Abstract
Phage display is known as a powerful methodology for the identification of targeting ligands that specifically bind to a variety of targets. The high-throughput screening of phage display combinatorial peptide libraries is performed through the affinity selection method of biopanning. Although phage display selection has proven very successful in the discovery of numerous high-affinity target-binding peptides with potential application in drug discovery and delivery, the enrichment of false-positive target-unrelated peptides (TUPs) without any actual affinity towards the target remains a major problem of library screening. Selection-related TUPs may emerge because of binding to the components of the screening system rather than the target. Propagation-related TUPs may arise as a result of faster growth rate of some phage clones enabling them to outcompete slow-propagating clones. Amplification of the library between rounds of biopanning makes a significant contribution to the selection of phage clones with propagation advantage. Distinguishing nonspecific TUPs from true target binders is of particular importance for the translation of biopanning findings from basic research to clinical applications. Different experimental and in silico approaches are applied to assess the specificity of phage display-derived peptides towards the target. Bioinformatic tools are playing a rapidly growing role in the analysis of biopanning data and identification of target-irrelevant TUPs. Recent progress in the introduction of efficient strategies for TUP detection holds enormous promise for the discovery of clinically relevant cell- and tissue-homing peptides and paves the way for the development of novel targeted diagnostic and therapeutic platforms in pharmaceutical areas.
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References
AC’t Hoen PA et al (2012) Phage display screening without repetitious selection rounds. Anal Biochem 421:622–631. doi:10.1016/j.ab.2011.11.005
Adey NB, Mataragnon AH, Rider JE, Carter JM, Kay BK (1995) Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene 156:27–31
Anni H, Nikolaeva O, Israel Y (2001) Selection of phage-display library peptides recognizing ethanol targets on proteins. Alcohol 25:201–209
Bastings MM, Helms BA, van Baal I, Hackeng TM, Merkx M, Meijer EW (2011) From phage display to dendrimer display: insights into multivalent binding. J Am Chem Soc 133:6636–6641. doi:10.1021/ja110700x
Bellotto S, Chen S, Rentero Rebollo I, Wegner HA, Heinis C (2014) Phage selection of photoswitchable peptide ligands. J Am Chem Soc 136:5880–5883. doi:10.1021/ja501861m
Berger S, Bannantine JP, Griffin JF (2007) Autoreactive antibodies are present in sheep with Johne’s disease and cross-react with Mycobacterium avium subsp. paratuberculosis antigens. Microbes Infect 9:963–970. doi:10.1016/j.micinf.2007.03.016
Brammer LA, Bolduc B, Kass JL, Felice KM, Noren CJ, Hall MF (2008) A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site. Anal Biochem 373:88–98. doi:10.1016/j.ab.2007.10.015
Brown KC (2010) Peptidic tumor targeting agents: the road from phage display peptide selections to clinical applications. Curr Pharm Des 16:1040–1054
Chen T, Hoffmann K, Ostman S, Sandberg AS, Olsson O (2011) Identification of gliadin-binding peptides by phage display. BMC Biotechnol 11:16. doi:10.1186/1472-6750-11-16
Christiansen A et al (2015) High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum. Sci Rep 5:12913. doi:10.1038/srep12913
Coordinators NR (2016) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 44:D7–D19. doi:10.1093/nar/gkv1290
Derda R, Tang SK, Whitesides GM (2010) Uniform amplification of phage with different growth characteristics in individual compartments consisting of monodisperse droplets. Angew Chem Int Ed Engl 49:5301–5304. doi:10.1002/anie.201001143
