Can you start by saying your name and your various hats?
Okay. So I'm David Stewart and I am joint head of the Division of Structural Biology in the Nuffield Department of Medicine and Dentistry.
Be known as tribute. Yes, that's right. And I'm also so I'm for quite a long time, I've been significantly funded by the Medical Research Council.
So they actually fund a large part of my salary as a MLC professor and that's 50% of my time.
And then the other 50% of my time is life science director at the Diamond Synchrotron, which is half an hour down the road from me.
Um, and being the life science director at Diamond for quite a long time,
over ten years and until the end of last year, until the end of 2021, I was also the director of Instructor Eric,
which is a pan-European structured biology research infrastructure, which I wasn't formally paid for,
but because because the UK is a member country, my contribution was part of the MLC contribution to to instruct.
Eric I stopped doing that at the end of 2014.
Hm hmm. Well, I think we're going to talk about all of those things. Okay.
But can we start by just very briefly telling me how you got to where you are now is
starting from your earliest interest in biological sciences and then structural biology?
Okay. Well, that's sort of quite long, but we need to keep it short.
So I started off my first year in biophysics at King's College in London, and I became interested at that point in methods for looking at structures.
And I, uh, Maurice Wilkins was the head of department.
Um, and, you know, I discuss things with him as well.
I was interested in the sort of psychology science as well, but,
but I decided to do a PhD and did that at Bristol University and that was in X-ray crystallography.
So looking at the structure of proteins at that point, there weren't a huge number of proteins, structures that had been done.
Um, and I worked on the structure of an enzyme glycol,
lytic enzyme and the basic sort of enzymes that manages the metabolism of cells and tissues throughout biology.
So I did that for my Ph.D. Then I was at a loss really what to do.
Um, I went to, came here to Oxford for a short period, but during that period I was organising to go and work in China,
and I was supported in that by um, Dorothy Hodgkin and David Phillips.
Um, and then so I went out to work in Beijing on getting structural biology in that case,
mainly looking at two versions of insulin insulin with the insulin group in China that had very strong links with Dorothy.
Um, in Oxford being that was in the early 1980s.
So there wasn't that there wasn't the same sort of social media that there is now.
So I was lucky that the end of that time I was offered a postdoc to return to Oxford by Liz Johnson.
Um, so I came back and started with Louise and then, uh, after a relatively short time,
I applied for a, uh, a lectureship that came up in Oxford and got a permanent position.
And when I was starting my group, I, I sort of had to decide what to do.
And it was a time when there was some developments in virology.
There was an excellent virology group at the institute, which was, yeah, it's not that far from Oxford.
And the person leading that group contacted David Phillips and said, Look,
we're trying to make a better vaccine, will make a useful vaccine for for next disease virus.
And we think the structure would be interesting.
And David Phillips directed me to work with them, which was, uh, very sort of generous and he was very supportive of that.
So that moved me and gave me the opportunity to do something which at the time was quite ambitious,
which was to do the structure of a complete and complete virus.
Um, so that, that, that put me into the sort of direction of doing.
Structural virology.
And in the early years, I worked on foot and mouth disease virus and also worked on it because at the time also there was the HIV epidemic came about.
So the MLC set up an H directed programme of research and we collaborated with the pharmaceutical sort of branch of Wellcome because they,
they were doing some, they produced the first of the antiviral drugs.
So we were collaborating with them on the structure of the reverse transcriptase,
which was the primary drug talked to that time along with the protease.
So, so I got into trying to, to, to help people working in industry on drug design and got into working with the people that also in industry.
Frank Brown and Dave Robbins, welcome. With the idea of using structure to help in vaccine design.
So let's just unpack that a little bit. I mean, first of all, very basic question.
Why is it important to know about the three dimensional structure of something like a virus or a protein?
Well, there's there's a fundamental there's a fundamental biology and the science to this.
There's two things there. And the. David Baltimore got the Nobel Prize for discovering retroviruses many years ago.
And what his what he said was that the fantastic thing about viruses is that they are biology sort of stripped down to the minimum.
So you can argue about whether they're alive or not, but they what they do have is the they have an evolutionary history.
