Phage Random Peptide Library Research Articles

Selection of peptides with affinity for the N-terminal domain of GATA-1: identification of a potential interacting protein

As most transcription factors, GATA-1 activities are mediated by interactions with multiple proteins. Those identified so far associate with the zinc-finger domain and/or surrounding sequences. In contrast, no proteins interacting with the N-terminal domain have been identified although several evidences suggest its involvement in the control of hematopoiesis. In an attempt to identify proteins that interact with the N-terminal transactivation domain of GATA-1, a random phage peptide library was screened with recombinant GATA-1 protein and the sequence of a selected peptide was used for database protein sequence retrieval. We selected a set of peptides sharing the core sequence φ–B (2–3)–ν (2–4) (where φ, B, and ν represent hydrophobic, basic, and neutral residues, respectively). Using the sequence of the most represented peptide (pep5) as query, we retrieved the HIV accessory protein Nef. We show that Nef binds GATA-1 and GATA-3 in vitro in virtue of its sequence homology with pep5.

Identification of novel carrier peptides for the specific delivery of therapeutics into cancer cells.

Cancer therapy is currently limited by the difficulty of achieving efficient delivery into target cells. To investigate whether therapeutics can be delivered specifically to cancer cells, we have explored the possibility of selecting small peptides that bind specifically, or preferentially, to breast cancer cell lines. By using random peptide phage libraries and an experimental approach that allows the selection of internalized peptides, cell-specific binding peptides have been identified. The peptides define a major core motif (LTVXPWY) that was not found in negative phages. Phage displaying LTVSPWY peptide sequence exhibited a specific binding to breast cancer cells. None of the selected peptides bound to human primary cells from different tissue origin (e.g., epithelial, endothelial, hematopoetic). The potential of the selected peptides to mediate cellular internalization in the context of phages and recombinant GFP-peptide fusions was demonstrated. By linking the LTVSPWY peptide to an antisense phosphorothioate oligonucleotide against the ErbB2 receptor, specific delivery to cancer cells was achieved. In contrast to free antisense, the peptide-antisense conjugates inhibited ErbB2 gene expression. Thus, efficient delivery of antisense oligonucleotides can be achieved by coupling them to cancer cell-specific peptides, identified by a method that did not require any knowledge about their corresponding receptors.

Identification of the amino acid residues in trichosanthin crucial for IgE response

Trichosanthin (TCS) is the major effective component from Chinese herb Trichosanthes kirilowii. TCS has been approved to be effective in clinical treatment of HIV infection and leukemia, but its allergenicity has limited its clinical usage. To identify amino acid residues in TCS with an important role in IgE induction, TCS-specific IgE mAb (TE1) was used to serve as a probe and TE1 epitope was determined by a random phage-peptide library. Based on phage peptide sequences, TE1 epitope was predicted at amino acid residues 169–174 ( QQIGKR) of TCS protein. Based on modeling data, two amino acids (Lys173 and Arg174) on TCS were considered to have a crucial role in binding to TE1. After lysine 173 and arginine 174 were mutated to glycine, the mutant TCS protein specifically lost the binding activity to TE1 mAb and exhibited reduced IgE induction in the immunized mice. The data showed that the IgE epitope of TCS was determined and shown to play a critical role in induction of IgE, and the modification of IgE-epitope may be a useful strategy to reduce the allergenicity of an allergen.

Selective alpha4beta7 integrin antagonists and their potential as antiinflammatory agents.

The accumulation of leukocytes in various tissues contributes to the pathogenesis of numerous human autoimmune diseases. The integrin alpha4beta7, expressed on the surface of B and T lymphocytes, plays an essential role in lymphocyte trafficking throughout the gastrointestinal (GI) tract via interaction with its primary ligand, mucosal addressin cell adhesion molecule (MAdCAM). Elevated MAdCAM expression in the intestines and liver has been linked to GI-associated autoimmune disorders, including Crohn's disease, ulcerative colitis, and hepatitis C. Monoclonal antibodies that block the interaction of alpha4beta7 with MAdCAM inhibit lymphocyte homing to murine intestines without effecting migration to peripheral organs; this suggests that alpha4beta7-selective antagonists might be useful as GI specific antiinflammatory agents. Here, we report the discovery of highly potent and selective alpha4beta7 antagonists affinity selected from a random peptide-phage library. Subsequent optimization of initial peptide leads afforded alpha4beta7-selective heptapeptide inhibitors that competitively inhibit binding to MAdCAM in vitro and inhibit lymphocyte homing to murine intestines in vivo. Substitution of a single carboxylate moiety alters selectivity for alpha4beta7 by more than 500-fold to afford a potent and selective alpha4beta1 antagonist. The antagonists described here are the first peptides to demonstrate potency and selectivity for alpha4beta7 compared to other integrins.

