Natural Prodcast Episode 17: Cassandra Quave

Dan Udwary: Hey everybody! Welcome back for Natural Prodcast episode 17. The guest we have this week is Professor Cassandra Quave from Emory University, with joint appointments in the School of Medicine and College of Arts and Sciences. She’s an ethnobotanist and the herbarium curator there, with a broad range of experimental work on plants for drug discovery in antibiotics, anticancer, and now COVID. We also wanted to talk to her because she’s written a book about her life and her science, called The Plant Hunter, and I have to say it’s so awesome! For those of you want to understand more about natural products and drug discovery, or the challenges of academia, or if you want to understand what it’s like to do field science as a woman and with a physical disability, you’re gonna love it and enjoy it and learn a ton. And for those of us who already work in natural products, you’re going to get a great look at the intersection of traditional medicines and medicinal plants with the pursuit of modern drug discovery. It’s also the kind of book we can hand off to family members and friends as a way to introduce them to the field. I really can’t recommend it enough to this audience. The hardcover version is out now in stores and online, and there’s an audio version, read by Cassandra, and the paperback version will be available in June. You can get more info on all of this at cassandraquave.com, and I’ll link out to everything in the show notes, as always, at naturalprodcast.com. And, if you can’t get enough Cassandra, you’ll also want to check out her podcast, “Foodie Pharmacology,” where she talks about history, medicine, cuisine and chemicals. The conversation today covers a lot of ground – her book, bioprospecting vs biopiracy, early stage drug discovery in general, and a possible data-driven future for plant natural products. Happy listening!

DAN UDWARY: Hey, Alison.

ALISON TAKEMURA: Hey, Dan.

DAN UDWARY: So Alison, I’m very excited today. Usually when we do these interviews, most of the people that I think we’ve talked to so far I either know personally, or have worked with directly, or have met at conferences, or just know through professional circles in some way or another.

But today, we have someone who, weirdly, I haven’t, I think, ever been in a room with or spoken directly to but I feel like I really know her. And that’s because she has a book called The Plant Hunter and I’ve read all 400 pages of her life and I feel like I have a new friend that I’m really eager to talk to. So our guest today is Cassandra Quave. 

ALISON TAKEMURA: I do just want to say that I also feel like Cassandra Quave has put herself on the page and made herself really knowable through her book. And it was such a great book, The Plant Hunter. And so I’m sure we’ll hear more about that today.

But it’s kind of amazing, just all of the things that Cassandra has done. And so hi, Cassandra, welcome. And I just want to start out with you have done so much, and you wear so many hats. So I just want to give you a chance to introduce yourself.

CASSANDRA QUAVE: OK, great. Well, hey, it’s so great to see both of you, Dan and Alison. And I strangely feel like I know you as well just from being on Twitter. It’s this weird virtual world where I’m like, oh–

DAN UDWARY: For sure, yeah. I told Alison that, Cassandra is kind of one of my Twitter friends, so–

CASSANDRA QUAVE: Yeah, Twitter friends are the best.

DAN UDWARY: Yeah, for sure.

CASSANDRA QUAVE: Yeah, and it’s funny. It’s kind of weird to me that people are actually reading the book, because it was this labor of love for so long. And I’m like, god, no one’s going to read this. And then people have, [CHUCKLES] and it’s just– yeah, it’s a weird feeling. It’s an exciting feeling. But I’m really happy to be here today.

So Alison you asked about my many hats. So let’s see from a professional stance I’m an associate professor of Dermatology in Human Health at Emory University based in Atlanta, Georgia. I’m also the herbarium curator, so I take care of a museum of dead plants. I’m really good at finding and killing plants, so if you haven’t figured that out already from the book, not so great at growing them, unfortunately. I also–

ALISON TAKEMURA: I don’t think that’s true. Based on the recounting of your garden, I think–

CASSANDRA QUAVE: My garden benefits greatly from my husband’s love and care. Yeah, and let’s see. I lead a research group at Emory, I teach classes here on food and health and botanical medicine. I’m also a mom of four kids now so ranging from 8 to 17 in age, so my home life is very busy. And I’m also a pet mom of a mini pig and a dog. So we have a lot of action happening now at home.

ALISON TAKEMURA: Wow, amazing. I don’t know how you found the time to write a book but based on your productivity and what was shared in the book, it seems like it’s par for the course.

CASSANDRA QUAVE: Yeah it was such an opportunity. I feel incredibly thankful and really, really blessed to have had the opportunity to tell this story. I know like just since I was little I’d always wanted to write a book but it’s really hard to break into that area.

I mean you have to secure an agent and there’s all these steps and it’s kind of a mystery of how you get there. And I just feel like I got super lucky and found an agent that was really a great fit for me and really supportive, and I found an amazing editor. And yeah, it just kind of came together in the most delightful and unexpected way. So I had to leave with that chance when it presented itself.

