Methods for the creation of cyclic peptide libraries for use in lead discovery

Journal of Biomolecular Screening

Volumn 20, Issue 5, 2015, Pages 563-576

  Foster, Andrew D ^a   Ingram, James D ^a   Leitch, Eilidh K ^a   Lennard, Katherine R ^a   Osher, Eliot L ^a   Tavassoli, Ali ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

cyclic peptide; high throughput screening; protein protein interactions; review

Indexed keywords

CYCLOPEPTIDE; FLEXIZYME; INTEIN; RIBOZYME; UNCLASSIFIED DRUG; PEPTIDE LIBRARY;

HIGH THROUGHPUT SCREENING; HUMAN; MOLECULAR LIBRARY; NONHUMAN; PEPTIDE LIBRARY; PHAGE DISPLAY; PHAGEMID; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW; SYNTHESIS; CELL SURFACE DISPLAY; DRUG DEVELOPMENT; IN VITRO STUDY; PROCEDURES; PROTEIN SYNTHESIS;

CELL SURFACE DISPLAY TECHNIQUES; DRUG DISCOVERY; IN VITRO TECHNIQUES; PEPTIDE LIBRARY; PEPTIDES, CYCLIC; PROTEIN BIOSYNTHESIS;

EID: 84930349374     PISSN: 10870571     EISSN: 1552454X     Source Type: Journal    
DOI: 10.1177/1087057114566803     Document Type: Review

References (98)

