Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Expanding the antibacterial selectivity of polyether ionophore antibiotics through diversity-focused semisynthesis

Nature Chemistry volume 13, pages 47–55 (2021)Cite this article

Subjects

Abstract

Polyether ionophores are complex natural products capable of transporting cations across biological membranes. Many polyether ionophores possess potent antimicrobial activity and a few selected compounds have the ability to target aggressive cancer cells. Nevertheless, ionophore function is believed to be associated with idiosyncratic cellular toxicity and, consequently, human clinical development has not been pursued. Here, we demonstrate that structurally novel polyether ionophores can be efficiently constructed by recycling components of highly abundant polyethers to afford analogues with enhanced antibacterial selectivity compared to a panel of natural polyether ionophores. We used classic degradation reactions of the natural polyethers lasalocid and monensin and combined the resulting fragments with building blocks provided by total synthesis, including halogen-functionalized tetronic acids as cation-binding groups. Our results suggest that structural optimization of polyether ionophores is possible and that this area represents a potential opportunity for future methodological innovation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Accessing structural diversity within the polyether ionophores.
Fig. 2: Building block synthesis.
Fig. 3: Fragment coupling via boron trifluoride-mediated Mukaiyama aldol reaction.
Fig. 4: Final coupling of tetronic acid derivatives.
Fig. 5: Oxidative deconstruction of monensin for hybrid polyether synthesis.

Similar content being viewed by others

Data availability

MIC and IC50 values for cell viability for each biological replicate are available in Supplementary Table 1. The morphological profiling data (aggregated profiles and correlation matrix), included in Supplementary Figs. 3–9, have been deposited at Mendeley Data (https://doi.org/10.17632/jv3sjk8wy4.2). The images from morphological profiling are too large to be deposited at Mendeley Data (which has a limit of 10 GB per data set), but can be obtained upon request. The X-ray crystallography data have been deposited in the Cambridge Crystallographic Data Centre (CCDC) using the following identifiers (www.ccdc.cam.ac.uk/structures/): 1920656 (6-Na), 1920657 (14), 1920658 (24), 1920659 (29-Na) and 1920660 (31-Na).

Code availability

Code/scripts for analysis of morphological profiling data and Cell Profiler pipelines have been deposited at Mendeley Data (https://doi.org/10.17632/jv3sjk8wy4.2).

References

  1. Huffman, B. J. & Shenvi, R. A. Natural products in the ‘marketplace’: interfacing synthesis and biology. J. Am. Chem. Soc. 141, 3332–3346 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Schreiber, S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964–1969 (2000).

    CAS  PubMed  Google Scholar 

  3. Wetzel, S., Bon, R. S., Kumar, K. & Waldmann, H. Biology-oriented synthesis. Angew. Chem. Int. Ed. 50, 10800–10826 (2011).

    CAS  Google Scholar 

  4. Könst, Z. A. et al. Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Nat. Chem. 9, 1140–1149 (2017).

    PubMed  PubMed Central  Google Scholar 

  5. Wilson, R. M. & Danishefsky, S. J. Small molecule natural products in the discovery of therapeutic agents: the synthesis connection. J. Org. Chem. 71, 8329–8351 (2006).

    CAS  PubMed  Google Scholar 

  6. Huigens, R. W. et al. A ring-distortion strategy to construct stereochemically complex and structurally diverse compounds from natural products. Nat. Chem. 5, 195–202 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Abbasov, M. E. et al. Simplified immunosuppressive and neuroprotective agents based on gracilin A. Nat. Chem. 11, 342–350 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Karageorgis, G., Foley, D. J., Laraia, L. & Waldmann, H. Principle and design of pseudo-natural products. Nat. Chem. 12, 227–235 (2020).

    CAS  PubMed  Google Scholar 

  9. Seiple, I. B. et al. A platform for the discovery of new macrolide antibiotics. Nature 533, 338–345 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Richter, M. F. et al. Predictive compound accumulation rules yield a broad-spectrum antibiotic. Nature 545, 299–304 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Westley, J. (ed.) Polyether Antibiotics—Naturally Occurring Acid Ionophores 1st edn (Marcel Dekker, 1982).

