Molecular Pharmacology and Toxicology Faculty of Health Sciences Allosteric modulation of GABAergic and glutamatergic metabotropic receptors — Thibaud Freyd A dissertation for the degree of Philosophiae Doctor – June 2018 Content Acknowledgments ...................................................................................................................... iii List of papers ................................................................................................................................. v Abbreviations ............................................................................................................................. vii Summary .......................................................................................................................................ix 1. Introduction ............................................................................................................................. 1 1.1. Glutamate and GABA neurotransmitters in the CNS ....................................................... 1 1.2. G-protein coupled receptors .................................................................................................... 4 1.2.1. G-protein coupled receptor families ................................................................................................................ 4 1.2.2. Activation of signalling pathways ..................................................................................................................... 5 1.2.3. General structural knowledge ............................................................................................................................ 8 1.3. Family C of G-protein coupled receptors ............................................................................. 9 1.3.1. General structure and Binding pockets .......................................................................................................... 9 1.3.2. The GABAB receptor ............................................................................................................................................. 10 1.3.3. MetaBotropic glutamate receptors ................................................................................................................ 11 1.4. Mechanism of GPCR activation .............................................................................................. 12 1.4.1. Family A ..................................................................................................................................................................... 13 1.4.2. Family C ..................................................................................................................................................................... 14 1.4.3. GPCR ligands ............................................................................................................................................................ 15 1.4.4. Allosteric GPCR modulation ............................................................................................................................. 16 1.4.5. Biased signalling .................................................................................................................................................... 19 1.5. Molecular modelling in preclinical drug discovery ....................................................... 20 1.5.1. Modern drug discovery ...................................................................................................................................... 20 1.5.2. Molecular mechanics and force fields .......................................................................................................... 22 1.5.3. Molecular modelling techniques .................................................................................................................... 24 2. Aim of the study ..................................................................................................................... 35 3. In silico methods in the studies ........................................................................................ 37 3.1. Software choices ......................................................................................................................... 37 3.1.1. Paper 1 ....................................................................................................................................................................... 37 3.1.2. Paper 2 ....................................................................................................................................................................... 37 3.1.3. Paper 3: ...................................................................................................................................................................... 37 i 3.2. Alignment and homology modelling (paper 1) ............................................................... 38 3.3. Virtual Ligand Screening ......................................................................................................... 38 3.4. Molecular dynamics simulations ......................................................................................... 39 4. Summary of results .............................................................................................................. 41 4.1. Paper 1 ........................................................................................................................................... 41 4.2. Paper 2 ........................................................................................................................................... 41 4.3. Paper 3 ........................................................................................................................................... 42 5. Discussion ............................................................................................................................... 45 5.1. Virtual screening in search for new GABAB allosteric modulators (paper 1 & 2) ........................................................................................................................................................................ 46 5.1.1. Ligand-Based approach (paper 2) ................................................................................................................. 46 5.1.2. Structure-Based approach (paper 1) ............................................................................................................ 47 5.1.3. Target-Based screening of the filtered dataBase ..................................................................................... 48 5.1.4. Conclusion and further studies ....................................................................................................................... 50 5.2. Mechanisms of allosteric modulation (paper 3) ............................................................. 51 5.2.1. Activations features ............................................................................................................................................. 53 5.2.2. Conclusion and perspective .............................................................................................................................. 56 6. Conclusion ............................................................................................................................... 57 7. References ............................................................................................................................... 59 Paper 1 ............................................................................................................................................ I Paper 2 ........................................................................................................................................... II Paper 3 ..........................................................................................................................................III ii Acknowledgments It is finally my turn to write this section of the actual thesis. A Ph.D. is said to Be a personal work, but in my opinion, it is the result of a long teamwork with all the people I worked with along the course, and also the ones I met on a personal level. I express my deepest gratitude to my supervisors who helped me achieve this Ph.D. Professor Ingebrigt Sylte, thank you for guiding me and for always keeping your door open, for answering my questions and wonders. Your good nature and optimism are gifts that helped me through the Ph.D. I thank Dr. Mari Gabrielsen, for her guidance and perseverance. Your attention to detail rescued me more than once. I enjoyed learning under the supervision of Both of Mari and Ingebrigt. You never gave up on me despite my franglish (:D)! I would also like to thank Associate Professor Kurt Kristiansen for his support with Linux and Dr. Imin Wushur for the incredible work he has done with the in vitro experiments. The work presented in this thesis would not have Been possible without our collaborators in Poland and France. I would like to thank the research group of Professor Andrzej J. Bojarski, with special thanks to Dr. Dawid Warszycki and Dr. Stephan Mordalski. The help of Johann Hendrickx (UMR CNRS 6286, France) was highly Beneficial for the results obtained in paper 3. I would like to thank all my office mates. Krishanthi, next time I see you I will Bring “pain” and “poisson”. Linn, please do not involve me in more Snapchat videos! I also want to