Computational Identification of Antigen-Binding Antibody Fragments

Abstract

Determining which parts of the Ab are essential for Ag recognition and binding is crucial for understanding B cell–mediated immunity. Identification of fragments of Abs that maintain specificity to the Ag will also allow for the development of improved Ab-based therapy and diagnostics. In this article, we show that structural analysis of Ab–Ag complexes reveals which fragments of the Ab may bind the Ag on their own. In particular, it is possible to predict whether a given CDR is likely to bind the Ag as a peptide by analyzing the energetic contribution of each CDR to Ag binding and by assessing to what extent the interaction between that CDR and the Ag depends on other CDRs. To demonstrate this, we analyzed five Ab–Ag complexes and predicted for each of them which of the CDRs may bind the Ag on its own as a peptide. We then show that these predictions are in agreement with our experimental analysis and with previously published experimental results. These findings promote our understanding of the modular nature of Ab–Ag interactions and lay the foundation for the rational design of active CDR-derived peptides.

Understanding differences between synthetic and natural antibodies can help improve antibody engineering

“…This has been shown also for specific examples like the interaction between HyHEL-10 and lysozyme, in which CDRH2 and CDRL1 display a dominant role, while CDRH3 shows very low binding contribution. 38 The fact that CDRH3 is not necessary for the versatility of Abs was ultimately demonstrated by a study that has shown that synthetic libraries can yield specific Abs against different Ags with diverse CDRL3 and fixed CDRH3. 47 In another study, the introduction of diversity into the sequence of anti ErbB2 Ab only at CDRH3 did not result in affinity enhanced variant, while beneficial mutants could be obtained by engineering one of the other contacting CDRs (CDRH1,H2,L1 or L3).…”

“…The CDRs binding contribution may be an important consideration for CDR grafting, Ab humanization, design of 2-in-one Abs and for identifying CDRderived peptides. 38 …”

“…38 "CDRs Analyzer" is available online in http://www.ofranlab.org/CDRs_Analyzer. Synthetic Abs rely heavily on CDRH3 at the expense of CDRH2 and CDRH1 CDRH3, which encompasses the V-D-J recombination site, is the most diverse component of natural Abs.…”

“…These parameters are used by the "CDRs Analyzer" to calculate the "Independent binding score," which measure the potential of a given CDR to bind the Ag as peptide. 38 For that purpose, the percentage of independent or integrated residues for a given CDR was calculated out of Ag residues contacting that CDR. Here, we aimed to evaluate the complexity of the Ab-Ag interaction.…”

Remediating agitation-induced antibody aggregation by eradicating exposed hydrophobic motifs

“…It is commonly thought that the major contributor to binding and activity of an antibody is the CDR_H3 loop, although we have found exceptions to this generality as have others. 21 Therefore, it would make sense to incorporate changes that introduce beneficial properties distant to CDR_H3 similar to the configuration of mAb_A_42. However, the next 2 most agitation stable and active antibodies included changes to W109 and W110, which were in CDR_H3 as defined by the Kabat CDR definition.…”