ALISON TAKEMURA: So I have an idea of where we could start, but Cassandra please let us know if you want to start somewhere else. You go into this in the book but can you share with listeners what made you interested in plants and the natural compounds that they make?

CASSANDRA QUAVE: Yeah, so I mean my path towards natural products and medical ethnobotany really began with early childhood experiences in science, right. So I was always an outdoorsy kid – I was often found in a tree or covered in dirt playing with my dog in the yard. But I was also a bit of an unusual kid too because I was born with a lot of different birth defects of my skeletal system. So I was missing bones and I had to have a lot of corrective surgeries as a young child. And so many of those times when I was out and about I was on crutches and because I couldn’t always wear my prosthetic leg.

I had my leg amputated when I was three and almost died of an infection following the amputation. So I had this kind of oddball childhood where I was in and out of the hospital all the time but I was– when I was well enough to be outdoors, that’s where you could find me. And really it was my third grade science fair project where I first looked into a microscope and just fell in love with this invisible world that was all around me because I was always an observant child like I just like to sit and look at things and observe insects. And when I saw what was going on under the microscope, that really got me excited.

And so flash forward to college and I’m on a pre-medical track. Actually at Emory is where I did my undergraduate and I was a double major in Biology and I got introduced to this field of anthropology at the time too. I’d never even heard of anthropology. This is– I grew up in a very rural, small town. We didn’t have AP or IB courses or any of these advanced things that my kids have opportunities to partake in today.

So there were all these new concepts that I was being introduced to. And in one of my courses, I had the opportunity to learn more about traditional ways of healing in the world, and that really caught my interest. And it was in another course, in a tropical ecology course, that I first encountered the term “ethnobotany.” And for the audience, ethnobotany is the scientific study of the ways that people interact with plants, whether it’s for plants to make clothing, or musical instruments, or food, or medicine, which was really where my passion was.

And so a path opened itself to me, just before my senior year of college, a chance to go to the Amazon and work with a traditional healer as a volunteer intern in his garden. And again, it’s one of those things where you have these paths available, and you have to either leap at it and go, or not. And for me, I just– there was just no way I wasn’t going. I had to do this. I just really felt such a compulsion to go.

And it was really a life-changing experience for me. I was very much a skeptic at the time. How can these plant-based medicines actually work? Because again, I was getting training in biochemistry, and organic chemistry, and all of these hardcore principles of Western medicine. But in the Amazon, I really started to understand how healers are able to interpret the language of ecology, and interpret the language of plants, and use that as a way of treating their patients.

And as I read more and experienced more, I came to really appreciate the fact that many of our modern medicines are derived from nature, and in many cases from plants. And so I think of nature as giving us the gift of blueprints to interesting natural products that we can use successfully, hopefully, in the future even more so as novel therapies. And that’s how I got on that path of instead of wanting to practice medicine, I decided I want to discover and make medicine.

DAN UDWARY: So, yeah I think that’s a really good definition of ethnobotany, which was one of the questions I wanted to probe you on. And it’s a really interesting field that I guess– so I’m more of a microbe guy, and as is Alison, or not a guy, but [LAUGHS] a microbe lady. And I think I’m always intrigued by the people aspects of things, because a lot of what we do at JGI in terms of the sequencing that we do is very people-disconnected, and culture-disconnected. Like we’ll take some soil samples and sequence all the bugs out of that or whatever.

And so I was intrigued by the small section in the book about the conflicts between ideas of biopiracy versus bioprospecting, and where that lies. And I don’t know, do you want to elaborate a little bit on that in terms of ethnobotany’s views? Because I think I’m asking because partially it’s a check-up on me. And I wonder how that intersects with bacterial bioprospecting that is often done, where we’re really just looking at DNA sequences, and we don’t always know necessarily or pay attention to where bacteria come from. And do people even know that the bacteria are there? They haven’t been used as medicines. But with botany, it’s very, very different. So I guess I don’t have a question. I’m just wanting to probe that topic a little bit.

CASSANDRA QUAVE: Oh, absolutely. This is a really pertinent question. So let’s explain first what is the difference between bioprospecting versus biopiracy. At its most fundamental level, the difference is really in whether or not the research materials that you’re working on or the products you’re developing are being worked on or accessed under the principles of access and benefit sharing. So are you taking something without giving any benefit back to the owners of that genetic material?

So this is also relevant to bacteria. If you go into another country and take soil and discover a new important drug from the microbes in that soil, there are now international regulations that provide a structure for ensuring that the countries that are the source of that soil can receive some recompense. So this convention I’m talking about is called the Convention on Biological Diversity. And there’s something called the Nagoya Protocol on access and benefit sharing.

And for a very long time, there were– it served as a guidepost, but there weren’t many examples. And there wasn’t much infrastructure available, especially to researchers just starting out as they’re trying to form collaborations in different countries. I think that’s changed a lot since the convention went– since the protocol went into force in 2014. There’s now a website that has a lot of resources that you can access.