  12. Dutton, C. J., Banks, B. J. & Cooper, C. B. Polyether ionophores. Nat. Prod. Rep. 12, 165–181 (1995).

    CAS  PubMed  Google Scholar 

  13. Nakata, T. et al. A total synthesis of lasalocid A. J. Am. Chem. Soc. 100, 2933–2935 (1978).

    CAS  Google Scholar 

  14. Fukuyama, T. et al. Total synthesis of monensin. 3. Stereocontrolled total synthesis of monensin. J. Am. Chem. Soc. 101, 262–263 (1979).

    CAS  Google Scholar 

  15. Faul, M. M. & Huff, B. E. Strategy and methodology development for the total synthesis of polyether ionophore antibiotics. Chem. Rev. 100, 2407–2473 (2000).

    CAS  PubMed  Google Scholar 

  16. Song, Z., Lohse, A. G. & Hsung, R. P. Challenges in the synthesis of a unique mono-carboxylic acid antibiotic, (+)-zincophorin. Nat. Prod. Rep. 26, 560–571 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Kasun, Z. A., Gao, X., Lipinski, R. M. & Krische, M. J. Direct generation of triketide stereopolyads via merged redox-construction events: total synthesis of (+)-zincophorin methyl ester. J. Am. Chem. Soc. 137, 8900–8903 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Wang, G. & Krische, M. J. Total synthesis of (+)-SCH 351448: efficiency via chemoselectivity and redox-economy powered by metal catalysis. J. Am. Chem. Soc. 138, 8088–8091 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Chen, L.-A., Ashley, M. A. & Leighton, J. L. Evolution of an efficient and scalable nine-step (longest linear sequence) synthesis of zincophorin methyl ester. J. Am. Chem. Soc. 139, 4568–4573 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Liu, H., Lin, S., Jacobsen, K. M. & Poulsen, T. B. Chemical syntheses and chemical biology of carboxyl polyether ionophores: recent highlights. Angew. Chem. Int. Ed. 58, 13630–13642 (2019).

    CAS  Google Scholar 

  21. Kevin, D. A. II, Meujo, D. A. & Hamann, M. T. Polyether ionophores: broad-spectrum and promising biologically active molecules for the control of drug-resistant bacteria and parasites. Expert Opin. Drug Discov. 4, 109–146 (2009).

    CAS  PubMed Central  Google Scholar 

  22. Chapman, H. D., Jeffers, T. K. & Williams, R. B. Forty years of monensin for the control of coccidiosis in poultry. Poultry Sci. 89, 1788–1801 (2010).

    CAS  Google Scholar 

  23. Goodrich, R. D. et al. Influence of monensin on the performance of cattle. J. Anim. Sci. 58, 1484–1498 (1984).

    CAS  PubMed  Google Scholar 

  24. Antoszczak, M. et al. Biological activity of doubly modified salinomycin analogs—evaluation in vitro and ex vivo. Eur. J. Med. Chem. 156, 510–523 (2018).

    CAS  PubMed  Google Scholar 

  25. Igarashi, Y. et al. Nonthmicin, a polyether polyketide bearing a halogen-modified tetronate with neuroprotective and antiinvasive activity from Actinomadura sp. Org. Lett. 19, 1406–1409 (2017).

    CAS  PubMed  Google Scholar 

  26. Wyche, T. P. et al. Chemical genomics, structure elucidation, and in vivo studies of the marine-derived anticlostridial ecteinamycin. ACS Chem. Biol. 12, 2287–2295 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Westley, J. W., Evans, R. H., Williams, T. & Stempel, A. Structure of antibiotic X-537A. Chem. Commun. 71–72 (1970).

  28. Westley, J. W., Evans, R. H., Williams, T. & Stempel, A. Pyrolytic cleavage of antibiotic x-537A and related reactions. J. Org. Chem. 38, 3431–3433 (1973).

    CAS  PubMed  Google Scholar 

  29. Gruenfeld, N. et al. Angiotensin converting enzyme inhibitors: 1-glutarylindoline-2-carboxylic acids derivatives. J. Med. Chem. 26, 1277–1282 (1983).

