1901 SMMKADFDEEPR(24) SMMKADFEEEPR(8) 2 Phage display (subtractive panning) 3 PMID:22123204 Anti-Bla g 2 monoclonal antibody 7C11 Aspartic protease Bla g 2 2NR6, Not determined. Ph.D.-12 phage display library (X12) Phages were precleared by incubation for 20 min at room temperature with mouse IgG mAb 6G-2 of unrelated specificity bound to protein G beads. Unbound phages were then incubated with 300 ng of purified mAb 7C11. The amino acid sequences of the peptides on selected phages differed at only one position, occupied by 1 of 2 negatively charged residues. The two 12-mer sequences bound to 7C11 with similar avidity and specificity. There was good concordance between the residues in the 3D clusters identified from our phage display/computational method with the co-crystal structural analysis. The Episearch analysis using peptide 1 identified 2 high-scoring patches centered at residue Asp100 (score = 1.0) and Asp87 (score = 0.87), respectively. Analysis with peptide 2 identified 1 high-scoring patch, centered at Pro61 (score = 1.0), and 1 low-scoring patch, centered at Arg83 (score = 0.67). The same 4 patches, centered at Asp100, Pro61, Asp87 and Arg83, were also identified using the sequences of peptides 1 and 2 simultaneously. After antibody binding, amino acids Lys60, Lys65, Ile67, Asp68 and Arg83 lost more than 50 Å(2) of their surface area, while Try66 and Lys132 lost 100 Å(2) or more of their surface area. 1902 SYPIPDT(14) HTSDQTN(9) AKLPIIP(5) AYHPPAM(4) EGMHYHT(2) EPAHMSL(1) WTPYSLV(1) SNYLMYI(1) HATSYFV(1) 9 Phage display (subtractive panning) 4 PMID:22136656 Epidermal growth factor receptor Pro-epidermal growth factor, EGF 1IVO,1NQL,3NJP, Not determined. Ph.D.-7 phage display library (X7) A-431 cells expressing epidermal growth factor receptor were used as the matrix in a cell-based subtractive biopanning approach using a 7-mer peptide displaying phage library. Human fetal foreskin fibroblast cells were used to carry out subtractive screening. Competitive binding of the selected peptides (SYPIPDT and HTSDQTN) was performed to determine the affinities of the peptides displayed by the phage particles toward EGFR. Two novel peptide ligands were identified and tested for their affinities and functional effects on epidermal growth factor receptor. The identified peptides were able to inhibit the epidermal growth factor-induced phosphorylation of epidermal growth factor receptor in a concentration-dependent manner. The results of affinity binding experiments showed that the natural ligand, that is epidermal growth factor, was able to inhibit competitively the binding of peptide-bearing phage to epidermal growth factor receptor expressing A-431 cells. Molecular modeling studies were used to calculate the free energies for the binding of peptides to the receptor-binding site as well as proposing the interaction modes for this binding. 1903 HPLSKHPYWSQP 1 Phage display (common panning) 3 PMID:22119929 Clusterin Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Competition experiment,NMR spectroscopy The phage-displayed P3378 (HPLSKHPYWSQP) and synthetic P3378 (HPLSKHPYWSQP) bind in a competitive manner. Besides, the results of DRP-NMR strongly suggest that the P3378 peptide and not the P3378R peptide (PYLHQSPHWKPS), interacts with rhsCLU in a sequence-specific manner. HEK293-E6 cells expressing recombinant human secreted (rhs)CLU were used as the target in a cell-based biopanning approach. A third panning round returned phage clones of which essentially 100% displayed the same peptide. Sequencing of the peptide revealed the unique amino acid sequence HPLSKHPYWSQP, which was designated peptide P3378. Differential resonance perturbation nuclear magnetic resonance using P3378 and a scrambled control peptide (designated P3378R) confirmed the P3378-sCLU interaction and demonstrated that it was sequence specific. P3378 and P3378R peptides were conjugated to an Alexa680 near infrared fluorophore (NIRF) and assessed for their tumor homing abilities in in vivo time-domain fluorescence optical imaging experiments using living 4T1 tumor bearing BALB/c mice. When injected in separate animals, both peptides accumulated at the tumor site, however the NIRF-labeled P3378 peptide was retained for a significant longer period of time than the P3378R peptide. Similar observations were made after simultaneously injecting the same tumor-bearing animal with a peptide mixture of P3378 DyLight (DL)680 and the P3378R-DL800. Coinjection of P3378-DL680 with excess unlabeled P3378 blocked tumor accumulation of fluorescent signal while excess P3378R control peptide did not confirming the sequence specificity of the tumor accumulation. Finally, ex vivo fluorescence microscopy of these tumors confirmed the presence of P3378-DL680 in the tumor and its colocalization with CLU. These results confirm the tumor targeting specificity of the P3378 CLU-binding peptide and suggest its usefulness for the in vivo monitoring of solid tumors secreting detectable levels of CLU. 1904 PSTRKK(1) TGGWRF(2) QWPMLV(1) WSGQDI(1) YRRGHL(1) RYRTSL(2) SWGRRG(1) VRKVAA(2) SRSCTA(1) LEALVV(1) SACLTG(1) CLKTEG(1) FRRPGG(1) RGWGTV(1) LRYVTY(1) GGRVVT(1) RVYLLS(1) RAQMGE(1) PVQKKH(1) VGRHLA(1) KGWEGC(1) 21 Phage display (common panning) 5 PMID:22132161 Serine protease 28 Not determined. Not determined. Not determined. X6 T7 phage display library Phage display peptide mimetics revealed an expanded but mixed substrate specificity of ISP1, including chymotryptic and elastase activity. Based upon targets observed using phage display, we hypothesised that ISP1 might signal to cells by cleaving and activating proteinase-activated receptors (PARs) and therefore assessed PARs 1, 2 and 4 as potential ISP1 targets. 1905 FHKHKSPALSPV(19) FHKPFFPKGSAR(13) 2 Phage display (common panning) 3 PMID:22138765 Tenascin, TN Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Most solid tumors express the large isoform of TNC which contains EGF domain, fibrinogen glob (fbg) and fibronectin III (FN III) domains with the inclusion of alternatively spliced exons in the middle. Due to the complexity and sizes of the tumor specific TNC protein, the authors utilized two different versions of TNC proteins and performed two independent selections. One is the tumor-specific large isoform of TNC (Full-length TNC) expressed in eukaryotic cells and the other is the alternatively spliced domain (A1-D) of TNC expressed in bacteria. Of the 35 clones derived from two independent selections, 19 had the same sequences (designated peptide #1), and 13 others were also identical (designated peptide #2), while the remainder had similar sequences. The selected peptide #1 specifically recognized tenascin C protein in xenograft mouse tissue. The authors also observed exclusive staining of tenascin C by the selected peptide in tumor patient tissues. Moreover, the peptide reduced tenascin C-induced cell rounding and migration. 1906 HVHPPLRPHSDK(1) YPTHHAHTTPVR(10) HATNHLPTPHNR(1) 3 Phage display (subtractive panning) 5 PMID:22163050 Bovine rotavirus Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) In the fourth round of panning, the coated viruses were replaced by the supernatant of MA104 culture. The phages were incubated with the supernatant at room temperature for 30 min prior to the fifth round of panning. Using the specific peptide-expressing phages, the authors developed a phage-based ELISA to differentiate BRV from other viruses. Compared with quantitative real-time PCR (qPCR), the phage-mediated ELISA was more suitable for the capture of BRV and the detection limitation of this approach was 0.1 μg/ml of samples. The high sensitivity, specificity and low cross-reactivity for the phage-based ELISA were confirmed in receiver operating characteristics (ROC) analysis. 1907 WHWRLPS(10) LHHKTHH(2) 2 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H2N2 monoclonal antibody C179 Anfluenza A virus strain H2N2 Not determined. Not determined. Ph.D.-7 phage display library (X7) 1908 WHTHKWSLSAKA(4) HHWKFFFSHPGA(2) HHWKFFFSHPGE(2) LPFHGHKKPVLS(1) WPWWPGHTHRTI(1) HPMKQYRWRPSI(1) SPNYWFNKIHQH(1) 7 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H2N2 monoclonal antibody C179 Anfluenza A virus strain H2N2 Not determined. Not determined. Ph.D.-12 phage display library (X12) 1909 CNLSSSWIC(9) CNSGMFVRC(3) 2 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H2N2 monoclonal antibody C179 Anfluenza A virus strain H2N2 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) 1910 QWTWTQY(4) DTLPLFI(1) MSLQQEH(1) ANTTPRH(1) MDAHHAL(1) ITAPHPH(1) QRNQTQD(1) QWNRTQY(1) NTAPHPH(1) 9 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H1N1 monoclonal antibody IV.C102 Anfluenza A virus strain H1N1 Not determined. Not determined. Ph.D.