Antigen-Specific IgG Antibodies in Stage IV Long-Time Survival Breast Cancer Patients

Profiling the immune responses in patients with cancer is expected to facilitate the design of diagnostic tests and therapeutic vaccines. Such studies usually require the parental antigens. We attempted to profile the immune responses in patients with breast cancer using a peptide phage display selection strategy, which identifies antibody specificities whether or not the antigens are known. A panel of random peptide phage libraries was panned on serum IgG antibodies from breast cancer patients with stage IV, seeking for disease specific IgG epitopes. ELISA, immunoscreening, and Western blotting techniques were the main approaches used. Phage-displayed peptides were specifically enriched for binding to IgG antibodies from patients with breast cancer. Several peptides have been identified, in particular the SQRIPARIHHFPTSI peptide, which was recognized by IgG antibodies from breast cancer patients, but not from normals (p < 0.0004). In patients who responded to the selected peptides, in particular the SQRIPARIHHFPTSI peptide, antibodies against a 66 kDa cellular protein were found. Interestingly, three out of six patients with the strongest immunoreactivity are still alive, with a mean survival time from first recurrence until now of 2553 days. In contrast, all the nonresponders (n = 10) are deceased. The mean survival time of these patients was 784 days, whereas the mean survival time of the three deceased responders was 1050 days (p < 0.02). The data provide the first example in which panning of peptide phage display libraries on patient IgG antibodies results in the isolation of breast cancer specific IgG epitopes, some of which correlate with patient survival time. Thus, the identified B-cell epitopes should be of great interest in vaccine development.

Improved methods for the application of random peptide phage libraries to the study of the oligoclonal bands in cerebrospinal fluid of patients with multiple sclerosis

The target antigens of the oligoclonal bands in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS) are unknown but may reflect important autoantigens in MS. One approach to identify candidate antigens is to allow CSF to select peptide motifs from a random phage library. To determine whether selected peptide motifs are related to the pathogenesis of MS, it is important to know if other MS patients and appropriate control patients have antibodies reactive with these sequences either in CSF or sera. Unfortunately, serologic screening of such sequences directly in phage clones gave non-specific reactions. Western blotting was found to obviate the non-specificity problem and together with isoelectric focusing, could also be used to demonstrate the co-migration of antigen specific oligoclonal bands with individual total IgG bands. Using 2D gel electrophoresis, absorption of CSF antibodies by specific peptide sequences selected from the phage library could be demonstrated. These techniques should facilitate the systematic study of the targets of the oligoclonal bands in CSF of patients with MS.

Isolation of leptin-binding peptides from a random peptide phage library.

Leptin plays a role in regulating the body weight in mice. Injection of recombinant mouse leptin expressed in Escherichia coli reduced the food intake and body weight in normal, ob/ob and diet-induced obesity mice. Hyperglycemia, hyperinsulinemia and hypothermia can also be corrected in ob/ob mice after leptin injection. Leptin is a 16-kDa secretory protein comprising 167 amino acids produced in adipose tissue and is secreted to blood stream. In this study, a recombinant mouse leptin was generated and purified from a baculovirus expression system. This protein was used to identify putative ligands using a phage library of random peptides. Three leptin-binding phage clones were found, which were characterized by DNA sequencing and ELISA methods. The amino acid sequences of the reactive peptides are: LAYCSDPVRCLVWWY, MFWISAVSFVDHALV and LVLVLSAFLCCGVG. All three clones bound to recombinant human and mouse leptins. These peptides may be useful tools to study leptin-receptor interaction, food intake and body weight regulation.

