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Assembly and clustering of natural antibiotics guides target identification

Nature Chemical Biology volume 12, pages 233–239 (2016)Cite this article

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Abstract

Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm. From this we also detail the directed mining of biosynthetic scaffolds and resistance determinants to reveal structures with a high likelihood of having previously unknown modes of action. Implementing this pipeline led to investigations of the telomycin family of natural products from Streptomyces canus, revealing that these bactericidal molecules possess a new antibacterial mode of action dependent on the bacterial phospholipid cardiolipin.

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Figure 1: Microbial natural products with specific antibacterial activity define a diverse range of antibacterial targets.
Figure 2: A retrobiosynthetic strategy for charting antibacterial natural products and identifying rare scaffolds with new molecular targets.
Figure 3: Telomycin is a nonribosomal peptide that lyses bacteria through an unknown mechanism.
Figure 4: Telomycin exerts bactericidal activity by interacting with cardiolipin.

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References

  1. Bush, K. et al. Tackling antibiotic resistance. Nat. Rev. Microbiol. 9, 894–896 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Fischbach, M.A. & Walsh, C.T. Antibiotics for emerging pathogens. Science 325, 1089–1093 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Newman, D.J. & Cragg, G.M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 75, 311–335 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Vining, C.L. Roles of secondary metabolites from microbes. in CIBA Foundation Symposium 171—Secondary Metabolites: Their Function and Evolution 184–198 (Wiley, Chichester, 1992).

  5. Fischbach, M.A. & Clardy, J. One pathway, many products. Nat. Chem. Biol. 3, 353–355 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Payne, D.J., Gwynn, M.N., Holmes, D.J. & Pompliano, D.L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat. Rev. Drug Discov. 6, 29–40 (2007).

    Article  CAS  PubMed  Google Scholar 

  7. Baumann, S. et al. Cystobactamids: myxobacterial topoisomerase inhibitors exhibiting potent antibacterial activity. Angew. Chem. Int. Edn. Engl. 53, 14605–14609 (2014).

    Article  CAS  Google Scholar 

  8. Lin, A.H., Murray, R.W., Vidmar, T.J. & Marotti, K.R. The oxazolidinone eperezolid binds to the 50S ribosomal subunit and competes with binding of chloramphenicol and lincomycin. Antimicrob. Agents Chemother. 41, 2127–2131 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Keller, S., Schadt, H.S., Ortel, I. & Süssmuth, R.D. Action of atrop-abyssomicin C as an inhibitor of 4-amino-4-deoxychorismate synthase PabB. Angew. Chem. Int. Edn. Engl. 46, 8284–8286 (2007).

    Article  CAS  Google Scholar 

  10. Li, J.W. & Vederas, J.C. Drug discovery and natural products: end of an era or an endless frontier? Science 325, 161–165 (2009).

    Article  CAS  PubMed  Google Scholar 

  11. Cundliffe, E. & Demain, A.L. Avoidance of suicide in antibiotic-producing microbes. J. Ind. Microbiol. Biotechnol. 37, 643–672 (2010).

    Article  CAS  PubMed  Google Scholar 

  12. D'Costa, V.M., McGrann, K.M., Hughes, D.W. & Wright, G.D. Sampling the antibiotic resistome. Science 311, 374–377 (2006).

    Article  PubMed  Google Scholar 

  13. Thaker, M.N. et al. Identifying producers of antibacterial compounds by screening for antibiotic resistance. Nat. Biotechnol. 31, 922–927 (2013).

    Article  CAS  PubMed  Google Scholar 

  14. Bibikova, M.V., Ivanitskaia, L.P. & Singal, E.M. [Directed screening of aminoglycoside antibiotic producers on selective media with gentamycin]. Antibiotiki 26, 488–492 (1981).

    CAS  PubMed  Google Scholar 

  15. Ivanitskaia, L.P., Bibikova, M.V., Gromova, M.N., Zhdanovich, IuV. & Istratov, E.N. [Use of selective media with lincomycin for the directed screening of antibiotic producers]. Antibiotiki 26, 83–86 (1981).

    CAS  PubMed  Google Scholar 

  16. Forsberg, K.J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Boucher, H.W. et al. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48, 1–12 (2009).

    Article  PubMed  Google Scholar 

  18. Doroghazi, J.R. et al. A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat. Chem. Biol. 10, 963–968 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Donadio, S., Maffioli, S., Monciardini, P., Sosio, M. & Jabes, D. Antibiotic discovery in the twenty-first century: current trends and future perspectives. J. Antibiot. 63, 423–430 (2010).

