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A naturally inspired antibiotic to target multidrug-resistant pathogens

Abstract

Gram-negative bacteria are responsible for an increasing number of deaths caused by antibiotic-resistant infections1,2. The bacterial natural product colistin is considered the last line of defence against a number of Gram-negative pathogens. The recent global spread of the plasmid-borne mobilized colistin-resistance gene mcr-1 (phosphoethanolamine transferase) threatens the usefulness of colistin3. Bacteria-derived antibiotics often appear in nature as collections of similar structures that are encoded by evolutionarily related biosynthetic gene clusters. This structural diversity is, at least in part, expected to be a response to the development of natural resistance, which often mechanistically mimics clinical resistance. Here we propose that a solution to mcr-1-mediated resistance might have evolved among naturally occurring colistin congeners. Bioinformatic analysis of sequenced bacterial genomes identified a biosynthetic gene cluster that was predicted to encode a structurally divergent colistin congener. Chemical synthesis of this structure produced macolacin, which is active against Gram-negative pathogens expressing mcr-1 and intrinsically resistant pathogens with chromosomally encoded phosphoethanolamine transferase genes. These Gram-negative bacteria include extensively drug-resistant Acinetobacter baumannii and intrinsically colistin-resistant Neisseria gonorrhoeae, which, owing to a lack of effective treatment options, are considered among the highest level threat pathogens4. In a mouse neutropenic infection model, a biphenyl analogue of macolacin proved to be effective against extensively drug-resistant A. baumannii with colistin-resistance, thus providing a naturally inspired and easily produced therapeutic lead for overcoming colistin-resistant pathogens.

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Fig. 1: Discovery of macolacin.
Fig. 2: Antibacterial activity of macolacin.
Fig. 3: In vitro and in vivo activity of biphenyl-macolacin.

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Data availability

Publicly available DNA sequence data used in this study are referenced accordingly. The macolacin BGC sequence is available in GenBank with accession number NZ_CP018620.1. The website can be accessed through https://www.ncbi.nlm.nih.gov/nuccore/CP018620.1. Other accession numbers for polymyxin-like BGCs are included in Supplementary Table 2. NMR spectra for macolacin and diphenyl-macolacin are presented as Supplementary Information. BGCs were collected from antiSMASH-db (v.2.0). The website can be accessed through https://antismash-db.secondarymetabolites.org/Source data are provided with this paper.

References

  1. Ventola, C. L. The antibiotic resistance crisis: part 1: causes and threats. P. T. 40, 277–283 (2015).

    PubMed  PubMed Central  Google Scholar 

  2. 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  Google Scholar 

  3. Deveson Lucas, D. et al. Emergence of high-level colistin resistance in an Acinetobacter baumannii clinical isolate mediated by inactivation of the global regulator H-NS. Antimicrob. Agents Chemother. 62, e02442-17 (2018).

    Article  Google Scholar 

  4. Aitolo, G. L., Adeyemi, O. S., Afolabi, B. L. & Owolabi, A. O. Neisseria gonorrhoeae antimicrobial resistance: past to present to future. Curr. Microbiol. 78, 867–878 (2021).

    Article  CAS  Google Scholar 

  5. Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318–327 (2018).

    Article  Google Scholar 

  6. Imai, Y. et al. A new antibiotic selectively kills Gram-negative pathogens. Nature 576, 459–464 (2019).

    Article  CAS  ADS  Google Scholar 

  7. Biswas, S., Brunel, J. M., Dubus, J. C., Reynaud-Gaubert, M. & Rolain, J. M. Colistin: an update on the antibiotic of the 21st century. Expert Rev. Anti Infect. Ther. 10, 917–934 (2012).

    Article  CAS  Google Scholar 

  8. Liu, Y. Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161–168 (2016).

    Article  Google Scholar 

  9. Jeannot, K., Bolard, A. & Plesiat, P. Resistance to polymyxins in Gram-negative organisms. Int. J. Antimicrob. Agents 49, 526–535 (2017).

    Article  CAS  Google Scholar 

  10. Liu, Y. Y. et al. Structural modification of lipopolysaccharide conferred by mcr-1 in Gram-negative ESKAPE pathogens. Antimicrob. Agents Chemother. 61, e00580-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  11. Schwarz, S. & Johnson, A. P. Transferable resistance to colistin: a new but old threat. J. Antimicrob. Chemother. 71, 2066–2070 (2016).

    Article  Google Scholar 

  12. Hameed, F. et al. Plasmid-mediated mcr-1 gene in Acinetobacter baumannii and Pseudomonas aeruginosa: first report from Pakistan. Rev. Soc. Bras. Med. Trop. 52, e20190237 (2019).

    Article  Google Scholar 

  13. Tian, G. B. et al. MCR-1-producing Klebsiella pneumoniae outbreak in China. Lancet Infect. Dis. 17, 577 (2017).

    Article  Google Scholar 

  14. Rutledge, P. J. & Challis, G. L. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat. Rev. Microbiol. 13, 509–523 (2015).

