Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against ‘undruggable’ targets such as protein–protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Driggers, E. M., Hale, S. P., Lee, J. & Terrett, N. K. The exploration of macrocycles for drug discovery — an underexploited structural class. Nat. Rev. Drug Discov. 7, 608–624 (2008).
Marsault, E. & Peterson, M. L. Macrocycles are great cycles: applications, opportunities, and challenges of synthetic macrocycles in drug discovery. J. Med. Chem. 54, 1961–2004 (2011).
Tavassoli, A. SICLOPPS cyclic peptide libraries in drug discovery. Curr. Opin. Chem. Biol. 38, 30–35 (2017).
Freidinger, R. M., Veber, D. F., Perlow, D. S., Brooks, J. R. & Saperstein, R. Bioactive conformation of luteinizing hormone-releasing hormone: evidence from a conformationally constrained analog. Science 210, 656–658 (1980).
Veber, D. F. et al. Nonreducible cyclic analogues of somatostatin. J. Am. Chem. Soc. 98, 2367–2369 (1976).
Foster, A. D. et al. Methods for the creation of cyclic peptide libraries for use in lead discovery. J. Biomol. Screen. 20, 563–576 (2015).
Mistry, I. N. & Tavassoli, A. Reprogramming the transcriptional response to hypoxia with a chromosomally encoded cyclic peptide HIF-1 inhibitor. ACS Synth. Biol. 6, 518–527 (2017).
Vinogradov, A. A., Yin, Y. & Suga, H. Macrocyclic peptides as drug candidates: recent progress and remaining challenges. J. Am. Chem. Soc. 141, 4167–4181 (2019).
Tapeinou, A., Matsoukas, M.-T., Simal, C. & Tselios, T. Review cyclic peptides on a merry-go-round; towards drug design. Pept. Sci. 104, 453–461 (2015).
Neri, D. & Lerner, R. A. DNA-encoded chemical libraries: a selection system based on endowing organic compounds with amplifiable information. Annu. Rev. Biochem. 87, 479–502 (2018).
Lam, K. S., Lebl, M. & Krchňák, V. The “one-bead-one-compound” combinatorial library method. Chem. Rev. 97, 411–448 (1997).
Qian, Z., Upadhyaya, P. & Pei, D. Synthesis and screening of one-bead-one-compound cyclic peptide libraries. Methods Mol. Biol. 1248, 39–53 (2015).
Rhodes, C. A. et al. Cell-permeable bicyclic peptidyl inhibitors against NEMO-IkappaB kinase interaction directly from a combinatorial library. J. Am. Chem. Soc. 140, 12102–12110 (2018).
Trinh, T. B., Upadhyaya, P., Qian, Z. & Pei, D. Discovery of a direct Ras inhibitor by screening a combinatorial library of cell-permeable bicyclic peptides. ACS Comb. Sci. 18, 75–85 (2016).
Lau, Y. H., de Andrade, P., Wu, Y. & Spring, D. R. Peptide stapling techniques based on different macrocyclisation chemistries. Chem. Soc. Rev. 44, 91–102 (2015).
Bashiruddin, N. K. & Suga, H. Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies. Curr. Opin. Chem. Biol. 24, 131–138 (2015).
Smith, G. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 (1985). This is the first report of phage display.
Nemoto, N., Miyamoto-Sato, E., Husimi, Y. & Yanagawa, H. In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett. 414, 405–408 (1997).
Roberts, R. W. & Szostak, J. W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl Acad. Sci. USA 94, 12297–12302 (1997). This is the first report of mRNA display.
McCafferty, J., Griffiths, A. D., Winter, G. & Chiswell, D. J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 348, 552–554 (1990).
Lawrence, S. Billion dollar babies — biotech drugs as blockbusters. Nat. Biotechnol. 25, 380–382 (2007).
Parmley, S. F. & Smith, G. P. Antibody-selectable filamentous fd phage vectors: affinity purification of target genes. Gene 73, 305–318 (1988).
Scott, J. K. & Smith, G. P. Searching for peptide ligands with an epitope library. Science 249, 386–390 (1990).
