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A synthetic lethal approach for compound and target identification in Staphylococcus aureus

Nature Chemical Biology volume 12, pages 40–45 (2016)Cite this article

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Abstract

The majority of bacterial proteins are dispensable for growth in the laboratory but nevertheless have important physiological roles. There are no systematic approaches to identify cell-permeable small-molecule inhibitors of these proteins. We demonstrate a strategy to identify such inhibitors that exploits synthetic lethal relationships both for small-molecule discovery and for target identification. Applying this strategy in Staphylococcus aureus, we have identified a compound that inhibits DltB, a component of the teichoic acid D-alanylation machinery that has been implicated in virulence. This D-alanylation inhibitor sensitizes S. aureus to aminoglycosides and cationic peptides and is lethal in combination with a wall teichoic acid inhibitor. We conclude that DltB is a druggable target in the D-alanylation pathway. More broadly, the work described demonstrates a systematic method to identify biologically active inhibitors of major bacterial processes that can be adapted to numerous organisms.

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Figure 1: The S. aureus cell envelope is a complex system that includes numerous components and interactions that are poorly understood.
Figure 2: PCA of high-throughput screening data enables rapid identification of strain-selective growth inhibitors.
Figure 3: The target of amsacrine was identified by exploiting synthetic lethality.
Figure 4: Amsacrine inhibits incorporation of 14C-D-alanine into LTA in wild-type S. aureus but not in dltB mutants.
Figure 5: Amsacrine potentiates activity of aminoglycosides.
Figure 6: Synthetic lethal chemical genetic discovery cycle identifies mutant-selective inhibitors and their targets.

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Acknowledgements

The authors thank T. Pang (Department of Microbiology and Immunobiology, Harvard Medical School) for providing plasmids and other reagents; C. Shamu, J. Smith and the staff at the ICCB-Longwood Screening Facility for compound screening; and the Harvard Medical School Biopolymers Facility and the Tufts University Core Facility for sequencing. This work was funded by U.S. National Institutes of Health grants U19AI109764 to S.W. and T.C.M., U54AI057159 to the ICCB-L Screening Facility, P01AI083214 and R01AI099144 to S.W. and F32AI118160 to S.H.M.

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  1. Lincoln Pasquina, John P Santa Maria Jr & Samir H Moussa

    Present address: Present addresses: Health Advances, LLC, Weston, Massachusetts, USA (L.P.); Merck Research Laboratories, Boston, Massachusetts, USA (J.P.S.M. Jr.); Entasis Therapeutics, Waltham, Massachusetts, USA (S.H.M.).,

Authors and Affiliations

  1. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

    Lincoln Pasquina, John P Santa Maria Jr, B McKay Wood, Samir H Moussa, Leigh M Matano, Marina Santiago, Sara E S Martin, Wonsik Lee, Timothy C Meredith & Suzanne Walker

  2. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA

    Timothy C Meredith

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Contributions

L.P. and J.P.S.M. performed the chemical screen; T.C.M. and M.S. prepared the transposon library; L.P., L.M.M., T.C.M. and M.S. performed the Tn-seq experiments; W.L. constructed the ΔypfP mutant used for validation; L.P. selected for resistance mutations and analyzed whole genome sequences; B.M.W. performed LTA D-alanylation and gyrase assays; S.H.M. constructed complementation mutants; L.M.M. carried out MIC and spot dilution assays; and S.E.S.M. synthesized o-AMSA. S.W. designed and supervised the project, and figure design, preparation, and writing was primarily done by L.P. and S.W. with important contributions from L.M.M., J.P.S.M. and B.M.W. All of the authors edited the manuscript.

Corresponding author

Correspondence to Suzanne Walker.

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Pasquina, L., Santa Maria, J., McKay Wood, B. et al. A synthetic lethal approach for compound and target identification in Staphylococcus aureus. Nat Chem Biol 12, 40–45 (2016). https://doi.org/10.1038/nchembio.1967

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