Derda R, Tang SK, Li SC, Ng S, Matochko W, Jafari MR (2011) Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules 16:1776–1803. doi:10.3390/molecules16021776
Desjobert C, de Soultrait VR, Faure A, Parissi V, Litvak S, Tarrago-Litvak L, Fournier M (2004) Identification by phage display selection of a short peptide able to inhibit only the strand transfer reaction catalyzed by human immunodeficiency virus type 1 integrase. Biochemistry 43:13097–13105. doi:10.1021/bi049385e
Dias-Neto E et al (2009) Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS One 4:e8338. doi:10.1371/journal.pone.0008338
Dyson MR, Murray K (1995) Selection of peptide inhibitors of interactions involved in complex protein assemblies: association of the core and surface antigens of hepatitis B virus. Proc Natl Acad Sci USA 92:2194–2198
Eldridge GM, Weiss GA (2015) Identifying reactive peptides from phage-displayed libraries. Methods Mol Biol 1248:189–199. doi:10.1007/978-1-4939-2020-4_13
Even-Desrumeaux K, Chames P (2012) Phage display and selections on cells. Methods Mol Biol 907:225–235. doi:10.1007/978-1-61779-974-7_12
Gebhardt K, Lauvrak V, Babaie E, Eijsink V, Lindqvist BH (1996) Adhesive peptides selected by phage display: characterization, applications and similarities with fibrinogen. Pept Res 9:269–278
Getz JA, Schoep TD, Daugherty PS (2012) Peptide discovery using bacterial display and flow cytometry. Methods Enzymol 503:75–97. doi:10.1016/B978-0-12-396962-0.00004-5
He B et al (2016) BDB: biopanning data bank. Nucleic Acids Res 44:D1127–D1132. doi:10.1093/nar/gkv1100
Hong SS, Boulanger P (1995) Protein ligands of the human adenovirus type 2 outer capsid identified by biopanning of a phage-displayed peptide library on separate domains of wild-type and mutant penton capsomers. EMBO J 14:4714–4727
Hu YF, Gao XC, Xu TQ, Dun Z, Yu XL (2016) Characterization of seven new polystyrene plates binding peptides from a phage-displayed random 12-peptide library. Comb Chem High Throughput Screen 19:283–289
Huang J, Ru B, Li S, Lin H, Guo FB (2010) SAROTUP: scanner and reporter of target-unrelated peptides. J Biomed Biotechnol 2010:101932. doi:10.1155/2010/101932
Huang J, Ru B, Dai P (2011) Bioinformatics resources and tools for phage display. Molecules 16:694–709. doi:10.3390/molecules16010694
Huang J et al (2012) MimoDB 2.0: a mimotope database and beyond. Nucleic Acids Res 40:D271–D277. doi:10.1093/nar/gkr922
Hyvonen M, Laakkonen P (2015) Identification and characterization of homing peptides using in vivo peptide phage display. Methods Mol Biol 1324:205–222. doi:10.1007/978-1-4939-2806-4_14
Jesaitis AJ, Gizachew D, Dratz EA, Siemsen DW, Stone KC, Burritt JB (1999) Actin surface structure revealed by antibody imprints: evaluation of phage-display analysis of anti-actin antibodies. Protein Sci 8:760–770. doi:10.1110/ps.8.4.760
Kanamori T, Fujino Y, Ueda T (2014) PURE ribosome display and its application in antibody technology. Biochim Biophys Acta 1844:1925–1932. doi:10.1016/j.bbapap.2014.04.007
Kenan DJ et al (2006) Peptide-PEG amphiphiles as cytophobic coatings for mammalian and bacterial cells. Chem Biol 13:695–700. doi:10.1016/j.chembiol.2006.06.013
Kenrick SA, Daugherty PS (2010) Bacterial display enables efficient and quantitative peptide affinity maturation. Protein Eng Des Sel 23:9–17. doi:10.1093/protein/gzp065
Khusal KG et al (2015) Prokineticin receptor identified by phage display is an entry receptor for Trypanosoma cruzi into mammalian cells. Parasitol Res 114:155–165. doi:10.1007/s00436-014-4172-6
Krook M, Mosbach K, Ramstrom O (1998) Novel peptides binding to the Fc-portion of immunoglobulins obtained from a combinatorial phage display peptide library. J Immunol Methods 221:151–157
