Fenpyroximate Binds to the Interface between PSST and 49 kDa Subunits in Mitochondrial NADH-Ubiquinone Oxidoreductase

Using a photoaffinity labeling technique, Nakamaru-Ogiso et al. demonstrated that fenpyroximate, a strong inhibitor of bovine heart mitochondrial NADH-ubiquinone oxidoreductase (complex I), binds to the ND5 subunit [Nakamaru-Ogiso, E., et al. (2003) <i>Biochemistry 42</i>, 746–754]. Considering that the main body of the ND5 subunit composed of transmembrane helixes 1–15 is located at the distal end of the membrane domain [Efremov, R. G., et al. (2010) <i>Nature 465</i>, 441–445], however, their result may be questionable. Because establishing the number and location of inhibitors and/or quinone binding sites in the membrane domain is necessary to elucidate the function of the enzyme, it is critical to clarify whether there is an additional inhibitor and/or quinone binding site besides the interface between the hydrophilic and membrane domains. We therefore performed photoaffinity labeling experiments using two newly synthesized fenpyroximate derivatives [[¹²⁵I]-4-azidophenyl fenpyroximate ([¹²⁵I]­APF) and [¹²⁵I]-3-azido-5-iodobenzyl fenpyroximate ([¹²⁵I]­AIF)] possessing a photoreactive azido group at and far from the pharmacophoric core moiety, respectively. Doubled sodium dodecyl sulfate–polyacrylamide gel electrophoresis revealed that [¹²⁵I]­APF and [¹²⁵I]­AIF bind to the PSST and 49 kDa subunits, respectively. Careful examination of the fragmentation patterns of the labeled PSST and 49 kDa subunits generated by limited proteolysis indicated that the residues labeled by [¹²⁵I]­APF and [¹²⁵I]­AIF are located in the Ser43–Arg66 (PSST) and Asp160–Arg174 (49 kDa) regions, respectively, which face the supposed quinone-binding pocket formed at the interface of the PSST, 49 kDa, and ND1 subunits. We conclude that fenpyroximate does not bind to the distal end of the membrane domain but rather resides at the interface between the two domains in a manner such that the pharmacophoric pyrazole ring and side chain of the inhibitor orient toward the PSST and 49 kDa subunits, respectively. This study answers a critical question relating to complex I