1. Academic Validation
  2. Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade

Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade

  • Cell Discov. 2017 Mar 7;3:17004. doi: 10.1038/celldisc.2017.4.
Fei Zhang 1 Hudie Wei 1 Xiaoxiao Wang 2 Yu Bai 2 Pilin Wang 2 Jiawei Wu 1 Xiaoyong Jiang 1 Yugang Wang 1 Haiyan Cai 1 Ting Xu 2 Aiwu Zhou 1
Affiliations

Affiliations

  • 1 Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of The Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China.
  • 2 Alphamab Co. Ltd. , Suzhou, Jiangsu, China.
Abstract

The use of Antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of Cancer Immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumor growth. The crystal structures of KN035 complexed with PD-L1 and free PD-L1, solved here at 1.7 and 2.7 Å resolution, respectively, show that KN035 competes with PD-1 (programmed death protein 1) for the same flat surface on PD-L1, mainly through a single surface loop of 21 Amino acids. This loop forms two short helices and develops key hydrophobic and ionic interactions with PD-L1 residues, such as Ile54, Tyr56 and Arg113, which are also involved in PD-1 binding. The detailed mutagenesis study identified the hotspot residues of the PD-L1 surface and provides an explanation for the stronger (~1 000-fold) binding of KN035 to PD-L1 than PD-1 and its lack of binding to PD-L2. Overall, this study reveals how a single immunoglobulin-variable scaffold of KN035 or PD-1 can bind to a flat protein surface through either a single surface loop or beta-sheet strands; and provides a basis for designing new immune checkpoint blockers and generating bi-specific Antibodies for combination therapy.

Keywords

Immunotherapy; Nanobody; PD-L1; Structural Biology.

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