Bazan, J., Całkosiński, I. & Gamian, A. Phage display — a powerful technique for immunotherapy. Hum. Vaccin. Immunother. 8, 1817–1828 (2012).
Hertveldt, K., Beliën, T. & Volckaert, G. General M13 phage display: M13 phage display in identification and characterization of protein–protein interactions. Methods Mol. Biol. 502, 321–339 (2009).
Luzzago, A., Felici, F., Tramontano, A., Pessi, A. & Cortese, R. Mimicking of discontinuous epitopes by phage-displayed peptides, I. Epitope mapping of human H ferritin using a phage library of constrained peptides. Gene 128, 51–57 (1993).
McLafferty, M. A., Kent, R. B., Ladner, R. C. & Markland, W. M13 bacteriophage displaying disulfide-constrained microproteins. Gene 128, 29–36 (1993).
Barry, M. A., Dower, W. J. & Johnston, S. A. Toward cell-targeting gene therapy vectors: selection of cell-binding peptides from random peptide-presenting phage libraries. Nat. Med. 2, 299–305 (1996).
Wu, C.-H., Liu, I.-J., Lu, R.-M. & Wu, H.-C. Advancement and applications of peptide phage display technology in biomedical science. J. Biomed. Sci. 23, 8 (2016).
Hansen, M. et al. A urokinase-type plasminogen activator-inhibiting cyclic peptide with an unusual P2 residue and an extended protease binding surface demonstrates new modalities for enzyme inhibition. J. Biol. Chem. 280, 38424–38437 (2005).
Andersen, L. M., Wind, T., Hansen, H. D. & Andreasen, P. A. A cyclic peptidylic inhibitor of murine urokinase-type plasminogen activator: changing species specificity by substitution of a single residue. Biochem. J. 412, 447–457 (2008).
Gho, Y. S., Lee, J. E., Oh, K. S., Bae, D. G. & Chae, C. B. Development of antiangiogenin peptide using a phage-displayed peptide library. Cancer Res. 57, 3733–3740 (1997).
O’Neil, K. T. et al. Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library. Proteins 14, 509–515 (1992).
Ho, K. L., Yusoff, K., Seow, H. F. & Tan, W. S. Selection of high affinity ligands to hepatitis B core antigen from a phage-displayed cyclic peptide library. J. Med. Virol. 69, 27–32 (2003).
Tan, W. S., Tan, G. H., Yusoff, K. & Seow, H. F. A phage-displayed cyclic peptide that interacts tightly with the immunodominant region of hepatitis B surface antigen. J. Clin. Virol. 34, 35–41 (2005).
Dyson, M. R. & Murray, K. Selection of peptide inhibitors of interactions involved in complex protein assemblies: association of the core and surface antigens of hepatitis B virus. Proc. Natl Acad. Sci. USA 92, 2194–2198 (1995).
Even-Desrumeaux, K. & Chames, P. Phage display and selections on cells. Methods Mol. Biol. 907, 225–235 (2012).
Mangini, M. et al. Peptide-guided targeting of GPR55 for anti-cancer therapy. Oncotarget 8, 5179–5195 (2017).
Hussain, S. et al. Antibiotic-loaded nanoparticles targeted to the site of infection enhance antibacterial efficacy. Nat. Biomed. Eng. 2, 95–103 (2018).
Mann, A. P. et al. Identification of a peptide recognizing cerebrovascular changes in mouse models of Alzheimer’s disease. Nat. Commun. 8, 1403 (2017).
Heinis, C., Rutherford, T., Freund, S. & Winter, G. Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat. Chem. Biol. 5, 502–507 (2009). This paper reports the generation and screening of a phage-displayed bicyclic-peptide library.
Rentero Rebollo, I. & Heinis, C. Phage selection of bicyclic peptides. Methods 60, 46–54 (2013).
Chen, S. et al. Bicyclic peptide ligands pulled out of cysteine-rich peptide libraries. J. Am. Chem. Soc. 135, 6562–6569 (2013).
