Evidence map›Paper›PMID 41415474›Full record

ArticlebioRxiv : the preprint server for biology2025

Discovery of Non-Degradative Covalent Molecular Glues for Transcriptional Reprogramming.

Tuong Nghi Duong, Edward Pandji, Qian Shao, Daniel K Nomura

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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
–field-weighted citation impact
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.

  1. Review
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

4 authors.

Tuong Nghi DuongDepartments of Chemistry and Molecular and Cell Biology. University of California, Berkeley, Berkeley, CA 94720 USA.
Edward PandjiDepartments of Chemistry and Molecular and Cell Biology. University of California, Berkeley, Berkeley, CA 94720 USA.
Qian ShaoDepartments of Chemistry and Molecular and Cell Biology. University of California, Berkeley, Berkeley, CA 94720 USA.
Daniel K NomuraDepartments of Chemistry and Molecular and Cell Biology. University of California, Berkeley, Berkeley, CA 94720 USA.ORCID 0000-0003-1614-8360

Funding

Tackling Undruggable Cancer Targets using Chemoproteomic PlatformsR35CA263814 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Daniel Nomura · 2022 to 2026
$4.6M
Harnessing E3 Ligases for Cancer TherapyR01CA240981 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Daniel Nomura · 2019 to 2026
$4.3M
Acquisition of a Cryoprobe and Related Accessories for a 600 MHz NMR Spectrometer to Support Health Research Activities at the University of California, BerkeleyS10OD024998 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI HARTWIG, JOHN F · 2018 to 2018
$265k
NCI NIH HHS R01 CA240981NCI NIH HHS R35 CA263814NIH HHS S10 OD024998
6 · The paper itself

Abstract

Transcriptional reprogramming through induced proximity has emerged as a powerful strategy for modulating the expression of oncogenic and tumor-suppressive genes. Inspired by transcriptional reprogramming approaches such as transcriptional/epigenetic chemical inducers of proximity (TCIPs) that link BCL6 inhibitors to transcriptional regulators, we sought to develop covalent ligands that rewire BCL6 proximity to selectively suppress MYC transcriptional output while derepressing BCL6 target loci. Through a chemistry-driven and chemoproteomics-enabled design strategy, we generated a panel of BCL6-based electrophile-bearing hybrid ligands and identified a nondegradative molecular glue, ZD-1-186, that potently suppresses MYC and robustly induces CDKN1A (p21) in diffuse large B-cell lymphoma cells. ZD-1-186 downregulates MYC more effectively than BCL6 inhibitors or degraders, while strongly derepressing canonical BCL6 targets, including p21. Through BCL6 pulldown proteomics, ZD-1-186 induced a selective recruitment of the noncanonical BAF complex subunit BRD9 to BCL6 and covalently modified BRD9 at C288. Pharmacologic inhibition or genetic knockdown of BRD9 attenuated ZD-1-186-mediated MYC suppression and blunted p21 induction. Transcriptomic profiling of ZD-1-186 showed simultaneous derepression of BCL6-repressive loci and suppression of MYC transcriptional programs. These findings demonstrated that ZD-1-186 acted as a transcriptional rewiring glue, recruiting BRD9 to BCL6-repressive loci to activate tumor-suppressive transcription, while also potentially redirecting BCL6 to BRD9-bound oncogenic loci. Overall, our work provides a blueprint for the rational discovery and design of electrophile-enabled, nondegradative molecular glues for targeted transcriptional rewiring.

Indexed as

BCL6BRD9induced proximitymolecular gluesTCIPtranscriptional chemical inducers of proximity

Identifiers

PMID41415474
PMCPMC12710638

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Registered trials

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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.