By Jocelyn Chong
Peptoids are synthetically produced polymers that mimic polypeptides, naturally occurring proteins. Think of them as designer proteins– scientists can control the exact chemical structure, designing any peptoid they want with customized properties and functions tailored to specific applications. Peptoid synthesis is fully automated, performed by machines. Beyond being remarkably easy to make, peptoids can be crafted with incredible chemical diversity, naturally mimic the structure of biological proteins, resist breakdown in harsh conditions, retain powerful biological activity, and even organize themselves into protein-like nanostructures.
Peptoids were discovered in 1992 by a team of scientists at Chiron, spearheaded by Berkeley Lab’s Dr. Ron Zuckermann (Researcher Emeritus, Molecular Foundry). I spoke with him about this journey and the potential for peptoids to accelerate new scientific discoveries.
Your team developed the first peptoid synthesis robot. Can you walk me through what that process was like? What were the biggest challenges you encountered, and how did you know you were on the right track?
Ron: As a chemist, I understood the chemical principles involved, but being an auto mechanic before college and grad school taught me how mechanical systems function.
When we first discovered peptoids, I quickly realized the chemical steps were very simple but highly repetitive. We envisioned automation and robots as a way to amplify the impact of that chemistry by making them automatically instead of me toiling away in the lab. So, we set out to automate the process at a time when there really wasn’t anybody doing automated chemistry. The only automated chemistry at that time was DNA synthesizers and peptide synthesizers, and those were developed because DNA and peptides are fundamental biopolymers. People had been studying them for decades and figured out how to make them.
Doing new synthetic chemistry on a machine was daunting at first. I knew as a chemist that the chemical steps in peptoid synthesis were actually so simple that it’s almost like making coffee– you pour liquid through a filter. The peptoids are not even heated up, just room temperature. It’s literally just pouring liquid over a small bed of beads, then filtering, and washing. It’s totally doable.
So there was never a question that it couldn’t work. It was a matter of how do you, as a chemist, get something like that to work? You really need an interdisciplinary team and you need to think like an engineer as well as a scientist.
Q: How important is interdisciplinary collaboration– for instance, with biologists, engineers, or data scientists– in advancing peptoid research?
Ron: In addition to chemistry, you need people who understand engineering and computer programming. And so at the beginning, I didn’t have that. I had to do everything myself. I wrote the first software in Basic, which now people frown on, but I thought it was great. And I built the first synthesizer with a drill press, some chromatography columns, and a ton of Teflon tubing.
All the first synthesizers were handmade, and then slowly, as we showed how promising peptoids were, I got more and more interest, and more and more support. And I had engineers and programmers, and it was great to have that expertise of different disciplines working together.
We had to make the chemistry as good on a machine as it would be if you were giving it love and attention and focus by hand. And we were able to do that. That was mostly because we always made sure to respect the chemistry first and build the automation to fit those requirements. Our breakthrough really was making the first fully automated peptoid in 1992, which was reported in the Journal of the American Chemical Society.
When we think about the impact of automation, it was huge. It turned peptoid synthesis into a way of rapidly synthesizing an enormous diversity of materials. And so as a chemist, I’m super proud of that, and that’s what I know how to do. But I don’t claim to know all the potential uses for them. I know how to make them. And so what I did early on in my career was to always collaborate with people who are primarily looking for utility, or some kind of function that they want. And then we could meet in the middle and I’d say, “Hey, I know how to make that.” And they’d go, “Well, great. I need a material that does this.” And then we could iterate. And so this iteration of going back and forth between somebody who’s looking for something and somebody who’s making something is really important to find viable opportunities.
Q: Some of the more widely known peptoid-based use cases are in biomedicine. What are your favorite use cases outside of the medical field?
Ron: Peptoids have been used in biomedicine because they’re very close structural mimics to proteins– they’re about as chemically close as you can get. We’ve simply moved the side chain over one atom on the backbone, so as you can imagine, there’s a lot of biological things you can do, which we’ll talk about later.
