Two research labs 6,000 miles away from each other are studying how herbal remedies work at the molecular level, which would pave the way for a new era of more personalized therapeutics to treat complex human diseases.


Fu-Shuang Li, a Chinese medicinal chemist, summits a mountain in the Guangxi province in south China, and kneels to identify a plant with hollow stems and oval, creamy white flowers. The plant’s name is Japanese Knotweed (Polygonum cuspidatum), and, like all plants, contains thousands of small molecules known as metabolites, which are responsible for qualities such as color, flavor and fragrances. For two thousand years, species of Japanese Knotweed have been used medically for treating Lyme disease, joint pain, bronchitis, jaundice, amenorrhea and hypertension. In traditional Chinese medicine (TCM), a broad range of ancient medical practices which includes acupuncture and Tai chi, a plant like Japanese Knotweed will be combined with other plants and herbs to concoct a tea-like remedy. About 7,000 herbs—derived from roots, leaves, twigs and fruit—are used in TCM for a wide range of diseases. Hoping this species of Japanese Knotweed contains active metabolites with unique medicinal properties, Fu-Shuang spent the afternoon clearing the peak of the plant, then brought a hundred kilograms of material to a factory for processing.

Plants didn’t evolve fangs or claws or legs, so for 400 million years they have relied on chemistry to combat environmental stressors, using their complex metabolisms as a source for inventing tailor-made metabolites to defend against ultraviolet rays, droughts and assaults from insects, pathogens and herbivores. Many of these metabolites have therapeutic effects in humans. For example, the active metabolite in aspirin known as salicylic acid was derived from the bark of the willow tree and is used to treat pain, fever and inflammation. Salicylic acid also interacts with platelets, making the blood less ‘sticky’ and susceptible to clotting, which helps prevent heart attacks and stroke.

Also derived from bark of the Pacific yew tree is Paclitaxel, a natural compound that interferes with the string-like molecules that help cells divide, a curious interaction that happens to also protect against ovarian and breast cancer. In the 1940s, Sidney Farber discovered the first chemotherapeutic agent at the Harvard Medical School when he gave the plant-derived metabolite Aminopterin to children with acute lymphoblastic leukemia, causing temporary remission.

When Fu-Shuang arrived at the factory, he subjected Japanese Knotweed to two hundreds gallons of ethanol. After the mixture evaporated, a two-pound mass remained. The scientist brought this solid extract to his lab in Beijing at the Institute for Materia Medica, run by the medicinal chemist Dr. Peicheng Zhang. The chemists of the Zhang lab passed the extract through tall columns to isolate the plant’s metabolites. Using the technique Nuclear Magnetic Resonance (NMR) Spectroscopy, they purified about 60 compounds, 23 of which were new to chemists, and many of which showed anti-diabetes, anti-inflammatory, anti-oxidization, anti-tumor, hepato-protective, neuro-protective and cardio-protective activities.

As Fu-Shuang wrote up his findings for publication, he stumbled over a review paper on a plant in the same family that he studied during his master’s degree, known as Selaginella or the spikemosses. The review paper was written by Dr. Jing-Ke Weng, a plant biologist and biochemist who studied the origin and evolution of metabolic systems in plants. Fu-Shuang sent Jing-Ke an email. At the time, Jing-Ke was a postdoc at the Salk Institute in California, but he had been offered a faculty position at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, an independent research organization composed of 21 principal investigators, probing a range of questions in the life sciences—from how a wound heals or a cell divides to the molecular and genetic causes of Alzheimer’s and cancer.

“It was pure serendipity hearing from Fu-Shuang,” says Jing-Ke. “He asked to join my lab, so I reviewed his work.” When Jing-Ke left China for the United States 10 years ago, he spent his college weekends looking through the scientific literature on the therapeutic benefits of herbal remedies. When his search turned up next-to-nothing, he decided that when he had a lab of his own he would explore the medicinal properties of plants, particularly those that have been used in traditional Chinese medicine.

