Development of Dual and Selective Degraders of Cyclin‐Dependent Kinases 4 and 6

Abstract

Cyclin-dependent kinases 4and 6(CDK4/6) are key regulators of the cell cycle,a nd there are FDA-approved CDK4/6 inhibitors for treating patients with metastatic breast cancer.H owever,d ue to conservation of their ATP-binding sites,d evelopment of selective agents has remained elusive. Here,w er eport 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.W e found that in mantle cell lymphoma cell lines,c ombined 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,w er eport here the first compounds capable of inducing selective degradation of CDK4 and CDK6 as tools to pharmacologically dissect their distinct biological functions.Cyclin-dependent kinases 4a nd 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] As such, CDK4/6 are attractive targets for cancer therapy,and the dual CDK4/6 inhibitors palbociclib,r ibociclib,a nd abemaciclib have been FDAapproved for treating patients with advanced or metastatic breast cancer, leading to prolonged progressionfree-survival. [2] These agents are also currently under investigation in subsets of lung cancers,sarcomas,and lymphomas, such as mantle cell lymphoma (MCL), that exhibit aberrant cell-cycle progression due to activation of CDK4/6. [3] Although CDK4 and CDK6 are highly homologous, CDK4-and CDK6-specific functions have been reported. Fore xample,i namouse 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] On the other hand, CDK6-specific functions include participating as part of at ranscription complex that regulates expression of p16INK4a and VEGF-A, [5] and acting as ac o-factor for NFkB-dependent gene expression. [6] We also recently demonstrated that CDK6, but not CDK4, phosphorylates NFAT-family transcription factors to promote T-cell activation and enhance the antitumor immune response. [7] Since current CDK4/6 inhibitors target their highly conserved ATP-binding pockets and are approximately equipotent inhibitors of both proteins,w eh ypothesized that achieving selectivity would require exploiting selectivity determinants outside of the ATP-binding pocket. One approach is to develop small-molecule degraders,bifunctional molecules that consist of an E3 ubiquitin ligase binding moiety and at arget-binding moiety connected via an optimizable linker.S uccessful degradation requires induced heterodimerization between the E3 ligase and the target of interest, resulting in the targetsp olyubiquitination and subsequent proteasomal degradation. [8] This strategy has been deployed to achieve select...

Systematic exploration of different E3 ubiquitin ligases: an approach towards potent and selective CDK6 degraders

“…Compound 21 (Table 1) represents a negative control bearing an N-methylated-pomalidomide moiety which is unable to bind to CRBN. Notably, the PROTAC structures have an acylated piperazine moiety, thus differing from previously reported CDK4/6d, [33][34][35][36][37] all of which possess an alkylated piperazine with basic properties. On the contrary, our synthesis resulted in compounds with a tertiary amide which are not protonated at physiological pH value.…”

“…These approaches, including the one that is reported herein, utilized 2-aminopyrimidines, palbociclib or ribociclib, as the CDK4/6addressing moiety. [33][34][35][36][37] The corresponding molecular design culminated in the discovery of the prototypical PROTACs 7 and 8 ( Fig. 1).…”

PROTACs: great opportunities for academia and industry

“…In 2019, Gray and coworkers varied the linkers of the bifunctional molecules to find dual CDK4/6 degraders (BSJ-03-204) and selective CDK4 and CDK6 degraders (BSJ-04-132 or BSJ-03-123, respectively) 172,173 (Fig. 14).…”

Design, Synthesis, and Biological Evaluation of Proteolysis Targeting Chimeras (PROTACs) for the Dual Degradation of IGF-1R and Src

“…To date, PROTACs have been successfully applied to various target proteins with different cellular locations, including estrogen and androgen receptors, BET proteins, tau protein, FKBP12, and kinases [2,11,12,17,20,21]. In particular, PROTACs, which hijack various cellular kinases, have resulted in effective target degradations [22][23][24][25][26]. Furthermore, the enhanced selectivity of kinase degraders, as compared to their parental kinase inhibitors, were implicated as having potential applications for clinical study [23,27].…”