    Article  CAS  Google Scholar 

  15. Sussmuth, R. D. & Mainz, A. Nonribosomal peptide synthesis – principles and prospects. Angew. Chem. Int. Ed. Engl. 56, 3770–3821 (2017).

    Article  Google Scholar 

  16. Stachelhaus, T., Mootz, H. D. & Marahiel, M. A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem. Biol. 6, 493–505 (1999).

    Article  CAS  Google Scholar 

  17. Rabanal, F. & Cajal, Y. Recent advances and perspectives in the design and development of polymyxins. Nat. Prod. Rep. 34, 886–908 (2017).

    Article  CAS  Google Scholar 

  18. Li, J., Nation, R. & Kaye, K. (eds) Polymyxin Antibiotics: From Laboratory Bench to Bedside Preface 1145, V–VI (Springer, 2019).

  19. Tomm, H. A., Ucciferri, L. & Ross, A. C. Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. J. Ind. Microbiol. Biotechnol. 46, 1381–1400 (2019).

    Article  CAS  Google Scholar 

  20. Chu, J. et al. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat. Chem. Biol. 12, 1004–1006 (2016).

    Article  CAS  Google Scholar 

  21. Chu, J., Vila-Farres, X. & Brady, S. F. Bioactive synthetic-bioinformatic natural product cyclic peptides inspired by nonribosomal peptide synthetase gene clusters from the human microbiome. J. Am. Chem. Soc. 141, 15737–15741 (2019).

    Article  CAS  Google Scholar 

  22. Chu, J. et al. Synthetic-bioinformatic natural product antibiotics with diverse modes of action. J. Am. Chem. Soc. 142, 14158–14168 (2020).

    Article  CAS  Google Scholar 

  23. Kang, K. N. et al. Colistin heteroresistance in Enterobacter cloacae is regulated by PhoPQ-dependent 4-amino-4-deoxy-l-arabinose addition to lipid A. Mol. Microbiol. 111, 1604–1616 (2019).

    Article  CAS  Google Scholar 

  24. McClerren, A. L. et al. A slow, tight-binding inhibitor of the zinc-dependent deacetylase LpxC of lipid A biosynthesis with antibiotic activity comparable to ciprofloxacin. Biochemistry 44, 16574–16583 (2005).

    Article  CAS  Google Scholar 

  25. Moffatt, J. H. et al. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob. Agents Chemother. 54, 4971–4977 (2010).

    Article  CAS  Google Scholar 

  26. Wei, J.-R. et al. LpxK is essential for growth of Acinetobacter baumannii ATCC 19606: relationship to toxic accumulation of lipid A pathway intermediates. mSphere 2, e00199–00117 (2017).

    Article  CAS  Google Scholar 

  27. Richie, D. L. et al. Toxic accumulation of LPS pathway intermediates underlies the requirement of LpxH for growth of Acinetobacter baumannii ATCC 19606. PLoS ONE 11, e0160918 (2016).

    Article  Google Scholar 

  28. US Department of Health and Human Services. Antibiotic Resistance Threats in the United States; https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf (2019).

  29. Ling, Z. et al. Epidemiology of mobile colistin resistance genes mcr-1 to mcr-9. J. Antimicrob. Chemother. 75, 3087–3095 (2020).

    Article  CAS  Google Scholar 

  30. Sakura, N. et al. The contribution of the N-terminal structure of polymyxin B peptides to antimicrobial and lipopolysaccharide binding activity. Bull. Chem. Soc. Jpn 77, 1915–1924 (2004).

    Article  CAS  Google Scholar 

  31. Tsubery, H., Ofek, I., Cohen, S. & Fridkin, M. N-terminal modifications of polymyxin B nonapeptide and their effect on antibacterial activity. Peptides 22, 1675–1681 (2001).

    Article  CAS  Google Scholar 

  32. Lutgring, J. D. et al. FDA-CDC antimicrobial resistance isolate bank: a publicly available resource to support research, development, and regulatory requirements. J. Clin. Microbiol. 56, e01415-17 (2018).

    PubMed  PubMed Central  Google Scholar 

  33. Devarajan, P. Neutrophil gelatinase-associated lipocalin (NGAL): a new marker of kidney disease. Scand. J. Clin. Lab. Invest. Suppl. 241, 89–94 (2008).

    Article  Google Scholar 

  34. Wang, J., Ishfaq, M., Fan, Q., Chen, C. & Li, J. 7-hydroxycoumarin attenuates colistin-induced kidney injury in mice through the decreased level of histone deacetylase 1 and the activation of Nrf2 signaling pathway. Front. Pharmacol. 11, 1146 (2020).

    Article  CAS  Google Scholar 

  35. Bolignano, D. et al. Neutrophil gelatinase-associated lipocalin (NGAL) as a marker of kidney damage. Am. J. Kidney Dis. 52, 595–605 (2008).