Krumpe LR et al (2006) T7 lytic phage-displayed peptide libraries exhibit less sequence bias than M13 filamentous phage-displayed peptide libraries. Proteomics 6:4210–4222. doi:10.1002/pmic.200500606
Larson RS, Brown DC, Ye C, Hjelle B (2005) Peptide antagonists that inhibit Sin Nombre virus and hantaan virus entry through the beta3-integrin receptor. J Virol 79:7319–7326. doi:10.1128/JVI.79.12.7319-7326.2005
Lee SK, Yun DS, Belcher AM (2006) Cobalt ion mediated self-assembly of genetically engineered bacteriophage for biomimetic Co-Pt hybrid material. Biomacromolecules 7:14–17. doi:10.1021/bm050691x
Li J, Feng L, Jiang X (2015a) In vivo phage display screen for peptide sequences that cross the blood-cerebrospinal-fluid barrier. Amino Acids 47:401–405. doi:10.1007/s00726-014-1874-0
Li W et al (2015b) The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res 43:W580–W584. doi:10.1093/nar/gkv279
Lindner T, Kolmar H, Haberkorn U, Mier W (2011) DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods. Molecules 16:1625–1641. doi:10.3390/molecules16021625
Liu M, Tada S, Ito M, Abe H, Ito Y (2012) In vitro selection of a photo-responsive peptide aptamer using ribosome display. Chem Commun (Camb) 48:11871–11873. doi:10.1039/c2cc36618e
Lunder M, Bratkovic T, Doljak B, Kreft S, Urleb U, Strukelj B, Plazar N (2005) Comparison of bacterial and phage display peptide libraries in search of target-binding motif. Appl Biochem Biotechnol 127:125–131
Lunder M, Bratkovic T, Urleb U, Kreft S, Strukelj B (2008) Ultrasound in phage display: a new approach to nonspecific elution. Biotechniques 44:893–900. doi:10.2144/000112759
Mandava S, Makowski L, Devarapalli S, Uzubell J, Rodi DJ (2004) RELIC—a bioinformatics server for combinatorial peptide analysis and identification of protein–ligand interaction sites. Proteomics 4:1439–1460. doi:10.1002/pmic.200300680
Mathonet P, Barrios H, Soumillion P, Fastrez J (2006) Selection of allosteric beta-lactamase mutants featuring an activity regulation by transition metal ions. Protein Sci 15:2335–2343. doi:10.1110/ps.062304406
Matochko WL, Derda R (2013) Error analysis of deep sequencing of phage libraries: peptides censored in sequencing. Comput Math Methods Med 2013:491612. doi:10.1155/2013/491612
Matochko WL, Derda R (2015) Next-generation sequencing of phage-displayed peptide libraries. Methods Mol Biol 1248:249–266. doi:10.1007/978-1-4939-2020-4_17
Matochko WL, Li SC, Tang SK, Derda R (2014) Prospective identification of parasitic sequences in phage display screens. Nucleic Acids Res 42:1784–1798. doi:10.1093/nar/gkt1104
Matsubara T, Hiura Y, Kawahito O, Yasuzawa M, Kawashiro K (2003) Selection of novel structural zinc sites from a random peptide library. FEBS Lett 555:317–321
Menendez A, Scott JK (2005) The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal Biochem 336:145–157. doi:10.1016/j.ab.2004.09.048
Meyer SC, Gaj T, Ghosh I (2006) Highly selective cyclic peptide ligands for NeutrAvidin and avidin identified by phage display. Chem Biol Drug Des 68:3–10. doi:10.1111/j.1747-0285.2006.00401.x
Newton-Northup J, Deutscher S (2012) Contending with target unrelated peptides from phage display. J Mol Imaging Dyn 2:1–3
Nguyen KT et al (2014) Identification and characterization of mutant clones with enhanced propagation rates from phage-displayed peptide libraries. Anal Biochem 462:35–43. doi:10.1016/j.ab.2014.06.007
Pande J, Szewczyk MM, Grover AK (2010) Phage display: concept, innovations, applications and future. Biotechnol Adv 28:849–858. doi:10.1016/j.biotechadv.2010.07.004
