1226 HWGMWSY(1) NWGMWSY(1) PHWTWVL(1) HMSKPVQ(1) SSGTHAK(1) YNINIRP(1) NYTQTVP(1) 7 Phage display (common panning) 4 PMID:11748221 HMG box 1 domain of high mobility group protein B1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Peptides were eluted unspecifically by low pH. A computer search of the protein data bases found peptide homologies with proteins already known to interact with HMGB1, like p53, and have allowed us to identify new potential candidates. Among them, transcriptional activators like the heterogeneous nuclear ribonucleoprotein K (hnRNP K), repressors like methyl-CpG binding protein 2 (MeCP2), and co-repressors like the retinoblastoma susceptibility protein (pRb) and Groucho-related gene proteins 1 (Grg1) and 5 (Grg5) can be found. 1227 SSPHNHS(6) HAIYPRH(6) QISFMAN(4) TLTTPIL(2) HWGMWSY(1) ISIPRTM(1) TPAHNDY(1) FHMGQPF(1) APTPVKL(1) HMALNXV(1) MHSLSYR(1) WHWWPXL(1) GETRAPL(1) VQASNSN(1) GNSLRWD(1) SAPQILL(1) DTDPPGL(1) 17 Phage display (competitive panning) 4 PMID:11748221 HMG box 1 domain of high mobility group protein B1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Peptides were eluted by affinity with the same HMG-box used for the biopanning. A computer search of the protein data bases found peptide homologies with proteins already known to interact with HMGB1, like p53, and have allowed us to identify new potential candidates. Among them, transcriptional activators like the heterogeneous nuclear ribonucleoprotein K (hnRNP K), repressors like methyl-CpG binding protein 2 (MeCP2), and co-repressors like the retinoblastoma susceptibility protein (pRb) and Groucho-related gene proteins 1 (Grg1) and 5 (Grg5) can be found. 1228 IQSPHFF(8) LPLTPLP(7) NQDVPLF(2) WPKLASH(2) SPAHAAK(1) ASMSVAI(1) AWLPWAK(1) MPNRTAN(1) NLPAYTS(1) CSSVETH(1) GTPTLXS(1) VMPWVHK(1) YAPRLRS(1) APPTRNQ(1) 14 Phage display (competitive panning) 4 PMID:11748221 HMG box 2 domain of high mobility group protein B1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Peptides were eluted by affinity with the same HMG-box used for the biopanning. A computer search of the protein data bases found peptide homologies with proteins already known to interact with HMGB1, like p53, and have allowed us to identify new potential candidates. Among them, transcriptional activators like the heterogeneous nuclear ribonucleoprotein K (hnRNP K), repressors like methyl-CpG binding protein 2 (MeCP2), and co-repressors like the retinoblastoma susceptibility protein (pRb) and Groucho-related gene proteins 1 (Grg1) and 5 (Grg5) can be found. 1229 HWGMWSY(5) HSWLWWP(5) LAMPQYE(2) KLWVIPQ(1) SHWFWSW(1) HAIYPRH(1) SRPHTSD(1) HYWWWPR(1) SSSSHPT(1) PGAQLTK(1) STTLRYF(1) 20 Phage display (competitive panning) 4 PMID:11748221 HMG box 2 domain of high mobility group protein B1 Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Peptides were eluted by affinity with the same HMG-box used for the biopanning. A computer search of the protein data bases found peptide homologies with proteins already known to interact with HMGB1, like p53, and have allowed us to identify new potential candidates. Among them, transcriptional activators like the heterogeneous nuclear ribonucleoprotein K (hnRNP K), repressors like methyl-CpG binding protein 2 (MeCP2), and co-repressors like the retinoblastoma susceptibility protein (pRb) and Groucho-related gene proteins 1 (Grg1) and 5 (Grg5) can be found. 