Design principles for cyclin K molecular glue degraders

Abstract

Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12–cyclin K to the DDB1–CUL4–RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure–activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors

“…While writing this manuscript, the Thomä group published work exploring the SAR of cyclin K degraders. Their work further supports the conclusion that a diverse range of solvent-exposed groups can be incorporated into cyclin K inhibitors and used to trigger cyclin K degradation . Our data expands on their findingswhile they report that aromatic groups are required for degradation, we have identified nonaromatic substituents that enable potent degradation, as well as a subset of degraders showing improved activity compared to CR8.…”

“…Their work further supports the conclusion that a diverse range of solvent-exposed groups can be incorporated into cyclin K inhibitors and used to trigger cyclin K degradation. 36 Our data expands on their findings�while they report that aromatic groups are required for degradation, we have identified nonaromatic substituents that enable potent degradation, as well as a subset of degraders showing improved activity compared to CR8. We demonstrate that degradation-inducing moieties can be transferred between structurally distinct series.…”

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

“…The formation of the ternary complex is the key mechanistic step in the mechanism of action of small molecule degraders. It is established that characteristics such as affinity and half-life of the ternary complex correlate well with degradation fitness (26,29,35,36,40), and potentiating ternary complex affinity, stability and favourability to target ubiquitination provides a powerful optimization strategy. This goal can be expediated through biophysical and structural insights of CRBN recruitment, ushering structure-guided design of novel chemical matter.…”

“…This is in striking contrast with the structural and biophysical enablement that supports design of PROTAC degraders recruiting the other popular E3 ligase, von Hippel Lindau (VHL), as illustrated by the many ternary complex co-crystal structures solved by us and others that have led to efficient structure-guided design of VHL-based PROTACs (28)(29)(30)(31)(32)(33)(34), and their biophysical characterization (28,35,36). Ternary co-crystal structures have also enabled structure-driven design of Cyclin K degraders which glue CDK12 to the CRL4 adaptor protein DDB1 (Damage specific DNA binding protein 1), to induce ubiquitination and degradation of CDK12complexed Cyclin K (37)(38)(39)(40). We therefore hypothesized that full structural enablement of CRBN could substantially accelerate the design of CRBN-based degraders, and so turned our attention to protein construct design.…”

Induced protein degradation for therapeutics: past, present, and future

“…As a result, CDK12 fills a new role as a neosubstrate receptor that presents cyclin K for ubiquitination (68)(69)(70). Structural studies revealed that the CDK inhibitor CR8 binds the active site of CDK12 and bridges the CDK12-DDB1 interface (68,71). Importantly, the compound-induced complex mimics the overall architecture of a typical CRL4 E3 ligase complex.…”