Molecular glue degraders of cyclin K

Molecular glue degraders are small, drug-like compounds that induce interactions between an E3 ubiquitin ligase and a target, leading to target ubiquitination and subsequent degradation by the proteasome. Unlike traditional enzyme inhibitors, degraders can act sub-stoichiometrically to catalyse the rapid depletion of previously inaccessible targets. Despite the clinical success of this modality, only two molecular glue degrader classes, thalidomide analogues and aryl sulphonamides, have been well-described thus far and molecular glue discovery remains largely serendipitous. Hence, novel molecular glue degrader examples, as well as methods for their prospective discovery and rational design are highly sought-after.
In this work, a systematic search for molecular glue degraders was performed through bioinformatic mining of drug cytotoxicity data for correlations with E3 ligase component expression levels across hundreds of human cancer cell lines. This led to the identification of CR8, a preclinical cyclin-dependent kinase (CDK) inhibitor, as a molecular glue degrader of cyclin K. CR8 was found to facilitate the formation of a complex between CDK12–cyclin K and the CUL4 adaptor protein DDB1, thereby bypassing a canonical substrate receptor and directly presenting cyclin K for ubiquitination and degradation. A solvent-exposed pyridyl moiety of the compound, one that is absent in related inhibitors, protrudes from the kinase pocket and engages DDB1, which suggests more broadly that chemical modification of surface-exposed moieties can confer gain of function glue properties to an inhibitor. Notably, several structurally distinct cyclin K degraders were reported shortly after, including the dCeMM2-4 compounds, whose discovery through differential compound toxicity profiling in hyponeddylated and wild-type cellular models is described herein.
To examine this unexpected chemical diversity, the cyclin K degrader structure-activity relationship (SAR) was further investigated through the evaluation of over 90 putative degraders, including novel scaffolds and published inhibitors. The crystallographic dissection of 29 ternary complexes revealed that cyclin K degraders share a common mechanism, whereby kinase-binding scaffolds acquire gain-of-function properties through the engagement of interfacial DDB1 residues. This work demonstrated that degrader SAR differs considerably from that of inhibitors, offering conceptual learnings about compound-induced interfaces applicable to other molecular glue degrader classes. The cellular evaluation of cyclin K degrader activity identified compounds more potent than CR8, and established that cyclin K degradation versus CDK12 inhibition give rise to distinct transcriptional signatures. These findings therefore not only define a novel, diverse class of molecular glue degraders but also yield next-generation, interface-leveraging scaffolds for the selective inactivation of the emerging therapeutic targets CDK12 and cyclin K.