576 QKTLAKSTYMSA(9) APHWKHKREPPT(1) MPSLNNTESKLG(1) MSQPTTNKMLLS(1) SKKRFPNTSFRQ(1) LPPWKHKTSGVA(1) APPPTHWKKQLY(1) SMEPRKGPKRRG(1) 8 Phage display (common panning) 3 PMID:19100827 Anti-MrkD monoclonal antibody E01 Fimbria adhesin protein Not determined. Not determined. Ph.D.-12 phage display library (X12) This monoclonal antibody was produced by the hybridoma technique using recombinant MrkD-GST as the immunogen. It had an IgG1 isotype and showed high specificity to MrkD protein with an affinity of about 0.3 mg/ml. Thirty-six phage clones were randomly selected and their specificity to mAb was verified by sandwich and competitive inhibition ELISA. Sixteen phage clones were sequenced. 577 GEPQTKLFSFPL(10)[1.13 ± 0.14] 1 Phage display (subtractive panning) 3 PMID:19103307 Anti-CTGF monoclonal antibody 7G2 Connective tissue growth factor Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Microtiter wells were coated with 2 μg/ml of ZD521 peptide, TrxA-ZD521, or TrxA and blocked with PBS containing 10% fetal bovine sera. 7G2(anti-CTGF antibody) in the concentrations of 0, 0.1, 0.5, 1, 2 μg/ml was added to the wells. Bound 7G2 was detected with HRP-conjugated anti-mouse IgG antibody and then with the substrate. The values are recorded at OD450 nm. SDs are indicated by error bars. Only the value of the binding of ZD521 peptide to 7G2 in the concentration of 2 μg/ml was shown. Data were reproduced from the graph. This monoclonal antibody was produced by the hybridoma technique using recombinant CTGF C-terminal domain as the immunogen. The results of ELISA assays and Westen-blot showed that 7G2 could specifically bind to TrxA-CTGF/C and kidney mesangial cell lysates, but not to TrxA. The phage library was reabsorbed by mouse serum IgG and BSA to remove non-specific binders, and then specifically absorbed with 7G2. After 3 rounds of selection, roughly 31.3% (10/32) of the phage clones analyzed exhibited 7G2 binding activity by ELISA. All 10 positive phage clones were sequenced, and the sequences of all clones were identical, i.e. GEPQTKLFSFPL. The antiserum from mice immunized with TrxA-GEPQTKLFSFPL could also bind to CTGF/C recombinant protein and native CTGF, as well as significantly inhibit the proliferation of kidney mesangial cells induced by CTGF/C. 578 SVSVGMLPSPRP(20)[24.07 ± 3.40] SSWILSPYHWGR(13)[34.59 ± 8.20] GSFASLTNPRVL(8)[15.13 ± 1.36] TIQHQNPPHYAV(7)[2.76 ± 0.20] SNPHTDNHWPGR(2)[16.18 ± 1.59] 5 Phage display (common panning) 5 PMID:19389430 Phytophthora capsici extract Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA The apparent dissociation constant (Kd, pM) was obtained from a binding saturation curve fitted from three independent experiments. After five rounds of biopanning, 50 plaques were selected and sequenced. All the phages showed high binding affinity for P. capsici in the picomolar range. Phages bearing SVSVGMLPSPRP, TIQHQNPPHYAV and GSFASLTNPRVL inserts showed high specificity toward P. capsici, whereas GSFASLTNPRVL and SNPHTDNHWPGR bearing phages also bound to some of the similar Phytophthora strains with comparable affinities. 579 NHNMHRTTQWPL(2) KVTLHHPPITRS(2) KHLNFLEGRPTF(2) TGLPLYINEGRP(2) YTPQKKIERAFG(1) NPLPSNSPPTRS(1) 6 Phage display (common panning) 3 PMID:19400768 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Phages with encoded peptides were eluted with 100 μl of 0.2 M glycine/HCl (pH 2.2). NHNMHRTTQWPL inhibited MurE ATPase activity with an IC50 value of 500 μM. The inhibition was shown to be time-dependent and was reversed by the addition of meso-A2pm or UDP-MurNAc-Ala-Glu during the pre-incubation step. MurEp1 was found to interfere in meso-A2pm and UDP-MurNAc-Ala-Glu binding necessary for amide bond formation. 