PFI-3

Protein target name:

SMARCA2, SMARCA4, PBRM1

Mechanism of action:

Antagonist

Recommended Concentration for use in cells:

1 uM

Probe Availability

Selleck Chemicals

MedChemExpress

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

Bromodomain

HUGO ID:

HGNC:11098 HGNC:11100 HGNC:30064

Entrez gene ID:

6595 6597 55193

UNIPROT ID:

P51531 P51532 Q86U86

Target alias:

BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a, BAF190, BAF190A, BRG1, CSS4, MRD16, RTPS2, SNF2, SNF2L4, SNF2LB, SWI2, hSNF2b, BAF180, PB1

Probe Details

Chemical Probes Portal ID:

CPP1415

Probe alias:

PFI 3

PubChem CID:

78243717

ChEMBL ID:

CHEMBL3752911

SMILES string:

C1[C@@H]2CN([C@H]1CN2C3=CC=CC=N3)/C=C/C(=O)C4=CC=CC=C4O

InChi Key:

INAICWLVUAKEPB-QSTFCLMHSA-N

Control compound:

PFI-oMet

Orthogonal probe:

SGC-SMARCA-BRDVIIIABCI1

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

54-97 nM

Potency assay:

SMARCA2(A, B): 81 nM, 86 nM; PB1(5): 54 nM, SMARCA4: 97 nM; ITC assay

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

5DKC, 5DKD

Structure-activity relationship:

Yes, see J. Med. Chem. paper

Off target activity

Potency assay (off target):

PFI-3 was also profiled against 40 Bromodomains in Tm assay and in BROMOscan assay (DiscoveRx); it had no significant activity against any other Bromodomain.

Probe Selectivity in Vitro:

In a Cerep panel containing 102 cellular receptors and 30 enzymes, PFI-3 had minimal off-target activity, with the most significant IC50s measured against four GPCRs in the micromolar range (alpha1A: 0.4 uM; alpha1B: 3.6 uM; k opioid receptor: 13 uM; 5-HT2B: 4 uM). In a DNA intercalating and unwinding assay, no activity was detected.

In cell validation

On target activity in cells

Potency assay (cells):

In U2OS cells, PFI-3 increased fluorescence recovery of GFP-tagged, full-length BRM protein in FRAP assay including wild-type but not mutant version of BRM (N1464F), which does not bind acetylated chromatin.

Target engagement assay (cells):

Yes, FRAP assay

Toxicity

Cytoxicity assay:

Yes

Notes on cytotoxicity:

In C2C12 and C3H10T1/2 cells, no significant cytotoxicity (MTT assay) was detected up to 50 uM. At 10 uM PFI-3, no toxicity was detected in NCI-60 panel of tumor cell lines.

Primary Reference

Reference (doi):

10.1126/sciadv.1500723 10.1021/acs.jmedchem.6b00012 10.1172/JCI123557 10.1158/0008-5472.CAN-14-3798

Reference (PMID):

26702435 27115555 26139243 30496141

External Resources

Available data:

GDSC1 GDSC2

Under Review

This probe is in the process of SAB review. Please continue to check back for new reviews and commentary.

SAB Rating

Rating for use in Cells

2 review(s)

Rating for use in Model Organisms

2 review(s)

SAB Members

SAB Comments

This is a first-in-class inhibitor of the BAF bromodomains BRG and BRM. Data is only available for cell-based interogations. In this setting, PFI-3 should enable a range of studies around the cell-based consequences of modulating these important epigenetic targets.

Apr 29 2020 - 8:14pm

PFI-3 represents a well-studied and selective probe for the targets listed, suitable for cellular work. Care is needed in choosing appropriate cellular concentrations – target engagement is reported at 1uM but other studies report effects at different concentration ranges (Ding et al <0.1uM; Vangamundi et al report 5uM cellular IC50). The use of the negative control PFI-3oMet is strongly recommended. The probe developers do not recommend in vivo use; Ding et al report efficacy in a mouse model at 50 mg/kg p.o. so this may be feasible. Obtaining good quality PK data (not presented) is strongly recommended prior to any in vivo work, particularly given the potential for hydrolytic instability in acid - the compound contains a potentially unstable enamide group. Stability is shown in PBS and cell media for 1 week at neutral pH so there should be no issue for cellular work, however care should be taken with long term storage in solution, or if use at acidic or basic pHs is required which could accelerate decomposition.

Apr 29 2020 - 8:17pm

PFI-3

Probe Availability

Probe Information

Target Details

BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a, BAF190, BAF190A, BRG1, CSS4, MRD16, RTPS2, SNF2, SNF2L4, SNF2LB, SWI2, hSNF2b, BAF180, PB1

Probe Details

In vitro validation

In cell validation

Toxicity

Primary Reference

External Resources

Supporting Organizations

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PFI-3

Probe Availability

Probe Information

Target Details

BAF190, BRM, NCBRS, SNF2, SNF2L2, SNF2LA, SWI2, Sth1p, hBRM, hSNF2a, BAF190, BAF190A, BRG1, CSS4, MRD16, RTPS2, SNF2, SNF2L4, SNF2LB, SWI2, hSNF2b, BAF180, PB1

Probe Details

In vitro validation

In cell validation

Toxicity

Primary Reference

External Resources

Supporting Organizations

Interested in supporting the portal?