As an ethnobotanist, a lot of our work obviously is spent on plants. And in my area of applied ethnobotany which is really focused on medicine, there’s a clear history of colonial exploitation of both plants and the peoples that have either cultivated or selected for certain varieties of those plants or who have informed others as to how to use them medicinally. And we all benefit from that in a weird way today. I mean, if you think about how much you enjoy that morning cup of coffee, that is a plant that has a functional activity. It’s a pharmacological agent that acts as a stimulant on your central nervous system that in some ways could be considered a medicinal plant because it has something other than just dietary implications.

So that’s one that’s taken a journey around the world starting in Ethiopia, and over into the Arabian Peninsula, and then into Europe, and everywhere now. But was there any reward to the people that originally discovered how coffee could be used? 

The same can be said for many of our spices. And you can look at the colonial history of what happened in Indonesia, in the Banda Islands, with everyone that’s enjoying their pumpkin spice lattes of the season. They may be shocked to know that some of those key ingredients, things like nutmeg, and mace, or cloves, actually led to the annihilation of an entire people, their enslavement, and murder, in the search for a monopoly on the trade of those plants. So there’s a lot of bloody, dirty history behind plants. And certainly, ethnobotanists today don’t want to follow in those footsteps. 

So there’s a lot of work that goes into establishing new field sites. And it’s also important to set expectations because I’ve worked on hundreds of plants in many different cultures. And just because you do a field study in a location doesn’t mean that you’re going to have this massive economic gain, or some benefit come out of that, necessarily.

And so I think the way I’d like to approach this is, number one, is I put a lot of emphasis in my program on research capacity building. And I think this is something I’d love more natural products scientists to think about, because if you look at the 36 hotspots, or terrestrial biodiversity hotspots that we have on Earth, most of those occur in nations that have very poor research infrastructures. That hurts us across the field of science because they’re the ones that have access to these natural resources, but they don’t necessarily have the support network, the equipment, the facilities to really apply the cutting edge science to these in investigations.

So some of the things that we do is really look for opportunities through grant funding programs to build up research capacity with our global partners. And I can just give one example of our work that’s been ongoing now in the Balkans in Kosovo where we’ve been able to work with the State Department to get funds to help encourage and support training, where we’ve done laboratory exchanges. We also recently were fortunate to get awarded one of the peer grants. And the peer mechanism is something that’s offered through the National Academies of Sciences, it’s supported also by USAID. And it’s basically a mechanism where you can piggyback onto one of your existing NSF or NIH grants and get funds that would go not really to you but that go to your partners and your other countries that are supported through these programs.

And so we’ve done this in Kosovo. They’ve been able to not only purchase their own HPLC to enable faster analysis of their plant extracts, but also establish their own microbiology lab so that they, on site, can really do more to assess the amazing biodiversity of that mountain region, rather than just having it be the Western person comes in and takes the plants and brings them back to their lab.

I think that’s my overall goal. And if I were to have a dream, that would be what it would be is to really help build a larger network of scientists across these countries. So that’s one way to support access and benefit sharing. 

DAN UDWARY: That’s a very cool resource that I’m not terribly familiar with, though I’ve been out of the grant writing game for a while. But yeah, no that’s a great idea and hopefully other people will take some inspiration from that. It’s awesome.

CASSANDRA QUAVE: Yeah, and I’m sorry if I’m using like acronyms to NSF, National Science Foundation, NIH, National Institutes of Health, for those. I figure most of the listeners are–

DAN UDWARY: Most of our listeners are probably intimately familiar. Yeah, I would expect but sure.

CASSANDRA QUAVE: So the other thing that we do on the ground with the communities themselves is really think about what are their needs, what are their desires? In many cases in discussions with elders and communities, and especially with healers, is they want to have the knowledge returned to them in some format. So for example, when I was doing my dissertation research, I gather data from all over this area of Southern Italy and in addition to the papers and things I published for my dissertation, I also wrote a book that was– it was actually trilingual, so English, Italian and had some of the plant terms in Arberesh, which is an endangered version of modern-day Albanian that comes from five centuries ago. That’s a long story.

But it had those words in there as well, and it was prepared almost like a coffee table book so that it was very, very visual, lots of information on how the grandmothers and the healers explained how they prepared these medicines, and we were able to– our partners were able to get money from the European Union to print 1,000 copies of this and we were able to distribute it across the community. So that’s been used in supporting educational initiatives and work with school children and understanding the plants and their environment. We also were able to build a botanical garden, like a small teaching ethnobotanical garden. So these are some things that even if you’re not like a big pharma company and you’re just like an assistant professor, or at the time I was just a grad student, there are definitely ways that you can support benefit sharing and bringing value back to these communities so that it’s not just an extractive process.

DAN UDWARY: That’s beautiful.

ALISON TAKEMURA: Yeah, Cassandra in your book you mentioned working on several antibiotic resistant microbes including a bacterium called methicillin-resistant Staphylococcus aureus. Can you share why finding treatments for these microbes is so important?

