1826 FHENWPS(15) 1 Phage display (common panning) 3 PMID:11839467 96-well immunoassay plate (polystyrene, PS) Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The authors' purpose is to identify phage peptides that recognize the HER modification on BSA. A single sequence FHENWPS, emerged after the third round for all 15 independent clones, which appeared in one clone in the second biopanning round. Screening of the clone against an array of positive and negative targets to determine binding efficiency showed high readings (OD>1.5) in ELISA analysis. However, there were no differences between either positive versus negative target-coated or target-coated versus BSA-blocked uncoated wells by ELISA, nor by a more sensitive method of plaque assay. They concluded that most probably the selected clone was a super-binder of polystyrene surfaces that grew preferentially in the third biopanning round, and a different biopanning strategy for BSA-HER in solution was developed. 1827 FHWTWYW 1 Phage display (common panning) http://www.neb.com/nebecomm/tech_reference/protein_tools/phdFaq.asp#4.13 96-well immunoassay plate (polystyrene, PS) Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The sequence FHWTWYW is a plastic binder discovered and characterized at New England BioLabs (NEB). 1828 APFYYSWFPSYMAEGLPSPSPLDPVQDNLY 1 Phage display (common panning) PMID:15620878 96-well immunoassay plate (polystyrene, PS) Not determined. Not determined. Not determined. Not determined. 1829 WHRWPWLVSG(1) WHWWYWALDR(1) WHWWXW 2 Phage display (common panning) 3 PMID:9237215 Petri dish (polystyrene, PS) Not determined. Not determined. Not determined. X10 phage display library Each selection was performed on the streptavidin-coated (Pierce, Rockford, IL) petri plates. The peptide sequences WHRWPWLVSG and WHWWYWALDR were isolated from streptavidin biopanning, each at a frequency of 1 of 43 phages sequenced. Most importantly, WHWWXW phage have been isolated repeatedly in biopannings in which no streptavidin was used. The amino acid composition and the presence of the WHXW motif suggest that their phage were also plastic binders. 1830 YKKPLLMDQILK GDIDSQGVRPHE IPDQGNKPKSRL THQKPSDLPIGH WTAASSVPSKSS LTPSVWSSKSHN AQVPYFSNHPSG FDPFLRTLQGTH 8 Phage display (common panning) 3 PMID:21600948 Mouse pooled sera immunized with VHBL plasmid DNA VHBL plasmid DNA Not determined. Not determined. Ph.D.-12 phage display library (X12) 1831 CLPWAQHMC CVSLPHRTC CPSPTRSAC CTKMSPHAC CFNRSPVVC CGIRRTPTC CPLSKFHVC CPLTLPATC CKQQPYLYC CTKCQKMAC CTKMSRHAC CTKCRNNAC CTTSLYRSC CNGFYATTC CWLGDITQC CHSWLIHNC 16 Phage display (common panning) 3 PMID:21600948 Mouse pooled sera immunized with VHBL plasmid DNA VHBL plasmid DNA Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) 1832 SCQLEGSRLRCP QCKLEGSRLRCV QCALEGARIRCS QCTMDQGRLRCR GCITEQGRSRCI SCKLEGSRLRCP TCATDQGRLRCT HCFHDQGRVRCA TCEMTQGRLRCV ACRSDQGRARCT NCTLEGTRFRCS RCKPDQGRLRCG SCMKDPSSPRCL HCTMDQGRLRCR SCMLDQGRSRCR TCRQTLTPAVCH QCQEDQGRRRCS 17 Phage display (common panning) 3 PMID:21763377 Anti-mut-II monoclonal antibody LmmAbB2D4 Mutalysin-II (mut-II) Not determined. Not determined. XCX8CX+X15+X8CX8+X30 M13 phage display library pool The DNA sequence and the deduced amino acid sequence were determined, showing that the peptides were selected from the (XCX8CX) library. LmmAb2D4 reactivity with cellulose-bound phage-display identified peptides was detected with an alkaline-phosphatase coupled anti-mouse antibody. Spot intensities were measured with the Scion Image software. The results identified the QCTMDQGRLRCR, TCATDQGRLRCT, HCFHDQGRVRCA, HCTMDQGRLRCR and SCMLDQGRSRCR sequences as possible epitopes. 