Innovative CDR grafting and computational methods for PD-1 specific nanobody design

Area of Science:

• Biotechnology
• Immunology
• Computational Biology

Background:

• Nanobodies targeting Programmed Cell Death Protein-1 (PD-1) represent a novel strategy in cancer immunotherapy.
• Developing effective PD-1 inhibitors is crucial for enhancing anti-tumor immune responses.

Purpose of the Study:

• To design and characterize a novel nanobody specific for PD-1 using an integrated computational and experimental approach.
• To evaluate the binding affinity, stability, and physicochemical properties of the engineered PD-1 nanobody.

Main Methods:

• In silico design involving Complementarity-Determining Region (CDR) grafting.
• Structure prediction (AlphaFold2), molecular docking (ClusPro), and molecular dynamics (MD) simulations.
• Experimental validation including protein production, purification, Western blotting, ELISA, and dot blot analysis.

Main Results:

• Computational analyses predicted favorable binding interactions, stability, and physicochemical properties for the designed nanobody.
• Experimental validation confirmed the nanobody's specific binding affinity to PD-1.
• ELISA and dot blot assays demonstrated robust interaction between the nanobody and PD-1.

Conclusions:

• The combination of computational and experimental methods is effective for engineering functional nanobodies.
• The engineered PD-1 nanobody exhibits promising characteristics for cancer immunotherapy applications.
• This nanobody is a strong candidate for further preclinical and clinical evaluation.