Development of dual and selective degraders of cyclin-dependent kinases 4 and 6
Open accessAbstract
Cyclin‐dependent kinases 4 and 6 (CDK4/6) are key regulators of the cell cycle, and there are FDA‐approved CDK4/6 inhibitors for treating patients with metastatic breast cancer. However, due to conservation of their ATP‐binding sites, development of selective agents has remained elusive. Here, we report imide‐based degrader molecules capable of degrading both CDK4/6, or selectively degrading either CDK4 or CDK6. We were also able to tune the activity of these molecules against Ikaros (IKZF1) and Aiolos (IKZF3), which are well‐established targets of imide‐based degraders. We found that in mantle cell lymphoma cell lines, combined IKZF1/3 degradation with dual CDK4/6 degradation produced enhanced anti‐proliferative effects compared to CDK4/6 inhibition, CDK4/6 degradation, or IKZF1/3 degradation. In summary, we report here the first compounds capable of inducing selective degradation of CDK4 and CDK6 as tools to pharmacologically dissect their distinct biological functions.
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Written from the paper’s full text.
TL;DR
The paper reports imide-based bifunctional degraders that recruit CRBN to induce dual CDK4/6 degradation or selective degradation of either CDK4 or CDK6, while also tuning IKZF1/3 degradation. In mantle cell lymphoma cell lines, combined CDK4/6 and IKZF1/3 degradation showed enhanced anti-proliferative effects compared with CDK4/6 inhibition, CDK4/6 degradation alone, or IKZF1/3 degradation.
Key findings
- Palbociclib-, ribociclib-, and abemaciclib-based degraders were generated; most maintained biochemical IC50 values of 1–50 nM, and each inhibitor could be converted into active CDK4/6 degraders in Jurkat cells after 4 h treatment with 1 µM.
- Selective degraders were identified: BSJ-01–187 selectively degraded CDK4, YKL-06–102 selectively degraded CDK6, and BSJ-02–162 degraded both CDK4 and CDK6. Analogs BSJ-03–204, BSJ-04–132, and BSJ-03–123 retained dual CDK4/6, selective CDK4, or selective CDK6 degradation, respectively, without degrading IKZF1/3.
- Degradation was CRBN-dependent: in CRISPR/Cas9-generated Crbn−/− Jurkat cells, CDK4/6 and/or IKZF1/3 protein levels were unaffected, and 100 nM BSJ-02–162 induced G1 arrest in wildtype but not Crbn−/− Jurkat cells after 24 h, whereas 100 nM palbociclib induced G1 arrest in both.
- In MCL cells, 1 µM BSJ-02–162 for 1 day degraded CDK4/6 and IKZF1/3, while BSJ-03–204 degraded only CDK4/6; both reduced phosphorylated Rb and induced G1 arrest. BSJ-02–162 showed increased anti-proliferative effects versus BSJ-03–204 in many MCL cell lines. In Molt4 proteomics at 250 nM for 5 h, BSJ-04–132 reduced CDK4 by ~1.9-fold, below the 2-fold threshold, but more than CDK6, IKZF1, and IKZF3.
Methods
- Degraders were designed by attaching PEG or alkyl linkers to the piperazine 4-nitrogen of palbociclib, ribociclib, or abemaciclib, terminating at the 4- or 5-position of thalidomide as the CRBN-recruiting moiety.
- Cellular assays used Jurkat cells (wildtype and Crbn−/−), Molt4 cells, Granta-519 cells, and a panel of MCL cell lines; readouts included enzymatic CDK4/6 kinase inhibition, immunoblotting, propidium iodide cell-cycle analysis, multiplexed mass spectrometry-based proteomics, and anti-proliferative assays.
- Main analyses compared degrader-induced protein loss, CRBN dependence, cell-cycle effects, and proteome-wide selectivity, with a minimum 2-fold change threshold used for proteomic scatterplot depiction.