Though Jing-Ke was still wrapping up his postdoc at Salk, it wasn’t too early to think about recruitment for his laboratory at the Whitehead Institute. Jing-Ke was an adept biochemist, but he didn’t have the expertise to isolate and identify the chemical constituents of plants the way Fu-Shuang could. He saw the training that Fu-Shuang had received in the Zhang lab and told the young scientist to pack his bags. Several months later, the two were side-by-side in Cambridge, brainstorming experiments in the 1,000-square-feet of lab space, which was still a mess of unpacked boxes.  

“This young man is a rare talent,” says Jing-Ke, a talent that was honed in Dr. Peicheng Zhang’s lab in Beijing. Peicheng is a world leader in a fairly obscure field known as natural products chemistry. The “talent” he and his lab members possess is the ability to transform a plant into its individual metabolites. After the Zhang lab acquires a medicinal plant, they use sophisticated chemistry and tools to purify an extract to its most basic chemical constituents. It’s molecular exploration. Like cartographers, they map the chemical landscape of plants.

You won’t find many natural products PhD programs in the States, according to Jing-Ke, but the field is hot in China whose government has been allocating large funds to research probing the pharmacological properties of plants used in ancient medicine ($4.9 billion in 2012). But the over 6,000 Chinese scientists that work in this field will admit that winnowing a plant down to its individual metabolites isn’t as easy as grinding a few leaves with a mortar and pestle. The compounds must be extracted through a method known as ultrasonic heating, then isolated via high-performance liquid chromatography (HPLC), and finally identified with several sophisticated techniques, including NMR as well as ultraviolet–visible (UV) spectroscopy, infrared spectroscopy (IR), and mass spectrometry (MS).

Peicheng established his lab in 2001 after earning his doctorate in medicinal chemistry at the Institute for Materia Medica. In his office, Peicheng retrieves a plastic bag of herbs called Lonicera japonica, or “Golden Silver Flower,” which is used medically to treat the common cold in China. Peicheng’s colleague of 30 years, a chemist named Dr. Ziming Feng, explains that Golden Silver Flower should be steeped in hot water and ingested like tea. Peicheng says, “There’s over a thousand chemical constituents in this plant, but we still don’t know which contribute to its efficacy.” Ziming adds that the most likely player is chlorogenic acid, a compound with Penicillin-like antibiotic properties.

“We study about 15 plants with medicinal properties in our lab,” says Peicheng. “We focus on these,” he says, presenting a slip of paper with the scientific names of six plants: Arctium lappa, Rhodiola rosea, Sophora flavescens, Polygonum cuspidatum, Carthamus tinctorius, and forsythia suspense. Ziming flashes a scholarly article their lab published in the Journal of Natural Products in 2013. “This is our pride,” he says. The paper describes the chemical structures of newly discovered chemical compounds (12 dibenzoyl derivatives and 5 isoflavone glycosides) that the Zhang lab isolated from the root of Sophora flavescens, a shrub with proven anti-inflammatory and anti-microbial properties. “This plant is used commonly in traditional Chinese medicine as an antipyretic (fever reducing) and diuretic agent, and for the treatment of skin and gynecological diseases,” says Ziming.

Peicheng sets another paper on his desk, this one published in Organic Letters in 2013, describing their discovery of a metabolite called Ternatusine in the root of Ranunculus ternatus, a plant native to China. Says Peicheng, “In traditional Chinese medicine, this plant is used to treat tuberculosis and faucitis (inflammation of the throat), and some extracts have shown strong anti-tumor activity.” Given Ternatusine’s intriguing bioactivity, Peicheng and Ziming learned how to synthesize the metabolite in lab, so that later they could make chemical modifications to enhance efficacy. Ziming says, “After we patent the compound, we hope to develop it into a new drug.”

