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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.

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.

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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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The authors declare no competing interests.

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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.

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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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