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

AuthorsTimmerman, Peter; Shochat, Susana Geifman; Desmet, Johan; Barderas, Rodrigo ; Casal, J. Ignacio ; Meloen, Rob H.; Altschuh, Danièle
Keywordspeptide binder
binding mode
surface plasmon resonance
monoclonal antibody
mutational studies
Issue DateNov-2010
PublisherJohn Wiley & Sons
CitationJournal of Molecular Recognition 23(6):559-568(2010)
AbstractWe 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
Description10 páginas, 6 figuras, 2 tablas -- PAGS nros. 559-568
Publisher version (URL)http://dx.doi.org/10.1002/jmr.1017
Appears in Collections:(CIB) Artículos
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