Category Archives: Biological Chemistry

Revised: Targeting Oxygen sensitive Hypoxia-inducible factors (HIF-1s) can help cure cancer

The 2019 medicine Nobel Prize winner Dr. Gregg L. Semenza found out that targeting the oxygen-regulated hypoxia-inducible factors (HIF-1s) in the cells can help cure cancers.

What are HIF-1s?

We all need oxygen to be alive. In our body, only red blood cells that contain hemoglobin can deliver oxygen for all the other cells. During a shortage of oxygen, erythropoietin (EPO) increases the production of red blood cells. Hence, more red blood cells are available to bind and deliver oxygen from the lung to the other parts of the body.

Besides, vascular endothelial growth factors (VEGFs) can stimulate the formation of blood vessels in response to the lack of oxygen. By forming more blood vessels, the body can ensure that oxygen can get to other cells in different parts of the body.

Red blood cells transport. Source: HealthLink Canada

 

HIFs are the oxygen sensing knob in our bodies. Hypoxia-inducible factors (HIF-1s) are composed of two different subunits-one being an oxygen-regulated HIF alpha subunit and the other being an oxygen insensitive HIF beta subunit.

The alpha subunit of the HIFs can sense the oxygen concentration changes. When the oxygen level is low, the two HIF subunits join to assemble the dimeric HIF-1s. The HIF-1s can then bind to genes that express EPOs and VEGFs. As a result, more EPOs and VEGFs are available to deliver limited oxygen to cells in different parts of the body. Meanwhile, when the oxygen level is high, fewer HIF subunits form the dimeric HIF-1s. Thus, fewer HIF-1s can bind to EPOs and VEGFs genes, which further leads to less EPOs and VEGFs proteins being expressed.

How can the researchers target HIF-1s to cure cancers?
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Nobel Prize Winner, Gregg Semenza on the discovery of HIF-1. Source: Johns Hopkins Medicine

Cancer is a group of diseases with abnormal cell growth. Many studies have shown that tumor metastasis strongly correlates to the elevated levels of HIF-1s. Unlike normal cells, cancer cells have adaptive responses to hypoxic stress, meaning that they can survive and divide under low oxygen levels.

Therefore, HIF-1s can be targeted to treat cancer. By inhibiting the dimeric HIF-1s, cancer cells will have fewer EPOs and VEGFs. Without the adaptive response to low oxygen level, cancer cells will die. The HIF-1s inhibitors can combine with other anti-cancer drugs to kill off cancer cells.

The discovery of this oxygen-sensitive knob HIF-1s is a milestone in cancer treatments. Cancers perhaps are not that scary.

Journal Reference:

Gregg L. Semenza. Pharmacological targeting of hypoxia-inducible factors. Annual Review of Pharmacology and Toxicology, 2019; 59: 379-403 DOI: https://doi.org/10.1146/annurev-pharmtox-010818-021637

Georgina N. Masoud and Wei Li. HIF-1α pathway: role, regulation and intervention for cancer therapy. Acta Pharmaceutica Sinica B, 2015; 5: 378-389 DOI: https://doi.org/10.1016/j.apsb.2015.05.007

 

-Pricia Ouyang

Feb 15th, 2020

Microplastic issues? PLA can solve the problems!

Did you know that less than 11% of plastics have been recycled in Canada since the 1950s? Many plastics, such as water bottles, bags, and takeaway coffee cups, are buried in landfills and are disposed of into the oceans.

Over a long period of exposure to air, sunlight, and moisture, they eventually “disappear” – becoming invisible to the naked eye. In this case, are plastics degradable? While we may use the word “degradation”, they do not actually disappear. The invisible ones have taken the form of microplastics, thereby still existing and still polluting our ecosystem.

Video clip 1. Microplastics as a food for baby fishes.

 

To mitigate this issue, chemists have made an effort to develop biodegradable polymers that can be applied to produce commercial plastics. In modern polymer chemistry, considerable attention has been paid to polylactic acid, so-called PLA. Polylactic acid is produced from lactide which is derived from renewable resources such as corn and potato starch.

Figure 1. Chemical structures of lactide (monomer) and polylactic acid (polymer)  . ROP stands for ring-opening polymerization (a type of polymerization). DOI:10.1021/acs.accounts.7b00447

 

Unlike petroleum-based polymers used in plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polypropylene (PP), PLA has biodegradability and biocompatibility.The enriched oxygen atoms in PLA and its structural flexibility make it undergo hydrolytic and enzymatic degradations, regenerating monomers and oligomers. The degraded substances are further broken down to water and carbon dioxide, precluding the formation of microplastics. Therefore, PLA is a great candidate to substitute for plastics derived from petroleum sources.

