De-immunization of therapeutic proteins by T-cell epitope modification

Many therapeutic proteins in clinical use have been shown to elicit antibody responses which in some cases have been linked to adverse events. Conventional animal models, although convenient, have rarely been predictive of immunogenicity in humans. New methods for predicting the potential immunogenicity of therapeutic proteins are needed. This treatise proposes a new approach which pairs in silico T-cell epitope analysis with in vitro studies. T-cell epitope mapping algorithms such as EpiMatrix can be used to evaluate a candidate therapeutic protein for T-helper eptopes, followed by confirmation of the T-helper epitopes using in vitro methods such as MHC binding assays and T-cell assays. Once these are identified, substitution of key amino acids in the T-cell epitopes may attenuate the immunogenicity of the protein, since modification of the amino acids in anchor position(s) can abrogate binding to human class II MHC molecules and presentation of the peptides, in the context of MHC, to T-helper cells. Following substitution of the key amino acids, immunogenicity of the modified protein can be evaluated in vitro. In parallel, the potential effect of the modifications on the structure of the protein can be evaluated using in silico modeling methods. This multi-step process has been termed DeFT for de-immunization of functional therapeutics. In this article we review the rationale for the approach, provide several retrospective examples that prove the approach in principle, and describe potential applications to therapeutic protein design. The demand for pre-clinical means of evaluating therapeutic proteins is expected to increase with the number of therapeutic proteins and monoclonal antibodies entering the pre-clinical pipeline. Examples provided offer some preliminary proof that the de-immunization approach may improve clinical outcomes.