580 KVTLHHPPITRS(2) YTPQKKIERAFG(1) KSASNHQAHWLK(1) TPWHFHSTNGFR(1) INKPFHKVMPYA(1) HSVHSKARHLYT(1) TGLPLYINEGRP(1) YTTSNTLQVIAR(1) SFSNLAPSTRGT(1) 9 Phage display (common panning) 3 PMID:19400768 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Phages with encoded peptides were eluted with 100 μl of 1mM ATP. NHNMHRTTQWPL inhibited MurE ATPase activity with an IC50 value of 500 μM. The inhibition was shown to be time-dependent and was reversed by the addition of meso-A2pm or UDP-MurNAc-Ala-Glu during the pre-incubation step. MurEp1 was found to interfere in meso-A2pm and UDP-MurNAc-Ala-Glu binding necessary for amide bond formation. 581 NHNMHRTTQWPL(6) YTPQKKIERAFG(2) YPHYSLPGSSTL(1) HWKHEMYPRTRL(1) 4 Phage display (common panning) 3 PMID:19400768 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Phages with encoded peptides were eluted with 100 μl of 1 mM meso-A2pm. NHNMHRTTQWPL inhibited MurE ATPase activity with an IC50 value of 500 μM. The inhibition was shown to be time-dependent and was reversed by the addition of meso-A2pm or UDP-MurNAc-Ala-Glu during the pre-incubation step. MurEp1 was found to interfere in meso-A2pm and UDP-MurNAc-Ala-Glu binding necessary for amide bond formation. 582 ATLTDLMWFWMG ITIPLYALRSTA 2 Phage display (subtractive panning) 4 PMID:19454218 Anti-GA4 monoclonal antibody 8/E9-Gibberellin A4 complex Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Before and after binding reaction with 8/E9 in the presence of GA4, clones that bind 8/E9 Ab in the absence of GA4 were removed with immunotubes that had been coated with 8/E9 Ab in the absence of GA4. The 2 peptides showed specific binding to the complex of the antibody and its ligand GA4; that is, the antibody could not be replaced with the other anti-GA4 antibody, and GA4 could not be replaced with GA1, another ligand of the antibody. ITIPLYALRSTA showed higher GA4 dependency for binding to 8/E9. 583 TMTPPTR(0.066) GNDWPHW(0.066) EHPYITV(0.066) SSLLPTT(0.066) NTNTLHL(0.066) SYPDLHL(0.066) SILPYPY(0.6) 7 Phage display (subtractive panning) 2 PMID:19576904 The idiosyncratic pseudoknot structure (h18) formed by the segment 500–545 of 16S rRNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) he library was initially counter-selected by pre-incubation with the streptavidin-coated solid carrier used in selection. Target-bound phages were released by DNase treatment. A synthetic 59-nt RNA/DNA hybrid that was composed of a 49-nt RNA segment representing h18 of Bacillus anthracis 16S rRNA followed by a 10-nt poly-dA tail with biotin attached at the 3′ end was used as a target for panning. SILPYPY was the only sequence found among 60 sequenced phages after the third round of selection. Such a rapid drop in library complexity was unexpected and might have reflected an unusual susceptibility of the poly-dA tail to DNase I when the RNA/DNA hybrid target was associated with the corresponding phage variant. The peptide SILPYPY moderately stimulated protein synthesis. 584 FPGHSGP(0.02) VQSLPSP(0.02) EPLQLKM(0.02) TPHNTST(0.02) QWTWTQY(0.02) LTHPRWP(0.02) TKTDTWL(0.02) LSPKLPT(0.02) NTPQGMT(0.03) THPLLLS(0.07) GHWEARE(0.07) AVPRASF(0.07) YHPMPVP(0.08) TPTTDGP(0.2) AGAAMSH(0.32) 15 Phage display (subtractive panning) 4 PMID:19576904 The idiosyncratic pseudoknot structure (h18) formed by the segment 500–545 of 16S rRNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The library was initially counter-selected by pre-incubation with the streptavidin-coated solid carrier used in selection. Target-bound phages were released by low-pH elution. A synthetic 59-nt RNA/DNA hybrid that was composed of a 49-nt RNA segment representing h18 of Bacillus anthracis 16S rRNA followed by a 10-nt poly-dA tail with biotin attached at the 3′ end was used as a target for panning. AGAAMSH efficiently interfered with both bacterial and eukaryotic translation. It exhibited a high affinity binding to the isolated small ribosomal subunit (Kd of 1.1 μM). 