Although there are some general issues to resolve from an economical perspective, the environmentally friendly outcomes and industrial applications have made PLA a more attractive material for plastics PLA certainly has the potential to save our future!

-Young Cho

These Ingredients in Sunscreen Might Promote Breast Cancer

Breast cancer is the most diagnosed cancer with an estimated diagnosis of 331,530 women and 2670 men this year in the US alone. Research by the University of Massachusetts Amherst published on January 15 2020 observed that chemicals in everyday items can increase the chances of breast cancer in women.

Cancer is a dangerous illness, caused by the uncontrolled division of cells in the body. It is predicted that this year 41,760 women and 500 men will die of breast cancer in the US.  These estimations may now have to take into consideration th

Chemical Structure of Benzophenone-3 aka Oxybenzone Source: Wikipedia

e dangers of sunscreen and cosmetics, including makeup, hair products, and moisturizers.These everyday products are known to contain the chemicals benzophenone-3 (BP-3) and propylparaben (PP).

The study indicates that previous research into the effects of BP-3 had shown that only extremely high concentrations could promote cancer growth. Since these concentrations were far beyond the n

Chemical Structure of Propylparaben Source: Wikipedia

ormal levels of exposure to women, there was no cause for concern.

However, the study showed that mice exposed to oils containing BP-3 and PP had an increase in cancer. The results suggest that BP-3 and PP effect cells that contain oestrogen receptors. High levels of oestrogen has previously been linked to an increase in breast cancer.  The exposure to BP-3 and PP at only a fraction of the cancer promoting concentration was shown to increase DNA damage by causing structures known as R-Loops.

Dr Joesph Jerry of UMass Amherst, science director of Pioneer Valley Institute, and co-director of Rays of Hope Centre for Breast Cancer. Source: UMass Amherst from EurekAlert!

Based on the results, Dr Joseph Jerry, the professor of Veterinary & Animal Sciences at the University of Massachusetts Amherst warns that, “There may be a risk at lower levels than we would have previously understood,”.

The study shows that DNA damage only occurs in cells containing oestrogen receptors, and that all other cells show no adverse effects.

It might be time to take a look at the ingredients in your everyday items!

– Chantell Jansz

Revised: Xenobots: World’s First Living ‘Flesh Robot’ was Created from Frog Cells

Scientists have created the world’s first living, self-healing robots using stem cells from frogs.

Published on  PNAS, a team of scientists from the University of Tufts and the University of Vermont created the first living robot named Xenobots without using any metals or plastics.

Those flesh robots constructed from frog cells can manipulate objects, move as directed and even interact with each other. The success of Xenobots promises advances in safe drug delivery, environmental remediation and understanding origins of life.

A New Star in Robotics

“They’re neither a traditional robot nor a known species of animal. It’s a new class of artifact: a living, programmable organism.”

explained by computer scientist Joshua Bongard, a collaborator of this project. Before Xenobots, genetic modifications on a single cell or 3D printing tissues have been attempted to construct living systems. Despite the success in simulating biological structures, those methods cannot predict any behaviors. So the question became how to construct a biological system that ‘knows’ what to behave.

A behavioral goal (e.g., maximize displacement), along with structural building blocks designed by computer. The blue and red regions indicate two types of cells. Source: PNAS

The Birth of Xenbots

Thanks to computer scientists, a method called ‘evolutionary algorism’ has been developed to achieve this goal.

During the robot design process, scientists first input some behavioral goals, for example, maximizing the moving area or leaving a hole in the center to carry drug molecules. The computer would then explore different building blocks with the assistance of evolutionary algorism. There are two types of frog cells for the building block, and by cleverly combining those cells, the robot may move as expected.

Xenobot under the microscope. The diameter is less than 1mm. Source: PNAS

Finally, from thousands of building block combinations, less than ten designs were selected for the experiment in vivo. The robots were manufactured under microscopy through a series of steps and tested in real conditions.

The result is surprising. Those robots can live for weeks in the water environment without additional energy. Once the energy dissipated, the cells die naturally and degrade as common organisms. Although they lack a nervous system, the robots can still change their motion regularly, and different individuals tend to exhibit various moving patterns.

YouTube Preview Image                                             Video from the University of Vermont

Will The Terminator Come True?

The incredible character of the living robot is the ability to self-repair in the face of damage. This feature is reflected in the Terminator, in which robots dominate the world.

