Use of phage display technology for the determination of the targets for small-molecule therapeutics

Expert Opinion on Drug Discovery

Volumn 5, Issue 4, 2010, Pages 361-389

  Takakusagi, Yoichi ^a   Takakusagi, Kaori ^a   Sugawara, Fumio ^a   Sakaguchi, Kengo ^a  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

Bioinformatics; Peptide; Phage display; Small molecule

Indexed keywords

PEPTIDE DERIVATIVE;

DRUG SCREENING; DRUG TARGETING; MOLECULAR LIBRARY; PHAGE DISPLAY; PRIORITY JOURNAL; REVIEW; TECHNOLOGY;

EID: 77950283408     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460441003653155     Document Type: Review

References (100)

1. Yang Y, Adelstein SJ, Kassis AI. Target discovery from data mining approaches. Drug Discov Today 2009;14:147-154
2. Osada H. Protein targeting with small molecules: chemical biology techniques and applications. Wiley 2009
3. Sioud M. Target discovery and validation reviews and protocols: emerging strategies for targets and biomarker discovery (Volume 1: Methods in molecular biology). New Jersey: Humana Press; 2006
4. Sioud M. Target discovery and validation reviews and protocols: emerging molecular targets and treatment options (Volume 2: Methods in molecular biology). New Jersey: Humana Press 2007
5. Gregory PT, Randall WK. Target identification strategies in chemical genetics. Comb Chem High Throughput Screen 2004;7:677-688
6. Butcher SP. Target discovery and validation in the post-genomic era. Neurochem Res 2003;28:367-371
7. Harding MW, Galat A, Uehling DE, et al. A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature 1989;341:758-760
8. Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 1985;228:1315-1317
9. Smith GP, Petrenko VA. Phage Display. Chem Rev 1997;97:391-410
10. Mao C, Liu A, Cao B. Virus-based chemical and biological sensing. Angew Chem Int Ed Engl 2009;48:6790-6810
11. Krumpe LR, Mori T. Potential of phage-displayed peptide library technology to identify functional targeting peptides. Expert Opin Drug Discov 2007;2:525-537
12. Jung HJ, Kwon HJ. Chemical genomics with natural products. J Microbiol Biotechnol 2006;16:651-659
13. Krumpe LR, Mori T. The use of phage-displayed peptide libraries to develop tumor-targeting drugs. Int J Pept Res Ther 2006;12:79-91
14. Paschke M. Phage display systems and their applications. Appl Microbiol Biotechnol 2006;70:2-11
15. Sidhu SS. Phage display in biotechnology and drug discovery. CRC Press; 2005
16. Szardenings M. Phage display of random peptide libraries: applications, limits, and potential. J Recept Signal Transduct Res 2003;23:307-349
17. Barbas III CF, Burton DR, Scott JK, et al. Phage display a laboratory manual. Cold Spring Harbor Laboratory Press; 2001
18. Sidhu SS. Phage display in pharmaceutical biotechnology. Curr Opin Biotechnol 2000;11:610-616
19. Rodi DJ, Makowski L. Phage-display technology-finding a needle in a vast molecular haystack. Curr Opin Biotechnol 1999;10:87-93
20. Kay BK, Winter J, McCafferty J. Phage display of peptides and proteins a laboratory manual. Academic Press, San Diego; 1996
21. Castagnoli L, Zucconi A, Quondam M, et al. Alternative bacteriophage display systems. Comb Chem High Throughput Screen 2001;4:121-133
22. Yamamoto M, Kominato Y, Yamamoto F. Phage display cDNA cloning of protein with carbohydrate affinity. Biochem Biophys Res Commun 1999;255:194-199
23. Santini C, Brennan D, Mennuni C, et al. Efficient display of an HCV cDNA expression library as C-terminal fusion to the capsid protein D of bacteriophage lambda. J Mol Biol 1998;282:125-135
