Category Archives: Organic Chemistry

Exploring Caffeine to Expand the Pharmaceutical World

What do the effects of the chemicals in caffeine tell us? Researchers at the University of British Columbia, led by Dr. Laurel Schafer, answers this question, in 2019, by developing an efficient method to produce a similar chemical, known to be used in various applications. 

A starting material reacts with a chemical in a determined set of conditions to yield a single product. This product identifies itself as a class of pseudoalkaloids.

Pseudoalkaloids can be described by their use for biological activity and exhibit enhanced properties compared to alkaloids, such as cancer treatment. Pharmaceutical industries often investigate biological activities of alkaloids to use them for drugs. 

If you are a coffee lover, you probably know the naturally occurring substance, caffeine, and its stimulating properties to our nervous system. Caffeine is classified as a pseudoalkaloid.

Using a special type of reaction, these alkaloids can be created with materials that are compatible with each other. Past studies can be improved to target specific types of pseudoalkaloids by changing the materials and methods used.

Pseudoalkaloids can be artificially made, but time-consuming multiple synthetic steps limit the production of  pseudoalkaloids. Importantly, the challenge lies in the reactivity of the starting materials, and whether it can react to produce the desired pseudoalkaloid without byproducts. 

This proves to be a challenge because structurally complex or large chemicals have a hard time to mingle with their pairs. As such, this gives rise to multiple unwanted products, as seen in similar studies.

The solution lies within the tantalum catalyst, a tool that speeds up and controls the reaction, which is tested on a reaction to observe its effectiveness on producing the final product. Existing studies experimented with different types of metal catalysts and show a high potential for great results.

An idea was proposed to add molecules that bind to the tantalum catalyst. This binding molecule improves the reactivity of the catalyst and proceeds the reaction, thereby converting as much initial material as possible to the final product.

After many attempts of finding the perfect combination of chemicals to react in the optimal conditions, Dr. Laurel Schafer’s group has synthesized the desired pseudoalkaloid of interest. For public use, the product is isolated and purified easily, since the reactivity of the reaction is maximized.

The experiment is deemed successful as it tackled all the problems faced from past researchers. One example is the selectivity of the reaction, where the reaction conditions can structurally change the final product and display undesired applications.

Evidence proves the benefits of developing pseudoalkaloids, like caffeine, and hold significant demand in the public. It is possible to design synthetic methods to produce different pseudoalkaloids with caffeine in mind. 

 

 Reference

Dipucchio RC, Rosca SC, Athavan G, Schafer LL. Exploiting Natural Complexity: Synthetic Terpenoid‐Alkaloids by Regioselective and Diastereoselective Hydroaminoalkylation Catalysis. ChemCatChem. 2019;11(16):3871–6.

-Group 9 (Wilson, Young, Rachel)

 

Sugars – The Key to Talking to Our Cells

We are one step closer to achieving communication with those 37.2 trillion tiny cells making up our bodies. Just last year, researchers at the University of British Columbia, led by Dr. Stephen Withers, found a way to modify the sugars essential to this communication by using chemicals found in bacteria. The same bacteria living in our gut!

WHAT EXACTLY ARE SUGARS?

No ambiguity here! Chemists work with sugars based off molecules in this sugar cube. Credits: The Verge

To be specific, the sugars Withers’ team studied were simple sugars; hexagonal-shaped molecules, often joined to other molecules known as “acceptors”. The problem chemists face is like the average love life. 

Similar to starting a relationship with someone, joining acceptors to sugars is also quite difficult. Luckily for sugars, Mother Nature has come up with some solutions: enzymes, which are helper molecules that speed up the pairing or unlinking of two molecules.

A SOLUTION UNDER OUR NOSES…

Instead of struggling to find ways of joining sugars and acceptors, Withers’ team thought: Why not hijack Mother Nature and use these enzymes? To make their idea a reality, they extracted sugar-specific enzymes from E. Coli, a type of bacteria that lives inside the human gut.

