PROTAC BRD4 Degrader-9

 CAS No.: 2417370-42-2  Cat No.: BP-400180  Purity: 98% 4.5  

PROTAC BRD4 Degrader-9 is a sophisticated chemical compound designed for targeted protein degradation, specifically targeting the bromodomain-containing protein 4 (BRD4). This degrader operates by binding to the BRD4 protein at its bromodomain site, a critical region for protein-protein interactions. Structurally, PROTAC BRD4 Degrader-9 is characterized by its bifunctional molecular architecture, which includes a ligand for BRD4 and an E3 ligase recruiting element. This dual binding capability facilitates the formation of a ternary complex that bridges BRD4 with an E3 ubiquitin ligase, leading to ubiquitination and subsequent proteasomal degradation of the target protein. The primary mechanism of action of PROTAC BRD4 Degrader-9 involves the hijacking of the cellular ubiquitin-proteasome system, enabling selective degradation of BRD4, thereby modulating transcriptional regulation pathways. This compound is invaluable for research applications focused on elucidating the role of BRD4 in disease pathogenesis and for the development of novel therapeutic strategies through PROTAC-mediated protein degradation. Its application in targeted degradation studies enhances our understanding of protein dynamics and regulatory mechanisms within cellular environments.

PROTAC BRD4 Degrader-9

Structure of 2417370-42-2

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Category
PROTAC
Molecular Formula
C59H71F2N9O15S4
Molecular Weight
1312.5
Appearance
Solid

* For research and manufacturing use only. Not for human or clinical use.

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Purity
98%
Appearance
Solid
Storage
Store at -20°C
IUPACName
[(3R,5S)-1-[(2S)-2-[[2-[2-[2-[2-[[8-(3,5-difluoropyridin-2-yl)-15-methyl-4-(methylsulfonylmethyl)-14-oxo-8,12,15-triazatetracyclo[8.6.1.02,7.013,17]heptadeca-1(16),2(7),3,5,10,13(17)-hexaene-5-carbonyl]amino]ethoxy]ethoxy]ethoxy]acetyl]amino]-3,3-dimethylbutanoyl]-5-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]pyrrolidin-3-yl] (2-methyl-2-methylsulfonylsulfanylpropyl) carbonate
Synonyms
S-(1-(((((3R,5S)-1-((S)-15-(tert-butyl)-1-(7-(3,5-difluoropyridin-2-yl)-2-methyl-10-((methylsulfonyl)methyl)-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulen-9-yl)-1,13-dioxo-5,8,11-trioxa-2,14-diazahexadecan-16-oyl)-5-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-3-yl)oxy)carbonyl)oxy)-2-methylpropan-2-yl) methanesulfonothioate
InChI Key
YJTABYQWTJXVHI-DEYDXPIJSA-N
InChI
InChI=1S/C59H71F2N9O15S4/c1-34-50(86-33-66-34)36-12-10-35(11-13-36)24-65-54(73)46-22-40(85-57(76)84-32-59(5,6)87-89(9,79)80)28-70(46)56(75)51(58(2,3)4)67-47(71)30-83-19-18-82-17-16-81-15-14-62-53(72)41-23-45-42(20-37(41)31-88(8,77)78)43-29-68(7)55(74)49-48(43)38(25-63-49)27-69(45)52-44(61)21-39(60)26-64-52/h10-13,20-21,23,25-26,29,33,40,46,51,63H,14-19,22,24,27-28,30-32H2,1-9H3,(H,62,72)(H,65,73)(H,67,71)/t40-,46+,51-/m1/s1
SMILES
CC1=C(SC=N1)C2=CC=C(C=C2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)COCCOCCOCCNC(=O)C4=CC5=C(C=C4CS(=O)(=O)C)C6=CN(C(=O)C7=C6C(=CN7)CN5C8=C(C=C(C=N8)F)F)C)OC(=O)OCC(C)(C)SS(=O)(=O)C
Mechanism

Target: Targets BET bromodomain proteins, especially BRD4, BRD3, and BRD2 for experimental targeted protein degradation studies.

Binding Site: Binds the BET bromodomain acetyl-lysine pocket and recruited E3 ligase ligand site to support productive ternary complex formation.

Mechanism of Action: PROTAC BRD4 Degrader-9 is designed for use in PROTAC or targeted protein degradation experiments directed toward BET bromodomain proteins, especially BRD4, BRD3, and BRD2. The bifunctional molecule links a target-recognition element to cereblon, promoting proximity between the protein of interest and ubiquitination machinery. Productive ternary-complex formation can drive polyubiquitination and proteasome-dependent target depletion, allowing researchers to compare pharmacological inhibition with protein removal. It is suitable for evaluating degradation potency, kinetics, pathway selectivity, and downstream signaling consequences in engineered or disease-relevant cellular models.

Applications

• PROTAC-Mediated BRD4 Degradation: PROTAC BRD4 Degrader-9 is designed to facilitate the selective degradation of the BRD4 protein, a key regulator in transcriptional control and cancer progression. This compound enables researchers to study the impact of BRD4 loss on cellular pathways, providing valuable insights into its role in disease mechanisms.

• Targeted Protein Degradation Studies: By employing PROTAC technology, PROTAC BRD4 Degrader-9 allows scientists to investigate the efficacy of targeted protein degradation in modulating transcriptional networks. This approach aids in understanding how specific protein depletion affects cellular functions and can inform the development of novel therapeutic strategies.

• Functional Genomics Research: Utilizing PROTAC BRD4 Degrader-9 facilitates the exploration of BRD4's involvement in gene expression regulation. Researchers can dissect the consequences of BRD4 degradation on chromatin dynamics and epigenetic modifications, contributing to the broader understanding of gene regulation processes.

• Drug Discovery and Development: PROTAC BRD4 Degrader-9 serves as a powerful tool in the drug discovery process, allowing for the evaluation of BRD4 as a potential therapeutic target. By observing the biological outcomes of targeted degradation, researchers can assess the viability of BRD4 inhibitors in preclinical models.

1. Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target BRD4
Jing Wang, Kevin Coleman, Kanak Raina, James D Winkler, Craig M Crews, Andrew P Crew, Yimin Qian, John Hines, Jing Lu, Hanqing Dong, Martha Altieri Chem Biol . 2015 Jun 18;22(6):755-63. doi: 10.1016/j.chembiol.2015.05.009.
BRD4, a bromodomain and extraterminal domain (BET) family member, is an attractive target in multiple pathological settings, particularly cancer. While BRD4 inhibitors have shown some promise in MYC-driven malignancies such as Burkitt's lymphoma (BL), we show that BRD4 inhibitors lead to robust BRD4 protein accumulation, which may account for their limited suppression of MYC expression, modest antiproliferative activity, and lack of apoptotic induction. To address these limitations we designed ARV-825, a hetero-bifunctional PROTAC (Proteolysis Targeting Chimera) that recruits BRD4 to the E3 ubiquitin ligase cereblon, leading to fast, efficient, and prolonged degradation of BRD4 in all BL cell lines tested. Consequently, ARV-825 more effectively suppresses c-MYC levels and downstream signaling than small-molecule BRD4 inhibitors, resulting in more effective cell proliferation inhibition and apoptosis induction in BL. Our findings provide strong evidence that cereblon-based PROTACs provide a better and more efficient strategy in targeting BRD4 than traditional small-molecule inhibitors.
2. Degradation of proteins by PROTACs and other strategies
Haopeng Sun, Yang Wang, Xueyang Jiang, Feng Feng, Wenyuan Liu Acta Pharm Sin B . 2020 Feb;10(2):207-238. doi: 10.1016/j.apsb.2019.08.001.
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
3. MDM2-Recruiting PROTAC Offers Superior, Synergistic Antiproliferative Activity via Simultaneous Degradation of BRD4 and Stabilization of p53
Schan Lartigue, Craig M Crews, Yimin Qian, John Hines, Hanqing Dong Cancer Res . 2019 Jan 1;79(1):251-262. doi: 10.1158/0008-5472.CAN-18-2918.
Although the number of proteins effectively targeted for posttranslational degradation by PROTAC has grown steadily, the number of E3 ligases successfully exploited to accomplish this has been limited to the few for which small-molecule ligands have been discovered. Although the E3 ligase MDM2 is bound by the nutlin class of small-molecule ligands, there are few nutlin-based PROTAC. Because a nutlin-based PROTAC should both knockdown its target protein and upregulate the tumor suppressor p53, we examined the ability of such a PROTAC to decrease cancer cell viability. A nutlin-based, BRD4-degrading PROTAC, A1874, was able to degrade its target protein by 98% with nanomolar potency. Given the complementary ability of A1874 to stabilize p53, we discovered that the nutlin-based PROTAC was more effective in inhibiting proliferation of many cancer cell lines with wild-type p53 than was a corresponding VHL-utilizing PROTAC with similar potency and efficacy to degrade BRD4. This is the first report of a PROTAC in which the E3 ligase ligand and targeting warhead combine to exert a synergistic antiproliferative effect. Our study highlights the untapped potential that may be unlocked by expanding the repertoire of E3 ligases that can be recruited by PROTAC. SIGNIFICANCE: These findings present the first BRD4-targeting MDM2-based PROTAC that possesses potent, distinct, and synergistic biological activities associated with both ends of this heterobifunctional molecule.

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