9K2A image
Entry Detail
PDB ID:
9K2A
Keywords:
Title:
Structure of ClpP from Staphylococcus aureus in complex with ZY27
Biological Source:
PDB Version:
Deposition Date:
2024-10-17
Release Date:
2025-02-19
Method Details:
Experimental Method:
Resolution:
2.19 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:ATP-dependent Clp protease proteolytic subunit
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N
Chain Length:201
Number of Molecules:14
Biological Source:Staphylococcus aureus (strain Mu3 / ATCC 700698)
Primary Citation
Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection.
J.Med.Chem. 68 1810 1823 (2025)
PMID: 39760203 DOI: 10.1021/acs.jmedchem.4c02562

Abstact

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.

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