Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale

Abstract

A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.

High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces

“…Modern high-density peptide arrays synthesized in situ by the combinatorial deposition of amino acids can contain up to a million different peptide spots on a single substrate and thus represent an ideal pool of diverse functional molecules 16 – 18 . This functionality can be substantially extended by the integration of artificial building blocks 19 , peptide cyclization 20 , 21 , or peptoid chemistry 22 .…”

Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

“…However, the statistically derived amino acid/nucleotide interaction preferences can be strongly biased toward the stable ribonucleoprotein complexes as a product of the modern ribosomal translation. In this work, we demonstrate a bottom-up approach to studying primordial RNA/peptide interactions with fully combinatorial high-density peptide arrays [ 25 , 26 , 27 , 28 ] to evaluate as many potential interactions as possible.…”

Selective Peptide Binders to the Perfluorinated Sulfonic Acid Ionomer Nafion

“…[22] In contrast to recombinant screening methods, ultra-high density peptide arrays have been successfully used to screen for hydrophobic peptides as off-target specific binders to therapeutic antibodies. [23] In this work, we use ultra-high density peptide arrays to screen for optimal selective peptide binders for an ionomer dissolved in solution, perform a substitutional analysis of the found sequences, evaluate their dissociation constants, and study the deposition of the selected hydrophobic peptide on the Nafion membrane.…”

“…[ 22 ] In contrast to recombinant screening methods, ultra‐high density peptide arrays have been successfully used to screen for hydrophobic peptides as off‐target specific binders to therapeutic antibodies. [ 23 ]…”