Development of Small Molecule Kinase Inhibitors: A Multi-Target Therapeutic Strategy for Cancer Treatment

Abstract

Dual-specificity tyrosine-regulated kinases (DYRKs) and CDC-like kinases (CLKs) play essential roles in oncogenic signaling, RNA splicing, and cancer stemness, particularly in aggressive malignancies such as colorectal cancer (CRC), glioblastoma (GBM), and acute myeloid leukemia (AML). This dissertation describes the design, synthesis, and biological evaluation of a diverse portfolio of small-molecule inhibitors and targeted degraders, guided by structure-based drug design, SAR exploration, and pharmacological profiling. Beginning with a selective DYRK1A inhibitor (DYR533), iterative medicinal chemistry efforts led to the development of pan-DYRK/CLK inhibitors (e.g., DYR747), with expanded kinase coverage and potent Wnt/?-catenin pathway suppression. Scaffold modifications, including quinazoline, aza-quinazoline, and quinoxaline cores, were systematically optimized to improve Wnt modulation, GBM and AML cytotoxicity, and surrogate ADME properties such as microsomal stability, solubility, and predicted oral bioavailability. Structural analyses informed further SAR campaigns across multiple regions of the pharmacophore, including region-specific modifications to improve metabolic stability and selectivity. The ‘flipped’ series was further derived from the non-orally bioavailable DYR747 and yielded analogs with enhanced oral bioavailability while retaining moderate Wnt inhibition. Notably, this series also generated the first EGFR inhibitor within the program, demonstrating unprecedented cytotoxicity against GBM. In parallel, the aryl-piperazine series produced DYR895, a proof-of-concept compound with demonstrated in vivo efficacy in a CRC model. Continued optimization led to the discovery of diamino-pyridine analogs, which further improved Wnt inhibition and cancer cell cytotoxicity while limiting CNS exposure, ideal for peripheral diseases. This body of work delivers a comprehensive medicinal chemistry strategy for targeting kinase-driven cancer stemness pathways using both inhibitor and degrader modalities. The findings establish foundational tools and translational leads for therapeutic intervention in cancers with a high unmet clinical need.