Limitations
- Stated: structural analysis of kinase-degrader-CRBN ternary complexes will be required to reveal the basis for the observed CDK4 versus CDK6 selectivity.
- Evident: all reported efficacy and degradation data are from cell lines; no in vivo animal or clinical data are reported.
- Evident: the proteomics analysis used a minimum 2-fold change threshold, and CDK4 reduction by BSJ-04–132 (~1.9-fold) did not meet this threshold, so its selective CDK4 degradation was inferred from Table S2 rather than the scatterplot.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
0 of 19 cited sources checked · 0 supported · 0 flagged
- Findingown data
In mantle cell lymphoma cell lines, combined IKZF1/3 degradation with dual CDK4/6 degradation exhibited enhanced anti-proliferative effects compared to CDK4/6 inhibition, CDK4/6 degradation, or IKZF1/3 degradation.
“We found that in mantle cell lymphoma cell lines, combined IKZF1/3 degradation with dual CDK4/6 degradation exhibited enhanced anti-proliferative effects compared to CDK4/6 inhibition, CDK4/6 degradation, or IKZF1/3 degradation.”
- Also stated in: § Abstract · boosted
“We also discovered that simultaneously degrading CDK4/6 and IKZF1/3 demonstrated enhanced anti-proliferation effect in MCL cell lines in comparison to palbociclib, lenalidomide, or a selective CDK4/6 degrader, similar to what was observed with a previously reported BTK degrader that also targeted IKZF1/3[13c].”
Quote in the paperSubstantial claim - Also stated in: § Abstract · boosted
- Findingown data
BSJ-01-187 selectively degraded CDK4.
“In contrast, BSJ-01–187, a ribociclib-based degrader with a 4-carbon alkyl linker, selectively degraded CDK4 (Figure 3C)”
Quote in the paperSubstantial claim - Findingown data
YKL-06-102 induced selective degradation of CDK6.
“while the extended PEG-3 linker of the palbociclib-derived compound YKL-06–102 induced selective degradation of CDK6 (Figure 3E).”
Quote in the paperSubstantial claim - Findingown data
BSJ-02-162 degraded both CDK4 and CDK6.
“For example, BSJ-02–162, which consists of an alkyl linker conjugated to palbociclib, degraded both CDK4 and CDK6 (Figure 3A).”
Quote in the paperSubstantial claim - Findingown data
By varying linkers for CDK4/6-targeted degraders, the authors identified molecules capable of acutely and selectively degrading either CDK4 or CDK6.
“Here, by varying the linkers for CDK4/6-targeted degraders, we identified molecules capable of acutely and selectively degrading either CDK4 or CDK6.”
Quote in the paperSubstantial claim- Rests on an assumption: The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.
- Findingown data
Treatment of Granta-519 cells with these degraders potently induced a G1 arrest.
“Finally, treatment of Granta-519 cells with these degraders also potently induced a G1 arrest (Figure 6B).”
Quote in the paperSubstantial claim - Findingown data
BSJ-02-162 induced loss of CDK4/6, IKZF1/3, and other zinc finger proteins known to be recruited to CRBN by imides in Molt4 cells.
“As expected, BSJ-02–162 induced loss of CDK4/6, IKZF1/3, and other zinc finger proteins known to be recruited to CRBN by imides (Figure 5A)[16].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [16] a An J, Ponthier CM, Sack R, Seebacher J, Stadler MB, Donovan KA, Fischer ES, Nat Commun 2017, 8, 15398; 28530236 PMC5458144 b Sievers QL, Petzold G, Bunker RD, Renneville A, Slabicki M, Liddicoat BJ, Abdulrahman W, Mikkelsen T, Ebert BL, Thoma NH, Science 2018, 362. PMC6326779 30385546
Not checked in the free run.
- Findingown data
Acute exposure to some degraders differentially affected the abundance of CDK4 and CDK6 as a function of inhibitor, linker length, and linker composition.
