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To the Depths of Drug Discovery

To the Depths of Drug Discovery

To the Depths of Drug Discovery

To the Depths of Drug Discovery

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The ocean: Earth’s “cradle of life”, home to some of the greatest biological and chemical diversity found on our planet.

Throughout the history of our existence, humanity has relied on the ocean as a source of oxygen, food, exploration, creativity and vitality. Over recent decades, a “new wave” of marine natural products research has emerged, demonstrating how the ocean may also be key in our fight against human disease.

Join us on this feature-length voyage to the depths of drug discovery.

Natural products in modern medicine

There are certain intrinsic biological processes that occur in living organisms that are essential for development, growth and reproduction. Examples are the synthesis and breakdown of nucleic acids, proteins and fats. Collectively, these processes are referred to as primary metabolism, and the subsequent products, primary metabolites.

Living organisms are also capable of making molecules outside of primary metabolism. Secondary metabolites – often used interchangeably with the term natural products – are biosynthesized via secondary metabolism, which describes processes that are “an expression of the individuality of a species,” as Dias, Urban and Roessner describe in A Historical Overview of Natural Products in Drug Discovery. Secondary metabolites are not essential for an organism’s survival, but require energy to produce, and therefore often confer an advantage for the organism to thrive in its particular habitat. Secondary metabolites may be the product of a biological defence mechanism or a process an organism has developed for nutrient acquisition, as examples. 

Natural products have been harnessed for their therapeutic properties throughout the history of medicine. Land-dwelling – or terrestrial organisms – such as plants and soil microbes have naturally dominated the focus of scientists wanting to access nature’s pharmacopeia.

But an untapped resource of natural products, large in size and potential, was close by – we just couldn’t access it.  

A new wave in natural products discovery  

Marine-derived natural products – secondary metabolites obtained from organisms of the ocean – have been utilized by humans for an array of different purposes. An ancient civilization – the Phoenicians – inhabited the coastlines of the Mediterranean Sea thousands of years ago. Sometimes referred to as “the purple people” these civilizations harnessed the secretions of a mollusc species found in abundance in the shallow shores – Murex brandaris – to produce a long-lasting purple dye.

The therapeutic potential of marine-derived natural products, particularly those from easily accessed fish and algae, was perhaps recognized early in the early twentieth century, but wasn’t demonstrated scientifically until much later. The advent and popularization of SCUBA marked the beginning of a “new wave” in natural products discovery, as scientists journeyed to unexplored regions and depths of the ocean.

“The origins of marine-derived natural products really stem back to the days when chemists were also SCUBA divers, or had an interest in the ocean,” says Professor William Gerwick, a distinguished professor in the Skaggs School of Pharmacy and Pharmaceutical Sciences and the Scripps Institution of Oceanography at the University of California San Diego (UCSD). Gerwick, considered a leading figure in natural products chemistry and pharmacognosy, has received numerous accolades for his contributions to natural products research.

“Really, the chemistry aspect was what drove the early days of questioning, ‘What’s out there? What are the potential materials being produced?’” he says.

As researchers were able to venture deeper into the ocean, and collect samples of increasingly smaller size, they uncovered many novel compounds with interesting structures. “Basically, everything that you picked up had new chemistry in it. So, there was this amazing period of people finding lots of interesting new structures and studying the biological properties of these molecules, Dr. Paul Jensen, a professor at the Scripps Institution of Oceanography, UCSD, describes in a recent podcast, Marine Science.

The “new chemistry” being discovered was a form of communication.

A sightless, soundless world 

It’s estimated that between 70,000–100,000,000 different marine species exist, ranging from the gloriously gigantic blue whale (~ 33 meters in length) to macroscopic marine bacteria (~ 1,000 nm in size). This number may be even higher, Gerwick says, “largely on the basis of so many bacteria being observed by DNA sequencing technologies.”  

