Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin

ABSTRACT: Chemical proteomics encompasses novel drug target deconvolution methods in which compound modification is not required. Herein we use Thermal Proteome Profiling, Functional Identification of Target by Expression Proteomics and multiplexed redox proteomics for deconvolution of auranofin targets to aid elucidation of its mechanisms of action. Auranofin (Ridaura®) was approved for treatment of rheumatoid arthritis in 1985. Because several clinical trials are currently ongoing to repurpose auranofin for cancer therapy, comprehensive characterization of its targets and effects in cancer cells is important. Together, our chemical proteomics tools confirmed thioredoxin reductase 1 (TXNRD1) as a main auranofin target, with perturbation of oxidoreductase pathways as the top mechanism of drug action. Additional indirect targets included NFKB2 and CHORDC1. Our comprehensive data can be used as a proteomic signature resource for further analyses of the effects of auranofin. Here we also assessed the orthogonality and complementarity of different chemical proteomics methods that can furnish invaluable mechanistic information and thus the approach can facilitate drug discovery efforts in general.

INSTRUMENT(S): Orbitrap Fusion, Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Melanocyte, Colon

DISEASE(S): Colon Cancer,Melanoma

SUBMITTER: Amir Ata Saei

LAB HEAD: Roman Zubarev

PROVIDER: PXD016776 | Pride | 2020-03-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Thermal Proteome Profiling Datasets for smarTPCA

Project description:Chemical biology and the application of small molecules has proven to be a potent perturbation strategy especially for the functional elucidation of proteins, their networks and regulators. In recent years, the cellular thermal shift assay (CETSA) and its proteome-wide extension, thermal proteome profiling (TPP), have proven to be effective tools for identifying interactions of small molecules with their target proteins as well as off-targets in living cells. Here, we asked the question if isothermal dose-response (ITDR) CETSA can be exploited to characterize secondary effects downstream of the primary binding event, such as changes in post-translational modifications or protein-protein interactions (PPI). Applying ITDR-CETSA to MAPK14 kinase inhibitor treatment of living HL-60 cells, we found similar dose-responses for the direct inhibitor target and its known interaction partners MAPKAPK2 and MAPKAPK3. Extension of the dose-response similarity comparison to the proteome wide level using TPP with compound concentration range (TPP-CCR) revealed not only the known MAPK14 interaction partners MAPKAPK2 and MAPKAPK3, but also the potentially new intracellular interaction partner MYLK. We are confident that dose-dependent small molecule treatment in combination with ITDR-CETSA or TPP-CCR similarity assessment will not only allow discrimination between primary and secondary effects, but also provide a novel method to study PPI in living cells without perturbation by protein modification, which we named "small molecule arranged thermal proximity coaggregation" (smarTPCA).

2022-06-09 | PXD032942 | Pride

Anticancer effect of deuterium depleted water - comprehensive proteomics analysis suggests a redox disbalance mechanism

Project description:The proteomics data is derived from 4 parts of samples prepared and analysed by nanoLC-MS/MS. In order to make appropriate statistical analysed could be performed, all treatments were performed in biological replicates. The number of replicates was 4 for protein abundances analysis (part 1), 2 for time course analysis (part 2), 3 for redox proteomics analysis (part 3) and 2 for TPP analysis (part 4). Each set of TMT10 labelling samples were combined and fractionationed into 10 fractions. In total, 113 TMT labelling samples including 11 sets of TMT10 and 3 sets of iodoTMT6 were performed with a 120 min gradient. In each part of the experiment, separate controls treated with the vehicle were included. Samples were analysed in random order to reduce the “order of injection” effect. In part 1, A549 cells were treated with CAMP, MTX, PCTL and 80 ppm DDW (20 samples). In part 2, the cells were treated 80 ppm DDW, MTX and PCTL for 4-48h (5 time points, 40 samples). In addition, 2 control samples treated with the vehicle for 48h were included in each set of TMT10 for normalization. In part 3, the cells were treated with 80 ppm DDW and auranofin (3 samples). Finally, in part 4, the cells were treated with 80 ppm DDW and afterwords the cells were treated with 10 temperatures (40 samples). Quality check was performed by calculating the variation (CV) between the replicates as well as by building PCA models to verify the small overall spread between the replicates.

