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Phage Selection of Bicyclic Peptides Based on Two Disulfide Bridges

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Peptide Libraries

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1248))

Abstract

Bicyclic peptides can bind with high affinity and selectivity to protein targets, making this format attractive for biotechnological and medicinal applications. The good binding properties are based to a large extent on the limited conformational flexibility of the two connected peptide rings. Bicyclic peptides with desired binding specificity can be isolated from phage display libraries that are generated by chemically cyclizing linear peptide on phage with alkylating reagents. Recently, we presented a strategy for the phage selection of bicyclic peptides based on two disulfide bridges. This approach allows the generation and screening of topologically highly diverse bicyclic peptide structures. Herein, we describe step-by-step protocols to clone and produce disulfide-cyclized bicyclic peptide libraries as well as to screen the libraries and to synthesize and characterize isolated bicyclic peptides.

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References

  1. Luckett S, Garcia RS, Barker JJ, Konarev AV, Shewry PR, Clarke AR, Brady RL (1999) High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds. J Mol Biol 290(2):525–533. doi:10.1006/jmbi.1999.2891

    Article  CAS  PubMed  Google Scholar 

  2. De La Cruz EM, Pollard TD (1996) Kinetics and thermodynamics of phalloidin binding to actin filaments from three divergent species. Biochemistry 35(45):14054–14061. doi:10.1021/Bi961047t

    Article  Google Scholar 

  3. Koba M, Konopa J (2005) Actinomycin D and its mechanisms of action. Postepy Hig Med Dosw (Online) 59:290–298

    Google Scholar 

  4. Heinis C, Rutherford T, Freund S, Winter G (2009) Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat Chem Biol 5(7):502–507. doi:10.1038/nchembio.184

    Article  CAS  PubMed  Google Scholar 

  5. Timmerman P, Beld J, Puijk WC, Meloen RH (2005) Rapid and quantitative cyclization of multiple peptide loops onto synthetic scaffolds for structural mimicry of protein surfaces. Chembiochem 6(5):821–824. doi:10.1002/cbic.200400374

    Article  CAS  PubMed  Google Scholar 

  6. Angelini A, Cendron L, Chen S, Touati J, Winter G, Zanotti G, Heinis C (2012) Bicyclic peptide inhibitor reveals large contact interface with a protease target. ACS Chem Biol 7(5):817–821. doi:10.1021/cb200478t

    Article  CAS  PubMed  Google Scholar 

  7. Baeriswyl V, Rapley H, Pollaro L, Stace C, Teufel D, Walker E, Chen S, Winter G, Tite J, Heinis C (2012) Bicyclic peptides with optimized ring size inhibit human plasma kallikrein and its orthologues while sparing paralogous proteases. ChemMedChem 7(7):1173–1176. doi:10.1002/cmdc.2012000710

    Article  CAS  PubMed  Google Scholar 

  8. Rebollo IR, Angelini A, Heinis C (2013) Phage display libraries of differently sized bicyclic peptides. MedChemComm 4(1):145–150. doi:10.1039/C2md20171b

    Article  CAS  Google Scholar 

  9. Chen S, Rentero Rebollo I, Buth SA, Morales-Sanfrutos J, Touati J, Leiman PG, Heinis C (2013) Bicyclic peptide ligands pulled out of cysteine-rich peptide libraries. J Am Chem Soc 135(17):6562–6569. doi:10.1021/ja400461h

    Article  CAS  PubMed  Google Scholar 

  10. Kather I, Bippes CA, Schmid FX (2005) A stable disulfide-free gene-3-protein of phage fd generated by in vitro evolution. J Mol Biol 354(3):666–678. doi:10.1016/j.jmb.2005.09.086

    Article  CAS  PubMed  Google Scholar 

  11. Smith GP, VA P (1997) Phage display. Chem Rev 97(2):391–410

    Article  CAS  PubMed  Google Scholar 

  12. Bratkovič T (2010) Progress in phage display: evolution of the technique and its applications. Cell Mol Life Sci 67(5):749–767. doi:10.1007/s00018-009-0192-2

    Article  PubMed  Google Scholar 

  13. Lowman HB, Bass SH, Simpson N, JA W (1991) Selecting high-affinity binding proteins by monovalent phage display. Biochemistry 30(45):10832–10838

    Article  CAS  PubMed  Google Scholar 

  14. Yanofsky SD, Baldwin DN, Butler JH, Holden FR, Jacobs JW, Balasubramanian P, Chinn JP, Cwirla SE, Peters-Bhatt E, Whitehorn EA, Tate EH, Akeson A, Bowlin TL, Dower WJ, Barrett RW (1996) High affinity type I interleukin 1 receptor antagonists discovered by screening recombinant peptide libraries. Proc Natl Acad Sci U S A 93(14):7381–7386

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Giebel LB, Cass RT, Milligan DL, Young DC, Arze R, Johnson CR (1995) Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry 34(47):15430–15435

    Article  CAS  PubMed  Google Scholar 

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Acknowledgment

The financial contribution from the Swiss National Science Foundation (SNSF Professorship PP00P3_123524/1 to C.H.) is gratefully acknowledged.

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Correspondence to Christian Heinis .

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© 2015 Springer Science+Business Media New York

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Chen, S., Heinis, C. (2015). Phage Selection of Bicyclic Peptides Based on Two Disulfide Bridges. In: Derda, R. (eds) Peptide Libraries. Methods in Molecular Biology, vol 1248. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2020-4_9

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  • DOI: https://doi.org/10.1007/978-1-4939-2020-4_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2019-8

  • Online ISBN: 978-1-4939-2020-4

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