Georg Winter, a chemical biologist at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, Austria, talks to science writer Geoff Marsh about his work on protein degradation. He describes his research on the notorious drug thalidomide, aiming to turn it into a ‘chemical knockout’ for cancer. This year’s ceremony took place at the EMBL Advanced Training Centre in Heidelberg, Germany, on 27 June, 2019.
Geoff Marsh: Congratulations for winning this year’s prize. You must be chuffed.
Georg Winter: It’s a huge honour, and a very humbling experience.
GM: The work you’re being celebrated for started with a key paper in 2015 in Science, detailing a new technique for targeting specific proteins for degradation. How does that work?
GW: It’s a relatively simple principle. We started out by making small molecules that have two ‘arms’, where one arm binds to a protein of interest, and the second binds to the protein degradation machinery, which is active in every cell. We call them ‘bifunctional molecules’, and we use them to reprogram the degradation machinery to eliminate a protein of interest.
GM: The drug you use to bind those two components is a phthalimide, which has a contentious history.
GW: Yes. The first phthalimide that you’ll have heard of is called thalidomide. It was marketed for morning sickness and as a sedative [in the 1950s], and it was taken by many pregnant women. Unfortunately, it turned out that if women took it in the first trimester of pregnancy, their babies were born with limb abnormalities. That particular molecule was withdrawn from the market, unfortunately only after around ten thousand babies were born with limb defects. For many decades, nobody wanted to touch thalidomide or its analogues. But it then became clear that they have very interesting anticancer activities.
GM: How does this phthalimide work?
GW: In 2010, a Japanese research group identified its cellular binding partner. This turned out to be a protein called cereblon which is a so-called E3 ligase. This is one of the proteins engaged in the cellular degradation machinery. Once we knew that thalidomide binds to this E3 ligase, the question was whether we could use this binding event to reprogram the machinery — by conjugating thalidomide to another small molecule that would bind to a protein of interest? Once that happens, we have these ‘heterobifunctional’ molecules that bind to both the degradation machinery and the protein of interest, bring the two together, and redirect the degradation activity to the target protein.
GM: In that 2015 paper, your target protein was one essential for the growth and survival of cancer, and you tested it in mice. How did that go?
GW: It was one of the key findings of the paper. We were already very excited to see that the molecule worked in a cancer-cell line in a dish. But the real test is in an animal model, to check whether it had some therapeutic potential. We were amazed by how well it worked. These mice already had a tumour growing. We took out the tumour and stained and quantified it for levels of a protein called BRD4. A couple of hours after a single treatment with this particular molecule, levels of the protein had decreased in the tumour; when we treated those tumour-bearing mice every day, the tumour growth was profoundly reduced. We slowed down the tumour growth by degrading a protein relevant to that cancer.
GM: Theoretically, could this phthalimide conjugation technique work for any protein target for which there is a ligand?
GW: That is a fair statement, and for some proteins we might even have ligands without knowing it. So far, we’ve only really cared about ligands that change protein function. But now, binding of the ligand can be entirely inconsequential — we just use it as an anchor to induce closeness to the protein degradation machinery. Often in cancer research we’re driven by genetic studies. For instance, we know that if we knock out a particular gene, we slow down cancer growth. But this particular gene might code for a protein with three different functionalities. Some of these functionalities might look like great targets for a small molecule ligand because they have been inhibited before. But it can be that inhibiting one functionality does not equate to knocking out or deleting the gene. We can now revisit all these cases because our chemical perturbation of degrading the protein is much closer to deleting it genetically than the conventional pharmacological way to just inhibit a protein’s function.
GM: So it’s kind of like a ‘chemical knockout’?
GW: Very much so.
GM: What do you think should be the next protein targets that would help the fight against cancer, using this technique?https://science.sciencemag.org/content/348/6241/1376.long
GW: We now have the tools to tackle some transcription co-activators and regulators of gene control. Ultimately, we should aim to target transcription factors for degradation. These will be the proteins with the highest bar, because for many of them we don’t have defined binding pockets to help us predict the ligand. But this will be the challenge and there are already strategies out there to tackle these limitations.
GM: How close is this technology to readiness for human trials?
GW: Not directly with the technology of phthalimide conjugation, but there have been some with other closely related heterobifunctional molecules that hijack another part of the protein degradation machinery and have similar functionality. There is one biotech company from Newhaven called Arvinas. They have started trials in humans to degrade a transcription factor, called the androgen receptor, in prostate cancer. This is, to the best of my knowledge, the first clinical trial. The entire field is eagerly waiting for the results.
GM: Finally, what’s next for you?