In the face of harsh environmental pressures, marine life has been forced to develop unique traits that aid survival. Some are physical, structural or behavioral. But largely, the language of the ocean is chemical, as Gerwick elegantly describes: “In the sightless and soundless world of most underwater life, the mechanism of communication by ocean creatures is through their chemicals.”

Take crustaceans for example. For many species, mating only occurs within a specific period, once the mature females have molted (a process where the hard outer layer of the shell is shed). Male crustaceans can detect the upcoming molting period via chemical signals produced by the female. This allows the males to “guard” the female until she is ready to mate. Research has shown that, when rocks and sponges are treated with female urine – which carries the compounds involved in this chemical signaling – male crustaceans will do their very best to attempt mating with the rock, or sponge.

Phytoplankton are microscopic marine algae that are central to the ocean’s balanced ecosystem. Colonies of the phytoplankton Phaeocystis globosa are vulnerable to attacks by other marine organisms. Copepods – small crustaceans – can consume whole colonies of the phytoplankton, whereas ciliates choose to consume only single cells. When copepods start to attack P. globosa, the phytoplankton can chemically detect that the attack is occurring, and that it is by copepods, rather than ciliates. As a result of these chemical signals, colony formation is suppressed, such that the phytoplankton grow as individual cells, too tiny for the copepods to attack.

Symbiotic microbes also have a role in the chemical communication of the ocean. Many marine organisms live in association with other micro and macroorganisms to enable their survival. For example, the shrimp species Palaemon macrodactylus carry embryos externally, on the abdomen. Scientists from the laboratory of Professor William Fenical, regarded as a “true pioneer” in the field of marine natural products chemistry – and Gerwick’s PhD mentor – discovered that symbiotic microbes covering the surface of the embryos produce a metabolite: 2,3-indolinedione (isatin). This metabolite functions by protecting the embryos from pathogenic marine fungi.

“In the sea, creatures are bathed in essentially a salty soup, filled with microorganisms and viruses with which they have intimate contact, but somehow, they seem to survive.  This is a result of the rich suite of adaptive chemicals that they produce,” says Gerwick.

It's this chemical language – and its rich diversity – that makes the ocean a treasure trove for secondary metabolites. Historically, terrestrial organisms had proven to be a valuable source of natural products that possess medicinal properties. Would this be reflected in the planet’s waters?

“Scientists found marine invertebrates such as sponges, corals and even snails produce molecules with significant pharmaceutical relevance,” Dr. Vikram Shende, a postdoctoral fellow in Professor Bradley Moore's lab at the Scripps Institution of Oceanography, explains. Shende studies the biosynthesis of secondary metabolites by marine eukaryotes and their associated microbes.

Marine-derived drugs authorized for human use

During the 1990s, the field really experienced a sense of intensification, both in terms of interest and sophistication, Gerwick describes. Emerging techniques and technologies – such as next-generation sequencing – evolved to new heights of speed and sensitivity, with lowering costs. Scientists could study the complexity of marine organisms at a new level of detail, gaining insights into the role of specific genes, encoding proteins, metabolic pathways and the subsequent molecules produced. “There was a realization that there really are drugs out there [in the ocean]. Or, if not drugs themselves, molecules that could inspire the production of a drug,” Gerwick recalls. Investments from large research organizations and “Big Pharma” further fuelled the search for therapeutics from the sea.

Fast-forward to 2022, and a growing number of marine-derived natural products have progressed to authorization for human use or are in clinical trials. The exact number of marine-derived (or inspired) compounds authorized is a little unclear and varies depending on whether a source cites global or region-specific authorizations. Gerwick believes that the total figure is currently 23. “I'm not quite sure why some people exclude certain drugs from the list, such as those used in China to treat millions of patients, or some of the various fish oil products, or even the anticancer agents based on arabinose sugars. I think our list of 23 is the most comprehensive at the present time,” he says.

Authorized marine-derived drugs are of various chemical classes, including peptides, alkaloids, nucleosides, fatty acids, oligosaccharides and antibody-drug conjugates. Some are synthesized by marine organisms themselves, while others are inspired by the chemical structures of secondary metabolites produced by marine organisms. Let’s explore a few examples.

