Structural Insights into PROTAC-Mediated Degradation of Bcl-xL

Abstract

The Bcl-2 family of proteins, such as Bcl-xL and Bcl-2, play key roles in cancer cell survival. Structural studies of Bcl-xL formed the foundation for the development of the first Bcl-2 family inhibitors and FDA approved drugs. Recently, Proteolysis Targeting Chimeras (PROTACs) that degrade Bcl-xL have been proposed as a therapeutic modality with the potential to enhance potency and reduce toxicity versus antagonists. However, no ternary complex structures of Bcl-xL with a PROTAC and an E3 ligase have been successfully determined to guide this approach. Herein, we report the design, characterization, and X-ray structure of a VHL E3 ligase-recruiting Bcl-xL PROTAC degrader. The 1.9 Å heterotetrameric structure, composed of (ElonginB:ElonginC:VHL):PROTAC:Bcl-xL, reveals an extensive network of neo-interactions, between the E3 ligase and the target protein, and between noncognate parts of the PROTAC and partner proteins. This work illustrates the challenges associated with the rational design of bifunctional molecules where interactions involve composite interfaces.

A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models

“…It is worth noting that, to the best of our knowledge, only a very limited number of degrader ternary complex structures have been reported to date (39,(42)(43)(44)(45)(46). Structure-based design to generate more effective degraders is even rarer.…”

Discovery and Characterisation of Highly Cooperative FAK‐Degrading PROTACs

“…Thelargest number of VHL ternary complex structures have been reported from bromodomaincontaining proteins,s uch as BRD4 [29b] and SMARCA4, [31] with an additional structure of an on-bromodomain protein also having been recently disclosed. [32] Theh igh ternary complex cooperativity induced by GSK215 can be explained by many neo-interactions between FAKa nd VHL that occur at both ends of the PROTAC Angewandte molecule (Figure 4b). As expected, the FAKb inding moiety of the PROTACi scompletely enclosed by the FAKp rotein.…”

Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues

“…Ligase-PROTAC-target complexes have also been solved for systems that do not appear to exhibit positive cooperativity in the ternary equilibria, suggesting avenues for potential optimization strategy. The recent structure of a VCB:PROTAC6:B-cell lymphoma-extra-large (Bcl-xL) complex shows the long PEG linker of PROTAC6 is forced to adopt an extended conformation, before folding back into itself via a compact turn (Figure 4c) [57 ]. The unfavourable linker conformational energy likely surpasses any favourable induced PPIs, resulting in the negative cooperativity observed with this system.…”

“…Zoomed section shows the structure-based design of PROTAC 2 (PDB: 6HAX[56 ]) aimed at rigidifying the linker through substitution of a flexible 5-atom portion of the linker with a phenyl ring. (c) Ternary complex of VCB-PROTAC6(cyan)-Bcl-xL(lime green) (PDB: 6ZHC[57 ]). (d) Crystal structure of CRBN(violet)-DDB1 (green) complex with bound PROTAC dBET23 (cyan) and Brd4 BD1 (magenta) (PDB: 6BN7[58]).…”