24. Jespers LS, De Keyser A, Stanssens PE. LambdaZLG6: a phage lambda vector for high-efficiency cloning and surface expression of cDNA libraries on filamentous phage. Gene 1996;173:179-181
25. Rosenberg A, Griffin K, Studier FW, et al. T7Select phage display system: a powerful new protein display system based on bacteriophage T7. Novations, Newsletter of Novagen, Inc. 1996;6:1-6
26. Novagen. T7Select®System Manual. TB178 2009;Rev. C 1009JN
27. Novagen. OrientExpressTM cDNA Manual. TB247 2009;Rev. B 1109JN
28. Krumpe LR, Atkinson AJ, Smythers GW, et al. T7 lytic phage-displayed peptide libraries exhibit less sequence bias than M13 filamentous phage-displayed peptide libraries. Proteomics 2006;6:4210-4222
29. Takakusagi Y, Ohta K, Kuramochi K, et al. Synthesis of a biotinylated camptothecin derivative and determination of the binding sequence by T7 phage display technology. Bioorg Med Chem Lett 2005;15:4846-4849
30. McKenzie KM, Videlock EJ, Splittgerber U, et al. Simultaneous identification of multiple protein targets by using complementary-DNA phage display and a natural-product-mimetic probe. Angew Chem Int Ed Engl 2004;43:4052-4055
31. Takakusagi Y, Takakusagi K, Sugawara F, et al. Validation of small-molecule/protein interactions by the T7 phage display strategy using a quartz-crystal microbalance device. Tanpakushitsu Kakusan Koso 2009;54:1203-1209
32. Takakusagi Y, Suzuki A, Sugawara F, et al. Self-assembled monolayer (SAM) of small organic molecule for efficient random-peptide phage display selection using a cuvette type quartz-crystal micobalance (QCM) device. World J Engineering 2009. In press
33. Nishiyama K, Takakusagi Y, Kusayanagi T, et al. Identification of trimannoside-recognizing peptide sequences from a T7 phage display screen using a QCM device. Bioorg Med Chem 2009;17:195-202
34. 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. Bioorg Med Chem 2008;16:9837-9846
35. Takakusagi Y, Kuroiwa Y, Sugawara F, et al. Identification of a methotrexate-binding peptide from a T7 phage display screen using a QCM device. Bioorg Med Chem 2008;16:7410-7414
36. Takakusagi Y, Takakusagi K, Kuramochi K, et al. Identification of C10 biotinylated camptothecin (CPT-10-B) binding peptides using T7 phage display screen on a QCM device. Bioorg Med Chem 2007;15:7590-7598
37. Piggott AM, Karuso P. Quality not quantity: the role of marine natural products in drug discovery and reverse chemical proteomics. Mar Drugs 2005;3:36-63
38. Sche PP, McKenzie KM, White JD, et al. Display cloning: functional identification of natural product receptors using cDNA-phage display. Chem Biol 1999;6:707-716
39. Morohashi K, Arai T, Saito S, et al. A high-throughput phage display screening method using a combination of real-time PCR and affinity chromatography. Comb Chem High Throughput Screen 2006;9:55-61
40. Kuramochi K, Miyano Y, Enomoto Y, et al. Identification of small molecule binding molecules by affinity purification using a specific ligand immobilized on PEGA resin. Bioconjug Chem 2008;19:2417-2426
41. Aoki S, Morohashi K, Sunoki T, et al. Screening of paclitaxel-binding molecules from a library of random peptides displayed on T7 phage particles using paclitaxel-photoimmobilized resin. Bioconjug Chem 2007;18:1981-1986
42. Johnson KM, Chen X, Boitano A, et al. Identification and validation of the mitochondrial F1F0-ATPase as the molecular target of the immunomodulatory benzodiazepine Bz-423. Chem Biol 2005;12:485-496