CASSANDRA QUAVE: Yeah, that’s a great question. 

DAN UDWARY: And personal.

CASSANDRA QUAVE: So staph is my old nemesis. It almost killed me when I was three. It wasn’t an MRSA strain at the time because that was in the 1980s. I’m showing my age now.

So early 1980s we didn’t have– there were some isolated cases but it wasn’t as widespread as we have today. And the sad truth is MRSA and staph in general kills more people than HIV/AIDS does every year in the US and it has since 2005 even though we technically have a number of different antibiotics in our arsenal to treat infections by MRSA. And then there are other infections that we really have almost nothing for. We’re also working on organisms, pathogenic fungi like Candida aureus in the lab and we work on carbapenem-resistant Acinetobacter baumannii, so that’s a mouthful. And those are really hard to kill. I mean, really, really hard to treat.

We’ve thrown our entire library at the A. baumannii and came up with just a few possible compounds to chase down, but there– the challenge is, as the listeners know, even when you find a highly potent active compound that has a good cytotoxicity profile, so a nice selectivity index, doesn’t necessarily mean it’s going to make a good systemic drug. So there’s just– we’re pushing closer and closer to the envelope. But you have to go through a lot of different options before you find something that could be viable for development as an antibiotic.

ALISON TAKEMURA: And so is that the main thrust of your research now looking through your library looking for compounds that could be active against these antibiotic resistant microorganisms?

CASSANDRA QUAVE: Yeah, that’s definitely one of the main thrusts. I think that there’s– the two thrusts that I see in the research group are, number one, is I really want to understand how these traditional medicines work because in my mind when I think about plants that are used for the treatment of infectious or inflammatory disease and these same species are being used not just by one generation but by many generations, and maybe there are some small alterations in the recipe of how the medicines are prepared, but this knowledge is getting passed down over and over and over again and in some cases many centuries, and we can find evidence of that by looking at historic text which we have done looking at old texts in Latin and also in Chinese block text as well. I think– so that’s one question is like how do these work, are they safe, and how can that inform people that use these as their primary form of medicine?

The second driving force is absolutely – I’m unabashedly applied in my research, which doesn’t strangely doesn’t always help me with grant applications. It’s a weird… it’s … yeah. But yes, I would love to find more drugs I like. That’s the main focus of our work, looking for new therapies that could be used to treat these highly resistant bacterial and fungal pathogens.

And we’ve actually just wrapped up a year, a years’ long screen, probably the largest screen ever attempted I think on COVID that we’re getting ready to submit for publication and have found some interesting hits for that as well. And so I think that there are really interesting small molecules in nature that are just waiting to be found. They’re hard to get at. You have to really– there are a lot of bottlenecks as you well when it comes to isolating compounds from these very complex mixtures, and in some cases, an isolated compound is not the answer. Some cases, it’s actually multiple compounds acting in synergy which is scientifically fascinating but a huge pain to deal with in the lab.

DAN UDWARY: Yeah, especially for advancing towards the clinic. Yeah. So then maybe the COVID stuff is a good example. What’s your approach toward … your scientific approach, I guess. Where do you start when you decide to tackle a new target or whatever? What’s your process for discovery?

CASSANDRA QUAVE: Right, so I think the process really begins with the construction of our library. So that’s something that’s ongoing. We have I think we’re over 700 species in the library now. It’s unique in that it is highly targeted towards, again, plants that are used in traditional medicine for infectious and inflammatory disease. So we have over 2,000 extracts.

Some labs like to prefractionate before screening. I do not. I would rather screen all of the crudes I’ve got. And then based on both activity and cytotoxicity, then we start the process of kneeling down on the activity. When it came to– when it comes to finding a new target to screen, I think having assays that are amenable to – high-throughput testing is really important for us. In this particular case, we are using a pseudovirion screen to look at the interaction between SARS-coV-2 spike protein and the ACE2 receptor, so we’re looking at viral entry inhibitors.

But the other important part of our approach is the ability to go back and forth as we screen and fractionate. So between the two labs, I have labs on different sides of campus, so that’s what I mean when I say “between the two labs.” They’re all under the same umbrella but physically apart from each other.

So in the phytochemistry lab, we’re preparing the drugs, the master plates for testing. In the micro lab, we’re screening. Once we have hits, we go back to phytochem, and we have folks working on fractionation, structure ID, all that jazz. In the meantime, we’re going back and forth.

I think that ability to do that in-house is really important because even with the best collaborators, there’s always a lag when you’re trying to get another lab to test your compounds. It’s just– so I’m able to avoid that by having it all done in-house. And then the other, I think, really important thing that we’ve done in our approach is I really try to find experts that are able to take it beyond that initial screen because I am not an expert in virology, OK. So I– but what I can do, and what I have done is I’ve teamed up with people that are experts in virology and immunology and we’re putting together a grant right now to look at some of these in non-human primates should they pass the next steps in terms of live virus testing.

