Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

Area of Science:

• Biochemistry
• Structural Biology
• Immunology

Background:

• PTPN2 and PTPN1 are key phosphatases and attractive immuno-oncology targets.
• Targeted protein degradation offers a novel therapeutic strategy for challenging targets like phosphatases.
• Deletion of Ptpn1 and Ptpn2 has shown promise in improving immunotherapy response in preclinical models.

Purpose of the Study:

• To develop potent PTPN2/N1 dual heterobifunctional degraders.
• To elucidate the mechanistic insights into the degrader-induced cooperative complex formation.
• To provide structural understanding of the ternary complex involving degraders, E3 ligase, and target phosphatases.

Main Methods:

• Development of novel heterobifunctional degraders (Cmpd-1 and Cmpd-2).
• Utilized X-ray crystallography to determine the structure of PTPN2 bound to the degrader.
• Employed single-particle cryo-electron microscopy (cryo-EM) to resolve the DDB1-CRBN/Cmpd-1/PTPN2 complex.
• Performed molecular dynamics (MD) simulations based on cryo-EM data.

Main Results:

• Successfully developed potent PTPN2/N1 dual degraders (Cmpd-1, Cmpd-2) mediating degradation in cells and mice.
• Crystal structure revealed specific recognition of PTPN2 by the degrader.
• Cryo-EM structure elucidated degrader-induced proximity between CRBN and PTPN2, despite conformational heterogeneity.
• MD simulations highlighted dynamic interactions and rigid body movements within the ternary complex.

Conclusions:

• Demonstrated the development of PTPN2/N1 heterobifunctional degraders with potential in cancer immunotherapy.
• The structural workflow provides insights into the dynamic nature of degrader-induced ternary complexes.
• These degraders represent a promising approach for targeting phosphatases in immuno-oncology.