43. Cooper MA, Singleton VT. A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions. J Mol Recognit 2007;20:154-184
44. Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008;21:355-400
45. Hengerer A, Decker J, Prohaska E, et al. Quartz crystal microbalance (QCM) as a device for the screening of phage libraries. Biosens Bioelectron 1999;14:139-144
46. Matsubara T, Ishikawa D, Taki T, et al. Selection of ganglioside GM1-binding peptides by using a phage library. FEBS Lett 1999;456:253-256
47. Olsen EV, Sorokulova IB, Petrenko VA, et al. Affinity-selected filamentous bacteriophage as a probe for acoustic wave biodetectors of Salmonella typhimurium. Biosens Bioelectron 2006;21:1434-1442
48. Gearhart DA, Toole PF, Warren Beach J. Identification of brain proteins that interact with 2-methylnorharman. An analog of the parkinsonian-inducing toxin, MPP +. Neurosci Res 2002;44:255-265
49. Smith MW, Smith JW, Harris C, et al. Phage display identification of functional binding peptides against 4-acetamidophenol (Paracetamol): an exemplified approach to target low molecular weight organic molecules. Biochem Biophys Res Commun 2007;358:285-291
50. Krumpe LR, Schumacher KM, McMahon JB, et al. Trinucleotide cassettes increase diversity of T7 phage-displayed peptide library. BMC Biotechnol 2007;7:65
51. Dai M, Temirov J, Pesavento E, et al. Using T7 phage display to select GFP-based binders. Protein Eng Des Sel 2008;21:413-424
52. Mandava S, Makowski L, Devarapalli S, et al. RELIC-a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics 2004;4:1439-1460
53. Rodi DJ, Janes RW, Sanganee HJ, et al. Screening of a library of phage-displayed peptides identifies human bcl-2 as a taxol-binding protein. J Mol Biol 1999;285:197-203
54. Rodi DJ, Agoston GE, Manon R, et al. Identification of small molecule binding sites within proteins using phage display technology. Comb Chem High Throughput Screen 2001;4:553-572
55. Rodi DJ, Makowski L. Similarity between the sequences of taxol-selected peptides and the disordered loop of the anti-apoptotic protein, Bcl-2. Pac Symp Biocomput 1999;532-541
56. Popkov M, Lussier I, Medvedkine V, et al. Multidrug-resistance drug-binding peptides generated by using a phage display library. Eur J Biochem 1998;251:155-163
57. Jin Y, Yu J, Yu YG. Identification of hNopp140 as a binding partner for doxorubicin with a phage display cloning method. Chem Biol 2002;9:157-162
58. Kim YK, Lee WK, Jin Y, et al. Doxorubicin binds to un-phosphorylated form of hNopp140 and reduces protein kinase CK2-dependent phosphorylation of hNopp140. J Biochem Mol Biol 2006;39:774-781
59. Wiederrecht G, Lam E, Hung S, et al. The mechanism of action of FK-506 and cyclosporin A. Ann NY Acad Sci 1993;696:9-19
60. Piggott AM, Kriegel AM, Willows RD, et al. Rapid isolation of novel FK506 binding proteins from multiple organisms using gDNA and cDNA T7 phage display. Bioorg Med Chem 2009;17:6841-6850
61. He QL, Jiang H, Zhang F, et al. Simultaneous identification of multiple receptors of natural product using an optimized cDNA phage display cloning. Bioorg Med Chem Lett 2008;18:3995-3998
62. Kwon HJ. Discovery of new small molecules and targets towards angiogenesis via chemical genomics approach. Curr Drug Targets 2006;7:397-405
63. Kwon HJ, Kakeya H. Chemical genomics on new angiogenesis inhibitors. Tanpakushitsu Kakusan Koso 2005;50:1056-1062
