ClpP Protease Modulators

Design, synthesis and characterization of novel modulators of ClpP proteases from Gram-negative bacteria (WP1/2)

Prof. Koen Augustyns
University of Antwerp

ClpP proteases inhibition has been shown to have potential as antibacterial strategy. Covalent binders have a proven track record as useful antibacterial drugs in the clinic but only a very limited number of chemotypes have been reported as covalent binders of ClpP. Therefore, the aim of this project is to design and synthesize novel covalent ClpP inhibitors. UA has extensive expertise in the design, synthesis and characterization of potent, selective, non-toxic, covalent inhibitors of several serine proteases. This research resulted in a focused library of irreversible serine protease inhibitors consisting of about 200 α-amino diaryl phosphonates. At first, this library will be enriched with hydrophobic substituents, based on the substrate specificity of ClpP. Next, these compounds will be screened for covalent inhibition of ClpP from E. coli. The irreversible nature of the compounds will also be investigated, as well as their activity on Gram-negative bacteria. The most promising diaryl phosphonates will be docked in the active site of the crystal structure of E. coli, ensuring a covalent bond with the active site serine hydroxyl group. For two selected compounds pharmacokinetic parameters will be determined using a single oral – single intravenous dose application in mice. The chemical diversity will also be enlarged to other irreversible covalent warheads (chloromethylketones) and reversible covalent warheads (nitriles, boronic acids).

Objectives: Design, synthesis and characterization of novel covalent inhibitors of ClpP proteases from Gram-negative bacteria.

Expected Results: A novel covalently binding ClpP protease inhibitor with activity against Gram-negative bacteria, thereby validating ClpP as therapeutic target.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No  642620
European Union