Why are the Zhang and Weng labs so interested in the natural products made by plants? Because, far and away, they are the best source of medicines. It’s widely known that most drugs fail in the drug discovery process not because they’re unsafe (though many certainly are), but because they simply don’t work, often for reasons not fully understood. “The current trend of drug development model is mechanism-based,” says Jing-Ke, a one-molecule-for-one-target approach that works well against acute diseases and infections, but rarely for chronic and degenerative diseases, such as cancer and Alzheimer’s.

Such diseases have foiled drug-makers, because they are multi-faceted, driven by a myriad of genetic and biochemical mechanisms, and are exceedingly clever in adapting to most pharmacological interventions. “Herbal medicines used in traditional Chinese medicine are not mechanism-based, but phenotype-based,” says Jing-Ke. By “phenotype,” he means what-you-can-observe. For two centuries traditional Chinese doctors have given patients concoctions of plants, minerals and animal parts, and then watched what happened. If a practice or herbal remedy did nothing for a patient’s symptoms, or made a patient sick, a therapy or concoction was tweaked and improved through trial and error. If a remedy worked, it became the front-line therapy. The fact that the doctors didn’t know how the mixture worked was of little significance. If a fever broke, or a wound healed, who cared about the underlying mechanism driving the problem?

“Right now, we are focused on Rhodiola Rosea, which has been used in Chinese medicine for fatigue and altitude sickness,” says Ziming. The lab has distilled the plant’s root to 140 compounds, which go by names such as phenols, rosavin and terpenoids as well as these compounds’ derivatives, including flavonoids, anthraquinones and alkaloids. As an example, a well-known phenol is capsaicin, the active component of chili peppers, is an irritant, and causes a burning sensation when eaten, but if packaged into a topical cream, the compound can reduce muscle pain by interfering with Substance P, a molecule that shuttles pain signals to the brain.

Jing-Ke says, “The enormous diversity of chemicals in plants could be an endless source for therapeutic agents for human diseases.” Pharmaceutical companies have spent decades exploiting Nature’s wisdom to develop blockbuster drugs, most of which have been derived from plants, such as the anti-cancer drug Taxol and morphine. In fact, of the 175 small molecules approved by the FDA for treating cancer since 1940, 74.8% have not been created synthetically, and 48.6%, have been natural products derived from plants. In 2010, 50% of the drugs approved by the FDA came from plants.

The fact that plants have pharmacological properties is no news to the Chinese. In the civilization’s 2,000 years of prescribing herbal remedies, traditional doctors have published their vast medical knowledge in about 20 classic texts, the earliest of which is Huangdi Neijing (The Emperor’s Classic of Internal Medicine). These ancient medical texts are still assigned reading in Chinese medical schools. The first book to cover herb-based treatments was Shennong Bencao Jing (The Divine Farmer’s Materia Medica Classic) written between about 200 and 250 AD by Shen Nong. The three-volume work details the distribution, collection methods, indications and contraindications, dosage and health benefits of 120 medicinal substances.

Peicheng pulls the Modern Study of Traditional Chinese Medicine (1998) from his bookshelf. He opens it randomly to a page describing Red Flower’s medicinal properties, and reads: “Red Flower purges fire, dispenses heat, and removes blood stasis.” He translates, “This plant treats cardiovascular disease very effectively. We actually have it in our lab.” Ziming then retrieves a tome above his mentor’s desk. “This is a very famous book,” he says, presenting The Compendium of Materia Medicina. “Many of these ancient therapies are still used today.” The Compendium was written in 1578 by China’s greatest herbologists, Li Shizhen, who spent 30 years experimenting with the therapeutic potential of plants, minerals, insects and animals. It remains today as the most comprehensive documentation of the use of medicinal substances, containing 1,892 therapeutic compounds and 11,000 prescriptions, complete with drawings, pharmacological properties, symptoms to look for and side effects to avoid.

