Conditional protein degradation with novel PROteolysis-TArgeting Chimeras (PROTACs)

Abstract

PROteolysis-TArgeting Chimeras (PROTACs) are novel heterobifunctional degraders that catalytically induce targeted protein degradation through the Ubiquitin-Proteasome System (UPS). Offering unique advantages over conventional small molecule inhibitors, PROTACs have successfully degraded a wide range of oncogenic proteins and showed potential as a promising paradigm in drug discovery. Despite the rapid expansion of the field, achieving conditional activation control of PROTAC-mediated protein degradation remains relatively unexplored. In this thesis, two novel PROTAC design strategies were developed to enhance spatiotemporal control and tissue specificity in PROTAC-mediated protein degradation. In the first design, a novel photoswitchable multi-kinase PROTAC, AP-PROTAC-2, was developed to enable conditional light-mediated control of protein degradation. This design incorporates a novel arylazopyrazole photoswitchable linker, combined with a multi-kinase inhibitor capable of engaging approximately 40% of the kinome. AP-PROTAC-2 can be reversibly switched between E and Z isomer-enriched states and exhibits superior photochemical properties compared to previous photoswitchable PROTACs. Multiplexed proteomics studies demonstrated that AP-PROTAC-2 selectively depleted four protein kinases in vitro in a light-switchable manner. This research marks the first instance of simultaneous photoswitchable degradation of multiple proteins, achieving selective spatiotemporal modulation of targeted kinase degradation. In the second design, peptide-based PROTACs were conjugated to monoclonal antibodies to design antibody-peptide degrader conjugates (Ab-peptides), building upon the concept of antibody-drug conjugates (ADCs). These Ab-peptides were designed to utilise ADC's antibody-mediated internalisation pathways for the targeted delivery of peptide payloads to antigen-positive cells. This approach aimed to enhance tissue specificity, cellular uptake, and intracellular degradation potency of peptide-based degraders. The development of three types of Ab-peptides targeting distinct proteins and employing different ADC linkers was reported. The resulting Ab-peptides exhibited enhanced target degradation efficacy surpassing that of unconjugated peptides, underscoring their promising potential. Collectively, these novel strategies offer valuable perspectives and insights into conditional protein degradation with a focus on photoswitchable multi-target PROTACs and peptide-based PROTACs.