Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1

Abstract

Pidilizumab is a monoclonal antibody tested against several types of malignancies, such as lymphoma and metastatic melanoma, showing promising results. In 2016, the FDA put Pidilizumab’s clinical studies on partial hold due to emerging evidence pointing to the antibody target uncertainty. Although initial studies indicated an interaction with the PD-1 checkpoint receptor, recent updates assert that Pidilizumab binds primarily to Notch ligand DLL1. However, a detailed description of which interactions coordinate antibody-antigen complex formation is lacking. Therefore, this study uses computational tools to identify molecular interactions between Pidilizumab and its reported targets PD-1 and DLL1. A docking methodology was validated and applied to determine the binding modes between modeled Pidilizumab scFvs and the two antigens. We used Molecular Dynamics (MD) simulations to verify the complexes’ stability and submitted the resulting trajectory files to MM/PBSA and Principal Component Analysis. A set of different prediction tools determined scFv interface hot-spots. Whereas docking and MD simulations revealed that the antibody fragments do not interact straightforwardly with PD-1, ten scFv hot-spots, including Met93 and Leu112, mediated the interaction with the DLL1 C2 domain. The interaction triggered a conformational selection-like effect on DLL1, allowing new hydrogen bonds on the β3-β4 interface loop. The unprecedented structural data on Pidilizumab’s interactions provided novel evidence that its legitimate target is the DLL1 protein and offered structural insight on how these molecules interact, shedding light on the pathways that could be affected by the use of this essential immunobiological.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pidilizumab
• PD-1
• DLL1
• MD Simulation
• immune
• antibody
• interaction

Acknowledgements

The authors thank the Oswaldo Cruz Foundation for their support in this study.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This research was financially supported through a master’s degree scholarship offered by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, an institution linked to the Brazilian Ministry of Education. The funding bodies did not play any role in this study’s design or development, the analysis and interpretation of data, or this manuscript’s writing. This article was funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior and Fundação Oswaldo Cruz.