Angelini, A. et al. Bicyclic peptide inhibitor reveals large contact interface with a protease target. ACS Chem. Biol. 7, 817–821 (2012).
Bertoldo, D. et al. Phage selection of peptide macrocycles against β-catenin to interfere with Wnt signaling. ChemMedChem 11, 834–839 (2016).
Josephson, K., Ricardo, A. & Szostak, J. W. mRNA display: from basic principles to macrocycle drug discovery. Drug Discov. Today 19, 388–399 (2014).
Barendt, P. A., Ng, D. T., McQuade, C. N. & Sarkar, C. A. Streamlined protocol for mRNA display. ACS Comb. Sci. 15, 77–81 (2013).
Cho, G., Keefe, A. D., Liu, R., Wilson, D. S. & Szostak, J. W. Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J. Mol. Biol. 297, 309–319 (2000).
Goto, Y., Katoh, T. & Suga, H. Flexizymes for genetic code reprogramming. Nat. Protoc. 6, 779–790 (2011). The paper describes the mRNA-display protocol in excellent detail.
Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755 (2001).
Josephson, K., Hartman, M. C. & Szostak, J. W. Ribosomal synthesis of unnatural peptides. J. Am. Chem. Soc. 127, 11727–11735 (2005).
Heckler, T. G. et al. T4 RNA ligase mediated preparation of novel “chemically misacylated” tRNAPheS. Biochemistry 23, 1468–1473 (1984).
Ohuchi, M., Murakami, H. & Suga, H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr. Opin. Chem. Biol. 11, 537–542 (2007).
Passioura, T. & Suga, H. Flexizyme-mediated genetic reprogramming as a tool for noncanonical peptide synthesis and drug discovery. Chem. Eur. J. 19, 6530–6536 (2013).
Katoh, T. & Suga, H. Ribosomal incorporation of consecutive beta-amino acids. J. Am. Chem. Soc. 140, 12159–12167 (2018).
Passioura, T., Liu, W., Dunkelmann, D., Higuchi, T. & Suga, H. Display selection of exotic macrocyclic peptides expressed under a radically reprogrammed 23 amino acid genetic code. J. Am. Chem. Soc. 140, 11551–11555 (2018). This paper details the use of flexizymes with mRNA display for the generation of a cyclic-peptide library containing multiple non-natural amino acids.
Goto, Y., Murakami, H. & Suga, H. Initiating translation with D-amino acids. RNA 14, 1390–1398 (2008).
Kawakami, T., Murakami, H. & Suga, H. Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem. Biol. 15, 32–42 (2008).
Ito, K., Passioura, T. & Suga, H. Technologies for the synthesis of mRNA-encoding libraries and discovery of bioactive natural product-inspired non-traditional macrocyclic peptides. Molecules 18, 3502–3528 (2013).
Guillen Schlippe, Y. V., Hartman, M. C., Josephson, K. & Szostak, J. W. In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J. Am. Chem. Soc. 134, 10469–10477 (2012).
Millward, S. W., Takahashi, T. T. & Roberts, R. W. A general route for post-translational cyclization of mRNA display libraries. J. Am. Chem. Soc. 127, 14142–14143 (2005).
Goto, Y. et al. Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem. Biol. 3, 120–129 (2008).
Seebeck, F. P., Ricardo, A. & Szostak, J. W. Artificial lantipeptides from in vitro translations. Chem. Commun. 47, 6141–6143 (2011).
Goto, Y., Iwasaki, K., Torikai, K., Murakami, H. & Suga, H. Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chem. Commun. 23, 3149–3421 (2009).
Yamagishi, Y., Ashigai, H., Goto, Y., Murakami, H. & Suga, H. Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction. ChemBioChem 10, 1469–1472 (2009).
Takatsuji, R. et al. Ribosomal synthesis of backbone-cyclic peptides compatible with in vitro display. J. Am. Chem. Soc. 141, 2279–2287 (2019).
McAllister, T. E. et al. Non-competitive cyclic peptides for targeting enzyme–substrate complexes. Chem. Sci. 9, 4569–4578 (2018).