    Article  CAS  Google Scholar 

  20. Walsh, C.T. & Wencewicz, T.A. Prospects for new antibiotics: a molecule-centered perspective. J. Antibiot. 67, 7–22 (2014).

    Article  CAS  Google Scholar 

  21. Goss, R.J.M., Shankar, S. & Fayad, A.A. The generation of “unnatural” products: synthetic biology meets synthetic chemistry. Nat. Prod. Rep. 29, 870–889 (2012).

    Article  CAS  PubMed  Google Scholar 

  22. Ling, L.L. et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Cociancich, S. et al. The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine. Nat. Chem. Biol. 11, 195–197 (2015).

    Article  CAS  PubMed  Google Scholar 

  24. Hamamoto, H. et al. Lysocin E is a new antibiotic that targets menaquinone in the bacterial membrane. Nat. Chem. Biol. 11, 127–133 (2015).

    Article  CAS  PubMed  Google Scholar 

  25. Weber, T. et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W1, W237-43 (2015).

    Article  CAS  Google Scholar 

  26. Medema, M.H. et al. Minimum Information about a Biosynthetic Gene cluster. Nat. Chem. Biol. 11, 625–631 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Hadjithomas, M. et al. IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio. 6, e00932–15 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Bérdy, J. et al. Handbook of Antibiotic Compounds Vols. I–X (CRC Press, Boca Raton, Florida, USA, 1980–1982).

  29. Bérdy, J. Thoughts and facts about antibiotics: where we are now and where we are heading. J. Antibiot. 65, 385–395 (2012).

    Article  CAS  Google Scholar 

  30. Koch, M.A. et al. Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc. Natl. Acad. Sci. USA 102, 17272–17277 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Over, B. et al. Natural-product-derived fragments for fragment-based ligand discovery. Nat. Chem. 5, 21–28 (2013).

    Article  CAS  PubMed  Google Scholar 

  32. Wilson, D.N. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat. Rev. Microbiol. 12, 35–48 (2014).

    Article  CAS  PubMed  Google Scholar 

  33. Srivastava, A. et al. New target for inhibition of bacterial RNA polymerase: 'switch region'. Curr. Opin. Microbiol. 14, 532–543 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Skinnider, M.A. et al. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res. 43, 9645–9662 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Gibson, M.K., Forsberg, K.J. & Dantas, G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 9, 207–216 (2015).

    Article  CAS  PubMed  Google Scholar 

  36. Nakao, M. et al. Pyloricidins, novel anti-Helicobacter pylori antibiotics produced by Bacillus sp. I. Taxonomy, fermentation and biological activity. J. Antibiot. 54, 926–933 (2001).

    Article  CAS  Google Scholar 

  37. Nakajima, M. et al. Mycoplanecins, novel antimycobacterial antibiotics from Actinoplanes awajinensis subsp. mycoplanecinus subsp. nov. II. Isolation, physico-chemical characterization and biological activities of mycoplanecin A. J. Antibiot. 36, 961–966 (1983).

    Article  CAS  Google Scholar 

  38. Misiek, M. et al. Telomycin, a new antibiotic. Antibiot. Annu. 5, 852–855 (1957–1958).

    PubMed  Google Scholar 

  39. Gourevitch, A. et al. Microbiological studies on telomycin. Antibiot. Annu. 5, 856–862 (1957–1958).

    PubMed  Google Scholar 

  40. Tisch, D.E., Huftalen, J.B. & Dickison, H.L. Pharmacological studies with telomycin. Antibiot. Annu. 5, 863–868 (1957–1958).

    PubMed  Google Scholar 

  41. Sheehan, J.C., Mania, D., Nakamura, S., Stock, J.A. & Maeda, K. The structure of telomycin. J. Am. Chem. Soc. 90, 462–470 (1968).

    Article  CAS  PubMed  Google Scholar 

  42. Oliva, B., Maiese, W.M., Greenstein, M., Borders, D.B. & Chopra, I. Mode of action of the cyclic depsipeptide antibiotic LL-AO341β1 and partial characterization of a Staphylococcus aureus mutant resistant to the antibiotic. J. Antimicrob. Chemother. 32, 817–830 (1993).

    Article  CAS  PubMed  Google Scholar 

  43. Fu, C. et al. Biosynthetic studies of telomycin reveal new lipopeptides with enhanced activity. J. Am. Chem. Soc. 137, 7692–7705 (2015).

    Article  CAS  PubMed  Google Scholar 

  44. Tsai, M. et al. Staphylococcus aureus requires cardiolipin for survival under conditions of high salinity. BMC Microbiol. 11, 13 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Machaidze, G., Ziegler, A. & Seelig, J. Specific binding of Ro 09-0198 (cinnamycin) to phosphatidylethanolamine: a thermodynamic analysis. Biochemistry 41, 1965–1971 (2002).

