Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity

Significance Nature produces a variety of proteins that could be tapped for therapeutic applications. This paper focuses on the bacterial enzyme β-lactamase, a component of antibody-directed enzyme prodrug therapies designed to activate cytotoxic prodrugs selectively at sites of malignancy. Unfortunately, like many other nonhuman proteins, β-lactamase evokes an antidrug immune response that limits its clinical potential. This paper demonstrates that a multiobjective library-design method enables incorporation of mutations throughout the protein, modifying portions that trigger immune recognition while simultaneously preserving stability and catalytic activity. The libraries were inherently enriched in beneficial variants, and they produced numerous candidates that were both highly functional and immunologically stealthy. The method is general purpose and could enable functional deimmunization of other biotherapeutic agents. Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide–MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 109 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening.