Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (V_HH) at the N-terminus of each heavy chain. This feature of the V_HH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better V_HH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of V_HH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of V_HH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of V_HH, an exciting view of various factors in structure prediction of V_HH, like template framework selection, is also discussed.

Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms

BACKGROUND

The existence of conformational changes in antibodies upon binding has been previously established. However, existing analyses focus on individual cases and no quantitative study provides a more global view of potential moves and repacking, especially on recent data. The present study focuses on analyzing the conformational changes in various antibodies upon binding, providing quantitative observations to be exploited for antibody-related modeling.

METHODS

Cartesian and dihedral Root-Mean-Squared Deviations were calculated for different subparts of 27 different antibodies, for which X-ray structures in the bound and unbound states are available. Elbow angle variations were also calculated. Previously reported results of four docking algorithms were condensed into one score giving overall docking success for each of 16 antibody-antigen cases.

RESULTS

Very diverse movements are observed upon binding. While many loops stay very rigid, several others display side-chain repacking or backbone rearrangements, or both, at many different levels. Large conformational changes restricted to one or more antibody hypervariable loops were found to be a better indicator of docking difficulty than overall conformational variation at the antibody-antigen interface. However, the failure of docking algorithms on some almost-rigid cases shows that scoring is still a major bottleneck in docking pose prediction.

CONCLUSIONS

This study is aimed to help scientists working on antibody analysis and design by giving insights into the nature and the extent of conformational changes at different levels upon antigen binding.

Rational design and generation of recombinant control reagents for bispecific antibodies through CDR mutagenesis

Developments in the field of bispecific antibodies have progressed rapidly in recent years, particularly in their potential role for the treatment of malignant disease. However, manufacturing stable molecules has proven to be costly and time-consuming, which in turn has hampered certain aspects of preclinical evaluation including the unavailability of appropriate "negative" controls. Bispecific molecules (e.g., bispecific tandem scFv) exhibit two specificities, often against a tumor antigen as well as an immune-activation ligand such as CD3. While for IgG antibodies, isotype-matched controls are well accepted, when considering smaller antibody fragments it is not possible to adequately control for their biological activity through the use of archetypal isotypes, which differ dramatically in affinity, size, structure, and design. Here, we demonstrate a method for the rapid production of negative control tandem scFvs through complementarity determining region (CDR) mutagenesis, using a recently described bispecific T-cell engager (BiTE) targeting a tumor-specific mutation of the epidermal growth factor receptor (EGFRvIII) as an example. Four independent control constructs were developed by this method through alteration of residues spanning individual CDR domains. Importantly, while target antigen affinity was completely impaired, CD3 binding affinity was conserved in each molecule. These results have a potential to enhance the sophistication by which bispecific antibodies can be evaluated in the preclinical setting and may have broader applications for an array of alternative antibody-derived therapeutic platforms.