PROTAC Mediated Protein Degradation—using small molecules to manipulate our cellular machinery

 As a medicinal chemist I have spent half my professional life trying to re-capitulate the phenotype observed in a genetically modified “knock-out” animal using a small molecule that blocks the function of the knocked out protein. Using medicinal chemistry techniques ensures that my small molecule reaches the protein of interest (POI) with sufficient potency and quantity to inhibit the function of the protein. 

Unfortunately using this small molecule approach does not always fully imitate what happens in the POI knock-out animal. One potential reason is that whilst the RNAi and CRISPR gene editing techniques remove the POI in its entirety my small molecule will only block its function.  And to borrow from Donald Rumsfeld, there are “the unknown unknowns – the one’s we don’t know we don’t know” impacts of removing the POI which may not be related to its function.  Is the protein involved with other processes unrelated to its function that generate the required phenotype?

Pioneering work from the laboratory of Craig Crews may now provide a means of removing the POI using small molecule techniques. What this group has developed is a means of hijacking the cell’s own garbage disposal system, the ubiquitin proteasome pathway (UPP), to selectively degrade our POI.  The degradation of a protein via the UPP involves a discrete two-step process – the first step requires the tagging of the protein with multiple ubiquitin molecules and  the second step recognizes  and subsequently destroys the proteasome.  The key step in the ubiquitin tagging of the protein involves an enzyme called the E3 ligase.  It is this E3 ligase that catalyses the transfer of the ubiquitin molecule from the ubiquitin-containing enzyme to our POI.  The discovery of small molecules, such as pomalidomide, that can bind to this E3 ligase has opened up the possibility of designing heterobifunctional molecules— capable of binding contemporaneously to two different targets—that can bind both to the E3 ligase and our POI. 

So in essence is it possible to take the small molecule that I would design to inhibit the function of the POI, connect it via an inert chemical linker to the small molecule that binds to E3 ligand and then use the UPP to remove the POI. The realization of this approach has given rise to the PROteolysis TArgeting Chimera (PROTAC) concept.  

Two further features of this PROTAC approach that offer exciting possibilities in the drug discovery world are the catalytic nature of the PROTAC process and the fact that the small molecule that I design only needs to bind with our POI; no longer would my small molecule need to inhibit the POI. The catalytic nature of the PROTAC has led to what Crews has termed “event-driven pharmacology” rather than the classical exposure driven pharmacology.  In the traditional drug design the efficacy of the drug is determined by a combination of pharmacokinetics (exposure), pharmacodynamics and target engagement.  With the PROTACs ability to eliminate the POI the desired efficacy need not match the exposure but driven by the re-synthesis rate of our POI (see image below).

 

The PROTAC approach would also allow for the possibilities to reach beyond the limits of the traditional drug discovery paradigm. With this approach we only have to design molecules that bind to our POI since the pharmacology is driven by removal of the POI. This will increase the number of protein targets we as medicinal chemists can target since it is suggested that current therapies only target 13% (400 out of 3000 genes) of the therapeutic proteome.

The versatility of the PROTAC approach has been demonstrated by various laboratories which have targeted kinases (e.g. RIPK1, TANK-Binding Kinase 1), previously difficult epigenetic targets (Sirt2 and BRD) and nuclear hormone receptors (Androgen and estrogen α receptor). Two fledgling biotech companies Arvinas (a 2015 Fierce 15 company) and C4 Therapeutics (a 2016 Fierce 15 company) have been formed to take this technology into the clinic. 

The PROTAC approach was the focus of a recent RSC/SCI conference, Targeting the Ubiquitin – Proteasome Pathway, and will also be featured in an upcoming issue of the Journal of Medicinal Chemistry.

We are currently awaiting the read-outs from the current clinical trial using the CRISPR technology and whilst the work from Arvinas and C4 Therapeutics is still in the preclinical stage of development we keenly await whether this chemistry-based technology will complement CRISPR.