585 AMSAPIP(94) GTMLAAV(4) MKHPPRI(2) 3 Phage display (subtractive panning) 4 PMID:19576904 The idiosyncratic pseudoknot structure (h18) formed by the segment 500–545 of 16S rRNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) The library was initially counter-selected by pre-incubation with the streptavidin-coated solid carrier used in selection. The phage-target complexes were captured in the wells of streptavidin-coated microtiter plate and were eluted with a low-pH buffer. A synthetic 59-nt RNA/DNA hybrid that was composed of a 49-nt RNA segment representing h18 of Bacillus anthracis 16S rRNA followed by a 10-nt poly-dA tail with biotin attached at the 3′ end was used as a target for panning. GTMLAAV and AMSAPIP reduced protein yield by 70-80%. 586 TLTYTWS 1 Phage display (in vivo) 2 PMID:19584266 MMP-2-processed pepsin-extracted collagen IV from human placenta Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) In a first step, a pool of potential tumor-homing phage was selected in vivo. In a second step, this phage pool was panned against immobilized MMP-2-processed pepsin-extracted collagen IV from human placenta in vitro. Seven individual phage clones from the second round of in vitro selection were isolated. The phage clone displayed the sequence TLTYTWS could bind to MMP-2-processed collagen IV but not to native collagen IV. 587 LVPPSFS(2) LPLTALP(2) LPLTPLP(2) HPVHHYQ(2) LPGIMSL(1) HKVVAYY(1) HSNTGYP(1) TIGLITS(1) TSGLASR(1) FPLLNML(1) NNLLPPY(1) SIVRLQV(1) SISVIQE(1) QPKQFFQ(1) AQCLRIP(1) 15 Phage display (subtractive panning) 3 PMID:19645415 Hp-AS-pwk RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Preselection was conducted with prewashed beads to remove streptavidin-binding phage. For screening, the hp-AS-pwkRNA was refolded and hybridized with the 50-biotin-DNA in a 1:1 molar ratio. \r\nThe phages were eluted nonspecifically with 100 μL of buffer B (0.2M glycine-HCl, pH2.2, 1mg/mL BSA) for exactly 9 min followed by neutralization with 15 μL of buffer C (1M Tris-HCl, pH 9.1). HPVHHYQ and LPLTPLP displayed selective binding to the A-site 16S rRNA with on-bead fluorescence assays. 588 LPLTPLP(2) LPLTALA(2) AQATALP(1) LPLTPLA(1) HPVHHYQ(1) TLHPAHP(1) TIGAITS(1) TQSLASR(1) GSWPSLL(1) NWSSLY(1) NAFHSHI(1) SHIMPPN(1) QPTSEGL(1) QCWSPSL(1) QSTLNPT(1) 15 Phage display (subtractive panning) 3 PMID:19645415 Hp-AS-pwk RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Preselection was conducted with prewashed beads to remove streptavidin-binding phage. For screening, the hp-AS-pwkRNA was refolded and hybridized with the 50-biotin-DNA in a 1:1 molar ratio. The phages were eluted specifically with 100 μL of buffer A containing 300 pmol of nonbiotin-labeled target RNA (hp-AS) for 1 h at room temperature. HPVHHYQ and LPLTPLP displayed selective binding to the A-site 16S rRNA with on-bead fluorescence assays. 