“Subsequently, we found that acute exposure to some degraders differentially affected the abundance of CDK4 and CDK6, as a function of inhibitor, linker length, and linker composition.”
Quote in the paperSubstantial claim - Findingown data
BSJ-03-204 was selective for CDK4/6 degradation.
“its non-IKZF1/3-recruiting analog BSJ-03–204 was verified to be selective for CDK4/6 degradation (Figure 5B).”
Quote in the paperSubstantial claim - Findingown data
The analogs BSJ-03-204, BSJ-04-132, and BSJ-03-123 did not induce IKZF1/3 degradation.
“none of which induced IKZF1/3 degradation.”
Quote in the paperSubstantial claim - Findingown data
Each CDK4/6 inhibitor (palbociclib, ribociclib, abemaciclib) could be successfully converted into active CDK4/6 degraders in Jurkat cells.
“Immunoblotting for CDK4/6 revealed that each inhibitor could be successfully converted into active CDK4/6 degraders (Figure 2).”
Quote in the paperSubstantial claim - Findingown data
BSJ-02-162 had increased anti-proliferative effects in many MCL cell lines compared to BSJ-03-204.
“Interestingly, BSJ-02–162, which degrades CDK4/6 and IKZF1/3, had increased anti-proliferative effects in many MCL cell lines in comparison to BSJ-03–204, which only degrades CDK4/6 (Figure 6C)”
Quote in the paperSubstantial claim - Findingown data
The authors were able to tune the activity of these degrader molecules against IKZF1 and IKZF3.
“We were also able to tune the activity of these molecules against Ikaros (IKZF1) and Aiolos (IKZF3), well-established targets of imide-based degraders.”
Quote in the paperSubstantial claim - Findingown data
Most synthesized degraders maintained biochemical CDK4/6 kinase inhibition IC50 values ranging from 1 to 50 nM.
“Most compounds maintained a biochemical IC50 ranging from 1 – 50 nM (Table S1), validating our choice of linker attachment site.”
Quote in the paperSubstantial claim - Findingown data
Dual CDK4/6 degraders reduced levels of phosphorylated Rb in Granta-519 cells, similar to palbociclib.
“Similar to palbociclib, these dual CDK4/6 degraders also reduced levels of phosphorylated Rb (Figure 6A).”
Quote in the paperSubstantial claim - Findingown data
Abemaciclib-based degraders also induced degradation of CDK9.
“Interestingly, abemaciclib-based degraders also induced degradation of CDK9, a known off-target[12].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [12] Gelbert LM, Cai S, Lin X, Sanchez-Martinez C, Del Prado M, Lallena MJ, Torres R, Ajamie RT, Wishart GN, Flack RS, Neubauer BL, Young J, Chan EM, Iversen P, Cronier D, Kreklau E, de Dios A, Invest New Drugs 2014, 32, 825– 837. 24919854 PMC4169866
Not checked in the free run.
- Findingown data
The authors developed a series of CDK4/6 degraders that largely recapitulated the cellular effects of CDK4/6 inhibition, including reduction in pRB levels, G1 arrest, and anti-proliferative activity.
“In sum, we developed a series of CDK4/6 degraders that largely recapitulated the cellular effects of CDK4/6 inhibition, including reduction in pRB levels, G1 arrest, and anti-proliferative activity.”
Quote in the paperSubstantial claim - Findingown data
Palbociclib (100 nM, 24 h) induced profound G1 arrest in both wildtype and Crbn−/− Jurkat cells.
“As expected, treatment of wildtype or Crbn−/− Jurkat cells with 100 nM palbociclib for 24h induced profound G1 arrest in both cell lines”
Quote in the paperSubstantial claim - Findingown data
Lenalidomide (100 nM, 24 h) had no effect on the cell cycle profile of wildtype or Crbn−/− Jurkat cells.
“while treatment with 100 nM lenalidomide for 24h had no effect.”
Quote in the paperSubstantial claim - Findingcitation
Simultaneously degrading CDK4/6 and IKZF1/3 demonstrated enhanced anti-proliferation effect in MCL cell lines compared to palbociclib, lenalidomide, or a selective CDK4/6 degrader.
“We also discovered that simultaneously degrading CDK4/6 and IKZF1/3 demonstrated enhanced anti-proliferation effect in MCL cell lines in comparison to palbociclib, lenalidomide, or a selective CDK4/6 degrader, similar to what was observed with a previously reported BTK degrader that also targeted IKZF1/3[13c].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13c]
Not checked in the free run.
- Premisecitation
In a mouse model of non-small cell lung carcinoma, genetic ablation of CDK4 but not CDK6 induced senescence in lung cancer cells expressing mutant K-Ras.
“For example, in a mouse model of non-small cell lung carcinoma, genetic ablation of CDK4 but not CDK6 induced senescence in lung cancer cells expressing mutant K-Ras[4].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [4] Puyol M, Martin A, Dubus P, Mulero F, Pizcueta P, Khan G, Guerra C, Santamaria D, Barbacid M, Cancer Cell 2010, 18, 63– 73. 20609353 source
Not checked in the free run.
- Premisecitation
CDK4/6 regulate the G1-S cell cycle transition by phosphorylating the tumor suppressor retinoblastoma (Rb), thereby triggering gene expression programs that promote S phase entry.
“Cyclin-dependent kinases 4 and 6 (CDK4/6) regulate the G1-S cell cycle transition by phosphorylating the tumor suppressor retinoblastoma (Rb), thereby triggering gene expression programs that promote S phase entry[1].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [1] O’Leary B, Finn RS, Turner NC, Nat Rev Clin Oncol 2016, 13, 417– 430. 27030077 source
Not checked in the free run.
- Interpretationown data
The authors report the first compounds capable of inducing selective degradation of CDK4 and CDK6 as tools to pharmacologically dissect their distinct biological functions.
“In sum, we report here the first compounds capable of inducing selective degradation of CDK4 and CDK6 as tools to pharmacologically dissect their distinct biological functions.”
Quote in the paperSubstantial claim- Rests on an assumption: The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.
- Interpretationown data
Compounds that target multiple vulnerabilities may be a promising therapeutic strategy, particularly for B-cell malignancies that are sensitive to IKZF1/3 degradation.
“Thus, compounds that target multiple vulnerabilities may be a promising therapeutic strategy, particularly for B-cell malignancies that are sensitive to IKZF1/3 degradation.”
Quote in the paperSubstantial claim - Premisecitation
Successful degradation by small molecule degraders requires induced heterodimerization between the E3 ubiquitin ligase and the target, resulting in the target's polyubiquitination and subsequent proteasomal degradation.
“Successful degradation requires induced heterodimerization between the E3 ligase and the target of interest, resulting in the target’s polyubiquitination and subsequent proteasomal degradation[8].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [8] Toure M, Crews CM, Angew Chem Int Ed Engl 2016, 55, 1966– 1973. 26756721 source
Not checked in the free run.
- Premisecitation
A BRD4 degrader achieves selectivity versus BRD2 and BRD3 by exploiting structural differences in the bromodomain/E3 ligase protein-protein interface.
“We also developed a BRD4 degrader that achieves selectivity versus BRD2 and BRD3 by exploiting structural differences in the bromodomain/E3 ligase protein-protein interface[10].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [10] Nowak RP, DeAngelo SL, Buckley D, He Z, Donovan KA, An J, Safaee N, Jedrychowski MP, Ponthier CM, Ishoey M, Zhang T, Mancias JD, Gray NS, Bradner JE, Fischer ES, Nat Chem Biol 2018, 14, 706– 714. 29892083 PMC6202246 source
Not checked in the free run.
- Interpretationown data
Co-targeting CDK4/6 and IKZF1/3 pathways may be a promising strategy for the treatment of MCL.
“suggesting that co-targeting these two distinct pathways may be a promising strategy for the treatment of MCL.”
Quote in the paperSubstantial claim
- May combine two claims. 16
- Classified as probably not a substantial claim. 6
May combine two claims.
Findingown dataTreatment of isogenic Jurkat cells in which CRBN was deleted by CRISPR/Cas9 had no effect on the abundance of CDK4/6 and/or IKZF1/3 protein, demonstrating that degradation was dependent on CRBN.
“Finally, we found that treatment of isogenic Jurkat cells in which CRBN was deleted by CRISPR/Cas9 had no effect on the abundance of CDK4/6 and/or IKZF1/3 protein, demonstrating that that degradation was dependent on CRBN (Figure 3).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataTreatment of Molt4 cells with BSJ-03-123 resulted in loss of CDK6, but not CDK4 or IKZF1/3.
“Finally, treatment of Molt4 cells with BSJ-03–123 resulted in loss of CDK6, but not CDK4 or IKZF1/3 (Figure 5D).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn cells treated with BSJ-04-132, CDK4 level was reduced to a greater extent than CDK6, IKZF1, and IKZF3, although CDK4 (~1.9-fold change) did not meet the minimum 2-fold change threshold.
“In cells treated with BSJ-04–132, CDK4 (~1.9-fold change) did not meet our minimum 2-fold change threshold to be depicted on the scatterplot (Figure 5C), but its level was reduced to a greater extent than those of CDK6, IKZF1 and IKZF3 (Table S2).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataTreatment of Granta-519 cells with BSJ-02-162 resulted in pronounced loss of CDK4/6 and IKZF1/3 protein, while BSJ-03-204 only resulted in degradation of CDK4/6.
“Treatment of Granta-519 cells with 1 µM BSJ-02–162 for 1d resulted in pronounced loss of CDK4/6 and IKZF1/3 protein, while treatment with BSJ-03–204 only resulted in degradation of CDK4/6 (Figure 6A).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataProfiling confirmed that the authors could achieve both dual and selective degradation of CDK4/6 across the proteome after acute compound treatment, and that they could tune degradation of IKZF1/3.
“Thus, profiling confirmed that we could achieve both dual and selective degradation of CDK4/6 across the proteome after acute compound treatment, and that we could tune degradation of IKZF1/3.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataBSJ-02-162, BSJ-01-187, and YKL-06-102 all induced degradation of IKZF1/3.
“found that BSJ-02–162, BSJ-01–187, and YKL-06–102 all induced degradation of IKZF1/3 (Figure 3).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe authors developed imide-based degrader molecules capable of degrading both CDK4 and CDK6, or selectively degrading either CDK4 or CDK6.
“Here, we report imide-based degrader molecules capable of degrading both CDK4/6, or selectively degrading either CDK4 or CDK6.”
- Also stated in: § Abstract · plain
“Here, we generated CRBN-recruiting degraders and identified molecules capable of inducing both dual CDK4/6 and selective CDK4 or CDK6 degradation.”
- Also stated in: § Abstract · plain
“Here, by varying the linkers for CDK4/6-targeted degraders, we identified molecules capable of acutely and selectively degrading either CDK4 or CDK6.”
Quote in the paperSubstantial claim- Rests on an assumption: The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.
- Also stated in: § Abstract · plain
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationCDK4/6 inhibitors are under investigation in subsets of lung cancers, sarcomas, and lymphomas such as mantle cell lymphoma (MCL), which exhibits aberrant cell cycle progression via activation of CDK4/6.
“These agents are also currently under investigation in subsets of lung cancers, sarcomas, and lymphomas, such as mantle cell lymphoma (MCL), that exhibits aberrant cell cycle progression via activation of CDK4/6[3].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [3] Sherr CJ, Beach D, Shapiro GI, Cancer Discov 2016, 6, 353– 367. 26658964 PMC4821753 source
Not checked in the free run.
May combine two claims.
PremisecitationThe dual CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib are FDA-approved for treating patients with advanced or metastatic breast cancer and lead to prolonged progression-free survival.
“As such, CDK4/6 are attractive targets for cancer therapy, and the dual CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib have been FDA approved for treating patients with advanced or metastatic breast cancer, leading to prolonged progression-free-survival[2].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [2] Laderian B, Fojo T, Semin Oncol 2017, 44, 395– 403. 29935901 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSelective degradation of CDK9 was achieved by converting the non-selective CDK inhibitor SNS-032 into a degrader.
“For example, selective degradation of CDK9 was achieved by converting the non-selective CDK inhibitor SNS-032 into a degrader[9].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [9] Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, Zhang Z, Zhang T, Kwiatkowski N, Boukhali M, Green JL, Haas W, Nomanbhoy T, Fischer ES, Young RA, Bradner JE, Winter GE, Gray NS, Nat Chem Biol 2018, 14, 163– 170. 29251720 PMC5912898 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThalidomide binds to the E3 ligase substrate adapter Cereblon (CRBN) and has often been used as the E3 ligase-binding moiety in degraders.
“The small molecule thalidomide, which binds to the ubiquitously expressed E3 ligase substrate adapter Cereblon (CRBN), has often been used as the E3 ligase-binding moiety in degraders[11].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [11] a An S, Fu L, EBioMedicine 2018, 36, 553– 562; 30224312 PMC6197674 b Cromm PM, Crews CM, Cell Chem Biol 2017, 24, 1181– 1190. 28648379 PMC5610075 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCDK6 participates as part of a transcription complex that regulates expression of p16INK4a and VEGF-A.
“On the other hand, CDK6-specific functions include participating as part of a transcription complex that regulates expression of p16INK4a and VEGF-A[5]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [5] Kollmann K, Heller G, Schneckenleithner C, Warsch W, Scheicher R, Ott RG, Schafer M, Fajmann S, Schlederer M, Schiefer AI, Reichart U, Mayerhofer M, Hoeller C, Zochbauer-Muller S, Kerjaschki D, Bock C, Kenner L, Hoefler G, Freissmuth M, Green AR, Moriggl R, Busslinger M, Malumbres M, Sexl V, Cancer Cell 2013, 24, 167– 181. 23948297 PMC3743049 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCDK6 acts as a co-factor for NFκB-dependent gene expression.
“and acting as a co-factor for NFκB-dependent gene expression[6].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [6] Handschick K, Beuerlein K, Jurida L, Bartkuhn M, Muller H, Soelch J, Weber A, Dittrich-Breiholz O, Schneider H, Scharfe M, Jarek M, Stellzig J, Schmitz ML, Kracht M, Molecular cell 2014, 53, 193– 208. 24389100 source
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May combine two claims.
InterpretationreasoningThese compounds may serve as selective probes for pharmacological dissection of the distinct CDK4 or CDK6 biological functions and as starting points for the development of therapeutic degrader molecules.
“These compounds may serve as selective probes for pharmacological dissection of the distinct CDK4 or CDK6 biological functions and as starting points for the development of therapeutic degrader molecules.”
Quote in the paperSubstantial claim- Rests on an assumption: The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.
May combine two claims.
PremisecitationMCL is an incurable B cell non-Hodgkin lymphoma whose molecular hallmark is the t(11;14)(q13;q32) chromosomal translocation that juxtaposes CCND1 with the Ig heavy chain gene locus, resulting in aberrant cell cycle progression via activation of CDK4/6.
“CDK4/6 inhibitors are currently being evaluated for MCL, an incurable B cell non-Hodgkin lymphoma whose molecular hallmark is the t(11;14)(q13;q32) chromosomal translocation that juxtaposes CCND1 (encoding cyclin D1) with the Ig heavy chain gene locus, resulting in aberrant cell cycle progression via activation of CDK4/6[17].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [17] Jares P, Colomer D, Campo E, Nat Rev Cancer 2007, 7, 750– 762. 17891190 source
Not checked in the free run.
May combine two claims.
PremisecitationCDK6, but not CDK4, phosphorylates NFAT family transcription factors to promote T cell activation and enhance the anti-tumor immune response.
“We also recently demonstrated that CDK6, but not CDK4, phosphorylates NFAT family transcription factors to promote T cell activation and enhance the anti-tumor immune response[7].”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [7] Deng J, Wang ES, Jenkins RW, Li S, Dries R, Yates K, Chhabra S, Huang W, Liu H, Aref AR, Ivanova E, Paweletz CP, Bowden M, Zhou CW, Herter-Sprie GS, Sorrentino JA, Bisi JE, Lizotte PH, Merlino AA, Quinn MM, Bufe LE, Yang A, Zhang Y, Zhang H, Gao P, Chen T, Cavanaugh ME, Rode AJ, Haines E, Roberts PJ, Strum JC, Richards WG, Lorch JH, Parangi S, Gunda V, Boland GM, Bueno R, Palakurthi S, Freeman GJ, Ritz J, Haining WN, Sharpless NE, Arthanari H, Shapiro GI, Barbie DA, Gray NS, Wong KK, Cancer Discov 2018, 8, 216– 233. 29101163 PMC5809273 source
Not checked in the free run.
May combine two claims.
Interpretationown dataBSJ-02-162 (100 nM, 24 h) induced G1 arrest in wildtype but not Crbn−/− Jurkat cells, indicating that the cytostatic effect of CDK4/6 degraders required CRBN-dependent degradation of CDK4/6.
“In contrast, treatment with 100 nM of BSJ-02–162 for 24h induced G1 arrest in wildtype but not Crbn−/− Jurkat cells, indicating that the cytostatic effect of CDK4/6 degraders required CRBN-dependent degradation of CDK4/6 (Figure 4).”
Quote in the paperSubstantial claimMay combine two claims.
Premiseown dataHigh-resolution crystal structures of palbociclib, ribociclib, and abemaciclib with CDK6 revealed similar binding modes where the aminopyrimidine moiety forms three hydrogen bonds with the backbones of Val101 and Asp163, and the piperazine ring is stabilized via direct interactions with a solvent-exposed ridge consisting of Asp104 and Thr107.
“High-resolution crystal structures of palbociclib [PDB ID: 5L2I], ribociclib [PDB ID: 5L2T], and abemaciclib [PDB ID: 5L2S] with CDK6 revealed similar binding modes where the aminopyrimidine moiety forms three hydrogen bonds with the backbones of Val101 and Asp163, and the piperazine ring is stabilized via direct interactions with a solvent-exposed ridge consisting of Asp104 and Thr107.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites PDB ID: 5L2I
Not checked in the free run.
- cites PDB ID: 5L2T
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- cites PDB ID: 5L2S
Not checked in the free run.
May combine two claims.
Interpretationown dataThe cellular effects of CDK4/6 degraders required the presence of CRBN and were dependent on target degradation rather than inhibition.
“As these effects required the presence of CRBN, they were dependent on target degradation rather than inhibition.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
PremisecitationPrevious studies indicated that varying the thalidomide aryl amine nitrogen to an oxylamide could prevent recruitment of IKZF1/3 to CRBN.
“As previous studies indicated that varying the thalidomide aryl amine nitrogen to an oxylamide could prevent recruitment of IKZF1/3 to CRBN[10, 13c]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [10, 13c]
Not checked in the free run.
The paper relies on this without support.
The ATP-binding pockets of CDK4 and CDK6 are highly conserved/homologous, and current CDK4/6 inhibitors are approximately equipotent for both proteins, making selective inhibition difficult.
“However, due to conservation of their ATP-binding sites, development of selective agents has remained elusive.”
“As current CDK4/6 inhibitors target their highly conserved ATP-binding pockets and are approximately equipotent inhibitors of both proteins, we hypothesized that achieving selectivity would require exploiting selectivity determinants outside of the ATP-binding pocket.”
“The highly homologous ATP-binding pockets of CDK4 and CDK6 has hindered the development of selective CDK4 or CDK6 probes.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Previous studies have shown that a nitrogen to oxygen modification on the thalidomide aryl attachment point can reduce or remove IMiD off-target effects in BTK and CDK4/6 targeted degraders.
“Previous studies have shown that a nitrogen to oxygen modification on the thalidomide aryl attachment point can reduce or remove IMiD off-target effects in BTK and CDK4/6 targeted degraders (Dobrovolsky et al., 2019; Jiang et al., 2019).”
From Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development (2020) · cites this paper as Jiang et al., 2019
Multiple studies have described numerous CRBN-recruiting dual-selective degraders and CDK6-selective degraders, but none report CDK4-selective degraders; the only reported CDK4-selective degraders are built on ribociclib.
“Whereas multiple studies have described numerous CRBN-recruiting dual-selective degraders and CDK6-selective degraders 70–73, none report CDK4-selective degraders; the only reported CDK4-selective degraders are built on a slightly different warhead, ribociclib 74.”
From Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta (2021) · cites this paper as [74]
Some CRBN-based PROTACs have been shown to degrade the natural substrates of CRBN such as IKZF1 and IKZF3.
“some CRBN-based PROTACs have been shown to degrade the natural substrates of CRBN such as IKZF1 and IKZF3 [86, 87].”
From PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics (2020) · cites this paper as [87]
Some CRBN-recruiting PROTACs have been shown to catalyse the degradation of the IMiD targets IKZF1 and IKZF3.
“and some CRBNrecruiting PROTACs have been shown to catalyse the degradation of the IMiD targets IKFZ1 and IKFZ3 (refs 40,41 ).”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [41]
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- Authors
- Jiang, B., Wang, E. S., Donovan, K. A., Liang, Y., Fischer, E. S., Zhang, T., & Gray, N. S.
- Affiliations
- Dana-Farber Cancer Institute (US)
- Corresponding author
- Zhang, Tinghu
- Gray, Nathanael S.
- ORCID
- Venue
- Angewandte Chemie International Edition
- Publisher
- Wiley
- Published
- 2019-03-29
- Volume
- 58
- Issue
- 19
- Pages
- 6321-6326
- ISSN
- 1433-7851 (ISSN-L)
- 1521-3773
- PMC
- PMC7678623
- OpenAlex
- W2917565897
- Semantic Scholar
- 453a25d8c1f9a6987f549b2e132dc50d712ec85d
- Cited by
- 272
- References
- 24
- Citations by year
- 2026: 19 · 2025: 46 · 2024: 39 · 2023: 26 · 2022: 38 · 2021: 47 · 2020: 43 · 2019: 14
- FWCI
- 12.49
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Angewandte Chemie International Edition (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Damon Runyon Cancer Research Foundation (DRG-2270-16, DRR-50-18)
- National Institutes of Health (R01CA218278)
- Dana-Farber Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Advanced Breast Cancer Therapies
- Keywords
- CDK4, CDK6, selective degradation, mantle cell lymphoma, metastatic breast cancer, cell cycle regulation, antiproliferative activity
- MeSH terms
- Humans, Imides, Piperazines, Pyridines, Cell Line, Tumor, Protein Kinase Inhibitors, Cell Proliferation, Cyclin-Dependent Kinase 4, Cyclin-Dependent Kinase 6, Ikaros Transcription Factor, Cell Cycle Checkpoints
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