Journal Article

Characterization and prediction of the mechanism of action of antibiotics through NMR metabolomics

Neugebauer, Ute, Poon, Karen K. H., Löffler, Bettina, Große, Christina, Duggan, Gavin E., Zbytnuik, Lori, Hoerr, Verena, Methling, Karen, Vogel, Hans J.

2016

Overview

Background The emergence of antibiotic resistant pathogenic bacteria has reduced our ability to combat infectious diseases. At the same time the numbers of new antibiotics reaching the market have decreased. This situation has created an urgent need to discover novel antibiotic scaffolds. Recently, the application of pattern recognition techniques to identify molecular fingerprints in ‘omics’ studies, has emerged as an important tool in biomedical research and laboratory medicine to identify pathogens, to monitor therapeutic treatments or to develop drugs with improved metabolic stability, toxicological profile and efficacy. Here, we hypothesize that a combination of metabolic intracellular fingerprints and extracellular footprints would provide a more comprehensive picture about the mechanism of action of novel antibiotics in drug discovery programs. Results In an attempt to integrate the metabolomics approach as a classification tool in the drug discovery processes, we have used quantitative 1 H NMR spectroscopy to study the metabolic response of Escherichia coli cultures to different antibiotics. Within the frame of our study the effects of five different and well-known antibiotic classes on the bacterial metabolome were investigated both by intracellular fingerprint and extracellular footprint analysis. The metabolic fingerprints and footprints of bacterial cultures were affected in a distinct manner and provided complementary information regarding intracellular and extracellular targets such as protein synthesis, DNA and cell wall. While cell cultures affected by antibiotics that act on intracellular targets showed class-specific fingerprints, the metabolic footprints differed significantly only when antibiotics that target the cell wall were applied. In addition, using a training set of E. coli fingerprints extracted after treatment with different antibiotic classes, the mode of action of streptomycin, tetracycline and carbenicillin could be correctly predicted. Conclusion The metabolic profiles of E. coli treated with antibiotics with intracellular and extracellular targets could be separated in fingerprint and footprint analysis, respectively and provided complementary information. Based on the specific fingerprints obtained for different classes of antibiotics, the mode of action of several antibiotics could be predicted. The same classification approach should be applicable to studies of other pathogenic bacteria.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Analysis / Anti-Bacterial Agents - pharmacology / Antibiotics / Bacteria / Bacterial infections / Biological Microscopy / Biomedical and Life Sciences / Biosynthesis / Carbenicillin - pharmacology / Drug Discovery / Drug resistance / E coli / Escherichia coli - classification / Escherichia coli - drug effects / Health aspects / Infectious diseases / Investigations / Life Sciences / Metabolism / Metabolites / Metabolomics - methods / Microbial biochemistry / Microbial Sensitivity Tests / Microbiology / Mode of action / Multivariate Analysis / Mycology / Nuclear magnetic resonance spectroscopy / Parasitology / Pathogens / Pattern recognition / physiology and metabolism / Pilot Projects / Protein synthesis / Proton Magnetic Resonance Spectroscopy - methods / Research Article / Solvents / Streptomycin - pharmacology / Tetracycline - pharmacology / Virology