BAY-598

Reagent Authentication Certificate:

Chemical Probes Portal BAY-598.pdf

Protein target name:

SMYD2

Mechanism of action:

protein-substrate competitive inhibitorSAM uncompetitive inhibitor

Recommended Concentration for use in cells:

50 nM - 2 uM

Probe Availability

MilliporeSigma (BAY-598)

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

Protein methyltransferase

HUGO ID:

HGNC:20982

Entrez gene ID:

56950

UNIPROT ID:

Q9NRG4

Target alias:

KMT3C, H5KM-B, ZMYND14

Probe Details

Chemical Probes Portal ID:

CPP47

Probe alias:

GTPL8953

PubChem CID:

117072551

ChEMBL ID:

23698919

SMILES string:

CCN([C@H]1CN(N=C1C2=CC(=C(C=C2)Cl)Cl)C(=NC3=CC(=CC=C3)OC(F)F)NC#N)C(=O)CO

InChi Key:

OTTJIRVZJJGFTK-SFHVURJKSA-N

Control compound:

BAY-369

Orthogonal probe:

LLY-507

PAINs evaluation:

PAINs free

Physico-chemical properties

NMR:

1H NMR (400 MHz, [D]6DMSO): δ =0.98–.10 (m, 3H), 3.17–.42 (m, 2H, partially under water signal), 3.94–.17 (m, 3H), 4.46 (t, J = 11.7 Hz, 1H), 4.75 (t, J = 5.7 Hz, 1H), 6.98 (dd, J = 7.8, 1.8 Hz, 1H), 7.18 (br t, 1H), 7.22 (m, 1H), 7.23 (t, J = 8.2 Hz, 1H), 7.40 (t, 1H), 7.62 (dd, J = 8.2, 1.8 Hz, 1H), 7.7 (d, J = 8.2 Hz, 1H), 8.11 (d, J = 1.4 Hz, 1H), 9.85 (br s, 1H).

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

27 nM

Potency assay:

Scintillation proximity assay

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

5ARG

Structure-activity relationship:

Yes, at least 15 compounds with in vitro IC50 data.

In cell validation

On target activity in cells

Potency in cells:

IC50

58 nM

Potency assay (cells):

in-cell quantification of substrate methylation by FLAG-tagged SMYD2

Target engagement assay (cells):

Yes, indirect. Inhibition of protein substrate methylation in cells.

Off target activity in cells

Potency in cells, off target:

IC50

Off target protein and potency (cells):

SMYD3 3 uM

Potency assay, off target (cells):

BAY-598 showed 100-fold selectivity for SMYD2 over 30 protein methyltranferases including SMYD3, SUV420H1, and SUV420H2.

Probe Selectivity in Cell:

No significant activity was detected in KINOMEscan (DiscoveRx) or LeadProfilingScreen (Eurofin Panlabs) assays.

In vivo validation

Organism:

rat and female BALB/c nude mice

Dose:

0.8 mg/kg (rat)10-100 mg/kg (mouse)

Route of delivery:

Oral

Systemic clearance:

1.6 L/h/kg (rat)

Organ of Interest

Organ (O):

subcutaneous tumor xenograft (mouse)

Target engagement assay:

Yes, indirect. Ex vivo protein substrate methylation assay in tumor cells overexpressing SMYD2.

Primary Reference

Reference (doi):

10.1021/acs.jmedchem.5b01890

Reference (PMID):

27075367

Endorsed probe

The Chemical Probes Portal endorses this compound as chemical probe for use in cells and in model organisms.

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

3 review(s)

SAB Members

SAB Comments

This is a potent, selective probe suitable for cellular studies with on-target activity expected between 50-1000 nM. If used above 5000 nM, there is a potential for SMYD3 inhibition (unconfirmed). The probe is also suitable for use in vivo in human tumour xenografts in mice with on-target activity expected between 30-100 mg/kg (oral dosing). Full mouse PK, plasma protein binding, and free drug PK-PD relationships in mouse models have not yet been reported. I recommend that the user determine free-drug exposure if dosing above 100 mg/kg (orally) to relate to pharmacology profile. Over the short term (48 h), the compound is chemically stable in standard conditions; racemisation has been observed in basic forcing conditions.

Jun 12 2016 - 3:04am

In KYSE-150 cells, BAY-598 reduces p53K370me (relative to p53K370) with IC50 = 50 nM. Use BAY-598 in parallel with its control compound BAY-369 in cell assays.

Jun 12 2016 - 3:05am

BAY-598

Probe Availability

Probe Information

Target Details

KMT3C, H5KM-B, ZMYND14

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?

Search form

BAY-598

Probe Availability

Probe Information

Target Details

KMT3C, H5KM-B, ZMYND14

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?