Several drugs authorized to treat cancers are derived from different species of molluscs and/ or symbiotic bacteria. Brentuximab vedotin (brand name Adcetris®), for example, is an antibody-drug conjugate authorized to treat lymphomas. “This drug uses an antibody to target tumor cells and deliver a small molecule ‘warhead’ based on a peptide molecule, dolastatin 10, isolated from a sea hare,” explains Kayla Wilson, a graduate student in the Moore lab at the Scripps Institution of Oceanography. Interestingly, the sea hare does not actually make this compound, but acquires it from its diet of marine cyanobacteria (blue-green algae).

Fatty acids extracted from fish, such as Omega-3-carboxylic acid (brand name Epanova®) and Eicosapentaenoic acid ethyl ester (brand name Vascepa®), are authorized for the treatment of hypertriglyceridemia, a common condition characterized by increased levels of serum triglycerides that can contribute to the development of cardiovascular disease.

Many bioactive compounds have also been extracted from sea sponges. “Sea sponges are fascinating to researchers from several different areas of science. Evolutionary biologists study them to learn how early animal life evolved on earth, materials scientists use them to build bioinspired scaffolds, and we as natural products chemists study them because they make medicines,” says Wilson.

Acyclovir, one of the first systemic antiviral medications to be approved by the US Food and Drug Administration (FDA), was heavily inspired by nucleosides isolated from a Caribbean sponge, Tectitethya crypta (formerly known as Cryptotheca crypta). The cancer medication Eribulin (brand name Halaven®), used to treat breast cancer and liposarcoma, is a synthetic form of halichondrin B, a compound first isolated from the Halichondria okadai sponge. Subsequent research identified that this compound is produced via a symbiotic relationship with bacteria. Indeed, this has been the case for many bioactive compounds extracted from sea sponges.

“Sponges have a complex microbiome – just like we have a complex human microbiome – and dozens of biologically active molecules have been discovered,” Wilson says. However, recent work by Wilson’s colleagues at the Moore lab, focusing on the terpene-producing sponge Axinella, suggests that the sponges themselves can synthesize many interesting compounds. Using long-read DNA sequencing, Wilson and team looked at the genes surrounding terpene synthases, enzymes critical for the production of terpenes. “These surrounding genes contained introns and had large non-coding regions between them – which are both characteristic of eukaryotic DNA,” she explains. The data imply that the sponge is the synthesizer of terpenes, not the bacteria that constitute its microbiome. This work demonstrates the constant evolution of our understanding of natural product synthesis.

Serving unmet needs in drug discovery

The list of authorized marine-derived drug examples provided is by no means exhaustive, but perhaps demonstrates the broad landscape of clinical applications and sources of these therapeutics.  

An interesting aspect of the field is how marine-derived natural products could offer a sense of renewed excitement for disease areas that currently lack efficacious treatments. An example is neuroscience drug discovery, where a high-profile “retreat” from research and development by Big Pharma has left an unmet clinical need for many patients. 

“Unfortunately, several costly failures have led pharmaceutical companies to largely exit neuroscience drug development over the last couple of decades, which has occurred as increased lifespans and increasing numbers of patients with neurological disorders leads to a large gap in what is needed vs. what is being done,” explains Dr. Marsha Pierce, an assistant professor at Midwestern University. Pierce’s research focus includes studying the role of oxytocin analogs, marine natural products in drug development and microRNAs in sensorineural development, function and maintenance.

Marine natural products from organisms and their symbiotic microorganisms display unique chemically active primary and secondary metabolite structures that are very different from those in synthetic chemical libraries,” – Pierce.

Could marine-derived natural products offer neuroscience drug discovery an opportunity for revival? It’s possible, and some success has already been had. In 2004, the FDA approved the analgesic Ziconotide (brand name Prialt®) – a synthetic version of the ω-conopeptide found in the venom of a giant marine snail, Conus magus – for the treatment of chronic pain.