1. Wender P. A., Mitchell D. J., Pattabiraman K., et al. The Design, Synthesis, and Evaluation of Molecules That Enable or Enhance Cellular Uptake: Peptoid Molecular Transporters. Proc. Natl. Acad. Sci. U.S.A. 2000 ; 97: 13003-13008
2. Giordano R. J., Cardó-Vila M., Salameh A., et al. From Combinatorial Peptide Selection to Drug Prototype (I): Targeting the Vascular Endothelial Growth Factor Receptor Pathway. Proc. Natl. Acad. Sci. U.S.A. 2010 ; 107: 5112-5117
3. Turner J. P., Lutz-Rechtin T., Moore K. A., et al. Rationally Designed Peptoids Modulate Aggregation of Amyloid-Beta 40. ACS Chem. Neurosci. 2014 ; 5: 552-558
4. Jahnsen R. D., Sandberg-Schaal A., Vissing K. J., et al. Tailoring Cytotoxicity of Antimicrobial Peptidomimetics with High Activity against Multidrug-Resistant Escherichia coli. J. Med. Chem. 2014 ; 57: 2864-2873
5. Mahato R. I., Narang A. S., Thoma L., et al. Emerging Trends in Oral Delivery of Peptide and Protein Drugs. Crit. Rev. Ther. Drug. 2003 ; 20: 153-214
6. Khafagy E. S., Morishita M.. Oral Biodrug Delivery Using Cell-Penetrating Peptide. Adv. Drug Deliv. Rev. 2012 ; 64: 531-539
7. Menegatti S., Hussain M., Naik A. D., et al. mRNA Display Selection and Solid-Phase Synthesis of Fc-Binding Cyclic Peptide Affinity Ligands. Biotechnol. Bioeng. 2013 ; 110: 857-870
8. Meyer S. C., Gaj T., Ghosh I.. Highly Selective Cyclic Peptide Ligands for NeutrAvidin and Avidin Identified by Phage Display. Chem. Biol. Drug Des. 2006 ; 68: 3-10
9. Liskamp R. M. J., Rijkers D. T. S., Kruijtzer J. A. W., et al. Peptides and Proteins as a Continuing Exciting Source of Inspiration for Peptidomimetics. Chembiochem. 2011 ; 12: 1626-1653
10. Lennard K. R., Tavassoli A.. Peptides Come Round: Using SICLOPPS Libraries for Early Stage Drug Discovery. Chemistry. 2014 ; 20: 10608-10614
11. Scott C. P., Abel-Santos E., Wall M., et al. Production of Cyclic Peptides and Proteins In Vivo. Proc. Natl. Acad. Sci. U.S.A. 1999 ; 96: 13638-13643
12. Tavassoli A., Benkovic S. J.. Split-Intein Mediated Circular Ligation Used in the Synthesis of Cyclic Peptide Libraries in E-coli. Nat. Protoc. 2007 ; 2: 1126-1133
13. Wilson D. S., Keefe A. D., Szostak J. W.. The Use of mRNA Display to Select High-Affinity Protein-Binding Peptides. Proc. Natl. Acad. Sci. U.S.A. 2001 ; 98: 3750-3755
14. Yamagishi Y., Shoji I., Miyagawa S., et al. Natural Product-Like Macrocyclic N-Methyl-Peptide Inhibitors against a Ubiquitin Ligase Uncovered from a Ribosome-Expressed De Novo Library. Chem. Biol. 2011 ; 18: 1562-1570
15. Guillen Schlippe Y. V., Hartman M. C. T., Josephson K., et al. In Vitro Selection of Highly Modified Cyclic Peptides That Act as Tight Binding Inhibitors. J. Am. Chem. Soc. 2012 ; 134: 10469-10477
16. Goto Y., Katoh T., Suga H.. Flexizymes for Genetic Code Reprogramming. Nat. Protoc. 2011 ; 6: 779-790
17. Desimmie B. A., Humbert M., Lescrinier E., et al. Phage Display-Directed Discovery of LEDGF/p75 Binding Cyclic Peptide Inhibitors of HIV Replication. Mol. Ther. 2012 ; 20: 2064-2075
18. 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. U.S.A. 2004 ; 101: 15591-15596
19. Kritzer J. A., Hamamichi S., McCaffery J. M., et al. Rapid Selection of Cyclic Peptides That Reduce [Alpha]-Synuclein Toxicity in Yeast and Animal Models. Nat. Chem. Biol. 2009 ; 5: 655-663
20. Ma Z., Hartman M. C.. In Vitro Selection of Unnatural Cyclic Peptide Libraries via mRNA Display. Methods Mol. Biol. 2012 ; 805: 367-390
