Binding of CDR-derived peptides is mechanistically different from that of high-affinity parental antibodies

Authors

  • Peter Timmerman,

    Corresponding author
    1. Pepscan Therapeutics B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
    2. Van't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
    • Pepscan Therapeutics B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands.
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    • These authors contributed equally in this work.

  • Susana G. Shochat,

    1. CNRS, University of Strasbourg, Biosensor group, ESBS, Bld Sébastien Brant, BP10413, 67412 Illkirch, France
    Current affiliation:
    1. School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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    • These authors contributed equally in this work.

  • Johan Desmet,

    1. Algonomics N.V., Technologiepark 4, 9052 Gent, Belgium
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    • These authors contributed equally in this work.

  • Rodrigo Barderas,

    1. Centro de Investigaciones Biológicas (CSIC), 28040 Madrid. Spain
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    • These authors contributed equally in this work.

  • Jose Ignacio Casal,

    1. Centro de Investigaciones Biológicas (CSIC), 28040 Madrid. Spain
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    • These authors contributed equally in this work.

  • Rob H. Meloen,

    1. Pepscan Therapeutics B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
    2. Academic Biomedical Centre, University Utrecht, Yalelaan 1, 3584 CL Utrecht, The Netherlands
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    • These authors contributed equally in this work.

  • Danièle Altschuh

    Corresponding author
    1. CNRS, University of Strasbourg, Biosensor group, ESBS, Bld Sébastien Brant, BP10413, 67412 Illkirch, France
    • CNRS, University of Strasbourg, Biosensor group, ESBS, Bld Sébastien Brant, BP10413, 67412 Illkirch, France.
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    • These authors contributed equally in this work.


  • This article is published in Journal of Molecular Recognition as a special issue on Affinity 2009, edited by Gideon Fleminger, Tel-Aviv University, Tel-Aviv, Israel and George Ehrlich, Hoffmann-La Roche, Nutley, NJ, USA.

Abstract

We present data that reveal crucial differences between the binding mode of anti-gastrin17 (G17, pyroEGPWLEEEEEAYGWMDF-NH2) monoclonal antibodies (mAbs) and their CDR-derived synthetic binders (SBs) with G17. The mAbs recognize the N-terminal sequence of G17 (pyroEGPWL) with nanomolar affinity and high sequence selectivity. Molecular simulations suggest that G17 recognition is based primarily on a multitude of weak antibody–ligand interactions (H-bonding, van der Waals, etc.) inside a structurally well-defined cleft-like binding pocket. Relatively small structural changes (e.g. G-2 to A for G17) have a drastic impact on affinity, which is characteristic for antibody-like binding. In contrast, SBs recognize various sequences, including G17-unrelated targets with affinities of 1:1 complexes estimated in the 0.1–1.0 mM range. In most cases however, the G17/SB complex stoichiometries are not well-defined, giving rise to multimer aggregate formation with high apparent complex stabilities. Mutational studies on both G17 and SBs reveal the importance of positively charged (K/R) and aromatic residues (W/Y/F) for G17/SB complex formation. We propose that the synthetic binders use combinations of electrostatic, hydrophobic, and/or cation–π interactions in a variety of ways due to their intrinsic flexibility. This may also be the reason for their relatively low target specificity. We speculate that our findings are of general relevance, in showing that high-affinity mAbs do not necessarily provide the optimal basis for functional mimics design. Copyright © 2010 John Wiley & Sons, Ltd.

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