Abstract
Programmed cell death 1 (PD-1) monoclonal antibodies have been approved by regulatory agencies for the treatment of various types of cancer, and the mechanism involves the restoration of T cell functions. We report herein the X-ray crystal structure of a fully human monoclonal antibody mAb059c fragment antigen-binding (Fab) in complex with the PD-1 extracellular domain (ECD) at a resolution of 1.70 Å. Structural analysis indicates 1) an epitope, comprising fragments from the C’D, BC and FG loops of PD-1, contributes to mAb059c interaction, 2) an unique conformation of the C’D loop and a different orientation of R86 enabling the capture of PD-1 by the antibody complementarity determining region (CDR) and the formation of one salt-bridge contact – ASP101(HCDR3):ARG86(PD-1), and 3) the contact of FG with light chain (LC) CDR3 is maintained by a second salt-bridge and two backbone hydrogen bonds. Interface analysis reveals that N-glycosylation sites 49, 74 and 116 on PD-1 do not contact mAb059c; while N58 in the BC loop is recognized by mAb059c heavy chain CDR1 and CDR2. Mutation of N58 attenuated mAb059c binding to PD-1. These findings and the novel anti-PD-1 antibody will facilitate better understanding of the mechanisms of the molecular recognition of PD-1 receptor by anti-PD-1 mAb and, thereby, enable the development of new therapeutics with an expanded spectrum of efficacy for unmet medical needs.
Highlights
Programmed cell death 1 (PD-1) monoclonal antibodies have been approved by regulatory agencies for the treatment of various types of cancer, and the mechanism involves the restoration of T cell functions
N58, which is on the BC loop of PD-1 and resides closest to the binding epitopes of pembrolizumab and nivolumab, was reported to be heavily glycosylated and most of the glycans consisted of two N-acetylglucosamines (GlcNac) and one fucose in the core position when PD-1 was expressed in both mammalian[11] and insect cells[1]
An in vivo efficacy study using the MC-38 model in human PD-1 knock-in mice showed that mAb059c was as efficacious as pembrolizumab and nivolumab references at a dose of 1 mg/kg (Fig. 1a,b) and 10 mg/kg (Supplementary Fig. S1)
Summary
Programmed cell death 1 (PD-1) monoclonal antibodies have been approved by regulatory agencies for the treatment of various types of cancer, and the mechanism involves the restoration of T cell functions. We report the X-ray crystal structure of a fully human monoclonal antibody mAb059c fragment antigen-binding (Fab) in complex with the PD-1 extracellular domain (ECD) at a resolution of 1.70 Å. N58, which is on the BC loop of PD-1 and resides closest to the binding epitopes of pembrolizumab and nivolumab, was reported to be heavily glycosylated and most of the glycans consisted of two N-acetylglucosamines (GlcNac) and one fucose in the core position when PD-1 was expressed in both mammalian[11] and insect cells[1]. Loss of core fucosylation caused PD-1 deprivation on the cellular surface and augmented T cell activation[15]. Both TCR and PD-1 are glycoproteins, and core fucosylation could be utilized to regulate PD-1 expression by modulating TCR signaling strength[20]
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