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PROTAC drug discovery – prior preparation and planning

“By failing to prepare, you are preparing to fail” so said Benjamin Franklin, and as a veteran of early stage drug discovery you can bet that I, like you, have seen my fair share of successes but also more failures than I’d like.  

The discovery of new drugs is inherently a difficult and risky proposition and researching any novel, or known, biological target or disease mechanism using new chemical matter brings many challenges.  

As a consequence of these challenges, many projects inevitably run into situations where scientific, financial or strategic reasons mean that the project will be suspended and team efforts will be refocused on other areas that are deemed to be of greater need or commercial opportunity (or a combination of the two).  

Failures have value but we should anticipate specific challenges

So, are failures in drug discovery really simply due to bad preparation?  Far from it, but there might often be a failure to anticipate the nature or the enormity of the specific challenges to be met.  In my opinion, rework and analysis of past projects is a valuable work practice and in drug discovery there are abundant opportunities to learn from mistakes which, whilst being expensive, are more valuable than serendipitous success where all challenges are easily resolved, not that I have anything against serendipity.

However, it’s good practice to try to be successful first time around and in an effort to reduce timelines, to enhance the probability of success, and to identify novel types of therapeutic agents. Our industry demands innovation to deliver new technology and new working paradigms that can improve our foresight, improve efficiency, limit financial risk, and hopefully facilitate the discovery of the new therapeutic agents that we and our competitors have been unable to hunt down to date. 

It is an unfortunate reality that many of the drug discovery technologies that are commercialized, or on which companies are founded, fail to deliver the promise that was so seductive in the first place.  Whilst new drug discovery technology is needed, the application of it can result in expensive failures so it’s important to approach implementation carefully. 

Delivering on the promise of PROTACs technology

With such cautionary words in mind, how should we consider using new drug discovery approaches such as PROTAC technology and how can we best plan for success?   

Our experience at Selvita in recent years has provided good opportunities to understand that whilst the concept of PROTACs is fabulously simple on paper it is highly complex in practice.

Nonetheless the PROTACs concept is enormously appealing; it promises the potential to evaluate specific biochemical pathways with high precision and to pharmacologically address biological targets in disease where traditional small molecules have failed to deliver new drugs. 

In my view the challenges in PROTACs are things for which we can prepare well and whilst nothing in science is guaranteed we’re happy to be exploring this new world of drug discovery.

Tom Coulter
What are the key challenges for consideration with potential PROTACs projects? 

First and foremost, with a specific protein target in mind we need to select a binding partner that efficiently allows us to “grab” the protein, ideally in a selective fashion over related protein. Finding a selective binding partner for a target protein is the bread and butter of medicinal chemistry and this is by no means trivial.

However, with PROTACs this is the ‘easy bit’ for several fortuitous reasons:

  • We should be able to exploit existing known ligands for the protein.
  • We don’t need the binding ligand to have a pharmacological role itself so it can be a reasonable binder, but be a poor inhibitor, and still perform adequately.
  • Reports in the literature show that selectivity for the target protein can actually improve when the ligand is incorporated into the bifunctional PROTAC molecule.  

These are all highly helpful observations and so, once we have found a ligand with adequate binding then the rest of our work can begin. 

Secondly, when it comes down to E3 ligase choices, at present only a small number have been tested as PROTAC components and only couple are in common use, mainly because we know a bit more about those and their associated ligands.  

An important consideration to explore is whether other ligases might provide an easier path to new intellectual property and also if they are better fits for the PROTAC due to better expression levels being found in the biological compartment where our targeted protein is found and to be degraded.  

Thirdly, we need to connect these pairs of binding partners usefully so that the target protein can interact with the bound ligase.  Once we’ve found ligands for our target protein and ligase it seems simple to envisage tethering the two ligands together with a simple string of atoms using some well-known chemistry such as amide formation but in practice this is one of the trickiest things to achieve. The length and conformational flexibility of the linker is critical, too much or too little can influence how well the PROTAC functions or indeed whether protein degradation is observed at all.   

The other important consideration about tethering of the two ligands is that it needs to be done such that the attachment points where each ligand connects to the linker is not involved in binding to the protein and such that the new substituent doesn’t diminish the ligand binding to the protein.  This is easier said than done.  

Often when introducing a substituent to a theoretically “safe” point on a ligand, binding is much reduced which brings me to the other important point: that highly floppy tethers can raise entropy to the point where binding to the ligand is completely ruined.  Ligand tethers thus need to be rigid enough not to compromise ligand binding but flexible enough to allow our target protein and the E3 enzyme to come into the correct proximately and with good orientation to each other.  Not so easy now eh?  

To a degree computational methodology can help but lots of trial and error will likely feature at this stage.  

When planning such a project it is therefore wise to factor in the trial synthesis and assembly of multiple linker variants. 

PROTACs: one of the most exciting innovations in drug discovery

So, there’s a lot to consider and doing a PROTAC project is almost like doing three or four projects in one but with correct planning, a successful outcome is tangible and could be highly valuable. In my view the challenges in PROTACs are things for which we can prepare well and whilst nothing in science is guaranteed we’re happy to be exploring this new world of drug discovery. So, what about having a closer scientific look at the refreshing field of PROTACs that is pitched to be one of the most exciting recent innovations in the world of drug discovery research.  

Dr Tom Coulter is Integrated Drug Discovery Director at Selvita where he is focused on development of enhanced drug discovery capabilities. Tom’s professional experience includes tenures at at Evotec, Syntaxin, Karus Therapeutics and Midatech Pharma.

Explore innovative new research in Protein Degradation and consider other novel approaches and applications in the drug discovery process at the 5th Medicinal Chemistry & Protein Degradation Summit. Discover the programme.

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