Selective degradation of CDK6 by a palbociclib based PROTAC

Abstract

Development of selective kinase inhibitors that target the ATP binding site continues to be a challenge largely due to similar binding pockets. Palbociclib is a cyclin-dependent kinase inhibitor that targets the ATP binding site of CDK4 and CDK6 with similar potency. The enzymatic function associated with the kinase can be effectively probed using kinase inhibitors however the kinase independent functions cannot. Herein, we report a palbociclib based PROTAC that selectively degrades CDK6 while sparing the homolog CDK4. We used competition studies to characterize the binding and mechanism of CDK6 degradation.

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– a game-changing technology

“…In 2014, the crystal structures of DDB1-CRBN complexes bound to thalidomide [14] and lenalidomide [15] were solved. Since then, PROTACs with IMiD small molecules targeting CRBN and diverse proteins of interest, including the bromodomain and extra-Terminal (BET) proteins (BRD2/3/4) [16][17][18], FKBP12 [16], BCR-ABL [19], BRD9 [20], Sirt2 [21], CDK9 [22,23], FLT3 [24], BTK [24,25], ALK [26], CDK4/CDK6 [27,28] and HDAC6 [29] have been reported.…”

“…For MDM2 -CRBN PROTACs, SARs were established regarding the length and the type of linker, modifications on the cereblon ligand and attachment point of the linker. The most potent compound, MD-224 (28), was the result of linker rigificiation; two methylene groups were converted into an alkyne group and this significantly improved the potency. The authors investigated also MDM2 -VHL PROTACs with the MDM2 inhibitor MI-1061, however in all cases MDM2 -VHL PROTACs were less potent than the corresponding MDM2 inhibitor.…”

Significance of Selective Protein Degradation in the Development of Novel Targeted Drugs and Its Implications in Cancer Therapy

“…[ 136 ] Moreover, SGK3‐PROTAC1, which was constructed by the SGK inhibitor 308R and the VHL ligand VH032, was shown to selectively degrade SGK3 at submicromolar concentrations. [ 137 ] Furthermore, other kinases, such as Bruton's tyrosine kinase, [ 138 ] anaplastic lymphoma kinase, [ 139 ] Fms‐like tyrosine kinase 3, [ 140 ] serine/threonine kinase TANK‐binding kinase 1 (TBK1), [ 141 ] CDK6, [ 142 ] and CDK9, [ 143 ] have been designed as effective PROTACs using kinase inhibitors and E3 ligands such as VHL, CRBN, and MDM2, respectively.…”