BAY-850 A chemical probe for ATAD2A

This probe is available from Cayman Chemical and Sigma (trihydrochloride).

overview
Probe Negative control

 

BAY-850

 

BAY-460

ATAD2 and ATAD2B are epigenetic regulators known to function as co-factors for oncogenic transcription factors. ATAD2 overexpression correlates with poor outcomes in several cancers. The bromodomain module of ATAD2 has been shown to be essential for its association with acetylated chromatin and presumable function.
BAY-850 is a chemical probe for the ATAD2A bromodomain which displaces acetylated H4 peptide from the ATAD2 bromodomain with an IC50 value of 20 nM (HTRF). MST and BROMOscan measurements indicate a Kd of 84.9 nM and 120 nM, respectively. BAY-850 displays exquisite selectivity over all other bromodomains (no hits in BROMOscan at 10 µM) and displaces full-length ATAD2 from chromatin in live cells at a concentration of 1 µM as determined by FRAP. To avoid potential unspecific off-target effects concentrations of ≥ 5 µM are not recommended.
BAY-460 is a companion control compound with strongly reduced potency against ATAD2 (HTRF IC50 = 16 µM, no activity in BROMOscan at 10 µM test concentration).

Properties

ATAD2H4AcK5/8/12/16 IC50 (HTRF)0.02 μM
LLElogD2.6
ATAD2 TSA ΔT(100μM)13.9°C
BRD4 BD1 IC50 (HRTF)>20 μM
BRD4BD2 IC50 (HTRF)>20 μM
DiscoverX BromoScanATAD2A @ 10 μM
DiscoverX ATAD2A KD0.12 μM
MST KD0.08 μM

 

Sw pH 6.5 [mg/L]>500*
log D (pH 7.5)2.9

*HCl salt

properties
Probe Negative control

 

BAY-850

 

BAY-460

Physical and chemical properties for BAY-850
Molecular weight653.3
Molecular formulaC38H44ClN5O3
IUPAC name4-(3-(4-amino-cyclohexylamino)-2-((2-chloro-4-methoxy-5-(5-((1-p-tolyl-ethylamino)-methyl)-furan-2-yl)-phenyl)-formylamino)-propyl)-benzonitrile
MollogP6.17
PSA98.59
No. of chiral centres2
No. of rotatable bonds15
No. of hydrogen bond acceptors8
No. of hydrogen bond donors5



 

Physical and chemical properties for BAY-460 (Negative Control)
Molecular weight

568.2

 

Molecular formulaC33H33ClN4O3
IUPAC name4-(2-((2-chloro-5-(5-((1-p-tolyl-ethylamino)-methyl)-furan-2-yl)-phenyl)-formylamino)-4-methylamino-4-oxo-butyl)-benzonitrile
MollogP5.533
PSA84.53
No. of chiral centres2
No. of rotatable bonds14
No. of hydrogen bond acceptors7
No. of hydrogen bond donors3
  • SMILES:
  • BAY-850: O=C(N[C@H](CC1=CC=C(C=C1)C#N)CN[C@H]2CC[C@H](CC2)N)C3=C(Cl)C=C(OC)C(C4=CC=C(CN[C@@H](C5=CC=C(C)C=C5)C)O4)=C3
  • BAY-460: CC1=CC=C([C@H](NCC2=CC=C(O2)C3=CC(C(N[C@@H](CC4=CC=C(C=C4)C#N)CC(NC)=O)=O)=C(Cl)C=C3)C)C=C1
  • InChI:
     