So in that sense,
they're really the sort of simplest embodiment of life so that you can see Darwinian sort of evolution work and in the case of the pandemic,
in sort of real time, you know, so that the thing is that the genome is very small.
So in RNA virus, most RNA viruses are not very accurate.
That polymerase that copies their genome makes errors so they can only support a relatively simple genome.
So there's a small number of proteins that a lot of the complications of cell life they don't do.
They don't make their own energy and stuff like that. So they they're so I know from my perspective,
they're a really interesting system because you can have this sort of crazy idea that you can sort
of understand them in a in more in a more complete way than you would a very complicated cell.
So that's the sort of fundamental science. And then, of course, there's there's also the the sort of health impact.
And and that's human and animal health. And the to understand the basic science of something like a virus structure.
I think everybody recognises now that that that's a sort of key aspect to hang your understanding on and for the therapeutic side to say the things.
Really there's sort of two aspects, major aspects of think of the vaccines and then the therapeutics are the small molecules or, or biologics.
And in a sense, both of those structures should be important.
And for small molecule drug design, the the argument is accepted really by the drug companies.
All the major drug companies have a a large amount of activity in the area.
And Steve Bury, the head of the protein database in Rutgers in the US, did an analysis and I can't remember the exact numbers,
but well over half of the drugs coming to market now have used structure at some point in their development.
And this is just because you need to you've got two things that have to interact.
Yes. So you can try to try to design a small molecule that's going to bind to a protein, usually a protein target, and stop it working.
So, you know, in the case of the HIV,
we've got the the key enzyme reverse transcriptase that's responsible for allowing that the virus to incorporate into the host genome.
So you have little chemical pieces that are like the chemical fragments that the virus uses to make replicate the genome, which bind,
but then inactivate the enzyme so that the whole sort of basis of that success is
based on the physical chemical recognition of of a large molecule by a small compound.
And so you could you can imagine you would you could do it you can do it all by chance.
But it is very inefficient.
And beyond that, you know, in principle, what happens with viruses, because because as I say, the error rate of the polymerase is very high,
the virus is able to mutate very quickly, an escape from antibodies or escape from small molecule therapeutics very often.
And that's that's one of the things that with the HIV story, we find that extremely quickly.
And and that that was something that was I was very impressed with was the way that even though welcome, you know,
they they were they they produced a drug and they thought that they were hoping to sell this and and
and hoping for it to be effective as soon as they discovered and they discovered it very quickly,
because the resistance comes up very quickly in tissue culture, they were completely open about it and made all the information available.
So but that escape, again, is explicable in terms of the simple, simple physicochemical processes.
There's a. Station in the in the viral protein.
And, you know,
you might have a bigger protein SIDECHAIN that's that's put in there by the mutation that then blocks the binding of the small molecule drug.
So one of the questions that we were looking at with with welcome and the one of the students that was looking at this was Andrew Hopkins,
who's now the CEO of Ciencia, one of the local drug companies.
Is can you can you build into your compound design a way of reducing the chance that the virus can escape from it?
And it's not a trivial question. It's still an open question. But in principle, if you have the structural information, you've got the tools,
then to start to think about those questions so that so the structure is,
is important for small molecules and the for the same with antibodies, you know, biological therapeutics essentially.
The but then, you know, we'll probably discuss this later.
One of the things we want you to understand is what how the virus changes to avoid being avoid recognition
by antibodies that the that the people generate and you know that again it's a very simple thing.
There's a there's a there's a recognition of the of the viral protein by the antigen.
And if you make a mutation in the viral protein, if it's well if it's well designed, prevent the antibody binding and then the vaccine side.
Because my my feeling from the beginning was that you should be it should be possible to improve the properties of the the the antigen,
which is the vaccine to to make more successful vaccines.
And there's various ways that you can go about doing that. You can get rid of the genetic material from a vaccine.
So you're not producing vast amounts of live virus, so it becomes safe.
And that then also reduces the requirement that that the antigen is capable of supporting life in a sense.
So you can make changes to its that stabiliser to making it a better vaccine but would be incompatible with it being a replication virus.
So the the recognition sites tend to be on the sort of outside envelope with the virus, whereas the genetic material is on the inside.