589 LPLTPLP(4) SAKLMGH(2) HPVHHYQ(2) LPVTPLP(1) NQDVPLF(1) VSSGPHW(1) TIGAITS(1) 7 Phage display (subtractive panning) 4 PMID:19645415 Hp-AS-pwk RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Preselection was conducted with prewashed beads to remove streptavidin-binding phage. For screening, the hp-AS-pwkRNA was refolded and hybridized with the 50-biotin-DNA in a 1:1 molar ratio. The phages were eluted nonspecifically with 100 μL of buffer B (0.2M glycine-HCl, pH2.2, 1mg/mL BSA) for exactly 9 min followed by neutralization with 15 μL of buffer C (1M Tris-HCl, pH 9.1). In the fourth round, the competitor RNA (hp-C, which is missing the triple A bulge at nucleotides 1492, 1493, and 1408,) was used in a counter-selection. HPVHHYQ and LPLTPLP displayed selective binding to the A-site 16S rRNA with on-bead fluorescence assays. 590 LPLTPLP(7) LPLTTLH(1) QLPTTLP(1) TIGAITS(1) 4 Phage display (subtractive panning) 4 PMID:19645415 Hp-AS-pwk RNA Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) Preselection was conducted with prewashed beads to remove streptavidin-binding phage. For screening, the hp-AS-pwkRNA was refolded and hybridized with the 50-biotin-DNA in a 1:1 molar ratio. The phages were eluted specifically with 100 μL of buffer A containing 300 pmol of nonbiotin-labeled target RNA (hp-AS) for 1 h at room temperature. In the fourth round, the competitor RNA (hp-C, which is missing the triple A bulge at nucleotides 1492, 1493, and 1408,) was used in a counter-selection. LPLTPLP displayed selective binding to the A-site 16S rRNA with on-bead fluorescence assays. 591 EGEVGLG(0.58) MRRSVGS(0.14) SSAVL(0.08) VLI(0.08) SAGSVAL(0.06) FGVR(0.03) GFWEGGL(0.03) 7 Phage display (in vivo) 4 PMID:19825959 Human breast cancer cell line MDA-MB-231 Not determined. Not determined. Not determined. X9 T7 phage display library Mice bearing MDA-MB-231 human breast tumors were subject to 40 mg/kg sunitinib given i.p. for 3 consecutive d. Treatment began 30 d after tumor implantation. The phage libraries were administered 4 h after the last treatment. Phages were recovered after being in circulation for 16h by harvesting the tumors in the mice. Phages recovered from excised tumors were amplified and subjected to three more rounds of selection. Thirty-six phage plaques were sequenced after the 4th round of panning. EGEVGLG was the dominant sequence isolated from biopanning. This peptide showed increased binding relative to control groups in two cancer cell lines (MDA-MB-435 and MCF-7 human breast) responding to sunitinib treatment, whereas no elevated binding occurred in vitro when samples were incubated with tumor cells that are unresponsive to sunitinib treatment (B16 melanoma and BxPC3 pancreatic). 592 EGEVGLG(0.67) MRRSVGS(0.12) SSAVL(0.18) FGVR(0.01) GFWEGGL(0.03) 5 Phage display (in vivo) 4 PMID:19825959 Human breast cancer cell line MCF-7 Not determined. Not determined. Not determined. X9 T7 phage display library Mice bearing MDA-MB-231 human breast tumors were subject to 40 mg/kg sunitinib given i.p. for 3 consecutive d. Treatment began 30 d after tumor implantation. The phage libraries were administered 4 h after the last treatment. Phages were recovered after being in circulation for 16h by harvesting the tumors in the mice. Phages recovered from excised tumors were amplified and subjected to three more rounds of selection with mice bearing MCF-7 human breast tumors. Thirty-six phage plaques were sequenced after the 4th round of panning. EGEVGLG was the dominant sequence isolated from biopanning. This peptide showed increased binding relative to control groups in two cancer cell lines (MDA-MB-435 and MCF-7 human breast) responding to sunitinib treatment, whereas no elevated binding occurred in vitro when samples were incubated with tumor cells that are unresponsive to sunitinib treatment (B16 melanoma and BxPC3 pancreatic). 