The Mechanism of Ligand-Induced Activation or Inhibition of - and -Opioid Receptors

G-protein-coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all-atom, long-time-scale molecular dynamics simulations on the -opioid and -opioid receptors (OR and OR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand-receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent-accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand.

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

Stefano Vanni

This thesis is devoted to the study of the activation mechanism of G-protein coupled receptors (GPCRs), one of the largest and most diverse protein families in mammalian genomes, by means of different computer-based simulation techniques. Using force field based classical molecular dynamics (MD), the time evolution of two prototypical GPCRs, rhodopsin and β adrenergic receptors, has been followed for microseconds under different external conditions. Within this approach, the non-native modifications induced by the different engineering techniques used to crystallize most of the known GPCR structures have been identified and some of the mechanisms through which these receptors have managed to optimize their function through evolution have been described and quantified. In detail, this has led to suggest a possible binding mode of agonists to β adrenergic receptors and to identify crucial micro-switches during receptor activation, as well as to describe an asymmetric pathway in the rhodopsin dimer that suggests oligomerization in GPCRs as a biological strategy to enhance activation efficiency. The increased knowledge of GPCR activation mechanism obtained from the classical molecular dynamics simulations hinted to a crucial role of chemical reactions inside the binding pocket of the receptors during the activation cycle. These events have been studied in this thesis using a hybrid quantum mechanics/molecular mechanics (QM/MM) protocol based on Density Functional Theory. Using this approach, it has been possible to characterize the optical properties of the different intermediates along the activation pathway of rhodopsin and to quantitatively estimate the barrier for the proton transfer reaction that induces active state formation. Finally, a novel activation mechanism in diffusible ligands class A GPCRs that indicates proton transfer from the bound ligand to the receptor as a crucial step to reach the active conformation is proposed.

EPFL2011

The Principles of Ligand Specificity on beta-2-adrenergic receptor

Shuguang Yuan

G protein-coupled receptors are recognized as one of the largest families of membrane proteins. Despite sharing a characteristic seven-transmembrane topology, G protein-coupled receptors regulate a wide range of cellular signaling pathways in response to various physical and chemical stimuli, and prevail as an important target for drug discovery. Notably, the recent progress in crystallographic methods led to a breakthrough in elucidating the structures of membrane proteins. The structures of beta(2)-adrenergic receptor bound with a variety of ligands provide atomic details of the binding modes of agonists, antagonists and inverse agonists. In this study, we selected four representative molecules from each functional class of ligands and investigated their impacts on beta(2)-adrenergic receptor through a total of 12 x 100 ns molecular dynamics simulations. From the obtained trajectories, we generated molecular fingerprints exemplifying propensities of protein-ligand interactions. For each functional class of compounds, we characterized and compared the fluctuation of the protein backbone, the volumes in the intracellular pockets, the water densities in the receptors, the domain interaction networks as well as the movements of transmembrane helices. We discovered that each class of ligands exhibits a distinct mode of interactions with mainly TM5 and TM6, altering the shape and eventually the state of the receptor. Our findings provide insightful prospective into GPCR targeted structure-based drug discoveries.

Nature Publishing Group2016

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

Stefano Vanni

EPFL2011