Natural products library to boost discovery of earthly compounds

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FREDERICK, Md. -- Tree bark, microbes, and mold are not simply the stuff you rake in the back yard and track in on the bottom of your shoes. They just might be a treatment for a rare disease. 

Products found in nature gave rise to some of our most familiar and relied-upon therapies including some antibiotics and decongestants and aspirin. There may be another treatment contained in a sea sponge or a leaf, but sifting through to isolate that compound is a complex undertaking. Scientists find natural products notoriously difficult to work with.

The team at a new state-of-the-art laboratory at the National Cancer Institute’s Natural Products Branch aims to change that, and to reinvigorate the study of natural products. 

Frederick National Laboratory scientists Tanja Grkovic, Ph.D. and John Britt oversee the highly automated laboratory designed to extract compounds from natural products, with the goal of making them easier to screen for activity against a target. The NCI’s Natural Product Discovery Program (NPNPD for short) launched a pre-fractionated extract library effort earlier this year with the goal of generating a library of 1 million natural products fractions in five years.

The 100,000 plants, marine organisms and microbes housed in the freezers and cabinets at the National Products Repository come from 50 countries worldwide. Collection agreements ensure if a product contains a compound that is ultimately commercialized, the source country will share in the profit from the drug. 

Isolating a Promising Compound from a Natural Product

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A single natural product fraction can contain upwards pf 20 compounds, Grkovic said, and it often turns out that just a single one is responsible for activity seen in the laboratory. Determining which compound is active involves multiple steps of simplifying the natural source into fractions, until the compound is finally isolated.

Grkovic likens it to starting with a forest, then zeroing down to a specific tree, to a leaf and finally to a blade of grass. 

Extracting compounds from a natural product begins with tools like hammers and chisels. Sometimes it calls for a bandsaw or a meat grinder. That kind of firepower is needed to break down a portion of a tree trunk or an enormous starfish that has been frozen after being removed from the ocean. 

Once the samples are a reasonable size and mixed with water, they are spun in a centrifuge, freeze dried and pulverized. The resulting jar of dry powder may contain a potent anti-cancer compound. But it’s still not ready for modern drug discovery.

Natural Products Research Has Lagged

Products gleaned from the Earth are have led to approved drugs in many areas of medicine, including cancer. One of the most successful natural products is the drug paclitaxel, which originates from the Pacific yew tree’s bark and has been used as a chemotherapy drug since it was approved by the Food and Drug Administration in 1993. The drug does not actually contain yew tree bark, rather it is manufactured from a compound derived from that bark.

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However, the high-throughput screening of natural products chemistry has not kept pace with the increasingly automated technology developed over the last 20 years. The technology can test 10,000 to 100,000 samples per day, an efficient way to screen for activity against a target, such as a protein involved in cancer. But crude natural product extracts are challenging to integrate into high-throughput screening programs.

Crude extracts such as ground-up tree bark are gummy and insoluble, and wind up clogging the liquid handlers. “They’re not high-throughput friendly,” Grkovic said.

The NCI’s new natural products fraction library, funded by the Cancer Moonshot, is set up to remedy that. Barry O’Keefe, Ph.D., chief of NCI’s Natural Products Branch and his colleagues in the Natural Product Support Group designed the highly automated process to carve out and isolate a product’s compounds into fractions. Tiny samples of the fractions are placed into 384-well plates, and they are ready to ship to researchers to conduct high-throughput screening. 

O’Keefe said the variety of natural products in the NCI library can lead to a broader discovery of chemicals than any synthetic compound library. 

“It really is a treasure trove of chemical diversity,” he said. 

To date, the fraction library has received requests for access to plated fractions from more than 40 research institutions around the world, studying multiple disease targets. The library is publicly accessible and samples are provided free of charge.