-7 phage display library (X7) 1911 DCWQMDRKTCPL(6) NTPAWLNHTTVI(3) LPAFFVTNQTQD(1) TVHWWZTHGPLS(1) SAIPTTWNPLAV(1) 5 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H1N1 monoclonal antibody IV.C102 Anfluenza A virus strain H1N1 Not determined. Not determined. Ph.D.-12 phage display library (X12) 1912 CPLHARLPC(10) CSLASLPAC(2) 2 Phage display (common panning) 3 PMID:22171803 Anti-influenza A H1N1 monoclonal antibody IV.C102 Anfluenza A virus strain H1N1 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) 1913 WPWHNHR(6) ASINSSL(2) QSERAIQ(1) TSLPTIV(1) AFSYHIH(1) NMWQALN(1) 6 Phage display (subtractive panning) 3 PMID:22171803 Anti-influenza A H3N2 polyclonal antibody IgG Influenza A virus (strain A/Texas/1/1977 H3N2) Not determined. Not determined. Ph.D.-7 phage display library (X7) Goat IgG were used in a subtractive biopanning approach. 1914 VWSTPPHADGPA(4) HAPWRHHQASPK(3) FPAHPAWTIGSM(1) YTPLSSASPWGP(1) GMSLLHGQRPHT(1) VSRHQSWHPHDL(1) EREAHQLHSHHK(1) 7 Phage display (subtractive panning) 3 PMID:22171803 Anti-influenza A H3N2 polyclonal antibody IgG Influenza A virus (strain A/Texas/1/1977 H3N2) Not determined. Not determined. Ph.D.-12 phage display library (X12) Goat IgG were used in a subtractive biopanning approach. 1915 CLGALSHTC(8) CSPVLPFLC(1) CTHEPSGRC(1) CSAPRQADC(1) CSLPLTGQC(1) 5 Phage display (subtractive panning) 3 PMID:22171803 Anti-influenza A H3N2 polyclonal antibody IgG Influenza A virus (strain A/Texas/1/1977 H3N2) Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Goat IgG were used in a subtractive biopanning approach. 1916 ETKAWWL(7) LASKPMP(4) QAHTIST(1) 3 Phage display (subtractive panning) 3 PMID:22171803 SIV sera from patients Swine-origin influenza virus A/2009 Not determined. Not determined. Ph.D.-7 phage display library (X7) Human IgG were used in a subtractive biopanning approach. 1917 QAHNWYNHKPLP(6) VHNNAARTGSPP(2) VHNHANDPGSPP(1) QELYPYSPHIHV(1) FSHELSWKPRKA(1) AHTHSKERVQTI(1) 6 Phage display (subtractive panning) 3 PMID:22171803 SIV sera from patients Swine-origin influenza virus A/2009 Not determined. Not determined. Ph.D.-12 phage display library (X12) Human IgG were used in a subtractive biopanning approach. 1918 CPLHARLPC(6) CRHLPLTPC(1) CSLPLTGQC(1) CPSYPLSFC(1) CRDISPLAC(1) CYGWPIYSC(1) CNLSSSWTC(1) 7 Phage display (subtractive panning) 3 PMID:22171803 SIV sera from patients Swine-origin influenza virus A/2009 Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Human IgG were used in a subtractive biopanning approach. 1919 CLRSGRFC(10) 1 Phage display (competitive panning) 3 PMID:22189418 C-X-C chemokine receptor type 1, CXCR-1 Interleukin-8, IL-8 1ILP,1ILQ, Not determined. CX6C fdMED1 phage display library In fact, hCXCR1-transfected murine pre-B cells were used to panning the phage library. In each round, bound phage were eluted with hCXCL8. Sequence analysis revealed homology between the linear hexapeptides and the N-terminal domain (1-SAKELR-6), whereas the constrained peptides are composed of non-contiguous amino acids mimicking spatial structure on the surface of folded C-terminal portion of hCXCL8 (50-CLDPKENWVQRVVEKFLKRAENS-72). The synthetic linear and structurally constrained peptides competed for 125I-hCXCL8 binding to hCXCR1 and hCXCR2 (IC50 comprised between 10 and 100 lM). Furthermore, they inhibited the intracellular calcium flux and the migration of hCXCR1/hCXCR2 transfectants; and desensitized hCXCR1 and hCXCR2 receptors on neutrophils, reducing their chemotactic responses induced by ELR-CXC chemokines (hCXCL8, hCXCL1, hCXCL2, hCXCL3, and hCXCL5). 1920 MSRAKE(10) 1 Phage display (competitive panning) 3 PMID:22189418 C-X-C chemokine receptor type 1, CXCR-1 Interleukin-8, IL-8 1ILP,1ILQ, Not determined. X6 fdMED1 phage display library In fact, hCXCR1-transfected murine pre-B cells were used to panning the phage library. In each round, bound phage were eluted with hCXCL8. Sequence analysis revealed homology between the linear hexapeptides and the N-terminal domain (1-SAKELR-6), whereas the constrained peptides are composed of non-contiguous amino acids mimicking spatial structure on the surface of folded C-terminal portion of hCXCL8 (50-CLDPKENWVQRVVEKFLKRAENS-72). The synthetic linear and structurally constrained peptides competed for 125I-hCXCL8 binding to hCXCR1 and hCXCR2 (IC50 comprised between 10 and 100 lM). Furthermore, they inhibited the intracellular calcium flux and the migration of hCXCR1/hCXCR2 transfectants; and desensitized hCXCR1 and hCXCR2 receptors on neutrophils, reducing their chemotactic responses induced by ELR-CXC chemokines (hCXCL8, hCXCL1, hCXCL2, hCXCL3, and hCXCL5). 