    CAS  PubMed  Google Scholar 

  30. Hiyama, T., Kimura, K. & Nozaki, H. Chromium(ii) mediated threo selective synthesis of homoallyl alcohols. Tetrahedron Lett. 22, 1037–1040 (1981).

    CAS  Google Scholar 

  31. Hansen, T. M. et al. Highly chemoselective oxidation of 1,5-diols to δ-lactones with TEMPO/BAIB. Tetrahedron Lett. 44, 57–59 (2003).

    CAS  Google Scholar 

  32. Brazeau, J.-F. et al. Stereocentrolled synthesis of C1–C17 fragment of narasin via a free radical-based approach. Org. Lett. 12, 36–39 (2010).

    CAS  PubMed  Google Scholar 

  33. Zografos, A. L. & Georgiadis, D. Synthetic strategies towards naturally occurring tetronic acids. Synthesis 3157–3188 (2006).

  34. Markó, I. E., Richardson, P. R., Bailey, M., Maguire, A. R. & Coughlan, N. Selective manganese-mediated transformations using the combination: KMnO4/Me3SiCl. Tetrahedron Lett. 38, 2339–2342 (1997).

    Google Scholar 

  35. Sabbah, M., Bernollin, M., Doutheau, A., Soulère, L. & Queneau, Y. A new route towards fimbrolide analogues: importance of the exomethylene motif in LuxR dependent quorum sensing inhibition. Med. Chem. Commun. 4, 363–366 (2013).

    CAS  Google Scholar 

  36. Roush, W. R. Concerning the diastereofacial selectivity of the aldol reactions of α-methyl chiral aldehydes and lithium and boron propionate enolates. J. Org. Chem. 56, 4151–4157 (1991).

    CAS  Google Scholar 

  37. Masamune, S., Choy, W., Petersen, J. S. & Sita, L. R. Double asymmetric synthesis and a new strategy for stereochemical control in organic synthesis. Angew. Chem. Int. Ed. 24, 1–30 (1985).

    Google Scholar 

  38. Evans, D. A., Yang, M. G., Dart, M. J., Duffy, J. L. & Kim, A. S. Double stereodifferentiating lewis acid-promoted (Mukaiyama) aldol bond constructions. J. Am. Chem. Soc. 117, 9598–9599 (1995).

    CAS  Google Scholar 

  39. Nicolaou, K. C., Estrada, A. A., Zak, M., Lee, S. H. & Safina, B. S. A mild and selective method for the hydrolysis of esters with trimethyltin hydroxide. Angew. Chem. Int. Ed. 44, 1378–1382 (2005).

    CAS  Google Scholar 

  40. Vögtle, F. & Weber, E. Multidentate acyclic neutral ligands and their complexation. Angew. Chem. Int. Ed. 18, 753–776 (1979).

    Google Scholar 

  41. Evans, D., Chapman, K. & Carreira, E. M. Directed reduction of β-hydroxy ketones employing tetramethylammonium triacetoxylborohydride. J. Am. Chem. Soc. 110, 3560–3578 (1988).

    CAS  Google Scholar 

  42. Cai, D. & Still, W. C. Synthesis of monensin. Reconstruction from degradation products. J. Org. Chem. 53, 4641–4643 (1988).

    CAS  Google Scholar 

  43. Baskaran, S., Islam, I., Raghaven, M. & Chandrasekaran, S. Pyridinium chlorochromate in organic synthesis. A facile and selective oxidative cleavage of enol ethers. Chem. Lett. 16, 1175–1178 (1987).

    Google Scholar 

  44. Bray, M.-A. et al. Cell painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc. 11, 1757–1774 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Svenningsen, E. B. & Poulsen, T. B. Establishing cell painting in a smaller chemical biology lab—a report from the frontier. Bioorg. Med. Chem. 27, 2609–2615 (2019).

    CAS  PubMed  Google Scholar 

  46. Hutz, J. E. et al. The multidimensional perturbation value: a single metric to measure similarity and activity of treatments in high-throughput multidimensional screens. J. Biomol. Screen. 18, 367–377 (2013).

