XMD-12

Protein target name:

AURKA, AURKB, AURKC

Mechanism of action:

Inhibitor

Recommended Concentration for use in cells:

up to 1 uM

Probe Availability

Available free here

Probe Information

Target and Probe Information

Target Details

Target class:

Protein kinase

Subclass:

cell cycle-regulated kinase

HUGO ID:

HGNC:11393 HGNC:11390 HGNC:11391

Entrez gene ID:

6790 9212 6795

UNIPROT ID:

O14965 Q96GD4 Q9UQB9

Target alias:

AIK, ARK1, AURA, BTAK, PPP1R47, STK15, STK6, STK7, AIK2, AIM-1, AIM1, ARK-2, ARK2, AurB, IPL1, PPP1R48, STK-1, STK12, STK5, aurkb-sv1, aurkb-sv2, AIE2, AIK3, ARK3, AurC, HEL-S-90, SPGF5, STK13, aurora-C

Probe Details

Chemical Probes Portal ID:

CPP2048

Probe alias:

DUN57447, Aurora-IN-1, ZTX

PubChem CID:

54592204

ChEMBL ID:

CHEMBL4649424

SMILES string:

CN(C1=CN=C(NC2=CC=C(N3CCC(O)CC3)C=C2)N=C1N(C)C4=C5C=CC=C4)C5=O

InChi Key:

DFQAJLQXPSPNJE-UHFFFAOYSA-N

Orthogonal probe:

MK-5108AMG900AZD1152

Physico-chemical properties

NMR:

1H NMR (600 MHz, CD3OD) δ 8.19 (s, 1H), 7.71 (dd, J = 1.8, 7.8 Hz, 1H), 7.51 (dd, J = 2.4, 7.2 Hz, 2H), 7.49-7.46 (m, 1H), 7.19 (d, J = 8.4 Hz, 1H), 7.14 (t, J = 7.2 Hz, 1H), 6.97 (d, J = 8.4 Hz, 2H), 3.75-3.69 (m, 1H), 3.49-3.44 (m, 5H), 3.36 (s, 3H), 2.248-2.80 (m, 2H), 1.98-1.95 (m, 2H), 1.70-1.40 (m, 2H).

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

5.6 (AURKA), 18.4 (AURKB), 24.6 (AURKC) nM

Potency assay:

Invitrogen biochemical assay

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

3ZTX

Structure-activity relationship:

yes

Off target activity

Potency (off target):

IC50

Off target protein and potency:

LRRK2 30.5 nM LRRK2 (G2019S) 10.7 nM

Potency assay (off target):

Invitrogen biochemical assay

Probe Selectivity in Vitro:

Profiled using KINOMEscan @ 1 uM across a panel of 442 kinases: revealed sub-100 nM IC50 against DCAMKL2, LRRK2, NUAK1, and TAOK1. Potent biochemical inhibitor of LRRK2 (IC50 = 30.5 nM), this should be considered if it is being employed in scenarios where LRRK2 is expressed. DCAMKL2 87.7 nM; MAP3K2 155 nM; MAP3K3 120 nM; NUAK1 52.2 nM; TAOK2 54.3 nM

In cell validation

On target activity in cells

Potency in cells:

EC50

16.7 nM

Potency assay (cells):

Dose-dependently inhibited Aurora A autophosphorylation monitored by T288 residue in HeLa S3 cell, completely inhibited Aurora A at 250 nM. Dose-dependently inhibited Aurora B autophosphorylation monitored by T232 residue in HeLa S3 cell, completely inhibited Aurora A at 250 nM. Dose-dependently inhibited HCT116/HT29/HeLa cell growth with EC50 of 9.5 nM, 55 nM and 16.7 nM respectively. Compound phenotypes were compared to literature. The cellular effects were correlated with in vitro biochemical activities.

Primary Reference

Reference (doi):

10.1021/cb200305u

Reference (PMID):

21992004

External Resources

Available data:

Nathanael Gray Lab - Cancer Chemical Biology

Endorsed probe

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

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

3 review(s)

SAB Members

SAB Comments

XMD-12 has good kinome-wide selectivity with DCAMKL2, LRRK2, NUAK1 and TAOK1 being the only off targets below 100 nM, but target engagement and cellular inhibition has not been demonstrated for these off targets. At low concentration (100 nM), this pan-Aurora Inhibitor induces a SAC silencing phenotype suggesting that phenotypically, XMD-12 behaves like an pan-Aurora Inhibitor. Due to the known off targets and the lack of a negative control, I recommend however using additional Aurora inhibitors such as VX-680 or MLN8054 as controls.

Oct 18 2020 - 11:23am

Compound 1 complements the set of known selective Aurora inhibitors and is among the most kinase selective pan-Aurora inhibitor reported. The established pan-Aurora inhibitor VX680 appears to have more off-target activities, such as Flt-3 and Abl, and the panel used in its original publication was significantly smaller (58 kinases). While compound 1 is a relatively kinase selective compound, it is not free of significant kinase off-target activities, e.g. LRRK2 IC50 = 30 nM. Apart from the kinases that IC50s were determined for, the Ambit panel had numerous additional hits that were not followed up on in an IC50 screen (ERK5, TNK1, RET, FGR, CSF1R), and IC50 data for these kinases would provide additional confidence in adequate selectivity of this probe. Antiproliferation cellular EC50s in three cancer cell lines (HCT116, HT29, HeLa) are between 10 and 55 nM, which seems more potent than what would be expected based on its biochemical Aurora B IC50, in light of ATP concentrations >30x higher in cells, serum binding, etc. but the observed small shift is in line with other reported Aurora inhibitors. Use of this probe is limited to cellular applications as in vivo use of this compound was not reported, possibly due to ADME property shortcomings, but no further information is provided in the corresponding paper.

Dec 2 2020 - 10:03am

XMD-12

Probe Availability

Probe Information

Target Details

AIK, ARK1, AURA, BTAK, PPP1R47, STK15, STK6, STK7, AIK2, AIM-1, AIM1, ARK-2, ARK2, AurB, IPL1, PPP1R48, STK-1, STK12, STK5, aurkb-sv1, aurkb-sv2, AIE2, AIK3, ARK3, AurC, HEL-S-90, SPGF5, STK13, aurora-C

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

External Resources

Supporting Organizations

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XMD-12

Probe Availability

Probe Information

Target Details

AIK, ARK1, AURA, BTAK, PPP1R47, STK15, STK6, STK7, AIK2, AIM-1, AIM1, ARK-2, ARK2, AurB, IPL1, PPP1R48, STK-1, STK12, STK5, aurkb-sv1, aurkb-sv2, AIE2, AIK3, ARK3, AurC, HEL-S-90, SPGF5, STK13, aurora-C

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

External Resources

Supporting Organizations

Interested in supporting the portal?