Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

14-3-3 immunoprecipitation followed by LC-MS in MCF7 cells treated CV2a (PROTAC)

ABSTRACT: Proteins lacking defined ligandable pockets remain challenging drug targets. Here, we develop a molecular glue-based PROTAC (MGPROTACs) approach that chemically conjugates a molecular glue stabilizer to a VHL-recruiting ligand to capture and ubiquitinate the 14-3-3/Estrogen Receptor α (ERα) complex. Our designed MGPROTACs engage a composite interface between 14-3-3 and the disordered F-domain of ERα, promoting cooperative complex formation and target ubiquitination. Biophysical characterization revealed distinct linker-dependent cooperativities across the MGPROTAC series, which influenced both cellular permeability and ubiquitination efficiency. Cryo-EM of the most cooperative MGPROTAC uncovers de novo VHL–14-3-3ζ contacts, while molecular dynamics simulations rationalize the stabilizing interactions underlying cooperativity. Strikingly, fine-tuning linker design enables selective ubiquitination of distinct complex subunits. These findings establish a structural and mechanistic framework for integrating molecular glue and PROTAC principles, expanding the scope of drug discovery to previously intractable protein complexes.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Laura Demmers

LAB HEAD: Christian Ottmann

PROVIDER: PXD075638 | Pride | 2026-07-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20241220_SA_168426_LD002_MCF7_1433IP.mzTab	Mztab
	20241220_SA_168426_LD002_MCF7_1433IP_A.raw	Raw
	20241220_SA_168426_LD002_MCF7_1433IP_B.raw	Raw
	20241220_SA_168426_LD002_MCF7_1433IP_C.raw	Raw
	20241220_SA_168426_LD002_MCF7_1433IP_D.raw	Raw

Items per page:

1 - 5 of 23

Similar Datasets

Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design

Project description:Proteins lacking defined ligandable pockets remain challenging drug targets. Here, we develop a molecular glue-based PROTAC (MGPROTACs) approach that chemically conjugates a molecular glue stabilizer to a VHL-recruiting ligand to capture and ubiquitinate the 14-3-3/Estrogen Receptor α (ERα) complex. Our designed MGPROTACs engage a composite interface between 14-3-3 and the disordered F-domain of ERα, promoting cooperative complex formation and target ubiquitination. Biophysical characterization revealed distinct linker-dependent cooperativities across the MGPROTAC series, which influenced both cellular permeability and ubiquitination efficiency. Cryo-EM of the most cooperative MGPROTAC uncovers de novo VHL–14-3-3ζ contacts, while molecular dynamics simulations rationalize the stabilizing interactions underlying cooperativity. Strikingly, finetuning linker design enables selective ubiquitination of distinct complex subunits. These findings establish a structural and mechanistic framework for integrating molecular glue and PROTAC principles, expanding the scope of drug discovery to previously intractable protein complexes

2026-07-07 | PXD071378 | Pride

TRIM24 as therapeutic target in endocrine treatment resistant breast cancer

Project description:While ERα+ breast cancer treatment is considered effective, resistance to endocrine therapy is common. Since in therapy-resistance tumors, ERα is still the main driver, alternative therapeutic strategies are needed to disrupt ERα transcriptional activity. In this work, we describe TRIM24 as a key player of the ERα transcriptional complex. TRIM24 interacts with ERα and other well-known ERα-cofactors to facilitate ERα chromatin interactions, and allows for maintenance of active histone marks including H3K23ac and H3K27ac. Consequently, genetic perturbation of TRIM24 abrogates ERα-driven transcriptional programs and reduces tumor cell proliferation capacity. Using a recently-developed PROTAC targeting TRIM24, ERα-driven transcriptional output and growth was blocked, effectively treating not only endocrine-responsive cell lines, but also drug resistant derivates thereof as well as cell line models bearing activating ESR1 point mutations. Finally, using human tumor-derived organoid models, we could show efficacy of TRIM24 PROTAC in the endocrine responsive and resistant setting, with no response in ERα-negative organoids. Overall, our study positions TRIM24 as a central component for integrity and activity of the ERα transcriptional complex, with PROTAC-mediated perturbation of TRIM24 as promising therapeutic avenue in the treatment of primary and endocrine resistance breast cancer.

2025-08-01 | PXD046736 | Pride

Genetic vulnerabilitis study in VHL mutant cells

Project description:VHL has been known as a tumour suppressor gene, also is an essential gene for some proteolysis-targeting chimera (PROTAC) degraders. Here by using CRISPR-cas9 genome wide screening we find that VHL mutation results in strong proliferation defect by HIF1A . VHL MUT shows malfunction of mitochondria which can be restored by HIF1A inhibition. VHL MUT bear specific genetic vulnerabilities which are druggable and mainly HIF1A dependent. In OE33 and MCF7, additional HIF1A inhibition on VHL MUT allows a complete ARV-771 drug resistance acquisition. Our study reports the consequence of VHL mutation and HIF1A dependent druggable genetic vulnerabilities in VHL mutant renal epithelial cells and possible PROTAC resistance acquisition mechanism in breast and oesophageal cancers, provides potential therapeutic targets and strategies for early precancerous and established cancerous cells.