  • BAY-850: InChI=1S/C38H44ClN5O3/c1-24-4-10-28(11-5-24)25(2)42-23-32-16-17-36(47-32)34-19-33(35(39)20-37(34)46-3)38(45)44-31(18-26-6-8-27(21-40)9-7-26)22-43-30-14-12-29(41)13-15-30/h4-11,16-17,19-20,25,29-31,42-43H,12-15,18,22-23,41H2,1-3H3,(H,44,45)/t25-,29-,30+,31-/m1/s1
  • BAY-460: InChI=1S/C33H33ClN4O3/c1-21-4-10-25(11-5-21)22(2)37-20-28-13-15-31(41-28)26-12-14-30(34)29(17-26)33(40)38-27(18-32(39)36-3)16-23-6-8-24(19-35)9-7-23/h4-15,17,22,27,37H,16,18,20H2,1-3H3,(H,36,39)(H,38,40)/t22-,27+/m1/s1
  • InChIKey:
  • BAY-850: BSISGUIVBKDTQO-QIKYYPRYSA-N
  • BAY-460: HBEUJCCOUJWRIC-AMGIVPHBSA-N

     

selectivity profile
in vitro potency
cell based assay data
references

Fernández-Montalván, A., Berger, M., Kuropka, B., Koo, S., Badock, V., & Weiske, J. et al. (2017). Isoform-Selective ATAD2 Chemical Probe with Novel Chemical Structure and Unusual Mode of Action. ACS Chemical Biology. http://dx.doi.org/10.1021/acschembio.7b00708

pk properties
co-crystal structures
synthetic schemes
materials and methods
19.12.2016

3D map of PC2 to jump-start drug discovery efforts in polycystic kidney disease

by: SGC

Oxford, UK, December 19, 2016, Scientists from the Structural Genomics Consortium (SGC) and Oxford University report a three-dimensional view of the Polycystin-2 (PC2), a protein that causes autosomal dominant polycystic kidney disease (ADPKD) when mutated, in an article published today in Nature Structural and Molecular Biology.

16.10.2016

Oxford AHSN recognizes the SGC with its annual Public-Private Collaboration Award

by: SGC

SGC wins Oxford AHSN Public-Private Collaboration Award
Shown left-to-right: John Harris (CEO of OBN), Dr. Rab Prinjha (VP of GSK Medicines Research Centre), Chas Bountra (Director SGC Oxford), Dr. Paul Durrands (COO Oxford AHSN), and Dr. Wen Hwa Lee (Director Disease Foundations Network & Strategic Alliances SGC).

12.09.2016

The SGC releases its first crop of TEPs to accelerate drug discovery

by: SGC

Target-enabling packages provide a crucial link between human genetics and disease biology to accelerate drug discovery in cancer and malaria

The SGC has released its first set of Target-Enabling Packages (TEPs) to the scientific community.

16.08.2016

The Alzheimer’s Research UK Drug Discovery Alliance and the SGC announce their collaboration in dementia research

by: SGC

We announce today a groundbreaking partnership between the Alzheimer’s Research UK Drug Discovery Alliance (DDA) 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 enabling new clinical trials, quickly.

16.07.2016

The Chemical Probes Portal Reboot

by: SGC

We are pleased to announce that an updated version of The Chemical Probes Portal is now live. Please visit the portal and look around. In addition to the site’s new look, we’ve added new content, including a lot more data about the existing probes, reviewer ratings and their comments.

NVS-PAK1-1 A Chemical Probe For PAK1

NVS-PAK1-1 is available from Sigma, Cayman Chemical and Tocris.

Its negative control (NVS-PAK1-C) is available for purchase from Tocris and Cayman Chemical.

overview
Probe Negative control

 

NVS-PAK1-1

 

NVS-PAK1-C

Biology of the PAK1 kinase

PAK kinases belong belong to the family of STE kinases, named after the yeast STE7, STE11 and STE20 genes, which form the MAPK cascade, transducing signals from the surface of the cell to the nucleus. The PAK family itself consist of 6 members and can be subdivided into 2 groups Group I PAKs (PAK1-3) and Group II PAKs (PAK 4-6). Group I PAKs (1-3) contain a N-terminal PBD-AIN domain and a kinase domain as well as two SH3-domains and one non-classical SH3-domain.