Hipolito, C. J., Tanaka, Y., Katoh, T., Nureki, O. & Suga, H. A macrocyclic peptide that serves as a cocrystallization ligand and inhibits the function of a MATE family transporter. Molecules 18, 10514–10530 (2013).
Tanaka, Y. et al. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 496, 247–251 (2013).
Hayashi, Y., Morimoto, J. & Suga, H. In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors. ACS Chem. Biol. 7, 607–613 (2012).
Morimoto, J., Hayashi, Y. & Suga, H. Discovery of macrocyclic peptides armed with a mechanism-based warhead: Isoform-selective inhibition of human deacetylase SIRT2. Angew. Chem. Int. Ed. 51, 3423–3427 (2012).
Yamagata, K. et al. Structural basis for potent inhibition of SIRT2 deacetylase by a macrocyclic peptide inducing dynamic structural change. Structure 22, 345–352 (2014).
Scott, C. P., Abel-Santos, E., Wall, M., Wahnon, D. C. & Benkovic, S. J. Production of cyclic peptides and proteins in vivo. Proc. Natl Acad. Sci. USA 96, 13638–13643 (1999). This paper reports the use of SICLOPPS inteins for cyclic-peptide generation.
Tavassoli, A. & Benkovic, S. J. Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli. Nat. Protoc. 2, 1126–1133 (2007).
Chong, S., Williams, K. S., Wotkowicz, C. & Xu, M.-Q. Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. J. Biol. Chem. 273, 10567–10577 (1998).
Paulus, H. The chemical basis of protein splicing. Chem. Soc. Rev. 27, 375–386 (1998).
Scott, C. P., Abel-Santos, E., Jones, A. D. & Benkovic, S. J. Structural requirements for the biosynthesis of backbone cyclic peptide libraries. Chem. Biol. 8, 801–815 (2001).
Townend, J. E. & Tavassoli, A. Traceless production of cyclic peptide libraries in E. coli. ACS Chem. Biol. 11, 1624–1630 (2016).
Lennard, K. R. & Tavassoli, A. Peptides come round: using SICLOPPS libraries for early stage drug discovery. Chem. Eur. J. 20, 10608–10614 (2014).
Horswill, A. R., Savinov, S. N. & Benkovic, S. J. A systematic method for identifying small-molecule modulators of protein–protein interactions. Proc. Natl Acad. Sci. USA 101, 15591–15596 (2004).
Tavassoli, A. & Benkovic, S. J. Genetically selected cyclic-peptide inhibitors of AICAR transformylase homodimerization. Angew. Chem. Int. Ed. 44, 2760–2763 (2005).
Spurr, I. B. et al. Targeting tumour proliferation with a small-molecule inhibitor of AICAR transformylase homodimerization. ChemBioChem 13, 1628–1634 (2012).
Asby, D. J. et al. AMPK activation via modulation of De Novo Purine biosynthesis with an inhibitor of ATIC homodimerization. Chem. Biol. 22, 838–848 (2015). This paper reports the in vivo activity of a small molecule derived from a cyclic peptide identified with SICLOPPS.
Miranda, E. et al. A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells. J. Am. Chem. Soc. 135, 10418–10425 (2013). This paper reports the use of SICLOPPS for the identification of the first HIF1-isoform-selective inhibitor.
Asby, D. J., Cuda, F., Hoakwie, F., Miranda, E. & Tavassoli, A. HIF-1 promotes the expression of its α-subunit via an epigenetically regulated transactivation loop. Mol. BioSyst. 10, 2505–2508 (2014).
Birts, C. N. et al. A cyclic peptide inhibitor of C-terminal binding protein dimerization links metabolism with mitotic fidelity in breast cancer cells. Chem. Sci. 4, 3046–3057 (2013).
Male, A. L. et al. Targeting Bacillus anthracis toxicity with a genetically selected inhibitor of the PA/CMG2 protein-protein interaction. Sci. Rep. 7, 3104 (2017).
Tavassoli, A. et al. Inhibition of HIV budding by a genetically selected cyclic peptide targeting the Gag–TSG101 interaction. ACS Chem. Biol. 3, 757–764 (2008).
