Evidence map›Paper›PMID 38110475›Full record

ArticleNature chemistry2024

Proteolysis-targeting chimeras with reduced off-targets.

Tuan M Nguyen, Vedagopuram Sreekanth, Arghya Deb, Praveen Kokkonda, Praveen K Tiwari, Katherine A Donovan, Veronika Shoba, Santosh K Chaudhary, Jaron A M Mercer, Sophia Lai and 6 more

Open access · greenAbstract read
In one paragraph

Article in Nature chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.

0numbers the graph read from it
0cells of the map it votes in
63citing papers in PubMed
16.3field-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

63 citing papers in PubMed, 109 citations in OpenAlex.

  1. Evolving CRBN ligands enhance the drug-like properties of protein degraders.Journal of enzyme inhibition and medicinal chemistry · 2026
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3 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

16 authors at 2 institutions in 1 country.

Tuan M Nguyen *Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-4879-3962
Vedagopuram Sreekanth *Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Arghya Deb *Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Praveen Kokkonda *Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Praveen K TiwariChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Katherine A DonovanDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-8539-5106
Veronika ShobaChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Santosh K ChaudharyChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-9979-9323
Jaron A M MercerMerkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7078-614X
Sophia LaiChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ananthan SadagopanChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-6306-4907
Max JanDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Eric S FischerDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
David R LiuMerkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9943-7557
Benjamin L EbertDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0003-0197-5451
Amit ChoudharyChemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA. achoudhary@bwh.harvard.edu.ORCID 0000-0002-8437-0150
Broad Institute · USHarvard University · US

Funding

Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human DiseaseRM1HG009490 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Brittany S. Adamson, Martin Joseph Ankrah Aryee · 2017 to 2026
$22.7M
Integrating Chemistry and Evolution to Illuminate Biology and Enable Novel TherapeuticsR35GM118062 · NIGMS · HARVARD UNIVERSITY · PI LIU, DAVID R · 2016 to 2025
$6.4M
ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potentialR01EB027793 · NIBIB · BROAD INSTITUTE, INC. · PI Ahmad Samir Khalil, DAVID R LIU · 2019 to 2026
$6.1M
Degrading therapeutically important kinases using small moleculesR01CA218278 · NCI · STANFORD UNIVERSITY · PI Eric Sebastian Fischer, NATHANAEL Schiander GRAY · 2019 to 2026
$4.6M
The molecular basis of IMiD induced neo-substrate recruitment to the CRL4CRBN ubiquitin E3 ligase.R01CA214608 · NCI · DANA-FARBER CANCER INST · PI Eric Sebastian Fischer · 2017 to 2026
$4.0M
Continuous Evolution of Proteins with Novel Therapeutic PotentialR01EB031172 · NIBIB · BROAD INSTITUTE, INC. · PI LIU, DAVID R · 2021 to 2024
$2.5M
Chemical approaches for precision genome editingR01GM137606 · NIGMS · BROAD INSTITUTE, INC. · PI CHOUDHARY, AMIT · 2021 to 2024
$1.5M
Development of synthetic gene drives using small moleculesR01GM132825 · NIGMS · BRIGHAM AND WOMEN'S HOSPITAL · PI AKBARI, OMAR SULTAN, CHOUDHARY, AMIT · 2019 to 2022
$1.4M
Enzymatic modification of nucleobases for single base pair editing in genomic DNAF32GM133088 · NIGMS · BROAD INSTITUTE, INC. · PI MERCER, JARON · 2019 to 2021
$192k
NCI NIH HHS R01 CA214608NCI NIH HHS R01 CA218278NHGRI NIH HHS RM1 HG009490NIBIB NIH HHS R01 EB027793NIBIB NIH HHS R01 EB031172NIGMS NIH HHS F32 GM133088NIGMS NIH HHS R01 GM132825NIGMS NIH HHS R01 GM137606NIGMS NIH HHS R35 GM118062
6 · The paper itself

Abstract

Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.

Indexed as

ProteinsUbiquitin-Protein LigasesProteolysisThalidomidepomalidomideProteinsThalidomideUbiquitin-Protein Ligases

Identifiers

PMID38110475
PMCPMC10913580
OpenAlexW4389894233

What OpenQuestion holds

Textmetadata
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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.