The Research of Natural Products

Scientists can discern something invisible to us? Don’t be frightened! This is not a scenario in a horror story. In fact, it exists in “the micro-world” of Nature. Dr. Hsiao-Ching Lin, an Assistant Research Fellow of Institute of Biological Chemistry at Academia Sinica, demonstrated a molecular model and took us into the imagination of how fungi build the natural product, which consists of complex molecular structures, like build Lego.


The Micro-World

“The most unforgettable experiment is usually the most frightening one as well.” Dr. Lin’s eyes glimmered, saying the words which disillusion the common image of scientists. “When I was in high school, my classmates were dissecting a bullfrog, while I could only stay in a distance and watch it…”

A scientist can come from everywhere. Dr. Lin, who is expert in natural product biosynthesis, was not created in the bubbling mixture “Chemical X”; instead, she came from the fields in her hometown, Yilan, Taiwan, which is considered as “the least chemical” place.

Growing up on the fields in Yilan, put it in an accurate way, growing up on fields with no homesteads and residential buildings, she could closely get along with Nature. She was interested the most in science and nature classes at school. There was a daily science column in Mandarin Daily News (國語日報) , introducing animals, plants, insects and natural phenomena. Dr. Lin read the newspaper with her round eyes in childhood, exploring the world with an enormous interest.

Once Upon a Time… Life was a cartoon depicting the micro-world of human bodies. Every cell was personified in the cartoon. There was a different theme in each episode. For example, white cells protect a human body when it is attacked by bacteria, or metabolism works to process carbohydrate and fat after humans consume food.” Dr. Lin recalled scenes in the cartoon like a child with endless curiosity, although it has been a long time since she watched the program.

There is a micro-world of our imagination in somewhere invisible. When growing up, I also discovered a lot of systems of micro-world which developed on their own, such as the biosynthesis pathway of natural products.

 

Naturally Synthesized Products

Natural Products,  types of organic compounds, can be explained in textbooks using several pieces of chemical structure graphs which look like written in aliens’ language. However, Dr. Lin explained it in a different way. “Some effects of Ginkgo biloba, which can prevent memory loss, and coffee happening on human bodies resulted from natural products.”

Those “effects” refer to the biological activity or pharmacological activity of natural products. How they can be effective on human bodies is an unexpected result when fungi, bacteria, and plants produce the natural products, because they produce the natural products actually for the purpose of themselves and the environment. For instance, they want to keep their enemies away or help their symbiotic host.

Natural products are the tools causing interaction between creatures, in a mutually beneficial or mutually harmful way.

Take okaramine, a type of natural product, as an example. It is a type of alkaloids containing nitrogen atoms possessing a particular “interaction function”. “Okara” means “bean dregs” in Japanese, and “amine” means the compounds containing nitrogen atoms. Scientist discovered that fungi of Penicillium species grew on bean dregs and produced okaramine, the natural product. And other scientists further learned that okaramine possessed the biological activity with a selective insecticidal effect.

Put it in an easily understandable way, fungi grow on bean dregs and produce okaramine, which means they declare the sovereignty to their bug competitors. “Only we can inhabit here! Those who trespass will be killed with no mercy!”

The phenomenon of fierce territory competition in the micro-world is interesting for scientists. They wonder whether such natural product can be artificially synthesized. But, to date, there is still no comprehensive chemical synthesis pathway that has been developed. In order to find the pathway, first we need to figure out what atoms and the process those creatures rely on to build up the structure of natural products like play Lego .

Build Up Okaramine With the Concept of Lego

Dr. Lin compares the research of natural products to playing Lego. Organic atoms, “carbon, hydrogen, oxygen, nitrogen, and so on”, are like pieces of Lego. At first, scientists discovered that fungi had built up a Lego battleship (natural product), which could have fought against invading enemy bugs. However, scientists had no idea about how fungi had built it up.

So the scientists used the same way to analyze backward with the same “carbon, hydrogen, oxygen, nitrogen and so on” pieces of Lego and speculated what had happened in the process. They finally revealed the secret of how to build up such a Lego battleship in the laboratory.

More than a century ago, scientists tried producing compounds composed of complicated structures with “chemical synthesis”, which meant to proceed chemical reaction at high temperature and pressure using hyperactive chemicals.

