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Background Information of CDK9-IN-3

CDK9-IN-3 (Compound 8d) is a CDK9 inhibitor, which inhibits MCF-7 (CDK9-rich) cell lines with an IC50 of 40±3.0 μM. Cyclin-dependent kinase 9 (CDK9) is a serine (Ser)/threonine kinase which forms a subunit of the P-TEFb complex with cyclin T. It can interact with many transcription factors (TFs) and regulate the expression of antiapoptotic proteins for the survival of cancer cells.

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Mechanism and Indications

Signaling Pathways Cell Cycle/DNA Damage
Target CDK
Research Area Cancer

Clinical Information

Product Name Sponsor & Collaborators Indications Start Date End Date Phase

Chemical Information

M.Wt Formula CAS No. Synonyms
695.71 C38H37N3O10 Compound 8d

Structure Information of CDK9-IN-3

InChI InChI=1S/C38H37N3O10/c42-26-20-28(44)34(35-33(26)27(43)21-29(51-35)22-12-7-6-8-13-22)50-19-10-5-3-1-2-4-9-16-30(45)39-24-15-11-14-23-32(24)38(49)41(37(23)48)25-17-18-31(46)40-36(25)47/h6-8,11-15,20-21,25,42,44H,1-5,9-10,16-19H2,(H,39,45)(H,40,46,47)

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CDK9-IN-6 1391855-95-0 C27H37ClN6O2 5
ML167 1285702-20-6 C19H17N3O3 15
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LEE011 (hydrochloride) 1211443-80-9 C23H31ClN8O 8
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Wogonin 632-85-9 C16H12O5 28
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WHI-P180 211555-08-7 C16H15N3O3 13
THZ1 1604810-83-4 C31H28ClN7O2 18
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Purvalanol B 212844-54-7 C20H25ClN6O3 22

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[1].Bian J, et al. Discovery of Wogonin-based PROTACs against CDK9 and capable of achieving antitumor activity. Bioorg Chem. 2018 Aug 30;81:373-381.
Wogonin is a natural product isolated from the Scutellaria baicalensis and has been proved to be a potent and selective inhibitor of CDK9. Using this scaffold, we designed and synthesized a series of proteolysis targeting chimeras (PROTACs) targeting CDK9 by recruiting ubiquitin E3 ligase cereblon (CRBN). For constructing diverse Wogonin-based PROTACs, a "click chemistry" approach was employed for the synthesis of CDK9-targeting PROTACs. The results of western blotting assays showed that compounds containing triazole group in the linker could selectively downregulate the intracellular CDK9 level. Among these compounds, 11c could selectively degrade CDK9 in a concentration-dependent manner. In addition, the application of the proteasome inhibitor MG132 and CRBN siRNA silencing confirmed that 11c could promote the proteasome-dependent and CRBN-dependent degradation. Consistent with the degradation of the CDK9 protein, 11c selectively inhibits proliferation of CDK9-overexpressed cancer cells. Thus, our Wogonin-based PROTAC would be an efficient probe that induces the degradation of CDK9.

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