PAK1 is involved in many intracellular signaling pathways downstream of integrins and receptor-type kinases and plays an important role in in cell adhesion, cytoskeleton dynamics, migration, proliferation, apoptosis, mitosis, and in vesicle-mediated transport processes. It also plays a role in the regulation of insulin secretion in response to elevated glucose levels. PAKs have been shown to activate components of ERK, AKT and WNT signaling pathway and functions as GTPase effector that links the Rho-related GTPases CDC42 and RAC1 to the JNK MAP kinase pathway. PAK1 phosphorylates and activates MAP2K1, and thereby mediates activation of downstream MAP kinases.

PAK1 has been found to be overexpressed and/or activated in many tumor types and its expression levels have been correlated with patient prognosis. In addition Group I PAKs have been implicated in neurodegenerative disorders like Alzheimer and Huntington diseases as well as FXS (fragile X syndrome).

We recommend using NVS1-PAK1-1 at 2.5 uM for PAK1/2 inhibition or 0.25 uM for PAK1 inhibition.

The inactive control at similar concentration has no effect on PAK1/2

NVS-PAK1-1: A Chemical Probe for PAK1

NVS1-PAK-1, a specific allosteric PAK1 inhibitor, has been developed by Novartis [1]

Chemical structure of NVS-PAK1-1 and its inactive control compound NVS-PAK1-C

Co-Crystal Structure

Details of the co-crystal structure of the hit compound and a related compound with the PAK1 kinase domain, click on the 'Co-Crystal structures' tab above for more details

Potency Against Target Family

NVS-PAK1-1 is a potent allosteric inhibitor of PAK1 with an IC 50 of 5 nM for dephosphorylated PAK1 and 6 nM for phosphorylated PAK1 as assessed in a Caliper assay. This data is in good agreement with KD of 7 nM assessed in DiscoverX kinome scan. Inhibition is ATP-competitive, most likely due to indirect competition due to incompatibility of ATP binding with the DFG-out binding conformation of the allosteric compound. The control compound NVS-PAK1-C has more than 100 fold less activity in the respective Caliper assays.

IC Activity against the closest PAK member, PAK2 is over 54 fold. NVS-PAK1-1 has an IC50 of 270 nM against dephosphorylated PAK2 and 720 nM against phosphorylated PAK2 respectively in Caliper assay.

Selectivity

Selectivity of NVS-PAK1-1 was assessed against a panel of 442 kinases (DiscoverX kinome scan) at 10 µM and the compound was found to be exquisitely selective.

Selectivity Beyond Target Family

NVS-PAK1-1 was found to be inactive vs 27 receptors (Novartis panel) at 10µM, with the most potent activity measured of 13 uM against H1 and M1. No activity at 10µM was found in a panel of 48 BRDs.

Cellular Activity

NVS-PAK1-1 potently inhibits autophosphorylation of PAK1 (S144) at 0.25 µM in the Su86.86 cell line and MEK S289 phosphorylation with an IC50 = 0.21 in Su86.86 cells in which PAK2 is downregulated.

properties
NVS-PAK1-1

(S)-3-((2-chloro-5-(2,2-difluoroethyl)-8-fluoro-5H-dibenzo[b,e][1,4]diazepin-11-yl)amino)-N-isopropylpyrrolidine-1-carboxamide

For SDF click here

selectivity profile

Selectivity Within Target family

KINOMEscan

NVS-PAK1-1 is highly selective against 442 kinases tested at 10 µM with a selectivity score (S10-score) of 0.003.

442 Kinases tested at 10 uM

S(35), 3 hits, Sscore = 0.008

S(10), 1 hit, Sscore = 0.003

Selectivity Beyond Target Family

NVS-PAK1-1 shows no cross-reactivity in a panel of 53 proteases (tested at 10 µM), 22 receptors (IC50> 13 µM against closest off-target Phosphodiesterase 4D) and a panel of 28 bromodomains.