1230 ACNMLRWDKTIPCR SCTSPVSQGTQPCK VCPHVAPYQTPLCK RCRKVLICRRICP CCTMPNCTLYVLCE VCEHPENKAPPCCP SCRLSTFSMRMVCN VCPTSEILAGATCR RCGPASREKHALCT VCAKGPPQLPRCP GCAIPQNAIRPPCS SCSPTVYLTSTKCP TCCLCSGKLALACE TCPLPDPDSQYCE RCQALSRLFREKCT FCPGVGRYPVRQCY DCQVRRCSRDSHCE NCQTKVTRITESCC PCSRAETNPTMQCP YCPPPLLNSGEPCS TCKQLKAHPPLACM SCTYSGRADAVVCR 22 Phage display (common panning) 2 PMID:18760481 Anti-WNV E protein monoclonal antibody E16 Envelope protein 1ZTX, Not determined. XC(X)10CX phage display library 1231 CGWASGMADGSSNC CAGWKTGEADGSSC CGWTSGKSDGSASC CTSLVADLDHLSSC CPNIGELSHYDPFC CAAWHTGKAEGNGC CAGRWEHGTAEGDC CTLWVLGLADGTRC 8 Phage display (common panning) PMID:17427229 Trastuzumab Receptor tyrosine-protein kinase erbB-2 1N8Z, Not determined. FMC12C phage display library 1232 CYDGSYRWAPC(3) CYDAQHHWTRC(2) CYNAFLNWVPC(2) CSSPFASC(19) CRLPGSAFTYC(1) CHIPGSIFHLC(4) CYPYGSTFGLC(2) CYAHASNFHMC(2) CRTTGSVFHLC(1) CRWQGSAFAYC(1) CSTSASNYYLC(1) 11 Phage display (common panning) 1 PMID:7685301 Anti-H Fer monoclonal antibody H107 Ferritin heavy chain Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) Comparison of the selected oligopeptides with one another allowed us to derive two consensus sequences characterized by conserved amino acid (aa) residues. Analysis of the distribution of the aa side chains exposed on the surface of H Fer reveals that most of the aa defining both consensus sequences are present either at the end of the big loop or at the end of the A helix. These two regions of the H Fer, though separated in the linear sequence, are very close in the folded molecule. 1233 GRRPNPPIP(4) GRAPNPNLP(2) GRSPGSHMA(5) 3 Phage display (common panning) 2 PMID:7685299 Anti-PTX S1 monoclonal antibody 1B7 Pertussis toxin subunit 1 (PTX S1) Not determined. Not determined. pVIII-9aa phage display library (X9) The selected recombinant phage are capable of mimicking the discontinuous epitope as far as binding to the corresponding mAb, but they are unable to elicit a detectable production of antibodies specific for the original antigen. 1234 CFLRFHPHVLC(1) CRGTSPMDATC(1) CSRTGRCGHGG(1) 3 Phage display (common panning) 2 PMID:7685299 Anti-PTX S1 monoclonal antibody 1B7 Pertussis toxin subunit 1 (PTX S1) Not determined. Not determined. pVIII-9aa.Cys phage display library (CX9C) The selected recombinant phage are capable of mimicking the discontinuous epitope as far as binding to the corresponding mAb, but they are unable to elicit a detectable production of antibodies specific for the original antigen. 1235 IPKSRKRRIPQR(1) PIQRKRRQMPLS(1) PQLRKRRQNSMM(2) SPQRRKRTRQIR(1) IPSRKRRNRIQQ(1) IKHRKRRLRMIL(1) HMRKRTKIKKIR(1) MMKKTRKRTKRR(2) RKR 8 Phage display (common panning) 3 PMID:20637107 Anti-capsid protein 1 monoclonal antibody C4 Capsid protein 1 Not determined. Not determined. Ph.D.-12 phage display library (X12) The epitope of VP1 is located in the N-terminal and contains the role amino acid sequence R-K-R. Immunization of mice indicated that the phage-displayed peptide induces antibodies against PPV. 1236 APWHLSSQYSRT(6) 1 Phage display (in vivo) 3 PMID:20808875 Mouse cardiac tissue Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) A cardiomyoblast cell line, H9C2, was incubated with a M13 phage 12 amino acid peptide display library. Internalized phage was recovered, amplified and then subjected to a total of three rounds of in vivo biopanning where infectious phage was isolated from cardiac tissue following intravenous injection. After the third round, 60% of sequenced plaques carried the peptide sequence APWHLSSQYSRT, termed cardiac targeting peptide (CTP). Authors demonstrate that CTP was able to transduce cardiomyocytes functionally in culture in a concentration and cell-type dependent manner. Mice injected with CTP showed significant transduction of heart tissue with minimal uptake by lung and kidney capillaries, and no uptake in liver, skeletal muscle, spleen or brain. The level of heart transduction by CTP also was greater than with a cationic transduction domain. 