A structure-based engineering approach to abrogate pre-existing antibody binding to biotherapeutics

Abstract

Development of biotherapeutics is hampered by the inherent risk of immunogenicity, which requires extensive clinical assessment and possible re-engineering efforts for mitigation. The focus in the pre-clinical phase is to determine the likelihood of developing treatment-emergent anti-drug antibodies (TE-ADA) and presence of pre-existing ADA in drug-naïve individuals as risk-profiling strategies. Pre-existing ADAs are routinely identified during clinical immunogenicity assessment, but their origin and impact on drug safety and efficacy have not been fully elucidated. One specific class of pre-existing ADAs has been described, which targets neoepitopes of antibody fragments, including Fabs, VH, or VHH domains in isolation from their IgG context. With the increasing number of antibody fragments and other small binding scaffolds entering the clinic, a widely applicable method to mitigate pre-existing reactivity against these molecules is desirable. Here is described a structure-based engineering approach to abrogate pre-existing ADA reactivity to the C-terminal neoepitope of VH(H)s. On the basis of 3D structures, small modifications applicable to any VH(H) are devised that would not impact developability or antigen binding. In-silico B cell epitope mapping algorithms were used to rank the modified VHH variants by antigenicity; however, the limited discriminating capacity of the computational methods prompted an experimental evaluation of the engineered molecules. The results identified numerous modifications capable of reducing pre-existing ADA binding. The most efficient consisted of the addition of two proline residues at the VHH C-terminus, which led to no detectable pre-existing ADA reactivity while maintaining favorable developability characteristics. The method described, and the modifications identified thereby, may provide a broadly applicable solution to mitigate immunogenicity risk of antibody-fragments in the clinic and increase safety and efficacy of this promising new class of biotherapeutics.

Trends in industrialization of biotherapeutics: a survey of product characteristics of 89 antibody-based biotherapeutics

“…Ahmed et al previously showed, through sequence and structural analysis, that non-redundant physicochemical descriptors can be used to flag Fv regions of antibodies for medicine-likeness. 203 There are numerous ways computer-aided drug design can contribute to the marketed antibody-based biotherapeutic landscape, 204 including sequence analysis (for example, see Figures S3 (a, b)), 205 structure analysis, 206 and machine learning. 207 …”

Immunogenicity assessment of bispecific antibody-based immunotherapy in oncology

“…47 A structurebased engineering approach has been used to abrogate pre-existing ADAs binding to the neoepitope of antibody fragments by small modifications, while maintaining favorable developability characteristics. 48…”

VHH Structural Modelling Approaches: A Critical Review

“…Studying the interaction and affinity between V H H and its target of interest was the major goal of these papers. Additional experimental information allowed refining the models and/or docking, e.g., V H H anti-MMP8 second poses were considered better in regards to ELISA data [ 121 ] and the development of a structure-based engineering approach to abrogate pre-existing antibody binding in Biotherapeutics [ 123 ]. Regarding the actual sanitary context, Modeller was used for the design of a V H H that neutralised SARS-CoV-2.…”