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Synthesis and reactivity of precolibactin 886

Nature Chemistry volume 11, pages 890–898 (2019)Cite this article

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Abstract

The clb gene cluster encodes the biosynthesis of metabolites known as precolibactins and colibactins. The clb pathway is found in gut commensal Escherichia coli, and clb metabolites are thought to initiate colorectal cancer via DNA crosslinking. Here we report confirmation of the structural assignment of the complex clb product precolibactin 886 via a biomimetic synthetic pathway. We show that an α-ketoimine linear precursor undergoes spontaneous cyclization to precolibactin 886 on HPLC purification. Studies of this α-ketoimine and the related α-dicarbonyl revealed that these compounds are unexpectedly susceptible to nucleophilic cleavage under mildly basic conditions. This cleavage pathway forms other known clb metabolites or biosynthetic intermediates and explains the difficulties in isolating fully mature biosynthetic products. This cleavage also accounts for a recently identified colibactin–adenine adduct. The colibactin peptidase ClbP deacylates synthetic precolibactin 886 to form a non-genotoxic pyridone, which suggests precolibactin 886 lies off the path of the major biosynthetic route.

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Fig. 1: Overview of (pre)colibactin reactivity, mechanism of genotoxicity and the synthetic strategy pursued herein.
Fig. 2: Synthesis of the azide 20 and the amino alcohol 9.
Fig. 3: Synthesis of precolibactin 886 (1) and reactivity of the α-ketoimine and α-dicarbonyl residues.
Fig. 4: The α-ketoimine 2 undergoes transformation to known clb metabolites or biosynthetic intermediates under mild conditions, and ClbP deacylation of precolibactin 886 (1) forms the non-genotoxic pyridone 35.
Fig. 5: Biosynthetic and chemical reactivity model based on the studies reported herein.

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Acknowledgements

We thank D. Spiegel for helpful discussions regarding the mechanism of the hydrolytic cleavage of 2. Financial support from the National Institutes of Health (R01GM110506 to S.B.H., 1DP2-CA186575 to J.M.C. and R01CA215553 to S.B.H. and J.M.C.), the Chemistry Biology Interface Training Program (T32GM067543 to K.M.W.), the Charles H. Revson foundation (postdoctoral fellowship to A.R.H.) and Yale University is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Chemistry, Yale University, New Haven, CT, USA

    Alan R. Healy, Kevin M. Wernke, Chung Sub Kim, Nicholas R. Lees, Jason M. Crawford & Seth B. Herzon

  2. Chemical Biology Institute, Yale University, West Haven, CT, USA

    Alan R. Healy, Chung Sub Kim & Jason M. Crawford

  3. Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA

    Jason M. Crawford

  4. Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA

    Seth B. Herzon

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Contributions

A.R.H., K.M.W. and N.R.L. carried out the synthetic experiments. C.S.K. conducted the purification of precolibactin 886 (1) and ClbP deacylation studies. S.B.H. and J.M.C. oversaw the project. S.B.H. wrote the manuscript. All the authors discussed the results and commented on the manuscript.

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Correspondence to Jason M. Crawford or Seth B. Herzon.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–8, Supplementary Tables 1 and 2, Supplementary synthetic procedures and characterization data (1H, 13C NMR, IR, HRMS) for all new compounds.

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Healy, A.R., Wernke, K.M., Kim, C.S. et al. Synthesis and reactivity of precolibactin 886. Nat. Chem. 11, 890–898 (2019). https://doi.org/10.1038/s41557-019-0338-2

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