Deep learning assessment of nativeness and pairing likelihood for antibody and nanobody design with AbNatiV2.

Clinical Snapshot

Key Findings

• P Value: Not reported in abstract

• Effect Size: Substantial outperformance of recent pairing prediction models

• Primary Outcome: Native antibody pair identification accuracy of 74% on held-out test sets

• Nnt Or Sensitivity: Improved sensitivity for detecting nativeness changes upon CDR grafting compared to AbNatiV1

• Confidence Interval: Not reported in abstract

Clinical Application

High feasibility as computational tool requiring no additional laboratory resources Relevant to Australian biotechnology sector and research institutions developing therapeutic antibodies, potentially supporting TGA regulatory submissions through improved developability assessment Researchers and pharmaceutical companies involved in antibody and nanobody drug development

Abstract

Most immune-system created antibodies balance good binding and stability with low toxicity and self-reactivity. Quantifying the nativeness of a candidate sequence - its likelihood of belonging to natural immune repertoires - has thus emerged as a valuable strategy for hit selection from synthetic libraries, optimization and humanization, and for guiding de novo design toward developable candidates. We previously introduced AbNatiV, a transformer-based VQ-VAE for nativeness assessment, which proved effective across multiple nanobody engineering tasks. However, AbNatiV1 operated on unpaired sequences, limiting applicability to conventional VH-VL antibodies. Moreover, its performance on nanobody nativeness was constrained by the limited number and diversity of nanobody repertoires available at the time. Here, we sequenced new camelid repertoires, curated additional recent datasets, and present AbNatiV2: an enhanced architecture comprising various models each trained on ≥20 million sequences. AbNatiV2 improves nanobody nativeness classification across held-out and diverse test sets, and more robustly detects nativeness changes upon CDR grafting. We also introduce p-AbNatiV2, a cross-attention model fine-tuned on 3.7 million paired human sequences. p-AbNatiV2 provides residue- and sequence-level humanness for VH/VL pairs and learns pairing-likelihood via noise-contrastive training. On held-out tests, it assigns the native pair a higher score in 74% of cases, substantially outperforming recent pairing models. Together, AbNatiV2 and p-AbNatiV2 extend nativeness assessment and engineering to both nanobodies and conventional antibodies, supporting design decisions at single-residue, Fv-sequence, and paired-domain levels. AbNatiV2 is available as downloadable software and webserver.