title: Contributions of ionic interactions and protein dynamics to cytochrome P450 2D6 (CYP2D6) substrate and inhibitor binding.
abstract: P450 2D6 contributes significantly to the metabolism of >15% of the 200 most marketed drugs. Open and closed crystal structures of P450 2D6 thioridazine complexes were obtained using different crystallization conditions. The protonated piperidine moiety of thioridazine forms a charge-stabilized hydrogen bond with Asp-301 in the active sites of both complexes. The more open conformation exhibits a second molecule of thioridazine bound in an expanded substrate access channel antechamber with its piperidine moiety forming a charge-stabilized hydrogen bond with Glu-222. Incubation of the crystalline open thioridazine complex with alternative ligands, prinomastat, quinidine, quinine, or ajmalicine, displaced both thioridazines. Quinine and ajmalicine formed charge-stabilized hydrogen bonds with Glu-216, whereas the protonated nitrogen of quinidine is equidistant from Asp-301 and Glu-216 with protonated nitrogen H-bonded to a water molecule in the access channel. Prinomastat is not ionized. Adaptations of active site side-chain rotamers and polypeptide conformations were evident between the complexes, with the binding of ajmalicine eliciting a closure of the open structure reflecting in part the inward movement of Glu-216 to form a hydrogen bond with ajmalicine as well as sparse lattice restraints that would hinder adaptations. These results indicate that P450 2D6 exhibits sufficient elasticity within the crystal lattice to allow the passage of compounds between the active site and bulk solvent and to adopt a more closed form that adapts for binding alternative ligands with different degrees of closure. These crystals provide a means to characterize substrate and inhibitor binding to the enzyme after replacement of thioridazine with alternative compounds.
authors.affiliation: From the Department of Molecular and Experimental Medicine and.
authors.forename: An
authors.initials: A
authors.lastname: Wang
authors.affiliation: the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
authors.forename: C David
authors.initials: CD
authors.lastname: Stout
authors.affiliation: the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
authors.forename: Qinghai
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: From the Department of Molecular and Experimental Medicine and. Electronic address: johnson@scripps.edu.
authors.forename: Eric F
authors.initials: EF
authors.lastname: Johnson
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D019389:Cytochrome P-450 CYP2D6 / Q000737:chemistry* / Q000235:genetics; D065690:Cytochrome P-450 CYP2D6 Inhibitors / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009930:Organic Chemicals / Q000737:chemistry*; D046948:Secologanin Tryptamine Alkaloids / Q000737:chemistry*
chemical_list: D065690:Cytochrome P-450 CYP2D6 Inhibitors; D009930:Organic Chemicals; D046948:Secologanin Tryptamine Alkaloids; C113282:prinomastat; C005709:raubasine; D019389:Cytochrome P-450 CYP2D6
keywords: Ajmalicine; Crystal Structure; Cytochrome P450; Cytochrome P450 2D6 (CYP2D6); Drug Metabolism; Enzyme Inhibitor; Protein Structure; Quinidine; Quinine; Thioridazine