1833 CRNADKFPC CLDNQRPKC CDCRGDCFC 3 Phage display (in vivo) 5 PMID:21768392 Rat synovial tissue Not determined. Not determined. Not determined. CX7C fUSE5 phage display library Authors identified and isolated phages specific for arthritic joints using a combination of ex vivo and in vivo phage screening. For ex vivo screening, authors used CD31-expressing endothelial cells from the joints of an arthritic rat. Two rounds of ex vivo enrichment produced a phage pool that bound 66-fold more efficiently to the endothelial cells compared with the nonrecombinant phage. The ex vivo selected phage was injected i.v. into an arthritic rat, and subsequent three rounds of in vivo selection yielded a 53-fold enrichment of the phage recovered from the synovial tissue, whereas no enrichment was observed in the control tissues, namely the lung and the kidney. Apparently NQR and ADK bind to different receptors/receptor domains on the endothelial cell surface than RGD. We draw this inference based on three findings: (i) no cross-inhibition of phage binding by these peptides; (ii) inhibition of attachment of HUVECs to vitronectin, which involves integrin αvβ3, by RGD peptide, but not by NQR or ADK peptide; and (iii) differential alterations in the MAP kinase signaling pathway events induced by NQR peptide versus RGD peptide. The precise identity of the receptors that bind NQR and ADK peptides to vascular endothelial cells remains to be determined. In terms of functional properties, NQR and RGD, but not ADK, suppressed arthritis. ADK peptide apparently binds to a receptor that does not trigger a detectable tissue response. The antiarthritic activity of NQR is likely attributable, at least in part, to inhibition of angiogenesis and resulting inhibition of leukocyte migration into the inflamed joint. 1834 SSKVYTPTGSLP(1) TLSWGLGSIRTA(1) EDQYLSSEDFLL(1) VFPNNGLALSHV(1) FPGAAGSNRSPL(1) HDTSETKGLTDT(1) TYPNKYTAITPD(1) MKTAMPIKTKWP(1) LPKGSTDSGNMK(1) TLSWGLGSIRTA(1) AEYSMYSAHRPR(1) WYPNKYSPFHQS(1) AQPPKSEGWTLR(1) ATEIIPIALSRP(1) AQPPKSEGWTLR(1) SWLQLVTSKSTL(1) TNSILFARAPAE(1) GYFPLRLPLLSL(1) 18 Phage display (common panning) 3 PMID:21781322 Anti-CAEV polyclonal antibody Caprine arthritis encephalitis virus (strain 63) (CAEV-63) Not determined. Not determined. Ph.D.-12 phage display library (X12) 1835 CTKLSHKNC(2) CHTALAPSC(1) CGTLINNQC(2) CGWHSPMYC(1) CAVFYTTNC(1) CYNRAMIGC(1) CNFFTEPLC(1) CSGKFYPVC(1) CNLPSDPFC(1) CPSHDPWVC(1) CLLQSDPFC(1) CLSKDPFVC(1) CNSDPWVC(1) CSWNHWSYC(3) CSWKHWSYC(1) L-x-SDP-[FY] and SW-[NK]-HWSY 18 Phage display (common panning) 3 PMID:21781322 Anti-CAEV polyclonal antibody Caprine arthritis encephalitis virus (strain 63) (CAEV-63) Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Authors obtained families of 7 mer constrained peptides with consensus motifs LxSDPF/Y and SWN/KHWSY and mapped the epitopes mimicked by them at the Env 6-LISDPY-11 and 67-WNTYHW-72 sites of the mature gp135 amino acid sequence. The first epitope fell into the N-terminal immunogenic aa1-EDYTLISDPYGFS-aa14 site identified previously with a synthetic peptide approach; the second epitope has not been described previously. The first epitope is mostly conserved across CAEV isolates whereas the second newly described epitope is extremely conserved in Small Ruminant Lentiviruses env sequences. As being immunodominant, the epitopes are candidate targets for mimotope-mediated diagnosis and/or neutralization. 1836 CRTLTVRKC CIKRGGKRC 2 Phage display (subtractive panning) 4 PMID:21781994 Recombinant 4e5 domain of human stabilin-2 Not determined. Not determined. Not determined. CX7C T7 phage display library For subtraction of non-specific binding, the 1.0e9 plaque-forming units (pfu) in 100????l of TBST (50 mM Trisa??a After 46 selected phage obtained in the second-to-fourth rounds were sequenced, authors identified the two most commonly occurring clones, with peptide sequences CRTLTVRKC and CIKRGGKLC. ClusterX alignment analysis of all identified peptide sequences did not reveal any shared motif. To confirm selective binding of the two phage clones to the 4e5 domain, a binding assay was conducted. The two clones bound strongly to the human stabilin-2_4e5 protein, compared with insertless phage, and did not bind to other control proteins including