21. Frost J. R., Smith J. M., Fasan R.. Design, Synthesis, and Diversification of Ribosomally Derived Peptide Macrocycles. Curr. Opin. Struct. Biol. 2013 ; 23: 571-580
22. Satyanarayana M., Vitali F., Frost J. R., et al. Diverse Organo-Peptide Macrocycles via a Fast and Catalyst-Free Oxime/Intein-Mediated Dual Ligation. Chem. Commun. 2012 ; 48: 1461-1463
23. Smith J. M., Hill N. C., Krasniak P. J., et al. Synthesis of Bicyclic Organo-Peptide Hybrids via Oxime/Intein-Mediated Macrocyclization followed by Disulfide Bond Formation. Organ. Biomol. Chem. 2014 ; 12: 1135-1142
24. Lian W. L., Upadhyaya P., Rhodes C. A., et al. Screening Bicyclic Peptide Libraries for Protein-Protein Interaction Inhibitors: Discovery of a Tumor Necrosis Factor-Alpha Antagonist. J. Am. Chem. Soc. 2013 ; 135: 11990-11995
25. Liu T., Joo S. H., Voorhees J. L., et al. Synthesis and Screening of a Cyclic Peptide Library: Discovery of Small-Molecule Ligands against Human Prolactin Receptor. Bioorgan. Med. Chem. 2009 ; 17: 1026-1033
26. Smith G. P.. Filamentous Fusion Phage: Novel Expression Vectors That Display Cloned Antigens on the Virion Surface. Science. 1985 ; 228: 1315-1317
27. Hall P. R., Hjelle B., Njus H., et al. Phage Display Selection of Cyclic Peptides That Inhibit Andes Virus Infection. J. Virol. 2009 ; 83: 8965-8969
28. Takakusagi Y., Kuramochi K., Takagi M., et al. Efficient One-Cycle Affinity Selection of Binding Proteins or Peptides Specific for a Small-Molecule Using a T7 Phage Display Pool. Bioorgan. Med. Chem. 2008 ; 16: 9837-9846
29. Sternberg N., Hoess R. H.. Display of Peptides and Proteins on the Surface of Bacteriophage Lambda. Proc. Natl. Acad. Sci. U.S.A. 1995 ; 92: 1609-1613
30. Efimov V., Nepluev I., Mesyanzhinov V.. Bacteriophage T4 as a Surface Display Vector. Virus Genes. 1995 ; 10: 173-177
31. Pansri P., Jaruseranee N., Rangnoi K., et al. A Compact Phage Display Human scFv Library for Selection of Antibodies to a Wide Variety of Antigens. BMC Biotechnol. 2009 ; 9: 6
32. Sepulveda J., Shoemaker C. B.. Design and Testing of PCR Primers for the Construction of scFv Libraries Representing the Immunoglobulin Repertoire of Rats. J. Immunol. Methods. 2008 ; 332: 92-102
33. Neelakantam B., Sridevi N. V., Shukra A. M., et al. Recombinant Human Antibody Fragment against Tetanus Toxoid Produced by Phage Display. Eur. J. Microbiol Immunol. 2014 ; 4: 45-55
34. Sheng J., Oyler G., Zhou B., et al. Identification and Characterization of a Novel Cell-Penetrating Peptide. Biochem. Biophys. Res. Commun. 2009 ; 382: 236-240
35. Qi H., Lu H., Qiu H.-J., et al. Phagemid Vectors for Phage Display: Properties, Characteristics and Construction. J. Mol. Biol. 2012 ; 417: 129-143
36. Sclavons C., Burtea C., Boutry S., et al. Phage Display Screening for Tumor Necrosis Factor-α-Binding Peptides: Detection of Inflammation in a Mouse Model of Hepatitis. Int. J. Peptides. 2013 ; 2013: 9
37. Timmerman P., Beld J., Puijk W. C., et al. Rapid and Quantitative Cyclization of Multiple Peptide Loops onto Synthetic Scaffolds for Structural Mimicry of Protein Surfaces. Chembiochem. 2005 ; 6: 821-824
38. Angelini A., Cendron L., Chen S., et al. Bicyclic Peptide Inhibitor Reveals Large Contact Interface with a Protease Target. ACS Chem Biol. 2012 ; 7: 817-821
39. Tavassoli A., Benkovic S. J.. Genetically Selected Cyclic-Peptide Inhibitors of AICAR Transformylase Homodimerization. Angew Chem. Int. Edit. 2005 ; 44: 2760-2763
