Identification of a Novel Cyclin K Degrader Molecule with Selective Anti-AML Activity

Acute Myeloid Leukemia (AML) is a poor prognosis type of leukemia with 5-year survival rate of only 30.5% in adults. To develop novel agents for this disease, we screened a library of 10,000 compounds across 56 genetically diverse primary AML specimens. We looked for active compounds with a selective profile of inhibition, to exclude general cytotoxic compounds, and with a unique fingerprint across the 10,000 molecules. We identified compound S656 as a selective anti-AML molecule with low toxicity to cord blood cells.

To identify the mechanism of action of S656, we performed a CRISPR/Cas9 genome-wide functional screen, and found all components of the Cullin4-RING E3 ubiquitin ligase (CRL4) complex as the top synthetic rescue genes. We thus hypothesized that S656 acts as a molecular glue, mediating proteolysis of its target protein. Total proteomic analysis revealed cyclin K as the most depleted protein upon short-time exposure to S656. Validation experiments showed that leukemic cells exposed 3 hours to S656 display a strong depletion of cyclin K and its binding partner CDK12, and consequently, reduced levels of ser2 RNA Pol2 phosphorylation levels. Ultimately, S656 suppresses expression of the DNA damage response genes and induces DNA lesions and apoptosis. Our data indicate that S656 is a cyclin K degrader acting through the recruitment of CRL4 complex, and that cyclin K loss mediates the biological activity of S656 molecule.

A small number of structurally distinct cyclin K degraders have been described in the last couple of years. We showed, by comparing their activity in primary AML samples, that cyclin K degrader molecules are not all equivalent, likely due to additional inhibitory activities (CDK inhibition for example). Most importantly, we showed that cyclin K degraders are not biologically equivalent to direct CDK12/13 inhibitors, thus providing an additional class of anti-proliferative molecules to investigate for therapeutic development.

Additionally, structure-activity relationship (SAR) around S656 molecule is ongoing to determine critical structural elements that confer its molecular glue properties, to discriminate cyclin K degrader functions from off-target activities, and to increase its potency.

Previous studies have highlighted the importance of cyclin K in the stability of the genome and promotion of cell proliferation. Our study thus provides a novel cyclin K degrader with potent anti-AML potential.

Hebert:BMS: Research Funding. Marinier:BMS: Research Funding. Sauvageau:ExCellThera: Consultancy, Current Employment, Current equity holder in private company, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; BMS: Research Funding.