MultiCASE extends its predictive toxicology expertise into a new frontier: flagging HLA class II-mediated immunogenicity for peptide sequences.
Peptides have therapeutic origins tracing back to the discovery of insulin in 1922. These medium-sized molecules, composed of short chains of amino acids, sit between small molecules and large antibodies and offer higher specificity, flexible half-lives, lower immunogenicity, and lower production costs than large biologics.1 Originally produced using recombinant DNA (rDNA), peptides can now be produced synthetically. Synthetic methods, however, can introduce new peptide-related impurities that differ from the active pharmaceutical ingredient (API).2 Because peptide-related impurities can trigger immunogenicity, the FDA Center for Drug Evaluation and Research published the guidance document “ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin” to help sponsors assess the risk of immunogenicity posed by peptide-related impurities.3
An immunogenic response to a peptide drug or its impurities can produce a range of effects, from reduced therapeutic efficacy to immunotoxicity such as anaphylaxis. These effects arise from the production of anti-drug antibodies (ADAs), the body’s response to the peptide drug. To address these potential adverse outcomes, regulatory agencies have published guidance for assessing the immunogenic risk of both the peptide therapeutic and its synthesis-related impurities, much of which stems from T-cell responses. 3–6
At the cellular level, a peptide that enters the body is taken up and bound to human leukocyte antigen (HLA) class II molecules, the human form of the major histocompatibility complex (MHC) class II. This new peptide/HLA complex is then presented to CD4+ T-cells on the surface of an antigen-presenting cell (APC). The individual’s HLA genetics, which are highly polymorphic, along with the behavior of their B and T-cells, contribute to their immune response, leading to high variability in immunogenicity among patients. This T-cell-dependent immunogenicity can be mitigated by identifying T-cell epitopes: peptide regions (9 amino acids) that bind to HLA class II molecules. The genetic diversity of HLA alleles across a population must also be considered when predicting immunogenicity.4
Seqtara is MultiCASE’s new in silico platform for predicting HLA class II-mediated immunogenicity. Using FASTA input, it scans peptide sequences in overlapping 9-amino-acid windows and identifies regions most likely to bind HLA class II molecules, while also evaluating whether those sequences are new to the human proteome by assessing the novelty of their TCR-facing parts (HLA + TCR face evaluation).
Seqtara helps discovery and clinical development teams evaluate immunogenicity risk. With Seqtara, scientists can:
Seqtara is a natural extension of the MultiCASE platform, applying advanced computational techniques to analyze molecular sequence and structure. For over a decade, scientists worldwide have trusted MultiCASE to predict the mutagenic risk of impurities in accordance with the ICH M7 regulatory framework. Seqtara addresses a new question: which peptide sequences are most likely to trigger an immune response? By flagging immunogenicity risk before it surfaces in costly late-stage trials, Seqtara helps select safer candidates, address synthetic impurities, and provide clear reporting with the necessary documentation for regulators.
Seqtara is available as a web application and a desktop application for Windows and macOS. See what Seqtara can flag in your peptide sequences today.
Interested in learning more? Explore Seqtara, request a demo, or contact our team to discuss your peptide immunogenicity assessment needs.
(1) Xiao, W.; Jiang, W.; Chen, Z.; Huang, Y.; Mao, J.; Zheng, W.; Hu, Y.; Shi, J. Advance in Peptide-Based Drug Development: Delivery Platforms, Therapeutics and Vaccines. Sig Transduct Target Ther 2025, 10 (1), 74. https://doi.org/10.1038/s41392-024-02107-5.
(2) Al Musaimi, O. Exploring FDA-Approved Frontiers: Insights into Natural and Engineered Peptide Analogues in the GLP-1, GIP, GHRH, CCK, ACTH, and α-MSH Realms. Biomolecules 2024, 14 (3), 264. https://doi.org/10.3390/biom14030264.
(3) U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER). ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin; Guidance for Industry; Silver Spring, MD, 2021; p 15. https://www.fda.gov/media/107622/download.
(4) Jawa, V.; Terry, F.; Gokemeijer, J.; Mitra-Kaushik, S.; Roberts, B. J.; Tourdot, S.; De Groot, A. S. T-Cell Dependent Immunogenicity of Protein Therapeutics Pre-Clinical Assessment and Mitigation–Updated Consensus and Review 2020. Front. Immunol. 2020, 11, 1301. https://doi.org/10.3389/fimmu.2020.01301.
(5) European Medicines Agency. Guideline on Immunogenicity Assessment of Therapeutic Proteins; Committee for Medicinal Products for Human Use (CHMP): London, UK, 2017. https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-immunogenicity-assessment-therapeutic-proteins-revision-1_en.pdf.
(6) U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER), Center for Biologics Evaluation and Research (CBER). Immunogenicity Testing of Therapeutic Protein Products – Developing and Validating Assays for Anti-Drug Antibody Detection; Guidance for Industry; Silver Spring, MD, 2019; p 37. https://www.fda.gov/media/119788/download.
