By Sheelagh Frame, CSO at Ubiquigent
Modulation of the ubiquitin-proteasome system (UPS) presents a rich source for drug discovery.
Recent years have seen the clinical validation of proteolysis-targeting chimeras (PROTACs) unlock the ability to drug the undruggable, by exploiting E3 ligases to mediate targeted protein degradation (TPD), paving the way to tackle exciting new drug targets and embrace new modalities.
Enter the deubiquitinase (DUB) enzyme family.
DUBs are proteases that regulate ubiquitination in the UPS. They are key to protein homeostasis, activity, and degradation, and thereby hold great potential as therapeutic targets. DUBs can be modulated by DUB inhibitors or DUB-targeting PROTACs to achieve TPD, or even harnessed for protein stabilization through DUB-targeting chimeras (DUBTACs).
Though largely underexploited to date, the design and discovery of DUB modulators is rapidly gaining pace in the development of powerful new medicines for areas of high unmet need.
DUB inhibitors enter the clinic
The dysregulation of DUBs is implicated in several disorders, including cancer, neurodegenerative and cardiovascular diseases, with DUB modulation offering a promising treatment modality.
USP1 is one of the best-characterized human DUBs. It regulates cellular response to DNA damage and is overexpressed in cancer cells, providing an exciting anticancer target — inhibition of USP1 is synthetically lethal with defects in homologous recombination repair (such as BRCA deficiency), can re-sensitise PARP resistant cancer cells, and is synergistic in combination with PARP inhibitors.
Using Ubiquigent’s DUBprofiler assay to demonstrate USP1 inhibition and selectivity, KSQ Therapeutics entered the clinic in late 2021 with the first DUB inhibitor (KSQ-4279), targeting USP1 to treat advanced solid tumors. Not only did this milestone open the door for USP1 modulation as a therapeutic strategy, but also increased the appetite for many other DUB targets to be brought closer to clinical evaluation.
USP30
Another prominent drug target is USP30, which regulates the clearance of damaged mitochondria in a process called mitophagy. In early 2022, Mission Therapeutics received regulatory approval to initiate clinical trials for their lead USP30 inhibitor (MTX652) in kidney disease and idiopathic pulmonary fibrosis. Kidney cells, for example, are mitochondrion rich and therefore highly vulnerable to injury if those mitochondria are dysfunctional; USP30 inhibition promotes mitophagy to improve cellular health and longevity.
Recently presented at the 2022 Society for Neuroscience (SfN) conference, new data from the Beth Israel Deaconess Medical Center (BIDMC) cements Parkinson’s disease (PD) as a key disorder for which USP30 inhibition may be a viable treatment modality. The study reports that USP30 knockout enhanced mitophagy whilst decreasing alpha-synucleinopathy and dopaminergic neuronal loss, key pathological hallmarks of PD.
2023 is likely to see new DUB inhibitors for USP1, USP30, and others enter preclinical and clinical evaluation, across a range of indications. These advancements will need to meet concerns surrounding selectivity, and the availability of robust cell-based and biochemical assays to rapidly evaluate DUB inhibitors will enable drug discovery scientists to overcome this barrier.
As seen with KSQ-4279, access to large panels of human enzymes, such as DUBprofiler, has already been transformative.
The rise of protein stabilization
TPD has effectively addressed proteins previously seen as undruggable, but what if protein degradation is the pathogenic mechanism? Loss of protein function through abnormal degradation, often resulting from a genetic mutation, drives the pathology of many disorders, including cystic fibrosis, monogenic diseases, and some forms of cancer. In these cases, protein stabilization is the therapeutic aim rather than degradation.
DUBTACs recruit DUBs to a target protein, removing ubiquitin chains to rescue the protein from degradation, thereby stabilizing protein levels and restoring protein function. 2021 and 2022 brought a surge in funding for companies harnessing DUBs to stabilize proteins, with Stablix and Vicinitas Therapeutics both raising more than $60m in series A funding to develop DUBTACs, and Entact Bio closing its series A financing at $81m to advance its proprietary Encompass platform.
DUBTACs comprise three components: a DUB recruiter and a target protein binder, connected via a linker. Selecting the ‘right’ DUB partner for a given target protein is one of the greatest challenges to the design and development of DUBTACs. Fortunately, solutions already exist to help drug discovery scientists address this question.
For example, assays such as DUBprofiler-Tissue and DUBprofiler-Cell use activity-based probes (ABPs) to profile which DUBs are expressed and active in a specific disease setting or subcellular location, without the need for genetic manipulation, effectively generating a ‘DUB tissue atlas,’ which will be instrumental in this field.
Recent funding for DUBTAC development will bring this promising modality one step closer to the clinic. Funding will drive further research into identifying novel DUB recruiters and optimizing the most effective DUB and target protein pairings, which could lead to the development of breakthrough therapies — as such, the DUBTAC space is likely to continue to attract the interest of life science investors.
DUBs: A new dawn for drug discovery
The role of DUBs in human diseases is well established, DUB inhibitors are entering clinical development, and DUBTACs have emerged as a new modality to harness DUBs for protein stabilization.
DUB-focused drug discovery presents an exciting area for new funding and innovative therapeutic developments — watch this space!