GW: We are very much interested in pushing this technology to the next limit and eventually being able to degrade proteins that we can’t bind. I’ll tell you how we plan to do this the next time we meet.
Find out more about Georg Winter’s work here.
This is a download from Nature Research, part of Springer Nature.
Hello again. It’s that time of year, and I’m back to a very sunny Heidelberg to meet another winner of the Eppendorf Young European Investigator Award at the European Molecular Biology Laboratory’s Advanced Training Centre. Eppendorf has been running these awards in partnership with Nature since 1995. This year’s winner is Georg Winter, and I had a sit-down chat with him in a nice quiet room after his speech. First of all, a big congratulations on winning the prize. You must be thrilled.
Yeah, thank you very much. It’s a huge honour. It’s a very humbling experience to be awarded this prize.
It is a very hot day as well.
Yes, it’s very hot. I feel bad for everyone who has to put on a suit and even a tie maybe, but we’ll have to fight through it.
Well, thank goodness, they’ve found us a nice air-conditioned room for the podcast.
Now, the work you’re being celebrated for here started off with a key paper, didn’t it, in 2015 in Science, detailing a new technique for targeting specific proteins relevant to cancer.
Yes, so it works via a relatively simple principle. So, we started out by making small molecules that have two arms, where one arm would bind to a protein of interest that we want to degrade and the second arm binds to the protein degradation machinery of a cell. This is a machinery that is active in every cell of your body but with these, as we call them, bifunctional molecules, we can reprogramme this degradation machinery basically to eliminate this protein of interest that we want to get rid of.
And the drug you used to bind those two components then is a phthalimide. These drugs have quite a contentious history, don’t they?
Yeah, exactly. I mean the first phthalimide that you would be hearing of is called thalidomide, and it was marketed for morning sickness and as a sedative, and they were taken by many pregnant women. Unfortunately, it turned out that if women took this medicine in the first trimester of their pregnancy, babies were born with horrible limb abnormalities, and so the particular molecule was obviously retracted from the market, but unfortunately only after I think more than 10,000 babies were born with these limb defects. And then for many years and decades, nobody wanted to touch thalidomide or any of its analogues basically with a ten-foot pole, but it then became clear that they have very interesting anti-cancer activities.
Tell me how this phthalimide actually works then.
Georg WinterSo, this was then only in 2010 when a Japanese research group identified the molecular mechanism of this drug, and in particular the cellular binding partner of the drug, and this turned out to be a protein called cereblon which is a so-called E3 ligase, and this is one of these proteins that are engaged in the cellular degradation machinery. Once we knew that thalidomide binds to this E3 ligase, so this degradation machinery, the question was whether we could use this binding event to reprogramme this machinery by simply just using the phthalimide part on one end and then conjugating thalidomide to another small molecule that would bind to a protein of interest. And so, then we have these heterobifunctional molecules that bind to the degradation machinery and bind to this protein of interest, bring the two together and thereby redirect this degradation activity to get rid of a target protein of interest.
And so, in that 2015 paper, your target protein was a protein essential for the growth and survival of a particular cancer, and you tested this in living mice, didn’t you?
Georg WinterExactly, this is really one of the, I think, key findings of this paper. I mean we were very excited to see that this molecule works in just a cancer cell line, in a dish, and it worked very fast and very potent, but the real proof and the real test for us was can we get this to work in an animal model of a disease because I think this is really the first box we needed to check to make sure that this has some therapeutic potential and we were amazed by how well it worked. I mean we basically treated mice once with this molecule – these were mice that had already a tumour growing. We took out the tumour and stained or quantified for levels of this protein called BRD4, and only a couple of hours after treating once with this particular molecule, we could see that levels of this protein were strongly decreased in the tumour. And we found that when we treated those tumour-bearing mice every day, the tumour growth was very profoundly reduced and so that we could really, basically shrink the tumours in those mice. So, we slowed down the tumour growth by degrading a protein relevant to that cancer in the tumour.
Now, that was, what, four years ago? Theoretically, this phthalimide conjugation technique could work for any protein target that we have a ligand for that we know binds to a ligand.
