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BioAssay: AID 224309

Inhibitory activity against SH2 domain of human p60 c-Src tyrosine kinase using surface plasmon resonance (SPR) assay.

Results from a novel approach which uses protein crystallography for the screening of a low affinity inhibitor fragment library are analyzed by comparing the X-ray structures with bound fragments to the structures with the corresponding full length inhibitors. The screen for new phospho-tyrosine mimics binding to the SH2 domain of (pp60)src was initiated because of the limited cell penetration of more ..
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 Tested Compounds
 Tested Compounds
All(28)
 
 
Active(10)
 
 
Unspecified(18)
 
 
 Tested Substances
 Tested Substances
All(28)
 
 
Active(10)
 
 
Unspecified(18)
 
 
 Related BioAssays
 Related BioAssays
AID: 224309
Data Source: ChEMBL (221663)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: Literature, Extracted
BioAssay Version:
Deposit Date: 2010-05-24
Modify Date: 2014-08-25

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 10
Description:
Title: Requirements for specific binding of low affinity inhibitor fragments to the SH2 domain of (pp60)Src are identical to those for high affinity binding of full length inhibitors.

Abstract: Results from a novel approach which uses protein crystallography for the screening of a low affinity inhibitor fragment library are analyzed by comparing the X-ray structures with bound fragments to the structures with the corresponding full length inhibitors. The screen for new phospho-tyrosine mimics binding to the SH2 domain of (pp60)src was initiated because of the limited cell penetration of phosphates. Fragments in our library typically had between 6 and 30 atoms and included compounds which had either millimolar activity in a Biacore assay or were suggested by the ab initio design program LUDI but had no measurable affinity. All identified fragments were located in the phospho-tyrosine pocket. The most promising fragments were successfully used to replace the phospho-tyrosine and resulted in novel nonpeptidic high affinity inhibitors. The significant diversity of successful fragments is reflected in the high flexibility of the phospho-tyrosine pocket. Comparison of the X-ray structures shows that the presence of the H-bond acceptors and not their relative position within the pharmacophore are essential for fragment binding and/or high affinity binding of full length inhibitors. The X-ray data show that the fragments are recognized by forming a complex H-bond network within the phospho-tyrosine pocket of SH2. No fragment structure was found in which this H-bond network was incomplete, and any uncompensated H-bond within the H-bond network leads to a significant decrease in the affinity of full length inhibitors. No correlation between affinity and fragment binding was found for these polar fragments and hence affinity-based screening would have overlooked some interesting starting points for inhibitor design. In contrast, we were unable to identify electron density for hydrophobic fragments, confirming that hydrophobic interactions are important for inhibitor affinity but of minor importance for ligand recognition. Our results suggest that a screening approach using protein crystallography is particularly useful to identify universal fragments for the conserved hydrophilic recognition sites found in target families such as SH2 domains, phosphatases, kinases, proteases, and esterases.
(PMID: 14613321)
Comment
Compounds with activity <= 50uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.
Putative Target:
ChEMBL Target ID: 10434
Target Type: SINGLE PROTEIN
Pref Name: Tyrosine-protein kinase SRC
Synonyms: p60-Src;pp60c-src;Proto-oncogene c-Src;Proto-oncogene tyrosine-protein kinase Src;
Gene Name: SRC;SRC1;
Protein Accession: P12931;
Protein GI: 125711;
Organism: Homo sapiens
Tax ID: 9606
Target Classification: enzyme kinase protein kinase tk src
Confidence: Homologous single protein target assigned
Relationship Type: Homologous protein target assigned
Categorized Comment - additional comments and annotations
From BioAssay Depositor:
Assay Type: Binding
Assay Data Source: Scientific Literature
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
1IC50*IC50 PubChem standard valueFloatμM
3BEIBinding Efficiency Index(nM)Float
2SEISurface Efficiency Index(nM)Float
4LELigand EfficiencyFloat
5LLELipophilic Ligand EfficiencyFloat
6IC50 activity commentIC50 activity commentString
7IC50 standard flagIC50 standard flagInteger
8IC50 qualifierIC50 qualifierString
9IC50 published valueIC50 published valueFloatmM
10IC50 standard valueIC50 standard valueFloatnM
11IC50 data validityIC50 data validityString
12IC50 activity commentIC50 activity commentString
13IC50 standard flagIC50 standard flagInteger
14IC50 qualifierIC50 qualifierString
15IC50 published valueIC50 published valueFloatnM
16IC50 standard valueIC50 standard valueFloatnM
17IC50 data validityIC50 data validityString

* Activity Concentration.

Data Table (Concise)
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