Insights Into Receptor-Based Anesthetic Pharmacophores and Anesthetic-Protein Interactions

• Published in: Methods in enzymology Vol. 602; p. 77
• Main Authors: Fahrenbach, Victoria S, Bertaccini, Edward J
• Format: Journal Article
• Language: English
• Published: United States 2018
• Subjects: Computational chemistry; GABA(A) receptor; ONIOM; LGIC; Molecular modeling; Homology model; Docking; Pharmacophore; Anesthesia binding site; Ligand–receptor interactions
• ISSN: 1557-7988
• DOI: 10.1016/bs.mie.2018.01.004

General anesthetics are thought to allosterically bind and potentiate the inhibitory currents of the GABA receptor through drug-specific binding sites. The physiologically relevant isoform of the GABA receptor is a transmembrane ligand-gated ion channel consisting of five subunits (γ-α-β-α-β linkage) symmetrically arranged around a central chloride-conducting pore. Although the exact molecular structure of this heteropentameric GABA receptor remains unknown, molecular modeling has allowed significant advancements in understanding anesthetic binding and action. Using the open-channel conformations of the homologous glycine and glutamate-gated chloride receptors as templates, a homology model of the GABA receptor was constructed using the Discovery Studio computational chemistry software suite. Consensus structural alignment of the homology templates allowed for the construction of a three-dimensional heteropentameric GABA receptor model with (γ -β -α -β -α ) subunit linkage. An anesthetic binding site was identified within the transmembrane α/β intersubunit space by the convergence of three residues shown to be essential for anesthetic activity in previous studies with mutant mice (β -N265, β -M286, α -L232). Propofol derivatives docked into this binding site showed log-linear correlation with experimentally derived GABA receptor potentiation (EC ) values, suggesting this binding site may be important for receptor activation. The receptor-based pharmacophore was analyzed with surface maps displaying the predominant anesthetic-protein interactions, revealing an amphiphilic binding cavity incorporating the three residues involved in anesthetic modulation. Quantum mechanics calculations of the bonding patterns found in complementary high-resolution receptor systems further elucidated the complex nature of anesthetic-protein interactions.