Optimized alkyne-modified pyridylpiperazine efflux pump inhibitors overcome intrinsic macrolide resistance in multidrug-resistant Klebsiella pneumoniae isolates
Abstract
Multidrug-resistant (MDR), ESBL- and carbapenemase-producing Enterobacterales represent a major global health concern requiring novel therapeutic strategies. One promising approach is the development of efflux pump inhibitors (EPIs) targeting the predominant AcrAB-TolC system to sensitize these pathogens to antibiotics predominantly used for Gram-positive infections. PyridylPiperazine (PyrPip)-based EPIs are novel allosteric AcrB inhibitors that block antibiotic efflux in Enterobacterales. Medicinal chemistry optimization identified BDM100004 ( 3 ), an alkyne-modified PyrPip analog with improved drug-like properties. In vitro susceptibility profiling of 48 clinical MDR Klebsiella pneumoniae isolates showed that BDM100004 ( 3 ) potentiated macrolide activity in most MDR isolates, with particularly strong effects observed for azithromycin. A small fraction of MDR isolates was found to be highly resistant to macrolides, and poorly potentiated by BDM100004 ( 3 ). Genome analysis revealed these isolates to carry specific macrolide resistance genes, and together with reverse genetics, it was validated that BDM100004 ( 3 ) could not reverse Mph(A) and Mph(E) mediated azithromycin resistance. Interestingly, however, BDM100004 ( 3 ) was found to overcome azithromycin resistance mediated by Erm(B), Msr(E) and Mrx. In vivo, BDM100004 ( 3 ) enhanced azithromycin efficacy both in a Galleria mellonella infection model and in a murine lung infection model of K. pneumoniae . Overall, these findings demonstrate the potential of a PyrPip EPI to repurpose azithromycin against ESBL- and carbapenemase-producing K. pneumoniae with limitations in mph(A) and mph(E) -expressing strains.
Related
- Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors
- Prevention of Klebsiella pneumoniae antibiotic resistance plasmid dissemination by prophylactic or simultaneous CRISPR-Cas9 treatment.
- Closely related ST11 Klebsiella pneumoniae isolates with transient attenuation and re-emergence of carbapenem resistance during prolonged hospitalization: a case report
- Genome-wide transposon screening uncovers phage resistance mechanisms and bidirectional effects on antibiotic susceptibility in carbapenem-resistant Klebsiella pneumoniae
- Characterisation of the novel transposon Tn7722 harbouring blaNDM-1: Insights into the evolutionary dynamics of resistance in Klebsiella pneumoniae
BibTeX
@article{sobieski2026optimized,
title = {{Optimized alkyne-modified pyridylpiperazine efflux pump inhibitors overcome intrinsic macrolide resistance in multidrug-resistant Klebsiella pneumoniae isolates}},
author = {Cécilia Sobieski and Virginie Meurillon and Jonathan Chatagnon and Rodolphe Vatinel and Elizabeth Pradel and Gabriele Lucca and Lea Lebre and Delphine Cayet and Reinke Müller and Catherine Piveteau and Julie Dumont and Florence Leroux and Klaas Pos and Benoit Deprez and Nicolas Willand and Richard Bonnet and Laurye van Maele and Marion Flipo and Ruben C. Hartkoorn},
journal = {npj Antimicrobials and Resistance},
year = {2026},
month = aug,
doi = {10.1038/s44259-026-00263-y},
url = {https://hal.science/hal-05780372v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Optimized alkyne-modified pyridylpiperazine efflux pump inhibitors overcome intrinsic macrolide resistance in multidrug-resistant Klebsiella pneumoniae isolates
AU - Cécilia Sobieski
AU - Virginie Meurillon
AU - Jonathan Chatagnon
AU - Rodolphe Vatinel
AU - Elizabeth Pradel
AU - Gabriele Lucca
AU - Lea Lebre
AU - Delphine Cayet
AU - Reinke Müller
AU - Catherine Piveteau
AU - Julie Dumont
AU - Florence Leroux
AU - Klaas Pos
AU - Benoit Deprez
AU - Nicolas Willand
AU - Richard Bonnet
AU - Laurye van Maele
AU - Marion Flipo
AU - Ruben C. Hartkoorn
PY - 2026
DA - 2026/08/31
JO - npj Antimicrobials and Resistance
DO - 10.1038/s44259-026-00263-y
UR - https://hal.science/hal-05780372v1
AB - Multidrug-resistant (MDR), ESBL- and carbapenemase-producing Enterobacterales represent a major global health concern requiring novel therapeutic strategies. One promising approach is the development of efflux pump inhibitors (EPIs) targeting the predominant AcrAB-TolC system to sensitize these pathogens to antibiotics predominantly used for Gram-positive infections. PyridylPiperazine (PyrPip)-based EPIs are novel allosteric AcrB inhibitors that block antibiotic efflux in Enterobacterales. Medicinal chemistry optimization identified BDM100004 ( 3 ), an alkyne-modified PyrPip analog with improved drug-like properties. In vitro susceptibility profiling of 48 clinical MDR Klebsiella pneumoniae isolates showed that BDM100004 ( 3 ) potentiated macrolide activity in most MDR isolates, with particularly strong effects observed for azithromycin. A small fraction of MDR isolates was found to be highly resistant to macrolides, and poorly potentiated by BDM100004 ( 3 ). Genome analysis revealed these isolates to carry specific macrolide resistance genes, and together with reverse genetics, it was validated that BDM100004 ( 3 ) could not reverse Mph(A) and Mph(E) mediated azithromycin resistance. Interestingly, however, BDM100004 ( 3 ) was found to overcome azithromycin resistance mediated by Erm(B), Msr(E) and Mrx. In vivo, BDM100004 ( 3 ) enhanced azithromycin efficacy both in a Galleria mellonella infection model and in a murine lung infection model of K. pneumoniae . Overall, these findings demonstrate the potential of a PyrPip EPI to repurpose azithromycin against ESBL- and carbapenemase-producing K. pneumoniae with limitations in mph(A) and mph(E) -expressing strains.
SN - 2731-8745
ER -