PXD053846

PXD053846 is an original dataset announced via ProteomeXchange.

Title	Pushing the Limits of Hydrogen/Deuterium Exchange Mass Spectrometry to Study Protein:Fragment Low Affinity Interactions
Description	Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
HostingRepository	PRIDE
AnnounceDate	2025-12-23
AnnouncementXML	Submission_2025-12-23_01:17:38.566.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alessio Bortoluzzi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-10 07:48:34	ID requested
⏵ 1	2025-12-23 01:17:39	announced

10.1038/S42004-025-01787-6;

submitter keyword: HDX-MS, Low Affinity Interactions, Fragments

Tiago M. Bandeiras
contact affiliation	iBET – Instituto de Biologia Experimental e Tecnológica, Av. da República, Oeiras, 2780-157, Portugal
contact email	tiago.bandeiras@ibet.pt
lab head
Alessio Bortoluzzi
contact affiliation	iBET
contact email	alessio.bortoluzzi@ibet.pt
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/2025/12/PXD053846

PRIDE project URI

• PRIDE
  1. PXD053846
     1. Label: PRIDE project
     2. Name: Pushing the Limits of Hydrogen/Deuterium Exchange Mass Spectrometry to Study Protein:Fragment Low Affinity Interactions