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

• Published in: Communications chemistry Vol. 7; no. 1; pp. 183 - 16
• Main Authors: Hao, Qi, Rathinaswamy, Manoj K, Klinge, Kelly L, Bratkowski, Matthew, Mafi, Amirhossein, Baumgartner, Christina K, Hamel, Keith M, Veits, Gesine K, Jain, Rinku, Catalano, Claudio, Fitzgerald, Mark, Hird, Alexander W, Park, Eunice, Vora, Harit U, Henderson, James A, Longenecker, Kenton, Hutchins, Charles W, Qiu, Wei, Scapin, Giovanna, Sun, Qi, Stoll, Vincent S, Sun, Chaohong, Li, Ping, Eaton, Dan, Stokoe, David, Fisher, Stewart L, Nasveschuk, Christopher G, Paddock, Marcia, Kort, Michael E
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 16.08.2024; Nature Portfolio
• Subjects: Complex formation; Crystal structure; Degradation; Heterogeneity; Immunotherapy; Molecular dynamics; Molecular structure; Oncology; Phosphatase; Proteins; Receptors; Rigid structures; Tyrosine; Workflow
• ISSN: 2399-3669; 2399-3669
• DOI: 10.1038/s42004-024-01263-7

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.