title: Exploring binding properties of agonists interacting with a δ-opioid receptor.
abstract: Ligand-receptor interactions are at the basis of the mediation of our physiological responses to a large variety of ligands, such as hormones, neurotransmitters and environmental stimulants, and their tuning represents the goal of a large variety of therapies. Several molecular details of these interactions are still largely unknown. In an effort to shed some light on this important issue, we performed a computational study on the interaction of two related compounds differing by a single methyl group (clozapine and desmethylclozapine) with a [Formula: see text]-opioid receptor. According to experiments, desmethylclozapine is more active than clozapine, providing a system well suited for a comparative study. We investigated stable configurations of the two drugs inside the receptor by simulating their escape routes by molecular dynamics simulations. Our results point out that the action of the compounds might be related to the spatial and temporal distribution of the affinity sites they visit during their permanency. Moreover, no particularly pronounced structural perturbations of the receptor were detected during the simulations, reinforcing the idea of a strong dynamical character of the interaction process, with an important role played by the solvent in addition.
authors.affiliation: CNR-IOM SLACS and Dipartimento di Fisica, Università degli Studi di Cagliari, Monserrato, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Collu
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
mesh_terms: D001665:Binding Sites; D003024:Clozapine / Q000031:analogs & derivatives* / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D017465:Receptors, Opioid, delta / Q000819:agonists / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D017465:Receptors, Opioid, delta; D012997:Solvents; D014867:Water; C058272:norclozapine; D003024:Clozapine