Yes. So you could that. Exactly. You can throw that away.
And in principle, if you do it right, it doesn't affect the what is seen by the immune system at all.
And we should just very quickly go with the tools that you use.
So you started out an X-ray crystallography and also the also involved with electron microscopy.
And these are ways of trying to see things that are smaller than the wavelength light.
Yes, yes. And and a virus viruses were not seen at all until electron microscopy was invented in the 1930s.
And I think it was only about eight years after the electron microscope was invented,
that risk of the person that built the first microscope looked and saw a virus for the first time.
So so electron microscopes were needed to see them at all.
And that was a really important thing to do,
because a lot of the classification of viruses was based on the morphological character seen in the in the end,
but that that was at a much to poorer level of detail to be able to to help in drug
design or vaccine design because you couldn't see the sort of chemical basis of them.
So that's, that's why crystallography became the first method to really sort of open up virus structures.
And the it did that because compared to so crystallography started with Bragg looking at salts and first version the whole history of course
you know we're going to have enough to know now about to do as a modern as a modern quiz what way do you think that the point is that,
Crystal, we started off with very simple things, yes.
And a virus is probably of something like two orders of magnitude more complicated than a protein,
which is where crystallography, you know, what what is bread and butter was a few years ago.
So that I was interested because it was sort of quite challenging to do crystallography on it,
but it's perfectly possible to do it if you can get the crystals that gives you a crystal structure with atomic detail.
So that's very useful. But then the you still have to grow a crystal.
So there's, there's that which can be problematic.
And you get a single structure out of that, which is the crystal structure.
Cryo electron microscopy really sort of completely changed from a sort of ability to recognise morphology to to see atomic detail with a series of,
of improvements in the electron microscopes in the ways the electrons were detected and the ways the samples were presented.
The electrons interact much more strongly with matter than X-rays, so the sample has to be extremely thin.
Otherwise the electrons are completely absorbed and extremely cold.
That's hot. And they have to be they have to be cold at cryo.
And that that's they in general.
What we what we learned from X-ray crystallography was that we get a 100 fold greater lifetime of the crystal of a biological sample,
because electrons and X-rays are both damaging of biological samples.
So they destroy the chemistry ultimately. And that's that that's the limitation compared to material science.
So on the other hand, with with electron microscopy, if if your sample, the key thing there is the electron microscope has to be at very high vacuum.
And if you just had a biological sample in liquid in high vacuum, the liquid evaporate so, so way and also the sample would move around.
So so that's the real sort of advantage there is that you sort of freeze and make it make the sample stationary.
You put it in a very thin film of water, so you buy it by proteins.
And also viruses very often need to stay hydrated, otherwise they they become inactivated.
So you can do that with this process of vitrification, which just means that instead of cooling the water down slowly and getting ice crystals,
you could it very quickly and it forms a glass, which then doesn't disturb that the the the proteins and viruses that you want to look at.
So so in the electron microscope, you get these very thin, vitrified cryo specimens.
You have a very, very beautiful sort of beam of electrons and you have a very high quality detector.
And over the last ten years, that's completely transformed the capability of the method.
And it's not finished that transformation process.
There's still more to go in the future, I think. And I think we just need a very quick one sentence description of what synchrotron
enable you to do that you couldn't do with old fashioned X-ray methods.
This same synchrotron gives diamond like.
Yeah, I mean diamond synchrotron.
A lot of this thing from develops actually sort of came about in the UK diamond it allows you
to it gives you a source of X-rays that that is all many orders of magnitude brighter than
a lamps also the sort of hospital X-ray source and that that means that that you can
essentially tackle structures such as viruses that would be almost impossible by a normal lab.
So so it's it's transformed. It's and in terms of the science response and the viral virology response,
the that increased brightness of the beam means that you can collect a data set for,
for instance, a viral protein in perhaps 2 minutes at the synchrotron.
So it alters the the holes. It's a game changer in that rather than just look at a single structure,
you can think about looking at many hundreds of structures of the targets with a number of different chemicals bound.
And then you can help. Then you can much more quickly learn what the basis of the recognition is and improve the chemical design for it.
So that's a wonderful introduction to virology and structural studies and your career so far, is it?
