KI-CDK9d-32 is a selective CDK9 PROTAC degrader ( IC50 = 3 nM; DC50 = 0.89 nM). KI-CDK9d-32 induces CDK9 degradation via the ubiquitin-proteasome pathway to abrogates CDK9 enzymatic and scaffolding functions, downregulates MYC expression and MYC-dependent signaling, represses TNF-alpha signaling pathways activity and pre-rRNA levels. KI-CDK9d-32 disrupts nucleolar homeostasis, blocks cell cycle progression and cellular translation by reducing 4EBP1 phosphorylation, and elicits cancer cell cytotoxicity in a CRBN -dependent manner, while high ABCB1 activity attenuates the efficacy. KI-CDK9d-32 can be used for the research of acute lymphoblastic leukemia, rhabdomyosarcoma, pancreatic adenocarcinoma [1]. (Pink: CDK9 ligand; Blue: Cereblon ligand; Black: linker ).
In Vitro, KI-CDK9d-32 (0.004-5000 nM; 1-12 h) potently degrades CDK9 in MOLT-4 cells with a DC50 of 0.89 nM after 4 h, achieves near-complete degradation sustained for at least 12 h, and exhibits a maximal degradation rate of 1.04 h-1 at 126 nM[1]. KI-CDK9d-32 (50 nM; 4 h) reduces CDK9 protein levels 5-fold and MYC protein levels 3-fold in MOLT-4 cells, along with downregulating MYC-regulated kinases and disrupting cell cycle and ribosome biogenesis pathways[1]. KI-CDK9d-32 (50 nM; 4 h) selectively inhibits CDK9-mediated phosphorylation in MOLT-4 cells, reduces 4EBP1 phosphorylation to inhibit translation, and disrupts phosphosites linked to mRNA and ribosome-related processes[1]. KI-CDK9d-32 (15-125 nM; 2-8 h) dose- and time-dependently suppresses MYC mRNA levels in MOLT-4 cells, bypassing the compensatory MYC increase seen with CDK9 inhibition, and reduces CDK9 mRNA levels by 5-fold at 8 h[1]. KI-CDK9d-32 (15 nM; 2-8 h) induces rapid, sustained downregulation of MYC mRNA (over 6-fold relative to inhibition) in MOLT-4 cells, downregulates TNF-α signaling via NF-κB across MOLT-4, PSN-1, and RH-4 cells, and disrupts MYC target pathways linked to ribosome biogenesis[1]. KI-CDK9d-32 (up to 1.5 μM; 120 h) has a mean IC50 of 82.6 nM across ~800 human cancer cell lines, with sensitivity driven by CRBN expression and resistance driven by ABCB1 expression[1]. KI-CDK9d-32 (2 h) induces rapid (within 2 h) disruption of nucleolar homeostasis in HeLa cells by compromising the NPM1-marked nucleolar rim, without affecting the DDX21-marked core granular compartment[1]. KI-CDK9d-32 (0.1-10 μM) potently inhibits CDK9/cyclin T1 with a biochemical IC50 of 3 nM at 10 mM ATP, exhibits >1403-fold selectivity over most tested kinases, and inhibits ~90% of CDK9 activity at 100 nM with no off-target kinase inhibition[1]. KI-CDK9d-32 (10-100 nM; 4 h) destabilizes nucleolar homeostasis in HeLa cells[1]. KI-CDK9d-32 (100 nM; 4 h) induces significant disruption and dissolution of nucleolar structure in HeLa cells[1]. KI-CDK9d-32 (100 nM; 4 h) significantly reduces pre-rRNA (5'-ETS) levels in HeLa cells[1]. KI-CDK9d-32 (15 nM; 4-8 h) significantly downregulates multiple core regulatory circuitry gene transcripts in MOLT-4, PSN-1, and RH-4 cells, with stronger effects observed at 8 h[1]. KI-CDK9d-32 (50 nM; 4 h) induces potent degradation of CDK9 (fold change -4.81), with no detectable degradation of other tested kinase targets in a quantitative mass spectrometry assay[1]. KI-CDK9d-32 (50 nM; 4 h) induces degradation of CDK9 and c-MYC, and reduces pSer2, POLR2A levels in PSN-1, RH-4, and HeLa cells, with degradation reversed by MG-132 co-treatment[1]. KI-CDK9d-32 (50 nM; 4 h) does not affect CDK7 protein levels in MOLT-4 cells, demonstrating selectivity for CDK9 over its homologue CDK7[1]. KI-CDK9d-32 (15-125 nM; 4 h) induces dose-dependent degradation of CDK9 and MYC in MOLT-4 cells[1]. KI-CDK9d-32 (15 nM; 4 h) induces significant enrichment of HALLMARK MYC TARGETS V2 and HALLMARK TNFA via NFKB gene sets in MOLT-4 cells, enrichment of these sets in PSN-1 cells, and enrichment of HALLMARK DNA REPAIR in RH-4 cells[1]. KI-CDK9d-32 (0.69 nM-1.5 µM) reduces viability of ~800 tested cancer cell lines in a dose-dependent manner, with cell line sensitivity correlated with CRBN expression and resistance correlated with ABCB1 expression, as measured via the Broad Institute PRISM high-throughput platform[1].
References:
[1]. Toure MA, et al. Targeted degradation of CDK9 potently disrupts the MYC-regulated network. Cell chemical biology. 2025 Apr 17;32(4):542-555.e10.
In Vitro, KI-CDK9d-32 (0.004-5000 nM; 1-12 h) potently degrades CDK9 in MOLT-4 cells with a DC50 of 0.89 nM after 4 h, achieves near-complete degradation sustained for at least 12 h, and exhibits a maximal degradation rate of 1.04 h-1 at 126 nM[1]. KI-CDK9d-32 (50 nM; 4 h) reduces CDK9 protein levels 5-fold and MYC protein levels 3-fold in MOLT-4 cells, along with downregulating MYC-regulated kinases and disrupting cell cycle and ribosome biogenesis pathways[1]. KI-CDK9d-32 (50 nM; 4 h) selectively inhibits CDK9-mediated phosphorylation in MOLT-4 cells, reduces 4EBP1 phosphorylation to inhibit translation, and disrupts phosphosites linked to mRNA and ribosome-related processes[1]. KI-CDK9d-32 (15-125 nM; 2-8 h) dose- and time-dependently suppresses MYC mRNA levels in MOLT-4 cells, bypassing the compensatory MYC increase seen with CDK9 inhibition, and reduces CDK9 mRNA levels by 5-fold at 8 h[1]. KI-CDK9d-32 (15 nM; 2-8 h) induces rapid, sustained downregulation of MYC mRNA (over 6-fold relative to inhibition) in MOLT-4 cells, downregulates TNF-α signaling via NF-κB across MOLT-4, PSN-1, and RH-4 cells, and disrupts MYC target pathways linked to ribosome biogenesis[1]. KI-CDK9d-32 (up to 1.5 μM; 120 h) has a mean IC50 of 82.6 nM across ~800 human cancer cell lines, with sensitivity driven by CRBN expression and resistance driven by ABCB1 expression[1]. KI-CDK9d-32 (2 h) induces rapid (within 2 h) disruption of nucleolar homeostasis in HeLa cells by compromising the NPM1-marked nucleolar rim, without affecting the DDX21-marked core granular compartment[1]. KI-CDK9d-32 (0.1-10 μM) potently inhibits CDK9/cyclin T1 with a biochemical IC50 of 3 nM at 10 mM ATP, exhibits >1403-fold selectivity over most tested kinases, and inhibits ~90% of CDK9 activity at 100 nM with no off-target kinase inhibition[1]. KI-CDK9d-32 (10-100 nM; 4 h) destabilizes nucleolar homeostasis in HeLa cells[1]. KI-CDK9d-32 (100 nM; 4 h) induces significant disruption and dissolution of nucleolar structure in HeLa cells[1]. KI-CDK9d-32 (100 nM; 4 h) significantly reduces pre-rRNA (5'-ETS) levels in HeLa cells[1]. KI-CDK9d-32 (15 nM; 4-8 h) significantly downregulates multiple core regulatory circuitry gene transcripts in MOLT-4, PSN-1, and RH-4 cells, with stronger effects observed at 8 h[1]. KI-CDK9d-32 (50 nM; 4 h) induces potent degradation of CDK9 (fold change -4.81), with no detectable degradation of other tested kinase targets in a quantitative mass spectrometry assay[1]. KI-CDK9d-32 (50 nM; 4 h) induces degradation of CDK9 and c-MYC, and reduces pSer2, POLR2A levels in PSN-1, RH-4, and HeLa cells, with degradation reversed by MG-132 co-treatment[1]. KI-CDK9d-32 (50 nM; 4 h) does not affect CDK7 protein levels in MOLT-4 cells, demonstrating selectivity for CDK9 over its homologue CDK7[1]. KI-CDK9d-32 (15-125 nM; 4 h) induces dose-dependent degradation of CDK9 and MYC in MOLT-4 cells[1]. KI-CDK9d-32 (15 nM; 4 h) induces significant enrichment of HALLMARK MYC TARGETS V2 and HALLMARK TNFA via NFKB gene sets in MOLT-4 cells, enrichment of these sets in PSN-1 cells, and enrichment of HALLMARK DNA REPAIR in RH-4 cells[1]. KI-CDK9d-32 (0.69 nM-1.5 µM) reduces viability of ~800 tested cancer cell lines in a dose-dependent manner, with cell line sensitivity correlated with CRBN expression and resistance correlated with ABCB1 expression, as measured via the Broad Institute PRISM high-throughput platform[1].
References:
[1]. Toure MA, et al. Targeted degradation of CDK9 potently disrupts the MYC-regulated network. Cell chemical biology. 2025 Apr 17;32(4):542-555.e10.