Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response

Mohammed M Al Qaraghuli,Paul A Mulheran,Karina Kubiak-Ossowska,Valerie A Ferro

doi:10.1038/s41598-020-70680-0

Mohammed M Al Qaraghuli, Paul A Mulheran + Show 2 more

Open Access

https://doi.org/10.1038/s41598-020-70680-0

Copy DOI

Journal: Scientific Reports	Publication Date: Aug 13, 2020
Citations: 32	License type: open-access

Affiliation: University of Strathclyde

Abstract

Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful structural analysis beyond the antibody binding site is required to develop a more efficacious antibody. In this work, we focused on protein antigens, since they induce the largest antibody changes, and provide interesting cases to compare and contrast. The structures of 15 anti-protein antibodies were analysed to compare the antigen-bound/unbound forms. Surprisingly, three different classes of binding-induced changes were identified. In class (B1), the antigen binding fragment distorted significantly, and we found changes in the loop region of the heavy chain’s constant domain; this corresponds well with expected allosteric movements. In class (B2), we found changes in the same loop region without the overall distortion. In class (B3), these changes did not present, and only local changes at the complementarity determining regions were found. Consequently, structural analysis of antibodies is crucial for therapeutic development. Careful evaluation of allosteric movements must be undertaken to develop better effector responses, especially during the transformation of these antibodies from small fragments at the discovery stage to full antibodies at the subsequent development stages.

Highlights

Lymphocyte function-associated antigen 1 (LFA-1)I domain, Form I Lymphocyte function-associated antigen 1 (LFA-1) I domain, Form II Chicken egg-white lysozyme Hen egg white lysozyme Interleukin 1 beta (IL-1β) Vascular endothelial growth factor (VEGF)
Focusing on protein antigens as a potential target-class for several biotherapeutic p rogrammes[17], and by detailed inspection of available structures that are amenable to analysis, we have found that the allosteric mechanism proposed in16 is not universally observed
The angle changes were confirmed by corresponding distance changes between key cysteine residues on each domain

Summary

Introduction

Lymphocyte function-associated antigen 1 (LFA-1)I domain, Form I Lymphocyte function-associated antigen 1 (LFA-1) I domain, Form II Chicken egg-white lysozyme Hen egg white lysozyme Interleukin 1 beta (IL-1β) Vascular endothelial growth factor (VEGF). Webster et al initially correlated the binding sites surface topography to various antigen types[7] These shapes include pockets to accommodate small haptens, grooves to enclose peptides, and flat surfaces to grasp large protein surfaces[8]. The generated antibodies’ affinity is largely dependent on the number and type of amino acids that form the CDRs loops, and determine the binding site surface topography[10]. The antigen-binding region (paratope) and the antigenic determinant (epitope) are held together by non-covalent forces, which dictate the affinity of these a ntibodies[11]. This interaction is orchestrated by complementarity in the paratope-epitope charge and s hape[1]. Somatic gene-recombination and mutations, antibody class-switching, and heavy and light chain dimerisation, are mechanisms that can craft the malleable binding sites to accommodate a wide range of antigens[12,13,14,15]

Methods

Results

Conclusion