Protease-resistant peptide ligands from a knottin scaffold library

ACS Chemical Biology

Volumn 6, Issue 8, 2011, Pages 837-844

  Getz, Jennifer A ^a,b   Rice, Jeffrey J ^a,b   Daugherty, Patrick S ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN; EPITOPE; KNOTTIN; LIGAND; MOLECULAR SCAFFOLD; PEPTIDE; PROTEINASE; TRYPSIN;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; DISULFIDE BOND; ENZYME ACTIVITY; ESCHERICHIA COLI; FLUORESCENCE ACTIVATED CELL SORTING; INCUBATION TIME; MOLECULAR LIBRARY; NONHUMAN; PRIORITY JOURNAL; PROTEIN STABILITY;

AMINO ACID SEQUENCE; ANTITHROMBINS; CATALYTIC DOMAIN; CYCLOTIDES; CYSTINE KNOT MOTIFS; CYSTINE-KNOT MINIPROTEINS; ESCHERICHIA COLI; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PEPTIDE LIBRARY; THROMBIN;

EID: 80052005787     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb200039s     Document Type: Article

References (52)

1. Pichereau, C. and Allary, C. (2005) Therapeutic peptides under the spotlight Eur. Biopharm. Rev. 88-91
2. Sato, A. K., Viswanathan, M., Kent, R. B., and Wood, C. R. (2006) Therapeutic peptides: technological advances driving peptides into development Curr. Opin. Biotechnol. 17, 638-642 (Pubitemid 44791908)
3. Werle, M. and Bernkop-Schnürch, A. (2006) Strategies to improve plasma half life time of peptide and protein drugs Amino Acids 30, 351-367 (Pubitemid 43886897)
4. McGregor, D. P. (2008) Discovering and improving novel peptide therapeutics Curr. Opin. Pharm. 8, 616-619
5. Stromstedt, A. A., Pasupuleti, M., Schmidtchen, A., and Malmsten, M. (2009) Evaluation of strategies for improving proteolytic resistance of antimicrobial peptides by using variants of EFK17, an internal segment of LL-37 Antimicrob. Agents Chemother. 53, 593-602
6. Clark, R. J., Fischer, H., Dempster, L., Daly, N. L., Rosengren, K. J., Nevin, S. T., Meunier, F. A., Adams, D. J., and Craik, D. J. (2005) Engineering stable peptide toxins by means of backbone cyclization: Stabilization of the α-conotoxin MII Proc. Natl. Acad. Sci. U.S.A. 102, 13767-13772 (Pubitemid 41377653)
7. Harris, A. G. (1994) Somatostatin and somatostatin analogues: pharmacokinetics and pharmacodynamic effects Gut 35, S1-S4 (Pubitemid 24157987)
8. Tang, Y. and Tirrell, D. A. (2001) Biosynthesis of a highly stable coiled-coil protein containing hexafluoroleucine in an engineered bacterial host J. Am. Chem. Soc. 123, 11089-11090 (Pubitemid 33042035)
9. Ramon, J., Saez, V., Baez, R., Aldana, R., and Hardy, E. (2005) PEGylated interferon-2b: A branched 40K polyethylene glycol derivative Pharm. Res. 22, 1375-1387
10. Nygren, P. and Skerra, A. (2004) Binding proteins from alternative scaffolds J. Immunol. Methods 290, 3-28 (Pubitemid 38922856)
11. Chiche, L., Heitz, A., Gelly, J. C., Gracy, J., Chau, P. T. T., Ha, P. T., Hernandez, J. F., and Le-Nguyen, D. (2004) Squash inhibitors: from structural motifs to macrocyclic knottins Curr. Protein Peptide Sci. 5, 341-349 (Pubitemid 39200164)
12. Christmann, A., Walter, K., Wentzel, A., Kratzner, R., and Kolmar, H. (1999) The cystine knot of a squash-type protease inhibitor as a structural scaffold for Escherichia coli cell surface display of conformationally constrained peptides Protein Eng. Des. Sel. 12, 797-806 (Pubitemid 29472087)
13. Krause, S., Schmoldt, H. U., Wentzel, A., Ballmaier, M., Friedrich, K., and Kolmar, H. (2006) Grafting of thrombopoietin-mimetic peptides into cystine knot miniproteins yields high-affinity thrombopoietin antagonists and agonists FEBS J. 274, 86-95 (Pubitemid 44952900)
