TY - JOUR T1 - Novel Binding Mode of the Acidic CYP2D6 Substrates Pactimibe and Its Metabolite R-125528 JF - Drug Metabolism and Disposition JO - Drug Metab Dispos SP - 1938 LP - 1943 DO - 10.1124/dmd.108.020776 VL - 36 IS - 9 AU - Masakatsu Kotsuma AU - Hiroyuki Hanzawa AU - Yoriko Iwata AU - Kenji Takahashi AU - Taro Tokui Y1 - 2008/09/01 UR - http://dmd.aspetjournals.org/content/36/9/1938.abstract N2 - Typical CYP2D6 substrates generally contain a basic nitrogen atom that interacts with Asp301 and/or Glu216 and an aromatic moiety adjacent to the site of metabolism. Recently, we found novel acidic substrates for CYP2D6, pactimibe, and its indole metabolite, R-125528, that are not protonated but are negatively charged at physiological pH. The Km value of R-125528 in CYP2D6-expressing microsomes was determined to be 1.74 μM, which was comparable with those of typical basic CYP2D6 substrates (1–10 μM). Pactimibe has lower affinity than R-125528; however, the Km value was comparable with that of metoprolol. Interestingly, their sites of metabolism, the ω-1 position of the N-octyl indoline/indole group, were relatively distant from the aromatic moiety. A pactimibe analog with an N-decyl chain was similarly labile against CYP2D6; however, analogs with N-hexyl or N-dodecyl chains were stable to CYP2D6. An induced fit docking of the ligands with an X-ray crystal structure of substrate-free CYP2D6 (Protein Data Bank code 2F9Q) indicated the involvement of an electrostatic interaction between the carboxyl group and Arg221 and hydrophobic interaction between the aromatic moiety and Phe483. The docking model correctly positioned the site of metabolism above the heme. The effect of the N-alkyl chain length of pactimibe analogs on their CYP2D6 metabolic stability was plausibly explained by the docking model. In conclusion, we report herein a novel CYP2D6 binding mode for the acidic substrates pactimibe and R-125528. Further investigation, such as a site-directed mutation, will be necessary to directly demonstrate the involvement of Arg221 in CYP2D6 binding. The American Society for Pharmacology and Experimental Therapeutics ER -