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

Publication Type:

Journal Article


Nat Commun, Volume 15, Issue 1, p.2743 (2024)


bcl-X Protein, Humans, Neoplasms, Proto-Oncogene Proteins c-bcl-2


<p>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.</p>

VCB/753b/BCL-xL, VCB/753b/BCL-2 and VCB/WH244/BCL-2 have been deposited in the Protein Data Bank (PDB) under accession number 8FY0, 8FY1, and 8FY2