Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection

Peritonitis caused by Staphylococcus aureus poses a severe threat to patients with end-stage renal failure.
Treating multidrug-resistant S. aureus infections requires the use of antibiotics with diverse mechanisms
of action. Caseinolytic protease P (ClpP) is a promising antibacterial
target; however, selective activation of S. aureus ClpP (SaClpP) over human ClpP
(HsClpP) remains challenging. We previously identified (R)-ZG197 as a
selective SaClpP agonist, but its potency was suboptimal.
Herein, we develop (R)-ZG197 analogs through a structure-guided approach and examine
their structure–activity relationships. Notably, ZY39 demonstrates improved activation of SaClpP and
superior binding affinity. Interestingly, while ZY39 facilitates
the enzymatic hydrolysis of SaClpP and HsClpP in vitro, it does not target HsClpP in cellular environments. Furthermore, ZY39 effectively
inhibits the growth of multidrug-resistant S. aureus strains and shows excellent therapeutic efficacy in a murine model
of peritonitis. These findings highlight ZY39 as a promising SaClpP agonist for combating staphylococcal infections.