The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study

Abstract

Proteolysis targeting chimera (PROTAC) technology has emerged over the last two decades as a powerful tool for targeted degradation of endogenous proteins. Herein we describe the development of PROTACs for receptor tyrosine kinases, a protein family yet to be targeted for induced protein degradation. The use of VHL-recruiting PROTACs against this protein family reveals several advantages of degradation over inhibition alone: direct comparisons of fully functional, target-degrading PROTACs with target-inhibiting variants that contain an inactivated E3 ligase-recruiting ligand show that degradation leads to more potent inhibition of cell proliferation and a more durable and sustained downstream signaling response, and thus addresses the kinome rewiring challenge seen with many receptor tyrosine kinase inhibitors. Combined, these findings demonstrate the ability to target receptor tyrosine kinases for degradation using the PROTAC technology and outline the advantages of this degradation-based approach.

The PROTAC technology in drug development

“…They showed that the PROTACs significantly decreased cellular levels of ALK fusion proteins in different cell lines including SU-DHL-1 (lymphoma) and NCI-H2228 (lung cancer). 94 Interestingly, the PROTAC mediated the internalization of EGFR and sorted to lysosomal degradation, 94 although the RTKs usually prefer to internalize into a recycle endosome. 80 Kang et al later on proved that a synthesized PROTACs against ALK (based on VHL) worked in vivo.…”

PROTACs: An Emerging Targeting Technique for Protein Degradation in Drug Discovery

“…Compound 3i can completely knockdown TBK1 in several cancer cell lines at a concentration of 100 nM, indicating the excellent efficiency of this compound (Figure d) . In addition, VHL‐based PROCTACs have been shown to target transmembrane receptor tyrosine kinases (RTKs) as well as mutants of RTKs …”

Molecular design opportunities presented by solvent‐exposed regions of target proteins

“…Targeted protein degradation, using heterobifunctional small molecules (PROTACs) to remove protein targets from within cells, has emerged as a novel strategy for drug development, with the opportunity of providing therapeutic interventions not achievable with existing occupancy‐based enzyme inhibition approaches . Small‐molecular‐weight synthetic PROTACs ( 185‐189 ) have been used to selectively degrade various specific proteins (Figure ), including pirin, sirt2, BET protein, androgen receptor, and BRD4 protein …”

“…into one molecule, to take advantage of the presence of large hydrophobic patches at the HDAC surface rim. 122 Some encouraging results have been reported (Figure 22), such as dual-acting HDAC and topoisomerase II inhibitor On the basis of these analyses, a structure-based hybridization strategy was used to discover novel Mcl-1/Bcl-xL dual inhibitors (159,160) with a suitable linker based on 157 and 158 ( Figure 22). Notably, compound 160 displayed the potent dual-inhibitory activities (Mcl-1, IC 50 = 0.088 μM; and Bcl-xL, IC 50 = 0.0037 μM) ( Figure 23).…”