Dynamic binding of acetogenin-type inhibitors to mitochondrial complex I revealed by photoaffinity labeling

Acetogenins isolated from the Annonaceae plant family are potent inhibitors of mitochondrial NADH-ubiquinone (UQ) oxidoreductase (complex I). Since acetogenins have a markedly different chemical framework from other complex I inhibitors, studying their inhibitory action offers valuable insights into the mechanism of complex I inhibition. A cryo-EM structure of mouse complex I with a bound ~35 Å-long acetogenin derivative suggested that acetogenins bind along the full length of the predicted UQ-accessing tunnel, with their γ-lactone ring orientating toward the iron‑sulfur cluster N2. However, this binding mode does not fully explain the structure–activity relationships of various acetogenin derivatives. To further elucidate their inhibition mechanism, we conducted photoaffinity labeling experiments in bovine heart SMPs using a photoreactive acetogenin derivative DLA-1, containing a small photolabile diazirine near the γ-lactone ring. DLA-1 labeled both the complex I subunits 49-kDa and ND1, which define the architecture of “top” and “bottom” regions of the canonical UQ-accessing tunnel, respectively. Proteomic analysis revealed that the labeled sites in ND1 are not within the tunnel's interior, whereas in the case of 49-kDa subunit, part of the tunnel's inner region is labeled. To investigate the molecular basis of acetogenin binding, we performed atomistic molecular dynamics simulations of DLA-1 and a natural-type acetogenin analog in the UQ-accessing tunnel. The simulation data indicate that DLA-1 is relatively rigid yet adopts multiple conformations and interacts with several regions in the tunnel including the residues identified by photoaffinity labeling. Based on these results, we discuss the binding modes of acetogenin analogs to complex I.