1237 KGHSLMP(1) IPTLPSS(1) GTTVIAR(1) QHSEGAL(1) YQDSAKT(1) KVSMNSS(1) LVQPHTR(1) MAHRHPQ(1) QLPGRSG(1) HAIYPRH(1) 10 Phage display (common panning) 4 PMID:20529562 Anti-Human KGF monoclonal antibody Keratinocyte growth factor, KGF Not determined. Not determined. Ph.D.-7 phage display library (X7) Thirty-three out of fifty-eight (56.9%) of the isolated monoclonal phages exhibited high binding activity by ELISA. Ten of fifteen obtained phage model peptides were similar to KGF or epidermal growth factor (EGF). MTT assay data showed that four (No. 1-4) of the ten phage model peptides could promote epidermal cell proliferation. 1238 KHMHWHPPALNT(4) HYQGVHSRYCYH(1) LTPTMFNMHGVL(1) VSRHQSWHPHDL(1) HWPRPDDSFWRP(1) HSTWKLLRLDME(1) GPYFPTHSFLKS(1) 10 Phage display (common panning) 4 PMID:20237096 Nucleocapsid protein Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The selected phages harboring specific peptides that recognize the N protein of PRRSV were able to efficiently distinguish PRRSV from other viruses in enzyme-linked immunosorbent assays. 1239 APWHLSSQYSRT(3) GYPHPWTLWHLN(1) LDVRPWYVTPLP(1) WAPEKDYMQLMK(1) TPLINMNALTVT(1) P-W-x-[LV] 5 Phage display (subtractive panning) 4 PMID:20711469 Mouse embryonic stem cell line M9 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) To exclude non-specific binding, we used the differentiated ES (dES) cells and primary mouse embryonic fibroblast (PMEF) cells, a feeder layer for the maintenance pluripotency of embryonic stem cells, as a control. Each round of biopanning included three subtraction steps with dES cells, three ubtractions steps with PMEFs and then a selection step with ES cells. Through a phage display screen, authors found phages that displayed an APWHLSSQYSRT peptide showed high affinity and specificity to undifferentiated primate embryonic stem cells in an enzyme-linked immunoabsorbent assay. 1240 VPLYSNTLRYGF SYLTTLRYGNMS TQQSVFSTTLMY IPLPPPSRPFFK QPVDMPYFRTHP TLRYG 5 Phage display (subtractive panning) 4 PMID:20639454 Anti-ARD1A polyclonal antibody N-alpha-acetyltransferase 10, NatA catalytic subunit Not determined. Not determined. Ph.D.-12 phage display library (X12) During each round, the library was preincubated with IgGs purified from normal serum pooled from five healthy volunteers and immobilized on Protein G Sepharose 4 Fast Flow (GE Health care, Uppsala, Sweden) to remove nonspecific binding clones. After the preclearing step, the phage library was selected onto the pool of IgGs purified from patient serum. After four rounds of selection, roughly 1% (10/1000) of phage clones exhibited binding activity to serum from patients with colon cancer. DNA from 10 positive clones that specifically reacted with serum from patients was sequenced. Among 10 phage clones examined, five types of peptides were obtained. The peptide VPLYSNTLRYGF showed significant homology to the residues 121-126 (LYSNTL) of ARD1A by BLAST homology search. Authors revealed that human arrest defective 1 (ARD1A) may serve as an indicator of unfavorable prognosis in colon cancer. 1241 WLSEAGPVVTVRALRGTGSW 1 Phage display (common panning) 6 PMID:15313615 Primary cardiac myocytes (PCM) Not determined. Not determined. Not determined. X20 fAFF1 phage display library The isolated phage, displays the peptide WLSEAGPVVTVRALRGTGSW, and binds these cells 180 times better than a control phage from the library. Furthermore, phage displaying this peptide preferentially bind to cardiomyocytes when compared with a panel of other cell types. A BLAST search revealed that this peptide contains a 12 amino acid segment with sequence identity to a peptide in tenascin-X, an extracellular matrix protein. 