Phage-displayed combinatorial peptide libraries in fusion to β-lactamase as reporter for an accelerated clone screening: Potential uses of selected enzyme-linked affinity reagents in downstream applications

Combinatorial Chemistry and High Throughput Screening

Volumn 13, Issue 1, 2010, Pages 75-87

  Shukla, Girja S ^a   Krag, David N ^a  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

Author keywords

lactamase reporter; Accelerated screening; Enzyme linked peptides; Peptide libraries; Phage display

Indexed keywords

BACTERIAL DNA; BETA LACTAMASE; CEPHALOSPORINASE; CYSTEINE; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; HYBRID PROTEIN; NITROCEFIN; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; BACTERIAL GENE; BACTERIUM TRANSFORMATION; BETA LACTAMASE P99 GENE; CELL CULTURE; CELL STRAIN; CELL STRAIN MCF 7; CELL STRAIN SK BR 3; COMBINATORIAL LIBRARY; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SEQUENCE; ENTEROBACTER CLOACAE; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME BINDING; ENZYME LINKED IMMUNOSORBENT ASSAY; ESCHERICHIA COLI; FLUORESCENCE IMAGING; FLUOROMETRY; GENE OVEREXPRESSION; HUMAN; HUMAN CELL; MOLECULAR CLONING; NONHUMAN; PHAGE DISPLAY; PHAGEMID; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; REPORTER GENE; SCREENING; WESTERN BLOTTING;

AMINO ACID SEQUENCE; BASE SEQUENCE; BETA-LACTAMASES; CELL LINE, TUMOR; GENE EXPRESSION; GENETIC VECTORS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PROTEIN BINDING; RECEPTOR, ERBB-2; SEQUENCE ALIGNMENT;

ENTEROBACTER CLOACAE;

EID: 77949822788     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/138620710790218258     Document Type: Article

References (70)

