MRK-740

Protein target name:

PRDM9

Mechanism of action:

Inhibitor

Recommended Concentration for use in cells:

up to 3 uM

Probe Availability

TOCRIS

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

Histone methyltransferase

HUGO ID:

HGNC:13994

Entrez gene ID:

56979

UNIPROT ID:

Q9NQV7

Target alias:

PFM6; KMT8B; MSBP3; ZNF899; MEISETZ

Probe Details

Chemical Probes Portal ID:

CPP1836

Probe alias:

MRK740

PubChem CID:

137331596

SMILES string:

Cc1cc(ccn1)N1CCC2(CC1)CN(CCN2C)c1nc(c2cc(cc(c2)OC)OC)no1

InChi Key:

NZYTZRHHBAJPKN-UHFFFAOYSA-N

Control compound:

MRK-740-NC

Physico-chemical properties

Solubility - preferred solvent:

DMSO

NMR:

1H NMR (400MHz, CD3OD) δ 7.98 (d, J = 6.2 Hz, 1H), 7.08 (d, J = 2.3 Hz, 2H), 6.68 (d, J = 2.6 Hz, 1H), 6.64 (dd, J = 6.3, 2.6 Hz, 1H), 6.61 (t, J = 2.3 Hz, 1H), 3.26 (ddd, J = 13.6, 10.7, 3.3 Hz, 2H), 2.87 – 2.83 (m, 2H), 2.38 (s, 3H), 2.38 (s, 3H), 1.98 (ddd, J = 14.8, 10.8, 4.6 Hz, 2H), 1.66 (dd, J = 13.9, 3.9 Hz, 2H)

Storage Recommendations

Storage (dry powder):

- 20C

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

80 ± 16 nM

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

6NM4

Structure-activity relationship:

yes

Off target activity

Potency assay (off target):

Enzyme Activity Assay

Probe Selectivity in Vitro:

Selectivity against 32 methyltransferases (MTs) were tested at 1 µM and 10 µM of compounds. PRDM9 was the only methyltransferase in a panel of MTs that was inhibited by MRK-740

In cell validation

On target activity in cells

Potency in cells:

IC50

0.8 uM

Potency assay (cells):

H3K4 methylation assay

Target engagement assay (cells):

NanoLuciferase thermal shift assay (NALTSA)

Off target activity in cells

Potency assay, off target (cells):

Eurofins Panlabs

Probe Selectivity in Cell:

MRK-740 was profiled in a customized panel of 108 enzymes and receptors at Eurofins Panlabs Discovery Services, Taiwan. MRK-740 demonstrated significant (>50% at 10 µM) binding only to Adrenergic α2B, Histamine H3, Muscarinic M2 and Opiate µ receptors. Functional assessment for these four GPCRs in agonist and antagonist mode revealed no functional activity on Adrenergic α2B, Histamine H3 & Muscarinic M2 receptors, and some potential agonistic activity at the Opiate µ receptor.

Toxicity

Cytoxicity assay:

Yes

Notes on cytotoxicity:

10 uM after 4 days.

Primary Reference

Reference (doi):

10.1038/s41467-019-13652-x

Reference (PMID):

31848333

Under Review

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

Part of SGC Chemical Probe Collection

SAB Rating

Rating for use in Cells

1 review(s)

Rating for use in Model Organisms

no rating

SAB Members

SAB Comments

MRK-740 is a probe that shows good biochemical target-based potency (80 nM), selectivity against other methyltransferases as well as against a customized panel of 108 enzymes and receptors at Eurofins Panlabs Discovery Services. Moreover, it has also been shown to be sufficiently potent (0.8 uM) to be a useful probe to study the biology of PRMD9 in whole cells. The fact that a crystal structure of MRK-740 bound to PRMT9 is available that shows the mode of target engagement is a strong positive. On the other hand, because it shows cytotoxicity in HEK293 cells at 10 uM, as noted above this probe should not be used at concentrations above ~5 uM. It is unclear what the mechanism of cytotoxicity (both it and its inactive counterpart MRK-740-NC show similar off-target cytotoxicity). While the probe has a good drug-like structure, the methylpyridine structure suggests that it may inhibit kinase targets at higher concentrations, and since no broad kinase data has been published, this possibility has not been definitively ruled out. In addition, no pharmacokinetic data is available which should be generated independently if this probe is to be used in vivo.

Nov 4 2020 - 10:56am

MRK-740

Probe Availability

Probe Information

Target Details

PFM6; KMT8B; MSBP3; ZNF899; MEISETZ

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Toxicity

Primary Reference

Supporting Organizations

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MRK-740

Probe Availability

Probe Information

Target Details

PFM6; KMT8B; MSBP3; ZNF899; MEISETZ

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Toxicity

Primary Reference

Supporting Organizations

Interested in supporting the portal?