Selectivity is essential in drug discovery for finding or developing more effective opioid modulators. Structure-based approaches and binding kinetics effectively identify potential druggable regions and determine ligand candidates for improved therapies. In this study, we combined molecular dynamics simulations and funnel-metadynamics with charge density analyses to identify unique structural aspects of the main opioid receptors (ORs), including the mu (μOR), delta (δOR), and kappa (κOR). We found distinct conformational dynamics between the receptors, with the κOR extracellular vestibule tending to form a lid that covers its orthosteric site. Furthermore, we investigated how morphinan-scaffold ligands with distinct pharmacological effects bind to OR orthosteric sites and extracellular vestibules, identifying intermediate ligand states. The lowest-energy states of each complex reproduced the morphinan-like orientation revealed by experimental structures and experimental free energy of binding. Moreover, we determined the role of orthosteric subpockets and extracellular loops (ECLs) in stabilizing ligand-bound states, shedding light on ligand selectivity. Our results provide a detailed description, from an energetic perspective, of the conformational dynamics and structure-based selectivity determination within the OR family. These regions can be rationally targeted for designing and developing functionally selective opioid modulators with improved pharmacological effects in pain treatment or other OR-related diseases.
Gomes et al. (Fri,) studied this question.