Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

• Published in: Communications biology Vol. 7; no. 1; pp. 922 - 25
• Main Authors: Bashour, Habib, Smorodina, Eva, Pariset, Matteo, Zhong, Jahn, Akbar, Rahmad, Chernigovskaya, Maria, Lê Quý, Khang, Snapkow, Igor, Rawat, Puneet, Krawczyk, Konrad, Sandve, Geir Kjetil, Gutierrez-Marcos, Jose, Gutierrez, Daniel Nakhaee-Zadeh, Andersen, Jan Terje, Greiff, Victor
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group 31.07.2024; Nature Publishing Group UK; Nature Portfolio
• Subjects: Amino acid sequence; Antibodies; Cartography; Drug development; Monoclonal antibodies; Physicochemical properties; Plasticity
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-024-06561-3

Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as “developability”, which reflects an antibody’s ability to progress through development stages based on its physicochemical properties. While natural antibodies may provide valuable guidance for mAb selection, we lack a comprehensive understanding of natural developability parameter (DP) plasticity (redundancy, predictability, sensitivity) and how the DP landscapes of human-engineered and natural antibodies relate to one another. These gaps hinder fundamental developability profile cartography. To chart natural and engineered DP landscapes, we computed 40 sequence- and 46 structure-based DPs of over two million native and human-engineered single-chain antibody sequences. We find lower redundancy among structure-based compared to sequence-based DPs. Sequence DP sensitivity to single amino acid substitutions varied by antibody region and DP, and structure DP values varied across the conformational ensemble of antibody structures. We show that sequence DPs are more predictable than structure-based ones across different machine-learning tasks and embeddings, indicating a constrained sequence-based design space. Human-engineered antibodies localize within the developability and sequence landscapes of natural antibodies, suggesting that human-engineered antibodies explore mere subspaces of the natural one. Our work quantifies the plasticity of antibody developability, providing a fundamental resource for multi-parameter therapeutic mAb design.Analysis of 2 million native antibodies reveals that human-engineered antibodies form subspaces of the natural developability space. This large-scale analysis allows the quantification of developability plasticity, accelerating antibody drug design.