Materials and Methods

Differential Scanning Fluorimetry (DSF)

Thermal melting experiments were carried out using an Mx3005p Real Time PCR machine (Stratagene). Proteins were buffered in 10 mM HEPES pH 7.5, 500 mM NaCl and assayed in a 96-well plate at a final concentration of 2 µM in 20 µl volume. Compounds were added at a final concentration of 10 µM. SYPRO Orange (Molecular Probes) was added as a fluorescence probe at a dilution of 1:1000. Excitation and emission filters for the SYPRO-Orange dye were set to 465 nm and 590 nm, respectively. The temperature was raised with a step of 3 °C per minute from 25 °C to 96 °C and fluorescence readings were taken at each interval. Data was analysed as previously reported [3]

KINOMEscan

NVS-PAK1-1  was profiled by KINOMEscan™, a platform that measures the interactions between test compounds and a panel of kinase assays (http://www.discoverx.com), against 442 kinases.

in vitro potency

Potency against Target

Caliper Assay

NVS-PAK1-1 is a potent allosteric inhibitor of PAK1 with an IC50 of 0.005 µM for dephoshorylated PAK1 and 0.006 µM for phosphorylated PAK1 as shown in a Caliper in vitro dephosphorylation assay.

KINOME scan PAK1 Binding Assay.

NVS-PAK1-1 binds to PAK1 with a KD of 7 nM.

Materials and Methods

Caliper assay

Inhibition of PAK1 kinase activity was measured using the Caliper (Caliper LC3000, PerkinElmer) assay. The assay was performed using 384-well microtiter plates. Compounds were tested as 8-point dose responses using PAK1 expressed in E.coli. IC50 values were derived from percent inhibition values at different compound concentrations by non-linear regression analysis.

Binding Assay

Binding assays were performed at DiscoverX coporation in the KINOMEscan assay. Inhibitor binding constants (Kd values) are calculated from duplicate 11-point dose-response curves using Hill equation. Curves were fitted using a non-linear least square fit with the Levenberg-Marquardt algorithm.

cell based assay data

The cellular efficacy of NVS-PAK-1-1 on PAK1 was investigated assessing autophosphorylation in the pancreatic duct carcinoma cell line Su86.86 expressing high levels of PAK1 and PAK2. PAK1 and PAK2 are activated by autophosphorylation on PAK1 (S144) and PAK2 (S141), respectively due to blockage of PDB-domain autoinhibition.

NVS-PAK-1-1 blocks autophosphorylkation at both sites in dose-dependent manner.

Substrate phosphorylation

NVS-PAK-1-1 also inhibits phosphorylation of the downstream substrate MEK1 at Ser289, but only at concentrations that inhibit both PAK1 and PAK2 (6-20 µM).

Antiproliferative effect

Pancreatic duct carcinoma Su86.86 cells treated with NVS-PAK1-1 for 5 days showed inhibition of proliferation with an IC50 of 2 μM due to inhibition of both PAK1 and partial inhibition of PAK2. NVS-PAK1-1 shows growth inhibition with an IC50 of 0.21 μM in SU86.86 cells treated with shPAK2.

We recommend using NVS1-PAK1-1 at 2.5 uM for PAK1/2 inhibition or 0.25 uM for PAK1 inhibition.

Materials and Methods

PAK1/2 SER141/144 TARGET MODULATION ASSAY

Su86.86 pancreatic cancer cell line was grown and seeded in 6-well plate at 500,000 cell density. 10 mM compound diluted in DMSO was further diluted to appropriate concentration (3 fold dilution for 8 concentrations) using growth media and added to each well with cells grown 1 day before. Cells were harvested after 30 minutes of compound treatment and lysed with RIPA buffer (Sigma cat# R0278). Protein concentration of lysates was normalized before loading on SDS-PAGE. Western blot was done as described. pPAK1/2 Ser144/141 antibodies were generated as described. PAK1 and PAK2 antibodies were purchased from Cell Signaling Technology (PAK1 Cat#2602; PAK2 Cat#2608) and were mixed in equal amounts for generation of PAK1/2 signal in western blot.