14. Gunasekera, S., Foley, F. M., Clark, R. J., Sando, L., Fabri, L. J., Craik, D. J., and Daly, N. L. (2008) Engineering stabilized vascular endothelial growth factor-A antagonists: Synthesis, structural characterization, and bioactivity of grafted analogues of cyclotides J. Med. Chem. 51, 7697-7704
15. 3 integrin with antibody-like affinities J. Mol. Biol. 385, 1064-1075
16. Markland, W., Ley, A. C., and Ladner, R. C. (1996) Iterative optimization of high-affinity protease inhibitors using phage display. 2. Plasma kallikrein and thrombin Biochemistry 35, 8058-8067 (Pubitemid 26202548)
17. Markland, W., Ley, A. C., Lee, S. W., and Ladner, R. C. (1996) Iterative optimization of high-affinity proteases inhibitors using phage display. 1. Plasmin Biochemistry 35, 8045-8057 (Pubitemid 26202547)
18. Kiczak, L., Kasztura, M., Koscielska-Kasprzak, K., Dadlez, M., and Otlewski, J. (2001) Selection of potent chymotrypsin and elastase inhibitors from M13 phage library of basic pancreatic trypsin inhibitor (BPTI) Biochim. Biophys. Acta 1550, 153-163 (Pubitemid 34038001)
19. Roberts, B. L., Markland, W., Ley, A. C., Kent, R. B., White, D. W., Guterman, S. K., and Ladner, R. C. (1992) Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage Proc. Natl. Acad. Sci. U.S.A. 89, 2429-2433
20. Lehmann, A. (2008) Ecallantide (DX-88), a plasma kallikrein inhibitor for the treatment of hereditary angioedema and the prevention of blood loss in on-pump cardiothoracic surgery Expert Opin. Biol. Ther. 8, 1187-1199
21. Werle, M., Schmitz, T., Huang, H. L., Wentzel, A., Kolmar, H., and Bernkop-Schnürch, A. (2006) The potential of cystine-knot microproteins as novel pharmacophoric scaffolds in oral peptide drug delivery J. Drug Targeting 14, 137-146 (Pubitemid 43878822)
22. Zheng, K., Lubman, D. M., Rossi, D. T., Nordblom, G. D., and Barksdale, C. M. (2000) Elucidation of peptide metabolism by on-line immunoaffinity liquid chromatography mass spectrometry Rapid Commun. Mass Spectrom. 14, 261-269 (Pubitemid 30100852)
23. Werle, M., Kafedjiiski, K., Kolmar, H., and Bernkop-Schnürch, A. (2007) Evaluation and improvement of the properties of the novel cystine-knot microprotein McoEeTI for oral administration Int. J. Pharm. 332, 72-79 (Pubitemid 46227767)
24. Colgrave, M. L. and Craik, D. J. (2004) Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot Biochemistry 43, 5965-5975 (Pubitemid 38669464)
25. Rosengren, K. J., Daly, N. L., Plan, M. R., Waine, C., and Craik, D. J. (2003) Twists, knots, and rings in proteins. Structural definition of the cyclotide framework J. Biol. Chem. 278, 8606-8616 (Pubitemid 36800615)
26. Daly, N. L. and Craik, D. J. (2000) Acyclic permutants of naturally occurring cyclic proteins J. Biol. Chem. 275, 19068-19075
27. Rice, J. J. and Daugherty, P. S. (2008) Directed evolution of a biterminal bacterial display scaffold enhances the display of diverse peptides Protein Eng. Des. Sel. 21, 435-442 (Pubitemid 351882133)
28. Kenrick, S. A. and Daugherty, P. S. (2010) Bacterial display enables efficient and quantitative peptide affinity maturation Protein Eng. Des. Sel. 23, 9-17
29. Patrick, W. M., Firth, A. E., and Blackburn, J. M. (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries Protein Eng. Des. Sel. 16, 451-457 (Pubitemid 36917359)
30. Boder, E. T. and Wittrup, K. D. (1998) Optimal screening of surface-displayed polypeptide libraries Biotechnol. Prog. 14, 55-62 (Pubitemid 28118264)
31. Georgiou, G. and Segatori, L. (2005) Preparative expression of secreted proteins in bacteria: status report and future prospects Curr. Opin. Biotechnol. 16, 538-545 (Pubitemid 41393835)
32. Bode, W., Turk, D., and Karshikov, A. (1992) The refined 1.9-angstrom X-ray crystal-structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin Protein Sci. 1, 426-471