So having that ability and willingness to collaborate across disciplines can’t be underestimated as really being just so incredibly important to advancing these discoveries. The idea that something can go literally from the field to the pharmacy in one lab is just not possible. You need to be able to work with other people. Yeah.

DAN UDWARY: Yeah, in the natural products field, we call that find and grind, then, it sounds like, very traditional kinds of—yeah. That’s in a bit of contrast to what we usually do with bacteria nowadays, which is we usually just get a DNA sequence first. And there are plenty of software tools to find natural product gene clusters, and even be able to somewhat predict the structures of the compounds that would be produced. But plants, it’s not that easy. There are still not that many plant genomes, certainly nowhere close to bacterial kinds of numbers. What’s your thought on the future of what you do then? And are there ways to do data-driven approaches at some point like that in the future?

CASSANDRA QUAVE: Yeah, that’s a great question. I don’t know how amenable plants are really to a genome-based approach for screening. I think a lot of our work has been focused on exploring the possibilities of bioinformatics and ways to mine spectroscopic data. So the listeners are probably quite familiar with GNPS as a tool, and using molecular network analysis, too, as an early step. That’s something that we do as an early step when we’re looking at more complex mixtures, we’ll see what kind of scaffolds are present in those mixtures.

We also are trying to move – I have another proposal in review right now with a fabulous set of collaborators with Hosea Nelson at Caltech, and Yi Tang at UCLA, and Julia Kubanek at Georgia Tech, where we’re proposing to take this newly emerging cryo-EM MicroED technology, a massive leap forward into using it as a tool for screening plant natural products, and other natural product libraries, so not relying on single crystal X-ray diffraction, but looking actually at powders. And we’ve had some promising preliminary data where we’ve done this.

If you think about the classic OK, find and grind technique where you have your crude extract, you have different layers your liquid like a partition layer, your flash chromatography, then multiple iterations of preparative LC until you get down to your bio-guided targets. We’ve been able to work our way back up from the bottom of that fractionation tree moving up closer, so like basically at each level it becomes more and more chemically complex. And we’ve looked at these compounds through classic spectroscopic technologies, NMR, mass spec, whatnot and then we’re comparing that to see what we’re able to pick out through this cryo-EM MicroED context.

And so, for me, when I first read that paper where they were starting to show the ability to really identify, and get crystal structures out of these mixed powders, my immediate thought was this is going to revolutionize plant natural products work. And I’m always thinking about plants. But I’m sure it’d be very useful to other areas of natural products work as well, and so taking a very different kind of approach to that.

And I think there’s more we need to do when it comes to our existing libraries. Some of the limitations of platforms like GNPS, it’s very poor in terms of annotations on plant natural products. Rich, rich in bacterial and marine stuff. So we need more people annotating. It will take more people working on these plants. 

I think if there’s anything in my book that hopefully comes across it’s my siren’s call of people to the field. We need more plant natural products chemist and more ethnobotanists to work on these areas. We have over 33,000 species of plants used by humans in medicine, and we know almost nothing about most of them.

DAN UDWARY: Yeah, I mean one of the fun things I really enjoyed about the book is just there’s the narrative of what’s going on through your life, but then there’s all these little sidebars of plants and what they’re doing and what their history is, and it’s almost like I can picture like the movie version of it where the things are happening, and then there’s all these little labels on the plants that are in the surroundings. And I feel like having that perspective on the way a scientist thinks about things and the way a natural products chemist has a perspective on what the heck is going on in the world around us, and what we don’t know, and what we do know, is a really … I thought was a really fun way to show how a scientist thinks.

I think your book is a really great example of that. I really, really enjoyed it. I’m going to buy a copy and give it to my daughter.

CASSANDRA QUAVE: Oh, thank you. Yeah, there’s a lot of scientific names in there and I was like I have to, it’s like I have to include these in the book. I can’t have them–

[LAUGHTER]

DAN UDWARY: No, there’s no reason to hide who we are. 

ALISON TAKEMURA: I had a question about the complexity of the problem so and the scale. So thinking about 33,000 plants, how many plants would you say we’ve characterized to a natural product level?

CASSANDRA QUAVE: Oh. [CHUCKLES] I don’t– oh, man, this is a hard question. It’s like, I could tell you this. During the early days of the pandemic, my team took on this crazy idea of asking, what do we actually know about plant-derived antibiotics? And this was for a Chemical Reviews paper. And it was just a massive amount of work.

But we looked at the literature from the ’40s [CHUCKLES] till now. And then my lab pleaded mercy, and I said, OK, we’ll just do 2011 to present day. And it was still like 4,000 articles we had to go through.

But here’s the problem. The literature when it comes to plant natural products is rife with really poorly designed studies. We have studies where people write about work on certain plants, but they have no authenticated voucher specimen. So whereas in your area, you get a genome of an organism, when it comes to the plant sciences, you need to have a physical copy of the plant, a physical specimen pressed and stored and authenticated by a botanist. And surprisingly, a high number of these studies are lacking that. And so there’s no way to be 100% sure that the chemistry that they’re even reporting on is from the plant they say they’re working on.