In terms of non-biological uses, we can still take advantage of the modularity of synthesis, meaning, how you can link monomers together in different orders and different combinations to alter the properties. Some of the most exciting sort of material science things we’re doing as a field is making crystalline nanosheet structures.
Two dimensional (2D) materials are well studied in material science, but oftentimes they are not really designed to be in water, like graphene or other types of semiconducting 2D materials. They don’t function well in water, which is where biology happens.
If you want to make materials that can take advantage of some of the amazing structures we see in biology, that do incredible things like catalysis and photochemistry, we can pull on those design principles and put them into materials.
For example, nanosheets can be used as simply as a flat substrate to put things on. Think of a piece of plywood. By itself, you may ask, what’s this good for? But, if you think about all the possible things you can use it for, you can build tons of different things. One of the first things we did was to adorn the surface of nanosheets with different chemical and biological groups to create 2D displays.
You can display things on the surface, meaning you can put a group, like a catalytic group, or a fluorescent or optically active group that reacts with light, on the surface. You could also display a nanoparticle or quantum dot on the surface. If you were to throw a nanoparticle in solution, it’ll move around. It might aggregate, but if you stick it like fly paper to a substrate like a nanosheet, then you can display things with high surface area. So that can be used for things like catalyzing the degradation of environmental toxins or immobilizing them to the surface.
You can make surfaces that can bind nasty pathogens like virus particles, which relates not just to biomedicine, but to public health and environmental cleanup as well. We’ve worked on nanosheets that could bind the Ebola virus and all sorts of horrible things– imagine if you could just have a material that itself is non-toxic, but can bind to these things like fly paper and neutralize them.
When the virus sticks to the surface, it can’t be active anymore. Even though you haven’t physically destroyed it, you’ve immobilized it. And then think of a flat material– you can stack them up and make filter beds. You can do filtration or separations to purify water. You can bind toxic metals, for example, and remove them from a water stream. So those are the kinds of things people have published on.
A lot of that stems from the ability to make a 2D nanosheet, and now, just recently we can make a 1D material, a peptoid nanofiber. These fibers and nanosheets are themselves crystals– they’re crystalline– and that’s why they persist in their structure.
They have a very stable structure, but they’re still soft materials. They’re not rigid– they can bend and move, meaning they can adapt.
Q: How do you see AI impacting the field of peptoid synthesis?
Ron: One of the themes of the Foundry is to synthesize materials with real world applications. The third piece is using computation to learn from and predict new materials. I’ve always been a fan of computer computational methods. Our dream is to get to a point where we can design structures proactively and say, “Okay, I need a structure that goes like this and this, and has this here.” And you sketch out what you want and then we can figure out how to make it.
The Nobel Prize last year, [in 2024], went to David Baker and others for designing novel proteins. This stems from a fundamental paradigm of biology: if you know the sequence of monomers in a chain, it can fold up into a unique structure, and that structure will have some function.
And that’s revolutionizing. We hope to do the same thing with peptoids. Peptoids are modular, meaning like Tinker toys, we can take different units, and snap them together in a common way. That means robots can make all kinds of different combinations, and computers can study different sequences in their activities and hopefully start to predict function from sequence.
Going from sequence to structure to function, is really difficult to do with just chemical intuition. We need AI, we need computational molecular dynamics, and coarse grade modeling and all these things. I would say that we’re just at the beginning because you need a learning set to train AI. You need a vast pool of examples to study and we just don’t have that many yet. It’s something that will be big in the future, but right now it’s a little early to say because we’re still in the process of getting data for AI to be trained on.
Still, we can look at what we have discovered and mine that for information. There are new motifs and recurring structures that we see in peptoids that are just due to the intrinsic chemical nature of a peptoid. A lot of that work was what I do here at the Foundry, using electron microscopy and modeling to study the exact chemical structures of peptoid nanostructures. And that’s been huge, so I think there’s a lot of exciting things to learn, and we are close to being at the designability stage.
