Bacterial proteolytic machinery unleashed by acyldepsipeptide antibiotics

In an attempt to evaluate the potential of underexploited natural product classes we investigated a group of 8 closely related antibacterial acyldepsipeptides (ADEPs) that was previously described as the “A54556 complex” in a patent. We determined the correct structure of “factor A”, the main component, and established a route for its de novo synthesis. A derivatization program yielded largely improved congeners that demonstrated remarkable antibacterial activities against multi‐resistant Gram‐positive bacterial isolates in vitro and in vivo as well as an unprecedented mechanism of action. Applying genetic, biochemical and proteomic techniques the target was identified as ClpP, the core unit of a major bacterial protease complex. In order to protect the cell from the destructive power of this universal protease, ClpP is tightly regulated and unable to degrade proteins on its own. It strictly requires a member of the family of Clp‐ATPases and often further accessory proteins for proteolytic activation. Binding of acyldepsipeptides to ClpP eliminates these safeguards. The acyldepsipeptide‐activated ClpP core is capable of proteolytic degradation in the absence of the regulatory Clp‐ATPases. This uncontrolled proteolysis leads to inhibition of bacterial cell division and eventually cell death.