Targeted Protein Degradation: Why Just Inhibit What Can Be Destroyed?

By Kyle Proffitt  

September 17, 2020 | At the Drug Discovery Chemistry Virtual conference last month, the topic of disease treatment through targeted protein degradation was discussed repeatedly. These efforts range from small molecules similar to thalidomide that act as “molecular glue” degraders to more advanced “beyond rule of 5” proteolysis-targeting chimeras (PROTACs) with bifunctional moieties that encourage protein interaction with its E3 ubiquitin ligase.

Eric Fischer from Dana Farber Cancer Institute discussed his group’s work toward identifying the full range of proteins that might be targeted with a protein degradation strategy, which is to culminate in a web-accessible “degradable proteome” community resource. He reviewed the ubiquitin-proteasome system responsible for protein degradation, with specificity conferred primarily by the ubiquitin E3 ligases, and discussed the various ways this system has been hijacked by viruses, PROTACs, plant hormones, and molecular glues. Fischer’s group established the degradable kinome project based on 57 degrader molecules targeting kinases, then treated 6 proteomically diverse cell lines to capture a wide range of effects. They performed tandem mass tag proteomic analysis to identify targeted molecules. Mapping their results on the kinome tree revealed that most branches are covered by this set of molecules. Fischer hopes that this resource will be useful to the community, and he pointed to the example of a casein kinase degrader that also shows activity against AURKA as a potential starting point for developing more specific inhibitors.

Robert Law from GlaxoSmithKline discussed efforts to target focal adhesion kinase (FAK), which is overexpressed in advanced tumors, using PROTACs. Law reported that FAK inhibitors targeting the kinase activity have had limited clinical efficacy and pointed to studies showing that even kinase-dead FAK provides a tumor growth advantage in animal models compared with FAK-depleted tumors. Thus, the complete degradation of FAK with PROTACs is worth pursuit. To achieve this, Law’s group started with VS-4718, a small molecule FAK inhibitor that was discontinued after phase 1 clinical trials, and attached a VHL-targeting domain. After SAR-based improvement of the linker and replacement of the molecule’s oxazine moiety with a piperazine, they demonstrated that a 100-nM concentration depleted >80% FAK within 2 hours. They also looked at the wider proteome and found very good selectivity at lower concentrations with other FAK signaling pathways affected as concentration increases. Further modification of the FAK-binding portion of the molecule to improve pharmacokinetics and solubility led to additional compounds, including one that maintained 24 hours of FAK depletion at a 2 mg/kg dose in mice. 

Upendra Dahal from Amgen discussed the improvement of oral bioavailability and ADME properties of PROTACs. Despite the promise of this method of protein targeting, which was developed nearly 20 years ago, it has unfortunately not yet led to any clinically-approved drugs. The advantages of small molecules in terms of permeability, oral bioavailability, low manufacturing cost, and global access currently outweigh the high potency and specificity offered by PROTACs. All of the PROTACs published in the literature have a molecular weight of  ~1000 Da, logP of 5 and above, and high numbers of hydrogen bond acceptors, according to Dahal, and thus none can be used as oral drugs. Typically, the individual fragments have acceptable PK properties, but the linker region ruins it for the rest of the molecule. Dahal emphasized that we must optimize the PK properties of the PROTAC and not just the fragments. He offered some approaches that can help, such as introducing intramolecular hydrogen bonds, cyclization, using a prodrug approach to block polar groups, and of course reducing molecule size, highlighting an example in which they reduced a PROTAC from 956 to 521 Da to improve permeability and oral bioavailability while maintaining comparable potency. He also offered the option of using permeability enhancers, such as BSA, sodium caprate, or methyl piperazine, to open epithelial tight junctions in the gut and increase uptake.

Of course not everything was focused on degrading proteins; working from the opposite end, Dehua Pei of Ohio State University reported efforts to prevent protein degradation using macrocyclic peptides. He reported the development of an inhibitor of the interaction between CFTR and CAL, which allows mutant CFTR to accumulate. In combination with a clinically approved agent from Vertex that enables the common Δ508 mutant to regain an open, active conformation, his group showed an additive effect in enhancing ion channel activity, which could further improve the outlook for patients suffering from cystic fibrosis. Separately, Pei reported a molecule of significance for our current times—an inhibitor of the calcineurin-NFAT interaction that could be used to overcome the acute respiratory distress syndrome associated with COVID-19 by stalling cytokine production. Pei said this molecule is in further development by Entrada Therapeutics. 

Editor’s Note: Did you miss the 2020 Drug Discovery Chemistry conference? Because the event was virtual, you can still access the event including all of the recorded sessions, presentations, and materials. Register for PREMIUM POST-EVENT ON-DEMAND.