Plant nomenclature is also very confusing. There are many synonyms many– and these get mixed up in the literature as well. And then when it comes to the actual methodologies, we just focused on looking at studies that assess the MIC or Minimum Inhibitory Concentration of plant extracts and individual compounds derived from plants. And that’s another area of weakness where a lot of people are using things like disk diffusion, which is not amenable, really, especially to complex extracts, because the way things diffuse across agar, of course, has to do a lot with the different properties of the different molecules in the mixture.

And so what we did, we really limited our review to those plant extracts or plant-derived compounds that were assessed through standardized methods, through broth microtiter dilution, and they had clear authentication parameters in place. And out of that, we found just under 1,000 plants that have been tested as crude extracts or slightly refined fractions for antibacterial activity.

And that was published in a Frontiers review paper. We tried to send this whole mega thing to Chemical Reviews, and they’re like, what? No, this is too much.

[LAUGHTER]

So it actually ended up being two papers that were both actually too much. We probably could have divided it into four. It was just so long. There was so much information we had to distill.

But in the Chemical Reviews paper, we found 459 isolated compounds. Now the weaknesses in a lot of those papers was that most of those were lacking counter-screening data against mammalian targets. So we don’t know what the selectivity indices are. We don’t know how cytotoxic they are, because this is something I’m sure many of the listeners in this audience know, that there’s a lot of things in nature that will kill bacteria, but they’ll also kill you. I’ve got a lot of things. That doesn’t necessarily mean that they’ll make a great antibiotic, because they’re so toxic.

So but at the same time, there’s a lot of interesting starting points for medicinal chemists to play with. And we tried to organize that data, and posted the SMILES data also with the Pew Charitable Trusts.

So back to your question of, what do we know? Well, we know that at least 900 have been looked at for infection that had some decent– met some parameters for testing. But in those, they didn’t get down to single compounds. There were only a few papers that got into single compounds.

And even of the plants that are heavily studied, like if you think about ingredients and dietary supplements, they’re still finding novel chemistries in those. I mean, we just– they’re so incredibly complex. There’s so much there to mine and work through. So when it comes to those that have some rigorous examination, I would say we’re still in the low 100s, would be my best estimate.

DAN UDWARY: How much of an issue is strain variants in plants? Do you see different natural product profiles across different, I don’t know, cousins or–

CASSANDRA QUAVE: Yeah, populations? Well, even same species. Let’s say you’re in the same species, different places, absolutely. There’s lots of studies, especially on volatile compounds. You can look at terpenoid profiles, and they’re going to differ if this tree grows on this side of the mountain versus the other side, absolutely. 

I think one thing we do see is that generally, the major secondary metabolites are there, they just are going to be there in different percentages of relative abundance. But again, going back to traditional medicine, healers are often very well attuned with where certain plants should be collected, what time of day they should be collected, what season they should be collected, what girth or size of the branches should be, there are all these other details locked up in folklore which I think actually really point to their understanding of the plants chemistry because all these factors affect the chemistry.

DAN UDWARY: That is something we do not have in bacteria. Yeah.

CASSANDRA QUAVE: Although I guess if you change the media, you change the environmental conditions, you would get different probably metabolite profiles in bacteria as well. Yeah.

DAN UDWARY: Yeah. Yeah, common root. 

ALISON TAKEMURA: And so is that how your ethnobotany studies inform what plant samples you look at and what crude extracts you look at?

CASSANDRA QUAVE: Yeah, absolutely. Not only like what samples, but also what tissues, because root tissue of a plant is going to have a very different chemical makeup than the leaf tissue because those tissues each serve a different purpose for the plant. And this is something else that healers are very well attuned with is like– and also I said the age. So like a young leaf might not have the same chemistry’s as an older leaf would have. We also pay a lot of attention to the ways that they’re processed, are they dried, are they used fresh, are they boiled into a tea, or are they steeped in alcohol? Because again, we try whenever possible to replicate that in the lab because an aqueous extract with heat is going to yield a different composition than a cold alcohol maceration.

DAN UDWARY: Sure. 

ALISON TAKEMURA: I’m curious if you have an example of a favorite plant preparation that led to an interesting scientific discovery.

CASSANDRA QUAVE: I can tell a story of something that I think was an interesting tale.

So I was working on one of my visits to the Balkans, working with our collaborators at the University of Pristina. And because I’m based in the medical school, I also get to supervise resident research. So these are dermatology residents that have finished medical school and are training to become board certified dermatologist.

And on one of these trips, I brought a great– one of the residents with me. And she helped with the field expedition. And while we’re in these high-montane areas, one of the plants that I kept seeing over and over again that had relevance to skin was St. John’s wort.

And St. John’s wort is something that I think many listeners are familiar with. It’s found in your health food stores, often as an extract or tincture. But the way that they prepare this in the Balkans is actually as an oleolite preparation. So basically, you take the enfleurage– which I love saying that, “enfleurage”– [LAUGHING] extracted in oil or fat.

