Ubiquitin Engineering for Interrogating the Ubiquitin–Proteasome System and Novel Therapeutic Strategies

Abstract

Protein turnover, a highly regulated process governed by the ubiquitin–proteasome system (UPS), is essential for maintaining cellular homeostasis. Dysregulation of the UPS has been implicated in various diseases, including viral infections and cancer, making the proteins in the UPS attractive targets for therapeutic intervention. However, the functional and structural redundancies of UPS enzymes present challenges in identifying precise drug targets and achieving target selectivity. Consequently, only 26S proteasome inhibitors have successfully advanced to clinical use thus far. To overcome these obstacles, engineered peptides and proteins, particularly engineered ubiquitin, have emerged as promising alternatives. In this review, we examine the impact of engineered ubiquitin on UPS and non-UPS proteins, as well as on viral enzymes. Furthermore, we explore their potential to guide the development of small molecules targeting novel surfaces, thereby expanding the range of druggable targets.

Targeting the Ubiquitin–Proteasome System and Recent Advances in Cancer Therapy

“…Following the same line of evidence, the exploitation of engineered ubiquitin variants (UbVs) will pave the way to improve target specificity and selectivity. In fact, in the last few years, several studies have demonstrated that UbVs that tightly bind to UPS–related enzymes (such as E2s, E3s, and DUBs) may serve as valuable tools to modulate the function of these enzymes [ 156 ], as exemplified by the UbVs which inhibit USP7 and USP2a deubiquitinases described in Section 6.1 .…”

“…The rationale of this strategy relies on several properties, including the presence of Ub-binding sites in the UPS proteins, the ability of Ub to engage in low-affinity but specific interactions with UPS components and the possibility of genetically engineering the ubiquitin molecules. Over the past few years, UbVs have been obtained and screened against multiple components of UPS, such as E2 conjugating enzymes, E3 ligases and DUBs [ 156 ]. UbVs show high affinity and selectivity in targeting specific UPS protein and they can act as inhibitors, activators or modulators of targeted proteins.…”

“…The intracellular expression of these UbVs in cancer cells inhibits endogenous USP7 and USP2a, thus promoting the proteasomal degradation of MDM2 and, consequently, p53 stabilization [ 157 , 158 , 159 ]. Although the UbVs targeting UPS components have demonstrated their anticancer efficacy in cellular models [ 156 ], their potential use as therapeutics in cancer treatment awaits further validation.…”