Theoretical study of 3-D molecular similarity and ligand binding modes of orthologous human and rat D2 dopamine receptors

Computers in Biology and Medicine

Volumn 41, Issue 7, 2011, Pages 537-545

  Soriano Ursa, Marvin A ^a   Ocampo López, Jorge O ^b   Ocampo Mendoza, Karina ^b   Trujillo Ferrara, Josx G ^a   Correa Basurto, Josx ^a  

^a INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

^b Laboratorio Mexdico Qumico Biolgico   (Mexico)

Author keywords

D2 dopamine receptor ligands; Drug development; Molecular modeling; Parkinsons disease; Rat striatum

Indexed keywords

3D MODELS; ADENOSINE RECEPTOR; BINDING AFFINITIES; BINDING MODES; CENTRAL NERVOUS SYSTEMS; DRUG DEVELOPMENT; DRUG-DEPENDENCE; EXPERIMENTAL DATA; LIGAND AFFINITY; LIGAND BINDING MODE; LIGAND RECOGNITION; MOLECULAR SIMILARITY; PARKINSON DISEASE; PARKINSONS DISEASE; PROTEIN RESIDUES; RAT STRIATUM; RECEPTOR LIGANDS; THEORETICAL STUDY;

BINDING ENERGY; BRAIN; DISEASES; HUMAN FORM MODELS; LIGANDS; RATS;

THREE DIMENSIONAL;

ADENOSINE A2A RECEPTOR; BETA ADRENERGIC RECEPTOR; DOPAMINE 2 RECEPTOR;

ARTICLE; BINDING AFFINITY; DRUG DEPENDENCE; HUMAN; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARKINSON DISEASE; PRIORITY JOURNAL; RAT; SCHIZOPHRENIA; THEORETICAL STUDY;

ANIMALS; HUMANS; LINEAR MODELS; MODELS, MOLECULAR; PROTEIN BINDING; RATS; RECEPTOR, ADENOSINE A2A; RECEPTORS, ADRENERGIC, BETA-2; RECEPTORS, DOPAMINE D2; SEQUENCE ALIGNMENT; STEREOISOMERISM; STRUCTURAL HOMOLOGY, PROTEIN;

RATTUS;

EID: 79959229562     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2011.04.018     Document Type: Article

References (58)

