SELECTIVITY
1 INTRODUCTION 1 1 G-protein coupled receptors 1 11 Pharmacology 1 111 Signaling 1 112 Intrinsic activity 2 113 Functional selectivity and bias 3 114 Subtype selectivity and Allosteric binding 5 12 Crystal structures 7 121 Co-crystallized ligands 7 122 Active-state GPCR 7 123 Nanobodies 8 124 Ternary complexes 8 13 Structure-based drug design 9 131 Homology modeling 9 132 Molecular docking 10 133 Biomolecular simulations 10 134 Molecular-dynamics simulations 11 1341 Force fields 11 1342 Software and hardware development 12 135 Enhanced sampling 13 1351 Accelerated molecular dynamics 15 1352 Steered molecular dynamics and adaptive biasing 15 1353 Metadynamics 16 136 Advances in the application of biomolecular simulations 16 2 A THREE-SITE MECHANISM FOR AGONIST/ANTAGONIST SELECTIVE BINDING TO VASOPRESSIN RECEPTORS 19 21 Abstract 20 22 Introduction 21 23 Results and discussion 22 24 Acknowledgements 28 25 Supplementary Materials and Methods 28 251 Homology Model of V2R 28 252 Molecular-Dynamics Simulation methodology 29 253 DASH analysis of AVP 29 254 Spontaneous association of AVP to the extracellular surface of V2R 29 255 Adaptive Biasing Force simulations to probe potential docking paths 30 256 Metadynamics simulation of AVP-V2R binding 31 257 A homology model of V1aR 31 258 Metadynamics simulation of non-peptide ligands 32 3 COMPUTATIONAL PREDICTION OF GPCR-LIGAND’S BINDING AFFINITY AND KINETICS 39 31 Abstract 40 33 Results and discussion 41 34 Materials and Methods 45 341 General set up of MD simulations 45 342 ADRB2 46 343 M2 Muscarinic acetylcholine receptor 46 344 ?-opioid receptor 47 345 Metadynamics simulation of ligand binding to ?-opioid, muscarinic M2 and ?2 adrenergic receptor 47 346 Vasopressin V2 receptor 48 4 HOW DIFFERENT ARE NANOBODY-STABILIZED GPCR STRUCTURES FROM THEIR G-PROTEIN-STABILIZED EQUIVALENTS? 50 41 Abstract 51 42 Introduction 52 43 Results and discussion 53 44 Materials and Methods 58 441 General set up of MD simulations 58 442 ADRB2 58 443 M2 Muscarinic acetylcholine receptor 59 444 ?-opioid receptor 59 445 Metadynamics simulations of ligand binding to ADRB2, M2 and ?-opioid receptors 59 5 MOLECULAR MECHANISM OF G-PROTEIN–AGONIST COOPERATIVE ACTIVATION OF G-PROTEIN COUPLED RECEPTORS 64 51 Abstract 65 52 Introduction 66 53 Results and discussion 67 54 Materials and Methods 70 541 General set up of MD simulations 70 542 ADRB2 70 543 M2 Muscarinic acetylcholine receptor 71 544 ?-opioid receptor 71 545 Metadynamics simulation of ligand binding to ADRB2 72 546 Metadynamics simulation of coupling of G?s and activation of ADBR2 72 6 INSIGHTS INTO CONFORMATIONAL AND FUNCTIONAL SELECTIVITY OF ?2-ADRENERGIC RECEPTOR BIAS FROM TERNARY COMPLEX SIMULATIONS 76 61 Abstract 77 62 Introduction 78 63 Results and discussion 79 64 Materials and Methods 88 641 General set up of MD simulations 88 642 ADRB2 Models 88 643 Metadynamics simulation of ligand binding to ADRB2 89 644 Metadynamics simulation of coupling of G?s and activation of ADBR2 90 645 Metadynamics simulation of coupling of the ?-arrestin and activation of the ADBR2 91 7 SUMMARY 99 71 Subtype selectivity at the Vasopressin–receptor subtypes 99 72 Inactive and G-protein stabilized GPCRs compared to the crystalized nanobody-stabilized complexes 100 73 Molecular cooperativity between agonist and G-protein on ?2–adrenergic receptor 101 74 Predicting functional selectivity from ternary complex simulations 101 8 ZUSAMMENFASSUNG 102 81 Subtyp-Selektivität an den Vasopressin-Rezeptor Subtypen 102 82 Inaktive und G-Protein stabilisierte GPCR im Vergleich zu Nanobody-stabilisierten Komplexen 103 83 Molekulare Kooperativität zwischen Agonisten und G-Proteine am ?2–Adrenorezeptor 104 84 Vorhersage der funktionalen Selektivität durch Simulationen von ternären Komplexen 105 9 REFERENCES 106