These bacteria manufactured 175 sugar-specific enzymes, and from these they chose eight enzymes that were compatible with the sugars and acceptors they were interested in.

It seemed like Withers’ team now had everything needed to join the desired acceptors to the sugars; however, there was still a problem. The sugar-specific enzymes they got from E. Coli did the exact opposite of what they wanted; instead of forming sugar-acceptor linkages, they specialized in breaking them.

Enzymes that break sugar-acceptor linkages are analogous to using a screwdriver to loosen a screw, while enzymes that form sugar-acceptor linkages are like tightening a screw.

A small modification changes the function of the enzyme. Credits: Blog post authors

To solve this problem, they reverse-engineered the enzymes specialized in breaking linkages into those that form linkages, by changing a small part of the enzymes’ structure, similar to changing the tips on a screwdriver. As a result, Withers’ team now had eight enzymes specialized in forming different sugar-acceptor linkages. 

MORE THAN JUST A BOND…

Now being able to freely and efficiently modify sugars, there is a big potential for researchers to join in on the conversations with our cells. Why is this important? Often, there is miscommunication within our cells which can lead to serious trouble. 

One example is cancer; which is partly caused by cancer cells using abnormal sugar molecules as a form of miscommunication, to avoid being cleared up by immune cells. One potential treatment is a sugar-based vaccine, which allows our immune cells to more efficiently target tumor cells.

The challenge of creating a sugar-based vaccine isn’t just relevant to cancer, but other diseases as well which also occur  as a result of miscommunication. With Withers’ research, designing these sugar-based drugs won’t be as difficult thanks to their novel way of bonding sugars to other molecules. This research brings us one step closer to talking to our cells, helping with the battle against diseases.

Story source

Armstrong, Z.; Liu, F.; Chen, H.-M.; Hallam, S. J.; Withers, S. G. Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 20199 (4), 3219–3227.

– Kenny Lin, Pricia Ouyang, Tom Hou, Aron Engelhard (CO-10)

Sugars – The Key to Talking to our Cells

We are one step closer to achieving communication with those 37.2 trillion tiny cells making up our bodies. Our cells communicate using sugars, and different modifications to these sugars can change the way our cells communicate with each other. Just last year, researchers at the University of British Columbia, led by Dr. Stephen Withers, did exactly this! They designed a unique way to tinker with sugars’ chemical structures by using chemicals found in bacteria. The same bacteria living in our gut.

what exactly are sugars?

No ambiguity here! Chemists work with sugars based off molecules in this sugar cube. Credits: The Verge

To be specific, the type of sugars Wither’s team studied were simple sugars; hexagonal-shaped molecules, often joined to other molecules known as “acceptors”. The problem chemists face is like the average love life. Similar to starting a relationship with someone, joining acceptors to sugars is also quite difficult. Luckily for sugars, Mother Nature has come up with some solutions: enzymes, which are helper molecules that speed up the pairing or unlinking of two molecules. 

A SOLUTION UNDER OUR NOSES…

Instead of struggling to find ways of joining sugars and acceptors, Wither’s team thought: Why not hijack Mother Nature and use these enzymes? To make their idea a reality, they extracted sugar-specific enzymes from E. Coli, a type of bacteria that lives inside the human gut. These bacteria manufactured 175 sugar-specific enzymes, and from these they chose eight enzymes that were compatible with the sugars and acceptors they were interested in.

It seemed like Wither’s team now had everything needed to join the desired acceptors to the sugars; however, there was still a problem. The sugar-specific enzymes they got from E. Coli did the exact opposite of what they wanted; instead of forming sugar-acceptor linkages, they were specialized in breaking them. Enzymes that break sugar-acceptor linkages are analogous to using a screwdriver to loosen a screw, while enzymes that form sugar-acceptor linkages are like tightening a screw.