references

[1] Karpov AS, Amiri P, Bellamacina C, Bellance MH, Breitenstein W, Daniel D, Denay R, Fabbro D, Fernandez C, Galuba I, Guerro-Lagasse S, Gutmann S, Hinh L, Jahnke W, Klopp J, Lai A, Lindvall MK, Ma S, Mobitz H, Pecchi S, Rummel G, Shoemaker K, Trappe J, Voliva C, Cowan-Jacob SW, Marzinzik AL. Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor. ACS medicinal chemistry letters. 2015;6:776-81.

[2] Radu M, Semenova G, Kosoff R, Chernoff J. PAK signalling during the development and progression of cancer.Nature reviews Cancer. 2014;14:13-25.

[3] Wang G, Zhang Q, Song Y, Wang X, Guo Q, Zhang J, Li J, Han Y, Miao Z, Li F. PAK1 regulates RUFY3-mediated gastric cancer cell migration and invasion. Cell death & disease. 2015;6:e1682.

[4] Fang F, Pan J, Li YP, Li G, Xu LX, Su GH, Li ZH, Feng X, Wang J. p21-activated kinase 1 (PAK1) expression correlates with prognosis in solid tumors: A systematic review and meta-analysis. Oncotarget. 2016.

[5] Pinto VI, Mohammadi H, Lee WS, Cheung AH, McCulloch CA. PAK1 is involved in sensing the orientation of collagen stiffness gradients in mouse fibroblasts. Biochimica et biophysica acta. 2015;1853:2526-38.

pk properties
co-crystal structures

The co-crystal structure of a related compound with PAK1 has been solved with a resolution of 1.99Å. The key features are

  • Binding in an allosteric binding site in DFG out conformation
  • NVS-PAK1-1 strengthens interaction with crucial β4 carbonyl
  • Shift of the aC helix opens pocket for tert-butyl group; non-conserved Asn affected by the move moving out into the solvent provides rationale for selectivity over PAK2, which has a Leu in the corresponding position

synthetic schemes
materials and methods

A-395 A Chemical Probe For EED

This probe (as hydrochloride) and its inactive control are available from Sigma (A-395 and A-395N) and Cayman (A-395).

overview
Probe Negative control

 

A-395

 

A-395N

A collaboration between Abbvie and the SGC has resulted in the discovery of A-395, the first potent and selective chemical probe for EED. The in vitro activity of A-395 includes potent binding to EED with Ki = 0.4 nM,  inhibits the PRC2 complex with IC50 = 34 nM for methylation of H3K27 and greater than 100-fold selectivity over other histone methyltransferases and non-epigenetic targets. In cellular assays, A-395 inhibits the PRC2 complex (thus inhibiting the formation of H3K27me3) with IC50 = 90 nM (RD rhabdoid tumor cell line; 3 days).

A closely related compound, A-395N, exhibits no activity in the biochemical and cellular assays, and is an ideal control compound for cellular studies.

in vitro potency

A-395 potently inhibited the formation of H3K27me3 (via antagonizing EED in the trimeric PRC2 complex (EZH2:EED:SUZ12)) with IC50 = 34 ± 2 nM (Hill Slope = 0.7)

properties
Probe Negative control

 

A-395

 

A-395N

Physical and chemical properties for A-395
Molecular weight486.2
Molecular formulaC26H35FN4O2S
IUPAC name1-(5-fluoro-bicyclo[4.3.0]nona-1,3,5-trien-7-yl)-N,N-dimethyl-4-(4-(4-methylsulfonyl-piperazin-1-yl)-phenyl)-pyrrolidin-3-amine
MollogP4.425
PSA39.69
No. of chiral centres3
No. of rotatable bonds5
No. of hydrogen bond acceptors7
No. of hydrogen bond donors0
Physical and chemical properties for A-395N
Molecular weight

442.2

 

