Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation
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ABSTRACT:
PROVIDER: PRJNA643772 | ENA |
REPOSITORIES: ENA
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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
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 | GSE153700 | GEO
Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [WES]
| PRJNA643782 | ENA
Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [CRISPR]
| PRJNA643767 | ENA
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 | PXD016187 | Pride
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
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
Project description: Not available
| S-EPMC7462607 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-07-03 | GSE153708 | GEO
Project description:RNA-sequencing analysis of CDK12 overexpressiong ZR-75-30 cell lines. Cyclin dependent kinase 12 (CDK12) is amplified in approximately 70-90% of HER2 amplified breast cancer. Results provide insight into the targets of CDK12 in HER2 positive breast cancer.
2019-07-21 | GSE117523 | GEO