A small modification changes the function of the enzyme. Credits: Blog post authors

To solve this problem, they reverse-engineered the enzymes specialized in breaking linkages into those that form linkages, by changing a small part of the enzymes’ structure, similar to changing the tips on a screwdriver. As a result, Wither’s team now had eight enzymes specialized in forming different sugar-acceptor linkages. 

More than just a bond…

Now being able to freely and efficiently modify sugars, there is a big potential for researchers to join in on the conversations with our cells. Why is this important? Often, there is miscommunication within our cells which can lead to serious trouble. 

One example is cancer; which is partly caused by cancer cells using abnormal sugar molecules as a form of miscommunication, to avoid being cleared up by immune cells. One potential treatment is a sugar-based vaccine, which tells our immune cells to ignore this miscommunication and target tumor cells.

The challenge of designing a sugar-based vaccine isn’t just relevant to cancer, but other diseases as well which occur also as a result of miscommunication. With Wither’s research, designing these sugar-based drugs won’t be as difficult thanks to their novel way of bonding sugars to other molecules. This research brings us one step closer to talking to our cells, helping with the battle against diseases.

Story source

Armstrong, Z.; Liu, F.; Chen, H.-M.; Hallam, S. J.; Withers, S. G. Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 20199 (4), 3219–3227.

– Kenny Lin, Pricia Ouyang, Tom Hou, Aron Engelhard (CO-10)

Magical Materials Revolutionize the Pharmaceutical World

What if there’s more to caffeine than meets the eye? What if we can chemically change the way caffeine works to create a better version of itself. 

If you are a coffee lover, you probably know the naturally occurring substance, caffeine, and its stimulating properties to our nervous system. Why and how does it happen?

Using a special type of reaction, the biological activity of caffeine can be transformed to suit a variety of different applications. Past studies can be improved by changing the materials needed and the methods used. 

Dr. Schafer’s team, at the University of British Columbia, examines an approach to synthesize pseudoalkaloids (Fig. 1), chemicals present in caffeine, with great accuracy.

Figure 1. Examples of pseudoalkaloids. The pseudoalkaloids on the left are produced naturally or synthetically. The pseudoalkaloids on the right are the researchers’ target molecules. (molecules were drawn with ChemDraw 19.0; Credits: Wilson, Young, and Rachel)

Pseudoalkaloids can be artificially made, but time-consuming multiple synthetic steps limit the production of  pseudoalkaloids. Importantly, the challenge lies in the reactivity of the starting materials, and whether it can react to produce the desired pseudoalkaloid without byproducts. 

Similar studies show different products have formed, which proves to be a problem. 

Existing studies experimented with different types of metal catalysts showing potential improvement for the results. A tantalum catalyst, a tool that speeds up the reaction, is tested on a reaction to observe its effectiveness on producing the final product. 

An idea was proposed to add molecules that bind to the tantalum catalyst. This binding molecule improves the reactivity of the catalyst, thereby converting as many initial materials as possible to the final product.

Of many possible starting materials, terpenes (Fig. 2) were used for the synthesis of pseudoalkaloids. In addition to the inactive alkene groups in terpenes, various chemical structures make them attractive starting substrates to explore a new synthetic route. 

Figure 2. Examples of terpenes. Terpenes are naturally occurring organic molecules, produced by plants. The terpenes on the right are starting materials chosen by the researchers. Every terpene has unsaturated functional groups which may react with other molecules.  (molecules were drawn with ChemDraw 19.0; Credits: Wilson, Young, and Rachel)

Another key building block, an amine, can be any, as long as the nitrogen atom of an amine is directly bound to one hydrogen atom. However, a clever choice can even make the final products useful building blocks, allowing further modifications (Fig. 3)

 Figure 3. Amines with varying R groups. After reacting with a terpene, the R group of pseudoalkaloid can be further modified to form a new molecule. (molecules were drawn with ChemDraw 19.0; Credits: Wilson, Young, and Rachel)

The catalytic reaction between amines and terpenes with the tantalum catalyst showed great selectivity. Without the help of the tantalum catalyst, an amine could potentially select any active spot on a terpene and react with it, causing a mixture of pseudoalkaloids at the end of the reaction.

