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

Felix Jenne, Sergey Biniaminov, Nathalie Biniaminov, Philipp Marquardt, Clemens von Bojničić-Kninski, Roman Popov, Anja Seckinger, Dirk Hose, Alexander Nesterov-Mueller

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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.

Originele taal-2English
Artikelnummer3515
Aantal pagina's13
TijdschriftInternational Journal of Molecular Sciences
Volume23
Nummer van het tijdschrift7
DOI's
StatusPublished - apr 2022

Bibliografische nota

Funding Information:
Acknowledgments: We acknowledge support from the KIT-Publication Fund of the Karlsruhe Institute of Technology.

Funding Information:
This research was funded by F?rderprogramm ?Zentrales Innovationsprogramm Mittel-stand? des Bundesministeriums f?r Wirtschaft und Energie (BMWi), grant number ZF4407505CR9 and DFG, grant number AOBJ655892.

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Copyright:
Copyright 2023 Elsevier B.V., All rights reserved.

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