Molecular formulaC24H34N4O2S
IUPAC name1-benzyl-N,N-dimethyl-4-(4-(4-methylsulfonyl-piperazin-1-yl)-phenyl)-pyrrolidin-3-amine
MollogP3.158
PSA40.58
No. of chiral centres2
No. of rotatable bonds6
No. of hydrogen bond acceptors7
No. of hydrogen bond donors0
  • SMILES:
  • A-395: CN([C@H]1CN(C2CCC3=CC=CC(F)=C23)C[C@@H]1C4=CC=C(N5CCN(S(C)(=O)=O)CC5)C=C4)C
  • A-395N: CN([C@@H]1CN(C[C@H]1C2=CC=C(N3CCN(S(C)(=O)=O)CC3)C=C2)CC4=CC=CC=C4)C
  • InChI:
  • InChIKey:
  • A-395: REVJNSVNICWODC-KIDMSAQOSA-N
  • A-395N: VEABDKBNQNHHCB-BJKOFHAPSA-N
selectivity profile

Selectivity 

Selectivity of A-395 against 32 methyltransferase enzymes


 

Selectivity of a) A-395 and b) A-395N relative to epigenetic readers using a thermal shift assay


A-395 inhibits the activity of the PRC2 complex in cells – high-content screening assay of RD Rhabdoid tumor cell line treated for 72 hours

in vitro potency
cell based assay data
references
pk properties
co-crystal structures

Please wait whilst the interactive viewer is loaded!

Main features

synthetic schemes
materials and methods

LLY-283 A Chemical Probe For PRMT5.

This probe is available from Sigma and Cayman Chemical.

Its negative control (LLY-284) is available for purchase from Sigma.

overview
Probe Negative control

 

LLY-283

 

LLY-284

A collaboration between Eli Lilly and the SGC has resulted in the identification of LLY-283, the first potent and selective SAM-competitive chemical probe for PRMT5. The in vitro activity of LLY-283 includes potent inhibition of PRMT5 enzyme activity with IC50 = 20 nM for methylation of an H4R3 derived peptide substrate, and greater than 100-fold selectivity over other histone methyltransferases and non-epigenetic targets. In cellular assays, LLY-283 inhibits the methylation of SmBB’  with IC50 = 25 nM (MCF7 cells; 3 days) and also affects MDM4 splicing with IC50-relative of 40 nM (A375 cells; 3 days).

A closely related compound, LLY-284, is less potent in the biochemical assay and is an ideal control compound for cellular studies.

properties
Probe Negative control

 

LLY-283

 

LLY-284

Physical and chemical properties for LLY-283
Molecular weight342.1
Molecular formulaC17H18N4O4
IUPAC name2-(5-amino-2,4,9-triaza-bicyclo[4.3.0]nona-1(6),2,4,7-tetraen-9-yl)-5-(hydroxy-phenyl-methyl)-tetrahydro-furan-3,4-diol
MollogP-0.1422
PSA98.65
No. of chiral centres5
No. of rotatable bonds3
No. of hydrogen bond acceptors6
No. of hydrogen bond donors5
Physical and chemical properties for LLY-284 (Negative Control)
Molecular weight342.1
Molecular formulaC17H18N4O4
IUPAC name2-(5-amino-2,4,9-triaza-bicyclo[4.3.0]nona-1(6),2,4,7-tetraen-9-yl)-5-(hydroxy-phenyl-methyl)-tetrahydro-furan-3,4-diol
MollogP-0.1422
PSA98.65
No. of chiral centres5
No. of rotatable bonds3
No. of hydrogen bond acceptors6
No. of hydrogen bond donors5
  • SMILES:
  • LLY-283: NC1=NC=NC2=C1C=CN2[C@H](O3)[C@H](O)[C@H](O)[C@H]3[C@@H](C4=CC=CC=C4)O
  • LLY-284: NC1=NC=NC2=C1C=CN2[C@H](O3)[C@H](O)[C@H](O)[C@H]3[C@H](C4=CC=CC=C4)O
  • InChI:
  • LLY-284: InChI=1S/C17H18N4O4/c18-15-10-6-7-21(16(10)20-8-19-15)17-13(24)12(23)14(25-17)11(22)9-4-2-1-3-5-9/h1-8,11-14,17,22-24H,(H2,18,19,20)/t11?,12-,13+,14?,17+/m0/s1
  • InChIKey:
  • LLY-283: WWOOWAHTEXIWBO-QFRSUPTLSA-N
  • LLY-284: WWOOWAHTEXIWBO-CNUKPYSBSA-N
selectivity profile
in vitro potency
cell based assay data