Georg WinterYeah, I think that is a fair statement, and I think for some proteins, we even might have ligands without knowing it because so far, we always have that filter where we said we really only care about the ligands that change protein function, and this is basically a hurdle that we have now eliminated because binding of the ligand can be entirely inconsequential because we just use ligand binding as an anchor to induce, again, closeness to the protein degradation machinery. And so by that logic, we were also talking about multidomain proteins and often in cancer research and also many other disease-relevant research fields, we are driven by genetic studies. So, we know that if in cancer B we knock out a particular gene, we slow down cancer growth and for instance, this particular gene can be a protein that has three different functionalities. And so then some of these functionalities might look like great targets for small molecule ligands, simply because, for instance, this functionality has been inhibited before, and then sometimes, the community makes very potent ligands against this functionality, but it can be that this particular inhibiting dysfunctionality does not equate to just knocking out or deleting that gene, and I think in all of these cases we can now recapitulate and revisit with a degradation technology because our chemical perturbation of degrading the protein is a much closer match to deleting it genetically than the conventional way of pharmacology where we just inhibit a protein function.
So, it’s kind of like a chemical knockout.
Georg WinterVery much so, yeah.
What do you think should be some of the protein targets that will help the fight against cancer that might use this technique?
Georg WinterI think I am biased in this because my research interest is in gene control, but I think we now have the tools, certainly, to take some of these transcription coactivators and regulators of gene control. I think ultimately, we should aim to target transcription factors for degradation and it has been achieved for some transcription factors but I think this will also be those proteins with the highest power because for many of them we don’t have defined ligand-binding pockets where we can predict that we can develop a ligand, whether its consequential or inconsequential, but this will be the challenge. But there are also already strategies out there how these limitations can be tackled.
How close is this technology to the clinic? Have we had clinical trials using phthalimide conjugation?
Georg WinterSo, not directly with the technology of phthalimide conjugation, but with other closely related heterobifunctional molecules that just hijack another part of the protein degradation machinery with a very similar functionality. There is one biotech startup, or biotech company, I should say, out of New Haven called Arvinas which a couple of months ago started the first clinical trials in humans for I think to degrade a transcription factor called the androgen receptor in prostate cancer. And this is, to the best of my knowledge, the first clinical trial and obviously, the entire field is very eagerly waiting for the results of this.
And finally, what’s next for you?
Georg WinterSo, we are very much interested in pushing this technology to the next limit and eventually be able to degrade proteins that we can’t bind, and I’ll tell you more next time we meet about how we plan to do this.
That was Georg Winter, who’s currently at the Research Centre for Molecular Medicine of the Austrian Academy of Sciences. Before I left, I wanted to speak to a member of the jury to hear what had made Georg’s work stand out. I pulled Professor Laura Machesky to the side and we went for a walk outside the training centre to sit among the chirping insects in the evening sunshine for a chat about Georg’s achievements.
Laura MacheskySo, I’m Professor Laura Machesky and I’m from the Beatson Institute for Cancer Research in Glasgow.
What was it this year then about Georg Winter’s work that really stood out above the crowd?
Laura MacheskySo, I was actually one of the most enthusiastic panel members, I think, about his work because I thought what he had done, which was to pioneer this ubiquitin-mediated degradation of proteins in cells in a specific way was unique among the applicants and was something that changed the way that we really could think about how to proceed with undruggable targets. So, his work caught the interest of many pharma companies and had really made a paradigm shift in the field, I think. For me, that stood out as something that was not only an interesting scientific discovery, but something that potentially could change the lives of patients for diseases like cancer, and could revolutionise, maybe, the way that pharma would target proteins in the cell that normally would be thought of as untargetable or undruggable.
What reaction do you have to someone like Georg when they display this kind of innovation?
Laura MacheskyI think it’s really exciting and I guess maybe being young, you’re a bit more fearless about what you can achieve, and so sometimes when you’re more experienced you might overthink things and talk yourself out of doing the risky, exciting science that young people can do, and so I think Georg really had the fearlessness to take on a very difficult problem in biology and to maybe go against the odds to try something that many people would have ruled out as just being too difficult to do.
Since his sort of key paper in 2015, what impact have you seen it have in the medical sphere?
Laura MacheskyI guess I knew about his discoveries before he applied for this award or before he was nominated for this award because it’s touched my own work as well in the lab, and I saw that lots of pharma companies were very excited about the idea of using the ubiquitin system to target protein destruction in cells, and that for my own work, we’ve been trying to develop a compound to target a protein called fascin in the cell, and that is obviously a protein interaction target which is considered not a druggable target. And so, his system has given hope to many basic researchers who are trying to target difficult proteins in cells, which might nevertheless be really important for diseases such as cancer or Alzheimer’s disease, so I think that was really striking for me.
That was Professor Laura Machesky from the Beatson Institute for Cancer Research in Glasgow in the UK, and before her, you heard this year’s award winner, Georg Winter, from the Research Centre for Molecular Medicine of the Austrian Academy of Sciences. This has been a special podcast from Nature Research, part of Springer Nature. I’m Geoff Marsh. Thank you for listening.