Development of next-generation peptide binders using in vitro display technologies and their potential applications

Frontiers in Immunology

Volumn 4, Issue AUG, 2013, Pages

  Wada, Akira ^a  

^a RIKEN   (Japan)

Author keywords

Antibody drug; In vitro display technology; Peptide binder; Peptide therapeutic; Target binding

Indexed keywords

CALMODULIN; STREPTAVIDIN; SYNTHETIC PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE; BINDING AFFINITY; COMBINATORIAL LIBRARY; CRYSTAL STRUCTURE; CYCLIZATION; HUMAN; NONHUMAN; PHAGE DISPLAY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS;

EID: 84883665742     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2013.00224     Document Type: Article

References (55)

1. Clark M. Antibody humanization: a case of the "Emperor's new clothes?" Immunol Today (2000) 21:397-402. doi:10.1016/S0167-5699(00)01680-7
2. Presta LG. Molecular engineering and design of therapeutic antibodies. Curr Opin Immunol (2008) 20:460-70. doi:10.1016/j.coi.2008.06.012
3. Cwirla SE, Balasubramanian P, Duffin DJ, Wagstrom CR, Gates CM, Singer SC, et al. Peptide agonist of the thrombopoietin receptor as potent as the natural cytokine. Science (1997) 276:1696-9. doi:10.1126/science.276.5319.1696
4. Su JL, Lai KP, Chen CA, Yang CY, Chen PS, Chang CC, et al. A novel peptide specifically binding to interleukin-6 receptor (gp80) inhibits angiogenesis and tumor growth. Cancer Res (2005) 65:4827-35. doi:10.1158/0008-5472.CAN-05-0188
5. Hyde-DeRuyscher R, Paige LA, Christensen DJ, Hyde-DeRuyscher N, Lim A, Fredericks ZL, et al. Detection of small-molecule enzyme inhibitors with peptides isolated from phage-displayed combinatorial peptide libraries. Chem Biol (2000) 7:17-25. doi:10.1016/S1074-5521(00)00062-4
6. Welch BD, VanDemark AP, Heroux A, Hill CP, Kay MS. Potent D-peptide inhibitors of HIV-1 entry. Proc Natl Acad Sci U S A (2007) 104:16828-33. doi:10.1073/pnas.0708109104
7. Matsubara T, Onishi A, Saito T, Shimada A, Inoue H, Taki T, et al. Sialic acid-mimic peptides as hemagglutinin inhibitors for anti-influenza therapy. J Med Chem (2010) 53:4441-9. doi:10.1021/jm1002183
8. Whaley SR, English DS, Hu EL, Barbara PF, Belcher AM. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature (2000) 405:665-8. doi:10.1038/35015043
9. Wang S, Humphreys ES, Chung SY, Delduco DF, Lustig SR, Wang H, et al. Peptides with selective affinity for carbon nanotubes. Nat Mater (2003) 2:196-200. doi:10.1038/nmat833
10. Rodi DJ, Janes RW, Sanganee HJ, Holton RA, Wallace BA, Makowski L. Screening of a library of phage-displayed peptides identifies human bcl-2 as a taxol-binding protein. J Mol Biol (1999) 285:197-203. doi:10.1006/jmbi.1998.2303
11. Smith GP, Petrenko VA. Phage display. Chem Rev (1997) 97:391-410. doi:10.1021/cr960065d
12. Hoess RH. Protein design and phage display. Chem Rev (2001) 101:3205-18. doi:10.1021/cr000056b
13. Eisenhardt SU, Schwarz M, Bassler N, Peter K. Subtractive single-chain antibody (scFv) phage-display: tailoring phage-display for high specificity against function-specific conformations of cell membrane molecules. Nat Protoc (2007) 2:3063-73. doi:10.1038/nprot.2007.455
14. Bradbury AR, Sidhu S, Dübel S, McCafferty J. Beyond natural antibodies: the power of in vitro display technologies. Nat Biotechnol (2011) 29:245-54. doi:10.1038/nbt.1791
15. Devlin JJ, Panganiban LC, Devlin PE. Random peptide libraries: a source of specific protein binding molecules. Science (1990) 249:404-6. doi:10.1126/science.2143033