However, the tantalum catalyst results in one dominating product. Although the final pot contains some residual starting materials, the target pseudoalkaloids are the major product that can be easily isolated.

By constructing a pathway to ultimately arrive at the designated point, new and better options can be achieved. Caffeine is one of many that can be innovated upon.

 

Reference

Dipucchio RC, Rosca SC, Athavan G, Schafer LL. Exploiting Natural Complexity: Synthetic Terpenoid‐Alkaloids by Regioselective and Diastereoselective Hydroaminoalkylation Catalysis. ChemCatChem. 2019;11(16):3871–6.

 

-Group 9 (Wilson, Young, Rachel)

 

The Next Step in Antibiotics

Did you know that not all types of bacteria in this world are harmful to humans? Some bacteria can be beneficial such as those used for the production of cheese and yogurt. Furthermore, these tiny creatures could even potentially be used to manufacture antibiotics for human use.

Antibiotics are used to cure bacterial infections by killing bacteria. For example, penicillin saved thousands of people in the 19th century.

Bacteria

As Amazing as they Sound, Antibiotics are not a Permanent Solution

The over-usage of antibiotics results in bacteria that can build resistance and cause the medication to be ineffective. The World Health Organization announced: “A serious threat is no longer a prediction for the future, it is happening right now in every region of the world and has the potential to affect anyone” on the development of drug-resistant bacteria.

Once a type of bacteria develops a resistance to a specific antibiotic, other antibiotics must be used to treat the infection. For example, nitroimidazole is a drug found in antibiotics such as azomycin. Due to its low resistance by bacteria, it has been used extensively to treat bacteria that have developed resistance to certain antibiotics.

Nitroimidazole

Research Looking into Nitroimidazole

Dr. Jason Hedges and Dr. Katherine Ryan of the University of British Columbia took a look into finding new ways to synthesize nitroimidazole. Their recent publication in 2019 showed how they were able to convert an amino acid (a building block of proteins) into azomycin. 

The researchers used bioinformatics, a data analysis tool, to find all previous work that has been done on this topic. Bioinformatic searches are performed on databases such as NCBI.

They found that back in 1953, azomycin was extracted from a strain of bacteria called Streptomyces eurocidicus. Furthermore, they found a specific gene in a separate strain of yeast called Streptomyces cattleya, which had similarities to S. eurocidicus

The two researchers aimed to find new ways to synthesize nitroimidazole, and proposed to synthesize nitroimidazole from L-arginine. Once a pathway had been developed, their end goal was to synthesize and extract azomycin in S. cattleya.

Hedges and Ryan were able to develop a multi-step pathway for the conversion of L-arginine to nitroimidazole through experimentation. However, they were unable to detect azomycin in S. cattleya. They noted that the gene of interest was unable to synthesize azomycin, and a separate drug may have synthesized in its place.

Synthesize of nitroimidazole from L-Arginine

A Bright Future

The significance of this research transcends the synthesis of azomycin. Although they failed to detect azomycin in S. cattleya, their work provides a stepping stone for further research to be conducted. This study provides insight on new biosynthetic pathways which is important to those currently in the field of life sciences and pharmacology. Furthermore, this study expands people’s knowledge of bacteria engineering and the biosynthetic pathway of other antibiotics. It also provides information about future antibiotic observations.

Future researchers could test their synthetic pathway on other bacteria such as E. coli to determine if azomycin could be synthesized.

Reference:

Hedges, J. B.; Ryan, K. S. In Vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angewandte Chemie International Edition 2019, 58 (34), 11647–11651.

-Adrian Emata/Jackson Kuan/Xinyu Gu/Yicheng Zhu

 

 

 

The Key to Treating Pneumonia can be Found in Soil?

