Ureadepsipeptides as ClpP Activators.

Acyldepsipeptides are a unique class of antibiotics that act via allosterically dysregulated activation of the bacterial caseinolytic protease (ClpP). The ability of ClpP activators to kill non-growing bacteria represents a new opportunity to combat deep-seated biofilm infections. However, the acyl depsipeptide scaffold is subject to rapid metabolism. Herein, we explore alteration of the potentially metabolically reactive α,β unsaturated acyl chain. Through targeted synthesis, a new class of phenyl urea substituted depsipeptide ClpP activators with improved metabolic stability is described. The ureadepsipeptides are potent activators of S. aureus ClpP and show activity against Gram-positive bacteria, including S. aureus biofilms. These studies demonstrate that a phenyl urea motif can successfully mimic the double bond, maintaining potency equivalent to acyldepsipeptides, but with a decreased metabolic liability. While removal of the double bond from acyldepsipeptides generally has a significant negative impact on potency, structural studies revealed that the phenyl urea depsipeptides can retain potency through the formation of a third hydrogen bond between the urea and the key Tyr63 residue in the ClpP activation domain. Ureadepsipeptides represent a new class of ClpP activators, with improved drug-like properties, potent antibacterial activity, and the tractability to be further optimized.