title: Relationship between potential aggregation-prone regions and HLA-DR-binding T-cell immune epitopes: implications for rational design of novel and follow-on therapeutic antibodies.
abstract: Aggregation and unwanted immunogenicity are hurdles to avoid in successful commercial development of antibody-based therapeutics. In this article, the relationship between aggregation-prone regions (APRs), capable of forming cross-β motifs/amyloid fibrils, and major histocompatibility complex class II-restricted human leukocyte antigen (HLA)-DR-binding T-cell immune epitopes (TcIEs) is analyzed using amino acid sequences of 25 therapeutic antibodies, 55 TcIEs recognized by T-regulatory cells (tregitopes), 1000 randomly generated 15-residue-long peptides, 2257 human self-TcIEs (autoantigens), and 11 peptides in HLA-peptide cocrystal structures. Sequence analyses from these diverse sources consistently show a high level of correlation between APRs and TcIEs: approximately one-third of TcIEs contain APRs, but the majority of APRs occur within TcIE regions (TcIERs). Tregitopes also contain APRs. Most APR-containing TcIERs can bind multiple HLA-DR alleles, suggesting that aggregation-driven adverse immune responses could impact a broad segment of patient population. This article has identified common molecular sequence-structure loci that potentially contribute toward both manufacturability and safety profiles of the therapeutic antibodies, thereby laying a foundation for simultaneous optimization of these attributes in novel and follow-on candidates. Incidence of APRs within TcIERs is not special to biotherapeutics, self-TcIEs from human proteins, involved in various diseases, also contain predicted APRs and experimentally proven amyloid-fibril-forming peptide sequence portions.
authors.affiliation: Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., Chesterfield, Missouri 63017, USA. Sandeep.Kumar@Pfizer.com
authors.forename: Sandeep
authors.initials: S
authors.lastname: Kumar
authors.forename: Mark A
authors.initials: MA
authors.lastname: Mitchell
authors.forename: Bonita
authors.initials: B
authors.lastname: Rup
authors.forename: Satish K
authors.initials: SK
authors.lastname: Singh
mesh_terms: D000595:Amino Acid Sequence; D000682:Amyloid / Q000737:chemistry / Q000276:immunology*; D000906:Antibodies / Q000737:chemistry / Q000276:immunology* / Q000627:therapeutic use*; D017076:Computer-Aided Design; D015195:Drug Design; D018984:Epitopes, T-Lymphocyte / Q000276:immunology*; D006684:HLA-DR Antigens / Q000276:immunology*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000276:immunology / Q000627:therapeutic use; D016415:Sequence Alignment
chemical_list: D000682:Amyloid; D000906:Antibodies; D018984:Epitopes, T-Lymphocyte; D006684:HLA-DR Antigens; D010455:Peptides