Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
Jingxian Liu1, Guiqun Wang2, Liu Liu2
1Shanghai ChemPartner Co.Ltd, Shanghai, 201203, The People's Republic of China. jxliu@chempartner.com.
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.
Insights
This study reveals the crystal structure of an anti-PD-1 antibody fragment (mAb059c Fab) bound to PD-1, detailing key interactions and the epitope. These findings advance understanding of antibody recognition for developing novel cancer immunotherapies.
Area of Science:
- Structural biology
- Immunology
- Biochemistry
Background:
- Monoclonal antibodies targeting Programmed Cell Death 1 (PD-1) are crucial in cancer immunotherapy by restoring T cell functions.
- Understanding the molecular interactions between anti-PD-1 antibodies and the PD-1 receptor is vital for developing more effective treatments.
Purpose of the Study:
- To determine the high-resolution X-ray crystal structure of a fully human anti-PD-1 antibody fragment (mAb059c Fab) in complex with the PD-1 extracellular domain (ECD).
- To elucidate the specific molecular interactions, epitope, and binding mechanisms involved in the recognition of PD-1 by mAb059c.
- To provide insights for the rational design of next-generation anti-PD-1 therapeutics.
Main Methods:
- X-ray crystallography was employed to obtain the complex structure at 1.70 Å resolution.
- Detailed structural analysis of the antibody-antigen interface, including epitope mapping and identification of key binding residues and interactions.
- Site-directed mutagenesis (N58 mutation) was performed to assess the functional significance of specific interactions.
Main Results:
- The crystal structure revealed the epitope on PD-1, involving the C'D, BC, and FG loops.
- Specific interactions were identified, including a salt bridge between ASP101(HCDR3) and ARG86(PD-1), and contacts involving the FG loop and light chain CDR3.
- The N58 glycosylation site in the BC loop was found to be recognized by mAb059c heavy chain CDR1 and CDR2, with its mutation attenuating antibody binding.
Conclusions:
- The structural insights provide a detailed understanding of how mAb059c recognizes the PD-1 receptor.
- The identified molecular interactions and epitope are critical for the antibody's function in blocking PD-1 signaling.
- These findings will aid in the development of novel anti-PD-1 antibodies with improved efficacy for cancer treatment.
