This probe is available from Tocris and Cayman Chemical.
The control may be requested by clicking here.
| Probe | Negative control | |
 |
|  |
TP-064 |
| TP-064N |
A collaboration between Takeda and the SGC has resulted in the discovery of TP-064, the first potent, selective and cell active chemical probe for PRMT4. The in vitro activity of TP-064 includes inhibition of PRMT4 with IC50 < 10nM for methylation of H3 (1-25) and greater than 100-fold selectivity over other histone methyltransferases and non-epigenetic targets. In cellular assays, TP-064 inhibits the methylation of MED12 with IC50 = 43 nM.
A closely related compound, TP-064N, exhibits no activity in the biochemical and cellular assays, and is an ideal control compound for cellular studies.
| Probe | Negative control | |
|
| |
TP-064 |
| TP-064N |
| Physical and chemical properties for TP-064 | |
| Molecular weight | 458.3 |
| Molecular formula | C28H34N4O2 |
| IUPAC name | (methyl-((2-(1-(2-methylamino-ethyl)-piperidin-4-yl)-pyridin-4-yl)-methyl)-amino)-(3-phenoxy-phenyl)-methanone |
| MollogP | 3.422 |
| PSA | 47.71 |
| No. of chiral centres | 0 |
| No. of rotatable bonds | 10 |
| No. of hydrogen bond acceptors | 6 |
| No. of hydrogen bond donors | 1 |
| Physical and chemical properties for TP-064N (Negative Control) | |
| Molecular weight | 459.3 |
| Molecular formula | C28H33N3O3 |
| IUPAC name | (((2-(1-(2-methoxy-ethyl)-piperidin-4-yl)-pyridin-4-yl)-methyl)-methyl-amino)-(3-phenoxy-phenyl)-methanone |
| MollogP | 4.051 |
| PSA | 44.24 |
| No. of chiral centres | 0 |
| No. of rotatable bonds | 10 |
| No. of hydrogen bond acceptors | 6 |
| No. of hydrogen bond donors | 0 |
Selectivity of TP-064N at 10 μM () and 1 μM () and of TP-064 at 10 μM () and 1 μM () for PRMT1, 3, 4, 5, 6, 7, 8, and 9 as well as for 24 histone and DNA methyltransferases was assessed. Dose response data are presented in the top panel as IC50s (μM).
TP-064 inhibits the dimethylation of PRMT4 substrates. HEK293 cells were treated with indicated concentrations of TP-064 for 3 days and dimethylation levels of BAF155 and MED12 in whole cell extracts were analyzed by western blotting. (B) Quantitation of data in (A). Graphs represent nonlinear curve fits of dimethyl-BAF155 and dimethyl-MED12 signal intensities normalized to total BAF155 or MED12, respectively. Data represent mean ± SEM of two independent experiments prepared in triplicate.
TP-064 (blue) inhibits PRMT4 activity with an IC50 value of < 10 nM under balanced conditions. TP-064N (red) has no effect on PRMT4 activity up to 100 nM. The binding of TP-064 to PRMT4 was confirmed by DSLS with stabilization at about 6°C. No binding was observed with TP-064N
SPR analysis of the TP-064 binding to PRMT4 in the presence of 50 μM SAM. A representative sensorgram (black dots) is shown with the kinetic fit (solid green). A Kd value of 7.1 ± 1.8 nM, with kon = 1.1 ± 0.1 × 105 M−1 s−1 and koff = 0.7 ± 0.1 × 10−3 s−1, was obtained from triplicate experiments. The steady state response (black circles) and 1:1 binding model fitting (red dashed line) is presented.
Mechanism of action of TP-064 was assessed by determining IC50 of both substrates values at various concentrations.
Kazuhide Nakayama, Magdalena M. Szewczyk, Carlo dela Sena, Hong Wu, Aiping Dong, Hong Zeng, Fengling Li, Renato Ferreira de Freitas, Mohammad S. Eram, Matthieu Schapira, Yuji Baba, Mihoko Kunitomo, Douglas R. Cary, Michiko Tawada, Akihiro Ohashi, Yasuhiro Imaeda, Kumar Singh Saikatendu, Charles E. Grimshaw, Masoud Vedadi, Cheryl H. Arrowsmith, Dalia Barsyte-Lovejoy, Atsushi Kiba, Daisuke Tomita and Peter J. Brown TP-064, a potent and selective small molecule inhibitor of PRMT4 for multiple myeloma. Oncotarget 9: 18480-93 (2018)
| Test compound | TP-064 |
| Animal | C.B-17/Icr-scid mouse, female, 7W, fed |
| Formulation | 10% DMSO/10% Cremophor EL /10% PropyleneGlycol (PG)/Distilled Water |
| Administration | i.p., 30 or 100 mg/kg as free body |
| Test items | Plasma |
| Sampling time | 0.25, 0.5, 1, 2, 4, 8, 24 hours after administration |
Main features
This probe is available from Tocris, Cayman Chemical and Sigma.
Its negative control (TP-472N) is available for purchase from Tocris and Sigma.
| Probe | Negative control | |
 |
|  |
TP-472 |
| TP-472N |
The bromodomain containing protein 9 (BRD9) has been reported as a component of the switch/sucrose non-fermentable (SWI/SNF) brahma-related gene 1-associated factor (BAF) complex, which plays a key role in chromatin remodelling and transcription control [1] although the precise biological role is unknown. The highly homologous bromodomain containing protein 7 (BRD7) is a component of the SWI/SNF polybromo-associated BAF (PBAF) complex and has been proposed as a tumor suppressor [2].
