Targeting Transcription Factors in Neuroblastoma: Development of Aurora Kinase A/N-Myc Degraders and ID2 Chemical Probes

Abstract

Transcription factors (TFs) are promising targets in oncology due to their critical rolesin dysregulated signaling pathways in tumor cells. However, targeting TFs with small molecules is challenging as they frequently lack endogenous ligands or amenable ligandbinding sites. The thesis will discuss our efforts in the development of novel chemical modulators of TFs in neuroblastoma using targeted protein degradation. N-Myc overexpression is the most frequent driver in neuroblastoma. Unique features of N-Myc biology offer innovative approaches for developing chemical modulators of this oncogenic TF. For example, N-Myc is stabilized from proteolytic degradation in neuroblastoma through binding to Aurora kinase A (Aurora-A). Chapters 2 – 3 will discuss the discovery of first-in-class Aurora-A/N-Myc degraders and the first proof-of-concept for targeting N-Myc with Aurora-A degraders. A highly selective and potent Aurora-A ligand 2.1 (HLB-0532261, HLB = Harki Lab) was developed through chemical modifications of the CDK4/6 inhibitor ribociclib. A series of Aurora-A/N-Myc degraders were subsequently developed using proteolysis targeting chimera (PROTAC) technology. The representative compound, 2.3 (HLB-0532259), potently decreases N-Myc protein levels following the induced degradation of Aurora-A. Tandem mass tag (TMT)-based proteomic analysis has demonstrated that 2.3 possesses excellent selectivity for degrading Aurora-A and N-Myc in neuroblastoma cells. Furthermore, 2.3 exhibits low nanomolar cytotoxicity against MYCN-amplified neuroblastoma cells, favorable pharmacokinetic properties, and potent in vivo anti-tumor efficacy. Continuous efforts on optimizing the Aurora-A targeting ligand for better kinase selectivity will be discussed in Chapter 4. And Chapter 5 will focus on the exploration of rigid and hydrophilic chemical linkers in Aurora-A/N-Myc PROTACs to improve the physicochemical properties of 2.3. Inhibitor of DNA-binding 2 (ID2) has been found to be critical for tumorigenesis and its expression is strongly predictive of poor prognosis for neuroblastoma patients. However, validation of ID2 as a viable protein target for neuroblastoma remains an understudied area in drug discovery, and no small molecule ID2 modulators have been published. Chapter 6 will discuss the serendipitous discovery of 6.1 (HLB-0534981), an abemaciclib analogue, that induces a potent downregulation of both ID2 and N-Myc. To decipher the unknown target(s) of 6.1, a diazirine photo-crosslinking probe, 6.6 (HLB-0535030), has been successfully developed and validated as a viable probe for the subsequent target identification studies. Finally, Appendix A reports the development of a cellular thermal shift assay for evaluating the target engagement of small-molecule compounds with Cyclin Kinase 1/2.