Abstract
Many biologically active peptides found in nature exhibit a bicyclic structure wherein a head-to-tail cyclic backbone is further constrained by an intramolecular linkage connecting two side chains of the peptide. Accordingly, methods to access macrocyclic peptides sharing this overall topology could be of significant value toward the discovery of new functional entities and bioactive compounds. With this goal in mind, we recently developed a strategy for enabling the biosynthesis of thioether-bridged bicyclic peptides in living bacterial cells. This method involves a split intein-catalyzed head-to-tail cyclization of a ribosomally produced precursor peptide, combined with inter-sidechain cross-linking through a genetically encoded cysteine-reactive amino acid. This approach can be applied to direct the formation of structurally diverse bicyclic peptides with high efficiency and selectivity in living Escherichia coli cells and provides a platform for the generation of combinatorial libraries of genetically encoded bicyclic peptides for screening purposes.
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References
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(7):608–624
London N, Raveh B, Schueler-Furman O (2013) Druggable protein-protein interactions—from hot spots to hot segments. Curr Opin Chem Biol 17(6):952–959
Bionda N, Fasan R (2015) Peptidomimetics of α-helical and β-strand protein binding epitopes. In: Czechtizky W, Hamley P (eds) Small molecule medicinal chemistry. Strategies and technologies. Wiley, Hoboken, NJ, pp 431–464
White CJ, Yudin AK (2011) Contemporary strategies for peptide macrocyclization. Nat Chem 3(7):509–524
Hipolito CJ, Suga H (2012) Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems. Curr Opin Chem Biol 16(1–2):196–203
Smith JM, Frost JR, Fasan R (2013) Emerging strategies to access peptide macrocycles from genetically encoded polypeptides. J Org Chem 78(8):3525–3531
Frost JR, Smith JM, Fasan R (2013) Design, synthesis, and diversification of ribosomally derived peptide macrocycles. Curr Opin Struct Biol 23(4):571–580
Baeriswyl V, Heinis C (2013) Polycyclic peptide therapeutics. ChemMedChem 8(3):377–384
Lennard KR, Tavassoli A (2014) Peptides come round: using SICLOPPS libraries for early stage drug discovery. Chemistry 20(34):10608–10614
Bowers AA (2012) Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries. Med Chem Commun 3(8):905–915
Josephson K, Ricardo A, Szostak JW (2014) mRNA display: from basic principles to macrocycle drug discovery. Drug Discov Today 19(4):388–399
Smith JM, Vitali F, Archer SA, Fasan R (2011) Modular assembly of macrocyclic organo-peptide hybrids using synthetic and genetically encoded precursors. Angew Chem Int Ed Engl 50(22):5075–5080
Satyanarayana M, Vitali F, Frost JR, Fasan R (2012) Diverse organo-peptide macrocycles via a fast and catalyst-free oxime/intein-mediated dual ligation. Chem Commun (Camb) 48(10):1461–1463
Frost JR, Vitali F, Jacob NT, Brown MD, Fasan R (2013) Macrocyclization of organo-peptide hybrids through a dual bio-orthogonal ligation: insights from structure-reactivity studies. Chembiochem 14(1):147–160
Smith JM, Hill NC, Krasniak PJ, Fasan R (2014) Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation. Org Biomol Chem 12(7):1135–1142
Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R (2015) Ribosomal synthesis of macrocyclic peptides in vitro and in vivo mediated by genetically encoded aminothiol unnatural amino acids. ACS Chem Biol 10(8):1805–1816
Bionda N, Cryan AL, Fasan R (2014) Bioinspired strategy for the ribosomal synthesis of thioether-bridged macrocyclic peptides in bacteria. ACS Chem Biol 9(9):2008–2013
Bionda N, Fasan R (2015) Ribosomal synthesis of natural-product-like bicyclic peptides in Escherichia coli. Chembiochem 16(14):2011–2016
Scott CP, Abel-Santos E, Wall M, Wahnon DC, Benkovic SJ (1999) Production of cyclic peptides and proteins in vivo. Proc Natl Acad Sci U S A 96(24):13638–13643
Liu CC, Schultz PG (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413–444
Nordgren IK, Tavassoli A (2014) A bidirectional fluorescent two-hybrid system for monitoring protein-protein interactions. Mol Biosyst 10(3):485–490
Horswill AR, Savinov SN, Benkovic SJ (2004) A systematic method for identifying small-molecule modulators of protein-protein interactions. Proc Natl Acad Sci U S A 101(44):15591–15596
Young TS, Ahmad I, Yin JA, Schultz PG (2010) An enhanced system for unnatural amino acid mutagenesis in E. coli. J Mol Biol 395(2):361–374
Zuger S, Iwai H (2005) Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Nat Biotechnol 23(6):736–740
Katz BA (1995) Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence. Biochemistry 34(47):15421–15429
Naumann TA, Savinov SN, Benkovic SJ (2005) Engineering an affinity tag for genetically encoded cyclic peptides. Biotechnol Bioeng 92(7):820–830
Acknowledgments
This work was supported by the US National Institutes of Health (grant R21 CA187502). MS instrumentation was supported by the US National Science Foundation (grants CHE-0840410 and CHE-0946653).
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Bionda, N., Fasan, R. (2017). Ribosomal Synthesis of Thioether-Bridged Bicyclic Peptides. In: Mootz, H. (eds) Split Inteins. Methods in Molecular Biology, vol 1495. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6451-2_5
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DOI: https://doi.org/10.1007/978-1-4939-6451-2_5
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