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Author Spotlight: Evaluating Biophysical Assays for Characterizing PROTACS Ternary Complexes
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Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

Qi Hao1, Manoj K Rathinaswamy2, Kelly L Klinge3

  • 1Calico Life Sciences LLC, South San Francisco, CA, 94080, USA. qhao@calicolabs.com.

Communications Chemistry
|August 16, 2024
PubMed

Insights

We developed novel dual degraders targeting PTPN2 and PTPN1 phosphatases, enhancing immunotherapy response. Structural studies reveal how these degraders induce protein-protein interactions for targeted degradation in cancer.

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.

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