PXD057431-1

PXD057431 is an original dataset announced via ProteomeXchange.

Title	A general workflow for E3 ligase ligand validation for PROTAC development
Description	PROteolysis TArgeting Chimeras (PROTACs) have gained considerable attention as a new modality in drug discovery. However, the development of PROTACs has been mainly focused on CRBN (Cereblon) and VHL (van Hippel-Lindau Ligase) ligands. The considerable size of the human E3 ligase family, newly developed E3 ligase ligands, as well as the favorable druggability of some E3 ligase families hold the promise that novel degraders with unique pharmacological properties will be designed in the future using this large target space. Here, we developed a workflow for the evaluation of E3 ligand efficiency for PROTAC development and the corresponding “degradable” target space using broad-spectrum kinase inhibitors and the well-established VHL ligand VH032. Our study revealed VH032 linker attachment points that are highly efficient for kinase degradation and highlighted some of the pitfalls when using protein degradation as a readout. For instance, cytotoxicity was identified as a major mechanism leading to PROTAC- and VHL-independent kinase degradation. The combination of E3-ligand negative controls, kinase parent compounds and other tool compounds such as neddylation and proteasome inhibitors was essential to distinguish between VHL-dependent and -independent kinase degradation events. We hope that this study will provide a blueprint for future evaluation of the efficacy of new E3 ligand systems for degrader development.
HostingRepository	PRIDE
AnnounceDate	2025-04-04
AnnouncementXML	Submission_2025-04-04_09:01:17.848.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thorsten Mosler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-01 09:26:12	ID requested
⏵ 1	2025-04-04 09:01:18	announced

10.1021/acschembio.4c00812;

Mileti, ć N, Weckesser J, Mosler T, Rathore R, Hoffmann ME, Gehrtz P, Schlesiger S, Hartung IV, Berner N, Wilhelm S, M, ü, ller J, Adhikari B, N, ě, mec V, Sivashanmugam SA, Elson L, Holzmann H, Schwalm MP, Hoffmann L, Abdul Azeez KR, M, ü, ller S, Kuster B, Wolf E, Đ, iki, ć I, Knapp S, Workflow for E3 Ligase Ligand Validation for PROTAC Development. ACS Chem Biol, 20(2):507-521(2025) [pubmed]

submitter keyword: PROTAC,VHL, promiscious kinase inhibitor

Stefan Knapp
contact affiliation	Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
contact email	knapp@pharmchem.uni-frankfurt.de
lab head
Thorsten Mosler
contact affiliation	Goethe University Clinics Frankfurt
contact email	thorstenmosler@googlemail.com
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/2025/04/PXD057431

PRIDE project URI

• PRIDE
  1. PXD057431
     1. Label: PRIDE project
     2. Name: A general workflow for E3 ligase ligand validation for PROTAC development