Both Peicheng and Jing-Ke use medical texts such as these as sources to uncover plants with medicinal potential. The approach has a famous precedent. In the 1960’s, the Chinese phytochemist Tu Youyou sifted through over 2,000 Chinese texts in her search for a malaria drug. In The Prescription for Emergencies (~341 AD), Youyou found an herb, sweet wormwood (Artemisia annua), that was written to relieve malaria-like symptoms. In the lab, she observed that the leaves of sweet wormwood reduced parasite numbers in rodent’s blood. In the following years, her research team isolated the active metabolite known as Artemisinin that significantly reduced the mortality rates in humans and remains today as the best weapon medicine has against the deadly disease. Youyou’s discovery won her the 2011 Lasker Award, and she won the Nobel Prize in Physiology or Medicine in 2015.

Of course, it’s one thing to know the chemical composition of a plant, it’s quite another to tease out how the several hundred, usually thousands, of chemicals achieve their physiological effects in the complex milieu of organismal chemistry. This is Jing-Ke’s quest. “Dr. Zhang’s lab does the important discovery work of isolating and identifying active compounds in plants. I hope to build on that by exploring the compounds’ mechanisms of action. Jing-Ke says that if we know how natural products function, we might be able to improve their efficacy and safety to treat chronic diseases such as cancer, diabetes and Alzheimer’s.”

Both Jing-Ke and Peicheng acknowledge the skepticism about traditional Chinese treatments and herbal remedies. “Traditional medicine has been tested by culture, not by modern experiments,” says Ziming. The Western medical and scientific community is traditionally critical of anecdotal evidence, or findings that can’t be measured or defined, often deeming traditional therapies as pseudoscientific, even mystical. “Ancient practices are not especially ‘scientific’ by today’s standard,” says Jing-Ke. “They are viewed very critically, which is why we need to show solid data,” something he thinks he can with the most cutting-edge tools available.

It’s an approach that has recently borne fruit. The lab of Dr. David Schubert at the Salk Institute recently chemically reinvented curcumin—the active compound in turmeric—based on data that showed curcumin’s ability to inhibit β-amyloid plaque formation in Alzheimer’s patients. The novel compound known as J147 is ready for clinical trials, but shows high potency to reverse symptoms to Alzheimer’s in mice.

With Fu-Shuang working busily at the lab bench, Jing-Ke’s lab has already begun to isolate and identify compounds in medicinal plants and herbal remedies, but Jing-Ke admits that it won’t be a walk in the park pinpointing exactly which compounds are responsible for therapeutic effects. Teasing out which compounds contribute to an herbal remedy’s effectiveness is challenging not only because the prescription is a cocktail of several plants, but because each herb contains a myriad of metabolites that have different targets and typically work synergistically to relieve symptoms. “When you ingest a plant, you don’t just get the active component, but all the thousands of metabolites.”

For instance, Realgar-Indigo naturalis is a traditional Chinese herbal medicine used to treat leukemia. The formula contains three active components: realgar and indigo minerals and sage root. When ingested, these compounds divide and conquer to kill cancer cells: the arsenic in realgar fights destructive proteins in leukemia cells; the indirubin in indigo slows the growth of leukemia cells; and the tanshinone in the sage root helps repair damaged pathways so the cancer cells can’t spread.

To dissect the complex activities within a mixture such as Realgar-Indigo naturalis, Jing-Ke employs a “systems biology” approach, an interdisciplinary sub-discipline of the biological sciences that involves analytical chemistry, biochemistry, genomics, and metabolomics, and employs advanced mathematical and computational algorithms. “With advanced technology,” say Jing-Ke, “we can observe proteins and metabolites and see how they work together at the molecular level.”

A recent study in the Weng lab focused on metformin, a widely prescribed diabetes medication. Metformin is a synthetic drug inspired by the French Lilac plant (Galega officilas), which has been used for centuries to treat symptoms of diabetes. In medieval Europe, French Lilac was given to patients with frequent and painful urination, a symptom of diabetes. In the 1920s, scientists discovered the active component of French Lilac as a metabolite known as galegine. In its natural form, galegine was too toxic, but scientists modified the structure to reduce the toxicity, thereby creating metformin. “But we still don’t know how metformin works,” says Jing-Ke. “If we know the molecular mechanisms that drive metformin’s efficacy, we might be able to devise ’smarter,’ more personalized herbal-based therapeutics.”

