Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4

Nile Red is sequentially metabolized by cytochrome P4503A4 to the N-monoethyl and N-desethyl products, which typifies the metabolism of many amine containing drugs. Sequential metabolism of a single substrate results in complex kinetics that confound predictive models of drug clearance. As a fluorescent model for drugs which undergo sequential metabolism, Nile Red provides the opportunity to monitor drug–CYP interactions wherein the fluorescent properties of Nile Red could, in principle, be exploited to determine individual rate and equilibrium constants for the individual reactions. Previously, it was shown that Nile Red binds at the active site and fluoresces (KD ≈ 50 nM) with maximum emission at ∼620 nm, but it was unclear whether a red-shifted emission, at ∼660 nm, consisted of only free Nile Red or Nile Red bound at a second site on the protein. Here, equilibrium binding studies, including ‘reverse titrations’ spanning low ratios of CYP3A4/Nile Red, indicate two binding sites for Nile Red with a contribution to the ‘red emission’ greater than can be accounted for by free Nile Red. Singular value decomposition affords basis spectra for both spectral components and fits well to the experimentally determined concentration dependence of Nile Red emission. In addition, the red spectral component, with an apparent KD = 2.2 μM, is selectively eliminated by titration with the known allosteric effectors of CYP3A4, α-napthoflavone and testosterone. Furthermore, the double mutant L2311F/D214E, previously demonstrated to perturb a peripheral allosteric site, lacks the red-emitting Nile Red binding site, but retains the blue-emitting site. Together these data indicate that a second Nile Red site competes with other effectors of CYP3A4 at a site that results in Nile Red emission at 660 nm.