    Article  CAS  PubMed  Google Scholar 

  46. Kawai, F. et al. Cardiolipin domains in Bacillus subtilis Marburg membranes. J. Bacteriol. 186, 1475–1483 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Mileykovskaya, E. & Dowhan, W. Cardiolipin membrane domains in prokaryotes and eukaryotes. Biochim. Biophys. Acta 1788, 2084–2091 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Oliver, P.M. et al. Localization of anionic phospholipids in Escherichia coli cells. J. Bacteriol. 196, 3386–3398 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Arias-Cartin, R., Grimaldi, S., Arnoux, P., Guigliarelli, B. & Magalon, A. Cardiolipin binding in bacterial respiratory complexes: structural and functional implications. Biochim. Biophys. Acta 1817, 1937–1949 (2012).

    Article  CAS  PubMed  Google Scholar 

  50. Stolpnik, V.G., Solovena, Y.V. & Antonenko, L.I. [Concentration of neothelomycin in the blood of rabbits following intramuscular or oral administration]. Antibiotiki 11, 567–568 (1966).

    CAS  PubMed  Google Scholar 

  51. Needleman, S.B. & Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970).

    Article  CAS  PubMed  Google Scholar 

  52. Steinbeck, C. et al. The Chemistry Development Kit (CDK): an open-source Java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43, 493–500 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).

    Article  CAS  PubMed  Google Scholar 

  54. Huson, D.H. & Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067 (2012).

    Article  PubMed  Google Scholar 

  55. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Capella-Gutiérrez, S., Silla-Martínez, J.M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Eddy, S.R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Magrane, M. & Consortium, U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, bar009 (2011).

    Article  CAS  Google Scholar 

  59. Finn, R.D., Clements, J. & Eddy, S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was funded through a Natural Sciences and Engineering Research Council (NSERC) of Canada Discovery grant (RGPIN 371576-2014) (N.A.M.) and a Joint Programme Initiative on Antimicrobial Resistance funded through the Canadian Institutes of Health Research (CIHR; N.A.M.). C.W.J. is funded through a CIHR Doctoral Research Award. E.D.B and N.A.M. are supported by the Canada Research Chairs Program. The authors acknowledge and thank R. Epand for valuable communications.

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Authors and Affiliations

  1. Department of Biochemistry & Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada

    Chad W Johnston, Michael A Skinnider, Chris A Dejong, Philip N Rees, Gregory M Chen, Chelsea G Walker, Shawn French, Eric D Brown, Dennis Y Liu & Nathan A Magarvey

  2. Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, Canada

    Chad W Johnston, Michael A Skinnider, Chris A Dejong, Philip N Rees, Gregory M Chen, Chelsea G Walker, Dennis Y Liu & Nathan A Magarvey

  3. Eötvös Loránd University, IVAX Drug Research Institute Ltd., Budapest, Hungary

    János Bérdy

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Contributions

C.W.J. performed telomycin studies, assisted in antibacterial library curation and development of scoring strategies, performed Antibioticome analysis, contributed to study design and wrote the manuscript. M.A.S. developed PRISM, developed the Antibioticome web application, assisted in resistance gene collection and contributed to study design. C.A.D. developed the retrobiosynthetic algorithm, devised scoring strategies for the Antibioticome, developed the Antibioticome web application and contributed to study design. P.N.R. curated the antibacterial library. G.M.C. developed the retrobiosynthetic algorithm and devised scoring strategies for the Antibioticome. C.W. collected resistance genes. S.F. performed microscopy studies. E.D.B. edited the manuscript. J.B. curated the antibacterial library. D.Y.L. assisted in resistance gene collection and curation of the antibacterial library. N.A.M. contributed to study design and wrote the manuscript.

Corresponding author

Correspondence to Nathan A Magarvey.

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Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–15 and Supplementary Tables 1–4. (PDF 969 kb)

Supplementary Note

Synthetic Procedures (PDF 4573 kb)

Supplementary Data Set 1

Results from retrobiosynthetic analysis of microbial modular natural product antibacterials (PDF 3440 kb)

Supplementary Data Set 2

Hidden Markov models used by PRISM to detect antibiotic resistance genes (XLSX 66 kb)

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Johnston, C., Skinnider, M., Dejong, C. et al. Assembly and clustering of natural antibiotics guides target identification. Nat Chem Biol 12, 233–239 (2016). https://doi.org/10.1038/nchembio.2018

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