Current strategies for the design of PROTAC linkers: a critical review

Abstract

PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an “anchor” to bind to an E3 ubiquitin ligase and a “warhead” to bind to a protein of interest, connected by a chemical linker. Targeted protein degradation by PROTACs has emerged as a new modality for the knock down of a range of proteins, with the first agents now reaching clinical evaluation. It has become increasingly clear that the length and composition of the linker play critical roles on the physicochemical properties and bioactivity of PROTACs. While linker design has historically received limited attention, the PROTAC field is evolving rapidly and currently undergoing an important shift from synthetically tractable alkyl and polyethylene glycol to more sophisticated functional linkers. This promises to unlock a wealth of novel PROTAC agents with enhanced bioactivity for therapeutic intervention. Here, the authors provide a timely overview of the diverse linker classes in the published literature, along with their underlying design principles and overall influence on the properties and bioactivity of the associated PROTACs. Finally, the authors provide a critical analysis of current strategies for PROTAC assembly. The authors highlight important limitations associated with the traditional “trial and error” approach around linker design and selection, and suggest potential future avenues to further inform rational linker design and accelerate the identification of optimised PROTACs. In particular, the authors believe that advances in computational and structural methods will play an essential role to gain a better understanding of the structure and dynamics of PROTAC ternary complexes, and will be essential to address the current gaps in knowledge associated with PROTAC design.

PROTACs and Building Blocks: The 2D Chemical Space in Very Early Drug Discovery

“…Therefore, an analysis of the degraders’ chemical space is extremely relevant to understand more about their potential as drugs. This was also very recently highlighted by Troup et al in their excellent review [ 14 ], which supports the relevance of physicochemical properties in the PROTAC drug optimization process. Moreover, two pivotal studies specifically focused on this topic have been published in the last two years.…”

“…The high number of linkers could be due to the evidence that a significant proportion of degraders were developed through mostly empirical optimization of linker composition, which usually requires the synthesis of large libraries of compounds containing linkers of various natures [ 14 ]. A second consideration on linkers is related to the different functionalization at either end [ 14 ]. A detailed analysis of the sites conjugating the linker with warheads and E3 ligands is beyond the scope of our study.…”

“…Therefore, the synthetic requirements and commercial availability of reagents suggest that the fragment proposal presented by the database is not representative enough. The high number of linkers could be due to the evidence that a significant proportion of degraders were developed through mostly empirical optimization of linker composition, which usually requires the synthesis of large libraries of compounds containing linkers of various natures [14]. A second consideration on linkers is related to the different functionalization at either end [14].…”

Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends

“…Engineered to induce degradation of disease causing proteins by ubiquitin proteasome pathway, PROTAC degrade disease-causing proteins through the cell's ubiquitin/proteasome system and functions by recruiting an E3 ligase to tag the target protein for ubiquitination. Gratifyingly, PROTACs can induce degradation of the target proteins at low exposures and are catalytic in their mode of action [309][310][311]. Epigenetic drug discovery field, at present, is flooded with numerous agents that have shown promise at preclinical or early stage clinical level.…”

Drug design targeting active posttranslational modification protein isoforms

“…It is worth noting that the molecular mechanisms underlying the selectivity profiles of certain PROTACs are far from being fully elucidated. It is not clear whether different degradation selectivity profiles were directly derived from the varying PROTAC structures, or whether the genetic, epigenetic, or proteomic backgrounds of different cell lines also impacted the observed potency and selectivity, and to what extent 362 . Therefore, there is a long way to design PRTOTACs for targeting specific PTM protein isoforms, which will be accelerated with the advancement of high‐resolution structures for PTM isoforms and systematic understanding of the cellular compartments across different cell lines.…”