Evidence map›Paper›PMID 30548204›Full record

ArticleChemMedChem2019

Chemical Space Overlap with Critical Protein-Protein Interface Residues in Commercial and Specialized Small-Molecule Libraries.

Yubing Si, David Xu, Khuchtumur Bum-Erdene, Mona K Ghozayel, Baocheng Yang, Paul A Clemons, Samy O Meroueh

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in ChemMedChem, 2019. 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

7 authors.

Yubing SiDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
David XuCenter for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Khuchtumur Bum-ErdeneDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Mona K GhozayelDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Baocheng YangHenan Provincial Key Laboratory of Nanocomposites and Applications, Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan, 450006, China.
Paul A ClemonsChemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
Samy O MerouehDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.ORCID 0000-0002-3948-7499

Funding

Small-Molecule Antagonists of Ral GTPases in CancerR01CA197928 · NCI · INDIANA UNIVERSITY INDIANAPOLIS · PI MEROUEH, SAMY · 2016 to 2020
$2.9M
NCI NIH HHS R01 CA197928
6 · The paper itself

Abstract

There is growing interest in the use of structure-based virtual screening to identify small molecules that inhibit challenging protein-protein interactions (PPIs). In this study, we investigated how effectively chemical library members docked at the PPI interface mimic the position of critical side-chain residues known as "hot spots". Three compound collections were considered, a commercially available screening collection (ChemDiv), a collection of diversity-oriented synthesis (DOS) compounds that contains natural-product-like small molecules, and a library constructed using established reactions (the "screenable chemical universe based on intuitive data organization", SCUBIDOO). Three different tight PPIs for which hot-spot residues have been identified were selected for analysis: uPAR⋅uPA, TEAD4⋅Yap1, and Ca

Indexed as

Adaptor Proteins, Signal TransducingBiological ProductsCalcium ChannelsDNA-Binding ProteinsDose-Response Relationship, DrugHumansMolecular StructureMuscle ProteinsPhosphoproteinsProtein BindingProtein Interaction MappingReceptors, Urokinase Plasminogen ActivatorSmall Molecule LibrariesStructure-Activity RelationshipTEA Domain Transcription FactorsTranscription FactorsAdaptor Proteins, Signal TransducingBiological ProductsCalcium ChannelsDNA-Binding ProteinsMuscle ProteinsPhosphoproteinsReceptors, Urokinase Plasminogen ActivatorSmall Molecule LibrariesTEAD4 protein, humanTEA Domain Transcription FactorsTranscription FactorsUrokinase-Type Plasminogen ActivatorYAP1 protein, humanYAP-Signaling Proteinscompound librariescomputational chemistryprotein-protein interactionsvirtual screening

Identifiers

PMID30548204
PMCPMC7175409

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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.