Q: If we fast forward 20 years, what do you think the average person’s interactions with peptoid-based technologies would look like?
Ron: Well, I think the biggest things are going to be antimicrobial drugs and cancer drugs. Peptoids are really good at selectively targeting certain cells and disrupting their membranes.
But therapeutics take a long time to develop. They have to go through so much testing and optimization, but in 20 years, I think you’ll see many examples of peptoids, either pure peptoids or small sequences of peptoids inserted into other structures.
Another application that will come soon is drug delivery. That problem is really a materials science question– like what kind of polymer or liposome can be used to take a drug, make it more tolerated by the body, survive longer, and get to where it needs to go?
A great example of this are the lipid nanoparticles used in the COVID-19 vaccine. Those are short, cationic polymers, whose simple features can be well captured in a peptoid. One of our users, in a company called Nutcracker Therapeutics, is actually developing peptoids in their products to deliver mRNA to cells.
They are getting close, but since they’re developing a commercial product, it still has to go through testing. But, overall, drug delivery and therapeutics I think will be the most prevalent areas of application. Another super new and promising area is the use of peptoids for organ preservation. Which I haven’t really talked about too much, but it’s a really cool application!
Q: I was actually going to ask you about that. I saw the story about the pig’s kidney and I would love to hear your thoughts on that.
Ron: Yeah, that’s a brilliant story because we set up the user facility on the fifth floor, now run by Dr. Michael Connolly, to allow users to come in and make any peptoids they need for whatever they thought was important. So here we had a user who said, “I want to make peptoids that can preserve organs” and I was like, “Wow, okay, that’s above my pay grade. But you come here, we’ll make whatever you think you want to design, and I’ll help you.”
They were very clever and just said, “Okay, we’re gonna make a family of different peptoids (inspired by antifreeze proteins) and we’re just gonna simply dissolve them in water and freeze them and they’re just going to make ice.” They had little 96 well plates, they froze them, then they took the ice samples to the ALS (The Advanced Light Source, one of Berkeley Lab’s facilities) and looked at the structure of the ice rings.
Since ice is crystalline when you shine x-rays at it, you get these rings, meaning the water molecules are frozen and they’re locked in a lattice. But they looked at all these different peptoid samples and they found ice where there was no ring or the rings were very diffused. This means the water molecules aren’t disorganized, they’re less organized.
So they found a peptoid that could disrupt the formation of ordered ice lattices. And this was Dr. Xiaoxi Wei and Dr. Mark Kline. They were some of our early industrial users and smart enough to ask, “If we were to soak an organ– or at first just a single cell– in this peptoid solution, could it survive freezing?”
It turns out that the peptoid changes the shape of ice crystals as they freeze. Like salt water, the peptoid in there makes it a little harder for the water to freeze. But it changes the shape of the crystal so they’re not these sharp spears and spiky points, they’re kind of soft rounded crystals. And that’s because of the way the peptoid is binding to the ice crystal as it forms in solution. It kind of prevents those edges from growing. So it’s a cool application of fundamental chemistry and physics and people brilliant enough to think of this application.
Q: Peptoids are often praised for their designability. Have you encountered a case where that flexibility worked against the intended function?
Ron: I can’t think of a reason why designability in itself is bad. There are problems where peptoids may not be the right solution.
But the fact that they’re biomimetic polymers, meaning they have the same modularity, polarity, and solubility as biological materials, the properties are roughly in a place where there’s a rich world to explore. So I would say designability is not a limitation. It’s always an advantage.
If I were to say, “Okay, if I need a polymer, that just needs to have a few aromatic groups and a few ionic groups. What could I make?” Peptoids is the obvious answer. You can make that in as little as five minutes (though more practically, one day). The coupling reactions are less than an hour per monomer. It’s automated, so it may not ultimately be the cheapest, ultimate material. But that flexibility allows us to test an idea really fast.