Lennard, K. R., Gardner, R. M., Doigneaux, C., Castillo, F. & Tavassoli, A. Development of a cyclic peptide inhibitor of the p6/UEV protein–protein interaction. ACS Chem. Biol. 14, 1874–1878 (2019).
Osher, E. L. et al. A genetically selected cyclic peptide inhibitor of BCL6 homodimerization. Bioorg. Med. Chem. 26, 3034–3038 (2018).
Leitch, E. K. et al. Inhibition of low-density lipoprotein receptor degradation with a cyclic peptide that disrupts the homodimerization of IDOL E3 ubiquitin ligase. Chem. Sci. 9, 5957–5966 (2018).
Kjelstrup, S., Hansen, P. M. P., Thomsen, L. E., Hansen, P. R. & Løbner-Olesen, A. Cyclic peptide inhibitors of the β-sliding clamp in Staphylococcus aureus. PLOS ONE 8, e72273 (2013).
Cheng, L. et al. Discovery of antibacterial cyclic peptides that inhibit the ClpXP protease. Protein Sci. 16, 1535–1542 (2007).
Kritzer, J. A. et al. Rapid selection of cyclic peptides that reduce alpha-synuclein toxicity in yeast and animal models. Nat. Chem. Biol. 5, 655–663 (2009).
Barreto, K. et al. A genetic screen for isolating “lariat” peptide inhibitors of protein function. Chem. Biol. 16, 1148–1157 (2009).
Bharathikumar, V. M., Barreto, K., DeCoteau, J. F. & Geyer, C. R. Allosteric lariat peptide inhibitors of Abl kinase. ChemBioChem 14, 2119–2125 (2013).
Kinsella, T. M. et al. Retrovirally delivered random cyclic peptide libraries yield inhibitors of interleukin-4 signaling in human B cells. J. Biol. Chem. 277, 37512–37518 (2002).
Al Musaimi, O., Al Shaer, D., De la Torre, B. G. & Albericio, F. 2017 FDA peptide harvest. Pharmaceuticals 11, 42 (2018).
Zorzi, A., Deyle, K. & Heinis, C. Cyclic peptide therapeutics: past, present and future. Curr. Opin. Chem. Biol. 38, 24–29 (2017).
Wrighton, N. C. et al. Small peptides as potent mimetics of the protein hormone erythropoietin. Science 273, 458–464 (1996).
Rader, C. & Barbas, C. F. III. Phage display of combinatorial antibody libraries. Curr. Opin. Biotechnol. 8, 503–508 (1997).
Dougherty, P. G., Sahni, A. & Pei, D. Understanding cell penetration of cyclic peptides. Chem. Rev. 119, 10241–10287 (2019).
Peraro, L. & Kritzer, J. A. Emerging methods and design principles for cell-penetrant peptides. Angew. Chem. Int. Ed. 57, 11868–11881 (2018).
Huang, Y., Wiedmann, M. M. & Suga, H. RNA display methods for the discovery of bioactive macrocycles. Chem. Rev. 119, 10360–10391 (2019).
Acknowledgements
A.T. thanks Cancer Research UK (A20185) for support.
Author information
Authors and Affiliations
Contributions
The authors contributed equally to all aspects of the article.
Corresponding author
Ethics declarations
Competing interests
A.T. and A.F. are employees and shareholders of Curve Therapeutics. C.S is a shareholder in Curve Therapeutics.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Sohrabi, C., Foster, A. & Tavassoli, A. Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 4, 90–101 (2020). https://doi.org/10.1038/s41570-019-0159-2
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41570-019-0159-2
This article is cited by
-
Beyond canonical PROTAC: biological targeted protein degradation (bioTPD)
Biomaterials Research (2023)
-
Nature-inspired protein ligation and its applications
Nature Reviews Chemistry (2023)
-
An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides
Nature Communications (2023)
-
High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays
Nature Communications (2023)
-
Single-chain tandem macrocyclic peptides as a scaffold for growth factor and cytokine mimetics
Communications Biology (2022)