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Exploring Effectiveness of KEAP1-based PROTAC Strategy

ABSTRACT: Targeted protein degradation (TPD) uses small molecules to recruit E3 ubiquitin ligases into proximity of proteins of interest, inducing ubiquitination-dependent degradation. A major bottleneck in the TPD field is the lack of accessible E3 ligase ligands for developing degraders. To expand the E3 ligase toolbox, we sought to convert the KEAP1 inhibitor KI696 into a recruitment handle for several targets. While we were able to generate KEAP1-recruiting degraders of BET family and murine FAK we discovered that the target scope of KEAP1 was narrow, as targets easily degraded by a cereblon (CRBN)-recruiting degrader were refractory to KEAP1-mediated degradation. Linking the KEAP1-binding ligand to a CRBN-binding ligand resulted in a molecule that induced degradation of KEAP1 but not CRBN. In sum, we characterize tool compounds to explore KEAP1-mediated ubiquitination and delineate the challenges of exploiting new E3 ligases for generating bivalent degraders.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Eric Fischer

LAB HEAD: Eric Fischer

PROVIDER: PXD034423 | Pride | 2022-09-07

REPOSITORIES: Pride

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Similar Datasets

Exploring Effectiveness of KEAP1-based PROTAC Strategy

Project description:Targeted protein degradation (TPD) uses small molecules to recruit E3 ubiquitin ligases into proximity of proteins of interest, inducing ubiquitination-dependent degradation. A major bottleneck in the TPD field is the lack of accessible E3 ligase ligands for developing degraders. To expand the E3 ligase toolbox, we sought to convert the KEAP1 inhibitor KI696 into a recruitment handle for several targets. While we were able to generate KEAP1-recruiting degraders of BET family and murine FAK we discovered that the target scope of KEAP1 was narrow, as targets easily degraded by a cereblon (CRBN)-recruiting degrader were refractory to KEAP1-mediated degradation. Linking the KEAP1-binding ligand to a CRBN-binding ligand resulted in a molecule that induced degradation of KEAP1 but not CRBN. In sum, we characterize tool compounds to explore KEAP1-mediated ubiquitination and delineate the challenges of exploiting new E3 ligases for generating bivalent degraders.

2022-09-07 | PXD034424 | Pride

Exploring Effectiveness of KEAP1-based PROTAC Strategy

2022-09-07 | PXD034378 | Pride

Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins

Project description:Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR/Cas9-based gene-editing studies. We observed that myeloma cell resistance to "degraders" of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; involves loss-of-function for the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for CRBN- vs. VHL-based degraders explains mechanistically the lack of cross-resistance for degraders targeting the same protein via different E3 ligase/CRLs.

2021-02-12 | GSE162205 | GEO

The Cyclimids: Degron-inspired cereblon binders for targeted protein degradation

Project description:Our studies establish the unique properties of the cyclimids as versatile warheads in TPD and a systematic biochemical approach for quantifying ternary complex formation to predict their cellular degradation activity, which together will accelerate the development of novel CRBN-targeting bifunctional degraders.

2024-01-26 | PXD041494 | Pride

Chemically induced cereblon (CRBN) degradation: efficacy of recruiting CRBN in comparison to VHL

Project description:As small molecule degrader technology has developed, it has raised the question of whether E3 ligases could be induced to self-ubiquitinate. To examine this question, we generated six CRBN-CRBN degraders (also referred to as homo-PROTACs) and six CRBN-VHL degraders (hetero-PROTACs). From these compounds we identified two potent and selective CRBN degraders (ZXH-4-130 and ZXH-4-137), both of which are CRBN-VHL compounds. Comparison of these compounds to previously reported small molecule CRBN degraders further validated our observation that CRBN-VHL compounds are more potent degraders of CRBN than CRBN-CRBN compounds.

2021-07-30 | PXD022022 | Pride

Chemically induced cereblon (CRBN) degradation: efficacy of recruiting CRBN in comparison to VHL

2021-07-30 | PXD022060 | Pride

Chemically induced cereblon (CRBN) degradation: efficacy of recruiting CRBN in comparison to VHL

2021-07-30 | PXD022058 | Pride

Chemically induced cereblon (CRBN) degradation: efficacy of recruiting CRBN in comparison to VHL

2021-07-30 | PXD022059 | Pride

Chemically induced cereblon (CRBN) degradation: efficacy of recruiting CRBN in comparison to VHL

2021-07-30 | PXD022021 | Pride

A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo

Project description:Targeted protein degradation offers an alternative modality to classical inhibition and holds the promise of addressing previously undruggable targets to provide novel therapeutic options for patients. Heterobifunctional molecules co-recruit the target and an E3 ligase, resulting in ubiquitylation and proteosome-dependent degradation of the target. The oral route of administration is the option of choice in the clinic, but has only been achieved so far by CRBN- recruiting bifunctional degrader molecules. We aimed to achieve orally bioavailable molecules that selectively degrade the BAF Chromatin Remodelling complex ATPase SMARCA2 over its closely related paralogue SMARCA4, to allow in vivo evaluation of the synthetic lethality concept of SMARCA2 dependency in SMARCA4 deficient cancers. Here we outline structure- and property-guided approaches that led to the first orally bioavailable VHL-recruiting degraders. Our tool compound, ACBI2, shows selective degradation of SMARCA2 over SMARCA4 in ex vivo human whole blood assays and in vivo efficacy in SMARCA4-deficient cancer models. This study demonstrates the feasibility for broadening the E3 ligase and physicochemical space that can be utilised for achieving oral efficacy with bifunctional molecules.

2022-06-20 | PXD032239 | Pride

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