    PubMed  Google Scholar 

  47. Golbek, T. W., Schmüsen, L., Rasmussen, M. H., Poulsen, T. B. & Weidner, T. Lasalocid acid antibiotic at a membrane surface probed by sum frequency generation spectroscopy. Langmuir 36, 3184–3192 (2020).

    CAS  PubMed  Google Scholar 

  48. Versini, A. et al. Chemical biology of salinomycin. Tetrahedron 74, 5585–5614 (2018).

    CAS  Google Scholar 

  49. Mai, T. T. et al. Salinomycin kills cancer stem cells by sequestering iron in lysosomes. Nat. Chem. 9, 1025–1033 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Wang, F. et al. Nucleolin is a functional binding protein for salinomycin in neuroblastoma stem cells. J. Am. Chem. Soc. 141, 3613–3622 (2019).

    CAS  PubMed  Google Scholar 

  51. Heathcock, C. H. & Flippin, L. A. Acyclic stereoselection. 16. High diastereofacial selectivity in Lewis acid mediated additions of enol silanes to chiral aldehydes. J. Am. Chem. Soc. 105, 1667–1668 (1983).

    CAS  Google Scholar 

  52. Lamprecht, M. R., Sabatini, D. M. & Carpenter, A. E. CellProfilerTM: free, versatile software for automated biological image analysis. Biotechniques 42, 71–75 (2007).

    CAS  PubMed  Google Scholar 

  53. Becker, T., Goodman, A., McQuin, C., Rohban, M. & Singh, S. cytominer: methods for image-based cell profiling. R package v.0.1.0 (2017); https://cran.r-project.org/package=cytominer

  54. R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2017); https://www.R-project.org/

  55. Warnes, G. R. et al. gplots: various R programming tools for plotting data. R package v.3.0.3 (2020); https://cran.r-project.org/package=gplots

  56. Wei, T. & Simko, V. R package ‘corrplot’: visualization of a correlation matrix. R package v.0.84 (2017); https://github.com/taiyun/corrplot

Download references

Acknowledgements

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 865738). Financial support from the Carlsberg Foundation (grant CF17-0800), Novo Nordisk Foundation (grant NNF19OC0054782) and Independent Research Fund Denmark (grants 9040-00117B and 6110-00600B) is acknowledged. We thank E. Jung and A. Johnbeck for technical assistance with the organic syntheses, A. Bodholt Nielsen for technical assistance with NMR spectroscopy, and I.C. Stensgaard Jensen for technical assistance with microbiology.

Author information

Author notes

  1. These authors contributed equally: S. Lin, H. Liu.

Authors and Affiliations

  1. Department of Chemistry, Aarhus University, Aarhus, Denmark

    Shaoquan Lin, Han Liu, Esben B. Svenningsen, Malene Wollesen, Kristian M. Jacobsen, Jaime Moyano-Villameriel, Christine N. Pedersen, Peter Nørby & Thomas B. Poulsen

  2. Department of Engineering—Microbial Biosynthesis, Aarhus University, Aarhus, Denmark

    Frederikke D. Andersen & Thomas Tørring

Authors
  1. Shaoquan Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Han Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Esben B. Svenningsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Malene Wollesen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kristian M. Jacobsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Frederikke D. Andersen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jaime Moyano-Villameriel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Christine N. Pedersen
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Peter Nørby
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Thomas Tørring
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Thomas B. Poulsen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

T.B.P. conceived and supervised the study. T.B.P., S.L., H.L. and E.B.S. designed the experiments. S.L., H.L., J.M.V. and C.N.P. performed the organic syntheses. E.B.S. and K.M.J. conducted the cell biology experiments and analysed data. M.W. and F.D.A. conducted the microbiology experiments. T.T. supervised the microbiology experiments and analysed data. P.N. carried out the X-ray crystallographic analyses. T.B.P., S.L., H.L. and E.B.S. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Thomas B. Poulsen.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Strategies for the synthesis of protected 5-(halo)methylidene tetronic acid building blocks and subsequent coupling.