In contrast to chemical synthesis, there are “enzymes” with various functions in natural creatures acting as catalysts for chemical reactions. Each creature has its own genome sequence, and the function of the specific enzyme is recorded in DNA. In recent years, along with the advance of genome sequencing, scientists are able to learn what genes and enzymes are involved in the process of biosynthesis, which produces various compounds.

Apart from genome mining, the technology of gene deletion, heterologous expression, and chemical structure analysis enable Dr. Lin and her research team to enter the micro-world and observe the key genes and enzymes responsible for synthesizing compounds in creatures and the roles they play in the process. She and team members can also simulate the Nature environment at normal temperature and pressure and try to catalyze biosynthesis reactions in an aqueous solution containing substrates and cofactors.

“The biosynthesis pathways we rely on here is different from the chemical synthesis in the past. It does not involve hyper-reactive and more toxic compounds.” Dr. Lin explained.

The biosynthesis pathways of natural products we want to study is that practically used in the world of Nature.

Dr. Lin demonstrated the model of okaramine compound, which looked like Lego. We can observe how chemical bonds are formed between black carbon atoms, blue nitrogen atoms, and red oxygen atoms. It is shown in the yellow circle as the following graph. When ascomycetes (one kind of fungi) are composing okaramine, they catalyze the synthesis process with OkaE, a type of enzyme, which is similar to how the joints of Lego work, to form a bond between two separate carbon atoms and combine with another carbon atom and a nitrogen atom to become a 4-membered cyclic compound.

Dr. Lin was holding the molecular  model of okaramine and trying connecting two carbon atoms on the model with her bare hands, which took some effort to stabilize the structure of the model. “It took some effort do it with bare hands, and it also took some energy for fungi to form a bond with 4-membered ring. And Nature utilizes OkaE enzyme as a catalyst for the process, which was first discovered by our team.” Dr. Lin said with a cheerful smile.

Only One Truth in Nature

Neither enzymes of natural products nor the biosynthesis pathways in Nature have we already known much about, but Dr. Lin believes that this is where the interest of the natural products research lies, which means there are a lot of secrets awaiting discovery. “Moreover, during the natural products research, I learn that there is only one truth!” At the moment when Dr. Lin said so, she looks like Detective Conan, a Japanese comic character, who is wearing glasses with glare.

It is a constant principle that the function of a certain enzyme will be proved the same in different experiments.

The other motivation of the research team is the potential in the pharmaceutical field. Take Paclitaxel, which can be the treatment of cancer, as an example. It is also a type of natural product. It can be extracted from the bark of Taxus brevifolia. Then it was discovered that a type of intermediate could be extracted from leaves of an akin tree species (Taxus baccata), and paclitaxel could be synthesized by means of semi-synthesis with the intermediate. However, only very little paclitaxel could be naturally produced before, which became the obstacle of clinical drug research and delayed the development of the medication.

If we are able to understand the biosynthesis pathways of natural products in Nature and the genes and the enzymes involved, we are on track to prepare the medicine through synthetic biology and have the access to the source of the medicine.

Does mass synthesis of natural products affect the natural environment? “Each natural product has its own biological activity, so if we decide to produce a large number of certain organic compounds, we need to think twice and understand the purpose of the production.” Dr. Lin answered the question after she considered carefully. She said that natural product is originally synthesized in Nature, so the corresponding biodegrading mechanism must lie in Nature as well.

Although it is invisible to the naked eyes, maybe the trees outside the window or the fungi around us are energetically playing with “Lego” now, and producing various natural products.

 

Reference

◎ Article translated from 真菌也會玩樂高?還組合出「天然物」戰艦! http://research.sinica.edu.tw/natural-products-okaramines-lin-hsiao-ching/

◎ The website of Hsiao-Ching Lin http://www.ibc.sinica.edu.tw/PI_DetailE.asp?Auto=55

◎ A green light for green chemistry: the discovery of new enzymes synthesizing alkaloid natural products http://www.ibc.sinica.edu.tw/Research_2017E3.asp

◎ Lai CY, Lo IW, Hewage RT, Chen YC, Chen CT, Lee CF, Lin S, Tang MC, (Lin HC) (2017-08) Angewandte Chemie-International Edition 56(32), 9478-9482 “Biosynthesis of Complex Indole Alkaloids: Elucidation of the Concise Pathway of Okaramines.” https://www.ncbi.nlm.nih.gov/pubmed/28631282?dopt=Citation

 

Editor: Ting-Hsien Lin

Art editor: Yu-Chen Chang

Translator: Man-Shu Huang