Of course there’s gonna be things you can’t do with a particular material. So I think the more interesting way to think of that question is: what’s limiting peptoids from being adopted where they would make an impact? I think a lot of it is word of mouth, which is why the Foundry’s user program is so important because people can come here to the Foundry and learn how to make them and take that knowledge back with them.
One of the challenges of a place like the Foundry is spreading the word and getting this technology into more people’s hands. We’re doing the best we can. We’re publishing papers and there’s a whole community of people working on this stuff.
It’s growing at its natural accelerating rate, which I’m delighted about. But the other limitation when you zoom out is that you need money to really make a worldwide impact. To get money, we have to convince investors to invest. There are granting agencies, which is the traditional route and we’ve been doing that.
But the biggest thing will be the development of peptoids in industrial applications. That’s where you can really get dedicated people and dedicated money to focus on solving these problems. This will require the key step of manufacturing peptoids, that’s something we don’t necessarily think about when we’re working here on the bench. But when you think about, okay, now we’ve got to produce a liter of solution for organ preservation, they not only have to manufacture the peptoid economically. They have to sterilize it, bottle it, and formulate it.
X-Therma has shown that it is feasible to manufacture peptoids at that scale. They chose an application that’s clever because you just need a bottle that’s a dilute peptoid solution in water. So a little peptoid goes a long way. I wouldn’t say the manufacturing of peptoids is a limitation, it’s just the next hurdle that we have to, as a community, make sure goes smoothly.
I know as a chemist, each step is going to work. But I’m not an expert on the economics of scaling.
Q: Which underexplored field do you think peptoids could revolutionize next, and why?
Ron: You’d call peptoids meso-materials. “Meso” means in between, not like miso soup. The traditional materials we think of are small molecules, like drugs like aspirin, or like proteins which are long chains of amino acids, and polymers, which are also long chains to make things like plastics. So those are three classes of materials that have different properties, but peptoids are neat because they can mimic all three of those classes of materials.
You can make short peptoids, which mimic small molecules. You make long peptoids, which mimic polymers, or you can make very specific sequence patterns, which mimic proteins. We have the ability to make these things synthetically, but the huge challenge in the field is choosing which peptoids to make out of all these gazillion choices – there are literally 200 monomers we can use, and we can link 50 of them together. So that’s 200 to the 50th power, which is way too many to choose!
The peptoids we’re looking for are in plain sight, but we don’t know which ones are the best. That’s why peptoid discovery is so important, where we can make lots of different peptoids, work with somebody who knows what they’re looking for, and iterate back and forth to find them.
That’s how we do it now. In the future, hopefully we can design them more directly with AI and so forth. Instead of searching for one, you can design the one that you need for your purpose. The way to think of it is, the computer wouldn’t just design one and be done.
It would focus us on a small sector of peptoid space. It would bring you closer to where you need to go. And then you always need experimental synthesis and testing – back and forth – to refine it. But I think discovering materials that are in that intermediate space– this meso peptoid space– is gonna be the future because peptoids are easy to synthesize, so that means we’re not limited by the question of “Can we make this?”
That’s what most chemists get stuck on. But peptoid synthesis is pretty doable, so it shifts the question of “can we make something” to, “what should we make and why?”
Q: If you could pass one piece of advice or a challenge to the next generation of peptoid researchers, what would it be?
Ron: I think an important concept is to think about accessibility and sustainability. We need functional materials in this world that are easy to make. And what I mean is that they use a low amount of energy to make, they’re cheap, they don’t cause environmental damage and they can be made in high yield, meaning you don’t waste a lot of energy and material resources trying to purify teeny amounts. So you need something available in abundance and not a rarefied material. Peptoids are not perfect, but the nice thing is, if you identify an active peptoid, we know it can be made readily. I would encourage people to really start thinking about how to design functions that they’re looking for based on accessible structure, not the perfect structure. That’s what nature does– it uses evolution to find something that’s pretty good and then iteratively tweak it to make it better and better.
