Beyond natural amino acids: Extending immunogenicity risk assessment to non-canonical peptide drugs through chemical feature encoding

Peptide therapeutics are increasingly used to treat challenging diseases, but immunogenicity risks limit their clinical success. In silico tools enable immunogenicity screening through prediction of peptide-MHCII binding, yet current methods fail to capture chemical properties of non-natural amino acids routinely incorporated to improve drug properties. Here, we present a machine learning approach combining chemical fingerprints with sequence information to predict MHC class II binding for both canonical and modified peptides. We propose two molecular representations (direct-encoding and similarity-based chemical fingerprints) that preserve positional information while encoding chemical diversity. These representations achieved performance comparable to sequence-based encodings (BLOSUM62 and one-hot) for canonical peptides while accurately identifying binding cores and motifs. Testing on citrullinated peptides, chemical fingerprints substantially improved quantitative prediction accuracy while maintaining comparable linear correlation across encoding methods, demonstrating the importance of explicit chemical representation for accurate absolute binding affinity prediction. These descriptors can be integrated into pan-allele prediction frameworks, enabling immunogenicity risk assessment across diverse modifications and therapeutic modalities, including peptide therapeutics, antibody-drug conjugates, and synthetic vaccines. The proposed chemistry-informed framework addresses a critical gap in preclinical drug development, facilitating early mitigation strategies before costly clinical trials.