Communication pathways bridge local and global conformations in an IgG4 antibody

Thomas Tarenzi,Raffaello Potestio,Marta Rigoli

doi:10.1038/s41598-021-02323-x

Abstract

The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). Recent evidence, however, points toward a nontrivial relation between the CDR and distal sites: variations in the binding strengths have been observed upon mutating residues separated from the paratope by several nanometers, thus suggesting the existence of a communication network within antibodies, whose extension and relevance might be deeper than insofar expected. In this work, we test this hypothesis by means of molecular dynamics (MD) simulations of the IgG4 monoclonal antibody pembrolizumab, an approved drug that targets the programmed cell death protein 1 (PD-1). The molecule is simulated in both the apo and holo states, totalling 4 μs of MD trajectory. The analysis of these simulations shows that the bound antibody explores a restricted range of conformations with respect to the apo one, and that the global conformation of the molecule correlates with that of the CDR. These results support the hypothesis that pembrolizumab featues a multi-scale hierarchy of intertwined global and local conformational changes. The analysis pipeline developed in this work is general, and it can help shed further light on the mechanistic aspects of antibody function.

Highlights

The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs)
The number of monoclonal antibodies employed for therapeutic applications dramatically increased in the recent years: from 1997 to 2013, 34 mAbs-based pharmaceuticals were approved in US or EU, while from 2014 to 2020, in only 7 years, the number of approved mAbs was 6 11. mAbs have been developed to treat a large variety of conditions, including cancer, autoimmune diseases and, very recently, COVID-192,3
This is true for the interplay between the molecule structure and its dynamics, which is extremely rich and varied, as several studies have recently shown[27,56,57,58]

Summary

Introduction

The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). The selection of the isotype, and those structural/dynamical features of the constant region that come with it, leads to different immune responses, and is performed on the basis of the planned a pplication[7,8]; on the other side, modifications of single residues can determine a higher therapeutic efficacy, as in the case of those mutations introduced in the Fc domain to enhance effector function and recruitment of additional p roteins[9,10,11]. A remarkable example is the single-residue mutation that, in the hinge of IgG4 antibodies, prevents Fab-arm e xchange[12,13,14] Modifications of this type, which may be distributed throughout the whole antibody sequence, are usually introduced for reasons that are not directly linked to antigen affinity modulation. The CDR loops are not the only possible loci of intervention; it is experimentally shown that both mutations near and far from the antigen-binding site can affect affinity[16]. In silico structural investigation of Scientific Reports | (2021) 11:23197

Methods

Results

Conclusion