PXD007094

PXD007094 is an original dataset announced via ProteomeXchange.

Title	Small molecule interactome mapping by photo-affinity labeling (SIM-PAL)
Description	Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most common pharmaceutical agents in the world. However, despite well-studied interactions with cyclooxygenase-2, little is known about the broader proteomic interactions and additional mechanisms that the NSAIDs elicit. Here we present a global binding site identification platform for the direct in cellulo characterization of NSAID binding sites. The platform uses (1) photochemical conjugation of NSAID derivatives in the whole proteome, (2) enrichment of the binding sides, for (3) targeted mass spectrometry-based assignment. Using our approach, we identified the NSAID “interactome” consisting of nearly 200 binding sites in Jurkat and K562 cells. We observed a binding site hotspot on the nucleosome where three NSAIDs (but not fragment-based small molecules) interacted. These data suggest that the NSAIDs may behave as a novel type of epigenetic mark. Our approach is potentially amenable to production of precise, whole proteome binding site maps for virtually any molecule of interest.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:39:40.515.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Woo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-21 06:04:10	ID requested
1	2019-01-25 00:43:39	announced
⏵ 2	2024-10-22 04:39:48	announced	2024-10-22: Updated project metadata.

Gao J, Mfuh A, Amako Y, Woo CM, Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs. J Am Chem Soc, 140(12):4259-4268(2018) [pubmed]

10.1021/jacs.7b11639;

curator keyword: Technical, Biomedical

submitter keyword: photo-crosslinking, NSAID, proteome, interactome,binding site

Christina May Woo
contact affiliation	Department of Chemistry and Chemical Biology, Woo Lab, Harvard University, US
contact email	cwoo@chemistry.harvard.edu
lab head
Christina Woo
contact affiliation	Harvard University
contact email	cwoo@chemistry.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/01/PXD007094

PRIDE project URI

• PRIDE
  1. PXD007094
     1. Label: PRIDE project
     2. Name: Small molecule interactome mapping by photo-affinity labeling (SIM-PAL)