Can it really be that simple? Can the answer really be in the ground beneath our feet?

Source: Soil Science Society of America

Discovery of a gene cluster commonly found in soil-dwelling bacteria may be the key to treating anaerobic bacterial infections such as appendicitis and pneumonia. Researchers Jason B. Hedges and Prof. Dr. Katherine S. Ryan from the University of British Columbia have isolated the antibiotic compound azomycin from a biosynthetic gene cluster found in the bacterium Streptomyces cattleya.

With this information they believe it can lead to engineering bacteria to produce a new line of antibiotics.

What is a gene cluster?

The term gene cluster is moreso semantics to describe a group of genes that share a common phenomenon.

Originally, azomycin was isolated from a similar bacterium Streptomyces eurocidicus back in 1953 and became the blueprint to synthetic nitroimidazoles. 

“Nitroimidazoles are one of the most effective ways to treat anaerobic bacterial infections”,[1] Hedges writes in his 2019 study. The most commonly used nitroimidazole, metronidazole, is an antibiotic used to treat pelvic inflammatory disease, endocarditis, and bacterial vaginosis.[2] It is also on the World Health Organization’s List of Essential Medicines, the safest and most effective medicines needed in a health system.[3]

Figure 1: Molecular Structure of Nitroimidazole. Source: Sigma Aldrich

Despite its use in antibiotics for over 60 years, the incidence of nitroimidazole resistance in anaerobes remains low, making it an essential component of the antibiotic arsenal. [1,4]

Since the isolation of azomycin back in 1953, synthesis of nitroimidazoles were limited to synthetic routes, most commonly involving reactions of an imidazole with nitric acid and sulfuric acid. 

Using bioinformatics, however, in 2019 Hedges and Ryan were able identify a biosynthetic gene cluster in the same bacterium that makes penicillin,[5] Streptomyces cattleya. They were able to find that this gene cluster containing azomycin is widely distributed among soil-dwelling actinobacteria and proteobacteria.

Because of this they theorize that azomycin and other nitroimidazoles may be important factors in ecology.

What are bioinformatics?

Bioinformatics is the science of collecting and analyzing complex biological data such as genetic codes. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data

In addition to the isolation of azomycin in a gene cluster, Hedges and Ryan were able to perform in vitro analysis in order to understand the enzymatic steps that take the primary protein L-arginine to become azomycin. 

Source: Washington Post

Their work opens the door to biocatalytic methods to synthesize azomycin and other nitroimidazoles. They believe this discovery can “lead to the possibility of engineering bacteria to produce nitroaromatic compounds”.[1]

In other words, this may lead to stronger antibiotics immune to drug resistance.

References

Hedges, J. B.; Ryan, K. S. In Vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angewandte Chemie International Edition 201958 (34), 11647–11651.

The American Society of Health-System Pharmacists. Archived from the original on 6 September 2015. Retrieved 31 July 2015.

World Health Organization model list of essential medicines: 21st list 2019. Geneva: World Health Organization

David I. Edwards, Nitroimidazole drugs-action and resistance mechanisms I. Mechanism of action, Journal of Antimicrobial Chemotherapy, Volume 31, Issue 1, January 1993, Pages 9–20, https://doi.org/10.1093/jac/31.1.9

Kahan, JS; Kahan, FM; Goegelman, R; Currie, SA; Jackson, M; Stapley, EO; Miller, TW; Miller, AK; Hendlin, D; Mochales, S; Hernandez, S; Woodruff, HB; Birnbaum, J (Jan 1979). “Thienamycin, a new beta-lactam antibiotic. I. Discovery, taxonomy, isolation and physical properties”. The Journal of Antibiotics32 (1): 1–12

-Adrian Emata

The magical “Ta” catalyst for pseudoalkaloids

If you are a coffee lover, you would probably know the naturally occurring substance, caffeine. But, were you aware that this substance is classified as a pseudoalkaloid?