Finally, we get to Kovac. Can you remember where you were, what you were doing, or how you first heard that something was going on in China?
And when you came to realise that it was something that you were going to have to engage with.
It's a tricky one because there's often things happening around the world with viruses and there was the first hint that something was happening,
I guess before the end of the year in 2019.
That wasn't at all obvious to me that this was going to develop into a into a problem.
It did in January 2020, started to become clear that this was this was a serious this was serious.
And. I we i my group at that time weren't working on coronaviruses.
We've done many years before. We've done some work on, uh, sales when, when that outbreak occurred.
Um, but so we were not, it wasn't something that we were particularly attuned to.
So we're probably, uh, you know, I guess perhaps I thought, well, you know,
unless this is really going to be a big thing, we, we'll carry on doing what we're doing.
But I got a call from, uh, a colleague of mine writes to her in China fairly late in January.
Um, and they, by that point, it was clear that this this was serious.
And we we so we were thinking, how should we engage with this?
And how was his he with some other peers were the first people to do a structure of SARS-CoV-2 protein,
which was the main protease, which is the target for the, the rush drug for, for instance, at the moment.
Um, so he phoned up because, uh, well, we do stay in touch, but in particular they'd, they'd got the structure.
And they, they worked extraordinarily quickly to, as soon as the sequences available,
they made the synthetic gene for the protein they wanted to work on.
They driven to the place where the gene was made and brought it back.
And within a few days it got crystals because they'd worked on the samples and the mouse versions of this.
That gave them a lot of sort of insight because it's a related protein.
So they're able to get a structure very quickly.
And they started to sort of think about how they might look at, uh, designing compounds that would inactivated.
But then they, they were using the synchrotron in China, the Shanghai Synchrotron.
And like any synchrotron that runs in, uh, sort of cycles, you have a run and you have a shutdown period, and they had a shutdown period coming up.
So they, he got in touch to see if there was a way this collaboration with Diamond to sort of keep things moving along.
And because of the difficulty of sort of exchanging things, materials,
what actually happened was we ended up using information from them to synthesise
everything over here and but essentially using all of their knowledge that they gained.
And we set up the, uh, a program at Diamond because of, over the years we set up a system at Diamond called X Chem,
which is basically adding a lab on to adjacent to the beamline so that people can come in and,
uh, use pre-made libraries of small chemical fragments,
which can then be dispensed to very high throughput and sort of quickly and easily and reliably onto protein crystals.
And then that there's a system for simulation, well,
helping people prepare those crystals and get them ready for the synchrotron and then those get shipped on to the very high throughput beamline.
So that was that process was set in motion very early on.
The the cloning and crystallisation work was was led by Martin Walsh at Diamond and my deputy at Diamond.
And then the person that leads the project, Frank Delft, who's joint appointment here with Department of Medicine,
was involved in the, uh, the making sure the X Games stuff worked efficiently.
And this was, was this just looking at the main protein? So initially it was just the one thing.
Yeah, because we just wanted to get something up and running and we, we didn't have any extra money for this,
so we just had to sort of people just repurposed what they were doing and then worry about it afterwards, you know.
Um, so that was set up initially. Yeah. And that went very quickly and the results just and right as soon as we got the structure actually
made the structure available even before the protein databank had sort of been overwritten,
which takes a week or so to, to, to review it and then make it available.
So made it available immediately to people. And then it was put on the PDB very quickly.
So in the same way with the with the fragment screen, as soon as the results came through,
they were made available from through from diamond before they could be sort of
put on the PDP because when you get large amounts of data for these things,
it doesn't fit into the deposition method. The president spoke very well.
So it was easier to to make a special sort of site that people could take the data from.
And then the that was to sort of let people know about that.
It was that that really took off through Twitter rather than anything else.
Martin sort of told people on Twitter about this.
And it was a time when probably a significant number of medicinal chemists that were not able to go into work.
So they picked up on the information that was there.
And essentially there was this sort of moonshot project that sort of fell together with people around the world,
particularly sort of led by groups in America. But that the initiative driven by this work in Diamond and that that meant
that the medicinal chemist could look at the results and come up with ideas,
come up with the next generation of compounds that should be better because the first compound should get out of a procedure like that,
a very poor, very weak binders. But you get something quickly and you get quite a lot of results to give you a heads and that.
