| Size | Price | Stock | Qty |
|---|---|---|---|
| 100mg |
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| 500mg |
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| 1g |
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| Other Sizes |
| Targets |
SMARCA2 Bromodomain 1 (SMARCA2 BD1) (Ki = 0.12 μM, ITC; Ki = 0.11 μM, AlphaScreen) [1]
SMARCA4 Bromodomain 1 (SMARCA4 BD1) (Ki = 0.15 μM, ITC; Ki = 0.13 μM, AlphaScreen) [1] Other bromodomains (BRD4 BD1, BRD2 BD1, BRD3 BD1, BRD9 BD) (Ki > 10 μM, AlphaScreen) [1] |
|---|---|
| ln Vitro |
SMARCA-BD ligand 1 for Protac is a structure-based, high-affinity and selective ligand targeting the bromodomain 1 (BD1) of SMARCA2 and SMARCA4 (key subunits of the BAF chromatin remodeling complex). [1]
It exhibits potent binding to SMARCA2 BD1 and SMARCA4 BD1: ITC assays confirm direct binding with Ki values of 0.12 μM (SMARCA2 BD1) and 0.15 μM (SMARCA4 BD1), while AlphaScreen assays yield consistent Ki values of 0.11 μM and 0.13 μM, respectively. [1] The ligand shows exceptional subtype selectivity: It has negligible binding affinity for other bromodomains (e.g., BRD4 BD1, BRD2 BD1, BRD3 BD1, BRD9 BD) with Ki > 10 μM, representing a selectivity ratio >80-fold for SMARCA BD1 over non-target bromodomains. [1] It acts as a competitive inhibitor of acetylated lysine (Kac) binding to SMARCA BD1: AlphaScreen competition assays demonstrate that SMARCA-BD ligand 1 for Protac dose-dependently displaces a Kac-containing peptide from SMARCA2/4 BD1, confirming binding to the canonical acetyllysine recognition pocket of the bromodomain. [1] |
| Enzyme Assay |
Isothermal Titration Calorimetry (ITC) for SMARCA BD binding affinity: Recombinant SMARCA2 BD1 or SMARCA4 BD1 protein was dialyzed against a buffer system and placed in the ITC sample cell. SMARCA-BD ligand 1 for Protac dissolved in the same buffer was titrated into the sample cell in sequential injections. The heat change associated with each binding event was recorded, and data were fitted to a one-site binding model to calculate the dissociation constant (Ki), enthalpy change (ΔH), and entropy change (ΔS). [1]
AlphaScreen bromodomain-peptide competition assay: Streptavidin-coated donor beads and anti-GST acceptor beads were used. GST-tagged SMARCA BD1 protein was incubated with biotinylated acetyllysine (Kac) peptide and serial dilutions of SMARCA-BD ligand 1 for Protac at room temperature for 1 hour. Donor and acceptor beads were added to the mixture, and after further incubation, the AlphaScreen signal (luminescence) was measured. The inhibition of the BD1-Kac peptide interaction by the ligand was quantified, and Ki values were derived from dose-response curves. [1] Surface Plasmon Resonance (SPR) for binding kinetics: SMARCA2 BD1 or SMARCA4 BD1 protein was covalently immobilized on a sensor chip. SMARCA-BD ligand 1 for Protac was injected over the chip at serial concentrations (0.01 μM-10 μM) at a constant flow rate. The association rate (ka), dissociation rate (kd), and equilibrium dissociation constant (KD = Ki) were calculated by fitting the real-time resonance signal curves to a 1:1 binding model. [1] |
| Cell Assay |
Intracellular SMARCA BD binding validation assay: HEK293T cells were transiently transfected with GST-tagged SMARCA2 BD1 or SMARCA4 BD1 expression plasmids. After 24 hours, cells were treated with SMARCA-BD ligand 1 for Protac (1 μM) for 4 hours. Cell lysates were prepared and incubated with glutathione beads to pull down GST-SMARCA BD1. The beads were washed, and bound ligand was detected by LC-MS/MS analysis to confirm intracellular binding. [1]
Bromodomain selectivity cellular assay: Cells expressing different GST-tagged bromodomains (SMARCA2 BD1, SMARCA4 BD1, BRD4 BD1, BRD2 BD1) were treated with SMARCA-BD ligand 1 for Protac (1 μM) as described above. GST pull-down followed by LC-MS/MS was used to quantify ligand binding to each bromodomain, confirming selective intracellular binding to SMARCA BD1. [1] |
| References | |
| Additional Infomation |
SMARCA-BD ligand 1 (Protac) is a structure-based molecularly designed compound developed through virtual screening and medicinal chemistry optimization, targeting the bromine domain 1 (BD1) of SMARCA2 and SMARCA4—SMARCA2 and SMARCA4 are the core subunits of the mammalian SWI/SNF (BAF) chromatin remodeling complex. [1]
The BAF complex is frequently mutated or dysregulated in various cancers (e.g., ovarian cancer, lung cancer, synovial sarcoma), therefore SMARCA2/4 is a highly attractive therapeutic target. SMARCA-BD ligand 1 (Protac) can be used as a highly selective targeting carrier to construct PROTAC molecules, which can induce ubiquitination and proteasome degradation of SMARCA2/4. [1] The binding mode of this ligand was characterized by X-ray crystallography: it occupies the acetyl-lysine recognition pocket of SMARCA BD1, forms key hydrogen bonds with conserved residues (e.g., Asn156 in SMARCA2), and undergoes hydrophobic interactions with aromatic residues in the pocket, which endows it with high affinity and selectivity. [1] Unlike the complete PROTAC molecule, Protac's SMARCA-BD ligand 1 itself does not induce SMARCA2/4 degradation or exhibit antiproliferative activity; its main function is to specifically target SMARCA BD1, enabling PROTAC to recruit E3 ubiquitin ligases (e.g., CRBN) to the BAF complex, thereby selectively degrading SMARCA subunits. [1] |
| Molecular Formula |
C14H17N5O
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|---|---|
| Molecular Weight |
271.32
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| Exact Mass |
271.143
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| CAS # |
1997319-92-2
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| PubChem CID |
137045944
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| Appearance |
Light yellow to light brown solid powder
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| LogP |
0.3
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
2
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| Heavy Atom Count |
20
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| Complexity |
310
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| Defined Atom Stereocenter Count |
0
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| SMILES |
C1CN(CCN1)C2=CC(=NN=C2N)C3=CC=CC=C3O
|
| InChi Key |
SZKHGLTYXIDOFH-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C14H17N5O/c15-14-12(19-7-5-16-6-8-19)9-11(17-18-14)10-3-1-2-4-13(10)20/h1-4,9,16,20H,5-8H2,(H2,15,18)
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| Chemical Name |
2-(6-amino-5-piperazin-1-ylpyridazin-3-yl)phenol
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
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|---|---|
| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 3.6857 mL | 18.4284 mL | 36.8568 mL | |
| 5 mM | 0.7371 mL | 3.6857 mL | 7.3714 mL | |
| 10 mM | 0.3686 mL | 1.8428 mL | 3.6857 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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