Discovery of Small-Molecule Degraders of the CDK9-Cyclin T1 Complex for Targeting Transcriptional Addiction in Prostate Cancer

Abstract

Aberrant hyperactivation of cyclins results in carcinogenesis and therapy resistance in cancers. Direct degradation of the specific cyclin or cyclin-dependent kinase (CDK)-cyclin complex by small-molecule degraders remains a great challenge. Here, we applied the first application of hydrophobic tagging to induce degradation of CDK9-cyclin T1 heterodimer, which is required to keep productive transcription of oncogenes in cancers. LL-K9-3 was identified as a potent small-molecule degrader of CDK9-cyclin T1. Quantitative and time-resolved proteome profiling exhibited LL-K9-3 induced selective and synchronous degradation of CDK9 and cyclin T1. The expressions of androgen receptor (AR) and cMyc were reduced by LL-K9-3 in 22RV1 cells. LL-K9-3 exhibited enhanced anti-proliferative and pro-apoptotic effects compared with its parental CDK9 inhibitor SNS032 and suppressed downstream signaling of CDK9 and AR more effectively than SNS032. Moreover, LL-K9-3 inhibited AR and Myc-driven oncogenic transcriptional programs and exerted stronger inhibitory effects on several intrinsic target genes of AR than the monomeric CDK9 PROTAC (Thal-SNS032).

Discovery of LL-K8-22: A Selective, Durable, and Small-Molecule Degrader of the CDK8-Cyclin C Complex

“…Compound LL-K8-16 was synthesized with a similar procedure as LL-K8-1 from 11 (44 mg, 0.1 mmol, 1 equiv) and 2,2-diphenylacetic acid (A9) (32 mg, 0.15 mmol, 1.5 equiv). LL-K8-16 was obtained as a yellow solid (37 44.19, 43.95, 41.65, 41.43, 41.38, 41.27.…”

“…Compound LL-K8-24 was synthesized with a similar procedure as LL-K8-15 from 11 (44 mg, 0.1 mmol, 1 equiv) and intermediate B1 (47 mg, 0.2 mmol, 2 equiv). LL-K8-24 was obtained as a white solid (37…”

“…33,36 We have previously demonstrated that synchronous degradation of CDK9 and its binding protein cyclin T1 can be achieved by the HyT approach. 37 The relatively slow degradation kinetics of HyT may facilitate the degradation of protein complexes, which avoids the rapid depletion of one free subunit of the protein complex before it is assembled into the protein complex. A recent study also showed that the bridged PROTAC approach enables degradation of undruggable targets, such as cyclin D1.…”

“…The HyT-based degrader contains a large hydrophobic moiety that is linked to the ligand of target protein by a linker . The hydrophobic moiety, attaching to the protein surface, mimics a denatured state of the target protein, resulting in proteasome system-mediated degradation of the target protein. , We have previously demonstrated that synchronous degradation of CDK9 and its binding protein cyclin T1 can be achieved by the HyT approach . The relatively slow degradation kinetics of HyT may facilitate the degradation of protein complexes, which avoids the rapid depletion of one free subunit of the protein complex before it is assembled into the protein complex.…”

Bridged Proteolysis Targeting Chimera (PROTAC) Enables Degradation of Undruggable Targets

“…We hypothesized that cyclin D1 and other traditionally undruggable proteins could be targeted by a novel PROTAC approach, termed bridged PROTAC, which utilizes a small-molecule binder that recruits a bridge protein and its binding partner (POI), thus bringing the protein complex into proximity with an E3 ligase and inducing preferential degradation of the POI over the bridge protein (Figure A). While protein complex degraders have been reported − such as EZH2 and EED PROTACs that also degraded other PRC2 (polycomb repressive complex 2) components − ,, and a hydrophobic tag-based CDK9 degrader that induced the degradation of both CDK9 and cyclin T1, none of these degraders preferentially degraded partner proteins over the protein that binds the degraders directly. In fact, the degradation of these partner proteins is likely the consequence of the initial degradation of the protein that directly binds the PROTAC and subsequent destabilization of the protein complex.…”