Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [CRISPR]

ABSTRACT: Molecular glues are small molecules that exert their biologic or therapeutic activities by inducing gain-of-function interactions between pairs of proteins. In particular, molecular-glue degraders, which mediate interactions between target proteins and components of the ubiquitin proteasome system to cause targeted protein degradation, hold great promise as a unique modality for therapeutic targeting of proteins that are currently intractable. Here, we report a new molecular glue HQ461 discovered by high-throughput screening of small molecules that inhibited NRF2 activity. Using unbiased loss-of-function and gain-of-function genetic screening followed by biochemical reconstitution, we show that HQ461 acts by promoting interaction between CDK12 and DDB1-CUL4-RBX1 E3 ubiquitin ligase, leading to polyubiquitination and proteasomal degradation of CDK12’s interacting protein Cyclin K (CCNK). Degradation of CCNK mediated by HQ461 compromised CDK12 function, leading to reduced phosphorylation of CDK12 substrate, downregulation of DNA damage response genes, and cell death. Structure-activity relationship analysis of HQ461 revealed the importance of a 5-methylthiazol-2-amine pharmacophore and resulted in an HQ461 derivate with improved potency. Our studies reveal a new molecular glue that engages its target protein directly with DDB1 to bypass the requirement of a substrate-specific receptor, presenting a new strategy for targeted protein degradation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE153700 | GEO | 2020/07/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [WES]

Project description:Molecular glues are small molecules that exert their biologic or therapeutic activities by inducing gain-of-function interactions between pairs of proteins. In particular, molecular-glue degraders, which mediate interactions between target proteins and components of the ubiquitin proteasome system to cause targeted protein degradation, hold great promise as a unique modality for therapeutic targeting of proteins that are currently intractable. Here, we report a new molecular glue HQ461 discovered by high-throughput screening of small molecules that inhibited NRF2 activity. Using unbiased loss-of-function and gain-of-function genetic screening followed by biochemical reconstitution, we show that HQ461 acts by promoting interaction between CDK12 and DDB1-CUL4-RBX1 E3 ubiquitin ligase, leading to polyubiquitination and proteasomal degradation of CDK12’s interacting protein Cyclin K (CCNK). Degradation of CCNK mediated by HQ461 compromised CDK12 function, leading to reduced phosphorylation of CDK12 substrate, downregulation of DNA damage response genes, and cell death. Structure-activity relationship analysis of HQ461 revealed the importance of a 5-methylthiazol-2-amine pharmacophore and resulted in an HQ461 derivate with improved potency. Our studies reveal a new molecular glue that engages its target protein directly with DDB1 to bypass the requirement of a substrate-specific receptor, presenting a new strategy for targeted protein degradation.

2020-07-03 | GSE153707 | GEO

The CDK12-inhibitor CR8 mediates Cyclin K degradation through the CUL4-RBX1-DDB1 E3 ubiquitin ligase

Project description:Small molecules have been identified that induce protein-protein interactions between a substrate and a ubiquitin ligase, resulting in targeted protein degradation. Such molecular glue compounds, unlike traditional enzyme inhibitors, act sub-stoichiometrically to catalyse rapid depletion of previously inaccessible targets. Molecular glue degraders have the potential for clinical efficacy, but have thus far only been discovered serendipitously. Through correlations between compound cytotoxicity and E3 ligase expression levels, we found that CR8, a cyclin-dependent kinase (CDK) inhibitor, acts as a molecular glue degrader. A surface-exposed pyridyl moiety of CR8 is sufficient to induce complex formation between CDK12-Cyclin K and DDB1, a component of CUL4 E3 ubiquitin ligase complexes, which presents Cyclin K for ubiquitination and degradation. Our results reveal that minor surface-exposed modifications confer gain-of-function glue properties to an inhibitor. We hypothesize that chemical alteration of surface-exposed moieties is a broad strategy to turn a target binder into a molecular glue.

2020-06-10 | PXD016188 | Pride

The CDK12-inhibitor CR8 mediates Cyclin K degradation through the CUL4-RBX1-DDB1 E3 ubiquitin ligase

2020-06-10 | PXD016187 | Pride

Design principles for cyclin K molecular glue degraders

Project description:Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. To investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical, and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

2023-10-20 | PXD041836 | Pride

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

Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation

| PRJNA643772 | ENA

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [WES]

Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [WES]

| PRJNA643782 | ENA

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [CRISPR]

Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [CRISPR]

| PRJNA643767 | ENA

Transcriptome and analysis of Wdr70 deletion by next-generation sequencing

Project description:CRL4 is a family of SCF-like ubiquitin ligase constituted by Cul4-Ddb1-RING finger scaffold and DCAF substrate adaptors. We revealed Wdr70 as a novel DCAF protein that assembles with Cul4-Ddb1 and functions as chromatin remodeling factor in Schizosaccharomyces pombe.Besides its function in DNA repair, CRL4Wdr70 is speculated to regulate gene expression in a subset of yeast transcriptome. Here we use the next-generation sequencing to show that deletion of Wdr70 gene disturbs the gene expression profile of G2-synchronised yeast cells. Examination of genome-wide gene expression in 2 different yeast strains using Illumina Hiseq2500.

2016-04-04 | E-GEOD-79830 | biostudies-arrayexpress

Selective Degradation of Splicing Factor CAPER-alpha by Anticancer Sulfonamides

Project description:Target protein degradation is an emerging field in drug discovery and development. In particular, the substrate receptor proteins of the cullin ubiquitin ligase system play a key role in selective protein degradation, which is an essential component of the anti-myeloma activity of immunomodulatory drugs (IMiDs) represented by lenalidomide. Here, we demonstrate that a series of anticancer sulfonamides NSC 719239 (E7820), indisulam, and NSC 339004 (chloroquinoxaline sulfonamide, CQS) induce proteasomal degradation of the U2AF-related splicing factor CAPER-alpha via DCAF15-DDB1-CUL4 CRL4-DCAF15 mediated ubiquitination in human cancer cell lines. Both CRISPR/Cas9-based knockout of DCAF15 and a single amino acid substitution of CAPER-alpha conferred resistance against sulfonamide-induced CAPER-alpha degradation and cell-growth inhibition. Thus, the these sulfonamides represent selective chemical probes for disrupting CAPER-alpha function and designate DCAFs as promising drug targets for promoting selective protein degradation in cancer therapy.

2017-01-20 | GSE93829 | GEO

Transcriptome and analysis of Wdr70 deletion by next-generation sequencing

2016-04-04 | GSE79830 | GEO