Population-specific design of de-immunized protein biotherapeutics.

Pierre Dönnes,Roland L Dunbrack,Thomas Hopf,Debora Marks,Oliver Kohlbacher,Charlotta Schärfe,Benjamin Schubert

doi:10.1371/journal.pcbi.1005983

Abstract

Immunogenicity is a major problem during the development of biotherapeutics since it can lead to rapid clearance of the drug and adverse reactions. The challenge for biotherapeutic design is therefore to identify mutants of the protein sequence that minimize immunogenicity in a target population whilst retaining pharmaceutical activity and protein function. Current approaches are moderately successful in designing sequences with reduced immunogenicity, but do not account for the varying frequencies of different human leucocyte antigen alleles in a specific population and in addition, since many designs are non-functional, require costly experimental post-screening. Here, we report a new method for de-immunization design using multi-objective combinatorial optimization. The method simultaneously optimizes the likelihood of a functional protein sequence at the same time as minimizing its immunogenicity tailored to a target population. We bypass the need for three-dimensional protein structure or molecular simulations to identify functional designs by automatically generating sequences using probabilistic models that have been used previously for mutation effect prediction and structure prediction. As proof-of-principle we designed sequences of the C2 domain of Factor VIII and tested them experimentally, resulting in a good correlation with the predicted immunogenicity of our model.

Highlights

Protein-based drugs are increasingly used to treat a wide variety of diseases [1, 2]
Therapeutic proteins have become an important area of pharmaceutical research and have been successfully applied to treat many diseases in the last decades
Biotherapeutics suffer from the formation of anti-drug antibodies, which can reduce the efficacy of the drug or even result in severe adverse effects

Summary

Introduction

Protein-based drugs (biotherapeutics) are increasingly used to treat a wide variety of diseases [1, 2]. The immunogenicity of the biotherapeutic is influenced by multiple factors that can be roughly divided into extrinsic—such as dosage, rout of administration, duration and production impurities—and intrinsic properties like the protein sequence or post-translational modifications [3]. This immune response involves the formation of anti-drug antibodies (ADAs) that target the biotherapeutic itself and cause loss of effect or adverse reactions[3,4,5]. This correlation between severity of the disease and lack of efficacy follows from the fact that the immune system is more likely to recognize the therapeutic Factor VIII as foreign the more severe the natural mutation is, where mutations that cause a total loss of Factor VIII production are most strongly associated with ADA development[7, 8]

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Results

Discussion

Conclusion