a, Chemical structure of the targeted 3-acyltetronic acid-derivatives found in nonthmicin/ecteinamycin and 6. No previous syntheses of the halogenated variants have been reported. b, Examples of known methods used to prepare non-halogenated variants. c, Failed attempts and model studies toward 5-chloromethylidene tetronate. I) Unsuccessful synthesis of 5-tributylstannylmethylidene tetronate. II) Unsuccessful chlorination of 5-dimethylaminomethylidene tetronate. III) Direct and indirect chlorination of 5-methylidene tetronate methyl ether. In practice, the removal of the methyl group from the chlorinated tetronate product using LiCl/DMSO or BBr3 was difficult. Thus, we moved to synthesize the tetronate derivatives bearing a TMSE group, which can be removed under much milder condition (TBAF/DMF). DMSO = dimethylsulfoxide DCC = N,N’-dicyclohexylcarbodiimide, DMAP = 4-dimethylaminopyridine, Ms = methanesulfonyl, MOM = methoxymethyl, DCE = 1,2-dichloroethane, DBU = 1,8-diazabicyclo[5.4.0]undec-7-ene, TMS = trimethylsilyl, NCS = N-chlorosuccinimide, AIBN = azobisisobutyronitrile.

Extended Data Fig. 2 Synthesis of hybrid polyether HL324 (32).

Preparation of analogue HL324 (32) was performed through anti-selective (Evans-Saksena) reduction of the ketone-functionality of 26 followed by DCC-mediated coupling with 5-chloromethylidene tetronate. rt = room temperature, TBAF = tetrabutylammonium fluoride, DMF = N,N-dimethylformamide, DCC = N,N’-dicyclohexylcarbodiimide, DMAP = 4-dimethylaminopyridine, HPLC = high pressure liquid chromatography.

Extended Data Fig. 3 Droplet screen for antibacterial activity in B. cereus.

a, Representative images of inhibition zones of all compounds from B. cereus. b, Heatmap representing no (red), slight (yellow) or large (green) inhibition zones. All compounds were tested at 10 mM in DMSO except monensin (1 mM) and HL160 (7 mM). c) Chemical structures of acid-containing synthetic fragments. SL382 = 27; SL415 = 26 – see Fig. 3.

Extended Data Fig. 4 Use of morphological profiling via cell painting to determine bioactivity threshold in U-2OS cells.

a, Plots of cell count (grey) and Mahalanobis distance (‘Bioactivity’; red and green) against concentration of compound. Green points indicate significant activity (mp-value < 0.01) while red points indicate no significant activity (mp-value > 0.01). Many ionophores induce an active profile without loss of cell viability while bioactivity of the hybrid ionophores is correlated with a loss of cells, indicating a profile representing toxicity. The bioactivity threshold is determined as the first concentration to reach significance (mp-value < 0.01). b, Dose-dependent morphological profiles from which the bioactivity threshold is determined. Note that some ionophores change profile at higher concentrations, for example calcimycin (Cal) and nanchangmycin (Nan), typically correlated with a loss of cells. See Supplementary Fig. 3–9 for representative images, all dose-response plots, profiles and correlation matrices in both U-2OS and Vero cells.

Supplementary information

Supplementary Information

Supplementary Figs. 1–9, X-ray crystallography methods and comments, morphological profiling imaging settings, synthesis protocols and characterization data, references and NMR spectra.

Reporting Summary

Supplementary Table 1

Complete data from MIC determinations and cell viability experiments.

Supplementary Data 1

Cif file for compound 6-Na.

Supplementary Data 2

Structure factors file for compound 6-Na.

Supplementary Data 3

Cif file for compound 14.

Supplementary Data 4

Structure factors file for compound 14.

Supplementary Data 5

Cif file for compound 24.

Supplementary Data 6

Structure factors file for compound 24.

Supplementary Data 7

Cif file for compound 29-Na.

Supplementary Data 8

Structure factors file for compound 29-Na.

Supplementary Data 9

Cif file for compound 31-Na.

Supplementary Data 10

Structure factors file for compound 31-Na.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lin, S., Liu, H., Svenningsen, E.B. et al. Expanding the antibacterial selectivity of polyether ionophore antibiotics through diversity-focused semisynthesis. Nat. Chem. 13, 47–55 (2021). https://doi.org/10.1038/s41557-020-00601-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41557-020-00601-1

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing