SGI-1027

DNMT inhibitor CAS# 1020149-73-8

SGI-1027

Catalog No. BCC4588----Order now to get a substantial discount!

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Chemical structure

SGI-1027

3D structure

Chemical Properties of SGI-1027

Cas No. 1020149-73-8 SDF Download SDF
PubChem ID 24858111 Appearance Powder
Formula C27H23N7O M.Wt 461.52
Type of Compound N/A Storage Desiccate at -20°C
Solubility DMSO : 27 mg/mL (58.50 mM; Need ultrasonic and warming)
H2O : < 0.1 mg/mL (insoluble)
Chemical Name N-[4-[(2-amino-6-methylpyrimidin-4-yl)amino]phenyl]-4-(quinolin-4-ylamino)benzamide
SMILES CC1=CC(=NC(=N1)N)NC2=CC=C(C=C2)NC(=O)C3=CC=C(C=C3)NC4=CC=NC5=CC=CC=C54
Standard InChIKey QSYLKMKIVWJAAK-UHFFFAOYSA-N
Standard InChI InChI=1S/C27H23N7O/c1-17-16-25(34-27(28)30-17)32-20-10-12-21(13-11-20)33-26(35)18-6-8-19(9-7-18)31-24-14-15-29-23-5-3-2-4-22(23)24/h2-16H,1H3,(H,29,31)(H,33,35)(H3,28,30,32,34)
General tips For obtaining a higher solubility , please warm the tube at 37 ℃ and shake it in the ultrasonic bath for a while.Stock solution can be stored below -20℃ for several months.
We recommend that you prepare and use the solution on the same day. However, if the test schedule requires, the stock solutions can be prepared in advance, and the stock solution must be sealed and stored below -20℃. In general, the stock solution can be kept for several months.
Before use, we recommend that you leave the vial at room temperature for at least an hour before opening it.
About Packaging 1. The packaging of the product may be reversed during transportation, cause the high purity compounds to adhere to the neck or cap of the vial.Take the vail out of its packaging and shake gently until the compounds fall to the bottom of the vial.
2. For liquid products, please centrifuge at 500xg to gather the liquid to the bottom of the vial.
3. Try to avoid loss or contamination during the experiment.
Shipping Condition Packaging according to customer requirements(5mg, 10mg, 20mg and more). Ship via FedEx, DHL, UPS, EMS or other couriers with RT, or blue ice upon request.

Biological Activity of SGI-1027

DescriptionSGI-1027 is an inhibitor of DNMT with IC50 values of 6, 8, 7.5 μM for DNMT1, DNMT3A, and DNMT3B, respectively
TargetsDNMT1DNMT3BDNMT3A   
IC506 μM7.5 μM8 μM    

Protocol

Kinase Assay [1]
To determine the nature of inhibition of DNMTase activity by SGI-1027, DNMT1 enzyme activity is measured in presence of a fixed concentration of SGI-1027 (0, 2.5, 5, and 10 μM) while one of the two (Ado-Met or DNA) is varied in a particular reaction mixture. At a fixed concentration of DNA (500 ng) varying concentrations of Ado-Met used are from 25-500 nM, respectively. Similarly, final DNA concentrations are varied from (25-500 ng) at 75 nM Ado-Met[1].

Cell Assay [1]
Rat hepatoma H4IIE cells are grown in DMEM supplemented with fetal bovine serum (10%) and calf serum (10%). Cells are seeded into 96-well plates and after 48 h exposed to SGI-1027 at concentrations ranging from 0 to 300 µM. The solubility is determined by Nephalometry techniques immediately after dosing and before harvesting the cells at 24 h. Following the exposure period, the cells or their supernatant (culture medium) are analyzed for changes in cell proliferation (propidium iodide), membrane leakage (α-GST), mitochondrial function [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and cellular ATP], oxidative stress (intracellular GSH and 8-isoprostane), and apoptosis (caspase-3). The half-maximal toxic concentration (TC50) is determined from the dose-response curves[1].

References:
[1]. Datta J, et al. A new class of quinoline-based DNA hypomethylating agents reactivates tumor suppressor genes by blocking DNA methyltransferase 1 activity and inducing its degradation. Cancer Res. 2009 May 15;69(10):4277-85. [2]. Rilova E, et al. Design, synthesis and biological evaluation of 4-amino-N- (4-aminophenyl)benzamide analogues of quinoline-based SGI-1027 as inhibitors of DNA methylation. ChemMedChem. 2014 Mar;9(3):590-601.

SGI-1027 Dilution Calculator

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SGI-1027 Molarity Calculator

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Preparing Stock Solutions of SGI-1027

1 mg 5 mg 10 mg 20 mg 25 mg
1 mM 2.1668 mL 10.8338 mL 21.6675 mL 43.3351 mL 54.1688 mL
5 mM 0.4334 mL 2.1668 mL 4.3335 mL 8.667 mL 10.8338 mL
10 mM 0.2167 mL 1.0834 mL 2.1668 mL 4.3335 mL 5.4169 mL
50 mM 0.0433 mL 0.2167 mL 0.4334 mL 0.8667 mL 1.0834 mL
100 mM 0.0217 mL 0.1083 mL 0.2167 mL 0.4334 mL 0.5417 mL
* Note: If you are in the process of experiment, it's necessary to make the dilution ratios of the samples. The dilution data above is only for reference. Normally, it's can get a better solubility within lower of Concentrations.

