PXD054057

PXD054057 is an original dataset announced via ProteomeXchange.

Title	Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor
Description	Inhibition of the mitochondrial deubiquitinating enzyme USP30 is neuroprotective and presents therapeutic opportunities for the treatment of idiopathic Parkinson’s Disease and mitophagy-related disorders. We have integrated structural and quantitative proteomics with biochemical assays to decipher the mode of action of covalent USP30 inhibition by a small molecule containing a cyanopyrrolidine reactive group, USP30-I-1. The inhibitor demonstrated high potency and selectivity for endogenous USP30 in neuroblastoma cells. Enzyme kinetics and Hydrogen Deuterium eXchange mass spectrometry (HDX-MS) infers that the inhibitor binds tightly to regions surrounding the USP30 catalytic cysteine and positions itself to form a binding pocket along the thumb and palm domains of the protein, thereby interfering its interaction with ubiquitin substrates. A comparison to a non-covalent USP30 inhibitor containing a benzosulfonamide scaffold revealed a slightly different binding mode closer to the active site Cys77, which may provide the molecular basis for improved selectivity towards USP30 against other members of the DUB enzyme family. Our results highlight advantages in developing covalent inhibitors, such as USP30-I-1, for targeting USP30 as treatment of disorders with impaired mitophagy.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_21:33:44.780.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Darragh O'Brien
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-19 00:17:46	ID requested
⏵ 1	2025-05-06 21:33:45	announced

10.1021/acs.jproteome.4c00618;

O'Brien DP, Jones HBL, Shi Y, Guenther F, Vendrell I, Viner R, Brennan PE, Mead E, Zarganes-Tzitzikas T, Davis JB, Pinto-Fern, á, ndez A, England KS, Murphy EJ, Turnbull AP, Kessler BM, Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor. J Proteome Res, 24(2):479-490(2025) [pubmed]

submitter keyword: Ubiquitin Specific Protease USP30

Cyanopyrrolidine Inhibitors, Activity-Based Protein Profiling Mass Spectrometry

Enzyme Kinetics

Hydrogen Deuterium eXchange-Mass Spectrometry

Molecular Docking,Mitophagy

Darragh O'Brien
contact affiliation	NDM Research Building | Old Road Campus | Oxford OX3 7FZ
contact email	darragh.obrien@ndm.ox.ac.uk
lab head
Darragh O'Brien
contact affiliation	Target Discovery Institute, University of Oxford
contact email	darragh.obrien@ndm.ox.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054057
     1. Label: PRIDE project
     2. Name: Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor