Name: XY-06-007
Brand: BOC Sciences
Rating: 5 (1 reviews)

Purity

≥95%

Solubility

Soluble in DMSO

Appearance

White Solid

Storage

Store at -20°C

IUPACName

(2R)-2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-[5-[[2-[2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindol-4-yl]oxyacetyl]amino]pentyl]propanamide

Synonyms

(2R)-2-((S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-benzo[f][1,2,4]triazolo[4,3-a][1,4]diazepin-4-yl)-N-(5-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)oxy)acetamido)pentyl)propanamide; 4H-[1,2,4]Triazolo[4,3-a][1,4]benzodiazepine-4-acetamide, 6-(4-chlorophenyl)-N-[5-[[2-[[2-(2,6-dioxo-3-piperidinyl)-2,3-dihydro-1,3-dioxo-1H-isoindol-4-yl]oxy]acetyl]amino]pentyl]-8-methoxy-α,1-dimethyl-, (αR,4S)-; (αR,4S)-6-(4-Chlorophenyl)-N-[5-[[2-[[2-(2,6-dioxo-3-piperidinyl)-2,3-dihydro-1,3-dioxo-1H-isoindol-4-yl]oxy]acetyl]amino]pentyl]-8-methoxy-α,1-dimethyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4-acetamide

Density

1.48±0.1 g/cm3

InChI Key

QTDHGBJLMBQHOW-BPJPHOPQSA-N

InChI

InChI=1S/C41H41ClN8O8/c1-22(35-37-48-47-23(2)49(37)29-15-14-26(57-3)20-28(29)36(46-35)24-10-12-25(42)13-11-24)38(53)44-19-6-4-5-18-43-33(52)21-58-31-9-7-8-27-34(31)41(56)50(40(27)55)30-16-17-32(51)45-39(30)54/h7-15,20,22,30,35H,4-6,16-19,21H2,1-3H3,(H,43,52)(H,44,53)(H,45,51,54)/t22-,30?,35+/m1/s1

SMILES

CC1=NN=C2N1C3=C(C=C(C=C3)OC)C(=NC2C(C)C(=O)NCCCCCNC(=O)COC4=CC=CC5=C4C(=O)N(C5=O)C6CCC(=O)NC6=O)C7=CC=C(C=C7)Cl

Mechanism

Target: XY-06-007 selectively targets engineered BRD4BD1L94V within bump-and-hole degradation systems.

Binding site: It binds the mutant BRD4 bromodomain acetyl-lysine recognition pocket selectively.

Mechanism of action: XY-06-007 is a selective bump-and-hole PROTAC optimized for degradation of engineered BRD4BD1L94V rather than endogenous bromodomain proteins. The molecule uses a bumped bromodomain ligand to recognize the mutant BRD4 bromodomain and a CRBN-recruiting element to engage cereblon E3 ligase machinery. This engineered complementarity supports selective ternary-complex formation, ubiquitination, and proteasomal degradation of the tagged or mutant target. XY-06-007 is useful for chemically controlled target validation, temporal depletion studies, and assessing protein function in systems where endogenous BET family degradation would confound interpretation.

Applications

• PROTAC-Mediated Kinase Degradation: XY-06-007 is designed to target and degrade specific kinases implicated in signaling pathways. By facilitating the ubiquitination and proteasomal degradation of these kinases, this PROTAC enables researchers to dissect kinase function and study signal transduction mechanisms with precision.

• Targeted Oncoprotein Degradation: Leveraging XY-06-007 allows for the selective degradation of oncoproteins that drive tumorigenesis. This application is crucial for investigating the role of these proteins in cancer progression and evaluating potential therapeutic strategies that involve their targeted removal.

• Degradation of Nuclear Receptors: XY-06-007 is effective in targeting nuclear receptors for degradation, offering insights into their regulatory roles in gene expression. This application supports research into receptor-mediated transcriptional control and its implications in various physiological and pathological contexts.

• Selective Protein Degradation in Drug Discovery: With XY-06-007, researchers can explore novel drug targets by inducing the degradation of proteins involved in disease pathways. This application is particularly valuable for identifying and validating new therapeutic targets through the lens of PROTAC technology.

1. Structure-Guided Design of a "Bump-and-Hole" Bromodomain-Based Degradation Tag

Nicholas A Eleuteri, Yuan Xiong, J Christine Yuan, Katherine A Donovan, Eric S Fischer, Radosław P Nowak, Nadia Kirmani, Joann Kalabathula J Med Chem . 2021 Aug 12;64(15):11637-11650. doi: 10.1021/acs.jmedchem.1c00958.

Chemical biology tools to modulate protein levels in cells are critical to decipher complex biology. Targeted protein degradation offers the potential for rapid and dose-dependent protein depletion through the use of protein fusion tags toward which protein degraders have been established. Here, we present a newly developed protein degradation tag BRD4BD1L94V along with the corresponding cereblon (CRBN)-based heterobifunctional degrader based on a "bump-and-hole" approach. The resulting compoundXY-06-007shows a half-degradation concentration (DC50, 6 h) of 10 nM against BRD4BD1L94V with no degradation of off-targets, as assessed by whole proteome mass spectrometry, and demonstrates suitable pharmacokinetics forin vivostudies. We demonstrate that BRD4BD1L94V can be combined with the dTAG approach to achieve simultaneous degrader-mediated depletion of their respective protein fusions. This orthogonal system complements currently available protein degradation tags and enables investigation into the consequences resulting from rapid degradation of previously undruggable disease codependencies.

Good evening, dear BOCSCI, would you please share with me its key features? thanks.

Key features: Highly potent: XY-06-007 has a DC50 (6h) of 10 nM against BRD4BD1L94V, meaning it can achieve 50% degradation of the protein at a concentration of just 10 nM after 6 hours. Selective: XY-06-007 does not degrade wild-type BRD4 or other off-target proteins, minimizing potential side effects. Promising therapeutic potential: BRD4 mutations are found in some cancers, and BRD4BD1L94V is a particularly aggressive form. XY-06-007 shows promise as a targeted therapy for these cancers.

9/2/2016

Hi, I would like to ask one technical question. could you explain to me its function as a PROTAC?

XY-06-007 is a PROTAC, which stands for proteolysis-targeting chimera. It works by hijacking the cell's natural degradation machinery to specifically target and eliminate the BRD4BD1L94V protein. One end of XY-06-007 binds to the mutant BRD4BD1L94V protein like a key fitting into a lock. The other end binds to an E3 ligase, a protein that tags other proteins for destruction by the proteasome. This brings the BRD4BD1L94V protein close to the E3 ligase, marking it for degradation. As a result, XY-06-007 effectively removes the mutant BRD4 protein from the cell.

3/8/2016

Hi, can XY-06-007 be used in vitro?

Yes, XY-06-007 can be used in vitro! Its potent and selective activity against BRD4BD1L94V with minimal off-target effects makes it suitable for studying its mechanism of action and potential therapeutic applications in cell-based assays.

20/12/2020

Sir, I want to know how does it work? thanks.

Here is a more detailed explanation of how XY-06-007 works: XY-06-007 binds to the BRD4BD1L94V protein. XY-06-007 then recruits another protein called cereblon to the BRD4BD1L94V protein. Cereblon is a protein that is involved in the degradation of other proteins in the cell. When cereblon is bound to BRD4BD1L94V, it tags BRD4BD1L94V for degradation. BRD4BD1L94V is then degraded by the cell's proteasome.

5/6/2021

Stock concentration: *

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* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C₁V₁ = C₂V₂