Rajik M, Jahanshiri F, Omar AR, Ideris A, Hassan SS, Yusoff K (2009) Identification and characterisation of a novel anti-viral peptide against avian influenza virus H9N2. Virol J 6:74. doi:10.1186/1743-422X-6-74
Ramanujam P, Tan WS, Nathan S, Yusoff K (2002) Novel peptides that inhibit the propagation of Newcastle disease virus. Arch Virol 147:981–993. doi:10.1007/s00705-001-0778-y
Rodi DJ, Soares AS, Makowski L (2002) Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries. J Mol Biol 322:1039–1052
Ru B et al (2010) MimoDB: a new repository for mimotope data derived from phage display technology. Molecules 15:8279–8288. doi:10.3390/molecules15118279
Ru B, AC’t Hoen PA, Nie F, Lin H, Guo FB, Huang J (2014) PhD7Faster: predicting clones propagating faster from the Ph.D.-7 phage display peptide library. J Bioinform Comput Biol 12:1450005. doi:10.1142/S021972001450005X
Serizawa T, Techawanitchai P, Matsuno H (2007) Isolation of peptides that can recognize syndiotactic polystyrene. Chembiochem Eur J Chem Biol 8:989–993. doi:10.1002/cbic.200700133
Shannon C (1948) A mathematical theory of communication, bell System technical Journal 27: 379-423 and 623–656. Math Rev (MathSciNet) MR10:133e
Shannon CE (1997) The mathematical theory of communication. 1963. MD Comput 14:306–317
Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R (2007) PepBank—a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinform 8:280. doi:10.1186/1471-2105-8-280
Siegel DL, Chang TY, Russell SL, Bunya VY (1997) Isolation of cell surface-specific human monoclonal antibodies using phage display and magnetically-activated cell sorting: applications in immunohematology. J Immunol Methods 206:73–85
Smith GP (2011) The phage nanoparticle toolkit. In: Petrenko V, Smith GP (eds) Phage nanobiotechnology. Royal Society of Chemistry, London, pp 1–11
Smith GP, Petrenko VA (1997) Phage Display. Chem Rev 97:391–410
Takenaka IM, Leung SM, McAndrew SJ, Brown JP, Hightower LE (1995) Hsc70-binding peptides selected from a phage display peptide library that resemble organellar targeting sequences. J Biol Chem 270:19839–19844
Thiel WH et al (2011) Nucleotide bias observed with a short SELEX RNA aptamer library. Nucleic Acid Ther 21:253–263. doi:10.1089/nat.2011.0288
Thomas WD, Golomb M, Smith GP (2010) Corruption of phage display libraries by target-unrelated clones: diagnosis and countermeasures. Anal Biochem 407:237–240. doi:10.1016/j.ab.2010.07.037
UniProt C (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212. doi:10.1093/nar/gku989
Valuev VP, Afonnikov DA, Ponomarenko MP, Milanesi L, Kolchanov NA (2002) ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res 30:200–202
Vodnik M, Zager U, Strukelj B, Lunder M (2011) Phage display: selecting straws instead of a needle from a haystack. Molecules 16:790–817. doi:10.3390/molecules16010790
Watanabe H, Yamasaki K, Honda S (2014) Tracing primordial protein evolution through structurally guided stepwise segment elongation. J Biol Chem 289:3394–3404. doi:10.1074/jbc.M113.530592
Wen F, Zhao H (2013) Construction and screening of an antigen-derived peptide library displayed on yeast cell surface for CD4+ T cell epitope identification. Methods Mol Biol 1061:245–264. doi:10.1007/978-1-62703-589-7_15
Zimmermann B, Gesell T, Chen D, Lorenz C, Schroeder R (2010) Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX. PLoS One 5:e9169. doi:10.1371/journal.pone.0009169
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Bakhshinejad, B., Zade, H.M., Shekarabi, H.S.Z. et al. Phage display biopanning and isolation of target-unrelated peptides: in search of nonspecific binders hidden in a combinatorial library. Amino Acids 48, 2699–2716 (2016). https://doi.org/10.1007/s00726-016-2329-6
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DOI: https://doi.org/10.1007/s00726-016-2329-6