Enzyme inhibition assay for LLY-283 and its negative control (LLY-284). The IC50 values of 22 ± 3 nM (Hill Slope of 1) and 1074 ± 53 nM (Hill Slope of 1.2) were determined for LLY-283 (x) and LLY-284 (x), respectively.

 

 

references

Zahid Q. Bonday, Guillermo S. Cortez, Michael J. Grogan, Stephen Antonysamy,  Ken Weichert, Thomas J. Raub, Wayne P. Bocchinfuso,  Fengling Li, Steven Kennedy, Binghui Li, Mary M. Mader, Cheryl H. Arrowsmith, Robert M. Campbell, Peter J. Brown,  Mohammad S. Eram, Magdalena M. Szewczyk, Masoud Vedadi, Dalia Barsyte-Lovejoy. LLY-283, a Potent and Selective Inhibitor of Arginine Methyltransferase 5, PRMT5, with antitumor activity. ACS Med. Chem. Lett. (2018) DOI: 10.1021/acsmedchemlett.8b00014

pk properties
co-crystal structures

Please wait whilst the interactive viewer is loaded!

PDB 6CKC
Main features

  1. Tetrameric structure of PRMT5 with LLY-283 
  2. Structure of SAM analog with substrate (PDB: 4GQB) 
  3. Details of LLY-283 binding pocket with H-bonds shown 
  4. Overlay of substrate, LLY-283, and EPZ015666 structures highlighting binding pocket differences 
synthetic schemes
materials and methods

BAY-299 A probe for BRD1 and TAF1

This probe is available from Tocris, Sigma and Cayman Chemical.

The inactive control is available from Sigma.

overview
Probe Negative control

 

BAY-299

 

BAY-364

The BRPF (BRomodomain and PHD Finger) family consists of 3 members BRPF1, BRPF2 (also known as BRD1) and BRPF3 that act as scaffolding proteins to assemble HAT complexes of the MOZ/MORF family (MOZ, Ybf2/Sas3, Sas2, and Tip60). These MYST complexes have a tetrameric core containing BRPF, the tumour suppressor ING and Eaf6/EPC (enhancer of polycomb)-related scaffold subunits. MYST complexes play crucial roles in DNA repair, recombination, and replication as well as in transcription activation. MOZ is frequently translocated in acute myeloid leukemia and has an essential role in development and maintenance of hematopoietic stem cells[1].

Transcription initiation factor TFIID subunits 1 (TAF1) is a component of the STAGA complex, which contains TRRAP, GCN5, TFIID, CBP/P300, mediator and Sp1, TAF1 is susceptible to oncogenic activation by MYC. Moreover, TAF1 has been shown to block p53 activity and inactivation of TAF1 triggers a DNA damage response. Additionally, the TFIID complex is vital to stem cell reprogramming. There have been few reports of selective inhibitors of TAF1 which are needed to help elucidate its biological role and potentially function to inhibit cancer cell growth and survival.

