Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation
The discovery of antibiotics has been slowing to a halt. Phenotypic screening is once again at the forefront of antibiotic discovery, yet Mechanism-Of-Action (MOA) identification is still a major bottleneck. As such, methods capable of MOA elucidation coupled with the high-throughput screening of wh...
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doaj-200b833736d64c6f92705fac3724bf9f2020-11-25T02:33:57ZengMDPI AGMetabolites2218-19892020-04-011014514510.3390/metabo10040145Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action ElucidationBernardo Ribeiro da Cunha0Luís P. Fonseca1Cecília R.C. Calado2iBB—Institute of Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, PortugaliBB—Institute of Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, PortugalISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa PortugalThe discovery of antibiotics has been slowing to a halt. Phenotypic screening is once again at the forefront of antibiotic discovery, yet Mechanism-Of-Action (MOA) identification is still a major bottleneck. As such, methods capable of MOA elucidation coupled with the high-throughput screening of whole cells are required now more than ever, for which Fourier-Transform Infrared (FTIR) spectroscopy is a promising metabolic fingerprinting technique. A high-throughput whole-cell FTIR spectroscopy-based bioassay was developed to reveal the metabolic fingerprint induced by 15 antibiotics on the <i>Escherichia coli</i> metabolism. Cells were briefly exposed to four times the minimum inhibitory concentration and spectra were quickly acquired in the high-throughput mode. After preprocessing optimization, a partial least squares discriminant analysis and principal component analysis were conducted. The metabolic fingerprints obtained with FTIR spectroscopy were sufficiently specific to allow a clear distinction between different antibiotics, across three independent cultures, with either analysis algorithm. These fingerprints were coherent with the known MOA of all the antibiotics tested, which include examples that target the protein, DNA, RNA, and cell wall biosynthesis. Because FTIR spectroscopy acquires a holistic fingerprint of the effect of antibiotics on the cellular metabolism, it holds great potential to be used for high-throughput screening in antibiotic discovery and possibly towards a better understanding of the MOA of current antibiotics.https://www.mdpi.com/2218-1989/10/4/145antibiotic discoverychemometrics<i>Escherichia coli</i>Fourier-Transform infrared (FTIR) spectroscopyhigh-throughput screeningmechanism-of-action (MOA) |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bernardo Ribeiro da Cunha Luís P. Fonseca Cecília R.C. Calado |
spellingShingle |
Bernardo Ribeiro da Cunha Luís P. Fonseca Cecília R.C. Calado Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation Metabolites antibiotic discovery chemometrics <i>Escherichia coli</i> Fourier-Transform infrared (FTIR) spectroscopy high-throughput screening mechanism-of-action (MOA) |
author_facet |
Bernardo Ribeiro da Cunha Luís P. Fonseca Cecília R.C. Calado |
author_sort |
Bernardo Ribeiro da Cunha |
title |
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation |
title_short |
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation |
title_full |
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation |
title_fullStr |
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation |
title_full_unstemmed |
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation |
title_sort |
metabolic fingerprinting with fourier-transform infrared (ftir) spectroscopy: towards a high-throughput screening assay for antibiotic discovery and mechanism-of-action elucidation |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2020-04-01 |
description |
The discovery of antibiotics has been slowing to a halt. Phenotypic screening is once again at the forefront of antibiotic discovery, yet Mechanism-Of-Action (MOA) identification is still a major bottleneck. As such, methods capable of MOA elucidation coupled with the high-throughput screening of whole cells are required now more than ever, for which Fourier-Transform Infrared (FTIR) spectroscopy is a promising metabolic fingerprinting technique. A high-throughput whole-cell FTIR spectroscopy-based bioassay was developed to reveal the metabolic fingerprint induced by 15 antibiotics on the <i>Escherichia coli</i> metabolism. Cells were briefly exposed to four times the minimum inhibitory concentration and spectra were quickly acquired in the high-throughput mode. After preprocessing optimization, a partial least squares discriminant analysis and principal component analysis were conducted. The metabolic fingerprints obtained with FTIR spectroscopy were sufficiently specific to allow a clear distinction between different antibiotics, across three independent cultures, with either analysis algorithm. These fingerprints were coherent with the known MOA of all the antibiotics tested, which include examples that target the protein, DNA, RNA, and cell wall biosynthesis. Because FTIR spectroscopy acquires a holistic fingerprint of the effect of antibiotics on the cellular metabolism, it holds great potential to be used for high-throughput screening in antibiotic discovery and possibly towards a better understanding of the MOA of current antibiotics. |
topic |
antibiotic discovery chemometrics <i>Escherichia coli</i> Fourier-Transform infrared (FTIR) spectroscopy high-throughput screening mechanism-of-action (MOA) |
url |
https://www.mdpi.com/2218-1989/10/4/145 |
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