Sam Kriegman, the first author of the study, admitted the moral issues brought by this project: the living robot variations may develop cognitive ability in the future. He also pointed out that, because this study is open to the public, society can discuss the topic and regulators should also formulate applicable policies. However, in the short term, this study is more likely to inspire future robotics and help us understand the innate creativity in life.

-Bokang Hou

Should you be worried?—An Outbreak of Novel Coronavirus!

Since December 2019, an unexplained pneumonia epidemic has occurred in Wuhan City, Hubei Province, China. An investigation found that these were related to Wuhan’s “South China Seafood Market”. Wuhan organized a multi-disciplinary expert consultation survey and used laboratory testing to identify pneumonia in Wuhan as viral pneumonia. On January 8, 2020, a new coronavirus was initially identified as the pathogen of the epidemic.

The spread of the novel Coronavirus

The outbreak of this infectious disease was first occured in Wuhan in December, 2019 and then spreaded globally since the huge flow og people in Wuhan during lunar new year. According to the New York Timesthere are more than 4,500 people in Asia infected the coronavirus as well as many other are suspected. At least 106 people have died as of Jan. 27, 20.Sources: National Health Commission of the People’s Republic of China; local governments. Note: Data as of 9 p.m E.T., Jan. 27

Evolutionary sources of coronavirus  and molecular pathways for infecting humans

To analyze the evolutionary source and possible natural host of the novel coronavirus, the researchers in this paper analyzed genetic evolution by comparing the novel coronavirus with collected large amount of coronavirus data. It was found that the novel coronavirus of Wuhan belongs to Betacoronavirus which is a RNA virus that parasitizes and infects higher animals (including humans). It is adjacent to the SARS virus and the SARS-like virus group in the position of the evolutionary tree. Interestingly, their evolutionarily common outgroup is an HKU9-1 coronavirus parasitic to Rousettus bats. Therefore, the common ancestor of Wuhan coronavirus and SARS or SARS-like coronavirus is a virus similar to HKU9-1. As the evolutionary neighbors and outgroups of Wuhan coronavirus have been found in various types of bats, it is speculated that the natural host of Wuhan coronavirus may also be bats and Wuhan coronavirus is likely to have unknown intermediate host vectors during the transmission from bat to human.

Phylogenetic tree (Source)

The authors used molecular computational simulation methods to perform structural docking studies on Wuhan coronavirus S-protein and human ACE2 protein, and found that although 4 of the 5 key amino acids that bind to ACE2 protein in Wuhan coronavirus S-protein have changed, the amino acids after the change have perfectly maintained the interaction between SARS virus S-protein and ACE2 protein. This result indicates that Wuhan coronavirus infects human respiratory epithelial cells through the molecular mechanism of S-protein interaction with human ACE2 protein, predicitng that Wuhan coronavirus has strong ability to infect humans.

Cα RMSD of 1.45 Å on the RBD domain compared to the SARS-CoV S-protein structure (Source)

Tips for prevention of coronavirus (source):

  • Wash your hands with soap for at least 20 seconds and avoid touching you mouth, nose and eyes with unwashed hands.
  • Keep a safe distance with people who are sick
  • Cover your cough or sneeze with tissue and throw the tissue in the trash
  • Clean frequently touched surfaces

-Xinyue Yang

Posted on Jan. 27th. 2020

Toxic Receipt – Another BPA Problem After Baby Bottles

Remember BPA was banned for making baby bottles by the Canadian government in 2010 due to its hormone-disrupting? You may think the problem is solved but BPA is still sneaking into people’s bodies and harm people’s health through a thing we are using daily—receipt.

Source: http://k.sina.com.cn/

After almost every payment is made, whether needed or not, the receipt will be printed out. These receipts are usually made of Bisphenol A (BPA)-containing thermal paper, which is an ink-free choice for most of the banks, supermarket, pos machine, etc.  You may think that is not a problem since you will only touch it for a few seconds rather than use it for daily drinking.

However, researchers at the University of Missouri have shown that BPA found on the heat-sensitive paper used in shopping receipts can be absorbed through the skin, significantly raising BPA levels in the body.

What is BPA Exactly?

BPA is the initial of Bisphenol A, it is a chemical raw material that can be added to plastics to make them colorless, transparent, durable, lightweight and impact resistant. BPA was widely used in the manufacture of baby bottles, water bottles, sealants for dental fillings, eye lenses and hundreds of other commodities until banned in 2010.