Structure and function of the third intracellular loop of the 5-hydroxytryptamine2A receptor: the third intracellular loop is alpha-helical and binds purified arrestins.

Understanding the precise structure and function of the intracellular domains of G protein-coupled receptors is essential for understanding how receptors are regulated, and how they transduce their signals from the extracellular milieu to intracellular sites. To understand better the structure and function of the intracellular domain of the 5-hydroxytryptamine2A (5-HT2A) receptor, a model G(alpha)q-coupled receptor, we overexpressed and purified to homogeneity the entire third intracellular loop (i3) of the 5-HT2A receptor, a region previously implicated in G-protein coupling. Circular dichroism spectroscopy of the purified i3 protein was consistent with alpha-helical and beta-loop, -turn, and -sheet structure. Using random peptide phage libraries, we identified several arrestin-like sequences as i3-interacting peptides. We subsequently found that all three known arrestins (beta-arrestin, arrestin-3, and visual arrestin) bound specifically to fusion proteins encoding the i3 loop of the 5-HT(2A) receptor. Competition binding studies with synthetic and recombinant peptides showed that the middle portion of the i3 loop, and not the extreme N and C termini, was likely to be involved in i3-arrestin interactions. Dual-label immunofluorescence confocal microscopic studies of rat cortex indicated that many cortical pyramidal neurons coexpressed arrestins (beta-arrestin or arrestin-3) and 5-HT2A receptors, particularly in intracellular vesicles. Our results demonstrate (a) that the i3 loop of the 5-HT2A receptor represents a structurally ordered domain composed of alpha-helical and beta-loop, -turn, and -sheet regions, (b) that this loop interacts with arrestins in vitro, and is hence active, and (c) that arrestins are colocalized with 5-HT2A receptors in vivo.

Novel peptide inhibitor of ecto-ADP-ribosyl cyclase of bone marrow stromal cell antigen-1 (BST-1/CD157)

cADP-ribose, which is produced by ecto-ADP-ribosyl cyclase of CD38 or bone marrow stromal cell antigen-1 (BST-1), is a key regulator of Ca2+-induced calcium release in an Ins(1,4,5)P3-independent manner. In the present study, we have identified a specific peptide inhibitor for ADP-ribosyl cyclase of BST-1. A 15-mer random peptide phage library was screened with a soluble form of BST-1 expressed in baculovirus-infected insect cells. After biopanning, two potent sequences reactive towards BST-1 were isolated. The two synthetic peptides corresponding to the identified sequences were shown to antagonize each other's ability to inhibit the binding of the two isolated phage to BST-1, suggesting that they bind at a common binding site on BST-1. One of the peptides (SNP-1) was shown to inhibit ADP-ribosyl cyclase activity of BST-1 in an uncompetitive manner with a Ki value of 180+/-40 nM (n=3). SNP-1 also inhibited cyclic ADP-ribose hydrolase activity of BST-1 dose-dependently. Selected phage did not cross-react with a soluble form of CD38. SNP-1 did not show any inhibitory effect on ADP-ribosyl cyclase activity of CD38, and therefore this peptide inhibitor will be useful to serve as a starting tool for understanding the roles of these intriguing ecto-enzymes. This is the first report of a specific ADP-ribosyl cyclase inhibitor.

A peptide isolated from a random phage peptide library is a structural mimic to the P1, P4-diadenosine 5'-tetraphosphate binding site on its receptor.

We have previously demonstrated that a monoclonal antibody (mAb TL4), which inhibits P1, P4-diadenosine 5'-tetraphosphate (Ap4A) binding to its receptor, selected a consensus RGS tripeptide from a random phage hexapeptide library. RGS interfered with Ap4A binding to its membrane receptor [Liu, G., Bryant, R. T. & Hilderman, R. H. (1996) Biochemistry 35, 197-201]. However the mechanism by which RGS interfered with Ap4A binding to its receptor was not determined. In this communication, we demonstrate that RGS interacts with Ap4A to prevent [3H]Ap4A binding to the Ap4A membrane receptor. To further characterize the mechanism by which RGS inhibits Ap4A binding to its receptor, we used mAb TL4 to screen a 15-residue random peptide phage library and DNAs from 24 clones were sequenced. 20 clones contain a RGSSS sequence while 17 of these clones contained an identical 15-amino-acid insert (clone A). Gel-filtration studies of previously equilibrated clone A phage and [3H]Ap4A support the idea that [3H]Ap4A interacts specifically with clone A phage while RGS effectively competes for [3H]Ap4A interaction on clone A phage. These data are consistent with RGS mimicking a sequence on the receptor essential for Ap4A binding.

