Affinity Maturation Enhances Antibody Specificity but Compromises Conformational Stability

Shehata, Laila; Maurer, Daniel P.; Wec, Anna Z.; Lilov, Asparouh; Champney, Elizabeth; Sun, Tingwan; Archambault, Kimberly; Burnina, Irina; Lynaugh, Heather; Zhi, Xiaoyong; Xu, Yingda; Walker, Laura M.

doi:10.1016/j.celrep.2019.08.056

Cited by 74 publications

(120 citation statements)

References 50 publications

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“…Various studies have discussed the effect of affinity maturation on structural and dynamic properties ( James and Tawfik, 2003 ; Cauerhff et al, 2004 ; Schmidt et al, 2013 ; Adhikary et al, 2015 ; Jeliazkov et al, 2018 ; Shehata et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Local and Global Rigidification Upon Antibody Affinity Maturation

Fernández‐Quintero

Loeffler

Bacher

et al. 2020

Front. Mol. Biosci.

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During the affinity maturation process the immune system produces antibodies with higher specificity and activity through various rounds of somatic hypermutations in response to an antigen. Elucidating the affinity maturation process is fundamental in understanding immunity and in the development of biotherapeutics. Therefore, we analyzed 10 pairs of antibody fragments differing in their specificity and in distinct stages of affinity maturation using metadynamics in combination with molecular dynamics (MD) simulations. We investigated differences in flexibility of the CDR-H3 loop and global changes in plasticity upon affinity maturation. Among all antibody pairs we observed a substantial rigidification in flexibility and plasticity reflected in a substantial decrease of conformational diversity. To visualize and characterize these findings we used Markovstates models to reconstruct the kinetics of CDR-H3 loop dynamics and for the first time provide a method to define and localize surface plasticity upon affinity maturation.

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Section: Resultsmentioning

confidence: 99%

Local and Global Rigidification Upon Antibody Affinity Maturation

Fernández‐Quintero

Loeffler

Bacher

et al. 2020

Front. Mol. Biosci.

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“…Besides developability traits that are constantly present in Abs, some unfavourable characteristics can be cryptic and thus become apparent only after exposure of Ab molecule to certain conditions. Thus, in addition to intrinsically polyreactive Abs that express their antigen-binding promiscuity constantly (18,19), a fraction of human Abs can acquire potent polyreactive behaviour posttranslationally upon in vitro or in vivo exposure to redox-active substances, including the physiologically-relevant cofactor heme (20)(21)(22)(23)(24). Notably, by analyses of a set of 9 therapeutic Abs approved for treatment of cancer, it was demonstrated that after exposure to heme most of the Abs acquired substantial polyreactivity (25).…”

Section: Introductionmentioning

confidence: 99%

Interaction of clinical-stage antibodies with heme predicts their physiochemical and binding qualities

Lecerf

Kanyavuz

Rossini

et al. 2020

Preprint

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Development of monoclonal antibody therapeutics is a sophisticated process. Early stage detection of negative traits of antibodies, which can impact the production, storage stability or therapeutic efficacy is of critical importance for saving time and resources in drug development programs. Since the developability issues of antibodies are diverse, including expression yield, chemical and physical stability, propensity for aggregation, antigen-binding polyreactivity, etc., a battery of experimental and in silico assays have been developed for thorough examination of drug candidates. Here, by using a set of 113 samples with variable region sequences matching clinical-stage therapeutic antibodies, we demonstrated that unique physicochemical properties of heme allow this cofactor molecule to be applied as a probe for simultaneous detection of different deleterious characteristics of antibodies i.e., antigen-binding polyreactivity, self-association, aggregation, hydrophobicity and expression yield. Moreover, our study demonstrates that similarly as antibody repertoires from healthy individuals, a fraction of therapeutic antibodies acquires use heme as cofactor for recognition of diverse antigens. These results reveal presence of a hidden vulnerability issue for some antibodies, which would not be detectable by standard analytical assays. This liability may be of concern for monoclonal antibodies intended to be use in patients with pathophysiological conditions where extracellular heme is present e.g. hemolysis or tissue damage. We provided evidence about the mechanistic basis of the unique features of heme and offer a powerful analytical tool for rapid and simple detection of important negative traits in candidate therapeutic antibodies.

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“…Elucidating the affinity maturation process has been the focus of numerous studies (Cauerhff et al, 2004;Cho et al, 2005;Acierno et al, 2007;Li et al, 2010;Wong et al, 2011;Adhikary et al, 2015;Jeliazkov et al, 2018;Mishra and Mariuzza, 2018;Fernández-Quintero et al, 2019b;Shehata et al, 2019;Chan et al, 2020). Upon affinity maturation (Figure 5), we observe for the matured F10.6.6 antibody in both V H -V L interface and elbow angle histograms ( Figure 5B) a narrower distribution, compared to the broader surface of the D44.1 Fab ( Supplementary Table S1).…”

Section: Discussionmentioning

confidence: 75%

Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments

Fernández‐Quintero

Kroell

Heiss

et al. 2020

Front. Mol. Biosci.

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Fab consist of a heavy and light chain and can be subdivided into a variable (VH and VL) and a constant region (CH1 and CL). The variable region contains the complementarity-determining region (CDR), which is formed by six hypervariable loops, shaping the antigen binding site, the paratope. Apart from the CDR loops, both the elbow angle and the relative interdomain orientations of the VH–VL and the CH1–CL domains influence the shape of the paratope. Thus, characterization of the interface and elbow angle dynamics is essential to antigen specificity. We studied nine antigen-binding fragments (Fab) to investigate the influence of affinity maturation, antibody humanization, and different light-chain types on the interface and elbow angle dynamics. While the CDR loops reveal conformational transitions in the micro-to-millisecond timescale, both the interface and elbow angle dynamics occur on the low nanosecond timescale. Upon affinity maturation, we observe a substantial rigidification of the VH and VL interdomain and elbow-angle flexibility, reflected in a narrower and more distinct distribution. Antibody humanization describes the process of grafting non-human CDR loops onto a representative human framework. As the antibody framework changes upon humanization, we investigated if both the interface and the elbow angle distributions are changed or shifted. The results clearly showed a substantial shift in the relative VH–VL distributions upon antibody humanization, indicating that different frameworks favor distinct interface orientations. Additionally, the interface and elbow angle dynamics of five antibody fragments with different light-chain types are included, because of their strong differences in elbow angles. For these five examples, we clearly see a high variability and flexibility in both interface and elbow angle dynamics, highlighting the fact that Fab interface orientations and elbow angles interconvert between each other in the low nanosecond timescale. Understanding how the relative interdomain orientations and the elbow angle influence antigen specificity, affinity, and stability has broad implications in the field of antibody modeling and engineering.

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Affinity Maturation Enhances Antibody Specificity but Compromises Conformational Stability

Cited by 74 publications

References 50 publications

Local and Global Rigidification Upon Antibody Affinity Maturation

Local and Global Rigidification Upon Antibody Affinity Maturation

Interaction of clinical-stage antibodies with heme predicts their physiochemical and binding qualities

Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments

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