Many other marine organisms produce toxins, either as a defence mechanism, or – if they are predators – to paralyze their prey prior to eating them. The target of several such toxin classes are voltage-gated ion channels, key mediators in a wide range of central and peripheral nervous system functions in humans, such as neuronal excitability and inhibition.

For Pierce, a key area of unmet clinical need, where marine-derived natural products could carry potential, is in the treatment of ischemic stroke: “There are no current pharmaceutical therapeutics for post-stroke recovery beyond the acute blockage-treating phase,” she says.

Post-stroke, the affected brain region demonstrates dynamic changes in excitability, new research suggests. “There is a period of recovery with characteristic heightened neuroplasticity in the peri-infarct region,” says Pierce. “However, this increased cortical excitability and plasticity is opposed by increases in tonic GABAergic inhibition.” Methods to prevent this opposition could enhance the potential for new synaptic connections to form, repairing the damaged brain region.

In 2020, Pierce and colleagues published a research project that examined whether Brevetoxin-2 (PbTx-2), a voltage-gated sodium channel modifier obtained from marine dinoflagellate Karenia brevis, could drive cortical excitability and promote neuronal plasticity in mice after a stroke. The research team showed that, in mouse models, epicortical application of the toxin resulted in increased neurite outgrowth and connectivity that corresponded with improved physical functioning.

“For neurological diseases, we’ve had few breakthroughs with the current synthetic chemical libraries largely because they work by generating derivatives of already existing compounds. In my opinion, it is the extreme conditions of marine organisms and unique structures of marine bioactive compounds that open the door for novel drug discovery,” says Pierce.

From sea-bed to patient-bed: Challenges and recent advances

Drug discovery and development is a nuanced area of scientific research that faces many bottlenecks, whether compounds are synthetically or biologically synthesized.

Shende speaks to the particular difficulties associated with natural products: “It’s definitely a long road to take a molecule from nature and get it into something that people will use every day,” he says. “Along with the traditional challenges of getting a drug into clinical trials, a big consideration especially for molecules from marine organisms or their microbiomes is supply. These organisms can be extremely slow growing, and in some cases rare or even endangered, so trying to harvest enough material for something like a clinical trial is not only economically unviable but can also be environmentally harmful.”

Despite these challenges, marine-derived drug discovery and development has demonstrated a respectable track record of bringing drugs to patients. Perhaps this can be attributed to the field’s enthusiasm to evolve? “One dimension of marine-derived natural products research that I think has been particularly positive is that it has continued to stay current and relevant. It’s adopted new technologies, new thinking and new research goals,” he says.

A notable example is the introduction of artificial intelligence (AI)-based methods, which Gerwick has been working on in collaboration with computer scientist Gary Cottrell and his students at UCSD.

Discovering and developing bioactive compounds from marine organisms is a process for which the methods vary between laboratories. Generally, methods can be characterized as either top-down – which Gerwick describes as a chemistry-driven process – and a bottom-up approach, which could be argued as being “more DNA-driven”.

“We use both approaches in my lab,” says Gerwick. “The top-down approach really starts with accessing the organism. We typically go on expeditions to various tropical locations where we scuba dive and collect samples. We store these samples to bring home, and we also try to take small samples that we may be able to grow in the laboratory.” He paints a visual picture of his laboratory, adorned with several hundred different strains of marine cyanobacteria of varying colors.

Organic solvents are used to extract compounds from organisms in the laboratory, which are then subjected to a variety of biological assays to search for useful activities. This could be anti-cancer activity, antiviral activity or antiparasitic activity. “When we find an extract or a fraction that shows activity, we then do further refinement to get to the actual active compound in that material using chromatography,” Gerwick adds. “These things are easy to say. But it can take weeks to months to years to accomplish. Once we get a pure compound, then we want to figure out what it is.”

The next step requires various spectroscopic techniques to study the size, orientation and arrangements of the atoms. It also stimulates a lot of new questions that, as Gerwick describes, can occupy a lifetime – or perhaps more than a lifetime – of further study.