During a recent talk at the Whitehead Institute, Jing-Ke examines a PowerPoint slide behind him that shows a piece of paper printed from an experiment known as Chromatography/Mass Spectrometry (LC/MS). The paper is littered with 1,788 dots, each of which represents a metabolite in a leaf extract of French Lilac. “It’s a galaxy of molecules,” says Jing-Ke. One dot is plumper than the others. “That’s galegine,” he explains. “It’s responsible for the anti-diabetic effects.” In order to try and understand the galegine’s mechanisms of action, he gives metformin to Arabidopsis, a plant that biologists often use as a model organism. He then uses Mass spectrometry (MS) to identify the genes and metabolic pathways galegine activates. “We are still far away from nailing down the full picture,” says Jing-Ke, “but we found another bioactive component in French Lilac. “It’s called peganine, and yet it has a different array of physiological effects in humans.”

Once scientists know the metabolites in a medicinal plant, and whether these metabolites have anti-inflammatory, anti-microbial, anti-viral, or immune-regulatory effects, there exists another far-off pursuit, perhaps The Holy Grail in the natural products field: being able to map all the metabolites in a plant as well as how they “talk” to each other in complex pathways. “It’s called the metabolome,” says Jing-Ke. A plant’s metabolome is mind-bogglingly complex, but Jing-Ke hopes he can make strides in this pursuit, as it would enable him to engineer plants to create new biomaterials or medicines. To help push this aim forward, Jing-Ke recently recruited a computer scientist-turned biologist named Tomáš Pluskal. “Tomáš is developing new methodology to ’digitize’ the chemical space of medicinal plants,” says Jing-Ke. “He’s using mathematic algorithms used in economics and sound engineering to ‘deconvolute’ the chemical complexity of plants, so that they can identify key metabolite features that drive efficacy.”

The western medical establishment is slowly embracing the potential of using modern tools to understand ancient herbal remedies. The National Institutes of Health (NIH) built the National Center for Complementary and Integrative Health, however they are still unsure of the best research to fund, according to Jing-Ke. Some pharmaceutical companies are exploring traditional Chinese medicine for drug candidates, including GlaxoSmithKline, a company that recently built a research base in Shanghai. To date, no drugs based on traditional remedies have been approved in the US or Europe. The closest is sinecatechins, an FDA-approved cream for genital and perianal warts derived from green tea extracts. Though clinical trials were positive, the ingredients responsible for the efficacy are still unknown.

The natural products field got a tremendous bump with Youyou’s Nobel Prize announcement, and generally seems poised for major breakthroughs. Both the Weng and Zhang lab continue to blaze the trail – Peicheng screening medicinal plants for drug candidates, and Jing-Ke trying to demystify the action mechanisms. “You need labs like mine and Dr. Zhang’s to do the exploratory work, to prove that this work is valuable,” says Jing-Ke. “Once we start producing valuable results, I think people will be convinced.”

Most of Fu-Shuang’s mountain climbing is metaphorical these days, but it is no less exhilarating. As the young scientist puts his skills to work at the lab bench, Jing-Ke plots out the peaks to summit. Holding The Compendium of Materia Medicina in his hands, Jing-Ke considers the three decades of tedious experimenting and writing it took Li Shizhen to complete his life’s work, and though it was written in the 16th century, it might now hold clues to the discovery of new medicines for complex diseases. Jing-Ke admits that the task of unscrambling and sorting the galaxy of metabolites in the plant kingdom will undoubtedly take longer than Li Shizen’s quest, but says, “If I figure out a handful of cases every 10 years, I will be happy.”