| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| 10mg |
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| Other Sizes |
| Targets |
SpCas9 ( IC50 = 22 μM )
BRD0539 targets Streptococcus pyogenes Cas9 (SpCas9), the CRISPR-associated endonuclease used in genome editing applications. The compound inhibits SpCas9 by disrupting the interaction between SpCas9 and the protospacer adjacent motif (PAM), which is required for DNA binding and cleavage. BRD0539 is cell-permeable and reversibly inhibits SpCas9. It does not interfere with the SpCas9:gRNA interaction. |
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| ln Vitro |
In a dose-dependent manner, BRD0539 inhibits the development of the DNA-bound state. The disruption brought about by the 4PAM DNA is weakened by BRD0539[1]. The interaction between SpCas9 and gRNA is not disrupted by BRD0539[1]. Further demonstrating the specificity of BRD0539, while it is able to inhibit SpCas9 in the eGFP-disruption experiment, it is unable to inhibit FnCpf1, a structurally distinct CRISPR-associated nuclease, in the same assay[1].
In vitro studies demonstrate that BRD0539 inhibits SpCas9 with an apparent IC50 of 22 μM in a DNA cleavage assay. The compound dose-dependently blocks the formation of the DNA-bound state. It disrupts the interaction between SpCas9 and PAM. BRD0539 is stable in human plasma and does not interfere with the SpCas9:gRNA interaction. The compound is cell-permeable. |
| ln Vivo |
No detailed in vivo activity data has been published for BRD0539. The compound has been primarily characterized in vitro as a research tool for modulating CRISPR-Cas9 activity. Its cell-permeable and non-toxic properties suggest that it could have potential for in vivo applications in genome editing research. Further studies would be needed to evaluate its efficacy in animal models.
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| Enzyme Assay |
The SpCas9 inhibitory activity of BRD0539 can be assessed using in vitro DNA cleavage assays. In a typical assay, recombinant SpCas9 protein is incubated with guide RNA, a DNA substrate containing the target sequence and PAM, and varying concentrations of BRD0539. The cleavage of the DNA substrate is analyzed by gel electrophoresis, and the IC50 is calculated. The IC50 for SpCas9 inhibition is 22 μM. The compound's ability to disrupt SpCas9-PAM interaction can be assessed using binding assays.
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| Cell Assay |
This eGFP-disruption assay reverses the BRD0539-mediated inhibition of SpCas9 by utilizing 2×105 U2OS.eGFP.The SpCas9:gRNA complex is nucleofected into PEST cells. In a 96-well plate, roughly 22,000 transfected cells/well are plated in four duplicates with 15 μM BRD0539 or DMSO. For the AcrIIA4 reversibility experiments, a preformed SpCas9:gRNA (10 pmol) is nucleofected into U2OS.eGFP.PEST cells using the previously described protocol after being incubated with AcrIIA4 (5×) for 10 min. At the designated time point (2–24 h), the media is replaced with new media that does not contain BRD0539/AcrIIA4, and the cells are allowed to grow until 24 h post-nucleofection.
The cellular activity of BRD0539 is assessed using cell-based genome editing assays. Cells are transfected with SpCas9 and guide RNA, and treated with varying concentrations of BRD0539. Genome editing efficiency is measured by sequencing or by using reporter assays. The compound's effect on SpCas9 activity is assessed. Cytotoxicity is assessed using MTT assays to confirm the compound's non-toxic profile. |
| Animal Protocol |
No detailed in vivo animal model data has been published for BRD0539. The compound has been primarily characterized in vitro as a research tool for inhibiting CRISPR-Cas9. Future studies may involve the use of animal models to assess the in vivo activity of BRD0539 in modulating genome editing. The compound's cell-permeable and non-toxic properties suggest potential for in vivo applications.
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| ADME/Pharmacokinetics |
No detailed pharmacokinetic data has been published for BRD0539. The compound has a molecular weight of approximately 435.5 g/mol and a molecular formula of C25H25FN2O3S. It is stable in human plasma. Further studies would be needed to characterize its absorption, distribution, metabolism, and excretion properties, including oral bioavailability, plasma protein binding, clearance, and half-life.
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| Toxicity/Toxicokinetics |
BRD0539 is a non-toxic inhibitor of CRISPR-Cas9. No detailed toxicity data has been published. The compound is cell-permeable and does not cause cytotoxicity in cell-based assays. Comprehensive toxicology studies would be required to evaluate its safety profile for potential therapeutic development. The compound is intended for research use only.
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| References | |
| Additional Infomation |
BRD0539 (CAS# 1403838-79-8) is a cell-permeable and non-toxic inhibitor of Streptococcus pyogenes Cas9 (SpCas9) with an apparent IC50 of 22 μM in an in vitro DNA cleavage assay. The compound reversibly inhibits SpCas9 by disrupting the SpCas9-PAM interaction. It is stable in human plasma and does not interfere with the SpCas9:gRNA interaction. The molecular formula is C25H25FN2O3S. BRD0539 is used as a research tool for modulating CRISPR-Cas9 activity.
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| Molecular Formula |
C25H25FN2O3S
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| Exact Mass |
452.16
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| Elemental Analysis |
C, 66.35; H, 5.57; F, 4.20; N, 6.19; O, 10.61; S, 7.08
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| CAS # |
1403838-79-8
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| PubChem CID |
54666326
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| Appearance |
Off-white to light yellow solid powder
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| LogP |
4.2
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
4
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| Heavy Atom Count |
32
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| Complexity |
751
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| Defined Atom Stereocenter Count |
3
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| SMILES |
CC1=CC=C(C=C1)S(=O)(=O)N2CC[C@H]3[C@@H]2C4=C(C=CC(=C4)C5=CC=CC=C5F)N[C@H]3CO
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| InChi Key |
CZOIXFMISSBIJL-DCEDVJGZSA-N
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| InChi Code |
InChI=1S/C25H25FN2O3S/c1-16-6-9-18(10-7-16)32(30,31)28-13-12-20-24(15-29)27-23-11-8-17(14-21(23)25(20)28)19-4-2-3-5-22(19)26/h2-11,14,20,24-25,27,29H,12-13,15H2,1H3/t20-,24+,25-/m1/s1
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| Chemical Name |
[(3aR,4R,9bR)-8-(2-fluorophenyl)-1-(4-methylphenyl)sulfonyl-2,3,3a,4,5,9b-hexahydropyrrolo[3,2-c]quinolin-4-yl]methanol
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| Synonyms |
BRD0539; BRD 0539; BRD-0539
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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) |
DMSO : 91~100 mg/mL (201.1~221 mM)
Ethanol : ~31 mg/mL (~68.5 mM) |
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (5.52 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 2.5 mg/mL (5.52 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. (Please use freshly prepared in vivo formulations for optimal results.) |
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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