MOLECULAR DYNAMICS STUDIES OF THE mu-OPIOID RECEPTOR IN COMPLEX WITH BIASED LIGANDS

The mu-opioid receptor (MOR) is a class A GPCR related to physiological processes, in particular analgesia. After activation by peptides or small molecules, downstream signaling is triggered and can occur via two distinct pathways. The G-protein pathway leads to the pain killing effect, while the beta-arrestin pathway is associated with known side effects such as respiratory depression, constipation, and tolerance. Some ligands are biased, that is, they can preferentially activate one of the pathways. In the case of MOR, ligands biased towards the G protein pathway are the most searched for. Kennedy et al. (2018) and Crowley et al. (2020) have studied a series of compounds that showed significant bias toward the MOR, and four of them (referred as K01, K44, K46 and C07) were selected for our simulations. The molecules had their geometry optimized and then docked to the receptor structure in the active conformation. The ligand bound receptor was inserted in a POPC membrane, followed by addition of water and ions. After equilibration, molecular dynamics (MD) simulations were performed using the amber-99-ildn (adapted for lipids and ligands) for 500 ns. Docking results showed binding energies (in kcal/mol) of -12.18, -10.57, -10.22 and -8.73 for C07, K46, K44, and K01, respectively. The receptor structures along the MD trajectories had their activation state determined by the method proposed by Ibrahim et al. (2019). It was observed that, for the complexes with C07, K01 and K46, the receptor changed conformation to the inactive state, while for the complex with K44 the receptor stayed in the regions corresponding to intermediate/active state. These results indicate that K44 might be an efficient agonist of the MOR. In order to investigate and better understand the biasing mechanism, simulations involving the G-protein will be considered.