the βig-h3 FAS domain, bovine serum albumin, or collagen, suggesting that the two clones bound specifically to the 4e5 domain. Authors examined whether selective binding of the CRTLTVRKC- or CIKRGGKLC-expressing phage to the human stabilin-2_4e5 domain was mediated by the peptides displayed by the phage. To this end, FITC-conjugated synthetic peptides were prepared. Fluorescence microscopic examination indicated that binding of the CRTLTVRKC (S2P) peptide to L/Stabilin-2 cells was significantly higher than to L/MOCK cells. However, the CIKRGGKRC peptide did not bind to either L/Stabilin-2 or L/MOCK cells, as was also the case with NSSSVDK, used as a control peptide. The peptide-binding to L/Stabilin-2 or L/MOCK cells was confirmed via FACS analysis. 1837 CTSTSAPYC(5) CVCCLAGLC(1) CNKWNLLNC(1) CTHDYPLVC(1) CPFGSPALC(1) CMRTHHMQC(1) CWANQPATC(1) CMTRHHLDC(1) 8 Phage display (in vivo) 4 PMID:21792566 ICR male mice brain parenchyma Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Following sequential rounds of isolation, a number of phages were sequenced and a peptide sequence (CTSTSAPYC, denoted as PepC7) was identified. Clone 7-1, which encodes PepC7, exhibited translocation efficiency about 41-fold higher than the random library phage. Immunofluorescence analysis revealed that Clone 7-1 had a significant superiority on transport efficiency into the brain compared with native M13 phage. Clone 7-1 was inhibited from homing to the brain in a dose-dependent fashion when cyclic peptides of the same sequence were present in a competition assay. Interestingly, the linear peptide (ATSTSAPYA, Pep7) and a scrambled control peptide PepSC7 (CSPATSYTC) did not compete with the phage at the same tested concentration (0.2-200 pg). Labeled by Cy5.5, PepC7 exhibited significant brain-targeting capability in in vivo optical imaging analysis. The cyclic conformation of PepC7 formed by disulfide bond, and the correct structure itself play a critical role in maintaining the selectivity and affinity for the brain. In conclusion, PepC7 is a promising brain-target motif never been reported before and it could be applied to targeted drug delivery into the brain. 1838 LPWWLPYRGESN(3) SPLSWWPHATVG(2) YGPWWYSSNAES(2) LPWWPQASISPP(1) LPWWPIQRVSHL(1) LPWWIPKEGWAV(1) LPWWLPPSLSRV(1) AGPWWHQTSVHV(1) NIPWWPFSLHAP(1) GGAWWPTSLVMY(1) APYSWWPYSAYN(1) SSVKSWWPAFTP(1) WYPQPFWPYRQA(1) YGKPFWPSSLWW(1) IPYWPFLPDTSM(1) LPYWLPYSSGNK(1) VPYWMPPPTVIP(1) PWWP 17 Phage display (common panning) 5 PMID:21816124 Plasmodium berghei ookinetes Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Fluorescence Specific peripheral immunofluorescence was uniformly observed on ookinetes incubated with selected phage clones 5 (LPWWPIQRVSHL) and 14 (SPLSWWPHATVG). Ookinetes incubated with non-selected phage clone and/or incubated with secondary antibody only showed no signal. The 21 selected phage peptides had adjacent residues of tryptophan (W) and proline (P) within their sequence, with proline residues flanking tryptophan. Prolines (8/21) were frequently associated with leucine (L) residues. A consensus peptide sequence (PWWP) was identified in phages that bound to the Plasmodium berghei ookinete surface and, in selected phages, bound to actin and enolase in overlay assays with ookinete protein extracts. Actin was localized on the surface of fresh live ookinetes by immunofluorescence and electron microscopy using specific antibodies. The overall results indicated that enolase and actin can be located on the surface of ookinetes, and suggest that they could participate in Plasmodium invasion of the mosquito midgut. 