Evidence map›Paper›PMID 31059647›Full record

ArticleACS chemical biology2019

Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications.

Carl C Ward, Jordan I Kleinman, Scott M Brittain, Patrick S Lee, Clive Yik Sham Chung, Kenneth Kim, Yana Petri, Jason R Thomas, John A Tallarico, Jeffrey M McKenna and 2 more

Open access · greenAbstract read
In one paragraph

Article in ACS chemical biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
162citing papers in PubMed, 1 pooled it
14.2field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

162 citing papers in PubMed, 1 synthesis or guideline pooled it, 325 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Nicotinamide-Based Covalent Inhibitors of tRNA (mACS medicinal chemistry letters · 2026
    Article
  5. Article
  6. Article
  7. Review
  8. Review
  9. Article
  10. Article
  11. Review
  12. Review
  13. Discovery of SKP2-Recruiting PROTACs for Target Protein Degradation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  14. Article
  15. Induced proximity-based therapeutic modalities.Nature reviews. Drug discovery · 2026
    Review
  16. Review
  17. Article
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  20. Review

102 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 2 institutions in 1 country.

Carl C WardDepartment of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States.
Jordan I KleinmanNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Scott M BrittainNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Patrick S LeeNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.ORCID 0000-0002-0517-120X
Clive Yik Sham ChungNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Kenneth KimDepartment of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States.
Yana PetriNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Jason R ThomasNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
John A TallaricoNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Jeffrey M McKennaNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.
Markus SchirleNovartis-Berkeley Center for Proteomics and Chemistry Technologies , University of California, Berkeley , Berkeley , California 94720 , United States.ORCID 0000-0003-4933-2623
Daniel K NomuraDepartment of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States.ORCID 0000-0003-1614-8360
Novartis (United States) · USUniversity of California, Berkeley · US

Funding

Expanding the scope of protein degradation and stability using chemoproteomic platformsF99CA245718 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI WARD, CARL · 2019 to 2020
$83k
Characterizing the Druggable Hotspots Targeted by Anti-Cancer Natural Product Withaferin AF31CA225173 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI WARD, CARL · 2018 to 2019
$52k
NCI NIH HHS F31 CA225173NCI NIH HHS F99 CA245718
6 · The paper itself

Abstract

Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.

Indexed as

Bromodomain Containing ProteinsCell Cycle ProteinsCoordination ComplexesCysteineHumansLigandsMolecular Docking SimulationNuclear ProteinsProteasome Endopeptidase ComplexProtein BindingProtein DomainsProteolysisSmall Molecule LibrariesStructure-Activity RelationshipTranscription FactorsUbiquitinationBRD4 protein, humanBromodomain Containing ProteinsCell Cycle ProteinsCoordination ComplexesCysteineLigandsNuclear ProteinsProteasome Endopeptidase ComplexRNF4 protein, humanSmall Molecule LibrariesTranscription FactorsUbiquitin-Protein LigasesZinc

Identifiers

PMID31059647
PMCPMC7422721
OpenAlexW2949862037

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.