16. Lam KS, Salmon SE, Hersh EM, Hruby VJ, Kazmierski WM, Knapp RJ. A new type of synthetic peptide library for identifying ligand-binding activity. Nature (1991) 354:82-4. doi:10.1038/354082a0
17. Weber PC, Pantoliano MW, Thompson LD. Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin. Biochemistry (1992) 31:9350-4. doi:10.1021/bi00154a004
18. Giebel LB, Cass RT, Milligan DL, Young DC, Arze R, Johnson CR. Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry (1995) 34:15430-5. doi:10.1021/bi00047a006
19. Katz BA. 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 (1995) 34:15421-9. doi:10.1021/bi00047a005
20. Heinis C, Rutherford T, Freund S, Winter G. Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat Chem Biol (2009) 5:502-7. doi:10.1038/nchembio.184
21. Henchey LK, Jochim AL, Arora PS. Contemporary strategies for the stabilization of peptides in the alpha-helical conformation. Curr Opin Chem Biol (2008) 12:692-7. doi:10.1016/j.cbpa.2008.08.019
22. Timmerman P, Shochat SG, Desmet J, Barderas R, Casal JI, Meloen RH, et al. Binding of CDR-derived peptides is mechanistically different from that of high-affinity parental antibodies. J Mol Recognit (2010) 23:59-68. doi:10.1002/jmr.1017
23. Smeenk LE, Dailly N, Hiemstra H, van Maarseveen JH, Timmerman P. Synthesis of water-soluble scaffolds for peptide cyclization, labeling, and ligation. Org Lett (2012) 14:1194-7. doi:10.1021/ol203259a
24. Zahnd C, Amstutz P, Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods (2007) 4:269-79. doi:10.1038/nmeth1003
25. Cotton SW, Zou J, Valencia CA, Liu R. Selection of proteins with desired properties from natural proteome libraries using mRNA display. Nat Protoc (2011) 6:1163-82. doi:10.1038/nprot.2011.354
26. Odegrip R, Coomber D, Eldridge B, Hederer R, Kuhlman PA, Ullman C, et al. CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Proc Natl Acad Sci U S A (2004) 101:2806-10. doi:10.1073/pnas.0400219101
27. Mattheakis LC, Bhatt RR, Dower WJ. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci U S A (1994) 91:9022-6. doi:10.1073/pnas.91.19.9022
28. Lamla T, Erdmann VA. Searching sequence space for high-affinity binding peptides using ribosome display. J Mol Biol (2003) 329:381-8. doi:10.1016/S0022-2836(03)00432-7
29. Wada A, Sawata SY, Ito Y. Ribosome display selection of a metal-binding motif from an artificial peptide library. Biotechnol Bioeng (2008) 101:1102-7. doi:10.1002/bit.21975
30. Hanes J, Schaffitzel C, Knappik A, Plückthun A. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat Biotechnol (2000) 18:1287-92. doi:10.1038/82407
31. Luginbühl B, Kanyo Z, Jones RM, Fletterick RJ, Prusiner SB, Cohen FE, et al. Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J Mol Biol (2006) 363:75-97. doi:10.1016/j.jmb.2006.07.027
32. Binz HK, Amstutz P, Plückthun A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol (2005) 23:1257-68. doi:10.1038/nbt1127
33. Tamaskovic R, Simon M, Stefan N, Schwill M, Plückthun A. Designed ankyrin repeat proteins (DARPins) from research to therapy. Methods Enzymol (2012) 503:101-34. doi:10.1016/B978-0-12-396962-0.00005-7
34. He M, Taussig MJ. Eukaryotic ribosome display with in situ DNA recovery. Nat Methods (2007) 4:281-8. doi:10.1038/nmeth0907-763
35. Douthwaite JA. Eukaryotic ribosome display selection using rabbit reticulocyte lysate. Methods Mol Biol (2012) 805:45-57. doi:10.1007/978-1-61779-379-0_3
36. Ueda T, Kanamori T, Ohashi H. Ribosome display with the PURE technology. Methods Mol Biol (2010) 607:219-25. doi:10.1007/978-1-60327-331-2_18
