GSK-5959

Protein target name:

BRPF1

Mechanism of action:

Antagonist

Reviewer suggested Concentration for use in cells:

between 500 nM and 5 uM

Probe Availability

MedChem Express (901245-65-6)

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

Bromodomain

HUGO ID:

HGNC:14255

Entrez gene ID:

7862

UNIPROT ID:

P55201

Target alias:

Bromodomain and PHD finger containing 1, BR140, IDDDFP

Probe Details

Chemical Probes Portal ID:

CPP1292

Probe alias:

GSK5959

PubChem CID:

15990224

ChEMBL ID:

CHEMBL1522313

SMILES string:

CN1C2=CC(=C(C=C2N(C1=O)C)N3CCCCC3)NC(=O)C4=CC=CC=C4OC

InChi Key:

LTUGYAOMCKNTGG-UHFFFAOYSA-N

Orthogonal probe:

NI-57

Physico-chemical properties

NMR:

1H NMR (600 MHz, CDCl3) δ 10.61 (s, 1H), 8.43 (s, 1H), 8.29 (dd, J = 7.9, 1.8 Hz, 1H), 7.50-7.52 (m, 1H), 7.14-7.17 (m, 1H), 7.07 (d, J = 8.1 Hz, 1H), 6.83 (s, 1H), 4.10 (s, 3H), 3.44 (s, 3H), 3.42 (s, 3H), 2.80-2.93 (m, 4H), 1.75-1.78 (m, 4H), 1.63 (br s, 2H).

13C NMR (151 MHz, CDCl3) δ 163.24 (s, 1C), 157.36 (s, 1C), 155.05 (s, 1C), 138.43 (s, 1C), 132.89 (s, 1C), 132.36 (s, 1C), 128.75 (s, 1C), 126.45 (s, 1C), 125.96 (s, 1C), 122.84 (s, 1C), 121.49 (s, 1C), 111.68 (s, 1C), 101.11 (s, 1C), 99.93 (s, 1C), 56.32 (s, 1C), 54.49 (s, 2C), 27.28 (s, 1C), 27.13 (s, 1C), 26.71 (s, 2C), 24.00 (s, 1C).

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

0.08 uM

Potency assay:

Time-resolved fluorescence resonance energy transfer (TR-FRET) binding assay, pIC50=7.1.

PDB ID for probe-target interaction (3D structure):

4UYE

Structure-activity relationship:

Yes, see PMID 25408830.

Off target activity

Potency (off target):

pIC50

Off target protein and potency:

BRPF2: 5.1, BRPF3 <4, BRD4 (1) <4.3, BRD4 (2) <4.3

Potency assay (off target):

TR-FRET binding assay

Probe Selectivity in Vitro:

In BROMOscan with 35 bromodomains (DiscoveRx), GSK-5959 was selective for BRPF1.

In cell validation

On target activity in cells

Potency in cells:

IC50

0.98 uM

Potency assay (cells):

NanoBRET assay; pIC50=6.0

Target engagement assay (cells):

Yes, direct: nanoBRET assay.

Off target activity in cells

Potency assay, off target (cells):

In nanoBRET assay, GSK-5959 is not active against BRPF1 isoform 2.

Primary Reference

Reference (doi):

10.1021/ml5002932

Reference (PMID):

25408830

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

no rating

SAB Members

SAB Comments

This is a good compound but it has been superseded by GSK6853 chemical probe, which has greatly improved solubility and cell activity.

Apr 14 2017 - 11:50am

This benzimidazolone probe inhibits BRPF1 (bromodomain and PHD finger-containing domain 1). Biochemical data using a TR-FRET format shows an IC50 of 80 nM against BRPF1 with 100X less potency against BRPF2 and high selectivity against BRPF3. Activity was measured against over 35 bromodomains, which also showed high selectivity. Further validation of binding to BRPF1 includes NMR and a X-ray co-crystal structure; however, the Kd was not mentioned. Cell-based data confirms cell penetration in a target-engagement assay (NanoBRET) with an IC50 ~ 1 uM. Further cell-based functional data would enhance confidence for the usefulness this probe in cell-based studies.

Apr 19 2017 - 11:34am

GSK-5959 is a reasonably potent (TR-FRET pIC50 7.1), selective (>100 fold over other BRDs) and cell permeable/cell active (NanoBRET pIC50 6.0). However, the compound has been superseded by GSK-6853 which is far more potent and well characterised. GSK-5959 poses as a useful in vitro tool molecule but as a broader profiling of its off-target activity has not been reported, users should approach screening at high cellular concentrations with caution. The cell target engagement of the compound has been measured using a NanoBRET displacement assay with a NanoLuc tagged Bromodomain-only construct of BRPF1- no mention is made why other constructs were not used. The benzimidazolones are a privileged scaffold for BRPF Brd inhibition (OF-1, PFI-4, BAY-299, GSK-5959, GSK-6853), whilst use of these molecules in concert to investigate BRPF biology is encouraged, ideally other structurally distinct chemotypes should be used. GSK-6853 superseding probe: 10.1021/acsmedchemlett.6b00092

Mar 12 2020 - 11:40am

GSK-5959

Probe Availability

Probe Information

Target Details

Bromodomain and PHD finger containing 1, BR140, IDDDFP

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

Supporting Organizations

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GSK-5959

Probe Availability

Probe Information

Target Details

Bromodomain and PHD finger containing 1, BR140, IDDDFP

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?