Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds

ABSTRACT: isoTOP-ABPP performed for a small library of cysteine-reactive compounds to assess cysteine ligandability of viral and host proteins towards these compounds.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Flowreen Shikwana

LAB HEAD: Keriann Marie Backus

PROVIDER: PXD046278 | Pride | 2024-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2020-1-13-kb-70min_FAIMS_100micron_3cv_-35_-45_-55--OTIT_AJ-JC19-1-isoTOP.mzML	Mzml
	2020-1-13-kb-70min_FAIMS_100micron_3cv_-35_-45_-55--OTIT_AJ-JC19-1-isoTOP.pepXML	Pepxml
	2020-1-13-kb-70min_FAIMS_100micron_3cv_-35_-45_-55--OTIT_AJ-JC19-2-isoTOP.mzML	Mzml
	2020-1-13-kb-70min_FAIMS_100micron_3cv_-35_-45_-55--OTIT_AJ-JC19-2-isoTOP.pepXML	Pepxml
	2020-1-13-kb-70min_FAIMS_100micron_3cv_-35_-45_-55--OTIT_AJ-c2-isoTOP.mzML	Mzml

Items per page:

1 - 5 of 166

Similar Datasets

An integrated chemoproteomic and screening platform identifies a functional and ligandable non-catalytic cysteine in caspase-2

Project description:Caspases are a highly conserved family of cysteine-aspartyl proteases known for their essential roles in regulating apoptosis, inflammation, cell differentiation and proliferation. Complementary to genetic approaches, small molecule inhibitors have emerged as useful tools for modulating caspase activity. Achieving high selectivity remains a central challenge for caspase-directed inhibitor development efforts, due to the high sequence and structure homology of all twelve human caspases. Here, using a chemoproteomic approach, we first identify a highly reactive non-catalytic cysteine that is unique to caspase-2. By combining both gel-based activity-based protein profiling (ABPP) and a TEV activation assay, we then identify covalent lead compounds that react preferentially with this cysteine and afford a complete blockade of caspase-2 activity. Inhibitory activity is restricted to the zymogen or precursor form of monomeric caspase-2, with compound treatment blocking intramolecular caspase interactions. Focused medicinal chemistry combined with chemoproteomic target engagement analysis in lysates and in cells yielded both caspase-2 selective and promiscuous caspase inhibitors, together with structurally matched inactive control compounds. Application of this focused set of tool compounds to stratify caspase contributions to activation of intrinsic apoptosis indicate likely compensatory caspase-9 activity driving etoposide-mediated cell death in the context of caspase-2 inactivation. More broadly, our study highlights the utility of targeting non-conserved and non-catalytic cysteine residues for achieving improved selectivity profiles for highly homologous families of enzymes.

2025-01-14 | PXD051381 | Pride

An integrated chemoproteomic and screening platform identifies a functional and ligandable non-catalytic cysteine in caspase-2

2025-01-14 | PXD042362 | Pride

Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds

Project description:Effects to protein homeostasis processes upon treatment with cysteine-reactive covalent small molecules in viral and host proteins

2024-10-24 | PXD046393 | Pride

A high-throughput screening approach identified a selective pro-caspase-10 probe that can inhibit its activity

Project description:Caspases are cysteine proteases that play a critical role in inflammation and apoptosis. Caspases have a functional role in either the intrinsic apoptotic pathway as initiators of apoptosis or in the extrinsic apoptotic pathway as executioners of apoptosis. Caspase-10 has been speculated to play a principal role as an initiator of apoptosis but the absence of adequate tools, i.e. selective probes, have hindered our understanding of this enzyme as well as the other caspases. Here, we engineered a tobacco etch virus (TEV)-cleavable construct that is compatible with high-throughput screening to identify selective caspase-10 inhibitors. We identified a set of promiscuous caspase inhibitors, including pifithrin-µ (PFT), an inhibitor of p53 transcriptional activity, as well as promising selective pro-caspase-10 and TEV protease inhibitors.

2025-02-04 | PXD053315 | Pride

A high-throughput screening approach identified a selective pro-caspase-10 probe that can inhibit its activity

2025-02-04 | PXD051710 | Pride

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

Project description:DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

| PRJNA1079738 | ENA

Protein-directed ABPP describing proteome-wide reactivities of WX-02-520 and WX-02-521 probes

Project description:More than half of the ∼20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.

2024-09-03 | PXD053077 | Pride

Stratifying the Cell Surface Cysteinome using Two-step Enrichment Proteomics

Project description:Cell surface cysteines represent an attractive class of residues for chemoproteomic studies due to their accessibility towards drugs and key roles they play in the structure and function of most human proteins. The redox sensitivity of cysteines also makes cell surface cysteines potential markers for cellular activities with altered redox states. However, cell surface cysteines are underrepresented in most of the cysteine proteomic dataset. While many mass spectrometry (MS) based techniques have been developed to enrich membrane proteins, current studies lack methods that can specifically inventory cysteines on cell surfaces. Here, we developed a novel dual enrichment method to achieve chemoproteomic profiling of cell Surface Cysteines - “Cys-Surf''. Combining cell surface capture (CSC) biotinylation and cysteine chemoproteomic biotinylation, this two-step biotinylation platform achieves identification of more than 1,900 cysteines with a specificity of about 50.0% in cell surface localization. In addition, Cys-Surf achieved quantitative analysis of oxidation states of cell surface cysteines, which reflect a completely different profile compared to that of the whole cysteinome. Redox sensitive cell surface cysteines were identified by applying reducing reagents and during T cell activation. Cys-Surf is also compatible with competitive small-molecule screening by isotopic tandem orthogonal activity-based protein profiling (isoTOP-ABPP) to evaluate the ligandability of cell surface cysteines. Altogether, these findings establish a platform that enables redox and ligandability analysis of the cell surface cysteinome and sheds light on future functional studies and drug discovery efforts targeting cell surface cysteines.

2024-01-26 | PXD042403 | Pride

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (ChIP-Seq)

Project description:DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (ChIP-Seq)

| PRJNA1079741 | ENA

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (RNA-Seq)

Project description:DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (RNA-Seq)

| PRJNA1079745 | ENA