Computational design of a synthetic PD-1 agonist
Cassie M Bryan1,2, Gabriel J Rocklin3,2, Matthew J Bick3,2
1Department of Biochemistry, University of Washington, Seattle, WA 98195; cassie.bryan@gmail.com.
Abstract:
Programmed cell death protein-1 (PD-1) expressed on activated T cells inhibits T cell function and proliferation to prevent an excessive immune response, and disease can result if this delicate balance is shifted in either direction. Tumor cells often take advantage of this pathway by overexpressing the PD-1 ligand PD-L1 to evade destruction by the immune system. Alternatively, if there is a decrease in function of the PD-1 pathway, unchecked activation of the immune system and autoimmunity can result. Using a combination of computation and experiment, we designed a hyperstable 40-residue miniprotein, PD-MP1, that specifically binds murine and human PD-1 at the PD-L1 interface with a Kd of ∼100 nM. The apo crystal structure shows that the binder folds as designed with a backbone RMSD of 1.3 Å to the design model. Trimerization of PD-MP1 resulted in a PD-1 agonist that strongly inhibits murine T cell activation. This small, hyperstable PD-1 binding protein was computationally designed with an all-beta interface, and the trimeric agonist could contribute to treatments for autoimmune and inflammatory diseases.
Insights
Researchers designed a novel miniprotein, PD-MP1, that binds to Programmed Cell Death protein-1 (PD-1). This protein acts as a PD-1 agonist, inhibiting T cell activation and offering potential treatments for autoimmune diseases.
Area of Science:
- Immunology
- Structural Biology
- Protein Engineering
Background:
- Programmed Cell Death protein-1 (PD-1) regulates T cell responses to prevent autoimmunity and excessive immune reactions.
- Tumor cells exploit the PD-1/PD-L1 pathway to evade immune surveillance.
- Dysregulation of the PD-1 pathway can lead to autoimmunity or impaired immune responses.
Purpose of the Study:
- To computationally design a hyperstable miniprotein that specifically targets the PD-1 receptor.
- To investigate the binding affinity and structural characteristics of the designed miniprotein.
- To evaluate the functional activity of the miniprotein as a PD-1 agonist.
Main Methods:
- Computational protein design was employed to create a 40-residue miniprotein (PD-MP1).
- Structural analysis using X-ray crystallography confirmed the designed fold of the miniprotein.
- Binding affinity was assessed using SPR (Kd of ~100 nM) for both murine and human PD-1.
- Functional assays measured the inhibition of murine T cell activation by trimerized PD-MP1.
Main Results:
- A hyperstable 40-residue miniprotein, PD-MP1, was successfully designed and validated structurally.
- PD-MP1 demonstrated specific binding to both murine and human PD-1 at the PD-L1 interface with high affinity (Kd ~100 nM).
- Trimerization of PD-MP1 yielded a potent PD-1 agonist that significantly inhibited T cell activation.
Conclusions:
- The designed miniprotein PD-MP1 is a stable and specific binder of PD-1.
- Trimeric PD-MP1 functions as a PD-1 agonist, inhibiting T cell activation.
- This novel protein scaffold holds promise for developing therapeutics for autoimmune and inflammatory conditions.
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