D.C. Osipovitch, A.S. Parker, C.D. Makokha, J. Desrosiers, W.C. Kett, L. Moise, C. Bailey-Kellogg, and K.E. Griswold, "Design and analysis of immune-evading enzymes for ADEPT therapy", Protein Eng. Des. Sel., 2012, 25:613-624. [paper]

The unparalleled specificity and activity of therapeutic proteins has reshaped many aspects of modern clinical practice, and aggressive development of new protein drugs promises a continued revolution in disease therapy. As a result of their biological origins, however, therapeutic proteins present unique design challenges for the biomolecular engineer. For example, protein drugs are subject to immune surveillance within the patient's body; this anti-drug immune response can compromise therapeutic efficacy and even threaten patient safety. Thus, there is a growing demand for broadly applicable protein deimmunization strategies. We have recently developed optimization algorithms that integrate computational prediction of T cell epitopes and bioinformatics-based assessment of the structural and functional consequences of epitope-deleting mutations. Here, we describe the first experimental validation of our deimmunization algorithms using Enterobacter cloacae P99 beta-lactamase, a component of ADEPT cancer therapies. Compared to wild-type or a previously deimmunized variant, our computationally optimized sequences exhibited significantly less in vitro binding to human MHC II immune molecules. At the same time, our globally optimal design exhibited wild-type catalytic proficiency. We conclude that our deimmunization algorithms guide the protein engineer towards promising immunoevasive candidates and thereby have the potential to streamline biotherapeutic development.