ALISON TAKEMURA: Is the “enfleurage,” is that “in flower”? What does that mean?

CASSANDRA QUAVE: Also “in flower,” yeah. So in this case, they’re taking the flowers. They’re putting them into transparent bottles, either glass or plastic. I think glass was more common.

And you stuff these bottles with fresh, bright yellow flowers of Hypericum perforatum, which is St John’s wort and flower, which grows abundantly in the wild there. Cover it in oil. Most cases are using olive oil, but sometimes they use other kind of canola, or other kind of kitchen oils. And they leave it exposed in the sun for 40 days.

And during that time, it goes from a clear oil, and it transforms into this bright blood red color. And there have been many other studies done by scientists in different countries that have shown that that blood red oil actually has a lot of wound healing properties. But for the dermatologist resident and I that were there, when I think of St John’s wort, my immediate thought was, well, what about phototoxicity? And here we have somebody putting this all over their skin because we know that hypericin can cause photosensitivities.

And I was like, this is strange because they’re exposed to the sun. They’re rubbing this all over their body. What’s going on? And so we brought the oil back to the lab and we assessed it. We analyzed it. We also analyzed the other kinds of preparations that you find more commonly in health food stores, as tinctures or other extracts. And we looked at both the chemistry and the pharmacological effects against bacteria. 

And what was interesting is that we found, indeed, that both formulations had some antimicrobial properties. But the one that was used in traditional medicine lacked the hypericin. So it had become– it had degraded into something else during this oil extraction process. So you didn’t have the risk of the same kind of phototoxicities that you would have if it were extracted in another way.

And for me, that just was such a great tale. Here you have the same starting ingredient. But depending on how it’s traditionally formulated, that can have huge differences on the final outcomes of the chemistry, and thus the pharmacology. And so yeah, I absolutely pay attention to those details when it comes to what parts are being used. And how is it made? How is the medicine being made, and stored, and applied?

DAN UDWARY: That’s fascinating.

CASSANDRA QUAVE: Yeah.

DAN UDWARY: I hadn’t thought about that added complexity of the idea that plants are out in the sun all day. And so even just that sun exposure probably has different spectrums of compounds between what’s in its stem or root or– yeah on top of the other, biological reasons for that.

CASSANDRA QUAVE: Yeah.

DAN UDWARY: Oh, very cool. 

ALISON TAKEMURA: Besides just getting more scientists into the field of plant natural products, how else can we evaluate so many plants at scale in high-throughput?

CASSANDRA QUAVE: Well, I’m glad you asked that because especially for this audience, I think there are some amazing resources they should be aware of. At the National Cancer Institute, they – actually, under the guidance of Dr. Barry O’Keefe – they have a massive project ongoing where they are pre-fractionating this mega library of plant natural products. So these are extracts that were originally collected from plants that globally I think in the ’80s and ’90s. And what’s great about that collection is they’ve already squared away all of the ethical considerations with country agreements.

So for those of you in the audience that really want to get your hands on more natural products, but perhaps the idea of running off into the forest and identifying different plants and bringing them back is not your jam, the good news is there’s this amazing resource that can be provided for free to scientists to use. They are actively looking for people to do more high-throughput testing with these libraries. They can be provided, I believe, in 96-well plates microarrayed out for you to test.

They also have onsite assistance if you find some interesting leads and need help with isolation or identification of those compounds. But again, for the natural products crowd, you could certainly pursue that on your own as well, once you find some interesting hits.

So I think there are resources out there and we should definitely keep looking because we’re in this weird paradox of a time where obviously humans are facing the health consequences of our destructive nature against planetary health. We’re losing a lot of biodiversity across the globe, a lot of our natural resources are at risk, this puts the future of human health at risk because of our– we just really haven’t looked at most of these resources and we don’t know what could be out there that could help us treat the next– some of these highly resistant forms of cancer or bacterial infections or even the next pandemic pathogen.

And I think it’s important to note just as critically that billions that’s with the B, billions of people across the globe rely on plants as their primary form of medicine. We think of it more as a novelty or this supplement to my diet that I can take in places like in the US or in Europe. But actually, the reality for many, many people across the globe is that is their medicine, and when those resources are put at risk, that really puts public health at risk on a global scale.

DAN UDWARY: People who listen to this podcast hear me say this every third podcast or so. But JGI, our focus as a DOE, Department of Energy, user facility is in energy and environment, and not necessarily in medicines. [CHUCKLES] Selfishly, what can or should we be doing to help the plant community to understand more about plant natural products? We have sequencing facilities, DNA synthesis, metabolomics. Where do you see the role of a big place like JGI in terms of helping out your research in your community?