In a collaborative effort Bayer and the SGC have identified and characterised BAY-299 as a potent and selective inhibitor of BRD1 (BROMOscan® [2] IC50 6nM) and the second bromodomain of TAF1 (BROMOscan® [2] IC50 13nM). BAY-299 is selective over other bromodomains; >30-fold selective over the other members of the BRPF family, >30-fold selective over close neighbours BRD9 and ATAD2 and >300-fold selective over BRD4. BAY-299 has <1uM activity in the BRD1 and TAF1 NanoBRET™ cell assays [3]. BAY-299 has a molecular weight of 429.5 and is soluble to 10mg/L in aqueous solutions. The structurally similar BAY-364  (MW 401.4) is inactive against BRD1 (>20uM), has moderate activity against TAF1 (3uM) and is suitable for use as a negative control.

properties
Probe Negative control

 

BAY-299

 

BAY-364

Physical and chemical properties for BAY-299
Molecular weight429.2
Molecular formulaC25H23N3O4
IUPAC name6-(3-Hydroxypropyl)-2-(1,3,6-trimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-1H-benzo[de]isoquinoline-1,3(2H)-dione
MollogP4.33
PSA62.28
No. of chiral centres0
No. of rotatable bonds4
No. of hydrogen bond acceptors7
No. of hydrogen bond donors1
Physical and chemical properties for BAY-364 (Negative Control)
Molecular weight401.1
Molecular formulaC23H19N3O4
MollogP3.844
PSA71.76
No. of chiral centres0
No. of rotatable bonds4
No. of hydrogen bond acceptors7
No. of hydrogen bond donors2
  • SMILES:
  • BAY-299: CC1=C(N2C(C3=CC=CC4=C(C=CC(C2=O)=C34)CCCO)=O)C=C(N(C(N5C)=O)C)C5=C1
  • BAY-364: CN1C(NC2=C1C=CC(N3C(C4=CC=CC5=C4C(C3=O)=CC=C5CCCO)=O)=C2)=O
  • InChI:
  • BAY-299: InChI=1S/C25H23N3O4/c1-14-12-20-21(27(3)25(32)26(20)2)13-19(14)28-23(30)17-8-4-7-16-15(6-5-11-29)9-10-18(22(16)17)24(28)31/h4,7-10,12-13,29H,5-6,11H2,1-3H3
  • BAY-364: InChI=1S/C23H19N3O4/c1-25-19-10-8-14(12-18(19)24-23(25)30)26-21(28)16-6-2-5-15-13(4-3-11-27)7-9-17(20(15)16)22(26)29/h2,5-10,12,27H,3-4,11H2,1H3,(H,24,30)
  • InChIKey:
  • BAY-299: OFWWWKWUCDUISA-UHFFFAOYSA-N
  • BAY-364: OGFBLTYSHLJDTR-UHFFFAOYSA-N
selectivity profile

Selectivity Against Non Target Family

BAY-299 and BAY-364 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. BAY-299 showed binding to A1 receptor (48%), Cl- channel (GABA-gated) (23%), PDE2A1 (49%) and PDE5 (-2%). BAY-364 was clean.


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in vitro potency
cell based assay data
references

1. Klein BJ, Lalonde ME, Côté J, Yang XJ, Kutateladze TG., Crosstalk between epigenetic readers regulates the MOZ/MORF HAT complexes. Epigenetics. 2014, 9(2), 186-93

2. DiscoverX https://www.discoverx.com/services/drug-discovery-development-services/epigenetic-profiling/bromoscan

3. Promega http://www.promega.com/a/forms/custom-assays/nanobret-protein-interaction.html

4. Benzo-isoquinoline-diones As Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains Léa Bouché, Clara D. Christ, Stephan Siegel, Amaury E. Fernández-Montalván, Simon J. Holton, Oleg Fedorov, Antonius ter Laak, Tatsuo Sugawara, Detlef Stöckigt, Cynthia Tallant, James M. Bennett, Octovia P Monteiro, Laura Díaz-Sáez, Paulina Siejka, Julia Meier, Vera Puetter, Joerg Weiske, Susanne Müller, Kilian Veit Marcus Huber, Ingo V. Hartung, and Bernard Haendler. J. Med. Chem .April 12, 2017

pk properties
co-crystal structures
synthetic schemes
materials and methods