Accelerating early antituberculosis drug discovery by creating mycobacterial indicator strains that predict mode of action

Maikel Boot, Susanna Commandeur, Amit K. Subudhi, Meriem Bahira, Trever C. Smith, Abdallah M. Abdallah, Mae van Gemert, Joël Lelièvre, Lluís Ballell, Bree B. Aldridge, Arnab Pain, Alexander Speer, Wilbert Bitter*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review

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Abstract

Due to the rise of drug-resistant forms of tuberculosis, there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole-cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on stricto sensu life/death screening that give little qualitative information. In doing so, promising compound scaffolds or nonoptimized compounds that fail to reach inhibitory concentrations are missed. To accelerate early tuberculosis (TB) drug discovery, we performed RNA sequencing on Mycobacterium tuberculosis and Mycobacterium marinum to map the stress responses that follow upon exposure to subinhibitory concentrations of antibiotics with known targets, ciprofloxacin, ethambutol, isoniazid, streptomycin, and rifampin. The resulting data set comprises the first overview of transcriptional stress responses of mycobacteria to different antibiotics. We show that antibiotics can be distinguished based on their specific transcriptional stress fingerprint. Notably, this fingerprint was more distinctive in M. marinum. We decided to use this to our advantage and continue with this model organism. A selection of diverse antibiotic stress genes was used to construct stress reporters. In total, three functional reporters were constructed to respond to DNA damage, cell wall damage, and ribosomal inhibition. Subsequently, these reporter strains were used to screen a small anti-TB compound library to predict the mode of action. In doing so, we identified the putative modes of action for three novel compounds, which confirms the utility of our approach.

Original languageEnglish
Article numbere00083-18
Pages (from-to)1-16
Number of pages16
JournalAntimicrobial Agents and Chemotherapy
Volume62
Issue number7
Early online date26 Jun 2018
DOIs
Publication statusPublished - Jul 2018

Funding

The research leading to these results has received funding from the Innovative Medicines Initiative Joint Undertaking under grant agreement 115337, the resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in-kind contribution. The grant was awarded to W. Bitter. This work was additionally supported by NIH grants (grant 1DP2LM011952 to B. B. Aldridge and grant T32 AI 7329-23). This work was supported by the Netherlands Organization for Scientific Research (NWO) through a VENI grant (016.Veni.171.090) awarded to A. Speer. We express our gratitude to Christina M. J. E. Vandenbroucke-Grauls for helpful discussions. We thank Francois Rustenburg and Coen Kuijl for technical assistance. The research leading to these results has received funding from the Innovative Medicines Initiative Joint Undertaking under grant agreement 115337, the resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in-kind contribution. The grant was awarded to W. Bitter. This work was additionally supported by NIH grants (grant 1DP2LM011952 to B. B. Aldridge and grant T32 AI 7329-23). This work was supported by the Netherlands Organization for Scientific Research (NWO) through a VENI grant (016.Veni.171.090) awarded to A. Speer. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

FundersFunder number
National Institutes of Health1DP2LM011952, T32 AI 7329-23
National Institute of Allergy and Infectious DiseasesT32AI007329
Seventh Framework Programme
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Seventh Framework ProgrammeFP7/2007-2013
Innovative Medicines Initiative115337

    Keywords

    • Antibiotics
    • Mycobacteria
    • RNA sequencing
    • Stress responses

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