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Meyer"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063666"],"tissue":["Epithelial Cell","Kidney"],"sample_protocol":["Proteins were digested according to a modified version of the sp3 protocol published by Hughes et al. In brief, 5 µg of protein was reduced in a solution of 2 % SDS and 20 mM TCEP. Protein was bound to paramagnetic beads (Sera-Mag Speed Beads, Cat. no. 4515-2105-050250, 6515-2105-050250), washed with 70% ethanol and retained on a 0.22 μm 96-well filter plate (MSGVN2210). On-bead overnight digestion was performed with 200 ng of lysyl endopeptidase and trypsin, each supplemented with 100 mM HEPES, 5 mM chloroacetamide and 1.25 mM TCEP. The digested peptides were labelled with 10-plex TMT-tags, using 72 µg of the respective label for each sample. After a quenching reaction with 0.01% hydroxylamine, samples from two neighbouring temperature treatments were pooled. Samples were desalted by solid phase extraction on a 96-well Oasis HLB µElution plate and the purified samples were dried in a vacuum centrifuge. Samples were subjected to additional high pH fractionation on an UltiMate 3000 (Dionex) by reversed-phase chromatography at pH 9-10 on a XBridge BEH C18 column (130Å, 3.5 µm, 2.1 mm X 250 mm). A total of 48 fractions were collected, with every twelfth fraction being pooled. Fractionated samples were further separated on an EASY-spray C18-column (25 cm, 75 μm inner diameter), using an acetonitrile/water gradient (0.1% formic acid) at 300 nL/min and 120 min of analysis time. The eluted peptides were analysed using the TopN method (full MS followed by ddMS2 scans) on an Orbitrap Q Exactive HF mass spectrometer operating in a data-dependent mode with survey scans at a resolution of 120,000, AGC target of 3 x 106 and maximum injection time of 120 ms. The 15 most abundant isotope patterns were selected from the survey scan with an isolation window of 0.7 m/z and fragmented with nCE at 32. MS/MS analysis was performed with a resolution of 60,000, AGC target of 2 x 105 and maximum injection time of 110 ms. The experimental metadata has been generated using lesSDRF."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The resulting MS data was processed with MaxQuant version 2.4.2.0 (https://www.maxquant.org/), where proteins were identified by searching MS and MS/MS data of the peptides against a human proteome reference database retrieved from the curated UniProtKB/Swiss-Prot database on 2023-08-09. Carboamido-methylation was set as fixed modification and oxidation and acetylation as variable modifications. The reporter intensity was corrected with isotope correction factors in MaxQuant."],"omics_type":["Proteomics"],"labhead":["Per Artursson"],"instrument_platform":[""],"labhead_affiliation":["Professor at Department of Pharmacy, Drug Delivery, Uppsala University"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["10.1111/BPH.70493"],"submitter_mail":["alina.meyer@farmaci.uu.se"],"submitter_affiliation":["Department of Pharmacy, Uppsala University"],"submitter_country":["Sweden"],"additional_accession":[]},"is_claimable":false,"name":"Identification of drug repurposing candidates for the treatment of polycystic kidney disease - Salicylic acid","description":"Autosomal dominant polycystic kidney disease (ADPKD) is a leading cause of end-stage renal disease with limited treatment options. Drug repurposing offers a promising strategy to find effective treatments. We identified birinapant, bardoxolone methyl and salicylic acid as repurposing candidates for ADPKD and applied thermal proteome profiling to identify disease-relevant targets. Our results uncovered shared effects between the three drugs, including a thermal shift in ADP/ATP translocases (SLC25A4/5/6) caused by reduced ATP production. As expected, salicylic acid displayed a polypharmacological profile but also engaged enzymes along the N-linked glycosylation pathway and inhibited PTK2, an activator of the proliferative PI3K/Akt/mTOR pathway. Orthogonal assays and computational modelling confirmed these findings and located the binding site (499-504) of salicylic acid within PTK2’s ATP-binding pocket. Engagement of several targets was achieved at clinically relevant concentrations. We have identified novel targets of three repurposing candidates that contribute to the cyst growth reducing effects in preclinical ADPKD models and identify salicylic acid, the metabolite of aspirin, as the repurposing candidate with the most promising mechanisms of action.This dataset contains files from thermal proteome profiling after salicylic acid exposure.","dates":{"publication":"2026-05-18","submission":"2025-05-06"},"accession":"PXD063666","cross_references":{"TAXONOMY":["NEWT:1773","NEWT:3555","NEWT:1182590","NEWT:10090","NEWT:749200","NEWT:35554","NEWT:4120","NEWT:5693","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:92867","NEWT:990346","NEWT:544496","NEWT:5334","NEWT:145953","NEWT:284812","NEWT:115104","NEWT:43330","NEWT:67825","NEWT:44544","NEWT:13076","NEWT:544404","NEWT:3702","NEWT:8839","NEWT:4232","NEWT:1736309","NEWT:4113","NEWT:7227","NEWT:11298","NEWT:885318","NEWT:4081","NEWT:876138","NEWT:554","NEWT:5691","NEWT:260710","NEWT:106592","NEWT:237561","NEWT:9913","NEWT:10036","NEWT:4100","NEWT:7574","NEWT:1351","NEWT:1076","NEWT:6763","NEWT:7215","NEWT:380394","NEWT:272563","NEWT:1639","NEWT:188229","NCBITaxon:79857","NEWT:746360","NEWT:6239","NEWT:135588","NEWT:135622","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:3880","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:146479","NEWT:1000589","NEWT:145943","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:7959","NEWT:2261","NEWT:3197","NEWT:9615","NEWT:884019","NEWT:4565","NEWT:1264690","NEWT:169963","NCBITaxon:38727","NEWT:36329","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:9606","NEWT:367830","NEWT:243230","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NEWT:470","NCBITaxon:79824","NCBITaxon:4563","NEWT:3218","NEWT:5759","NEWT:9838","NCBITaxon:9615","NEWT:1736231","NEWT:1193501","NEWT:6287","NEWT:6326","NEWT:9796","NEWT:2762","NEWT:5476","NEWT:562","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:29760","NEWT:260705","NEWT:1148","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:39946","NEWT:11676","NEWT:9823","NEWT:100226","NCBITaxon:6073","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:573","NEWT:6282","NEWT:7091"],"pubmed":[],"ORCID":["https://orcid.org/0009-0000-2097-6295"]}}