1839 CVKWRGVVVC 1 Phage display (common panning) 4 PMID:21821708 Membrane primary amine oxidase Sialic acid-binding Ig-like lectin 9 (Siglec-9) Not determined. Not determined. CX8C phage display library After 4 rounds of panning using recombinant VAP-1 as a bait, we obtained a 400-fold enrichment of phages bound to VAP-1 compared with the control (BSA-coated wells). Of the 23 randomly selected phages sequenced, 19 gave a sequence. Database searches with the sequence derived from the phage clones revealed similarities to the amino acid sequence of Siglec-9 (residues 289-295). In the binding assays, the phage peptide bound selectively to recombinant VAP-1. The binding between Siglec-9 and VAP-1 was confirmed by in vitro and ex vivo adhesion assays. The interaction sites between VAP-1 and Siglec-9 were identified by molecular modeling and confirmed by further binding assays with mutated proteins. 1840 RGR RQR RRY TRR RPR RRA QRR RRG 8 Phage display (common panning) 5 PMID:21821948 Soluble 37/48kDa oligomer formation of Aβ(1-42) Not determined. Not determined. Not determined. X3 T7 phage display library After the fifth round, arginine-containing peptides were enriched in phage library. 1841 RRRA RGKK KAVR RFRK RRRL RSKK RRKV KRAS 8 Phage display (common panning) 5 PMID:21821948 Soluble 37/48kDa oligomer formation of Aβ(1-42) Not determined. Not determined. Not determined. X4 T7 phage display library After the fifth round, arginine-containing peptides were enriched in phage library. SDS-PAGE and size-exclusion chromatography indicated that the inhibitory activities of 4-residue peptides against the soluble 37/48kDa oligomers of Aβ42 were higher than those of the 3-residue peptides, and RFRK exhibited strong inhibitory activity as well as SRPGLRR. SEPGLRR, a 7-residue peptide found by phage display, exhibited inhibitory activity against soluble 37/48kDa oligomers of Aβ42 (Mimotope Set ID: 1317) 1842 CLRSHPLGC CTFASVMTC 2 Phage display (common panning) PMID:21829538 Soluble ectodomain of APP isoform sAPPα695 Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Five out of 28 individually picked sAPPa-binding clones contained the peptide sequence LRSHPLG. An additional sAPPa-binding clone comprising amino acid sequence TFASVMT was isolated. The sequences of both peptides were then compared to human protein sequences in the NCBI databank using BLAST. This analysis revealed that both peptides presented significant sequence homologies to several members of the human semaphorin protein family. Interestingly, the TFASVMT peptide is homologous to a region of semaphorin 3A that has been shown to be important for receptor recognition, while the region that is homologous to the LRSHPLG peptide lies very close to that same important site. These initial results suggested that sAPPa binds to semaphorins at a domain that is important for receptor recognition and biological activity. 1843 CLLGTRWPC CFMESVGRC CLTPEFHIC CLAVGEVLC CFVSPPVGC CMPGWEVLC CKRGNSGSC CQRLVGFAC CLQASPNFC CNGSVRSFC CPGFGLAYC CFLFTFEAC CRGVLMRYC CRAFVVASC CQSHSAFVC 15 Phage display (subtractive panning) 4 PMID:21829599 Human thymic CD4+CD25+ T cells Not determined. Not determined. Not determined. fUSE5-based CX7C phage display library Screening of the phage library was performed by the BRASIL method, which allows the separation of cell-bound from unbound phage in one step. CD4+CD25- cells were used for preclearing. Among the phages sequenced a specific phage peptide for further analysis due to its sequence similarity to the Vitamin D receptor (VDR). This was the first choice because although Vitamin D has been extensively reported to display immunoregulatory functions in different contexts, its role has not been well-defined for human thymic T regs, opening an interesting area for research. The results from the ELISA assay showing that VDR phage was able to bind to active Vitamin D strongly supports our hypothesis. When phages were preincubated with Vitamin D we did not observe binding to VDR, confirming that the peptide, in fact, mimic the Vitamin D binding pocket in VDR and is able to prevent Vitamin D from binding to its native receptor. 1844 HWGNHSKSHPQR(3) HTLHRQVPKHWL(2) HYQHNTHHPSRW(2) HSSSASDRSRPL(1) STHHRHYHDTLA(1) GHIHSMRHHRPT(2) KHMHWHPPALNT(28) 7 Phage display (common panning) 5 PMID:21856287 PreS1 protein Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of H-(X)n-H-(X)m-H-P/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. 