2025-11-05 | GSE213241 | GEO

TRIM24 as therapeutic target in endocrine treatment resistant breast cancer (RNA-Seq)

2025-08-01 | GSE246793 | GEO

The efflux pump ABCC1/MRP1 constitutively restricts PROTAC sensitivity in cancer cells

Project description:Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce selective protein degradation by linking an E3 ubiquitin ligase enzyme to a target protein. This approach allows scope for targeting “undruggable” proteins and several PROTACs have reached the stage of clinical candidates. However, the roles of cellular transmembrane transporters in PROTAC uptake and efflux remain underexplored. Here, we utilized transporter-focused genetic screens to identify the ATP binding cassette transporter ABCC1/MRP1 as a key PROTAC resistance factor. Unlike the previously identified inducible PROTAC exporter ABCB1/MDR1, ABCC1 is highly expressed among cancers of various origins and constitutively restricts PROTAC bioavailability. Moreover, in a genome-wide PROTAC resistance screen, we identified candidates involved in processes such as ubiquitination, mTOR signaling and apoptosis as genetic factors involved in PROTAC resistance. In summary, our findings reveal ABCC1 as a crucial constitutively active efflux pump limiting PROTAC efficacy in various cancer cells, offering insights for overcoming drug resistance.

2025-07-17 | MTBLS11394 | MetaboLights

Identification of ubiquitination site in BCL-XL after PROTAC DT2216 treatment

Project description:The availability of a suitable lysine for PROTAC-mediated ubiquitination can also determine the degradative ability of a protein target and the selectivity of a PROTAC. PROTAC DT2216 selectively triggers ubiquitination and degradation of BCL-XL. In this study, we identify K87 is the key ubiquitinated lysine under DT2216 treatment through LC-MS/MS.

2019-10-08 | PXD015454 | Pride

A general workflow for E3 ligase ligand validation for PROTAC development

Project description:PROteolysis TArgeting Chimeras (PROTACs) have gained considerable attention as a new modality in drug discovery. However, the development of PROTACs has been mainly focused on CRBN (Cereblon) and VHL (van Hippel-Lindau Ligase) ligands. The considerable size of the human E3 ligase family, newly developed E3 ligase ligands, as well as the favorable druggability of some E3 ligase families hold the promise that novel degraders with unique pharmacological properties will be designed in the future using this large target space. Here, we developed a workflow for the evaluation of E3 ligand efficiency for PROTAC development and the corresponding “degradable” target space using broad-spectrum kinase inhibitors and the well-established VHL ligand VH032. Our study revealed VH032 linker attachment points that are highly efficient for kinase degradation and highlighted some of the pitfalls when using protein degradation as a readout. For instance, cytotoxicity was identified as a major mechanism leading to PROTAC- and VHL-independent kinase degradation. The combination of E3-ligand negative controls, kinase parent compounds and other tool compounds such as neddylation and proteasome inhibitors was essential to distinguish between VHL-dependent and -independent kinase degradation events. We hope that this study will provide a blueprint for future evaluation of the efficacy of new E3 ligand systems for degrader development.

2025-04-04 | PXD057431 | Pride

An estrogen receptor α-derived peptide improves glucose homeostasis during obesity

Project description:Estrogen improves insulin sensitivity and increases energy expenditure, contributing to sexual dimorphism regarding type 2 diabetes mellitus (T2DM) susceptibility. Estrogen receptor α (ERα) plays a crucial role in mediating estrogen action on glucose and energy homeostasis. However, the underlying mechanisms remain incompletely understood. Here, we found a ligand-independent effect of ERα on the regulation of glucose homeostasis and identified an ERα-derived peptide as a potential insulin sensitizer. Deficiency of ERα but not ERβ in the liver impaired glucose homeostasis in male, female, and ovariectomized (OVX) female mice. Mechanistic studies revealed that ERα promoted hepatic insulin sensitivity by suppressing ubiquitination-induced IRS1 degradation. The ERα 1-280 domain mediated the ligand-independent effect of ERα on insulin sensitivity. Furthermore, we designed a peptide based on ERα 1-280 domain and found that ERα-derived peptide interacted with IRS1, increased IRS1 stability through suppressing its ubiquitination, and enhanced insulin sensitivity. Importantly, administration of ERα-derived peptide into obese mice significantly increased insulin sensitivity, attenuated glucose intolerance, and improved serum lipid profiles. These findings pave the way for the therapeutic intervention of T2DM by targeting the ligand-independent effect of ERα and indicate that ERα-derived peptide is a potential insulin sensitizer for the treatment of T2DM.

2024-04-05 | GSE262841 | GEO

Modeling CRL4A ligase complex to predict target protein ubiquitination induced by CRBN-recruiting PROTACs

Project description:PROteolysis TArgeting Chimeras (PROTACs) are bifunctional small molecules that can simultaneously recruit target protein and E3 ligase to form a ternary complex (target protein / PROTAC / E3 ligase), leading to target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities enabling targeting of previously "undruggable" proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by CRBN-based PROTACs,

2022-05-19 | PXD030213 | Pride

BRD4 inhibitor GNE987 exerts anti-cancer effects in Osteosarcoma

Project description:GNE987 is a newly developed von Hippel-Lindau tumor suppressor (VHL)-based pan-BET-targeting PROTAC, which can bind to the target proteins (BET proteins, including BRD2, BRD3, and BRD4) and recruit them to the ubiquitin/proteasome system for selective degradation. In the our study, ChIP-Seq analysis was performed to explore the effect of GNE987 on osteosarcoma cells.

2024-08-08 | GSE243673 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data