1. Bradbury, A. Display technologies expand their horizons. Trends Biotechnol., 1999, 17, 137-138.
2. de Bruin, R.; Spelt, K.; Mol, J.; Koes, R.; Quattrocchio, F. Selection of high-affinity phage antibodies from phage display libraries. Nat. Biotechnol., 1999, 17, 397-399.
3. Smothers, J.F.; Henikoff, S.; Carter, P. Tech.Sight. Phage display. Affinity selection from biological libraries. Science, 2002, 298, 621-622.
4. Hoogenboom, H.R.; Chames, P. Natural and designer binding sites made by phage display technology. Immunol. Today, 2000, 21, 371-378.
5. Petrenko, V. Evolution of phage display: from bioactive peptides to bioselective nanomaterials. Expert Opin. Drug Deliv., 2008, 5, 825-836.
6. Shukla, G.S.; Krag, D.N. Selection of tumor-targeting agents on freshly excised human breast tumors using a phage display library. Oncol. Rep., 2005, 13, 757-764.
7. Smith, G. P.; Petrenko, V.A. Phage display. Chem. Rev., 1997, 97, 391-410.
8. Paschke, M. Phage display systems and their applications. Appl. Microbiol. Biotechnol., 2006, 70, 2-11.
9. Shukla, G.S.; Krag, D.N. Selective delivery of therapeutic agents for the diagnosis and treatment of cancer. Expert Opin. Biol. Ther., 2006, 6, 39-54.
10. Aina, O.H.; Liu, R.; Sutcliffe, J.L.; Marik, J.; Pan, C.X.; Lam, K.S. From combinatorial chemistry to cancer-targeting peptides. Mol. Pharm., 2007, 4, 631-651.
11. Sidhu, S.S.; Koide, S. Phage display for engineering and analyzing protein interaction interfaces. Curr. Opin. Struct. Biol., 2007, 17, 481-487.
12. Newton, J.; Deutscher, S.L. Phage peptide display. In Handbook of Experimental Pharmacology; Springer Berlin Heidelberg: Berlin, 2008, pp. 145-163.
13. Landon, L.A.; Zou, J.; Deutscher, S.L. Is phage display technology on target for developing peptide-based cancer drugs? Curr. Drug Discov. Technol., 2004, 1, 113-132.
14. Pero, S.C.; Shukla, G.S.; Armstrong, A.L.; Peterson, D.; Fuller, S.P.; Godin, K.; Kingsley-Richards, S.L.; Weaver, D.L.; Bond, J.; Krag, D.N. Identification of a small peptide that inhibits the phosphorylation of ErbB2 and proliferation of ErbB2 overexpressing breast cancer cells. Int. J. Cancer, 2004, 111, 951-960.
15. Taki, T.; Ishikawa, D.; Ogino, K.; Tanaka, M.; Oku, N.; Asai, T.; Popa, I.; Portoukalian, J. A new approach for drug discovery from glycobiology and phage-displayed peptide library technology. Biochim. Biophys. Acta, 2008, 1780, 497-503.
16. Rowley, M.J.; O'Connor, K.; Wijeyewickrema, L. Phage display for epitope determination: a paradigm for identifying receptorligand interactions. Biotechnol. Annu. Rev., 2004, 10, 151-188.
17. Tonikian, R.; Zhang, Y.; Boone, C.; Sidhu, S.S. Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat. Protoc., 2007, 2, 1368-1386.
18. Buckler, D.R.; Park, A.; Viswanathan, M.; Hoet, R.M.; Ladner, R.C. Screening isolates from antibody phage-display libraries. Drug Discov. Today, 2008, 13, 318-324.
19. Kay, B.K.; Kasanov, J.; Yamabhai, M. Screening phage-displayed combinatorial peptide libraries. Methods, 2001, 24, 240-246.
20. Shukla, G.S.; Krag, D.N. Phage display selection for cell-specific ligands: development of a screening procedure suitable for small tumor specimens. J. Drug Target., 2005, 13, 7-18.
21. Kretzschmar, T.; Geiser, M. Evaluation of antibodies fused to minor coat protein III and major coat protein VIII of bacteriophage M13. Gene, 1995, 155, 61-65.
22. Jacoby, G.A.; Munoz-Price, L.S. The new beta-lactamases. N. Engl. J. Med., 2005, 352, 380-391.
23. Hribar, G.; Smilovic, V.; Zupan, A.L.; Gaberc-Porekar, V. Beta-lactamase reporter system for selecting high-producing yeast clones. Biotechniques, 2008, 44, 477-484.
24. Campbell, R.E. Realization of beta-lactamase as a versatile fluorogenic reporter. Trends Biotechnol., 2004, 22, 208-211.
25. Qureshi, S.A. Beta-lactamase: an ideal reporter system for monitoring gene expression in live eukaryotic cells. Biotechniques, 2007, 42, 91-96.
26. Siemers, N.O.; Kerr, D.E.; Yarnold, S.; Stebbins, M.R.; Vrudhula, V.M.; Hellstrom, I.; Hellstrom, K.E.; Senter, P.D. Construction, expression, and activities of L49-sFv-beta-lactamase, a single-chain antibody fusion protein for anticancer prodrug activation. Bioconjug. Chem., 1997, 8, 510-519.
27. Harding, F.A.; Liu, A.D.; Stickler, M.; Razo, O.J.; Chin, R.; Faravashi, N.; Viola, W.; Graycar, T.; Yeung, V.P.; Aehle, W.; Meijer, D.; Wong, S.; Rashid, M.H.; Valdes, A.M.; Schellenberger, V. A beta-lactamase with reduced immunogenicity for the targeted delivery of chemotherapeutics using antibody-directed enzyme prodrug therapy. Mol. Cancer Ther., 2005, 4, 1791-1800.
