Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL

• Published in: Nature communications Vol. 15; no. 1; pp. 2743 - 17
• Main Authors: Nayak, Digant, Lv, Dongwen, Yuan, Yaxia, Zhang, Peiyi, Hu, Wanyi, Nayak, Anindita, Ruben, Eliza A., Lv, Zongyang, Sung, Patrick, Hromas, Robert, Zheng, Guangrong, Zhou, Daohong, Olsen, Shaun K.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29-03-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 13; 13/95; 631/154; 631/45/173; 631/45/535; 631/535; 96; Apoptosis; Bcl-2 protein; Bcl-x protein; bcl-X Protein - metabolism; Cancer; Crystal structure; Crystallization; Degradation; Design; Drug resistance; Functional analysis; Humanities and Social Sciences; Humans; Ligands; multidisciplinary; Neoplasms; Proteins; Proto-Oncogene Proteins c-bcl-2; Science; Science & Technology - Other Topics; Science (multidisciplinary); Toxicity; Tumorigenesis; Tumors; Ubiquitin-protein ligase
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-46922-4

Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.
Here, the authors have determined structures of 753b PROTAC, BCL-xL/BCL-2 and VHL E3 ligase ternary complexes which reveal the basis for the dual degrader activity of 753b. The structures and subsequent functional analyses facilitated design of WH244 PROTAC, with enhanced degrader activity in cells.