Many pseudoalkaloids can often have biological activities like caffeine stimulates our nervous system. Ultimately, pseudoalkaloids can be used as building blocks to produce useful drugs.

In 2019, researchers at the University of British Columbia, led by Dr. Schafer, uncovered a new pathway to produce structurally simple terpenoid-alkaloids, which belong to pseudoalkaloids.

This study can be simply summarized as a reaction between a terpene and an amine with the help of a tantalum catalyst. But, let’s first explore key ingredients to deeply understand how the synthetic route works!

 

An organotantalum compound with a ureate salt
The researchers developed a catalytic reaction run by a metallic compound. Based on other known studies, they chose an organoctantalum compound to produce terpenoid-alkaloids. As like an engine is the heart of a car, the tantalum compound is an engine to drive reactions to the final products, terpenoid-alkaloids

The choice of a metallic compound is of course crucial. However, it is more important for the compound to have complete catalytic potential. How could a bare metallic compound become a complete catalyst? The answer is associating a metallic compound with a ligand such as organic molecules or salts, which can coordinate to a metal center. Of numerous possible candidates of ligands, the researchers found that a specific salt can improve the efficiency and selectivity of the bare organotantalum compound, thereby allowing it to have a complete catalytic ability.


Figure 1.The ureate salt that improved selectivity and efficiency of the organotantalum compound, Ta(CH2SiMe3)3Cl2. Of several ureate salts, the above salt was the most suitable for this study due to its solubility.

Terpenes and anilines
As the name of final products, terpenoid-alkaloids, reflects the use of terpenes, one of key ingredients is a terpene, a naturally occurring molecule. By limiting the scope of terpenes to enantiopure limonene and pinene, the types of anilines were varied and reacted with the terpenes

Now, here comes a question. What is the consequence of mixing these ingredients together?

 

Fascinating results
This study is fascinating not only for the reason that a catalytic amination of terpenes is unexplored, but also the final products are not chaotic mixtures.

What does it mean by a chaotic mixture? Some catalysts have potential to alter an intrinsic structure of a staring substance. For example, if a catalyst was able to influence the chiral center of (R)-limonene by changing its stereochemistry, a reaction batch would contain both (S) and (R)-limonenes. Consequently, the occurrence of two products is equally probable.

Also, unexplored magical ability of the tantalum catalyst in the study allows anilines to react with one specific spot of an alkene moiety in terpenes. This astonishing selectivity gives a rise to one major product.

           Figure 2.The reaction of an enantiopure limonene with six different anilines (left). The reaction of an enantiopure pinene with six different anilines (right). Both reactions result in high regio- and diastereoselectivity.

Reference
Dipucchio RC, Rosca SC, Athavan G, Schafer LL. Exploiting Natural Complexity: Synthetic Terpenoid‐Alkaloids by Regioselective and Diastereoselective Hydroaminoalkylation Catalysis. ChemCatChem. 2019;11(16):3871–6.

-Young Cho

No Medicine to Cure

Can you imagine the world without medicine?

Nowadays, more and more bacteria begin to show resistance against antibiotics. Azomycin, a type of antibiotics used to treat multi-drug resistance is found to be used more and more frequently. What if bacteria start to grow resistance against Azomycin? However, it is actually nailed fact, the only question is when. In order to solve this problem, in 2019, Dr. Jason Hedges and Dr. Katherine Ryan of the University of British Columbia engaged in finding a new way to synthesize the nitroimidazole, the main component of azomycin.

source:https://www.reactgroup.org/toolbox/understand/how-did-we-end-up-here/few-antibiotics-under-development/

The study of antibiotics can be traced back to the 19th century. For these two centuries, antibiotics saved countless lives from all kinds of diseases. However, antibiotics can not kill all the bacteria. Every time when one bacteria survived from the massacre of the antibiotic, they grow the resistance against the antibiotic. Then it split, split and split. Finally, the survived bacteria become countless bacteria that can not be defeated by the antibiotic again. Thus, more and more bacteria begin to survive from the war with antibiotics, and more and more antibiotics become useless. Herein, the race between the evolving of antibiotics and evolving of bacteria begins. 

