title: Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate.
abstract: Biotherapeutics are subject to immune surveillance within the body, and anti-biotherapeutic immune responses can compromise drug efficacy and patient safety. Initial development of targeted antidrug immune memory is coordinated by T cell recognition of immunogenic subsequences, termed "T cell epitopes." Biotherapeutics may therefore be deimmunized by mutating key residues within cognate epitopes, but there exist complex trade-offs between immunogenicity, mutational load, and protein structure-function. Here, a protein deimmunization algorithm has been applied to P99 beta-lactamase, a component of antibody-directed enzyme prodrug therapies. The algorithm, integer programming for immunogenic proteins, seamlessly integrates computational prediction of T cell epitopes with both 1- and 2-body sequence potentials that assess protein tolerance to epitope-deleting mutations. Compared to previously deimmunized P99 variants, which bore only one or two mutations, the enzymes designed here contain 4-5 widely distributed substitutions. As a result, they exhibit broad reductions in major histocompatibility complex recognition. Despite their high mutational loads and markedly reduced immunoreactivity, all eight engineered variants possessed wild-type or better catalytic activity. Thus, the protein design algorithm is able to disrupt broadly distributed epitopes while maintaining protein function. As a result, this computational tool may prove useful in expanding the repertoire of next-generation biotherapeutics.
authors.affiliation: Thayer School of Engineering, Dartmouth College, 14 Engineering Dr., Hanover, NH, 03755, USA.
authors.forename: Regina S
authors.initials: RS
authors.lastname: Salvat
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Parker
authors.forename: Andrew
authors.initials: A
authors.lastname: Guilliams
authors.forename: Yoonjoo
authors.initials: Y
authors.lastname: Choi
authors.forename: Chris
authors.initials: C
authors.lastname: Bailey-Kellogg
authors.forename: Karl E
authors.initials: KE
authors.lastname: Griswold
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004355:Drug Stability; D004358:Drug Therapy / Q000379:methods; D018604:Epitope Mapping; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology; D006801:Humans; D011355:Prodrugs / Q000627:therapeutic use; D015202:Protein Engineering / Q000379:methods; D017384:Sequence Deletion; D013696:Temperature; D001618:beta-Lactamases / Q000235:genetics / Q000276:immunology / Q000627:therapeutic use
chemical_list: D018984:Epitopes, T-Lymphocyte; D011355:Prodrugs; D001618:beta-Lactamases