Development of CDK1-selective degraders for the treatment of T-cell malignancies

Cyclin-dependent kinases (CDKs) are serine/threonine kinases which play important roles in the control of cell division and transcription modulation. Among the members that regulate the cell cycle, CDK1 is considered the most essential, because its functions cannot be compensated by other CDKs, whereas CDK1 is capable of recapitulating their functions in regulating cell cycle transitions. Overexpression of CDK1 or its hyperactivation allows evasion of the G2/M phase checkpoint (DNA structure checkpoint) even in cases of cells with faulty DNA. This leads to the propagation of cells that possess damaged DNA eventually culminating in tumorigenesis. Numerous investigations have indeed demonstrated that the levels of CDK1 are upregulated in various tumors, including T-cell malignancies, which are aggressive hematological cancers with limited treatment options. Targeting CDK1, therefore, represents an appealing strategy for the development of novel therapeutics for T-cell cancers. Because the conventional inhibitor-based concept has limitations due to high inhibitor concentrations that must be maintained to ensure the target’s active site occupancy, innovative strategies to develop drugs are needed. In the proposed project, we intend to utilize targeted protein degradation (TPD) approaches to achieve selective chemically-induced depletion of CDK1. Proteolysis targeting chimeras (PROTACs) are currently deemed as the most promising TPD modality in drug discovery due to a range of advantages over inhibitors, such as catalytic mode of action, increased selectivity, as well as degradation of overexpressed and mutated proteins. PROTACs are heterobifunctional compounds consisting of an E3 ligase ligand, which is linked to a ligand that binds the target protein. Thus, PROTACs recruit the target protein to the E3 ligase resulting in the formation of a ternary complex ‘target-PROTAC-E3 ligase’. This promotes ubiquitination of the target protein and its subsequent proteasomal degradation. Recent progress in the TPD field uncovered two additional types of heterobifunctional compounds, which can exploit endogenous machineries to deplete intracellular proteins, namely hydrophobic tags (HyTs), and heat shock protein 90 (Hsp90)-mediated targeting chimeras (HEMTACs). The former mimic the unfolded protein response, while the latter hijack Hsp90 for induced degradation of cancer-related proteins. The scientific aim of the proposed project is to develop first-in-class degraders for the targeted depletion of the key cell cycle regulator, CDK1, as potential therapeutics or as powerful tools to probe the complex biology of this protein. The specific project objectives are: (i) to design and synthesize new heterobifunctional compounds capable of binding and degrading CDK1 using literature-guided knowledge, computational techniques, and medicinal chemistry; (ii) to evaluate the prepared CDK1 degraders for their anticancer activity in different T-cell malignancy models; (iii) to develop high-quality lead compound(s) as CDK1 degraders with good physico-chemical properties and potent anticancer activity. To achieve these goals, we will focus on the design and development of three complementary types of CDK1 degraders, i.e. PROTACs, HyTs, and HEMTACs. The modular way in which these chimeric compounds can be assembled will enable efficient synthesis of a variety of heterobifunctional degraders, which will be subsequently thoroughly evaluated in a number of in vitro functional cell-based assays. The project will be implemented by an international and complementary consortium of three scientific partners with highly interdisciplinary expertise. These facts raise prospects both in terms of feasibility of the project and scientifically successful outcome. The advanced CDK1 degraders will undoubtedly be of paramount scientific importance and will represent a valuable contribution to the development of a research field focused on novel T-cell malignancy treatments.