40. Desharnais J., Hwang I., Zhang Y., et al. Design, Synthesis and Biological Evaluation of 10-CF3CO-DDACTHF Analogues and Derivatives as Inhibitors of GAR Tfase and the De Novo Purine Biosynthetic Pathway. Bioorg. Med. Chem. 2003 ; 11: 4511-4521
41. Spurr I. B., Birts C. N., Cuda F., et al. Targeting Tumour Proliferation with a Small-Molecule Inhibitor of AICAR Transformylase Homodimerization. Chembiochem. 2012 ; 13: 1628-1634
42. Miranda E., Nordgren I. K., Male A. L., et al. A Cyclic Peptide Inhibitor of HIF-1 Heterodimerization That Inhibits Hypoxia Signaling in Cancer Cells. J. Am. Chem. Soc. 2013 ; 135: 10418-10425
43. Birts C. N., Nijjar S. K., Mardle C. A., et al. A Cyclic Peptide Inhibitor of C-Terminal Binding Protein Dimerization Links Metabolism with Mitotic Fidelity in Breast Cancer Cells. Chem. Sci. 2013 ; 4: 3046-3057
44. Kinsella T. M., Ohashi C. T., Harder A. G., et al. Retrovirally Delivered Random Cyclic Peptide Libraries Yield Inhibitors of Interleukin-4 Signaling in Human B Cells. J. Biol. Chem. 2002 ; 277: 37512-37518
45. Morimoto J., Hayashi Y., Iwasaki K., et al. Flexizymes: Their Evolutionary History and the Origin of Catalytic Function. Accounts Chem. Res. 2011 ; 44: 1359-1368
46. Shimizu Y., Kanamori T., Ueda T.. Protein Synthesis by Pure Translation Systems. Methods. 2005 ; 36: 299-304
47. Hipolito C. J., Suga H.. Ribosomal Production and In Vitro Selection of Natural Product-Like Peptidomimetics: The FIT and RaPID Systems. Curr. Opin. Chem. Biol. 2012 ; 16: 196-203
48. Kawakami T., Ohta A., Ohuchi M., et al. Diverse Backbone-Cyclized Peptides via Codon Reprogramming. Nat. Chem. Biol. 2009 ; 5: 888-890
49. Katoh T., Goto Y., Reza M. S., et al. Ribosomal Synthesis of Backbone Macrocyclic Peptides. Chem. Commun. (Camb). 2011 ; 47: 9946-9958
50. 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. 2013 ; 18: 3502-3528
51. Kang T. J., Hayashi Y., Suga H.. Synthesis of the Backbone Cyclic Peptide Sunflower Trypsin Inhibitor-1 Promoted by the Induced Peptidyl-tRNA Drop-Off. Angewandte Chemie. 2011 ; 50: 2159-2161
52. Valencia C. A., Cotten S. W., Dong B., et al. mRNA-Display-Based Selections for Proteins with Desired Functions: A Protease-Substrate Case Study. Biotechnol. Prog. 2008 ; 24: 561-569
53. Roberts R. W., Szostak J. W.. RNA-Peptide Fusions for the In Vitro Selection of Peptides and Proteins. Proc. Natl. Acad. Sci. U.S.A. 1997 ; 94: 12297-12302
54. Millward S. W., Fiacco S., Austin R. J., et al. Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity. ACS Chem. Biol. 2007 ; 2: 625-634
55. Smith J. M., Vitali F., Archer S. A., et al. Modular Assembly of Macrocyclic Organo-Peptide Hybrids Using Synthetic and Genetically Encoded Precursors. Angew Chem. Int. Edit. 2011 ; 50: 5075-5080
56. Smith J. M., Frost J. R., Fasan R.. Designer Macrocyclic Organo-Peptide Hybrids Inhibit the Interaction between p53 and HDM2/X by Accommodating a Functional Alpha-Helix. Chem. Commun. 2014 ; 50: 5027-5030
57. Lam K. S., Salmon S. E., Hersh E. M., et al. A New Type of Synthetic Peptide Library for Identifying Ligand-Binding Activity. Nature. 1991 ; 354: 82-84
58. Lam K. S., Lebl M., Krchnak V.. The "One-Bead-One-Compound" Combinatorial Library Method. Chem. Rev. 1997 ; 97: 411-448
59. Lam K. S., Liu R., Miyamoto S., et al. Applications of One-Bead One-Compound Combinatorial Libraries and Chemical Microarrays in Signal Transduction Research. Accounts Chem. Res. 2003 ; 36: 370-377
60. Lebl M., Krchnak V., Sepetov N. F., et al. One-Bead-One-Structure Combinatorial Libraries. Biopolymers. 1995 ; 37: 177-198
61. Liu T., Qian Z. Q., Xiao Q., et al. High-Throughput Screening of One-Bead-One-Compound Libraries: Identification of Cyclic Peptidyl Inhibitors against Calcineurin/NFAT Interaction. ACS Comb. Sci. 2011 ; 13: 537-546
62. Brenner S., Lerner R. A.. Encoded Combinatorial Chemistry. Proc. Natl. Acad. Sci. U.S.A. 1992 ; 89: 5381-5383
63. Nielsen J., Brenner S., Janda K. D.. Synthetic Methods for the Implementation of Encoded Combinatorial Chemistry. J. Am. Chem. Soc. 1993 ; 115: 9812-9813
64. Needels M. C., Jones D. G., Tate E. H., et al. Generation and Screening of Oligonucleotide-Encoded Synthetic Peptide Libraries. Abstr. Pap. Am. Chem. S. 1993 ;:
65. Melkko S., Scheuermann J., Dumelin C. E., et al. Encoded Self-Assembling Chemical Libraries. Nat. Biotechnol. 2004 ; 22: 568-574
66. Halpin D. R., Harbury P. B.. DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution. PLoS Biol. 2004 ; 2: E174
67. Gartner Z. J., Liu D. R.. The Generality of DNA-Templated Synthesis as a Basis for Evolving Non-Natural Small Molecules. J. Am. Chem. Soc. 2001 ; 123: 6961-6963
68. Clark M. A., Acharya R. A., Arico-Muendel C. C., et al. Design, Synthesis and Selection of DNA-Encoded Small-Molecule Libraries. Nat. Chem. Biol. 2009 ; 5: 647-654
69. Buller F., Zhang Y., Scheuermann J., et al. Discovery of TNF Inhibitors from a DNA-Encoded Chemical Library Based on Diels-Alder Cycloaddition. Chem. Biol. 2009 ; 16: 1075-1086
70. Buller F., Steiner M., Frey K., et al. Selection of Carbonic Anhydrase IX Inhibitors from One Million DNA-Encoded Compounds. ACS Chem. Biol. 2011 ; 6: 336-344
71. Mannocci L., Zhang Y., Scheuermann J., et al. High-Throughput Sequencing Allows the identification of Binding Molecules Isolated from DNA-Encoded Chemical Libraries. Proc. Natl. Acad. Sci. U.S.A. 2008 ; 105: 17670-17675
72. Mannocci L., Melkko S., Buller F., et al. Isolation of Potent and Specific Trypsin Inhibitors from a DNA-Encoded Chemical Library. Bioconjug. Chem. 2010 ; 21: 1836-1841
73. Gartner Z. J., Tse B. N., Grubina R., et al. DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles. Science. 2004 ; 305: 1601-1605
74. Kleiner R. E., Dumelin C. E., Tiu G. C., et al. In Vitro Selection of a DNA-Templated Small-Molecule Library Reveals a Class of Macrocyclic Kinase Inhibitors. J. Am. Chem. Soc. 2010 ; 132: 11779-11791
75. Tse B. N., Snyder T. M., Shen Y., et al. Translation of DNA into a Library of 13,000 Synthetic Small-Molecule Macrocycles Suitable for In Vitro Selection. J. Am. Chem. Soc. 2008 ; 130: 15611-15626
76. Daguer J. P., Ciobanu M., Alvarez S., et al. DNA-Templated Combinatorial Assembly of Small Molecule Fragments Amenable to Selection/Amplification Cycles. Chem. Sci. 2011 ; 2: 625-632
77. Ciobanu M., Huang K. T., Daguer J. P., et al. Selection of a Synthetic Glycan Oligomer from a Library of DNA-Templated Fragments against DC-SIGN and Inhibition of HIV gp120 Binding to Dendritic Cells. Chem. Commun. 2011 ; 47: 9321-9323
78. Margulies M., Egholm M., Altman W. E., et al. Genome Sequencing in Microfabricated High-Density Picolitre Reactors. Nature. 2005 ; 437: 376-380
