Novel binding mode of the acidic CYP2D6 substrates pactimibe and its metabolite R-125528

Typical CYP2D6 substrates generally contain a basic nitrogen atom that interacts with Asp(301) and/or Glu(216) 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 mu M, which was comparable with those of typical basic CYP2D6 substrates (1-10 mu M). Pactimibe has lower affinity than R-125528; however, the Km value was comparable with that of metoprolol. Interestingly, their sites of metabolism, the omega-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 Arg(221) and hydrophobic interaction between the aromatic moiety and Phe(483). 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.