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Updated: May 26, 2025

Quadruple-Checkerboard: A Modification of the Three-Dimensional Checkerboard for Studying Drug Combinations
Published on: July 24, 2021
Exploring the principles behind antibiotics with limited resistance
Elvin Maharramov1,2, Márton Simon Czikkely1,3,4, Petra Szili1
1Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre Szeged, Szeged, Hungary.
Abstract:
Antibiotics that target multiple cellular functions are anticipated to be less prone to bacterial resistance. Here we hypothesize that while dual targeting is crucial, it is not sufficient in preventing resistance. Only those antibiotics that simultaneously target membrane integrity and block another cellular pathway display reduced resistance development. To test the hypothesis, we focus on three antibiotic candidates, POL7306, Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we show that resistance evolution against these antibiotics is limited in ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, while dual-target topoisomerase antibiotics are prone to resistance. We discover several mechanisms restricting resistance. First, de novo mutations result in only a limited elevation in resistance, including those affecting the molecular targets and efflux pumps. Second, resistance is inaccessible through gene amplification. Third, functional metagenomics reveal that mobile resistance genes are rare in human gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial populations upon toxic exposure to membrane targeting antibiotics. We conclude that resistance mechanisms commonly found in natural bacterial pathogens provide only limited protection to these antibiotics. Our work provides guidelines for the future development of antibiotics.
Insights
New antibiotics targeting both membrane integrity and another cellular pathway show limited resistance development in key pathogens. This dual-action approach is crucial for overcoming antibiotic resistance challenges.
Area of Science:
- Microbiology
- Drug Discovery
- Molecular Biology
Background:
- Antibiotic resistance is a growing global health threat.
- Antibiotics targeting multiple cellular functions are predicted to reduce resistance.
- Dual-targeting strategies are crucial but may not be sufficient alone.
Purpose of the Study:
- To test the hypothesis that antibiotics simultaneously targeting membrane integrity and another cellular pathway exhibit reduced resistance.
- To evaluate the efficacy of three novel antibiotic candidates (POL7306, Tridecaptin M152-P3, SCH79797) against ESKAPE pathogens.
- To identify mechanisms that restrict resistance evolution to these dual-targeting antibiotics.
Main Methods:
- Testing antibiotic candidates against ESKAPE pathogens (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa).
- Investigating resistance mechanisms including de novo mutations, gene amplification, and mobile resistance genes via functional metagenomics.
- Assessing bacterial population eradication upon exposure to membrane-targeting antibiotics.
Main Results:
- Limited resistance evolution observed against POL7306, Tridecaptin M152-P3, and SCH79797 in ESKAPE pathogens.
- Dual-targeting topoisomerase antibiotics showed higher susceptibility to resistance development.
- Mechanisms restricting resistance include limited impact of target mutations/efflux pumps, inaccessibility via gene amplification, and rarity of mobile resistance genes.
- Rapid bacterial eradication was observed with membrane-targeting antibiotics.
Conclusions:
- Antibiotics simultaneously targeting membrane integrity and another cellular pathway demonstrate reduced resistance development.
- Common resistance mechanisms in pathogens offer limited protection against these novel antibiotics.
- These findings provide critical guidelines for developing next-generation antibiotics to combat resistance.
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