1. Jackson D.M., Wetilind-Danielsson A. Dopamine receptors: molecular biology, biochemistry and behavioural aspects. Pharmacol. Ther. 1994, 64:291-370.
2. Missale C., Nash S.R., Robinson S.W., Jaber M., Caron M.G. Dopamine receptors: from structure to function. Physiol. Rev. 1998, 78:189-225.
3. Seeman P., Nam D., Ulpian C., Liu I.S., Tallerico T. New dopamine receptor, D2(Longer), with unique TG splice site, in human brain. Brain Res. Mol. Brain Res. 2000, 76:132-141.
4. Lane J.R., Powney B., Wise A., Rees S., Milligan G. G protein coupling and ligand selectivity of the D2L and D3 dopamine receptors. J. Pharmacol. Exp. Ther. 2008, 325:319-330.
5. Wang Y.T., Su Z.Y., Hsieh C.H., Chen C.L. Predictions of binding for dopamine D2 receptor antagonists by the SIE method. J. Chem. Inf. Model. 2009, 49:2369-2375.
6. Kalani M.Y., Vaidehi N., Hall S.E., Trabanino R.J., Freddolino P.L., Kalani M.A., Floriano W.B., Kam V.W., Goddard W.A. , The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proc. Natl. Acad. Sci. USA 2004, 101:3815-3820.
7. Teeter M.M., Froimowitz M., Stec B., DuRand C.J. Homology modeling of the dopamine D2 receptor and its testing by docking of agonists and tricyclic antagonists. J. Med. Chem. 1994, 37:2874-2888.
8. Cherezov V., Rosenbaum D.M., Hanson M.A., Rasmussen S.G., Thian F.S., Kobilka T.S., Choi H.J., Kuhn P., Weis W.I., Kobilka B.K., Stevens R.C. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 2007, 318:1258-1265.
9. Warne T., Serrano-Vega M.J., Baker J.G., Moukhametzianov R., Edwards P.C., Henderson R., Leslie A.G., Tate C.G., Schertler G.F. Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 2008, 454:486-492.
10. 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 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008, 322:1211-1217.
11. Chien E.Y.T., Liu W., Zhao Q., Katritch V., Han G.W., Hanson M.A., Shi L., Newmann A.H., Javitch J.A., Cherezov V., Stevens R.C. Structure of the human dopamine D3 receptor in complex with a D2/D3 antagonist. Science 2010, 330:1091-1095.
12. J.C. Mobarec, R. Sanchez, M. Filizola, Modern homology modeling of G-protein coupled receptors: which structural template to use? J. Med. Chem. 10.1021/jm9005252.
13. van Munster B.C., de Rooij S.E., Yazdanpanah M., Tienari P.J., Pitkala K.H., Osse R.J., Adami D., Smit O., van der Steen M.S., van Houten M., Rahkonen T., Sulkava R., Laurila J.V., Strandberg T.E., Tulen J.H., Zwang L., Macdonald A.J., Treloar A., Sijbrands E.J., Zwinderman A.H., Korevaar J.C. The association of the dopamine transporter gene and the dopamine receptor 2 gene with delirium, a meta-analysis. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2010, 153:648-655.
14. Florea L., Di Francesco V., Miller J., Turner R., Yao A., Harris M., Walenz B., Mobarry C., Merkulov G.V., Charlab R., Dew I., Deng Z., Istrail S., Li P., Sutton G. Gene and alternative splicing annotation with AIR. Genome Res. 2005, 15:54-66.
15. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
16. Altschul S.F., Wootton J.C., Gertz E.M., Agarwala R., Morgulis A., Schäffer A.A., Yu Y.K. Protein database searches using compositionally adjusted substitution matrices. FEBS J. 2005, 272:5101-5109.
17. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
18. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007, 8:108-117.
19. Wu S., Skolnick J., Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology 2007, 5:17.
20. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 2006, 22:195-201.
21. Schwede T., Kopp J., Guex N., Peitsch M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 2003, 31:3381-3385.
22. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997, 18:2714-2723.
23. Chen C.C., Hwang J.K., Yang J.M. (PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics 2009, 10:366.
24. 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 2.8A structure of the human beta2-adrenergic receptor. Structure 2008, 16:897-905.
25. Zhang Y., Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57:702-710.
26. Lovell S.C., Davis I.W., Arendall W.B., de Bakker P.I., Word J.M., Prisant M.G., Richardson J.S., Richardson D.C. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 2003, 50:437-450.
27. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., Schulten K. Scalable molecular dynamics with NAMD. J. Comp. Chem. 2005, 26:1781-1802.
28. Wishart D.S., Knox C., Guo A.C., Cheng D., Shrivastava S., Tzur D., Gautam B., Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008, 36:D901-D906.
29. Suiko M., Sakakibara Y., Nakajima H., Sakaida H., Liu M.C. Enzymic sulphation of dopa and tyrosine isomers by HepG2 human hepatoma cells: stereoselectivity and stimulation by Mn2+. Biochem. J. 1996, 314:151-158.
30. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Zakrzewski V.G., Montgomery J.A., Stratmann R.E., Burant J.C., et al. Gaussian 98, version A.7 1998, Gaussian, Pittsburgh, PA.
31. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart E., Belew R.K., Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comp. Chem. 1998, 19:1639-1662.
32. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14:33-38.