1845 QDEERVSSCPKVAWTFC NCNKNDHLFACW ECKSDWMPPYCP ECTQKYDWLFCM 4 Phage display (common panning) 3 PMID:21872636 Anti-Li venom monoclonal antibody LimAb7 Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1bi Not determined. Not determined. LX-8, X15, X8CX8, X30 phage display library pool These mimotopes, together with a 3D model of LiD1, were used to predict with the MIMOP bioinformatics tool the putative epitope region (residues C197, Y224, W225, T226, D228, K229, R230, T232 and Y248 of LiD1) recognized by LimAb7. This analysis and results of alanine-scanning experiments highlighted a few residues (such as W225 and D228) that are found in the active site of different SMases D and that may be important for LiD1 enzymatic activity. 1846 HAWDPIPARDPF(4) AAWHLIVALAPN(1) ATSHLHVRLPSK(5) 3 Phage display (subtractive panning) 5 PMID:21887228 Influenza A virus (A/goose/Jilin/hb/2003(H5N1)) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Since the viruses were harvested from the cells, therefore, a subtract panning was conducted. In the fourth round of panning, the coated viruses were replaced by the supernatant form Madin-Darby canine kidney (MDCK) cells culture. Putative binding motifs to H5N1 viruses were identified by DNA sequencing. In terms of the minimum quantity of viruses, the phage-based ELISA was better than antiserum-based ELISA and a manual, semi-quantitative endpoint RT-PCR for detecting H5N1 viruses. More importantly, the selected phages bearing the specific peptides to H5N1 viruses were capable of differentiating this virus from other avian viruses in enzyme-linked immunosorbent assays. 1847 CTGSTQHQC CHSALTKHC CSTHFIDTC 3 Phage display (common panning) 5 PMID:21903933 Porcine skin Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Screening studies were performed on porcine skin in Franz diffusion cells (FDCs, PermeGear). The phage display library was placed in the donor compartment of the FDC. After 24 h, phage which had penetrated through the skin were collected from the receiver compartment, amplified, and again placed in the donor compartment for an additional round of screening to further narrow down the library. Peptides that penetrate the SC were identified using in vitro phage display, which were labeled a skin permeating and cell entering (SPACE) peptide. In vitro studies indicated that the SPACE peptide, when conjugated to cargoes such as small molecules and proteins, was able to facilitate their penetration across the SC into epidermis and dermis. 1848 CKTGSHNQC(0.3) CMGPSSMLC(0.3) CTDPNQLQC(0.2) 3 Phage display (common panning) 5 PMID:21903933 Porcine dermis Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) For the dermis screen, the phage display library was also placed in the donor compartment of the FDC. After 24 h, the liquid from the donor compartment was removed and the skin was placed at 60 °C for 90 s. The epidermis was then removed from the dermis. To extract phage from the dermis, the dermis was cut up into small pieces and then homogenized (IKA disperser). Phage screening was performed to isolate phage that localized in the dermis. 1849 CDPSPHTHC(7) CPSSLTPAC(2) CFPHGLGLC(1) CSPAVPMLC(1) 4 Phage display (common panning) 3 PMID:21906439 Ig-like C2-type 1-3 domain of c-kit Kit ligand 2E9W, Not determined. Ph.D.-C7C phage display library (CX7C) The synthesized peptides CDPSPHTHC and CPSSLTPAC, particularly CPSSLTPAC, stimulated UT-7 cell proliferation. 1850 HEPSSFVFFPLS(1) NALKPQGLHSWY(1) AVSSFERDNFVQ(2) TPLKAHLHSQRH(1) NSFHVPRLLIAG(1) THSFIPRLPLLK(1) WPKYTPRVFPHF(1) 7 Phage display (common panning) 3 PMID:21906439 Ig-like C2-type 1-3 domain of c-kit Kit ligand 2E9W, Not determined. Ph.D.-12 phage display library (X12) The synthesized peptides AVSSFERDNFVQ and THSFIPRLPLLK, particularly THSFIPRLPLLK, stimulated UT-7 cell proliferation.