1921 CLPWKENC(10) 1 Phage display (competitive panning) 3 PMID:22189418 C-X-C chemokine receptor type 2, CXCR-2 Interleukin-8, IL-8 Not determined. Not determined. CX6C fdMED1 phage display library In fact, hCXCR2-transfected murine pre-B cells were used to panning the phage library. In each round, bound phage were eluted with hCXCL8. Sequence analysis revealed homology between the linear hexapeptides and the N-terminal domain (1-SAKELR-6), whereas the constrained peptides are composed of non-contiguous amino acids mimicking spatial structure on the surface of folded C-terminal portion of hCXCL8 (50-CLDPKENWVQRVVEKFLKRAENS-72). The synthetic linear and structurally constrained peptides competed for 125I-hCXCL8 binding to hCXCR1 and hCXCR2 (IC50 comprised between 10 and 100 lM). Furthermore, they inhibited the intracellular calcium flux and the migration of hCXCR1/hCXCR2 transfectants; and desensitized hCXCR1 and hCXCR2 receptors on neutrophils, reducing their chemotactic responses induced by ELR-CXC chemokines (hCXCL8, hCXCL1, hCXCL2, hCXCL3, and hCXCL5). 1922 CAKELR(10) 1 Phage display (competitive panning) 3 PMID:22189418 C-X-C chemokine receptor type 2, CXCR-2 Interleukin-8, IL-8 Not determined. Not determined. X6 fdMED1 phage display library In fact, hCXCR2-transfected murine pre-B cells were used to panning the phage library. In each round, bound phage were eluted with hCXCL8. Sequence analysis revealed homology between the linear hexapeptides and the N-terminal domain (1-SAKELR-6), whereas the constrained peptides are composed of non-contiguous amino acids mimicking spatial structure on the surface of folded C-terminal portion of hCXCL8 (50-CLDPKENWVQRVVEKFLKRAENS-72). The synthetic linear and structurally constrained peptides competed for 125I-hCXCL8 binding to hCXCR1 and hCXCR2 (IC50 comprised between 10 and 100 lM). Furthermore, they inhibited the intracellular calcium flux and the migration of hCXCR1/hCXCR2 transfectants; and desensitized hCXCR1 and hCXCR2 receptors on neutrophils, reducing their chemotactic responses induced by ELR-CXC chemokines (hCXCL8, hCXCL1, hCXCL2, hCXCL3, and hCXCL5). 1923 MLRQTR(2) HASILP(5) KKEPWI(3) 3 Phage display (common panning) 3 PMID:22189418 Interleukin-8, IL-8 Not determined. Not determined. Not determined. X6 fdMED1 phage display library These peptides similarly displaced the binding of 125I-hCXCL8 to hCXCR1 in a dose-dependent manner, inhibited hCXCL8 induced increases in the intracellular calcium, and migration of hCXCR1- and hCXCR2-transfected cells. 1924 LSTHTTESRSMV LEPRWGFGWWLK 2 Phage display (common panning) 3 PMID:22227343 Prestin Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Prestin was adsorbed to polypropylene Petri dishes, these were used to perform the first two of three rounds of biopanning. The 3rd round of biopanning was performed using Cos-7 cells transiently transfected with a cCFP-prestin plasmid, to eliminate false-positives affinitive to intracellular loops and trans-membrane helices of the prestin that may have been obtained using soluble prestin. The binding properties of LSTHTTESRSMV and LEPRWGFGWWLK shown by flow cytometry demonstrated selectivity to prestin-expressing Chinese hamster ovary cells. PEG6K-b-PCL19K polymersomes covalently labelled with these peptides demonstrated effective targeting to outer hair cells in a rat cochlear explant study. 1925 IMVTESSDYSSY 1 Phage display (common panning) 4 PMID:22233341 Graphite flakes Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) As a novel approach, the authors demonstrate here that short dodecapeptides selected by phage display are capable of self-assembly on graphite and form long-range-ordered biomolecular nanostructures. Using atomic force microscopy and contact angle studies, they identify three amino acid domains along the primary sequence that steer peptide ordering and lead to nanostructures with uniformly displayed residues. The peptides are further engineered via simple mutations to control fundamental interfacial processes, including initial binding, surface aggregation and growth kinetics, and intermolecular interactions. Tailoring short peptides via their primary sequence offers versatile control over molecular self-assembly, resulting in well-defined surface properties essential in building engineered, chemically rich, bio-solid interfaces.