NI-42

Protein target name:

BRPF1, BRD1, BRPF3

Mechanism of action:

Antagonist

Recommended Concentration for use in cells:

1-10 uM

Probe Availability

Tocris (1884640-99-6)

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

Bromodomain

HUGO ID:

HGNC:14255 HGNC:1102 HGNC:14256

Entrez gene ID:

7862 23774 27154

UNIPROT ID:

P55201 O95696 Q9ULD4

Target alias:

Bromodomain and PHD finger containing 1, BR140, bromodomain containing 1, BRL, BRPF1, BRPF2, bromodomain and PHD finger containing 3

Probe Details

Chemical Probes Portal ID:

CPP1001

PubChem CID:

126961736

SMILES string:

CC1=CC2=C(C=CC(=C2)NS(=O)(=O)C3=CC=C(C=C3)[N+]#[C-])N(C1=O)C

InChi Key:

ZLTQCDRXWXUYHJ-UHFFFAOYSA-N

Control compound:

NI-198

Orthogonal probe:

OF-1PFI-4GSK6853

Physico-chemical properties

NMR:

1H NMR (400 MHz, DMSO-d6): δ 10.52 (1H, s), 8.06 - 8.00 (2H, m), 7.90 - 7.84 (2H, m), 7.73 (1H, s), 7.41 (1H, d, J = 9.1 Hz), 7.33 (1H, d, J = 2.5 Hz), 7.23 (1H, dd, J = 9.1, 2.5 Hz), 3.57 (3H, s), 2.09 (3H, d, J = 1.0 Hz);

13C NMR (126 MHz, DMSO-d6): δ 161.4, 143.3, 136.3, 135.0, 133.5, 130.8, 130.0, 127.4, 123.5, 120.3, 119.9, 117.5, 115.5, 115.3, 29.4, 17.3.

Storage Recommendations

Storage (dry powder):

Store at -20°C

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

ITC KD

BRPF1 40 nM; BRD1 210 nM; BRPF3 940 nM

Potency assay:

Potency was also determined in Bromoscan assay and Alphascreen activity assays. Bromoscan IC50s: BRPF1=7.9 nM, BRD1=48 nM, BRPF3=260 nM; Alpha assay IC50s: BRPF1=140 nM, BRD1=760 nM, BRPF3=2,000 nM.

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

5T4U, 5T4V

Structure-activity relationship:

Yes, SAR is available in both DSF and BROMOscan assays in the paper.

Off target activity

Potency (off target):

IC50

Off target protein and potency:

BRD9 310 nM; BRD4 4,500 nM; BRD7 82 nM

Potency assay (off target):

NI-42 was screened in Bromoscan assay and with differential scanning fluorimetry (DSF) against a panel of 48 BRDs and showed excellent selectivity. For the latter assay, all activity was confined to the class IV family of BRDs with ∆Tm < 1 oC stabilization for all non-class IV BRDs.

Probe Selectivity in Vitro:

NI-42 was tested for activity against 8 ion channels (Eurofins CardiacProfile: Nav1.5, Kv4.3/KChIP2, Cav1.2, hKv1.5, KCNQ1/mink, HCN4, Kiv2.1 and hERG) yiedling 45.6% inhibition of hERG current amplitude at 30 uM.

In cell validation

On target activity in cells

Potency assay (cells):

An indexed cell panel of 211 cancer cell lines (CLIMB panel) was treated with NI-42 for 72 h and observed modest and selective inhibition of proliferation of certain AML cell lines (OCI-AML2, Nomo-1, THP-1, KG-1, MV-4-11) with GI50s 1-10 uM.

Target engagement assay (cells):

Yes, in FRAP assays, NI-42 displaced BRPF1B-BRDx3 from chromatin at 1 µM using BRPF1B-GFP fusion protein.

In vivo validation

Organism:

mouse CD-1 (female)

Dose:

3 mg/kg (oral)1 mg/kg (IV)

Route of delivery:

Oral

Other route of delivery:

Plasma half life:

2.0 h (IV)

Systemic clearance:

4 mL/min/kg (IV)

Fraction of probe bound to plasma protein:

97 %

Cmax:

3.95 uM (oral)

Tmax:

1.0 h (oral)

Primary Reference

Reference (doi):

10.1021/acs.jmedchem.6b01583

Reference (PMID):

28068087

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

3 review(s)

SAB Members

SAB Comments

The chemical probe NI-57, which is closely related to NI-42, inhibits BRPF1, BRD1, BRPF3 and is the preferred probe for these targets. Although NI-57 is not yet published, it is commercially available. Details for NI-57 are available on the SGC website http://www.thesgc.org/chemical-probes/NI-57.

Mar 28 2017 - 7:15pm

NI-42 is a moderately potent BRPF1 inhibitor (exact potency unclear as it is assay format dependent, but presuming ITC is preferred format, KD ~40 nM) with moderate selectivity: ~6X selectivity over BRPF2, ~10X over BRD7, ~20-40X selectivity over BRPF3 and BRD9, and much greater selectivity over remaining BRD-containing proteins screened. GSK6853 (http://pubs.acs.org/doi/full/10.1021/acsmedchemlett.6b00092) would appear to be the preferred probe for cellular use, as it is more potent and selective. NI-42 may be the best in vivo tool available for models that require chronic dosing, however, as its pharmacokinetics was compatible with oral dosing, unlike GSK6853 (limited to IP dosing).

Mar 28 2017 - 8:03pm

As other SAB members have pointed out, it is difficult to obtain a clear view on the suitability of this probe for cellular work. Different biochemical IC50s are cited and whilst target engagement is demonstrated, no quantitative target engagement (IC50) has been reported. It is thus not possible to say to which extent the target is likely inhibited at a given concentrations or if near-complete inhibition in cells can be achieved without affecting other class IV bromodomains. As other SAB members pointed out, improved probes have been published for this target, though this seems to be the only one with decent mouse PK making it potentially usable in vivo. However, it should be noted, that without quantitative target engagement data, it is difficult to determine the dose for in vivo experiments.

Jul 25 2017 - 12:20pm

NI-42

Probe Availability

Probe Information

Target Details

Bromodomain and PHD finger containing 1, BR140, bromodomain containing 1, BRL, BRPF1, BRPF2, bromodomain and PHD finger containing 3

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?

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NI-42

Probe Availability

Probe Information

Target Details

Bromodomain and PHD finger containing 1, BR140, bromodomain containing 1, BRL, BRPF1, BRPF2, bromodomain and PHD finger containing 3

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?