Computational protocol: Racemic Salsolinol and its Enantiomers Act as Agonists of the μ-Opioid Receptor by Activating the Gi Protein-Adenylate Cyclase Pathway

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Protocol publication

[…] Molecular docking simulations were performed using the crystal structure of the mouse μ-opioid receptor bound to the morphinan high-affinity agonist BU72 (Neilan et al., ), obtained from the protein data bank as a PDB file (ID: 5C1M; Huang et al., ). For the simulations, water molecules near the receptor were conserved, but BU72 and any other co-crystallized molecules were removed. After that, polar hydrogens were added to the protein coordinates (not resolved in the crystal structure). The studied molecules, morphine, (R)-SAL and (S)-SAL, were prepared and optimized to their energy minima using SPARTAN 10. Docking simulations were performed using Autodock Vina (Trott and Olson, ), which renders the ligand fully flexible, while to the target protein a rigid structure. The search space was 24 Å3 around a side-chain oxygen of Asp147, regarded as a critical residue for the binding of ligands to this receptor (Li et al., ; Manglik et al., ; Shim et al., ; Huang et al., ). The searching exhaustiveness was 800 (default 8). Ligand-protein interactions analyses and 3D figures were prepared using PyMOL (DeLano, ). […]

Pipeline specifications

Software tools AutoDock Vina, PyMOL
Application Protein interaction analysis
Chemicals Ethanol, Morphine, Naltrexone