37. Cho G, Keefe AD, Liu R, Wilson DS, Szostak JW. Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J Mol Biol (2000) 297:309-19. doi:10.1006/jmbi.2000.3571
38. Huang BC, Liu R. Comparison of mRNA-display-based selections using synthetic peptide and natural protein libraries. Biochemistry (2007) 46:10102-12. doi:10.1021/bi700220x
39. Horisawa K, Tateyama S, Ishizaka M, Matsumura N, Takashima H, Miyamoto-Sato E, et al. In vitro selection of Jun-associated proteins using mRNA display. Nucleic Acids Res (2004) 32:e169. doi:10.1093/nar/gnh167
40. Fujimori S, Hirai N, Ohashi H, Masuoka K, Nishikimi A, Fukui Y, et al. Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. Sci Rep (2012) 2:691. doi:10.1038/srep00691
41. Li S, Roberts RW. A novel strategy for in vitro selection of peptide-drug conjugates. Chem Biol (2003) 10:233-9. doi:10.1016/S1074-5521(03)00047-4
42. Millward SW, Fiacco S, Austin RJ, Roberts RW. Design of cyclic peptides that bind protein surfaces with antibody-like affinity. ACS Chem Biol (2007) 2:625-34. doi:10.1021/cb7001126
43. Shimizu Y, Inoue A, Tomaril Y, Suzuki T, Yokogawa T, Nishikawa K, et al. Cell-free translation reconstituted with purified components. Nat Biotechnol (2001) 19:s751-5.
44. Josephson K, Hartman MC, Szostak JW. Ribosomal synthesis of unnatural peptides. J Am Chem Soc (2005) 127:11727-35. doi:10.1021/ja0515809
45. Kajihara D, Abe R, Iijima I, Komiyama C, Sisido M, Hohsaka T. FRET analysis of protein conformational change through position-specific incorporation of fluorescent amino acids. Nat Methods (2006) 3:923-9. doi:10.1038/nmeth945
46. Schlippe YV, Hartman MC, Josephson K, Szostak JW. In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J Am Chem Soc (2012) 134:10469-77. doi:10.1021/ja301017y
47. Patch JA, Barron AE. Mimicry of bioactive peptides via non-natural, sequence-specific peptidomimetic oligomers. Curr Opin Chem Biol (2002) 6:872-7. doi:10.1016/S1367-5931(02)00385-X
48. Sit CS, Yoganathan S, Vederas JC. Biosynthesis of aminovinyl-cysteine-containing peptides and its application in the production of potential drug candidates. Acc Chem Res (2011) 44:261-8. doi:10.1021/ar1001395
49. Baeriswyl V, Heinis C. Polycyclic peptide therapeutics. ChemMedChem (2013) 8:377-84. doi:10.1002/cmdc.201200513
50. Kawakami T, Murakami H, Suga H. Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem Biol (2008) 15:32-42. doi:10.1016/j.chembiol.2007.12.008
51. Yamagishi Y, Shoji I, Miyagawa S, Kawakami T, Katoh T, Goto Y, 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) 18:1562-70. doi:10.1016/j.chembiol.2011.09.013
52. Mochizuki Y, Biyani M, Tsuji-Ueno S, Suzuki M, Nishigaki K, Husimi Y, et al. One-pot preparation of mRNA/cDNA display by a novel and versatile puromycin-linker DNA. ACS Comb Sci (2011) 13:478-85. doi:10.1021/co2000295
53. Ueno S, Yoshida S, Mondal A, Nishina K, Koyama M, Sakata I, et al. In vitro selection of a peptide antagonist of growth hormone secretagogue receptor using cDNA display. Proc Natl Acad Sci U S A (2012) 109:11121-6. doi:10.1073/pnas.1203561109
54. Kondo E, Saito K, Tashiro Y, Kamide K, Uno S, Furuya T, et al. Tumour lineage-homing cell-penetrating peptides as anticancer molecular delivery systems. Nat Commun (2012) 3:951. doi:10.1038/ncomms1952
55. Kondo E, Tanaka T, Miyake T, Ichikawa T, Hirai M, Adachi M, et al. Potent synergy of dual antitumor peptides for growth suppression of human glioblastoma cell lines. Mol Cancer Ther (2008) 7:1461-71. doi:10.1158/1535-7163.MCT-07-2010