33. Paborsky, L. R., McCurdy, S. N., Griffin, L. C., Toole, J. J., and Leung, L. L. (1993) The single-stranded DNA aptamer-binding site of human thrombin J. Biol. Chem. 268, 20808-20811 (Pubitemid 23292253)
34. Petrera, N. S., Stafford, A. R., Leslie, B. A., Kretz, C. A., Fredenburgh, J. C., and Weitz, J. I. (2009) Long range communication between exosites 1 and 2 modulates thrombin function J. Biol. Chem. 284, 25620-25629
35. Parry, M. A. A., Maraganore, J. M., and Stone, S. R. (1994) Kinetic mechanism for the interaction of hirulog with thrombin Biochemistry 33, 14807-14814
36. Souriau, C., Chiche, L., Irving, R., and Hudson, P. (2005) New binding specificities derived from Min-23, a small cystine-stabilized peptidic scaffold Biochemistry 44, 7143-7155 (Pubitemid 40656659)
37. Warkentin, T. E. (2004) Bivalent direct thrombin inhibitors: hirudin and bivalirudin Best Pract. Res., Clin. Haematol. 17, 105-125 (Pubitemid 38780070)
38. Maritz-Olivier, C., Stutzer, C., Jongejan, F., Neitz, A. W. H., and Gaspar, A. R. M. (2007) Tick anti-hemostatics: targets for future vaccines and therapeutics Trends Parasitol. 23, 397-407 (Pubitemid 47268890)
39. Macedo-Ribeiro, S., Almeida, C., Calisto, B. M., Friedrich, T., Mentele, R., Sturzebecher, J., Fuentes-Prior, P., and Pereira, P. J. B. (2008) Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick PLoS One 3, e1624
40. Maraganore, J. M., Bourdon, P., Jablonski, J., Ramachandran, K. L., and Fenton, J. W. (1990) Design and characterization of hirulogs: a novel class of bivalent peptide inhibitors of thrombin Biochemistry 29, 7095-7101 (Pubitemid 20241158)
41. Clark, R. J., Daly, N. L., and Craik, D. J. (2006) Structural plasticity of the cyclic-cystine-knot framework: implications for biological activity and drug design Biochem. J. 394, 85-93 (Pubitemid 43259658)
42. Simonsen, S. M., Sando, L., Rosengren, K. J., Wang, C. K., Colgrave, M. L., Daly, N. L., and Craik, D. J. (2008) Alanine scanning mutagenesis of the prototypic cyclotide reveals a cluster of residues essential for bioactivity J. Biol. Chem. 283, 9805-9813
43. Iwai, H. and Plückthun, A. (1999) Circular β-lactamase: stability enhancement by cyclizing the backbone FEBS Lett. 459, 166-172 (Pubitemid 29475024)
44. Daugherty, P. S. (2007) Protein engineering with bacterial display Curr. Opin. Struct. Biol. 17, 474-480 (Pubitemid 47451767)
45. Gai, S. A. and Wittrup, K. D. (2007) Yeast surface display for protein engineering and characterization Curr. Opin. Struct. Biol. 17, 467-473 (Pubitemid 47454774)
46. Guzman, L. M., Belin, D., Carson, M. J., and Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter J. Bacteriol. 177, 4121-4130
47. Casadaban, M. J. and Cohen, S. N. (1980) Analysis of gene control signals by DNA fusion and cloning in Escherichia coli J. Mol. Biol. 138, 179-207 (Pubitemid 10044378)
48. Kenrick, S., Rice, J., and Daugherty, P. (2007) Flow cytometric sorting of bacterial surface-displayed libraries Curr. Protoc. Cytometry 42, 4.6.1-4.6.27
49. Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., and Toole, J. J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin Nature 355, 564-566
50. Daly, N. L., Love, S., Alewood, P. F., and Craik, D. J. (1999) Chemical synthesis and folding pathways of large cyclic polypeptides: studies of the cystine knot polypeptide kalata B1 Biochemistry 38, 10606-10614
51. Copeland, R. A. (2000) Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis, 2 nd ed., Wiley-VCH, New York.
52. Boulware, K. T. and Daugherty, P. S. (2006) Protease specificity determination by using cellular libraries of peptide substrates (CLiPS) Proc. Natl. Acad. Sci. U.S.A. 103, 7583-7588