A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes

Sela-Culang, Inbal; Alon, Shahar; Ofran, Yishai

doi:10.4049/jimmunol.1201493

Cited by 104 publications

(90 citation statements)

References 62 publications

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“…42 Residues of the second framework loop on the light chain may play a particular role. [42][43][44] This loop corresponds to residues LysL157 to LysL163 in Fv IL4 and LysL43 to LysL49 in Fv IL13 . These critical residues are not involved in direct domain contacts.…”

Section: Resultsmentioning

confidence: 99%

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

Steinmetz

Vallée

Beil

et al. 2016

mAbs

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Bispecific immunoglobulins (Igs) typically contain at least two distinct variable domains (Fv) that bind to two different target proteins. They are conceived to facilitate clinical development of biotherapeutic agents for diseases where improved clinical outcome is obtained or expected by combination therapy compared to treatment by single agents. Almost all existing formats are linear in their concept and differ widely in drug-like and manufacture-related properties. To overcome their major limitations, we designed cross-over dual variable Ig-like proteins (CODV-Ig). Their design is akin to the design of circularly closed repeat architectures. Indeed, initial results showed that the traditional approach of utilizing (G4S) x linkers for biotherapeutics design does not identify functional CODV-Igs. Therefore, we applied an unprecedented molecular modeling strategy for linker design that consistently results in CODV-Igs with excellent biochemical and biophysical properties. CODV architecture results in a circular self-contained structure functioning as a self-supporting truss that maintains the parental antibody affinities for both antigens without positional effects. The format is universally suitable for therapeutic applications targeting both circulating and membrane-localized proteins. Due to the full functionality of the Fc domains, serum half-life extension as well as antibody-or complement-dependent cytotoxicity may support biological efficiency of CODV-Igs. We show that judicious choice in combination of epitopes and paratope orientations of bispecific biotherapeutics is anticipated to be critical for clinical outcome. Uniting the major advantages of alternative bispecific biotherapeutics, CODV-Igs are applicable in a wide range of disease areas for fast-track multi-parametric drug optimization.

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Section: Resultsmentioning

confidence: 99%

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

Steinmetz

Vallée

Beil

et al. 2016

mAbs

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“…[42][43][44] CDRH3 is also located at the center of the binding site and is the CDR loop that undergoes the most significant conformational changes upon binding. 45 Thus, it is commonly assumed that CDRH3 accounts for the ability of Abs to recognize and bind specific epitopes. Understandably, Ab engineering methods often focus on CDRH3.…”

Section: Discussionmentioning

confidence: 99%

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

Burkovitz

Ofran

2015

mAbs

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Synthetic libraries are a major source of human-like antibody (Ab) drug leads. To assess the similarity between natural Abs and the products of these libraries, we compared large sets of natural and synthetic Abs using "CDRs Analyzer," a tool we introduce for structural analysis of Ab-antigen (Ag) interactions. Natural Abs, we found, recognize their Ags by combining multiple complementarity-determining regions (CDRs) to create an integrated interface. Synthetic Abs, however, rely dominantly, sometimes even exclusively on CDRH3. The increased contribution of CDRH3 to Ag binding in synthetic Abs comes with a substantial decrease in the involvement of CDRH2 and CDRH1. Furthermore, in natural Abs CDRs specialize in specific types of non-covalent interactions with the Ag. CDRH1 accounts for a significant portion of the cation-pi interactions; CDRH2 is the major source of salt-bridges and CDRH3 accounts for most hydrogen bonds. In synthetic Abs this specialization is lost, and CDRH3 becomes the main sources of all types of contacts. The reliance of synthetic Abs on CDRH3 reduces the complexity of their interaction with the Ag: More Ag residues contact only one CDR and fewer contact 3 CDRs or more. We suggest that the focus of engineering attempts on CDRH3 results in libraries enriched with variants that are not naturallike. This may affect not only Ag binding, but also Ab expression, stability and selectivity. Our findings can help guide library design, creating libraries that can bind more epitopes and Abs that better mimic the natural antigenic interactions.

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“…Of the three heavy chain loops, H3 is considered to be the most important to antigen recognition. 1,2 The contribution of each of the six CDR loops to antigen recognition is different from each other, and even within a single CDR loop, each residue position plays a different role in antigen binding. 3,4 It is necessary, therefore, to characterize the sequence and structural properties of each position in a CDR loop for estimating the utilization of each position in antigen binding and for understanding antigen recognition in more detail.…”

Section: Introductionmentioning

confidence: 99%

The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops

Tsuchiya

Mizuguchi

2016

Protein Science

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Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops.

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A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes

Cited by 104 publications

References 62 publications

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

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

The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops

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