Co-opting the E3 ligase KLHDC2 for targeted protein degradation by small molecules

Targeted protein degradation (TPD) by PROTAC (proteolysis-targeting chimera) and molecular glue small molecules is an emerging therapeutic strategy. To expand the roster of E3 ligases that can be utilized for TPD, we describe the discovery and biochemical characterization of small-molecule ligands targeting the E3 ligase KLHDC2. Furthermore, we functionalize these KLHDC2-targeting ligands into KLHDC2-based BET-family and AR PROTAC degraders and demonstrate KLHDC2-dependent target-protein degradation. Additionally, we offer insight into the assembly of the KLHDC2 E3 ligase complex. Using biochemical binding studies, X-ray crystallography and cryo-EM, we show that the KLHDC2 E3 ligase assembles into a dynamic tetramer held together via its own C terminus, and that this assembly can be modulated by substrate and ligand engagement.

PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models

The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo. Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM (PLAU and KRT80) also supported this conclusion.

Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers

The mammalian SWItch/Sucrose Non-Fermentable (SWI/SNF) helicase SMARCA4 is frequently mutated in cancer and inactivation results in a cellular dependence on its paralog, SMARCA2, thus making SMARCA2 an attractive synthetic lethal target. However, published data indicates that achieving a high degree of selective SMARCA2 inhibition is likely essential to afford an acceptable therapeutic index, and realizing this objective is challenging due to the homology with the SMARCA4 paralog. Herein we report the discovery of a potent and selective SMARCA2 proteolysis-targeting chimera molecule (PROTAC), A947. Selective SMARCA2 degradation is achieved in the absence of selective SMARCA2/4 PROTAC binding and translates to potent in vitro growth inhibition and in vivo efficacy in SMARCA4 mutant models, compared to wild type models. Global ubiquitin mapping and proteome profiling reveal no unexpected off-target degradation related to A947 treatment. Our study thus highlights the ability to transform a non-selective SMARCA2/4-binding ligand into a selective and efficacious in vivo SMARCA2-targeting PROTAC, and thereby provides a potential new therapeutic opportunity for patients whose tumors contain SMARCA4 mutations.

Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase

PROteolysis-TArgeting Chimeras (PROTACs) are hetero-bifunctional molecules that recruit an E3 ubiquitin ligase to a given substrate protein resulting in its targeted degradation. Many potent PROTACs with specificity for dissimilar targets have been developed; however, the factors governing degradation selectivity within closely-related protein families remain elusive. Here, we generate isoform-selective PROTACs for the p38 MAPK family using a single warhead (foretinib) and recruited E3 ligase (von Hippel-Lindau). Based on their distinct linker attachments and lengths, these two PROTACs differentially recruit VHL, resulting in degradation of p38α or p38δ. We characterize the role of ternary complex formation in driving selectivity, showing that it is necessary, but insufficient, for PROTAC-induced substrate ubiquitination. Lastly, we explore the p38δ:PROTAC:VHL complex to explain the different selectivity profiles of these PROTACs. Our work attributes the selective degradation of two closely-related proteins using the same warhead and E3 ligase to heretofore underappreciated aspects of the ternary complex model.

In vivo and in vitro studies of the binding of antibody/dsDNA immune complexes to rabbit and guinea pig platelets

The in vivo and in vitro binding of prepared antibody/dsDNA immune complexes to rabbit and guinea pig cellular blood components was examined. The in vitro binding in these two nonprimates was almost entirely due to platelets, and required homologous, intact complement; furthermore, no appreciable binding was observed for neutrophils, mononuclear cells, or erythrocytes at normal blood concentrations. The in vivo binding reaction occurred quite rapidly (less than 1 min for maximal binding) and the majority of the injected counts were cleared from the circulation in 3 to 5 min. Over this time period, however, a large fraction of the counts remaining in the circulation also remained bound to the animals' cells (presumably platelets), and this result was most pronounced for complement-fixing immune complexes prepared with high m.w. dsDNA. In vitro studies confirmed that immune complexes prepared with such dsDNA are rather slowly released from the animal platelets in the presence of homologous serum, and this result is in marked contrast to the considerably greater lability of bovine serum albumin/anti-bovine serum albumin immune complexes that are bound to complement receptors on animal and human cells. These observations suggest that the fate of immune-complexed dsDNA in the circulation may be very different from that of free dsDNA, and in the case of nonprimates may involve a platelet-mediated immune complex clearance mechanism analogous to the erythrocyte-mediated immune complex clearance mechanism which is believed to be operative in primates.

In vivo and in vitro studies of the binding of antibody/dsDNA immune complexes to rabbit and guinea pig platelets

The in vivo and in vitro binding of prepared antibody/dsDNA immune complexes to rabbit and guinea pig cellular blood components was examined. The in vitro binding in these two nonprimates was almost entirely due to platelets, and required homologous, intact complement; furthermore, no appreciable binding was observed for neutrophils, mononuclear cells, or erythrocytes at normal blood concentrations. The in vivo binding reaction occurred quite rapidly (less than 1 min for maximal binding) and the majority of the injected counts were cleared from the circulation in 3 to 5 min. Over this time period, however, a large fraction of the counts remaining in the circulation also remained bound to the animals' cells (presumably platelets), and this result was most pronounced for complement-fixing immune complexes prepared with high m.w. dsDNA. In vitro studies confirmed that immune complexes prepared with such dsDNA are rather slowly released from the animal platelets in the presence of homologous serum, and this result is in marked contrast to the considerably greater lability of bovine serum albumin/anti-bovine serum albumin immune complexes that are bound to complement receptors on animal and human cells. These observations suggest that the fate of immune-complexed dsDNA in the circulation may be very different from that of free dsDNA, and in the case of nonprimates may involve a platelet-mediated immune complex clearance mechanism analogous to the erythrocyte-mediated immune complex clearance mechanism which is believed to be operative in primates.

Suramin inhibits the binding of complement-fixing antibody/double-stranded DNA immune complexes to CR1

The effects of varying concentrations of heparin and suramin on the complement-mediated binding of antibody/double-stranded DNA immune complexes to red blood cells (RBCs) and Raji cells have been investigated. If the immune complexes are briefly opsonized with complement, suramin can block binding to both cell types, and heparin can block binding to RBCs. In addition, if these complexes are first allowed to bind to RBCs or Raji cells, relatively brief incubations in suramin are sufficient to cause release of the complexes from the cells' C3b receptors. The potential clinical and diagnostic implications of these findings are discussed.