Discovery of a novel thrombopoietin mimic agonist peptide.

A random phage peptide library was constructed for the filamentous bacteriophage fuse5. The library was made by inserting a degenerate oligonucleotide which encodes 15 variable amino acids into the NH2-terminal region of the phage gene III protein. This library, containing 1x10(9) different phages, was screened with a human immunoglobulin fusion protein containing the extracellular region of human thrombopoietin receptor. Several phages were isolated following four cycles of enrichment and amplification. These phages specifically bound to the fusion protein. One phage peptide acted as an agonist of the thrombopoietin receptor, since it stimulated the proliferation of thrombopoietin-dependent cells and the differentiation of mouse bone marrow cells to megakaryocytes. The amino acid sequence of this peptide is not present in the primary amino acid sequence of thrombopoietin. This discovery may lead to the design of a small-molecular mimic of thrombopoietin.

Epitope mapping by phage display: Random versus gene-fragment libraries

We present a comparative study on epitope mapping of four monoclonal antibodies directed against four different antigens using alternative phage display techniques and peptide scanning: mAb215 reacts with the largest subunit of RNA polymerase II, mAbBp53-11 with the tumor suppressor protein p53, mAbGDO5 with the Hantaan virus glycoprotein G2 and mAbL13F3 with the Hantaan virus nucleocapsid protein. Epitopes were determined (i) by gene-fragment phage display libraries, constructed by DNaseI digested random gene fragments cloned into the 5′ terminus of the pIII-gene of fd phage and (ii) by random peptide phage libraries displaying 6mer and 15mer peptides at the N-terminus of the pIII protein. Using the gene-fragment phage display libraries a single round of affinity selection resulted in the determination of the corresponding epitopes for all monoclonal antibodies tested. In contrast, biopanning of 6mer and 15mer random peptide libraries was only successful for two of the antibodies (mAbBp53-11 and mAbGDO5) after three or four rounds of selection. For the anti-p53 antibody we recovered the epitope from both the 6mer and 15mer library, for mAbGDO5 only the 6mer library displayed the epitope sequence. However, screening of the random peptide libraries with mAb215 and mAbL13F3 failed to yield immunopositive clones. Fine mapping of the epitopes by peptide scan revealed that the minimal epitopes recognized by mAbBp53-11 and mAbGDO5 consist of four and five amino acids, respectively, whereas mAb215 requires a minimal epitope of 11 amino acids for antigen recognition. In contrast, mAbL13F3 did not react with any of the synthesized 15mer peptides. The limits of the different methods of epitope mapping tested in this study are compared and the advantages of the gene-fragment phage display system are discussed.

Mapping epitopes of neutralizing monoclonal antibodies using phage random peptide libraries.

Identification of protective determinants from microbial proteins is a necessary step in the rational design of subunit vaccines. We have previously used a synthetic peptide scan (Pepscan) assay to map a panel of eight neutralizing monoclonal antibodies (mAb; designated as C1.1 to C1.8) to a common motif sequence from Chlamydia trachomatis. In the present study, five of the eight mAbs were used to screen phage random peptide libraries. mAbs C1.1 and C1.3 selected a motif sequence of G-L-X-N-D from a pIII-based phage random peptide library and a motif sequence of G-X-X-N-D from a pVIII-based random peptide library while mAbs C1.6 to C1.8 failed to select recognizable motifs from either of the phage libraries. However, C1.6 to C1.8 bound to the same motif sequence displayed on phage when the appropriate conformational constraints were imposed onto the motif sequence. Thus the specificity of the mAbs identified on Pepscan assays correlates with the mAbs' dependence on local epitope constraints displayed on the phage surface.

