Drugging the undruggables: exploring the ubiquitin system for drug development

Abstract

Dynamic modulation of protein levels is tightly controlled in response to physiological cues. In mammalian cells, much of the protein degradation is carried out by the ubiquitin-proteasome system (UPS). Similar to kinases, components of the ubiquitin system are often dysregulated, leading to a variety of diseases, including cancer and neurodegeneration, making them attractive drug targets. However, so far there are only a handful of drugs targeting the ubiquitin system that have been approved by the FDA. Here, we review possible therapeutic intervention nodes in the ubiquitin system, analyze the challenges, and highlight the most promising strategies to target the UPS.

Figure 1

Summary of the ubiquitin system and possible intervention nodes. Ubiquitination is an ATP-dependent process carried out by three classes of enzymes. E1 activating enzymes form a thioester bond with ubiquitin, followed by subsequent binding of ubiquitin to E2 conjugating enzymes, and ultimately the formation of an isopeptide bond between the carboxyl-terminal glycine of ubiquitin and a lysine residue on the substrate protein, which requires E3 ubiquitin ligases. Multiple intervention nodes in the reaction cascade have been proposed to either block or enhance ubiquitination.

Figure 2

SCF^SKP2 as a possible anti-cancer target. (A) The crystal structure of SCF^SKP2 highlights potential interfaces (pockets 1-3) that small molecule inhibitors can bind to and block its E3 ligase function. (B) Compound 25 has been identified to be a selective SCF^SKP2 inhibitor. It blocks ubiquitination and degradation of p27, as well as ubiquitination and activation of AKT. Together, this compound exhibits potent antitumor activities in multiple animal models.

Figure 3

MDM2 as a potential anti-cancer target. p53 is rapidly ubiquitinated by MDM2 and degraded via the proteasome. Nutlins (and other MDM2/p53 interaction inhibitors) disrupt the interaction between MDM2 and p53, resulting in accumulation of p53 and its anti-tumor effect.

Figure 4

Rationales of enhancing ubiquitination. (A) Auxin is a plant hormone that directly binds to the F-box protein TIR1. With the support of co-factor InsP₆, auxin promotes TIR1 interaction with the substrate proteins, AUX/IAAs, leading to enhanced ubiquitination and degradation of substrates. (B) Binding of endogenous substrates to CRBN is blocked by IMiDs molecules, whereas IMiDs recruit neo-substrates (for example: IKZF1 and IKZF3) to CRBN, leading to the stabilization of endogenous substrates but degradation of neo-substrates.

Figure 5

PROTAC as an anti-cancer strategy. (A) PROTACs are bifunctional molecules that are comprised of a targeting ligand tethered to an E3 ligase-recruiting moiety through a short linker. (B) dBET1 as an example of PROTAC. dBET1 is comprised of JQ1 that binds to oncoprotein BRD4, and thalidomide that recruits CRL4^CRBN, an E3 ubiquitin ligase.

Figure 6

Hydrophobic tagging as an anti-cancer strategy. A partially unfolded protein is assisted by the chaperone machinery to refold back into its native conformation. Proteasome-dependent degradation is triggered if chaperone machinery fails to refold a damaged protein. Hydrophobic tagging molecules are bifunctional molecules comprised of a substrate-recruiting ligand connected with a hydrophobic moiety, such as adamantane. A protein binding to a hydrophobic tagging molecule mimics partially unfolded state to trigger target protein degradation by either directly escorting target to proteasome or initiating ubiquitination of target protein.