Skip to main content
SpringerLink
Log in

Peptide Cyclization Catalyzed by Cyanobactin Macrocyclases

  • Protocol
  • First Online:
Enzyme-Mediated Ligation Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2012))

Abstract

Cyclic peptides are an emerging class of therapeutics that can modulate targets not amenable to traditional small molecule intervention (e.g., protein–protein interactions). However, N-to-C macrocyclization of peptides is a challenging and often a low yielding chemical transformation. Several macrocyclases from cyanobactin biosynthetic clusters have been used to catalyze this reaction.

This chapter provides practical guidance to the processes of heterologous expression and purification of these enzymes as well as performing in vitro biochemical reactions. Finally, approaches to recover the final product from an enzymatic reaction mixture are also discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D, Vajda S et al (2014) How proteins bind macrocycles. Nat Chem Biol 10:723–731

    Article  Google Scholar 

  2. Gao M, Cheng K, Yin H (2015) Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 104:310–316

    Article  Google Scholar 

  3. Kotz J (2012) Bringing macrocycles full circle. SciBX 5(45):2–8

    Google Scholar 

  4. Driggers EM, Hale SP, Lee J, Terrett NK (2008) The exploration of macrocycles for drug discovery-an underexploited structural class. Nat Rev Drug Discov 7:608–624

    Article  Google Scholar 

  5. Zorzi A, Deyle K, Heinis C (2017) Cyclic peptide therapeutics: past, present and future. Curr Opin Chem Biol 38:24–29

    Article  Google Scholar 

  6. White CJ, Yudin AK (2011) Contemporary strategies for peptide macrocyclization. Nat Chem 3:509–524

    Article  Google Scholar 

  7. Martí-Centelles V, Pandey MD, Isabel Burguete M, Luis SV (2015) Macrocyclization reactions: the importance of conformational, configurational, and template-induced preorganization. Chem Rev 115:8736–8834

    Article  Google Scholar 

  8. Alexandru-Crivac C, Dalponte L, Houssen WE, Idress M, Jaspars M, Rickaby KA et al (2017) Cyclic peptides – a look to the future. In: Koehnke J, Naismith J, van der Donk WA (eds) Cyclic peptides: from bioorganic synthesis to applications. The Royal Society of Chemistry, London

    Google Scholar 

  9. Houssen WE, Jaspars M (2010) Azole-based cyclic peptides from the sea squirt Lissoclinum patella: old scaffolds, new avenues. ChemBioChem 11:1803–1815

    Article  Google Scholar 

  10. Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G et al (2013) Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 30:108–160

    Article  Google Scholar 

  11. Leikoski N, Liu L, Jokela J, Wahlsten M, Gugger M, Calteau A et al (2013) Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides. Chem Biol 20:1033–1043

    Article  Google Scholar 

  12. Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG et al (2005) Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc Natl Acad Sci U S A 102:7315–7320

    Article  Google Scholar 

  13. Donia MS, Ravel J, Schmidt EW (2008) A global assembly line for cyanobactins. Nat Chem Biol 4:341–343

    Article  Google Scholar 

  14. Koehnke J, Bent A, Houssen WE, Zollman D, Morawitz F, Shirran S et al (2012) The mechanism of patellamide macrocyclization revealed by the characterization of the PatG macrocyclase domain. Nat Struct Mol Biol 19:767–772

    Article  Google Scholar 

  15. Lee J, McIntosh J, Hathaway BJ, Schmidt EW (2009) Using marine natural products to discover a protease that catalyzes peptide macrocyclization of diverse substrates. J Am Chem Soc 131:2122–2124

    Article  Google Scholar 

  16. Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X et al (2013) The cyanobactin heterocyclase enzyme: a processive adenylase that operates with a defined order of reaction. Angew Chem Int Ed 52:13991–13396

    Article  Google Scholar 

  17. Bent AF, Mann G, Houssen WE, Mykhaylyk V, Duman R, Thomas L et al (2016) Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD. Acta Crystallogr D Struct Biol 72:1174–1180

