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Theoretical Study of the Interaction of Agonists with the 5-HT2A Receptor

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Theoretical Study of the Interaction of Agonists with the 5-HT2A Receptor Theoretical study of the interaction of agonists with the 5-HT2A receptor Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat) der Fakultät für Chemie und Pharmazie der Universität Regensburg vorgelegt von Maria Elena Silva aus Buccinasco Regensburg 2008 Die vorliegende Arbeit wurde in der Zeit von Oktober 2004 bis August 2008 an der Fakultät für Chemie und Pharmazie der Universität Regensburg in der Arbeitsgruppe von Prof. Dr. A. Buschauer unter der Leitung von Prof. Dr. S. Dove angefertigt Die Arbeit wurde angeleitet von: Prof. Dr. S. Dove Promotiongesucht eingereicht am: 28. Juli 2008 Promotionkolloquium am 26. August 2008 Prüfungsausschuß: Vorsitzender: Prof. Dr. A. Buschauer 1. Gutachter: Prof. Dr. S. Dove 2. Gutachter: Prof. Dr. S. Elz 3. Prüfer: Prof. Dr. H.-A. Wagenknecht I Contents 1 Introduction ......................................................................................................... 1 1.1 G protein coupled receptors .....................................................................................1 1.1.1 GPCR classification ............................................................................................2 1.1.2 Signal transduction mechanisms in GPCRs .......................................................4 1.2 Serotonin (5-hydroxytryptamine, 5-HT) ....................................................................7 1.2.1 Historical overview ..............................................................................................7 1.2.2 Biosynthesis and metabolism .............................................................................8 1.3 Serotonin receptors (5-HTR) ..................................................................................10 1.3.1 5-HTR classification..........................................................................................10 1.4 5-HT2 receptors (5-HT2R) .......................................................................................13 1.4.1 5-HT2A receptor.................................................................................................14 1.4.1.1 5-HT2A receptor structure............................................................................15 1.4.1.2 5-HT2AR distribution, signal transduction and pharmacology......................18 1.5 5-HT2AR agonists and antagonists .........................................................................20 1.5.1 5-HT2AR agonists ..............................................................................................20 1.5.1.1 Tryptamines ................................................................................................20 1.5.1.2 Phenylalkylamines ......................................................................................22 1.5.1.3 Quinazolinediones – a new partial agonistic structure................................24 1.5.2 5-HT2AR antagonists..........................................................................................25 1.6 References .............................................................................................................28 2 Scope and Objective......................................................................................... 37 2.1 References .............................................................................................................40 3 Computational Methods ................................................................................... 41 3.1 GPCR homology models in medicinal chemistry....................................................41 3.2 Protein Database....................................................................................................43 3.3 Sequence alignment...............................................................................................44 3.4 3D structure generation ..........................................................................................44 3.5 Model validation......................................................................................................46 3.6 3D Quantitative Structure-Activity Relationships (3D QSAR) .................................47 II 3.7 References .............................................................................................................50 4 Docking of representative partial agonists at 5-HT2A receptor models based on rhodopsin ..................................................................................................... 53 4.1 Introduction...................................................................................................................53 4.2 Material and Methods..................................................................................................55 4.2.1 Model construction ................................................................................................55 4.2.2 Ligand selection, structure generation and docking ..............................................56 4.3 Results and Discussion ................................................................................................58 4.3.1 5-HT2A receptor models.........................................................................................58 4.3.2 Docking of representative partial agonists.............................................................59 4.4 Conclusion....................................................................................................................63 4.1 References .............................................................................................................65 5 5-HT2A receptor partial agonists: QSAR and interactions with the binding site...................................................................................................................... 69 5.1 Introduction.............................................................................................................69 5.2 The β2 adrenoceptor, a new template for GPCR homology modeling....................70 5.2.1 Crystal structures of the β2 adrenoceptor .........................................................70 5.2.2 Comparison of β2AR and rhodopsin crystal structures .....................................72 5.3 Material and Methods .............................................................................................74 5.3.1 Data set.............................................................................................................74 5.3.2 Fragment Regression Analysis (FRA) ..............................................................75 5.3.3 Generation of 3D structure models of 5-HT2A receptors ...................................77 5.3.4 Ligand selection, structure generation and docking..........................................78 5.3.5 3D QSAR Approaches: CoMFA and CoMSiA...................................................80 5.4 Results and Discussion ..........................................................................................81 5.4.1 Fragment Regression Analysis .........................................................................81 5.4.2 Comparison between 5-HT2AR models derived from β2AR and from bovine rhodopsin ..........................................................................................................84 5.4.3 Docking of representative partial agonists ........................................................87 5.4.4 3D-QSAR models .............................................................................................90 5.5 Conclusions ............................................................................................................98 5.6 References .............................................................................................................99 III 6 Modeling of the human 5-HT2A receptor in different active state and of interaction with ligands.................................................................................. 103 6.1 Introduction...........................................................................................................103 6.2 Material and methods ...........................................................................................107 6.2.1 Model construction..........................................................................................107 6.2.2 Docking of 5-HT2A receptor agonists and partial agonists ..............................110 6.3 Results..................................................................................................................111 6.3.1 Comparison of h5-HT2AR models in different states .......................................111 6.3.2 Analysis of the fully active h5-HT2AR model in complex with 5-HT .................116 6.3.3 Analysis of the partially active h5-HT2AR model in complex with a partial agonist ........................................................................................................................117 6.4 Conclusions ..........................................................................................................120 6.5 References ...........................................................................................................121 7 Summary...................................................................Error! Bookmark not defined. 8 Appendix.......................................................................................................... 129 8.1 Abbreviations........................................................................................................129 8.2 List of publications ................................................................................................131
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