Evaluation of peptide-HLA binding by an enzyme-linked assay and its application to the detailed peptide motifs for HLA-DR9 (DRB1 *0901)

In our recent studies, we identified HLA-DRB1 *0901-binding peptides by affinity-based selection of a phage random peptide library and showed that two major anchors (WxxS, where x is any amino acid) play an essential role in binding to DR9, determined using a radioactive peptide in combination with column chromatography. In the current study, we established an ELISA-based peptide-HLA binding assay system, with a new index (relative binding affinity; r.b.a.) for quantitation of peptide-HLA binding, using standard curves of competitive inhibition, an approach which enabled handling of a larger number of samples simultaneously. Quantitation of binding between HLA-DR9 molecules and 39 synthetic peptides showed that: (a) this system yields results which correlate with those obtained using the previous assay system (Spearman's rank correlation coefficient; the p value of the putative first anchor <0.001, and the putative second anchor <0.001); and (b) substituting the putative first (the most N-terminal) anchor Trp to Y, M, F, I, L, V, or C, and the putative second anchor Ser to T, G, A, V, F, or H, allow high-affinity binding to DR9.

Differential binding of peptides substituted at putative C-terminal anchor residues to HLA-DQ8 and DQ9 differing only at β 57

HLA-DQ8 (DQA1 *0302-DQB1 *0302: DQβ 57Ala) and DQ9 (DQA1 *0302-DQB1 *0303: DQβ 57Asp) differ only at β 57, at which polymorphism reportedly confers distinct susceptibility to insulindependent diabetes mellitus (IDDM). To identify the differential peptide binding affected by β 57, we determined DQ9-binding peptides by affinity-based selection of a phage random peptide library using the biotinylated DQ9 complex. Nonconservative single-residue substitution of a high-affinity DQ8and DQ9-binding peptide (1KLPD YVL WSSS TVVGLGAAGA 21) at the underlined residues significantly decreased the peptide binding to DQ8 and DQ9. Affinities of the wild-type 21-mer K 4D YVL WSSS TV 13 and K 4A YAA WAAA TA 13 to DQ8 and DQ9 were practically the same. The K 4D YVL WSSS TV 13-based analogue peptides with substitutions at 12T showed that residues R, K, H, E, D, Q, N, T, S, V, L, I, F, M, W, and Y permitted binding to DQ8, whereas only R, T, V, L, I, F, M, W, and Y did so to DQ9. Thus, significant differences exist between DQ9 and DQ8, in that the majority of polar residues, regardless of their static charges at the residue 12, permitted binding to IDDM-susceptible DQ8. which is not the case for DQ9. The affinities of K 4D YVL WSSS XV 13 and K 4A YAA WAAAA X 13 (where X is T, A, K, D, or I) were almost equal to DQ8 and DQ9, suggesting that DQ8 and DQ9-binding peptide motifs could accept both the 8-mer and 9-mer frames depending on intervening sequences between Nand C-terminal anchor residues. The biochemical basis of peptide-HLA interactions determined by DQβ 57 is discussed.

Antigen binding peptides derived from long random peptide phage libraries mimic antibodies and can generate mimetopes : Vernon L. Alvarez, J. Mark Carater, Steven J. McConnell, CYTOGEN Corp., 307 College Rd. East, Princeton, NJ 08540, USA

Antigen binding peptides derived from long random peptide phage libraries mimic antibodies and can generate mimetopes : Vernon L. Alvarez, J. Mark Carater, Steven J. McConnell, CYTOGEN Corp., 307 College Rd. East, Princeton, NJ 08540, USA

New Stimulation Ligand of the Adenovirus 2 Protease

The catalytic activity of the adenovirus cysteine peptidase is increased by a specific 11-amino-acid peptide adduct (GVQSLKRRRCF, referred to as pVIc). To identify additional peptides which might bind and alter the activity of the protease, a cysteine-constrained random peptide phage library was screened. Of 29 different phages which were isolated, 7 contained the consensus sequence VEGGS. Despite a superficial similarity to the substrate cleavage site of the protease, the peptide was not digested by the enzyme. VEGGS and pVIc altered protease activity similarly without sharing sequence similarity. To similar degrees, pVIc and VEGGS (a) stimulated the activity of the recombinant protease, (b) had no effect on viral protease, (c) increased the fluorescence emission of tryptophan residues in the protease, suggesting a conformational change, and (d) inhibited wt virus infection, but rescued ts1 infection at the nonpermissive temperature. The experiments also suggest that once the protease has been stimulated by one peptide, the other peptide has no further activity on the recombinant adenovirus cysteine protease, suggesting that the two peptides bring about the same change on the protease via different binding sites.