    Article  Google Scholar 

  18. Sardar D, Hao Y, Lin Z, Morita M, Nair SK, Schmidt EW (2017) Enzymatic N- and C-protection in cyanobactin RiPP natural products. J Am Chem Soc 139:2884–2887

    Article  Google Scholar 

  19. Parajuli A, Kwak DH, Dalponte L, Leikoski N, Galica T, Umeobika U et al (2016) A unique tryptophan C-prenyltransferase from the kawaguchipeptin biosynthetic pathway. Angew Chem Int Ed 55:3596–3599

    Article  Google Scholar 

  20. McIntosh JA, Donia MS, Nair SK, Schmidt EW (2011) Enzymatic basis of ribosomal peptide prenylation in cyanobacteria. J Am Chem Soc 133:13698–13705

    Article  Google Scholar 

  21. Donia MS, Schmidt EW (2011) Linking chemistry and genetics in the growing cyanobactin natural products family. Chem Biol 18:508–519

    Article  Google Scholar 

  22. Houssen WE, Bent AF, McEwan AR, Pieiller N, Tabudravu J, Koehnke J et al (2014) An efficient method for the in vitro production of azol(in)e-based cyclic peptides. Angew Chem Int Ed 53:14171–14174

    Article  Google Scholar 

  23. Ruffner DE, Schmidt EW, Heemstra JR (2015) Assessing the combinatorial potential of the RiPP cyanobactin tru pathway. ACS Synth Biol 4:482–492

    Article  Google Scholar 

  24. Koehnke J, Mann G, Bent AF, Ludewig H, Shirran S, Botting C et al (2015) Structural analysis of leader peptide binding enables leader-free cyanobactin processing. Nat Chem Biol 11:558–563

    Article  Google Scholar 

  25. Houssen WE, Koehnke J, Zollman D, Vendome J, Raab A, Smith MCM et al (2012) The discovery of new cyanobactins from Cyanothece PCC 7425 defines a new signature for processing of patellamides. ChemBioChem 13:2683–2689

    Article  Google Scholar 

  26. Agarwal V, Pierce E, McIntosh J, Schmidt EW, Nair SK (2012) Structures of cyanobactin maturation enzymes define a family of transamidating proteases. Chem Biol 19:1411–1422

    Article  Google Scholar 

  27. McIntosh JA, Donia MS, Schmidt EW (2010) Insights into heterocyclization from two highly similar enzymes. J Am Chem Soc 132:4089–4091

    Article  Google Scholar 

  28. Bent AF, Koehnke J, Houssen WE, Smith MCM, Jaspars M, Naismith JH (2013) Structure of PatF from Prochloron didemni. Acta Crystallogr F Struct Biol Commun 69:618–623

    Article  Google Scholar 

  29. Mann G, Koehnke J, Bent AF, Graham R, Houssen W, Jaspars M et al (2014) The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster. Acta Crystallogr F Struct Biol Commun 70:1597–1603

    Article  Google Scholar 

  30. Koehnke J, Bent AF, Houssen WE, Mann G, Jaspars M, Naismith JH (2014) The structural biology of patellamide biosynthesis. Curr Opin Struct Biol 29:112–121

    Article  Google Scholar 

  31. Donia MS, Hathaway BJ, Sudek S, Haygood MG, Rosovitz MJ, Ravel J et al (2006) Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nat Chem Biol 2:729–735

    Article  Google Scholar 

  32. Brás NF, Ferreira P, Calixto AR, Jaspars M, Houssen W, Naismith JH et al (2016) The catalytic mechanism of the marine-derived macrocyclase PatGmac. Chem A Eur J 22:13089–13097

    Article  Google Scholar 

  33. Schechter I, Berger A (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 27:157–162

    Article  Google Scholar 

  34. Booth J, Alexandru-Crivac C, Rickaby K, Nneoyiegbe A, Umeobika C, McEwan AR et al (2017) A blind test of computational technique for predicting the likelihood of peptide sequences to cyclize. J Phys Chem Lett 8:2310–2315

    Article  Google Scholar 

  35. Sivonen K, Leikoski N, Fewer DP, Jokela J (2010) Cyanobactins—ribosomal cyclic peptides produced by cyanobacteria. Appl Microbiol Biotechnol 86:1213–1225

