Evidence map›Paper›PMID 38456036›Full record

ArticleRSC chemical biology2024

Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening.

Gloria Ortiz, James E Longbotham, Sophia L Qin, Meng Yao Zhang, Gregory M Lee, R Jeffrey Neitz, Mark J S Kelly, Michelle R Arkin, Danica Galonić Fujimori

Open access · goldAbstract read
In one paragraph

Article in RSC chemical biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 35% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. Development of Dimethylsulfonium Probes for Broad Profiling of Methyllysine Reader Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
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

9 authors at 1 institution in 1 country.

Gloria OrtizDepartment of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA danica.fujimori@ucsf.edu.ORCID https://orcid.org/0000-0001-8189-0137
James E LongbothamDepartment of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA danica.fujimori@ucsf.edu.
Sophia L QinDepartment of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA danica.fujimori@ucsf.edu.
Meng Yao ZhangDepartment of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA danica.fujimori@ucsf.edu.
Gregory M LeeSmall Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA.ORCID https://orcid.org/0000-0002-2398-6648
R Jeffrey NeitzSmall Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA.
Mark J S KellyDepartment of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA.
Michelle R ArkinSmall Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA.ORCID https://orcid.org/0000-0002-9366-6770
Danica Galonić FujimoriDepartment of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA danica.fujimori@ucsf.edu.ORCID https://orcid.org/0000-0002-4066-9417
University of California, San Francisco · US

Funding

Discovery of Small Molecule Ligands for PHD1 Reader Domain of Histone Demethylase KDM5AR01CA250459 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ARKIN, MICHELLE, FUJIMORI, DANICA GALONIC · 2020 to 2023
$2.3M
NCI NIH HHS R01 CA250459
6 · The paper itself

Abstract

PHD fingers are a type of chromatin reader that primarily recognize chromatin as a function of lysine methylation state. Dysregulated PHD fingers are implicated in various human diseases, including acute myeloid leukemia. Targeting PHD fingers with small molecules is considered challenging as their histone tail binding pockets are often shallow and surface-exposed. The KDM5A PHD1 finger regulates the catalytic activity of KDM5A, an epigenetic enzyme often misregulated in cancers. To identify ligands that disrupt the PHD1-histone peptide interaction, we conducted a high-throughput screen and validated hits by orthogonal methods. We further elucidated structure-activity relationships in two classes of compounds to identify features important for binding. Our investigation offers a starting point for further optimization of small molecule PHD1 ligands.

Identifiers

PMID38456036
PMCPMC10915964
OpenAlexW4389898858

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.