E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points

Abstract

Proteolysis-targeting chimeras (PROTACs) have received tremendous attention as a new and exciting class of therapeutic agents that promise to significantly impact drug discovery. These bifunctional molecules consist of a target binding unit, a linker, and an E3 ligase binding moiety. The chemically-induced formation of ternary complexes leads to ubiquitination and proteasomal degradation of target proteins. Among the plethora of E3 ligases, only a few have been utilized for the novel PROTAC technology. However, extensive knowledge on the preparation of E3 ligands and their utilization for PROTACs has already been acquired. This review provides an in-depth analysis of synthetic entries to functionalized ligands for the most relevant E3 ligase ligands, i.e. CRBN, VHL, IAP, and MDM2. Less commonly used E3 ligase and their ligands are also presented. We compare different preparative routes to E3 ligands with respect to feasibility and productivity. A particular focus was set on the chemistry of the linker attachment by discussing the synthetic opportunities to connect the E3 ligand at an appropriate exit vector with a linker to assemble the final PROTAC. This comprehensive review includes many facets involved in the synthesis of such complex molecules and is expected to serve as a compendium to support future synthetic attempts towards PROTACs.

Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation

“…As depicted by Scheepstra M. et al in their 2019 review, the PROTAC-targeted ligases are CRL4 CRBN , cIAP1, MDM2, and CRL2 VHL , as they present known ligands that can be functionalized to add the needed linker and POI ligand (Figure 12) [38]. Arrows in Figure 13 indicate the most common position for the functionalization of these inhibitors; however, other positions can be succesfully functionalized for the obtention of different PROTACs, as very recently hightlighted by Bricelj A. et al [164]. Of all the E3 ligases that can be hijacked by PROTACs, in order to achieve selective degradation of HDACs, only CRL4 CRBN and CRL2 VHL have been targeted [38,60,61,75,[165][166][167][168][169][170].…”

Molecular Mechanisms of Cereblon-Interacting Small Molecules in Multiple Myeloma Therapy

“…PRO-TAC chemistry is a rapidly evolving area of drug development and beyond the scope of this review to describe in detail. We direct the reader to recent reviews and the PROTAC-DB online database as contemporary resources [114][115][116].…”

Targeted Protein Degradation: An Important Tool for Drug Discovery for “Undruggable” Tumor Transcription Factors

“… 5 The ubiquitin-proteasome system (UPS) consists of ubiquitin (Ub), the 26S proteasome, substrates, and 3 Ub cascade enzymes, namely Ub-activating enzyme (E1), Ub-conjugating enzyme (E2), and Ub ligase (E3). 6 Ubs are a class of small proteins that exist in most eukaryotes and are conjugated to other target proteins at their lysine residues. Protein ubiquitination may lead to degradation, localization, or modulation of signal transduction.…”

“… 7 Ub can be activated by E1 with the energy provided by ATP, Ub, and ATP, which are composed of ubiquitin adenylate complexes, after which it is transferred to the cysteine residue of E1. 5 – 7 E1 then transfers activated Ub to E2 via a transthioesterification reaction. In the last step of the ubiquitination cascade, E3 catalyzes the formation of an amide bond between Ub and the lysine residue of the POI.…”

“…In the last step of the ubiquitination cascade, E3 catalyzes the formation of an amide bond between Ub and the lysine residue of the POI. 6 – 8 Several Ub molecules are then added to form a polyubiquitin chain in the POI that is recognized by the 26S proteasome, which finally degrades the POI into small peptides. 9 – 11 …”