    Article  Google Scholar 

  36. McIntosh JA, Robertson CR, Agarwal V, Nair SK, Bulaj GW, Schmidt EW (2010) Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst. J Am Chem Soc 132:15499–15501

    Article  Google Scholar 

  37. Oueis E, Jaspars M, Westwood NJ, Naismith JH (2016) Enzymatic macrocyclization of 1,2,3-triazole peptide mimetics. Angew Chem Int Ed 55:5842–5845

    Article  Google Scholar 

  38. Koehnke J, Morawitz F, Bent AF, Houssen WE, Shirran SL, Fuszard MA et al (2013) An enzymatic route to selenazolines. ChemBioChem 14:564–567

    Article  Google Scholar 

  39. Oueis E, Nardone B, Jaspars M, Westwood NJ, Naismith JH (2017) Synthesis of hybrid cyclopeptides via enzymatic macrocyclization. Chemistry Open 6:11–14

    Google Scholar 

  40. Oueis E, Stevenson H, Jaspars M, Westwood NJ, Naismith JH (2017) Bypassing the proline/thiazoline requirement of the macrocyclase PatG. Chem Commun 53:12274–12277

    Article  Google Scholar 

  41. Ziemert N, Ishida K, Quillardet P, Bouchier C, Hertweck C, de Marsac NT et al (2008) Microcyclamide biosynthesis in two strains of Microcystis aeruginosa: from structure to genes and vice versa. Appl Environ Microbiol 74:1791–1797

    Article  Google Scholar 

  42. Alexandru-Crivac C, Umeobika C, Leikoski N, Jokela J, Rickabi K, Grilo AM et al (2017) Cyclic peptide production using a macrocyclase with enhanced substrate promiscuity and relaxed recognition determinants. Chem Commun 53:10656–10659

    Article  Google Scholar 

  43. Falorni M, Conti S, Giacomelli G, Cossu S, Soccolini F (1995) Optically active 4-oxaproline derivatives: new useful chiral synthons derived from serine and threonine. Tetrahedron Asymmetry 6:287–294

    Article  Google Scholar 

  44. Weinstein AB, Schuman DP, Tan ZX, Stahl SS (2013) Synthesis of vicinal aminoalcohols by stereoselective aza-wacker cyclizations: access to (-)-acosamine by redox relay. Angew Chem Int Ed 52:11867–11870

    Article  Google Scholar 

  45. Liu H, Naismith JH (2009) A simple and efficient expression and purification system using two newly constructed vectors. Protein Expr Purif 63:102–111

    Article  Google Scholar 

  46. Studier FW (2005) Protein production by auto-induction in high-density shaking cultures. Protein Expr Purif 41:207–234

    Article  Google Scholar 

  47. Dalponte L, Parajuli A, Younger E, Mattila A, Jokela J, Wahlsten M, Leikoski N, Sivonen K, Jarmusch SA, Houssen WE, Fewer DP (2018) N-prenylation of tryptophan by an aromatic prenyltransferase from the cyanobactin biosynthetic pathway. Biochemistry 57(50):6860–6867

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Marine Biodiscovery Centre, Chemistry Department, University of Aberdeen, Aberdeen, UK

    Wael E. Houssen

  2. Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK

    Wael E. Houssen

  3. Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt

    Wael E. Houssen

Authors
  1. Wael E. Houssen
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. EnzyPep B.V., Geleen, The Netherlands

    Timo Nuijens  & Marcel Schmidt  & 

Additional information

I dedicate this chapter to the memory of my colleagues Dr. Andrew Bent (University of St Andrews, UK) and Dr. Mostafa Abdelrahman (University of Aberdeen, UK & Al-Azhar University, Egypt) who died from cancer.

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Houssen, W.E. (2019). Peptide Cyclization Catalyzed by Cyanobactin Macrocyclases. In: Nuijens, T., Schmidt, M. (eds) Enzyme-Mediated Ligation Methods. Methods in Molecular Biology, vol 2012. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9546-2_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9546-2_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9545-5

  • Online ISBN: 978-1-4939-9546-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation