Degradation of Cyclin K/CDK12 is a druggable vulnerability of colorectal cancer (H012)
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PROVIDER: EGAS00001004517 | EGA |
REPOSITORIES: EGA
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Project description:The CDK12 inhibitor, SR-4835, promotes the proteasomal degradation of cyclin K, contingent on the presence of CDK12 and the CUL4-RBX1-DDB1 E3 ligase complex. The inhibitor displays molecular glue activity, which correlates with its enhanced ability to inhibit cell growth. This effect is achieved by facilitating the formation of a ternary complex that requires the small molecule SR-4835, CDK12, and the adaptor protein DDB1, leading to the subsequent ubiquitination and degradation of cyclin K. We have successfully solved the structure of the ternary complex, enabling the de novo design of molecular glues that transform four different CDK12 scaffold inhibitors, including the clinical pan-CDK inhibitor dinaciclib, into cyclin K degraders. These results not only deepen our understanding of CDK12's role in cell regulation but also underscore significant progress in designing molecular glues for targeted protein degradation, paving the way for more precise and effective therapeutic strategies in cancer treatment.
2025-05-07 | PXD053505 | Pride
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: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: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:Cyclin-dependent kinase 12 (CDK12) overexpression is implicated in breast cancer, but whether it has a primary or only a cooperative tumorigenic role is unclear. Here, we show that transgenic CDK12 overexpression in the mouse mammary gland per se is sufficient to drive the emergence of multiple and multifocal tumors, while, in cooperation with known oncogenes or chemical carcinogens, it promotes earlier tumor onset and metastasis. Integrative transcriptomic, metabolomic and functional data revealed that enhanced glycolysis and hyperactivation of the serine-glycine-one- carbon network are metabolic hallmarks inherent to CDK12-induced tumorigenesis, which impose distinct metabolic dependencies in CDK12-transformed mammary epithelial cells. Consistently, in the retrospective analysis of adjuvant and neoadjuvant breast cancer patient cohorts and in prospective preclinical studies using primary-derived human breast tumor xenografts, CDK12-overexpressing breast cancers showed a more favorable disease course in response to methotrexate- based chemotherapy targeting CDK12-induced metabolic alterations, while appearing intrinsically refractory to other types of chemotherapy. Even more clinically relevant, in patients with hormone receptor-negative and lymph node-positive breast cancer who were randomized in an adjuvant phase III trial to 1-year low-dose metronomic methotrexate-based maintenance chemotherapy or no chemotherapy after standard adjuvant treatments, a high CDK12 status predicted a dramatic reduction in distant metastasis rate in the chemotherapy-treated vs. not-treated arm. Thus, by coupling tumor progression with metabolic reprogramming, CDK12 creates an actionable vulnerability for breast cancer therapy and might represent a suitable companion biomarker for targeted antimetabolite therapies in naturally occurring human breast cancers.
2022-02-22 | GSE189274 | GEO
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:Cyclin-dependent kinase 12 (CDK12) interacts with Cyclin K to form a a functional nuclear kinase complex, which has been reported to phosphorylate the carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) for transcriptional regulation and co-transcriptional RNA processing. However, the precise mechanisms and targets of CDK12 action remain largely unknown. Here, we combined a chemical genetic screen and phosphoproteomic strategies and identified a landscape of nuclear CDK12 substrates, which included proteins that regulate transcription, chromatin organization, and RNA splicing. Next, we confirmed that the LEO1 subunit of the transcription elongation factor PAF1 complex (PAF1C) is a bona fide substrate of CDK12. Acute depletion of LEO1 reduces Pol II occupancy on the chromatin, while mutations of LEO1 phosphorylation sites to non-phosphorylatable alanine residues attenuated the association of PAF1C with elongating Pol II and chromatin, resulting in impaired processive transcription elongation. Furthermore, LEO1 C-terminus could interact with and be dephosphorylated by the Integrator-PP2A complex (INTAC), while acute depletion of INTAC in cells promotes the association between PAF1C and elongating Pol II on the chromatin. Together, this study provides a novel transcriptional regulatory mechanism that the CDK12-INTAC axis fine-tunes LEO1 phosphorylation for processive transcription elongation.
2023-05-19 | GSE217544 | GEO
Project description:The design of selective small-molecules is often stymied by similar ligand binding pockets. Here we report the first cyclin-dependent kinase 6 (CDK6) degrader, BSJ-03-123, that uses phthalimide-conjugation to exploit protein-interface determinants to achieve proteome-wide degradation selectivity. Pharmacologic CDK6 degradation targets a selective dependency of acute myeloid leukemia cells, and coupling acute degradation with transcriptomics and phosphoproteomics enabled dynamic mapping of the immediate role of CDK6 in coordinating signaling and transcription.
2018-11-20 | GSE116187 | GEO
Project description:Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation
| PRJNA643772 | ENA