64. Shim JS, Lee J, Park HJ, et al. A new curcumin derivative, HBC, interferes with the cell cycle progression of colon cancer cells via antagonization of the Ca2+/ calmodulin function. Chem Biol 2004;11:1455-1463
65. Finkelstein R, Reeves W, Ariizumi T, et al. Molecular aspects of seed dormancy. Annu Rev Plant Biol 2008;59:387-415
66. Dilly SJ, Bell MJ, Clark AJ, et al. A photoimmobilisation strategy that maximises exploration of chemical space in small molecule affinity selection and target discovery. Chem Commun (Camb) 2007;2808-2810
67. Ladwa SR, Dilly SJ, Clark AJ, et al. Rapid identification of a putative interaction between beta2-adrenoreceptor agonists and ATF4 using a chemical genomics approach. ChemMedChem 2008;3:742-744
68. Pirrung MC, Liu Y, Deng L, et al. Methyl scanning: total synthesis of demethylasterriquinone B1 and derivatives for identification of sites of interaction with and isolation of its receptor(s). J Am Chem Soc 2005;127:4609-4624
69. Webster NJ, Park K, Pirrung MC. Signaling effects of demethylasterriquinone B1, a selective insulin receptor modulator. Chembiochem 2003;4:379-385
70. Kim H, Deng L, Xiong X, et al. Glyceraldehyde 3-phosphate dehydrogenase is a cellular target of the insulin mimic demethylasterriquinone B1. J Med Chem 2007;50:3423-3426
71. López-Macià A, Jiménez JC, Royo M, et al. Synthesis and structure determination of kahalalide F (1,2). J Am Chem Soc 2001;123:11398-11401
72. Martín-Algarra S, Espinosa E, Rubió J, et al. Phase II study of weekly Kahalalide F in patients with advanced malignant melanoma. Eur J Cancer 2009;45:732-735
73. Piggott AM, Karuso P. Rapid identification of a protein binding partner for the marine natural product kahalalide F by using reverse chemical proteomics. Chembiochem 2008;9:524-530
74. Boitano A, Ellman JA, Glick GD, et al. The proapoptotic benzodiazepine Bz-423 affects the growth and survival of malignant B cells. Cancer Res 2003;63:6870-6876
75. Nakanishi T, Masuda A, Suwa M, et al. Synthesis of derivatives of NK109, 7-OH benzo[c]phenanthridine alkaloid, and evaluation of their cytotoxicities and reduction-resistant properties. Bioorg Med Chem Lett 2000;10:2321-2323
76. Fukuda M, Inomata M, Nishio K, et al. A topoisomerase II inhibitor, NK109, induces DNA single- and double-strand breaks and apoptosis. Jpn J Cancer Res 1996;87:1086-1091
77. Kanzawa F, Nishio K, Ishida T, et al. Anti-tumour activities of a new benzo[c] phenanthridine agent, 2,3-(methylenedioxy)-5-methyl- 7-hydroxy-8-methoxybenzo[c]phena nthridini um hydrogensulphate dihydrate (NK109), against several drug-resistant human tumour cell lines. Br J Cancer 1997;76:571-581
78. Morohashi K, Yoshino A, Yoshimori A, et al. Identification of a drug target motif: an anti-tumor drug NK109 interacts with a PNxxxxP. Biochem Pharmacol 2005;70:37-46
79. Fu Y, Li S, Zu Y, et al. Medicinal chemistry of paclitaxel and its analogues. Curr Med Chem 2009;16:3966-3985
80. Oberlies NH, Kroll DJ. Camptothecin and taxol: historic achievements in natural products research. J Nat Prod 2004;67:129-135
81. Pazdur R, Kudelka AP, Kavanagh JJ, et al. The taxoids: paclitaxel (Taxol) and docetaxel (Taxotere). Cancer Treat Rev 1993;19:351-386
82. Wall ME. Camptothecin and taxol: discovery to clinic. Med Res Rev 1998;18:299-314
83. Boehmerle W, Splittgerber U, Lazarus MB, et al. Paclitaxel induces calcium oscillations via an inositol 1,4,5-trisphosphate receptor and neuronal calcium sensor 1-dependent mechanism. Proc Natl Acad Sci USA 2006;103:18356-18361