1242 GRFLIRVTSSPLGPD(1) TGSGLYLHQMVYLYQ(1) FLIDSPLASIGPTSM(12) FMIDSPLASIGPTSM(2) VIDLSGTRKSSSGTM(1) VRKTTSHPPSYALLH(1) TPPYRAALATPVLLL(1) 7 Phage display (subtractive panning) 3 PMID:20682764 Campylobacter jejuni Not determined. Not determined. Not determined. f88-15mer phage display library (X15) The phage-display library was ubtracted twice against C.jejuni strain ACM 3393 in 3 ml PBSg in a Petri dish, prior to being added to C.jejuni strain C338. Non-binding phages were washed away using PBSg as the wash buffer. Cell surface bound phages were recovered with a low pH elution buffer and amplified by infection in E.coli K91BlueKan cells and used in subsequent rounds of affinity selection. In the second and third rounds of affinity selection, non-binding phage were washed away with PBSg. 1243 FSPFRISELVYTLHP(1) LPFNLAKPELYIFVQ(1) LSAPSPMFLPPVNPH(1) HRPVKTPANAPTTMM(1) CFNDPLDIVPPMLLL(2) 5 Phage display (subtractive panning) 3 PMID:20682764 Campylobacter jejuni Not determined. Not determined. Not determined. f88-15mer phage display library (X15) The phage-display library was ubtracted twice against C.jejuni strain ACM 3393 in 3 ml PBSg in a Petri dish, prior to being added to C.jejuni strain C338. Non-binding phages were washed away using PBSg as the wash buffer. Cell surface bound phages were recovered with a low pH elution buffer and amplified by infection in E.coli K91BlueKan cells and used in subsequent rounds of affinity selection. In the second and third rounds of affinity selection, non-binding phage were washed away with TBST. 1244 FLSDPPAPPTSPGVV(5) 1 Phage display (subtractive panning) 3 PMID:20682764 Campylobacter jejuni Not determined. Not determined. Not determined. f88-15mer phage display library (X15) The phage-display library was ubtracted twice against C.jejuni strain ACM 3393 in 3 ml PBSg in a Petri dish and an extra round of subtraction was carried out against C.jejuni strain C338, prior to being added to C.jejuni strain C338. Non-binding phages were washed away using PBSg as the wash buffer. Cell surface bound phages were recovered with a low pH elution buffer and amplified by infection in E.coli K91BlueKan cells and used in subsequent rounds of affinity selection. In the second and third rounds of affinity selection, non-binding phage were washed away with PBSg. 1245 ITAPHPH NPHAHLQ KPHPHVP TPHLHRD LQPHLHR TPHPHLP TPHPHLR LPHVHSR HQSPWHH HRPPHHW TQPHHTP HAIYPRH AAYTHAR YITHPPH YTFPHWH YWNHNHE SPTHGHD SPSHLHL SPHLHGS SPHLHGA SSPLHVH SSPHNHS ISAHEHL SSLLHVH SKLHMHL KSVQHPH TSLHPHP TGAHVHP EGWHAHT TGAHGHP QFTSLLH QLSHTHI QPQYHTS QSIYVRH QYVRHNH 35 Phage display (subtractive panning, competitive panning) 3 PMID:20863124 Toxin A Transforming protein RhoA Not determined. Not determined. Ph.D.-7 phage display library (X7) Since direct surface immobilization of target proteins can lead to partial denaturation, an affinity capture method was used, immobilizing the recombinant catalytic fragment (rTcdA540) to Ni-NTA resin. A preclearance step was performed prior to +each round of panning to remove plastic and Ni2+ binders from the phage pool. The biopanning protocol was specifically designed to identify those phage that bind rTcdA within the substrate binding pocket by requiring direct competition with RhoA. 1246 MLESHAWPPRAI(3) YISPLPNAATIS(1) TFDRHILDTRGS(1) STVASLGKPTKI(1) ASTIGNLMPGHS(2) FDPHEPTNTRSP(2) LTKEPATGRAML(4) YNKPSFQDHSVI(2) DHIRISTSYKSP(1) TPTRSLDSPHNM(2) DRFTSDLRAPDS(1) 11 Phage display (common panning) 3 PMID:20839946 Phakopsora pachyrhizi urediniospores Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Two peptides, MLESHAWPPRAI and YNKPSFQDHSVI, were identified that inhibit germ tube development when displayed as fusions with the coat protein of M13 phage or as fusions with maize cytokinin oxidase/dehydrogenase (ZmCKX1). 