That’s where AI-based programs, like the deep learning of NMR spectra called Small Molecule Accurate Recognition Technology (SMART), can help. “I see our use of AI in this field as a way to enhance and accelerate that process of figuring out what a new molecular structure is, or to enhance and figure out what the target of a compound is,” Gerwick says. “We're also developing some AI software that would enable you to take a new molecule and predict what biological activity it might have – could it have anti-cancer potential, and to what type of cancer would it be effective?”

He emphasizes that AI doesn’t necessarily give us solutions, but it helps to create hypotheses that need to be taken into evaluation. However, an essential requirement for AI – and a potential bottleneck here – is a need for good quality data from which you can train the system. This is a current shortcoming, according to Gerwick.

If this shortcoming can be overcome, AI looks set to “make waves” in marine-derived drug discovery, and natural products research more generally: “A process that used to take weeks to months now can be done in eight seconds. We're still working on the technology, but the dream is that [it] will really make a difference in the efficiency of the process,” Gerwick emphasizes.

The impact of climate change and biodiversity loss

Natural products as drugs will continue to be a critical – if not increasingly important – aspect of human health care. But success in natural products discovery is intrinsically linked with thriving biodiversity, and the planet is facing a biodiversity crisis.

The rate of species extinction on Earth is estimated to be 10–100 times higher than it has been over the last 10 million years, and only continues to rise. The catastrophic impact of this decline in biodiversity can be seen in terrestrial organisms, but also in marine life.

In April, researchers published a report in Science exploring extinction risks for marine species using ecophysiological modeling. The study data suggest that, if the “business-as-usual” global temperature continues to increase, it is likely that marine systems will undergo mass extinction on a similar level to the end-Permian extinction (EPME), in which ~80% of marine biodiversity was lost.

A threat to marine biodiversity is of course a threat to marine-derived natural products, explains Pierce: “Adaptation to their unique habitat contributes to marine organisms and their symbiotic microorganisms producing a wide variety of biologically active primary and secondary metabolites,” she says. “Climate change is leading to a rapid loss of marine organism abundance and diversity, as well as the symbiotic microorganisms inhabiting many of these marine organisms and producing some of these bioactive structures." If a species disappears, we will never know what it had the capacity to produce.

Natural product discovery and development cannot continue in a sustainable manner without efforts to tackle biodiversity conservation. Global and local efforts are ongoing here. “Partnering biodiversity preservation with drug discovery has been a long-standing focus of the International Cooperative Biodiversity Groups (ICBG) program of the Fogarty International Center, the international arm of the National Institutes of Health (NIH),” says Gerwick.

The future of the pharmasea

Over the last few decades, the efficacy of marine natural products as therapeutics has been demonstrated against a wide variety of human diseases. The growing preclinical and clinical pipeline of marine-derived drugs points to a bright future for this fascinating field of research, and we’re likely only just scratching the surface.

Humans have mapped a greater percentage of the Moon’s surface than we have the seas of our planet; we can’t possibly foresee the full extent of chemical diversity living within this vast, underwater realm. As for the future, the integration of sophisticated technologies – such as AI – and continued collaboration across a wide variety of scientific disciplines will no doubt elevate the study of marine natural products to new heights.

All the while, we must maintain – and bolster – our efforts to protect Earth’s biodiversity. “I hope that by discovering new medicines from the marine environment, we can show the public why they should care about protecting the ocean,” says Wilson. “The technologies we have to explore the chemistry and DNA of marine organisms are rapidly expanding and if we can keep our marine ecosystems healthy, it will be really exciting to see what we can learn in the coming decades.”

Her thoughts are echoed by Gerwick: “As rich as this field is with promise for drug discovery, I think it's even richer in capacity for human development and understanding our planet” – this, he explains, is his mantra. 

This article was originally published in issue fourteen of The Scientific Observer, Technology Networks' free monthly magazine. 

Meet the Author
Molly Campbell
Molly Campbell
Senior Science Writer