    Article  CAS  Google Scholar 

  36. Blin, K. et al. The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 47, D625–D630 (2019).

    Article  CAS  Google Scholar 

  37. Blin, K. et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–W87 (2019).

    Article  CAS  Google Scholar 

  38. Testing, E. C. O. A. S. Recommendations for MIC Determination of Colistin (Polymyxin E) as Recommended by the Joint CLSI-EUCAST Polymyxin Breakpoints Working Group (EUCAST, 2016).

  39. Wikler, M. A. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically: approved standard. CLSI document M07-A7 (2006).

  40. Bojkovic, J. et al. Characterization of an Acinetobacter baumannii lptD deletion strain: permeability defects and response to inhibition of lipopolysaccharide and fatty acid biosynthesis. J. Bacteriol. 198, 731–741 (2015).

    Article  Google Scholar 

  41. Carmichael, J., DeGraff, W. G., Gazdar, A. F., Minna, J. D. & Mitchell, J. B. Evaluation of a tetrazolium-based semiautomated colorimetric assay: assessment of chemosensitivity testing. Cancer Res. 47, 936–942 (1987).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the Y. Doi (pMQ124-mcr-1 and pMQ124xlab-mcr-1) and J. M. Boll (E. cloacae 13047-phoP/Q and E. cloacae13047-phoP/Q+phoP/Q) laboratories for providing strains and plasmids. We thank the CDC and FDA Antibiotic Resistance (AR) Isolate Bank for providing A. baumannii resistant strains (0282, 0286, 0287, 0295, 0296 and 0301). We thank the Comparative Bioscience Center at the Rockefeller University for their help with the animal studies. This work was supported by the National Institutes of Health (1U19AI142731 and 5R35GM122559).

Author information

Authors and Affiliations

Authors

Contributions

S.F.B. and Z.W. designed the study and analysed the data. Z.W. performed the biochemical experiments. B.K. performed the peptide synthesis. Z.W. and Y.H. performed the bioinformatic analysis. M.Z. performed the pharmacokinetic analysis. S.F.B., Z.W., S.P. and D.S.P. designed the animal study. All authors were involved in discussing the results. S.F.B. and Z.W. prepared the manuscript.

Corresponding author

Correspondence to Sean F. Brady.

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Nature thanks Gerry Wright and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Proposed macolacin biosynthetic pathway.

The predicted biosynthetic scheme for macolacin based on detailed bioinformatic analysis of the mac BGC is depicted.

Extended Data Fig. 2 Phylogenetic trees constructed from A-domain sequences associated with complete colistin and macolacin BGC.

Phylogenetic trees constructed from A domain sequences associated with complete colistin and macolacin A BGC. a) A1 domain; b) A3 domain; c) A7 domain and d) A10 domain. Each A-domain sequence was extracted from the polymyxin-like BGCs was then aligned together with known characterized polymyxin BGCs (for example, MIBIG IDs: BGC0000408, BGC0001192, BGC0001153) using the MUSCLE alignment software. The resulting phylogenetic tree was visualized using iTOLv5 software. Red color represents hits in polymyxin clade. Blue color represents hits in macolacin clade.

Extended Data Fig. 3 Structures of all synthetic macolacin derivates.

Structural differences compared to macolacin are depicted in blue.

Extended Data Fig. 4 Cytotoxicity and pharmacokinetic evaluation of macolacin and biphenyl-macolacin.

a) Cytotoxicity of macolacin and biphenyl-macolacin against HEK293. Data are presented as means ± SD. n = 3 technical replicates. b) Pharmacokinetic assessment of macolacin and biphenyl-macolacin. Total plasma concentrations of macolacin, biphenyl-macolacin or colistin versus time after administration of a single subcutaneous dose (10 mg/kg) to neutropenic mice. n = 2 biologically independent mice. Data are presented as mean of two independent assays. c) The level of serum NGAL in colistin or biphenyl-macolacin treated mice. Significant differences between groups were determined by one-way analysis of variance (ANOVA) (*P<0.05) (n = 6 biologically independent mice). Data are presented as means ± SD. Vehicle vs. Colistin, P value = 0.0069; Vehicle vs. Biphenyl-macolacin, P value = 0.0104; Colistin vs. Biphenyl-macolacin, P value = 0.9773.

Source data

Extended Data Table 1 Macolacin A-domain specificity analysis.
Extended Data Table 2 MIC values for macolacin analogs with different lipid substituents.
Extended Data Table 3 MIC data for XDR A. baumannii with and without mcr-1.
Extended Data Table 4 SAR of amino acid differences between macolacin and colistin.
Extended Data Table 5 High-resolution mass spectrometry data for all syn-BNP peptides.

Supplementary information

Supplementary Information

Supplementary Tables 1 and 2 and Figs 1–4.

Reporting Summary

Source data

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Wang, Z., Koirala, B., Hernandez, Y. et al. A naturally inspired antibiotic to target multidrug-resistant pathogens. Nature 601, 606–611 (2022). https://doi.org/10.1038/s41586-021-04264-x

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