Application of molecular dynamics to elucidate key binding interactions for the development of therapeutics against opioid overdose

Opioid overdose has been a long-standing public health issue in the United States. This crisis has only been exacerbated by the Covid-19 pandemic, with overdose deaths involving opioids increasing from an estimated 70,029 in 2020 to 80,816 in 2021. While there are treatments for opioid overdose, there are currently no therapeutic tools to prevent it. Moreover, these treatments are limited to emergency scenarios, most notably due to induction of withdrawal and loss of analgesia. Fatal opioid overdoses are primarily attributed to opioid-induced respiratory depression (OIRD). As part of an ongoing collaboration, a class of cysteine esters have been identified that reverse OIRD without blocking the analgesic effects of the opioid or inducing withdrawal. Our working hypothesis is that these esters function by binding β-arrestin and altering either its interaction with the opioid receptor, downstream proteins, or both. Accordingly, we have used “flooding” molecular dynamics simulations to identify candidate binding sites for several related ligands on the surface of β-arrestin 1 and 2, which we then validate using alchemical ligand binding free energy calculations. The results will be used to suggest mutations that would disrupt binding and to better understand the mechanism by which these compounds combat opioid overdose.