PFI-3 A selective chemical probe for SMARCA bromodomains

This probe is available from Cayman Chemical, Sigma and Tocris

For any inquiries please contact proberequests@thesgc.org.

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Overview

PFI-3

PFI-3oMet

In vitro Potency
Assay	K_d/IC50 (nM)
SMARCA4 (ITC)	89
PB1(5) (ITC)	48

SMARCA4 (SWI/SNF related, Matrix associated, Actin dependent Regulator of Chromatin, subfamily A, member 4), also known as BRG1 (Brahma-Related Gene 1), is part of the SWI/SNF (SWItch/Sucrose NonFermentable) family of proteins. Multiple transcript variants encoding different isoforms have been found for this gene in normal tissue as well as in cancer. SMARCA4 and the related protein SMARCA2 (BRM, BRahMa) contain a bromo and helicase domain and both proteins are central components of the large ATP-dependent SNF/SWI chromatin remodelling complex, which plays a key role in chromatin remodelling and transcription control. PB1 (PolyBromo 1) can also be part of the SWI/SNF complex.

Loss of function of SMARCA4 and components of SWI/SNF has been linked to cancer development suggesting a tumour suppressor function for BRG1. SMARCA4 has also been shown to interact with the breast cancer gene BRCA1 (BReast CAncer 1, early onset), as well as to regulate the expression of the tumorigenic protein CD44.

We have developed an inhibitor, PFI-3, against the SMARCA2/4 and PB1(5) bromodomains.

Properties

Structure of 2-methoxy-N-(3-methyl-2-oxo-1,2,3,4-tetrahydroquinazolin-6-yl)benzenesulfonamide

(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]prop-2-en-1-one
Click here to download SDF file

Physical and chemical properties
Molecular weight	321.4
Molecular formula	C ₁₉H ₁₉N ₃O ₂
IUPAC name	(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]prop-2-en-1-one
logP (ChemBioDraw Ultra)	2.39
PSA (ChemBioDraw Ultra)	56.14
Storage	-20°C as powder. NB making aliquots rather than freeze-thawing is recommended
Dissolution	Soluble in DMSO at least up to 10mM
Stability* at 37°C	t _1/2 > 15 days
Stability* at 20°C	t _1/2 > 200 days

*as measured by LCMS

SMILES:

OC1=CC=CC=C1C(/C=C/N2[C@H](C3)CN(C4=NC=CC=C4)[C@H]3C2)=O

InChI:

InChI=1S/C19H19N3O2/c23-17-6-2-1-5-16(17)18(24)8-10-21-12-15-11-14(21)13-22(15)19-7-3-4-9-20-19/h1-10,14-15,23H,11-13H2/b10-8+/t14-,15-/m1/s1

InChIKey:

INAICWLVUAKEPB-QSTFCLMHSA-N

Selectivity Profile

PFI-3 only shows a significant Tm shift with PB1(5) and SMARCA2/4. No interaction was observed with PB1(2-4), and there was no cross-reactivity in a kinase panel of 36 kinases.

Selectivity
Bromodomains
Target	Tm shift °C @ 10 µM
SMARCA2	6.4
SMARCA4	5.1
PB1 1st Bromodomain	-0.5
PB1 2nd Bromodomain	1.1
PB1 3rd Bromodomain	0.9
PB1 5th Bromodomain	7.5
PB1 6th Bromodomain	0.4
PCAF	0.5
BRD4 1st Bromodomain	0.3
BRD4 2nd Bromodomain	0.4
CREBBP	-0.0
BRD1	0.0
TIF1alpha	0.7
TRIM2B	0.3
TAF1L 1st Bromodomain	0.2
TAF1L 2nd Bromodomain	0.3
Other proteins
Invitrogen kinase panel	No activity

Cell-based Assay Data

Selectivity
SMARCA2 (Frap Assay)	Accelerated FRAP recovery at 1 uM
SMARCA2 (Frap Assay) *	Accelerated FRAP recovery at 1 uM
SMARCA2 (Frap Assay) #	Accelerated FRAP recovery at 1 uM

*24 hour compound incubation on cells
^1 hour compound incubation on cells preceded by 24 hour pre-incubation of the compound in medium

PFI-3 is stable in cells for >24h.

References

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance. Oleg Fedorov, Josefina Castex, Cynthia Tallant, Dafydd R. Owen, Sarah Martin, Matteo Aldeghi, Octovia Monteiro, Panagis Filippakopoulos, Sarah Picaud, John D. Trzupek, Brian S. Gerstenberger, Chas Bountra, Dominica Willmann, Christopher Wells, Martin Philpott, Catherine Rogers, Philip C. Biggin, Paul E. Brennan, Mark E. Bunnage, Roland Schüle, Thomas Günther, Stefan Knapp, Susanne Müller

Science Advances 13 Nov 2015:
Vol. 1, no. 10, e1500723
DOI: 10.1126/sciadv.1500723