28. Gschwind, A.; Fischer, O.M.; Ullrich, A. The discovery of receptor tyrosine kinases: targets for cancer therapy. Nat. Rev. Cancer, 2004, 4, 361-370.
29. Shukla, G.S.; Murray, C.J.; Estabrook, M.; Shen, G.P.; Schellenberger, V.; Krag, D.N. Towards a ligand targeted enzyme prodrug therapy: single round panning of a beta-lactamase scaffold library on human cancer cells. Int. J. Cancer, 2007, 120, 2233-2242.
30. Cwirla, S.E.; Peters, E.A.; Barrett, R.W.; Dower, W.J. Peptides on phage: a vast library of peptides for identifying ligands. Proc. Natl. Acad. Sci. USA, 1990, 87, 6378-6382.
31. Kristensen, P.; Winter, G. Proteolytic selection for protein folding using filamentous bacteriophages. Fold. Des., 1998, 3, 321-328.
32. Hayashi, N.; Kipriyanov, S.; Fuchs, P.; Welschof, M.; Dorsam, H.; Little, M. A single expression system for the display, purification and conjugation of single-chain antibodies. Gene, 1995, 160, 129-130.
33. Duez, C.; Frere, J.M.; Ghuysen, J.M.; Van Beeumen, J.; Delcambe, L.; Dierickx, L. Purification and properties of the exocellular beta-lactamase of Actinomadura strain R39. Biochim. Biophys. Acta, 1982, 700, 24-32.
34. Rigoutsos, I.; Floratos, A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 1998, 14, 55-67.
35. Mandava, S.; Makowski, L.; Devarapalli, S.; Uzubell, J.; Rodi, D.J. RELIC-a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics, 2004, 4, 1439-1460.
36. Shukla, G.S.; Krag, D.N. Developing bifunctional ß-lactamase molecules with built-in target-recognizing module for prodrug therapy: Identification of Enterobacter cloacae P99 cephalosporinase loops suitable for randomization and phage-display selection. J. Mol. Recognit., 2009, 22, 425-436.
37. Steiner, D.; Forrer, P.; Stumpp, M.T.; Pluckthun, A. Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat. Biotechnol., 2006, 24, 823-831.
38. Rodi, D.J.; Soares, A.S.; Makowski, L. Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries. J. Mol. Biol., 2002, 322, 1039-1052.
39. Yamane, K.; Mizushima, S. Introduction of basic amino acid residues after the signal peptide inhibits protein translocation across the cytoplasmic membrane of Escherichia coli. Relation to the orientation of membrane proteins. J. Biol. Chem., 1988, 263, 19690-19696.
40. Peters, E.A.; Schatz, P.J.; Johnson, S.S.; Dower, W.J. Membrane insertion defects caused by positive charges in the early mature region of protein pIII of filamentous phage fd can be corrected by prlA suppressors. J. Bacteriol., 1994, 176, 4296-4305.
41. Pluckthun, A.; Knowles, J.R. The consequences of stepwise deletions from the signal-processing site of beta-lactamase. J. Biol. Chem., 1987, 262, 3951-3957.
42. Barkocy-Gallagher, G.A.; Cannon, J.G.; Bassford, P.J., Jr. Beta-turn formation in the processing region is important for efficient maturation of Escherichia coli maltose-binding protein by signal peptidase I in vivo. J. Biol. Chem., 1994, 269, 13609-13613.
43. Nilsson, I.; von Heijne, G. A signal peptide with a proline next to the cleavage site inhibits leader peptidase when present in a sec-independent protein. FEBS Lett., 1992, 299, 243-246.
44. Shukla, G.S.; Krag, D.N. A sensitive and rapid chemiluminescence ELISA for filamentous bacteriophages. J. Immunoassay Immunochem., 2005, 26, 89-95.
45. Wright, R. M.; Dudas, D.; Gavin, B.; Dottavio, D.; Hexham, J. M.; Lake, P. A high-capacity alkaline phosphatase reporter system for the rapid analysis of specificity and relative affinity of peptides from phage-display libraries. J. Immunol. Methods, 2001, 253, 223-232.
46. Han, Z.; Karatan, E.; Scholle, M.D.; McCafferty, J.; Kay, B. K. Accelerated screening of phage-display output with alkaline phosphatase fusions. Comb. Chem. High Throughput Screen., 2004, 7, 55-62.
47. Gonzalez-Techera, A.; Umpierrez-Failache, M.; Cardozo, S.; Obal, G.; Pritsch, O.; Last, J. A.; Gee, S. J.; Hammock, B.D.; Gonzalez-Sapienza, G. High-throughput method for ranking the affinity of peptide ligands selected from phage display libraries. Bioconjug. Chem., 2008, 19, 993-1000.
48. Berezov, A.; Chen, J.; Liu, Q.; Zhang, H.T.; Greene, M.I.; Murali, R. Disabling receptor ensembles with rationally designed interface peptidomimetics. J. Biol. Chem., 2002, 277, 28330-28339.
49. Roskoski, R., Jr. The ErbB/HER receptor protein-tyrosine kinases and cancer. Biochem. Biophys. Res. Commun., 2004, 319, 1-11.
50. Griep, R.A.; van Twisk, C.; van der Wolf, J.M.; Schots, A. Fluobodies: green fluorescent single-chain Fv fusion proteins. J. Immunol. Methods, 1999, 230, 121-130.
