The alternative oxidase (AOX) is a monotopic diiron carboxylate protein that catalyses the oxidation of ubiquinol and the reduction of oxygen to water. Although a number of AOX inhibitors have been discovered, little is still known about the ligand–protein interaction and essential chemical characteristics of compounds required for a potent inhibition. Furthermore, owing to the rapidly growing resistance to existing inhibitors, new compounds with improved potency and pharmacokinetic properties are urgently required. In this study we used two computational approaches, ligand–protein docking and Quantitative Structure–Activity Relationships (QSAR) to investigate binding of AOX inhibitors to the enzyme and the molecular characteristics required for inhibition. Docking studies followed by protein–ligand interaction fingerprint (PLIF) analysis using the AOX enzyme and the mutated analogues revealed the importance of the residues Leu 122, Arg 118 and Thr 219 within the hydrophobic cavity. QSAR analysis, using stepwise regression analysis with experimentally obtained IC₅₀ values as the response variable, resulted in a multiple regression model with a good prediction accuracy. The model highlighted the importance of the presence of hydrogen bonding acceptor groups on specific positions of the aromatic ring of ascofuranone derivatives, acidity of the compounds, and a large linker group on the compounds on the inhibitory effect of AOX.

替代氧化酶 (AOX) 是一种单一的二铁羧酸盐蛋白，可催化泛醇的氧化和氧还原为水。尽管已经发现了许多 AOX 抑制剂，但对于有效抑制所需的化合物的配体-蛋白质相互作用和基本化学特征仍知之甚少。此外，由于对现有抑制剂的快速增长的抗性，迫切需要具有改进效力和药代动力学特性的新化合物。在这项研究中，我们使用了两种计算方法，配体-蛋白质对接和定量结构-活性关系 (QSAR) 来研究 AOX 抑制剂与酶的结合以及抑制所需的分子特征。对接研究随后使用 AOX 酶和突变类似物进行蛋白质-配体相互作用指纹 (PLIF) 分析，揭示了疏水腔内 Leu 122、Arg 118 和 Thr 219 残基的重要性。QSAR 分析，使用逐步回归分析和实验获得的 IC_{50 个}值作为响应变量，得到了具有良好预测精度的多元回归模型。该模型强调了在呋喃酮衍生物的芳环的特定位置上存在氢键受体基团、化合物的酸性以及化合物上的大连接基团对 AOX 抑制作用的重要性。