Structure of Staphylococcus aureus ClpP Bound to the Covalent Active‐Site Inhibitor Cystargolide A

The caseinolytic protease is a highly conserved serine protease, crucial to prokaryotic and eukaryotic protein homeostasis, and a promising antibacterial and anticancer drug target. Herein, we describe the potent cystargolides as the first natural β‐lactone inhibitors of the proteolytic core ClpP. B...

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Bibliographic Details
Published in:Angewandte Chemie International Edition 2024-01, Vol.63 (3), p.e202314028-n/a
Main Authors: Illigmann, Astrid, Vielberg, Marie‐Theres, Lakemeyer, Markus, Wolf, Felix, Dema, Taulant, Stange, Patrik, Kuttenlochner, Wolfgang, Liebhart, Elisa, Kulik, Andreas, Staudt, Nicole D., Malik, Imran, Grond, Stephanie, Sieber, Stephan A., Kaysser, Leonard, Groll, Michael, Brötz‐Oesterhelt, Heike
Format: Article
Language:English
Subjects:
Anti-Virulence
Antitumor agents
Caseinolytic Protease
Catalytic Domain
Dipeptides - metabolism
Endopeptidase Clp - metabolism
Homeostasis
In vitro methods and tests
Inhibitors
Lactones
Molecular modelling
Natural Products
Protease
Protein Crystallography
Proteolysis
Serine proteinase
Staphylococcus aureus
Staphylococcus aureus - metabolism
Therapeutic targets
Virulence
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Summary:The caseinolytic protease is a highly conserved serine protease, crucial to prokaryotic and eukaryotic protein homeostasis, and a promising antibacterial and anticancer drug target. Herein, we describe the potent cystargolides as the first natural β‐lactone inhibitors of the proteolytic core ClpP. Based on the discovery of two clpP genes next to the cystargolide biosynthetic gene cluster in Kitasatospora cystarginea, we explored ClpP as a potential cystargolide target. We show the inhibition of Staphylococcus aureus ClpP by cystargolide A and B by different biochemical methods in vitro. Synthesis of semisynthetic derivatives and probes with improved cell penetration allowed us to confirm ClpP as a specific target in S. aureus cells and to demonstrate the anti‐virulence activity of this natural product class. Crystal structures show cystargolide A covalently bound to all 14 active sites of ClpP from S. aureus, Aquifex aeolicus, and Photorhabdus laumondii, and reveal the molecular mechanism of ClpP inhibition by β‐lactones, the predominant class of ClpP inhibitors. Two clpP genes next to the biosynthetic genes for the cystargolides in Kitasatospora cystarginea provided the impetus to test the natural products for anti‐ClpP activity. Cystargolides emerged as covalent ClpP inhibitors and are the first β‐lactones for which ClpP co‐crystal structures could be solved. The molecular inhibition mechanism is presented.
ISSN:1433-7851
1521-3773
1521-3773
DOI:10.1002/anie.202314028