51. Morino, K.; Katsumi, H.; Akahori, Y.; Iba, Y.; Shinohara, M.; Ukai, Y.; Kohara, Y.; Kurosawa, Y. Antibody fusions with fluorescent proteins: a versatile reagent for profiling protein expression. J. Immunol. Methods, 2001, 257, 175-184.
52. Alting-Mees, M.A.; Risseeuw, E.P.; Liu, E.; Desautels, M.; Crosby, W.A.; Hemmingsen, S.M. Intracellular expression of recombinant antibody fluorescent protein fusions for localization of target antigens in Schizosaccharomyces pombe. Methods Mol. Biol., 2006, 313, 97-105.
53. Chuman, Y.; Uren, A.; Cahill, J.; Regan, C.; Wolf, V.; Kay, B.K.; Rubin, J.S. Identification of a peptide binding motif for secreted frizzled-related protein-1. Peptides, 2004, 25, 1831-1838.
54. Kuhne, S.A.; Hawes, W.S.; La Ragione, R.M.; Woodward, M.J.; Whitelam, G.C.; Gough, K.C. Isolation of recombinant antibodies against EspA and intimin of Escherichia coli O157:H7. J. Clin. Microbiol., 2004, 42, 2966-2976.
55. Velappan, N.; Martinez, J.S.; Valero, R.; Chasteen, L.; Ponce, L.; Bondu-Hawkins, V.; Kelly, C.; Pavlik, P.; Hjelle, B.; Bradbury, A.R. Selection and characterization of scFv antibodies against the Sin Nombre hantavirus nucleocapsid protein. J. Immunol. Methods, 2007, 321, 60-69.
56. El-Mousawi, M.; Tchistiakova, L.; Yurchenko, L.; Pietrzynski, G.; Moreno, M.; Stanimirovic, D.; Ahmad, D.; Alakhov, V. A vascular endothelial growth factor high affinity receptor 1-specific peptide with antiangiogenic activity identified using a phage display peptide library. J. Biol. Chem., 2003, 278, 46681-46691.
57. O'Callaghan, C.H.; Morris, A.; Kirby, S.M.; Shingler, A.H. Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate. Antimicrob. Agents Chemother., 1972, 1, 283-288.
58. Jones, R.N.; Wilson, H.W.; Novick, W.J., Jr.; Barry, A.L.; Thornsberry, C. In vitro evaluation of CENTA, a new beta-lactamase-susceptible chromogenic cephalosporin reagent. J. Clin. Microbiol., 1982, 15, 954-958.
59. Gao, W.; Xing, B.; Tsien, R.Y.; Rao, J. Novel fluorogenic substrates for imaging beta-lactamase gene expression. J. Am. Chem. Soc., 2003, 125, 11146-11147.
60. Xing, B.; Khanamiryan, A.; Rao, J. Cell-permeable near-infrared fluorogenic substrates for imaging beta-lactamase activity. J. Am. Chem. Soc., 2005, 127, 4158-4159.
61. Zlokarnik, G.; Negulescu, P.A.; Knapp, T.E.; Mere, L.; Burres, N.; Feng, L.; Whitney, M.; Roemer, K.; Tsien, R.Y. Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. Science, 1998, 279, 84-88.
62. Cartwright, S.J.; Waley, S. G. Purification of beta-lactamases by affinity chromatography on phenylboronic acid-agarose. Biochem. J., 1984, 221, 505-512.
63. Svensson, H.P.; Vrudhula, V.M.; Emswiler, J.E.; MacMaster, J.F.; Cosand, W. L.; Senter, P.D.; Wallace, P.M. In vitro and in vivo activities of a doxorubicin prodrug in combination with monoclonal antibody beta-lactamase conjugates. Cancer Res., 1995, 55, 2357-2365.
64. Vrudhula, V.M.; Kerr, D.E.; Siemers, N.O.; Dubowchik, G.M.; Senter, P.D. Cephalosporin prodrugs of paclitaxel for immunologically specific activation by L-49-sFv-beta-lactamase fusion protein. Bioorg. Med. Chem. Lett., 2003, 13, 539-542.
65. Hanessian, S.; Wang, J. Design and synthesis of a cephalosporincarboplatinum prodrug activable by a β-lactamase. Can. J. Chem., 1993, 71, 896-906.
66. Kerr, D.E.; Schreiber, G.J.; Vrudhula, V.M.; Svensson, H.P.; Hellstrom, I.; Hellstrom, K.E.; Senter, P.D. Regressions and cures of melanoma xenografts following treatment with monoclonal antibody beta-lactamase conjugates in combination with anticancer prodrugs. Cancer Res., 1995, 55, 3558-3563.
67. Meyer, D.L.; Jungheim, L.N.; Law, K.L.; Mikolajczyk, S.D.; Shepherd, T.A.; Mackensen, D.G.; Briggs, S.L.; Starling, J.J. Sitespecific prodrug activation by antibody-beta-lactamase conjugates: regression and long-term growth inhibition of human colon carcinoma xenograft models. Cancer Res., 1993, 53, 3956-3963.
68. Vrudhula, V.M.; Svensson, H.P.; Kennedy, K.A.; Senter, P.D.; Wallace, P.M. Antitumor activities of a cephalosporin prodrug in combination with monoclonal antibody-beta-lactamase conjugates. Bioconjug. Chem., 1993, 4, 334-340.
69. Vrudhula, V.M.; Svensson, H.P.; Senter, P.D. Cephalosporin derivatives of doxorubicin as prodrugs for activation by monoclonal antibody-beta-lactamase conjugates. J. Med. Chem., 1995, 38, 1380-1385.
70. Yao, H.; So, M.K.; Rao, J. A bioluminogenic substrate for in vivo imaging of beta-lactamase activity. Angew. Chem. Int. Ed. Engl., 2007, 46, 7031-7034.