Identification of HLA-DR9 (DRB1∗0901)-binding peptide motifs using a phage fUSE5 random peptide library

We identified HLA-DRB1 ∗0901-binding peptides by affinity-based selection of a phage random peptide library using the biotinylated DR9 complex. Analogue peptides with single amino acid residue substitutions of a DR9 binder revealed that two major anchors (WxxS, where x is any amino acid) play an essential role in binding to DR9. Determination of the binding affinity of synthetic wild-type-based analogue peptides showed that substituting W to F or L, and S to A, V, or F allow high affinity binding with DR9. Collectively, DR9-binding peptide motifs identified in this study are characteristic in that (a) only two anchors of the NH 2-terminal half of binding peptides play important roles in binding, and (b) small neutral hydrophilic Ser is allowed as the second anchor for high-affinity binding, unlike the other DR-binding motifs heretofore reported. The implications of our results are discussed in light of the HLA-DR9-associated susceptibility to juvenile-onset myasthenia gravis and systemic lupus erythematosus with antiphospholipid syndrome, in particular, T-cell responses to au-toantigens.

Determination of sintering parameters by image analysis: J.L. Quenec'h, M. Coster (ISMRA, Caen, France)

Contrary to lower species that recapitulate some of the developmental programs, in mammals, functional recovery after spinal cord injury is impaired by a non-permissive environment and the lack of plasticity of adult neurons. The developmental plasticity associated linear homopolymer of alpha 2,8-linked sialic acid (PolySialic Acid, PSA), represents a permissive determinant that could contribute to recovery. We previously showed that a PSA cyclic mimetic peptide (PR-21) displayed PSA-like biological functions (Torregrossa, P., Buhl, L., Bancila, M., Durbec, P., Schafer, C., Schachner, M., Rougon, G., 2004. Selection of poly-alpha 2,8-sialic acid mimotopes from a random phage peptide library and analysis of their bioactivity. J. Biol. Chem. 279, 30707–30714.). In the present study we investigated the therapeutic potential of PR-21 in young adult mice after dorsal hemisection at the T9 level. We show that PR-21 fulfills several criteria for an in vivo use as it is not toxic, not immunogenic and displays good stability in biological fluids or tissue. Delivery of PR-21 to the lesion site decreased the time of the animals' return to continence, and enhanced motor functions, sensorimotor control and coordination of hindlimbs with forelimbs when compared to a control peptide. At the cellular level, PR-21 increased serotonergic axon density at and caudal to the lesion site, and decreased reactive gliosis in vivo. In an in vitro model of reactive astrocytes, PR-21 increased NCAM expression in strongly GFAP positive cells. Our data point to the unique features of a carbohydrate mimicking peptide, and support the notion that PSA can be considered as an important factor in recovery from spinal cord injury.

Structural Characterization of Peptides That Bind Synovial Fluid Antibodies from RA Patients: A Novel Strategy for Identification of Disease-Related Epitopes Using a Random Peptide Library

Phage epitope library technology has become a powerful tool for identifying determinants recognized by homogenous antibodies. Screening of human sera or fluids with random peptide phage libraries is a novel approach that can dissect common features at the amino acid level in individuals infected by the same etiological agent(s). In this study we have analyzed the specificity of antibodies in synovial fluids (SF) obtained from patients with rheumatoid arthritis (RA). We found that a high proportion of the peptides binding SF antibodies differ from those binding serum antibodies, suggesting that synovial B cells are expanded as a result of local antigen stimulation. When all the selected phages (enriched library) that bind the SF antibodies from a seropositive RA patient were further screened by the use of different SF antibodies with or without rheumatoid factor activity, we identified common SF antibody specificities (IRRSETPRA, RRRVRNSDT, PVSSTRGNM). Antibodies against these common specificities are also found in SF from other RA patients. Taken together, the present results open the possibility of defining the entire set of synovium antibody specificities and also common SF specificities between RA patients.