Regulation of bacterial virulence

Group: Sieber

In the search for compounds that block bacterial virulence we focus on a major regulator of toxin production termed caseinolytic protease P (ClpP). Genetic knockouts of ClpP led to the attenuation of S. aureus virulence and we identified the first chemical inhibitor class specific for this enzyme. These inhibitors attenuated virulence of Staphylococcus aureus and multiresistant isolates. In numerous follow-up studies, we have identified novel inhibitor generations, obtained structural information on the binding mode, and unraveled protein dynamics and conformational changes essential to understand the enzyme mechanism of action. In addition, we have also looked for alternative virulence-regulating mechanisms including small molecule-driven sensing of bacteria and the human stress hormone dynorphin.

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Moreover, we are interested in the identification of novel antibiotic targets. Small molecules with antibacterial activity, either of natural or synthetic origin, are synthetically equipped with chemical tags to yield probes for target identification via activity-based protein profiling (pioneered by the Cravatt and Bogyo labs) in living bacteria. For example, a recent strategy focussed on the repurposing of existing drugs, i.e. human kinase inhibitors, to kill bacteria. Here we chemically optimized a hit compound of such a screen to yield a potent derivative, termed “PK150”. PK150 is active against methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates, kills difficult-to-treat persister cells, eradicates biofilms, and does not develop resistance in the lab. In depth mode of action studies with a corresponding PK150 probe revealed at least two cellular targets addressed by PK150: overactivation of protein secretion and inhibition of energy metabolism, a so far unprecedented dual mechanism of action. We believe that dysregulation of these targets causes rapid cell death and complicates the development of resistance.

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1. Le, P., Kunold, E., Macsics, R., Rox, K., Jennings, M., Ugur, I., Reinecke, M., Chaves-Moreno, D., Hackl, M.W., Fetzer, C., Mandl, F.A.M., Lehmann, J., Korotkov, V.S., Hacker, S.M., Küster, B., Antes, I., Pieper, D., Rohde, M., Wuest, W.M., Medina, E., Sieber, S.A., "Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms", Nat. Chem., 2020, 12, 145-158. PMID: 31844194, PMCID: PMC6994260

2. Gatsogiannis, C.°, Balogh, D.°, Merino, F., Sieber, S.A.*, Raunser, S.*, "Cryo-EM structure of the ClpXP protein degradation machinery", Nat. Struct. Mol. Biol., 2019, 26, 946-954. PMID: 31582852,  PMCID: PMC6783313


3. Fetzer, C., Korotkov, V.S., Thänert, R., Lee, K.M., Neuenschwander, M., von Kries, J.P., Medina, E., Sieber, S.A., "A Chemical Disruptor of the ClpX Chaperone Complex Attenuates the Virulence of Multidrug-Resistant Staphylococcus aureus", Angew. Chem. Int. Ed., 2017, 56, 15746-15750. PMID: 28906057


4. Gersch, M., Famulla, K., Dahmen M., Göbl, C., Malik, I., Richter, K., Korotkov, V. S., Sass, P., Rübsamen-Schaeff, H., Madl, T., Brötz-Oesterhelt*, H., Sieber, S.A.*, "AAA+ chaperones and acyldepsipeptides activate the ClpP protease via conformational control", Nat. Comm., 2015, 6, 6320, doi:10.1038/ncomms7320. PMID: 25695750