Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae

• Published in: EMBO molecular medicine 2024-01, Vol.16 (1), p.93-111
• Main Authors: Vieira Da Cruz, Anais, Jiménez-Castellanos, Juan-Carlos, Börnsen, Clara, Van Maele, Laurye, Compagne, Nina, Pradel, Elizabeth, Müller, Reinke T, Meurillon, Virginie, Soulard, Daphnée, Piveteau, Catherine, Biela, Alexandre, Dumont, Julie, Leroux, Florence, Deprez, Benoit, Willand, Nicolas, Pos, Klaas M, Frangakis, Achilleas S, Hartkoorn, Ruben C, Flipo, Marion
• Format: Article
• Language: English
• Subjects: Animals; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Biomedical and Life Sciences; Biomedicine; EMBO08; EMBO23; EMBO40; Escherichia coli; Escherichia coli Proteins - metabolism; Escherichia coli Proteins - pharmacology; Klebsiella pneumoniae - metabolism; Life Sciences; Mice; Molecular Medicine; Multidrug Resistance-Associated Proteins - metabolism; Multidrug Resistance-Associated Proteins - pharmacology
• ISSN: 1757-4684; 1757-4676; 1757-4684
• DOI: 10.1038/s44321-023-00007-9

Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump is the dominant constitutive system by which Enterobacterales like Escherichia coli and Klebsiella pneumoniae extrude antibiotics. Here, we describe the medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor. In vitro evaluation of BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression. Using cryo-EM, BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor. Finally, proof of concept studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection. Synopsis Bacterial efflux pumps are responsible for both basal and acquired broad-spectrum antibiotic resistance in K. pneumoniae . In the fight against drug resistance, efflux pump inhibitors such as pyridylpiperazines could offer a solution to potentiate antibiotic activity and revert resistance. The structure-based medicinal chemistry is presented to identify a pyridylpiperazine efflux pump inhibitor, BDM91288, with improved pharmacokinetic properties. BDM91288 is shown to inhibit the AcrB component of the primary K. pneumoniae efflux pump and allows for broad spectrum antibiotic boosting. Single-particle Cryo-EM-based structural biology shows BDM91288 binding to the transmembrane domain of K. pneumoniae AcrB. BDM91288 is shown to revert resistance in K. pneumoniae mediated by clinically relevant mutations in the transcriptional regulator RamR that confers efflux pump overexpression. Using in vivo murine models of K. pneumoniae lung infection, BDM91288 was demonstrated to potentiate the activity of the efflux substrate levofloxacin. Bacterial efflux pumps are responsible for both basal and acquired broad-spectrum antibiotic resistance in K. pneumoniae . In the fight against drug resistance, efflux pump inhibitors such as pyridylpiperazines could offer a solution to potentiate antibiotic activity and revert resistance.