1247 HKQPWYDYWLLR(12) SPPTLYEAWLRF(1) YITPYAHLRGGN(1) SLCLSSAVCWPC(1) SLSSEKLAYWGL(1) 5 Phage display (subtractive panning) 3 PMID:20660187 MLV/HIV 89.6 pseudovirions Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) In order to enrich for phage binding to CD4i epitopes, two negative selections were performed, one with MLV/89.6 in the absence of sCD4 and one with sCD4 alone. Each round of positive selection was followed by two consecutive negative selections. During HIV-1 entry, binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor triggers conformational changes resulting in exposure of new epitopes, the highly conserved CD4-induced (CD4i) epitopes that are essential for subsequent binding to chemokine receptor CCR5 or CXCR4. Due to their functional conservation, CD4i epitopes represent attractive viral targets for HIV-1 entry inhibition. Selected peptides showed partial identity with amino acids in the extracellular domains of CCR5/CXCR4, including motifs rich in tyrosines and aspartates at the N terminus known to be important for gp120 binding. 1248 CPLLSAWPC(2) CKSSSPIWC(1) CPPWYYPRC(1) CQSPDKTHC(1) 4 Phage display (subtractive panning) 3 PMID:20660187 MLV/HIV 89.6 pseudovirions Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) In order to enrich for phage binding to CD4i epitopes, two negative selections were performed, one with MLV/89.6 in the absence of sCD4 and one with sCD4 alone. Each round of positive selection was followed by two consecutive negative selections. During HIV-1 entry, binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor triggers conformational changes resulting in exposure of new epitopes, the highly conserved CD4-induced (CD4i) epitopes that are essential for subsequent binding to chemokine receptor CCR5 or CXCR4. Due to their functional conservation, CD4i epitopes represent attractive viral targets for HIV-1 entry inhibition. Selected peptides showed partial identity with amino acids in the extracellular domains of CCR5/CXCR4, including motifs rich in tyrosines and aspartates at the N terminus known to be important for gp120 binding. 1249 CRPDPGSPC(1) CLPLWPGAC(1) CSSRTMHHC(1) CTRTPAKVC(1) CPNMFSTSC(1) CMSGPPNMC(1) CPNIRAPLC(1) 7 Phage display (subtractive panning) 3 PMID:20802991 B16F10-Nex2 melanoma cell Not determined. Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) Melanoma B16F10-Nex2 cells were used as an affinity matrix for selection of C7C random peptide phage library, and the melanocytic melan-A cell line was used for unspecific phage depletion. After a few rounds of enrichment, 50 phages were randomly selected, amplified, and tested for inhibition of tumor cell proliferation. Seven were active, and the corresponding peptide of each phage was chemically synthesized in the cyclic form and tested in vitro. Three peptides were able to preferentially inhibit the melanoma lineage. A unique peptide, [-CSSRTMHHC-], exhibited in vivo antitumor inhibitory activity against a subcutaneous melanoma challenge, rendering 60% of mice without tumor growth. Further, this peptide also markedly inhibited in vitro and in vivo the tumor cell invasion and cell-to-cell adhesiveness in vitro. 1250 LTGKNFPMFHRN MHRMPSFLPTTL 2 Phage display (common panning) 4 PMID:20890540 Extracellular domain of TβR1 (TβR1-ED) Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) The output phage from the third round were used as the input for the fourth round without amplification. After four rounds of panning, 24 phage plaques were sequenced and 7 unique clones were identified. Authors evaluated these clones using a phage enzyme-linked immunosorbent assay (ELISA). Two clones exhibited specificity for the target over BSA.