Pyruvate dehydrogenase kinase (PDK) isoforms are molecular switches that downregulate the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation in mitochondria. We have determined structures of human PDK1 or PDK3 bound to the inhibitors AZD7545, dichloroacetate (DCA), and radicicol. We show that the trifluoromethylpropanamide end of AZD7545 projects into the lipoyl-binding pocket of PDK1. This interaction results in inhibition of PDK1 and PDK3 activities by aborting kinase binding to the PDC scaffold. Paradoxically, AZD7545 at saturating concentrations robustly increases scaffold-free PDK3 activity, similar to the inner lipoyl domain. Good DCA density is present in the helix bundle in the N-terminal domain of PDK1. Bound DCA promotes local conformational changes that are communicated to both nucleotide-binding and lipoyl-binding pockets of PDK1, leading to the inactivation of kinase activity. Finally, radicicol inhibits kinase activity by binding directly to the ATP-binding pocket of PDK3, similar to Hsp90 and Topo VI from the same ATPase/kinase superfamily.

中文翻译：

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AZD7545、二氯乙酸盐和根二酚抑制丙酮酸脱氢酶激酶亚型的不同结构机制。

丙酮酸脱氢酶激酶 (PDK) 亚型是通过线粒体中的可逆磷酸化下调丙酮酸脱氢酶复合物 (PDC) 的分子开关。我们已经确定了与抑制剂 AZD7545、二氯乙酸 (DCA) 和根核二酚结合的人 PDK1 或 PDK3 的结构。我们显示 AZD7545 的三氟甲基丙酰胺末端投射到 PDK1 的硫辛酰结合口袋中。这种相互作用通过中止激酶与 PDC 支架的结合来抑制 PDK1 和 PDK3 活性。矛盾的是，AZD7545 在饱和浓度下会显着增加无支架的 PDK3 活性，类似于内部硫辛酰结构域。良好的 DCA 密度存在于 PDK1 N 末端结构域的螺旋束中。结合的 DCA 促进局部构象变化，这些变化与 PDK1 的核苷酸结合和硫辛酰结合口袋相关，导致激酶活性失活。最后，根核酚通过直接结合 PDK3 的 ATP 结合口袋来抑制激酶活性，类似于来自同一 ATP 酶/激酶超家族的 Hsp90 和 Topo VI。