84. Wall ME, Wani MC, Cook CE, et al. Plant antitumor agents I. The isolation and structure of camptothecin, a novel alkaloidal leukemia and tumor inhibitor from Camptotheca acuminata. J Am Chem Soc 1966;88:3888-3890
85. Yoon KJ, Hyatt JL, Morton CL, et al. Characterization of inhibitors of specific carboxylesterases: development of carboxylesterase inhibitors for translational application. Mol Cancer Ther 2004;3:903-909
86. Hsiang YH, Hertzberg R, Hecht S, et al. Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I. J Biol Chem 1985;260:14873-14878
87. Jaxel C, Kohn KW, Wani MC, et al. Structure-activity study of the actions of camptothecin derivatives on mammalian topoisomerase I: evidence for a specific receptor site and a relation to antitumor activity. Cancer Res 1989;49:1465-1469
88. Harel M, Hyatt JL, Brumshtein B, et al. The crystal structure of the complex of the anticancer prodrug 7-ethyl-10-[4-(1-piperidino)- 1-piperidino]-carbonyloxycamptothecin (CPT-11) with Torpedo californica acetylcholinesterase provides a molecular explanation for its cholinergic action. Mol Pharmacol 2005;67:1874-1881
89. Takakusagi Y, Kobayashi S, Sugawara F. Camptothecin binds to a synthetic peptide identified by a T7 phage display screen. Bioorg Med Chem Lett 2005;15:4850-4853
90. Videlock EJ, Chung VK, Mohan MA, et al. Two-dimensional diversity: screening human cDNA phage display libraries with a random diversity probe for the display cloning of phosphotyrosine binding domains. J Am Chem Soc 2004;126:3730-3731
91. Videlock EJ, Chung VK, Hall JM, et al. Identification of a molecular recognition role for the activation loop phosphotyrosine of the SRC tyrosine kinase. J Am Chem Soc 2005;127:1600-1601
92. Takakusagi K, Takakusagi Y, Ohta K, et al. A sulfoglycolipid beta-sulfoquinovosyldiacylglycerol (betaSQDG) binds to Met1-Arg95 region of murine DNA polymerase lambda (Mmpol lambda) and inhibits its nuclear transit. Protein Eng Des Sel 2010;23:51-60
93. Aoki S, Ohta K, Yamazaki T, et al. Mammalian mitotic centromere- associated kinesin (MCAK): a new molecular target of sulfoquinovosylacylglycerols novel antitumor and immunosuppressive agents. FEBS J 2005;272:2132-2140
94. Yamazaki T, Aoki S, Ohta K, et al. Synthesis of an immunosuppressant SQAG9 and determination of the binding peptide by T7 phage display. Bioorg Med Chem Lett 2004;14:4343-4346
95. Morimura T, Noda N, Kato Y, et al. Identification of antibiotic clarithromycin binding peptide displayed by T7 phage particles. J Antibiot (Tokyo) 2006;59:625-632
96. Feng L, Jin J, Zhang LF, et al. Analysis of the resveratrol-binding protein using phage-displayed random peptide library. Acta Biochim Biophys Sin (Shanghai) 2006;38:342-348
97. Saitoh T, Kuramochi K, Imai T, et al. Podophyllotoxin directly binds a hinge domain in E2 of HPV and inhibits an E2/E7 interaction in vitro. Bioorg Med Chem 2008;16:5815-5825
98. Savinov SN, Austin DJ. The cloning of human genes using cDNA phage display and small-molecule chemical probes. Comb Chem High Throughput Screen 2001;4:593-597
99. Cheng J, Zhou X, Chou TF, et al. Identification of the amino acid-AZT-phosphoramidase by affinity T7 phage display selection. Bioorg Med Chem Lett 2009;19:6379-6381
100. Tsuzuki S, Wada A, Ito Y. Photo-immobilization of biological components on gold-coated chips for measurements using surface plasmon resonance (SPR) and a quartz crystal microbalance (QCM). Biotechnol Bioeng 2009;102:700-707