Selection of peptidic mimics of digoxin from phage-displayed peptide libraries by anti-digoxin antibodies

Development of a heterologous enzyme-linked immunosorbent assay for organophosphorus pesticides with phage-borne peptide

An enzyme-linked immunosorbent assay (ELISA) was developed to detect organophosphorus pesticides using a phage-borne peptide that was isolated from a cyclic 8-residue peptide phage library. The IC₅₀ values of the phage ELISA ranged from 1.4 to 92.1 μg L^-1 for eight organophosphorus pesticides (parathion-methyl, parathion, fenitrothion, cyanophos, EPN, paraoxon-methyl, paraoxon, fenitrooxon). The sensitivity was improved 120- and 2-fold compared to conventional homologous and heterologous ELISA, respectively. The selectivity of the phage ELISA was evaluated by measuring its cross-reactivity with 23 organophosphorus pesticides, among which eight were the main cross-reactants. The spike recoveries were between 66.1% and 101.6% for the detection of single pesticide residues of parathion-methyl, parathion and fenitrothion in Chinese cabbage, apple and greengrocery, and all of the coefficient of variation were less than or equal to 15.9%. Moreover, the phage ELISA results were validated by gas chromatography. The results indicate that isolating phage-borne peptides from phage display libraries is an alternative method for the development of a heterologous immunoassay and that the developed assay has a lower limit of detection than the chemically synthesized competitor assay.

Peptide mimics of hapten DNP: the effect of affinity of anti-DNP monoclonal antibodies for the selection of phage-displayed mimotopes

Biopanning of two linear (6- and 15-mer) and two constrained (10- and 17-mer) phage-displayed peptide libraries with two anti-DNP monoclonal antibodies (mAbs) selected seven unique peptide sequences using only the low affinity anti-DNP monoclonal antibody. The selected peptides contained two of 6, one of 10, two of 15 and two of 17 amino acids in length. They were all rich in hydrophobic residues. Both 15-mer peptides had antigenic regions of eight amino acids as revealed by a spot scan assay. Two of the 17-mer and one of the 10-mer peptides displayed on phage competed with free DNP for the low affinity anti-DNP mAb. These findings highlight (i) the selective power of phage displayed peptide libraries to identify peptides that mimic the shape of a small hapten molecule such as DNP, (ii) the possible preferential bias of phage libraries towards low affinity antibodies, (iii) the importance of using a panel of phage libraries for selecting peptide mimics.

Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures

Mimotopes mimic the three-dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody-antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In this study, we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies, which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the parental antigen (175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs on these V(NAR)s presented at the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody. These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing. We rationalize the higher affinity of the V(NAR)s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity, through interactions with other CDR regions on the antibody, though of course definitive support of this hypothesis will rely on co-crystallographic studies. Alternatively, the selection of mimotopes from a large (<4 x 10(8)) constrained library may have allowed selection of variants with even more favorable epitope topologies than present in the original antigenic structure, illustrating the power of in vivo selection of mimotopes from phage-displayed molecular libraries.

Synthetic antibody libraries focused towards peptide ligands

Synthetic antibody libraries have proven immensely useful for the de novo isolation of antibodies without the need for animal immunization. Recently, focused libraries designed to recognize particular classes of ligands, such as haptens or proteins, have been employed to facilitate the selection of high-affinity antibodies. Focused libraries are built using V regions encoding combinations of canonical structures that resemble the structural features of antibodies that bind the desired class of ligands and sequence diversity is introduced at residues typically involved in recognition. Here we describe the generation and experimental validation of two different single-chain antibody variable fragment libraries that efficiently generate binders to peptides, a class of molecules that has proven to be a difficult target for antibody generation. First, a human anti-peptide library was constructed by diversifying a scaffold: the human variable heavy chain (V(H)) germ line gene 3-23, which was fused to a variant of the human variable light chain (V(L)) germ line gene A27, in which L1 was modified to encode the canonical structure found in anti-peptide antibodies. The sequence diversity was introduced into 3-23 (V(H)) only, targeting for diversification residues commonly found in contact with protein and peptide antigens. Second, a murine library was generated using the antibody 26-10, which was initially isolated based on its affinity to the hapten digoxin, but also binds peptides and exhibits a canonical structure pattern typical of anti-peptide antibodies. Diversity was introduced in the V(H) only using the profile of amino acids found at positions that frequently contact peptide antigens. Both libraries yielded binders to two model peptides, angiotensin and neuropeptide Y, following screening by solution phage panning. The mouse library yielded antibodies with affinities below 20 nM to both targets, although only the V(H) had been subjected to diversification.

Ouabain-binding protein(s) from human plasma

Conservation of the binding site on mammalian Na+,K+-ATPase for cardiac glycosides and the importance of the Na+ pump in mammalian cellular physiology has stimulated the search for a mammalian analog of these plant compounds. One candidate, isolated from brain and blood, appears to be ouabain itself or a closely related isomer, the ouabain-like compound. Little is known about the circulating form. Because human steroid hormones circulate with carrier proteins, we produced a ouabain-specific monoclonal antibody (mAb 1-10) and used it to probe normal human plasma for ouabain-protein carrier complex. Ouabain-like biological activity was isolated in association with protein bands of 80, 50, and 25 kDa. These proteins appear to be human immunoglobulins or immunoglobulin-like because they are recognized by anti-human immunoglobulin antibodies, but not by anti-mouse immunoglobulin antibodies. The protein-containing fractions inhibit the binding of mAb 1-10 to immobilized ouabain, and with further purification on protein A, the immunoglobulin-like protein binds radioactive ouabain with an IC50 of 200 to 600 nmol/L, but binds digoxin with 100-fold less affinity, suggesting specificity for ouabain or its isomer. Active protein fractions after purification on C18 inhibit Na+ pump activity in human erythrocytes (IC50 approximately 4 nmol/L, ouabain equivalents), and this chromatography appears to dissociate the ouabain-like compound from the immunoglobulin protein(s). These immunoglobulin-like molecules may represent a subset of immunoglobulins (< or =0.5% of total protein A immunoglobulin) that function as a reservoir and delivery system for ouabain-like compounds in the modulation of human Na+, K+-ATPase in vivo.