79. Buller F., Steiner M., Scheuermann J., et al. High-Throughput Sequencing for the Identification of Binding Molecules from DNA-Encoded Chemical Libraries. Bioorgan. Med. Chem. Lett. 2010 ; 20: 4188-4192
80. Li X., Liu D. R.. DNA-Templated Organic Synthesis: Nature's Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules. Angewandte Chemie. 2004 ; 43: 4848-4870
81. Giudicessi S. L., Gurevich-Messina L. M., Martinez-Ceron M. C., et al. Friendly Strategy to Prepare Encoded One Bead-One Compound Cyclic Peptide Library. ACS Comb. Sci. 2013 ; 15: 525-529
82. Joo S. H., Xiao Q., Ling Y., et al. High-Throughput Sequence Determination of Cyclic Peptide Library Members by Partial Edman Degradation/Mass Spectrometry. J. Am. Chem. Soc. 2006 ; 128: 13000-13009
83. Xiao Q., Pei D. H.. High-Throughput Synthesis and Screening of Cyclic Peptide Antibiotics. J. Med. Chem. 2007 ; 50: 3132-3137
84. Zhang Y. Y., Zhou S. G., Wavreille A. S., et al. Cyclic Peptidyl Inhibitors of Grb2 and Tensin SH2 Domains Identified from Combinatorial Libraries. J. Comb. Chem. 2008 ; 10: 247-255
85. Liu T., Liu Y., Kao H. Y., et al. Membrane Permeable Cyclic Peptidyl Inhibitors against Human Peptidylprolyl Isomerase Pin1. J. Med. Chem. 2010 ; 53: 2494-2501
86. Hayashi Y., Morimoto J., Suga H.. In Vitro Selection of Anti-Akt2 Thioether-Macrocyclic Peptides Leading to Isoform-Selective Inhibitors. ACS Chem. Biol. 2012 ; 7: 607-613
87. 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. Edit. 2012 ; 51: 3423-3427
88. Tavassoli A., Lu Q., Gam J., et al. Inhibition of HIV Budding by a Genetically Selected Cyclic Peptide Targeting the Gag-TSG101 Interaction. ACS Chem. Biolo. 2008 ; 3: 757-764
89. Cheng L., Naumann T. A., Horswill A. R., et al. Discovery of Antibacterial Cyclic Peptides That Inhibit the ClpXP Protease. Protein Sci. 2007 ; 16: 1535-1542
90. Naumann T. A., Tavassoli A., Benkovic S. J.. Genetic Selection of Cyclic Peptide Dam Methyltransferase Inhibitors. Chembiochem. 2008 ; 9: 194-197
91. Millward S. W., Takahashi T. T., Roberts R. W.. A General Route for Post-Translational Cyclization of mRNA Display Libraries. J. Am. Chem. Soc. 2005 ; 127: 14142-14143
92. Takahashi T. T., Austin R. J., Roberts R. W.. mRNA Display: Ligand Discovery, Interaction Analysis and Beyond. Trends Biochem. Sci. 2003 ; 28: 159-165
93. Li S. W., Millward S., Roberts R.. In Vitro Selection of mRNA Display Libraries Containing an Unnatural Amino Acid. J. Am. Chem. Soc. 2002 ; 124: 9972-9973
94. Ishizawa T., Kawakami T., Reid P. C., et al. TRAP Display: A High-Speed Selection Method for the Generation of Functional Polypeptides. J. Am. Chem. Soc. 2013 ; 135: 5433-5440
95. Kawakami T., Ishizawa T., Fujino T., et al. In Vitro Selection of Multiple Libraries Created by Genetic Code Reprogramming To Discover Macrocyclic Peptides That Antagonize VEGFR2 Activity in Living Cells. ACS Chem. Biol. 2013 ; 8: 1205-1214
96. Kawakami T., Ishizawa T., Murakami H.. Extensive Reprogramming of the Genetic Code for Genetically Encoded Synthesis of Highly N-Alkylated Polycyclic Peptidomimetics. J. Am. Chem. Soc. 2013 ; 135: 12297-12304
97. Heinis C., Rutherford T., Freund S., et al. Phage-Encoded Combinatorial Chemical Libraries Based on Bicyclic Peptides. Nat. Chem. Biol. 2009 ; 5: 502-507
98. Baeriswyl V., Calzavarini S., Gerschheimer C., et al. Development of a Selective Peptide Macrocycle Inhibitor of Coagulation Factor XII toward the Generation of a Safe Antithrombotic Therapy. J. Med. Chem. 2013 ; 56: 3742-3746