Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

Abstract

The anti-cancer agent Indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which Indisulam mediates DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-Indisulam-RBM39(RRM2) complex structure to 2.3 Å. DCAF15 has a novel topology which embraces the RBM39(RRM2) domain largely via nonpolar interactions, and Indisulam binds between DCAF15 and RBM39(RRM2) and coordinates additional interactions between the two proteins. Studies with RBM39 point mutants and Indisulam analogs validated the structural model and defined the RBM39 alpha-helical degron motif. The degron is found only in RBM23 and RBM39 and only these proteins were detectably downregulated in Indisulam-treated HCT116 cells. This work further explains how Indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade novel targets.

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation

“…Several common themes have emerged from this limited set of molecular glues. First, molecular glues often bind to their target proteins with modest or even undetectable affinities, while enhanced affinities are usually observed once a regulatory protein is also present in the system ( Bussiere et al, 2020 ; Du et al, 2019 ; Faust et al, 2020 ). Such unique binding characteristics can be explained by induced protein-protein interactions and pre-existing protein surface complementarity as revealed by structural analysis of molecular glue-bound protein complexes ( Bussiere et al, 2020 ; Du et al, 2019 ; Faust et al, 2020 ; Tan et al, 2007 ).…”

“…First, molecular glues often bind to their target proteins with modest or even undetectable affinities, while enhanced affinities are usually observed once a regulatory protein is also present in the system ( Bussiere et al, 2020 ; Du et al, 2019 ; Faust et al, 2020 ). Such unique binding characteristics can be explained by induced protein-protein interactions and pre-existing protein surface complementarity as revealed by structural analysis of molecular glue-bound protein complexes ( Bussiere et al, 2020 ; Du et al, 2019 ; Faust et al, 2020 ; Tan et al, 2007 ). Second, molecular glues can target transcription factors and splicing factors, by recognizing either relatively flat surfaces or disordered regions of these proteins ( Han et al, 2017 ; Krönke et al, 2014 ; Lu et al, 2014 ; Tan et al, 2007 ).…”

Proteolysis‐targeting chimeras in drug development: A safety perspective

“…Indisulam forms a tripartite complex with DCAF15 and RBM39, where DCAF15 and RBM39 bind together mainly through non‐polar interactions. The observation that anti‐cancer sulfonamides make contact with both proteins simultaneously illustrates a diversity in this so‐called molecular glue mechanism and also highlights the challenge to hijack DCAF15 as a novel E3 ligase (Bussiere et al, ). Indisulam has been shown to be highly selective and in HCT116 cells showed degradation of RBM39 as the primary target together with RBM23 (https://doi.org/10.1101/737510).…”

Aryl Sulfonamides Induce Degradation of Aryl Hydrocarbon Receptor Nuclear Translocator through CRL4DCAF15 E3 Ligase

“…3E). Sulfonamides have been shown to promote ternary complex formation with DCAF15 and RBM39 or RBM23 (Bussiere et al, 2020;Du et al, 2019;Faust et al, 2020). Accordingly, we examined whether degradation of both RBM39 and RBM23 is a prerequisite for indisulam-mediated ARNT degradation.…”