Induced protein degradation: an emerging drug discovery paradigm

Abstract

Small-molecule drug discovery has traditionally focused on occupancy of a binding site that directly affects protein function, and this approach typically precludes targeting proteins that lack such amenable sites. Furthermore, high systemic drug exposures may be needed to maintain sufficient target inhibition in vivo, increasing the risk of undesirable off-target effects. Induced protein degradation is an alternative approach that is event-driven: upon drug binding, the target protein is tagged for elimination. Emerging technologies based on proteolysis-targeting chimaeras (PROTACs) that exploit cellular quality control machinery to selectively degrade target proteins are attracting considerable attention in the pharmaceutical industry owing to the advantages they could offer over traditional small-molecule strategies. These advantages include the potential to reduce systemic drug exposure, the ability to counteract increased target protein expression that often accompanies inhibition of protein function and the potential ability to target proteins that are not currently therapeutically tractable, such as transcription factors, scaffolding and regulatory proteins.

Figure 1. Mechanism of induced protein degradation technologies

A) Hydrophobic tagging (HyT) using bifunctional adamantane-based molecules. One proposal for the mode of action is that the hydrophobic tag destabilizes the protein of interest (POI), thereby recruiting endogenous chaperones to the unfolded protein. The protein is then shuttled for degradation to the proteasome. An alternative proposal is that chaperones recognize the hydrophobic tag directly and mediate the proteasomal degradation of the tagged protein. B) PROTAC technology works through active recruitment of an E3 ligase in order to tag proteins for disposal. Bifunctional PROTAC molecules bind to the POI with one end while the other end binds an E3 ligase to form a ternary complex. The recruited E3 ligase then mediates the transfer of ubiquitin from an E2 enzyme to the POI. The ternary complex dissociates, the ubiquitinated POI is removed by the proteasome and the PROTAC can bind another POI (assuming the interaction with the POI is non-covalent). C) The traditional ‘occupancy-driven pharmacology’ model is predicated upon stoichiometric drug binding to the POI in order to modulate protein function. With non-covalent inhibitors, the drug is capable of dissociating from the POI, leading to restoration of protein function. Furthermore, inhibitors based on ‘occupancy-driven’ pharmacology typically bind to an active site on the POI (although allosteric inhibitors and inhibitors targeting protein–protein interactions are an exception). By contrast, induced protein degradation technologies are ‘event-driven’, and can potentially exploit binding anywhere on the POI in order to achieve degradation.

Figure 2. Structures of compounds used for induced protein degradation technologies

A) Hydrophobic tags (HyTs) utilized to recruit chaperones to a protein of interest (POI): adamantane and Arg-Boc₃. B) E3 ligase recruiting ligands employed to hijack E3 ligases to ubiquitinate and degrade POIs. The wavy line illustrates the attachment point utilized in the studies discussed. C) The chemical structures of proteolysis-targeting chimeras (PROTACs) utilizing different E3 ligases to target the POIs for degradation. The POI ligands are shown in blue; the linkers are shown in black; and the E3 ligase recruiting ligands are shown in red.

Figure 3. Timeline of the induced protein degradation field

Selected events related to selective estrogen receptor degraders are highlighted in blue; proteolysis-targeting chimeras (PROTAC) technology in red,; hydrophobic tagging (HyT) in green,; and biotechnology company launches in yellow. MetAP-2, methionine aminopeptidase-2; ER, estrogen receptor; MDM2, mouse double minute 2 homolog; AR, androgen receptor; CRBN; Cereblon; cIAP1, cellular inhibitor of apoptosis protein 1; CRABP, cellular retinoic acid-binding protein; VHL, Von Hippel-Lindau; GST, glutathione-S-transferase; DHFR, dihydrofolate reductase; IKZF, Ikaros family zinc finger; ErbB3, erythroblastosis oncogene B3.