8U32

Crystal structure of PD-1 in complex with a Fab

Summary for 8U32

• Entry DOI: 10.2210/pdb8u32/pdb
• Descriptor: Programmed cell death protein 1, Fab light chain, Fab heavy chain, ... (5 entities in total)
• Functional Keywords: pd-1, fab, structural protein, structural protein-immune system complex, structural protein/immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 127014.39

Authors

Sun, D.,Masureel, M. (deposition date: 2023-09-07, release date: 2024-06-19, Last modification date: 2024-11-13)

Primary citation

Liang, W.C.,Xi, H.,Sun, D.,D'Ascenzo, L.,Zarzar, J.,Stephens, N.,Cook, R.,Li, Y.,Ye, Z.,Matsumoto, M.,Payandeh, J.,Masureel, M.,Wu, Y.
Structure- and machine learning-guided engineering demonstrate that a non-canonical disulfide in an anti-PD-1 rabbit antibody does not impede antibody developability.
Mabs, 16:2309685-2309685, 2024

PubMed Abstract: Rabbits produce robust antibody responses and have unique features in their antibody repertoire that make them an attractive alternative to rodents for in vivo discovery. However, the frequent occurrence of a non-canonical disulfide bond between complementarity-determining region (CDR) H1 (C35a) and CDRH2 (C50) is often seen as a liability for therapeutic antibody development, despite limited reports of its effect on antibody binding, function, and stability. Here, we describe the discovery and humanization of a human-mouse cross-reactive anti-programmed cell death 1 (PD-1) monoclonal rabbit antibody, termed h1340.CC, which possesses this non-canonical disulfide bond. Initial removal of the non-canonical disulfide resulted in a loss of PD-1 affinity and cross-reactivity, which led us to explore protein engineering approaches to recover these. First, guided by the sequence of a related clone and the crystal structure of h1340.CC in complex with PD-1, we generated variant h1340.SA.LV with a potency and cross-reactivity similar to h1340.CC, but only partially recovered affinity. Side-by-side developability assessment of both h1340.CC and h1340.SA.LV indicate that they possess similar, favorable properties. Next, and prompted by recent developments in machine learning (ML)-guided protein engineering, we used an unbiased ML- and structure-guided approach to rapidly and efficiently generate a different variant with recovered affinity. Our case study thus indicates that, while the non-canonical inter-CDR disulfide bond found in rabbit antibodies does not necessarily constitute an obstacle to therapeutic antibody development, combining structure- and ML-guided approaches can provide a fast and efficient way to improve antibody properties and remove potential liabilities.

PubMed: 38356181
DOI: 10.1080/19420862.2024.2309685

Experimental method

X-RAY DIFFRACTION (2.51 Å)