ONIOM2 approach for IH NMR chemical shift calculations including a polar solvent. J. Mol, Struct.: THEOCHEM. 2007, 806, 99-104.
38. (38) Lu, Q.; Tan, Y. H.; Luo, R. Molecular dynamics simulations of p53 DNA-binding domain. J.Phys. Chem. B 2007, 111, 11538-11545. (Pubitemid 47598337)
39. Li, W.; Ode, H.; Hoshino, T.; Liu, H.; Tang, Y.; Jiang, H. Reduced catalytic activity of P450 2A6 mutants with Coumarin: a computational investigation, J. Chem. Theory Comput. 2009, 5, 411-1420.
40. Olson, A. J.; Hu, Y. H.; Keinan, E. Chemical mimicry of viral capsid self-assembly. Pjpc. Natl. Acad Sd. 2007, 104, 20731-20736.
41. Gaussian 03, version C.02; Gaussian, Inc.: Wallingford, CT, 2004.
42. Wang, J. M.; Wang, W.; Kollman, P. A. Antechamber: An accessory software package for molecular mechanical calculations. Abstr. Pap. Am. Chem. Soc. 2001, 222, U403-U403.
43. Ryckaert, J. P.; Ciccotti, G. Andersen's canonical-ensemble molecular dynamics for molecules with constraints. Mol Phys. 1986, 58, 11251136.
44. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. integration of the cartesian equations of motion of a system with constrains: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
45. Wolber, G.; Dornhofer, A. A.; Langer, T. Efficient overlay of small organic molecules using 3D pharmacophores. J.comput.-Aided Mol Des. 2007, 20, 773-788.
46. Perdih, A.; Bren, U.; Solmajer, T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase. J. Mol, Model. 2009, 15, 983-996.
47. Bren, U.; Martínek, V.; Florián, J. Free energy simulations of uncatalyzed DNA replication fidelity: structure and stability of T-G and dTTP-G terminal DNA mismatches flanked by a single dangling nucleotide, Phys. Chem. B 2006, 110, 10557-10566.
48. (48) Åqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drag design. Protein Eng. 1994, 7, 385-391. (Pubitemid 24063137)
49. Naïm, M.; Bhat, S.; Rankin, K. N.; Dennis, S.; Chowdhury, S. F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C.; Jakalian, A.; Purisima, E. O. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. J. Chem. Inf. Model 2007, 47, 122-133.
50. Purisima, E. O. Fast Summation Boundary Element Method for Calculating Solvation Free Energies of Macromolecules. J. Comput. Chem. 1998, 19, 1494-1504.
51. Purisima, E. O.; Nilar, S. H. A. simple yet accurate boundary element method for continuum dielectric calculations. J. Comput. Chem. 1995, 16, 681-689.
52. Bhat, S.; Purisima, E. O. Molecular surface generation using a variableradius solvent probe. Proteins: Struct., Fund., Bioinf. 2006, 62, 244261.
53. Cui, Q.; Sulea, T.; Schrag, J. D.; Munger, C.; Hung, M.-N.; Naïm, M.; Cygler, M.; Purisima, E. O. Molecular Dynamics and Solvated Interaction Energy Studies of Protein-Protein Interactions: the MP1-pl4 Scaffolding Complex. J. Mol. Biol, 2008, 379, 787-802.