So, let’s take a look at what did Dr. Jason Hedges and Dr. Katherine Ryan do and what did they find.

By doing a lot of research, Dr. Jason Hedges and Dr. Katherine Ryan found that the development of nitroimidazole can be dated back to 1953 when azomycin was first found. And they noticed that when strain Streptomyces eurocidicus was produced, L-arginine is converted to azomycin. Therefore, they came up with a plan to synthesis nitroimidazoles by linking L-arginine to azomycin via in vitro reconstitution. 

In vitro reconstitution process of nitroimidazole. Source: Hedges and Ryan, 2019

Through the experiment, Dr. Jason Hedges and Dr. Katherine Ryan successfully synthesized nitroimidazole via in vitro reconstitution. But unfortunately, no azomycin was produced via Streptomyces cattleya. 

Although the experiment is failed to synthesis azomycin through Streptomyces cattleya, it still provides a lot of valuable information for further researchers. It points a direction on the biocatalytic pathway of azomycin synthesis and set the stage for the discovery of new antibiotics.

Reference:

Hedges, J. B.; Ryan, K. S. In Vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angewandte Chemie International Edition 201958 (34), 11647–11651.

 

Yicheng Zhu

 

 

 

 

 

Biosynthetic Pathway Found to Synthesize Anaerobic Antibiotics!

Fig 1. Image of Azomycin. source

Scientists found the biosynthetic pathway to the Nitroimidazole Antibiotic Azomycin. A steppingstone towards the revolution of anaerobic bacterial infection treatments.

Scientists from the University of British Columbia found the biosynthetic pathway to the Nitroimidazole antibiotic Azomycin. The enzymatic mechanism from L-Arginine to Nitroimidazole has now been proved and present to the public. Their formal paper was published online on July 17th, 2019. Nitroimidazole is an essential component for the modern antibiotics, it is crucial to know its synthetic pathway for further pharmaceutical studies. The result of their study set the stage for further development of important anaerobic antibiotic Azomycin.

What is it? Why do we need to know about this?

Nitroimidazole is an essential antibiotic specifically to treat anaerobic bacterial infections. They are widely used to treat diseases such as Amoebiasis, Parasitic infections, skin infections, diarrhea and so on. The low redox potential of anaerobic bacteria cells allowed nitroimidazole to act as the electron sink and form the radical species. The resultant radical species would induce the bacteria cells’ death by damaging their DNA. Antibiotic is the most powerful “weapon” to fight against bacterial infections. However, according to the World Health Organization, there are more than 700000 people die every year due to antibiotic resistance. Despite the several decade’s usages of Nitroimidazole antibiotics, the drug resistance of it still remains low relatively. Thus, Nitroimidazole antibiotics are increasingly used to treat multi-drug resistant bacteria as well.

 

Previous research established that L-Arginine is converted to azomycin by 2-aminioimidazole. They determined that the intermediate of the reaction is 4-hydroxy-2-ketoarginine (2). Furthermore, they also observed the accumulation of pyruvate(3) side products and 2-aminoimidazole(5) from the intermediate(2). However, the actual enzymatic synthetic pathway has not been determined detailly yet. Jason and Katherine in the research group determined that PLP-dependent enzymes, RohP,RohR,RohQ and RohS plays esstential role in the catalytic pathway of the reaction. Researchers examined the in vitro activity of RohP, RohR, RohQ and RohS. They put in these enzymes separately and stepwise to different reactants. For example, in order to test whether RohR could catalyze a retro-aldol cleavage of 2 into 3 and guanidinoacetaldehyde (4), they added purified RohR instead of RohP. Then according to activity analysis and also the mass spectrum, the result shows that RohP yields a bigger portion of 2.