33. Wilcox R.E., Huang W.H., Brusniak M.Y., Wilcox D.M., Pearlman R.S., Teeter M.M., DuRand C.J., Wiens B.L., Neve K.A. CoMFA-based prediction of agonist affinities at recombinant wild type versus serine to alanine point mutated D2 dopamine receptors. J. Med. Chem. 2000, 43:3005-3019.
34. Charuchinda C., Supavilai P., Karobath M., Palacios J.M. Dopamine D2 receptors in the rat brain: autoradiographic visualization using a high-affinity selective agonist ligand. J. Neurosci. 1987, 7:1352-1360.
35. Wong D.T., Bymaster F.P., Lane P.T., Kau D., Bach N.J., Kornfeld E.C. Binding of [3H] pergolide mesylate to dopamine receptors of mammalian brains. Res. Commun. Chem. Pathol. Pharmacol. 1980, 30:195-210.
36. Lima V.T., Macedo D.S., Nogueira C.R., Vasconcelos S.M., Viana G.S., Sousa F.C. Buspirone increases D2-like dopaminergic receptor density in rat corpus striatum. Arq. Neuropsiquiatr. 2002, 60:38-40.
37. Seeman P., Corbett R., Van Tol H.H. Atypical neuroleptics have low affinity for dopamine D2 receptors or are selective for D4 receptors. Neuropsychopharmacology 1997, 16:93-110.
38. Zhang Y., Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33:2302-2309.
39. Whisstock J.C., Lesk A.M. Prediction of protein function from protein sequence and structure. Q. Rev. Biophys. 2003, 36:307-340.
40. Javitch J.A., Fu D., Chen J. Residues in the fifth membrane-spanning segment of the dopamine D2 receptor exposed in the binding-site crevice. Biochemistry 1995, 34:16433-16439.
41. Javitch J.A., Fu D., Chen J. Differentiating dopamine D2 ligands by their sensitivities to modification of the cysteine exposed in the binding-site crevice. Mol. Pharmacol. 1996, 49:692-698.
42. Simola N., Morelli M., Carta A.R. The 6-hydroxydopamine model of Parkinsons disease. Neurotox. Res. 2007, 11:151-167.
43. Ungerstedt U., Arbuthnott G.W. Quantitative recording of rotational behavior in rats after 6-hydroxy-dopamine lesions of the nigrostriatal dopamine system. Brain Res. 1970, 24:485-493.
44. Liu X.Y., Chu X.P., Mao L.M., Wang M., Lan H.X., Li M.H., Zhang G.C., Parelkar N.C., Fibuch E.E., Haines M., Neve K.A., Liu F., Xiong Z.G., Wang J.Q. Modulation of D2R-NR2B interactions in response to cocaine. Neuron 2006, 52:897-909.
45. Nikiforovich G.V., Taylor C.M., Marshall G.R., Baranski T.J. Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins 2009, 78:271-285.
46. Dong C., Filipeanu C.M., Duvernay M.T., Wu G. Regulation of G protein-coupled receptor export trafficking. Biochim. Biophys. Acta 2007, 1768:853-870.
47. Lutteke T., Bohne-Lang A., Loss A., Goetz T., Frank M., von der Lieth C.W. GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 2006, 16:71R-81R.
48. Johnston C.A., Siderovski D.P. Structural basis for nucleotide exchange on G alpha i subunits and receptor coupling specificity. Proc. Natl. Acad. Sci. USA 2007, 104:2001-2006.
49. Fishburn C.S., Elazar Z., Fuchs S. Differential glycosylation and intracellular trafficking for the long and short isoforms of the D2 dopamine receptor. J. Biol. Chem. 1995, 270:29819-29824.
50. Blom N., Sicheritz-Ponten T., Gupta R., Gammeltoft S., Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4:1633-1649.
51. Katritch V., Reynolds K.A., Cherezov V., Hanson M.A., Roth C.B., Yeager M., Abagyan R. Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J. Mol. Recognit. 2009, 22:307-318.
52. Soriano-Ursúa M.A., Trujillo-Ferrara J.G., Alvarez-Cedillo J., Correa-Basurto J. Docking studies on a refined human beta(2) adrenoceptor model yield theoretical affinity values in function with experimental values for R-ligands, but not for S-antagonists. J. Mol. Model. 2010, 16:401-409.
53. Campiani G., Butini S., Gemma S., Nacci V., Fattorusso C., Catalanotti B., Giorgi G., Cagnotto A., Goegan M., Mennini T., Minetti P., Di Cesare M.A., Mastroianni D., Scafetta N., Galletti B., Stasi M.A., Castorina M., Pacifici L., Ghirardi O., Tinti O., Carminati P. Pyrrolo[1,3]benzothiazepine-based atypical antipsychotic agents. Synthesis, structure-activity relationship, molecular modeling, and biological studies. J. Med. Chem. 2002, 45:344-359.
54. Nygaard R., Frimurer T.M., Holst B., Rosenkilde M.M., Schwartz T.W. Ligand binding and micro-switches in 7TM receptor structures. Trends Pharmacol. Sci. 2009, 30:249-259.
55. Soriano-Ursúa M.A., Trujillo-Ferrara J.G., Correa-Basurto J. Scope and difficulty in generating theoretical insights regarding ligand recognition and activation of the beta 2 adrenergic receptor. J. Med. Chem. 2010, 53:923-932.
56. Bokoch M.P., Zou Y., Rasmussen S.G., Liu C.W., Nygaard R., Rosenbaum D.M., Fung J.J., Choi H.J., Thian F.S., Kobilka T.S., Puglisi J.D., Weis W.I., Pardo L., Prosser R.S., Mueller L., Kobilka B.K. Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor. Nature 2010, 463:108-112.
57. Wacker D., Fenalti G., Brown M.A., Katritch V., Abagyan R., Cherezov V., Stevens R.C. Conserved binding mode of human Β2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J. Am. Chem. Soc. 2010, 132:11443-11445.
58. Rasmussen S.G., Choi H.J., Fung J.J., Pardon E., Casarosa P., Chae P.S., Devree B.T., Rosenbaum D.M., Thian F.S., Kobilka T.S., Schnapp A., Konetzki I., Sunahara R.K., Gellman S.H., Pautsch A., Steyaert J., Weis W.I., Kobilka B.K. Structure of a nanobody-stabilized active state of the Β(2) adrenoceptor. Nature 2011, 469:175-180.