CASSANDRA QUAVE: Wow, that’s a big question. Well, I guess ways that these platforms I think could be leveraged better could be perhaps to take deeper looks at the interactions that organisms have, not just within the same kingdom, but actually cross kingdom. So I’m thinking about what are the interactions that bacteria have with plants, what’s going on between plants and mycorrhizal fungi? This has become something I think it’s always fascinating to me. But it’s becoming more and more discussed is the relationships that fungi have with plants and how that affects overall forest health and ecosystem health.

How cool would it be if you can use those metabolomics platforms to create a better system for reading the language of nature, like how are they signaling with one another, what are they saying to one another, and what does that mean overall for the environment? Those are very ambiguous questions. But I think, in general, it would be really neat if we could keep pushing the envelope on not just identifying compounds, but also really identifying their roles within these complex communication systems across kingdoms of life.

ALISON TAKEMURA: OK. This may have– you may have already answered this sufficiently Cassandra but just in case– what made you want to write this book?

CASSANDRA QUAVE: Wow, so I guess there were a couple of reasons. I have a lot to say about my passionate call. I want more people to think about exploring plants as a source of medicine. And really, we need more scientists working on this issue.

I think also there’s an urgency behind that call, because at the same time that we have just a tremendous amount of biodiversity loss, and linguistic loss, cultural loss. We’re losing languages. We’re losing species. We’re losing ways of knowing.

So there’s not just a need for scientists to investigate the chemistries and pharmacological promise of plants, but also for those to really document and understand the role of different environmental resources in human survival. In fact, ethnobotany is the science of survival. That’s how it’s been defined.

The other reason I wanted to write this book is, honestly, there aren’t that many books about science written by women, and even fewer books written by women scientists. And I really felt like this is something that we need to have more of. And I hope more and more women scientists have the opportunities to do that.

And I think from my individual perspective, too, as not only being a woman in science, but also being a disabled woman in science, that I was able to bring in another perspective also. And I hope that this book is useful not just to women in science or scientists in general, but also to anyone that identifies as “other,” whatever other is for them, that whatever your identity is, there are inherent challenges that we have to face in life. And above all else, I think my advice is to chase your passion because that’s what I’m doing, and I’m so very grateful for the opportunity to do so.

DAN UDWARY: Yeah, that’s lovely. All right, cool. Is there anything that we haven’t asked you that you want to talk about.

CASSANDRA QUAVE: No, this was great. This is a lot of fun to be able to speak to the natural products community. It’s great. Yeah.

DAN UDWARY: Yeah, great.

ALISON TAKEMURA: What about your book? So when do people pick it up at in their local bookstores?

CASSANDRA QUAVE: Yeah, you can find the book. You can find the link on my website at cassandraquave.com that’s C-A-S-S-A-N-D-R-A Q-U-A-V-E.com. I’m realizing now I probably should have come up with an easier website handle. I’m also on Twitter @QuaveEthnobot, that’s Q-U-A-V-E E-T-H-N-O-B-O-T, also on Instagram at the same handle.

The book will be out on October 19th in the US, Canada, and UK. And we’ve already got a couple of translation deals happening in Asia. And I’m hoping we’ll have this in many languages soon. And you can find all of that information on virtual and in-person events again on my website.

You can also– I’d also encourage listeners to check out my podcast. It’s called Foodie Pharmacology. And in that podcast, we explore the relationships between food and medicine and the food medicine continuum.

I get lots of ethnobotanists on the line. This week we were talking about hallucinogenic plants in the Amazon. We’ve talked about all kinds of really cool stuff on the show. So you can check that out, too, if you’re interested.

DAN UDWARY: It’s a good listen. I’ve enjoyed quite a few of those. I always grab on to the fermented foods things and any brewing or anything like that, because that’s my bag for sure, little hobby.

CASSANDRA QUAVE: That’s awesome. [CHUCKLES]

DAN UDWARY: I’m Dan Udwary, and you’ve been listening to Natural Prodcast, the podcast produced by the US Department of Energy Joint Genome Institute, a DOE Office of Science user facility located at Lawrence Berkeley National Lab. You can find links to transcripts, more information on this episode and our other episodes at naturalprodcast.com.

Special thanks, as always, to my co-host Alison Takemura. If you like Alison, you want to hear more science from her, check out her podcast Genome Insider. She talks to lots of great scientists outside of secondary metabolism, and if you like what we’re doing here, you’ll probably enjoy Genome Insider too. So check it out.

My intro and outro music are by Jazzar. Please help spread the word by leaving a review of Natural Prodcast on Apple Podcasts, Google, Spotify, or wherever you got the podcast. If you have a question, or want to give us feedback, tweet us @JGI or to me @danudwary. That’s D-A-N U-D-W-A-R-Y.

If you want to record and send us a question that we might play on air, email us at JGI-comms. That’s JGI dash C-O-M-M-S @lbl.gov. And, because we’re a user facility, if you’re interested in partnering with us, we want to hear from you. We have projects in genome sequencing, DNA synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, and microorganisms. If you want to collaborate, let us know. Find out more at jgi.doe.gov/user-programs. Thanks and see you next time.