593 CGYWRSEWGLC(11)[1.34] CTGYWPKAWGLC(7)[1.37] CTGFWEREWGLC(4)[0.82] CLYWPRLWGLC(1)[0.29] CYWAVRWGLLGC(1)[0.26] CGYWADVWQIHC(1)[0.50] [YF]-W-x(3)-W-G-L 6 Phage display (common panning) 5 PMID:19233852 Human IgG-Fc acid conformer Not determined. Not determined. Not determined. CX7-10C T7 phage display library ELISA The absorbance at 450 nm was measured using a microplate reader. Data were reproduced from the graph. These peptides recognized the non-native conformer (acid conformer) of human IgG that was generated by the low pH treatment, but not the native conformer. 594 CSSAFYPKC(8) CTRQPDRSC(1) CTLQPDRSC(1) CSLQPDRSC(1) 4 Phage display (common panning) 4 PMID:19290051 Anti-BoNT monoclonal antibody F1-40 Botulinum neurotoxin type A, BoNT/A Not determined. Not determined. Ph.D.-C7C phage display library (CX7C) 595 IGKIDRV(4) RILASRV(4) IGRRSRV(4) RLRASRV(2) SPRQSRV(2) IGKISRV(2) RLRASWV(2) SRRVSEV(1) AHRVSRI(1) KGRMTRV(1) AGRTTQV(1) SHRQSRV(1) IRRPSIV(1) VIVVSSV(1) TLRESVI(1) WDRASSV(1) PVKFSAV(1) [RK]-x-S-R-V 17 Phage display (common panning) 3 PMID:19235856 PDZ10 domain of Multiple PDZ domain protein 5-hydroxytryptamine receptor 2C Not determined. Not determined. X7 T7 phage display library IGRISRV displayed a two-fold improved affinity over the octapeptide derived from the carboxy terminus of the hc-Kit protein, which was demonstrated as among the highest affinity ligands reported to date for that domain. 596 AWKQTSV(7) FEMGTPV(5) SPRQSRV(3) MVGNMLV(2) EFRESSV(2) AWKQTTV(1) RRVESSV(1) RVRESKV(1) VVIGTSV(1) SEDPIAV(1) WDNGTRV(1) DLRTTSV(1) RDKGTRV(1) RFQETQI(1) 14 Phage display (common panning) 3 PMID:19235856 PDZ3 domain of Postsynaptic density protein 95 (PSD-95) Cysteine-rich PDZ-binding protein Not determined. Not determined. X7 T7 phage display library FEMGTPV possessed a reduced affinity, which was about 10-fold lower than that of benchmark KKETEV peptide, but comparable with the smallest recognizable CRIPT peptide fragment (KQTSV) binding. 597 CQQSNRGDRKRC(3) CMGNKRSAKRPC(3) CESHRQRRAKC(2) CKRTSKCGGKC(1) CLRKRRENTKC(1) CHHWTFRKTTC(1) CSPNNTRRPNK(1) 7 Phage display (common panning) 5 PMID:19123480 Embryonal Rhabdomyosarcoma cell line RD Not determined. Not determined. Not determined. CX7-10C T7 phage display library Sixteen clones were sequenced. CQQSNRGDRKRC and CMGNKRSAKRPC binded to rhabdomyosarcoma and to other tumour cell lines, but not to normal skeletal muscle cells and fibroblasts. 598 RCMTSRS(9) LATTVPH(4) TATTIPT(1) 3 Phage display (common panning) 3 PMID:19811729 Ouabain Not determined. Not determined. Not determined. Ph.D.-7 phage display library (X7) RCMTSRS could reverse the growth inhibition and death induction of ouabain in EAhy926 cells. 599 TPMNHHSQHAER(16)[1.12 ± 0.02] AHLPIVRASLPS(12)[1.33 ± 0.07] FPSSLIIPPLPN(7)[0.32 ± 0.06] GNIIPDRPMHPT(5)[0.64 ± 0.03] 4 Phage display (subtractive panning) 4 PMID:19550037 Disintegrin domain of ADAM 15 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) ELISA Binding was detected using the anti-M13 antibody and expressed as the absorbance (405 nm). Results are expressed as the mean ± SD of triplicate experiments. Data were reproduced from the graph. Two rounds of subtractive selection with streptavidin were performed. AHLPIVRASLPS was found to be homologous with integrin 600 VRKRSECLGAHD(19) 1 Phage display (subtractive panning) 3 PMID:19778796 Hepatocellular carcinoma cell line HepG2 Not determined. Not determined. Not determined. Ph.D.-12 phage display library (X12) Subtractive selection with human liver cell line L02 cells was performed. Among 30 clones picked, 27 clones have proper insetions. However, only the most frequent sequence is given in the original paper. Immunocytochemistry and immunohistochemistry confirmed the specificity of the VRKRSECLGAHD bearing phage binding to the hepatoma cells.