Fig 2. Reaction scheme from L-Arginine to Nitroimidazole. Source

Antibiotics are the most powerful “weapon” to kill bacteria in modern pharmaceutical studies. As early as in the 20th century, the observation of penicillin saved millions of people injured in the World War. Yet, the enormous benefits of antibiotics cause the consequences of drug-resistance. Azomycin, consider as a low-resistance antibiotic, it is crucial to understand its enzymatic reaction mechanism. Reaction mechanism allows scientist to have a more detail interpretation of the synthesis. It is crucial to find the catalytic cycle of the reaction, in order to allow scientists to develop and derive further study.

The study done by Jason and Katherine at the University of British Columbia provides the public with a steppingstone in future nitroimidazole anti-biotics study. Their study expanded people’s knowledge of the biosynthetic pathway to nitro-compounds. It also makes bacteria engineering to produce nitroaromatic compounds possible. This study will open the new door in enzymatic synthesis and biochemistry synthesis.

Cited article:

Hedges, J. B.; Ryan, K. S. In Vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angewandte Chemie International Edition 201958 (34), 11647–11651.

An Innovative Method to Optimize New Products

Can you make anything you want? You might be able to, with a modified blueprint.

Following instructions step-by-step can can be challenging, especially if there are multiple pathways. A specialized method can be used to selectively hand-pick specific products.

A design is invented from existing functional methods to counteract the difficulties of multiple products. Dr. Schafer at the University of British Columbia implements a system to accurately isolate the desired product.

The study urges the importance of terpenoid-alkaloids, compounds used for their pharmacological properties, compared to individual terpenes and alkaloids. The problem lies in the mechanism of producing terpenoid-alkaloids.

Past studies show the use of catalysts, a tool that promotes reactions to occur, result in multiple products to be formed. To selectively form a single product, the catalyst must be optimized.

A tantalum-based, metal catalyst, precursor was used to test its reactivity to terpene substrates, and shows promising results. The terpenoid-alkaloid conversion rate for the Ta(CH2SiMe3)3Cl catalyst is higher than the other precursors, as seen in Figure 1.

Figure 1. (a) Addition of Ta-based precursors in 1-octene and limonene (b) Ta-based precursor with N,O-chelating ligands in 1-octene and limonene (Source: Schafer)

An addition of various chelating ligands, molecules that attach to metal ion centers, to the Ta catalyst further increased the conversion rate. Different ligands show varying rates.

The reaction to synthesize terpenoid-alkaloids is called hydroaminoalkylation. Alongside the most optimal catalyst system created, terpenoid-alkaloids are produced with various yields and conversion rates on terpene substrates.

The selectivity factor can be supported by using NMR spectroscopy, a method that can determine the structure of the product. A chiral high performance liquid chromatography (HPLC) is used to determine if the product present is oriented in only one form.

The data is analyzed to determine the best possible reaction mechanism to accurately produce the desired product. The isolation and purification process is simple because the reaction went through to form one product.

The study experiments with different substrates of similar structure to further confirm their suspicions. The specificity of the reaction is recorded, including exact amounts of chemicals used and the reaction parameters studied in.

The hydroaminoalkylation reaction is chemically altered to regulate the formation of one specific product of terpenoid-alkaloids. More research is required to investigate reactivities of different substrates in various conditions to determine an even more optimal mechanism.

The act of modifying concrete steps to selectively isolate a distinct product is proven to succeed. The end result can offer enhanced properties to be applied.

 

Reference

Dipucchio, R. C.; Rosca, S. C.; Athavan, G.; Schafer, L. L. Exploiting Natural Complexity: Synthetic Terpenoid‐Alkaloids by Regioselective and Diastereoselective Hydroaminoalkylation Catalysis. ChemCatChem 2019, 11 (16), 3871–3876.

-Wilson Wong