2019-09-26 | PXD011085 | Pride

Protocol for performing and analyzing TPP-TR and TPP-CCR experiments

Project description:Explore the effect of Panobinostat on the thermal stability of the proteins of the K562 cell line proteome.

2019-05-24 | PXD013774 | Pride

Off-target profiling of Olaparib using Thermal Proteome Profiling

Project description:Explore off-targets of Olaparib using 2D Thermal Proteome Profiling (2D-TPP)

2024-05-13 | PXD046614 | Pride

New antiviral small molecule inhibitors disturb interactions between cellular HSP70 and virus proteins

Project description:RNA virus outbreaks such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), Ebola virus (EBOV) and Zika virus (ZIKV) causing worldwide health emergencies have highlighted the urgent need of new antiviral strategies. Upon outbreaks with new, unmet viruses where knowledge of virus biology is limited, targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds. Here, we present a strategy to identify novel host-targeted small molecule inhibitors using image-based phenotypic antiviral assay followed by characterization of structure-activity-relationship, mechanism-of-action and molecular targets of the novel antiviral compound using thermal proteome profiling.

2021-01-04 | PXD021494 | Pride

Thermal proteome profiling of sponge whole-body movement

Project description:Sponges (Porifera) are early-branching Metazoa who do not possess muscles or neurons, however are able to undergo a whole-body movement that involves the closure of their canal system and collapse of an epithelial tent. In this study we profile proteomic responses of the freshwater sponge Spongilla lacustris during nitric oxide (NO) and agitation induced movements to elucidate the early evolution of coordination. Specifically, we measure condition-dependent changes in protein thermal stability and abundance using Thermal proteome profiling (TPP). These changes are the result of proteins undergoing stabilizing or destabilizing conformational changes broadly caused by e.g. the binding or dissociation of small molecules to the proteins, the formation or loss of protein-protein interactions or a change in post-translational modifications.

2024-01-04 | PXD044169 | Pride

The Golgi stacking protein GRASP55 is targeted by the natural compound prodigiosin

Project description:The bacterial secondary metabolite prodigiosin has been shown to exert anticancer, antimalarial, antibacterial and immunomodulatory properties. With regard to cancer, it has been reported to affect cancer cells but not non-malignant cells, rendering prodigiosin a promising lead compound for anticancer drug discovery. However, a direct protein target has not yet been experimentally identified. Thus, we used mass spectrometry-based thermal proteome profiling and identified the Golgi stacking protein GRASP55 as target protein of prodigiosin. We show that prodigiosin treatment severely affects Golgi morphology and functionality, and that prodigiosin-dependent cytotoxicity is partially reduced in GRASP55 knockout cells. We also found that prodigiosin treatment results in decreased cathepsin activity and overall blocks autophagic flux, whereas co-localization of the autophagosomal marker LC3 and the lysosomal marker LAMP1 is clearly promoted. Finally, we observed that autophagosomes accumulate at GRASP55-positive structures, pointing towards an involvement of an altered Golgi function in the autophagy-inhibitory effect of this natural compound. Taken together, we propose that prodigiosin affects autophagy and Golgi apparatus integrity in an interlinked mode of action involving the regulation of organelle alkalization and the Golgi stacking protein GRASP55.

2023-10-24 | PXD043247 | Pride

Clemastine Fumarate in Plasmodium

Project description:The binding target for clemastine fumarate in Plasmodium Falciparum 3D7 strain is identified by two techniques: SPROX and TPP.

2020-02-21 | PXD014308 | Pride

Circadian rhythms of sense and antisense transcription in a highly polyploid crop.

Project description:Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h. Samples were collected from 24 h in constant light to 68 h in constant light and were labelled accordingly. Two biological replicates of each time point were made, with a dye swap with the reference. The reference used was a equimolar solution of all samples.

2013-11-21 | E-GEOD-42725 | biostudies-arrayexpress

Entamoeba histolytica and auranofin treatment

Project description:2 million E. histolytica HM1:IMSS was treated with 0.5% DMSO for 3 h and 2 million E. histolytica HM1:IMSS was treated with 1 M-5M auranofin for 3 h

2012-02-03 | E-MEXP-3494 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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