Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications

Abstract

Hetero-bifunctional PROteolysis TArgeting Chimeras (PROTACs) represent a new emerging class of small molecules designed to induce polyubiquitylation and proteasomal-dependent degradation of a target protein. Despite the increasing number of publications about the synthesis, biological evaluation, and mechanism of action of PROTACs, the characterization of the pharmacokinetic properties of this class of compounds is still minimal. Here, we report a study on the metabolism of a series of 40 PROTACs in cryopreserved human hepatocytes at multiple time points. Our results indicated that the metabolism of PROTACs could not be predicted from that of their constituent ligands. Their linkers’ chemical nature and length resulted in playing a major role in the PROTACs’ liability. A subset of compounds was also tested for metabolism by human cytochrome P450 3A4 (CYP3A4) and human aldehyde oxidase (hAOX) for more in-depth data interpretation, and both enzymes resulted in active PROTAC metabolism.

Applications of Bacterial Degrons and Degraders — Toward Targeted Protein Degradation in Bacteria

“…The design should take into consideration features such as the length, flexibility, and also the attachment sites of the linker to both ligands, and typically requires optimization for each PROTAC (Cyrus et al, 2011;Maple et al, 2019;Donoghue et al, 2020). The length of the linker not only influences PROTAC action and affinity toward the binding partners but also the compound stability (Goracci et al, 2020;Pike et al, 2020). Another important factor is the cell permeability of PROTAC molecules.…”

Novel advances in biotransformation and bioactivation research—2019 year in review

“…The work by Goracci et al (Goracci et al 2020) represents the first published comparison of the in vitro human hepatocyte metabolism of multiple proteolysis targeting chimeras (PROTACS). The authors employed a systematic approach to profile and compare the metabolism in cryopreserved hepatocytes across a total of 40 structurally diverse PROTAC molecules; reporting both the half-life and structures of biotransformation products formed for each compound.…”

“…When making their comparisons of structural differences on PROTAC half-lives, Goracci et al hypothesized how the changes would impact the interactions of these molecules with their drug metabolizing enzymes (Goracci et al 2020). Another possible factor not addressed by this work would be changes in compound membrane permeability, which would limit substrate availability to intracellular drug metabolizing enzymes in cryopreserved hepatocytes.…”

A Reliable and Sustainable Multicomponent Access to Protein Degraders

“…Besides degradation efficiency, similarly to any other medicinal chemistry campaign, properties such as solubility, metabolic stability and cell permeability represent an additional challenge to achieve an optimal in vivo effect, with far more reason since PROTACs lie outside the rule-of-five space [14][15][16] .…”

“…Hence, efforts have been devoted to rationally explore the role of the different structural elements in conferring favorable pharmacokinetic properties and a special attention has been given to the chemistry of the linker, whose optimization has a crucial impact on the ADME profile throughout the R&D process 14,17,18 . Linear aliphatic and PEG-based linkers are commonly used in the early phases of development to assess the most favorable length to form an efficient ternary complex, while at a later stage they are usually refined and enriched with rigidifying motifs (e.g.…”