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Background on SGI-1027

SGI-1027 is an inhibitor of DNMT with IC50 values of 12.5μM, 8μM and 7.5μM, respectively for DNMT1, DNMT3A and DNMT3B [1].

SGI-1027 shows inhibition with mammalian DNMTs and bacterial M. SssI in vitro. Both the endogenous and recombinant DNMTs can be inhibited by SGI-1027. The mechanism of this inhibition is that SGI-1027 competes with Ado-Met but not the substrate DNA within the cofactor binding site of the enzyme. SGI-1027 inhibits DNA methylation through directly inhibiting DNMTs [1].

In cancer cells, many TSGs are silenced due to hypermethylation of CpG islands in their promoters. SGI-1027 can demethylates these CpG islands and reactivate the silenced TSGs. In RKO cells, prolonged treatment of SGI-1027 induces reexpression of P16 and TIMP3 genes. Moreover, SGI-1027 is found to cause selective degradation of DNMT1 via proteasomal pathway [1].

References:
[1] Datta J, Ghoshal K, Denny WA, Gamage SA, Brooke DG, Phiasivongsa P, Redkar S, Jacob ST. A new class of quinoline-based DNA hypomethylating agents reactivates tumor suppressor genes by blocking DNA methyltransferase 1 activity and inducing its degradation. Cancer Res. 2009 May 15;69(10):4277-85.

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References on SGI-1027

Synthetic approaches to DNMT inhibitor SGI-1027 and effects on the U937 leukemia cell line.[Pubmed:23402879]

Bioorg Med Chem Lett. 2013 Mar 15;23(6):1631-5.

The known DNMT inhibitor SGI-1027 4 has been synthesized using as key steps Pd-catalyzed Ar-N bond formation reactions performed in a sequential or convergent manner. In the former approach, a by-product, which corresponds to the incorporation of two units of 4-chloroquinoline, was also isolated. The biological effects of compound 4 in the U937 human leukemia cell line are also described.

Molecular modeling studies of the novel inhibitors of DNA methyltransferases SGI-1027 and CBC12: implications for the mechanism of inhibition of DNMTs.[Pubmed:23637988]

PLoS One. 2013 Apr 25;8(4):e62152.

DNA methylation is an epigenetic modification that regulates gene expression by DNA methyltransferases (DNMTs). Inhibition of DNMTs is a promising approach for cancer therapy. Recently, novel classes of the quinolone-based compound, SGI-1027, and RG108-procainamide conjugates, CBC12, have been identified as potent DNMT inhibitors. In this work, we report comprehensive studies using induced-fit docking of SGI-1027 and CBC12 with human DNMT1 and DNMT3A. The docking was performed in the C-terminal MTase catalytic domain, which contains the substrate and cofactor binding sites, in the presence and absence of other domains. Induced-fit docking predicts possible binding modes of the ligands through the appropriate structural changes in the receptor. This work suggests a hypothesis of the inhibitory mechanisms of the new inhibitors which is in agreement with the reported autoinhibitory mechanism. The insights obtained in this work can be used to design DNMT inhibitors with novel scaffolds.

Design, synthesis and biological evaluation of 4-amino-N- (4-aminophenyl)benzamide analogues of quinoline-based SGI-1027 as inhibitors of DNA methylation.[Pubmed:24678024]

ChemMedChem. 2014 Mar;9(3):590-601.

Quinoline derivative SGI-1027 (N-(4-(2-amino-6-methylpyrimidin-4-ylamino)phenyl)-4-(quinolin-4-ylamino)benzamid e) was first described in 2009 as a potent inhibitor of DNA methyltransferase (DNMT) 1, 3A and 3B. Based on molecular modeling studies, performed using the crystal structure of Haemophilus haemolyticus cytosine-5 DNA methyltransferase (MHhaI C5 DNMT), which suggested that the quinoline and the aminopyridimine moieties of SGI-1027 are important for interaction with the substrates and protein, we designed and synthesized 25 derivatives. Among them, four compounds-namely the derivatives 12, 16, 31 and 32-exhibited activities comparable to that of the parent compound. Further evaluation revealed that these compounds were more potent against human DNMT3A than against human DNMT1 and induced the re-expression of a reporter gene, controlled by a methylated cytomegalovirus (CMV) promoter, in leukemia KG-1 cells. These compounds possessed cytotoxicity against leukemia KG-1 cells in the micromolar range, comparable with the cytotoxicity of the reference compound, SGI-1027. Structure-activity relationships were elucidated from the results. First, the presence of a methylene or carbonyl group to conjugate the quinoline moiety decreased the activity. Second, the size and nature of the aromatic or heterocycle subsitutents effects inhibition activity: tricyclic moieties, such as acridine, were found to decrease activity, while bicyclic substituents, such as quinoline, were well tolerated. The best combination was found to be a bicyclic substituent on one side of the compound, and a one-ring moiety on the other side. Finally, the orientation of the central amide bond was found to have little effect on the biological activity. This study provides new insights in to the structure-activity relationships of SGI-1027 and its derivative.

Description

SGI-1027 is a DNA methyltransferase (DNMT) inhibitor, with IC50s of 7.5 μM, 8 μM, and 12.5 μM for DNMT3B, DNMT3A, and DNMT1 with poly(dI-dC) as substrate.

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