In a collaborative effort Takeda and the SGC have identified and characterised TP-472 as a BRD9/7 probe. This molecule is of a different chemotype to the BRD9/7 probes previously available, has a structurally similar negative control available (TP-472N), has a good PK profile and is suitable for in vivo applications and is synthetically tractable.
TP-472 has excellent potency (BRD9 KD 33nM; BRD7 340nM by ITC), selectivity >30 fold over all other bromodomain family members except BRD7 and is cell active (EC50 320 nM in a BRD9 NanoBRET assay). The negative control TP472N is inactive against other bromodomains (>20uM against BRD9)
| Probe | Negative control | |
|
| |
TP-472 |
| TP-472N |
| Physical and chemical properties for TP-472 | |
| Molecular weight | 333.1 |
| Molecular formula | C20H19N3O2 |
| IUPAC name | 1-(7-(5-(cyclopropylamino-formyl)-2-methyl-phenyl)-1,5-diaza-bicyclo[4.3.0]nona-2,4,6,8-tetraen-9-yl)-ethanone |
| MollogP | 3.102 |
| PSA | 46.85 |
| No. of chiral centres | 0 |
| No. of rotatable bonds | 5 |
| No. of hydrogen bond acceptors | 5 |
| No. of hydrogen bond donors | 1 |
| Physical and chemical properties for TP-472N (Negative Control) | |
| Molecular weight | 306.1 |
| Molecular formula | C19H18N2O2 |
| IUPAC name | 1-(7-(2-(cyclopropyl-methoxy)-phenyl)-1,5-diaza-bicyclo[4.3.0]nona-2,4,6,8-tetraen-9-yl)-ethanone |
| MollogP | 3.673 |
| PSA | 30.22 |
| No. of chiral centres | 0 |
| No. of rotatable bonds | 5 |
| No. of hydrogen bond acceptors | 4 |
| No. of hydrogen bond donors | 0 |
Selectivity beyond target family
TP-472 and TP-472N were screened in the Eurofins CEREP Diversity Profile to measure binding to a range of Receptors, Ion Channels and enzymes @10 uM. The Inhibition as the mean % of control is shown below, results showing an inhibition or stimulation lower than 50% are considered to represent significant effects. TP-472 showed binding to Adenosine A1 receptor (14%), Benzodiazepine receptor (47%), PDE2A1 (h) (25%), PDE3A (h) (48%) and PDE4D2 (h) (28%). TP-472N showed binding to A1 receptor (35%), A3 receptor (23%), Melatonin receptor MT1 (47%) and Cl- channel (GABA-gated) (20%).
For a second year, SGC Toronto hosted a team of senior law students from the University of Toronto's Faculty of Law as part of an externship clinic to help SGC draft new agreements protecting our open access ethos and promoting our open science.
Oxford, UK (April 23rd, 2016) -FOP patient groups have announced an extension of their support to the FOP research team in SGC Oxford led by Dr Alex Bullock since 2008. The team, currently comprising two postdoctoral fellows, is working towards developing a treatment for the rare monogenic disease Fibrodysplasia Ossificans Progressiva (FOP), a disorder that causes severely debilitating extraskeletal bone formation and impairs movement.
Farnborough, Hampshire UK (April 13th, 2016) -We are delighted to announce a groundbreaking partnership between The Brain Tumour Charity and the Structural Genomics Consortium (SGC), an international group of academic and industrial researchers with a strong track record in uncovering new drug targets and initiating clinical trials within unusually short timeframes.
Rachel Harding, a researcher at SGC Toronto, appears on Global News discussing her open science experiment. She's welcomed the world to view her research progress in real-time by placing her lab notes online and explaining her results on her blog Lab Scribbles.
Fremont, CA – February 29, 2016 – DiscoverX Corporation, the leading supplier of innovative cell-based assays and services for drug discovery and development, today announced its partnership with the Structural Genomics Consortium (SGC), a public-private organization established in 2003, to develop selective and potent chemical probes for the unexplored human kinome and to promote open sharing of these probes with the scientific community.
TORONTO, February 26, 2016 — University of Toronto researcher Rachel Harding will be the first known biomedical researcher to welcome the world to review her lab notes in real time. The post-doctoral fellow with U of T’s Structural Genomics Consortium (SGC) is also explaining her findings to the general public through her blog. She hopes her open approach will accelerate research into Huntington’s disease.
This month, we talk to Dr Wen Hwa Lee, Strategic Alliances Manager at the Structural Genomics Consortium (SGC), part of the Nuffield Department of Clinical Medicine, about how the SGC is revolutionising the way we think about drug discovery.
We have recently heard a lot about open innovation in drug discovery and biomedicine – with the Structural Genomics Consortium (SGC) being one of the shining examples, mentioned in industry and strategic reports (including RAND, Deloitte and the recent Dowling Report) – can you tell us a bit more about it?
Myeloma UK and the Structural Genomics Consortium (SGC) have entered into an open-access research partnership to discover and characterise novel drug targets for myeloma using structural biology and chemical proteomics.
In this first partnership of its kind in Europe, Myeloma UK and the SGC have explicitly agreed not to file for patents on any of the collaborative research and to make all reagents and knowledge available without restriction to the wider research community, including pharmaceutical, biotech, and academic research groups.