And then there was also a company that makes chemicals sort of engaged as well to help get the next generation of compounds made.
And that that was the company and Amine, which is a company based in the north of Kiev.
So that they've not not been in action recently.
But they they they were extraordinary helpful in this process.
And that that then sort of went on. And, of course, you know, at each stage, you kind of there's there's different things needed.
And I think the process is sort of what it was done in a sort of open way.
Not it not as a not in a company. So at each stage for the next stage, there had to be a sort of collaboration set up where you had,
you know, how do you do the assays had to be set up and that was done, particularly people in Oxford.
Chris Schofield was, was great in that and is great and Chris is still very heavily involved in lots of aspects of this.
It's it's also spawned further work.
So there's now some some in H projects that were launched a week or two ago which Oxford and Diamond are heavily involved in, where they engage,
recognise that they want to expand this sort of activity to cover not just sociology too,
but to think about other viruses that are potential pandemic threats.
Um, so, so that, that was, that took off.
But of course, because Diamond is a use facility that lots of people came in with expertise in other proteins.
And over the period, I think most of the obvious targets within SARS-CoV-2 have been looked at now with those and those are going forward.
But so the protein that most people seem to hear about is the spike protein.
Now, that's yeah, that's that's that's not really a drug target.
That's just something that's what with your interest, that's what we worked with as well.
Yeah. Yeah. Now we've done we've, we've done a huge amount to this atomic spike protein.
Yeah. Well, so yeah.
Because I'm interested in structure of, of, of whole viruses and the spike is a key component on the virus.
The spike is the protein that recognises receptors on the cell.
So and each virus has lots of spikes. Yes, it's a good one, but no, no, there's quite, quite a lot.
I mean, how many is it is probably still the sort of subject of some discussion,
but there's a good number of spikes and each spike it's it's it's attached at one end into the virus.
The virus has a membrane which surrounds it and the spike has a little tail that, that is anchored in the membrane.
And then and then there is a substantial amount of protein.
It's a big protein, it's a trimer. So there's three protein chains that are identical to each other, arranged in a cluster.
Uh, and at the top of the spike there is one particular bit, but only about a sixth of the total protein, about 200 residues out to 1200.
That is critical for binding to the sort of main, I guess or you know, really key internalisation receptor, which is called ace2.
So this is a molecule on the on our cells that the virus has to recognise to get into the cell.
Um, so that recognition, recognition event is, is critical for cell entry to the virus.
Once that's happened, then the rest of the protein has a different job to do, which is to get the virus into the cell.
And it does that by a series of conformational changes that essentially anchor the the virus into to the host
membrane and then pull the two membranes together so that the viral genome is is released into the host cell.
It's a bit like a search. Yeah, yeah, yeah, yeah, yeah.
So, so, so that. But all of that depends on the initial recognition of the receptor via this the
receptor binding domain RBD as it's known on the top of the top of the spike.
So the spike a three of the sitting on the top and they're they're, they're, they're little,
little domains that can move around when, when they move up, they expose the bit that binds to the ace2 receptor.
When they're down, they don't they can't see the receptor. So it's it's a complicated, dynamic process.
And clearly you, you might expect that, uh,
antibodies that would bind to the place where the receptor normally binds would block the entry of the virus.
And so those would be so-called neutralising antibodies.
Um, so that's, and that's been entirely borne out a huge amount of work that's, that's followed and all the things you've just told me just now,
did we know that already from studies of other coronaviruses or has that come about?
We knew that we knew the basics of we as soon as the sequence came out, you could align it with the first solid virus.
So that's why it was relatively simple to name it.
And not all coronaviruses have the same receptor binding domain structure, but the cells have something that's pretty similar.
And in fact, there are one or two antibodies that neutralise source that can also neutralise SARS-CoV-2, the very, very small number.
But it's sufficiently similar that there are, you know, recognisable, structural.
Things that some some antibodies could recognise between the two viruses.
So much of that was and that and that knowledge was was absolutely critical
for the for a lot of things that follow that if we just started from scratch,
it would have slowed everything down. But so, again,
just as I've had experience with the the enzyme that was experienced from other groups on doing structural biology as spikes of cells and nerves,
which they did,
they knew that these were difficult proteins to work with and they knew that there were some tricks that you could do to stabilise the protein,
make it easier to work with so those and, you know, fold it in the trimeric form when it's taken off the virus or expressed with that the virus.
So there was a series of things that could immediately be applied from what we knew about the other viruses to making this.
It was still it's still a big and, you know, slightly floppy protein.
It was still not trivial to to make high quality reagents.
And that was really quite important, being able it was very important to be able to do that.
And in the early days there was a lot of stuff that, you know, they were they were low quality, simple,
low quality reagents around, which somewhat muddied the waters with some of the work and the screw, be it.
Yeah. The big strengths in structural biology is to be a sort of twofold.
One is the structural virology and the other is cell surface proteins.
And the cell surface proteins are the cell version of the spike.
Essentially. No, they're not the same, but the problems are similar so that our proteins that have a lot of sugars on the outside,
they are associated with membranes and they need to be made in special ways.
So so we were in a good position to be to have expertise in making these proteins.
So we had the very, very early days you going, who's a sort of post.
This worked with me and also with Yvonne.
He looked at this and came up with designs for the protein based on other people's experience.
And people in America were doing the same thing and we sort of use their ideas
and as well and were able to try to make the protein relatively quickly,
get to get the protein in the right formulation and stable enough to do the to do structural work by electron microscopy.
Took a bit of time, but we got there and as I say, there was a lot of groups working on it and the information was shared very rapidly because um,
the, you know, the journals published have responded very quickly in terms of the peer review process.
So there's been very compared to sometimes when it might take a year to get the paper through the whole thing.
It now it can be tender is being turned around very quickly because everybody's recognising importance.
But also the journals encourage people to make the papers available on preprint service.
So it meant that there was an open exchange of information, which was, uh, very good, so that we were able to, to relatively quickly.
I can't remember exactly when, but we were able to get some, some high quality spike and start on structural work.
And and what were the main questions that he were seeking to answer about, about this spike?
Well, I think the part of it was. Was.
Getting the being able to have the reagents.
The because although with structural biologists, high quality reagents like the spike are useful for a lot of other things.
So they're useful for diagnostics that useful for serology testing.
Um, and so actually the, when we were able to, to, to make this stuff,
we then were asked for material by a number of companies that were trying to set up tests,
whether it was sort of lateral flow tests or, or serology tests.
Um, so, so that, that was, that was something that, it was, it was a useful reagent so we could make reasonable or not massive amounts.
We can make enough, enough of the reagents to give to people to do a proof of principle experiment.
So I finally understood. Sorry, I've noticed that your name appears on a lot of these enormous studies, right,
that are looking at serology, that looking at the prevalence of infection in the population.
And I, I hadn't understood why that was. And nowadays. Right.
But and and it was sort of one of one of those one of those things was relatively early on.
I was approached by, um, the person that leads biology,
the biology activity at the Pool Scherrer Institute in, in Switzerland, who I've known for many years.
And he was collaborating with somebody at a hospital in Zurich, and they had a very high throughput serology assay,
robotic assay that they they that they were looking to repurpose, but they didn't have access to the reagents.
So we, we, we, we sent them some reagents.
And then I established contact with people that were developing the assay, you know, really, really nice people out there.
And also established contact with Daniel Hepner in the top of Discovery Institute.
And we sort of I, I, I don't, you know, I'm not, I don't do serology normally, but it just seemed that there was an opportunity to set something up.
So Daniel worked really hard and then set aside some of his robotic equipment.
And, you know, we the club, we work with the people in Switzerland and, and,
and then because it starts to become a, you know, you've got to think about how you run this as a project.
We Diamond donated one of their senior project managers to help sort of set up some of the structures of the thing in the early days.
Um, and, and we set up, we set up that, uh, robotic platform to enable us to do a few thousand, uh, serology tests a day.
Um, and that's, that's now run by, uh, Derek Crook.
Yes. So, and it's, it's I, I think it's, it's, it's, it's been a successful leasing rule,
which is that it's not nontrivial to do that, especially in a sort of academic environment.
But, um, but I think it contributed some useful information is provided a lot of data for the Office for National Statistics.
So that was one example of the value of the reagent.
But then yeah, the sort of questions that you do, the thing the structural balances don't quite know what the questions it's not,
it's often not entirely hypothesis driven but discovery science.
So one of the things was, you know, well, what will what will we learn by doing it?
And that's one of the things that we did wonder was whether there was the possibility for designing small molecule therapeutics against a spike.
And that's proved really difficult.
And we've not been successful in that.
We've got you know, we we came I thought we were getting close at one point because we we found that within the receptor binding domain,
there was a little lipid molecule, a little sort of fatty acid that was bound within it.
And and when when the fatty acid was there,
the receptor binding mates were locked in a down conformations would not be accessible to the two to find the cell.
So I thought that might be a way to, to, to get some.
Uh, if you could replace the fatty acid with something that bind much more tightly, then it could inactivate the virus.
And there are precedents for that type of mechanism from other viruses that work.
Um, but we were never able to reproducibly sort of, uh, get the spike in the right conformation,
were never able to reproducibly bind things into the receptor binding domain.
Once the lipid comes out it by thought and it's this suspect,
all the people probably agree is that the lipid is put in there as the thing comes out of the
cell through a membrane and then probably slowly falls out and that would then activate it,
for instance, might help the virus get out of the cell because it was minimising chance of reattaching, for instance.
Um, so. So that didn't go anywhere. But, but we did, we did try and we collaborated with, uh, with, with a company to try and find something.
Um, but having said that, at the same time, as we stumbled upon this grouping,
Bristol, observe the same thing and, and they, they've taken that much further.
And, and I think they've demonstrated that the principle that you can inhibit the virus by using that binding site.
So so in a sense because they were, they picked this up and they were in a much better position to take it forward.
We just sort of let them do it and good luck. I hope we can do something.
But, um, but you also looked at the interaction of antibodies as well.
That was that those are the sort of major, major thing. Yeah. And that was that that as you hinted, sort of brought together an awful lot of people.
Um, so Gavin Scruton and, and Gavin Ju have, have their group in this building that had moved back to Oxford from Imperial College for a while before.
And we'd sat around and then said, Oh, you know what?
Can we collaborate on that? And he was mainly working on flaviviruses things.
I think the virus that at that time we had ideas, but we didn't, you know, somehow we were busy with other things.
And then when this happened, Gavin's group sort of repurposed and the the spike production and all RBD production was,
well, I didn't say you quangos involved, but from the beginning it was a joint effort with Gavin's group.
So we've worked, we've worked extraordinarily closely together on this and.
So that it was a case of making those reagents and then that enabled and Gavin's group were involved in really doing the gold standard
serology not at such high throughput but slightly lower throughput which which was then used to calibrate the robotic stuff.
But also that underpinned all of the work with the the variants and the, you know,
thing that the whole different cohorts of people that had different sort of vaccination histories and infection histories and stuff like that.
Um, so that was serology, but also because of the expertise of this group, they could, where they had access to, to, to serum samples,
they could then do a book that they could do single cell sequencing from, from blood and get the sequence of antibodies.
And then again using the the spike as a sort of a screen could filtrate.
Those antibodies interact with Spike and then the live virus work was set up
in a pic green suites because the soon after we set up TRUBEE we got money
from welcome to set up a pic of the Oxford Particle Imaging Centre as a place where we could look at viruses in by electron microscopy in containment.
So that's there's areas where we can use electron microscope containment, but there's also tissue culture labs in other parts of.
And this just means a high level of biological safety. Yeah. So so that so so Gavin's group were using those contained labs.
So they they then again repurposed and, and set up, set up the work with live virus.
And then they also set up work with Pseudovirus, which is a sort of safe version where you just take a bit of the,
the spike bits and put it on another, another biological system so that all of those pieces were set up again.
You know, some of these things took longer than you'd hope, but but they came together.
And, um, so the, so we were, we were also working with, we've also worked with other people.
Jim Naismith Um, not, this wasn't his area of science, but he, he, he was,
he's been developing the camera antibodies, the nanavati side for, for some years,
particularly with Ray Owen's, who was initially we recruited to run the ultra protein production facility,
which then sort of migrated down to how well did you say come alive? Yeah, this is to do with most.
And he said, No, no, no. It's just that it's camels, llamas, camelids have special antibodies.
Do you know about the Nanobodies? Because a normal antibody has two chains or like chain and have a chain and both.
Both of those have variable domains, which are all the things that are swapped around genetically to give the variation and
also subjected to somatic mutation in the general centres to optimise the interaction.
So, so that that sort of the interaction area is, it's essentially two protein domains.
The commonest antibodies just have a subset of their antibodies, just have one of those domains which is called the V H.
So that means that there's a very small bit of protein.
It's only 100 residues and it's not that much bigger than the insulin, um, that is responsible for recognition.
So that is a useful reagent because it's so tiny.
It might, you know, it's the sort of thing that you can imagine given giving a guy an inhaler or something to get, to get it into the airways.
So so this was something that people had been working on for some time and the gentleman just got it right, just got money to set this up properly.
So so they they they switched initially.
So we were closer and closer with them to, to, to help initially.
And then they, they got all their own stuff so they could quickly sort of do everything themselves.
Um, and then they, they, they, they worked to develop very high affinity nanobodies as potential therapeutics.
And I don't know whether I'm sure that's at Jim.
Jim's hoping to, to get that. I think in to in to use but it's not so easy.
They the be the big sort of pharmaceutical companies.
You know, they tend to have very well-defined pipelines of what they do.
So if you fit into there, then that normal sort of expectation of what products are, that is much easier.
This is anything a little bit off track is quite a bit slower.
That's but yeah. So. So there was, there was there was that that side.
But yeah. So, so. So then so Gavin's group could then start to pull out antibodies and because they got the live virus,
these thought all these assays, they could select those that would have high affinity.
And then we, we had the ability to do crystallography,
to look at the binding of those to receptor binding domain and do electron microscopy to see and interact with the spike.
So it was an extremely sort of good collaboration because we just went back and forwards and,
you know, came up with ideas and tried to sort of understand these things.
And, you know, we started off with the original sort of early pandemic virus and we've somehow tracked through a lot of work since then.
I noticed that it's 11:00. It's almost got. So I'm just going to one final question.
I just have to skip most it, which is really just a summary of what you've learned really about how to how to do science from working in the pandemic.
I mean, everything you've told me about has involved massive collaboration and sharing and openness.
Was that typical of how you were working before, or do you think there's been a sea change and will it continue?
I, I, I've been really lucky to have had fantastic collaborations and to work with consortia for a long, long time.
So, so that sort of thing is not new to me.
The vaccine work that we're doing for matches with a consortium of the vaccine work in partnership
with a consortium of the European work has always been very consortia like but but what was this was.
But what was really good here was that the consortium was sort of so joined up and and broader than what you used to.
And Richard Cornell was really sort of made, I think I think did some fantastic stuff because as soon as it was clear what was happening,
he set up a sort of group within the Department of Medicine.
We would meet very regularly, you know, and have completely sort of open discussions.
And the interaction that I've had with medics and all of these people around has been completely transformed by this.
And it made it made a huge difference because, as you say, you know, if you look at the people involved, the people that work with, you know,
working with the patients with getting their consent,
making sure that the right samples were obtained and putting those things together, it normally is is terribly hard.
So it's really effective. And and, you know, that extends to the to to the sort of vaccine work as well.
You know, so we'd have these regular meetings when we find out what was happening from from Sarah.
And, you know, and I think that there was that that was really sort of refreshing to have that and and,
you know, something like Derek Crook, I mean, I knew about it, but I've never worked before.
So, you know, it's brilliant. You get to know these fantastic people and, you know,
it was so so that so that that that was I think that that it's that's been one I think that's been a really wonderful thing.
What you know, one of the questions is what have what happens next?
And I think I think I hope it'll be possible to to hold onto the realisation that by
putting all these pieces together you can actually sort of progress things through to a,
to a much sort of richer outcome than you would if you just looking through an area.
But let's see.