Cystobactamid off-target profiling reveals favorable safety, superoxide reduction, and SCARB1 inhibition in eukaryotes

Risch, T.; Hellwinkel, B.; Mostert, D.; Kany, A. M.; Solga, D.; Seedorf, T.; Heimann, D.; Hoppstädter, J.; Kohnhäuser, D.; Hilgers, J.-S.; Fries, F.; Deschner, F.; Brönstrup, M.; Kirschning, A.; Sieber, S. A.; Pietschmann, T.; Kiemer, A. K.; Herrmann, J.; Müller, R.

doi:10.1101/2024.10.10.617689

bioRxiv · 10.1101/2024.10.10.617689

Cystobactamid off-target profiling reveals favorable safety, superoxide reduction, and SCARB1 inhibition in eukaryotes

Risch, T.·Hellwinkel, B.·Mostert, D.·Kany, A. M.·Solga, D.·Seedorf, T.·Heimann, D.·Hoppstädter, J.·Kohnhäuser, D.·Hilgers, J.-S.·Fries, F.·Deschner, F.·Brönstrup, M.·Kirschning, A.·Sieber, S. A.·Pietschmann, T.·Kiemer, A. K.·Herrmann, J.·Müller, R.

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Abstract

Antimicrobial resistance (AMR) poses a fundamental global threat, necessitating new strategies for effective therapies. Cystobactamids (CYS), a class of antibacterial agents targeting bacterial gyrase and topoisomerase IV, represent a non-traditional chemical scaffold with broad-spectrum activity. For toxicological de-risking, we performed a comprehensive profiling on eukaryotic cells, focusing on cytotoxicity, genotoxicity, and mitochondrial toxicity, demonstrating cellular safety and superoxide scavenging properties. Studies in zebrafish embryos assessed developmental, cardiovascular, and hepatic toxicity, indicating a favorable in vivo safety profile. Metabolism studies revealed glucuronidation and amide bond hydrolysis as key pathways, whereby CYS metabolic stability substantially improved by cobicistat co-treatment. Affinity-based protein profiling identified the cholesterol- and HCV-receptor scavenger receptor class B member 1 (SCARB1) as a primary eukaryotic off-target protein, with cystobactamids shown to inhibit SCARB1s function, preventing hepatitis C virus pseudoparticle entry into cells. These findings suggest a high therapeutic potential for cystobactamids and highlight SCARB1 as a primary eukaryotic target.

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Risch, T., Hellwinkel, B., Mostert, D., Kany, A. M., Solga, D., Seedorf, T., Heimann, D., Hoppstädter, J., Kohnhäuser, D., Hilgers, J.-S., Fries, F., Deschner, F., Brönstrup, M., Kirschning, A., Sieber, S. A., Pietschmann, T., Kiemer, A. K., Herrmann, J., Müller, R.. 2024-10-17. Cystobactamid off-target profiling reveals favorable safety, superoxide reduction, and SCARB1 inhibition in eukaryotes. https://doi.org/10.1101/2024.10.10.617689

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