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Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting

Nature Chemical Biology volume 5, pages 849–856 (2009)Cite this article

Abstract

One of the most significant hurdles to developing new chemical probes of biological systems and new drugs to treat disease is that of understanding the mechanism of action of small molecules discovered with cell-based small-molecule screening. Here we have assembled an ordered, high-expression clone set of all of the essential genes from Escherichia coli and used it to systematically screen for suppressors of growth inhibitory compounds. Using this chemical genomic approach, we demonstrate that the targets of well-known antibiotics can be identified as high copy suppressors of chemical lethality. This approach led to the discovery of MAC13243, a molecule that belongs to a new chemical class and that has a unique mechanism and promising activity against multidrug-resistant Pseudomonas aeruginosa. We show that MAC13243 inhibits the function of the LolA protein and represents a new chemical probe of lipoprotein targeting in bacteria with promise as an antibacterial lead with Gram-negative selectivity.

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Figure 1: Chemical genetic interactions of six known antibiotics and MAC13243 discovered by high copy suppression.
Figure 2: Suppression analysis of MAC13243 by high copy LolA.
Figure 3: MAC13243 blocks lipoprotein targeting in E. coli.
Figure 4: Interaction of MAC13243 with LolA by NMR.

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Acknowledgements

We thank B. Wanner and H. Mori of Purdue University and the Nara Institute, respectively, for providing the ordered genomic library (ASKA library) used in these studies and for inspiring discussion. We thank H. Zgurskaya at University of Oklahoma for the polyclonal antibodies against TolC, we thank D. Andrews at McMaster University for the YidC antibodies and we thank G. Wright at McMaster University for the clinical isolates of P. aeruginosa. This work was supported by an operating grant from the Canadian Institutes of Health Research (MOP-81330) and by a Canada Research Chair award to E.D.B.

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Author notes

  1. Ranjana Pathania

    Present address: Present address: Department of Biotechnology, Indian Institute of Technology, Roorkee Uttaranchal, India.,

Authors and Affiliations

  1. Department of Biochemistry and Biomedical Sciences,

    Ranjana Pathania, Soumaya Zlitni, Courtney Barker, Giuseppe Melacini & Eric D Brown

  2. Michael G. DeGroote Institute of Infectious Disease Research,

    Ranjana Pathania, Soumaya Zlitni, Courtney Barker, David A Gerritsma, Julie Lebert, Emilia Awuah, Fred A Capretta & Eric D Brown

  3. Department of Chemistry, McMaster University, Hamilton, Ontario, Canada

    Rahul Das, David A Gerritsma, Julie Lebert, Emilia Awuah, Giuseppe Melacini & Fred A Capretta

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Contributions

R.P. designed and performed the high-expression array experiments, lipoprotein targeting studies and antibacterial activity determinations for MAC13243 and analogs and co-wrote the manuscript. S.Z. conducted the efflux susceptibility tests, analyzed the SAR data and the activity of MAC13243 against the pseudomonal isolates and co-wrote the manuscript. C.B. performed the suppression analysis of MAC13243 by high copy LolA and analyzed the SAR data. D.A.G., J.L. and E.A. performed the synthesis and characterization of MAC13243 and analogs under the guidance of F.A.C. R.D. performed the NMR spectroscopy studies of MAC13243 and LolA under the guidance of G.M. F.A.C. and G.M. co-wrote the manuscript. E.D.B. conceived and oversaw the project and co-wrote the manuscript.

Corresponding author

Correspondence to Eric D Brown.

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Supplementary Figures 1–4, Supplementary Tables 1 and 2, and Supplementary Methods (PDF 854 kb)

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Pathania, R., Zlitni, S., Barker, C. et al. Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. Nat Chem Biol 5, 849–856 (2009). https://doi.org/10.1038/nchembio.221

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