BPA is an endocrine disruptor that can interfere with the body’s endocrine system by mimicking the effects of estrogen. When BPA shows hormone-like effects, the real hormones in the body may not work properly.

And what’s worse is….

BPA Absorption Increased Significantly After Using Hand Sanitizer 

One study showed that using hand sanitizer or other skincare products before handling receipts increases the absorption of BPA by up to 185 times, reaching levels that can lead to obesity, diabetes, coronary heart disease, infertility, and cancer.

The study mimics a common behavior seen in fast-food restaurants: wash your hands with hand sanitizer, hold the receipt for a while, and then eat with that hand.

By testing BPA on hands, they found that after using hand sanitizer, large amounts of BPA were transferred from heat-sensitive paper to hands in just a few seconds. BPA transfers hundreds of times faster than in dry hands.

Source: https://doi.org/10.1371/journal.pone.0110509.g002

This is because hand sanitizers and skincare products (such as soaps, sunscreens, lotions) contain “dermal osmotic enhancers” used to enhance the delivery of the active ingredients in the products. This enhanced effect leads to a rapid transfer of BPA through the skin.

BPA passed on to the hands is absorbed through the skin and under the tongue when eating, leading to higher levels of the chemical in the blood and urine.

Source: https://doi.org/10.1371/journal.pone.0110509.g002

So, next time, remember to dry your hands before touching the receipt and wash your hands afterward. Or simply tell the waiter that you don’t need the receipt.

—–Yicheng Zhu

 

Is Your Headache “Normal”?

If you experience a sudden and severe headache, be careful! It could be an intracranial aneurysm. An intracranial aneurysm is the ballooning of a weakened blood vessel in the brain, which causes an intense headache upon rupturing. Around 3% of the population have unruptured aneurysms, which should be treated before they rupture. In 2011, Aoki’s group at Kyoto University suggested that nonsteroidal anti-inflammatory drugs (NSAIDs) may be an alternative to surgical repair, which is currently the only treatment for aneurysms.

Unruptured aneurysm (left) vs. Ruptured aneurysm (right)
(Credit: Mayo Clinic)

Mechanism of NSAIDs

Inflammation leads to the growth and rupture of intracranial aneurysms, but NSAIDs reduce inflammation by inhibiting the cyclooxygenase (COX) enzymes, specifically the COX-2 pathway. When this pathway is activated by inflammatory stimuli, the COX-2 enzyme converts arachidonic acid to prostaglandin, which then upregulates sequential reactions to promote inflammation, and enlarges intracranial aneurysms. Aoki’s team observed that NSAIDs decreased the formation of intracranial aneurysms in mice within the first six weeks.

Risks associated with NSAIDs and surgical repair

Although this treatment seems promising, long-term use of NSAIDs may lead to cardiovascular and gastrointestinal side effects. There are two surgical options to treating aneurysms: endovascular coiling and clipping. A major risk for coiling is that it may develop vasospasm, which occurs when the vessel constricts and leads to tissue death; whereas clipping increases the risk of infection and death, as it is an open surgery.

Two surgical procedures: Coiling an unruptured aneurysm (left) vs. Clipping a ruptured aneurysm (right)
(Created with Notability)

Both surgical and potential pharmacological treatments come with their risks, but hopefully our advancing knowledge will soon bring forth safer therapies.

 

Athena Wang

Dayvigo, A Novel Approach to Insomnia Therapy

Sleep is an inherently simple process that is often enjoyed, yet there is still a possibility that it can become so inexplicably difficult. For instance, consider insomnia, a condition where falling asleep can often become practically impossible. Even though many potential factors and causes can induce the disorder, the consequences tend to all be the same. However, with the FDA’s recent approval of a new drug called DAYVIGOTM, which contains the active ingredient lemborexant, improvement of the current insomnia treatment modalities is possible.

What causes insomnia?

To understand the causes of insomnia, it is necessary to first acknowledge that it is defined in terms of both a symptom and a disorder. Making the distinction is vital, as it can adjust our conceptualisation of it entirely. For instance, considering insomnia as a disorder, one of the causes is likely to be stress. On the other hand, if we choose to define insomnia as a symptom, pain or even sleep apnoea are both likely causes. Be that as it may, some of the major causes are listed as follows: stress, anxiety, depression, poor sleep hygiene, other health issues, stimulants and lack of exercise. Although we are developing a better understanding of the condition, it is beginning to affect more people. In fact, one study has even estimated that the prevalence of the symptoms alone is roughly 30%, hence the need for remedies such as DAYVIGOTM.

DAYVIGOTM and the role of Lemborexant

According to the label on the FDA website, the drug has been designed to treat adult patients that are having difficulties with inducing or maintaining sleep. It is worth mentioning though that the effects produced by this drug are attributed to lemborexant, which is an orexin receptor antagonist. The IUPAC name is (1R, 2S)-2-{[(2,4-dimethylpyrimidin-5-yl)oxy]methyl}-2-(3-fluorophenyl)-N-(5-fluoropyridin-2-yl) cyclopropanecarboxamide, and the molecular formula is C22H20F2N4O2. What is interesting about the drug’s structure is the presence of a 3-membered cyclopropane ring at the very centre.

Structure of lemborexant

Chem Spider ID:34500836, (accessed 03:33, Jan 28, 2020)

Certain pharmacological tests conducted with the compound illustrate the efficacy of the drug in the onset and sustenance of sleep. For instance, the molecule selectively binds to the orexin receptors, which are thought to be involved in sleep regulation. Essentially what the drug does is it binds to the receptors, preventing the “wake-promoting neuropeptides orexin A and orexin B” from interacting and therein suppressing the feeling of wakefulness.

The billion-dollar question

Is the drug worth it? A study conducted by the Tufts Center for the Study of Drug Development estimated the cost of producing novel compounds at $1.395 billion (2013 USD). Even without factoring in today’s inflationary pressures, that number is staggering. Furthermore, there are several drugs currently available to treat insomnia. However, it has been shown that DAYVIGOTM is one of the first FDA approved substance to report safety data for 12 months. Furthermore, the drug is rapidly absorbed, binds with a high affinity and is selective. Hence, in my opinion, the use of the drug is warranted.

-Akash Panjabi

Targeting Oxygen sensitive Hypoxia-inducible factors (HIF-1s) can help cure Anemia and Cancers

The 2019 medicine Nobel Prize winner Dr. Gregg L. Semenza found out that cancers and Anemia can be cured by targeting the oxygen-regulated hypoxia-inducible factors (HIF-1s) in the cells.

What are HIF-1s and how are they related to oxygen? 

We all need Oxygen to be alive. At a cellular level, oxygen is essential to cell viability as it provides an energy source (ATP) for important cellular activities. In our body, only red blood cells that contain hemoglobin can deliver oxygen for all the other cells. During a shortage of oxygen, erythropoietin (EPO) increases the production of red blood cells. Hence, more red blood cells are available to bind and deliver oxygen from the lung to the other parts of the body. Besides, vascular endothelial growth factors (VEGFs) can stimulate the formation of blood vessels in response to the lack of oxygen. By forming more blood vessels, the body can ensure that oxygen can get to other cells in different parts of the body.

HIFs are the oxygen sensing knob in our bodies. Hypoxia-inducible factors (HIF-1s) are composed of two different subunits-one being an oxygen-regulated HIF alpha subunit and the other being an oxygen insensitive HIF beta subunit.

The alpha subunit of the HIFs can sense the oxygen concentration changes. When the oxygen level is low, the two HIF subunits join to assemble the dimeric HIF-1s. The HIF-1s can then bind to genes that express EPOs and VEGFs. As a result, more EPOs and VEGFs are available to deliver limited oxygen to cells in different parts of the body. Meanwhile, when the oxygen level is high, fewer HIF subunits form the dimeric HIF-1s. Thus, fewer HIF-1s can bind to EPOs and VEGFs genes, which further leads to less EPOs and VEGFs proteins being expressed.

How can the researchers target the HIF-1s to cure cancer and Anemia?

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Cancer is a group of diseases with abnormal cell growth. HIF-1s can be targeted to treat cancer because by inhibiting the dimeric HIF-1s, the cancer cells will have fewer EPOs and VEGFs. Therefore, the cancer cells will have much harder time oxygen and without enough oxygen, these cancer cells can die.

 “By adding a small molecule that inhibits HIF-1s, added on to the other cancer drugs that patients are receiving, will allow those other drugs to be more effective in fighting cancer,’ said Dr. Semenza

“And as for Anemia, targeting the HIF-1s could show promising effect.”

 He added: “Anemia is associated with the lower-than-normal amount of red blood cells or hemoglobin. By taking a pill of a drug that increases HIF-1s activity and turns on EPO.”

The discovery of this oxygen-sensitive knob HIF-1s is a milestone in cancer and Anemia treatments. Cancers and Anemia perhaps are not that scary.

 

Journal Reference :

Gregg L. Semenza. Pharmacological targeting of hypoxia-inducible factors. Annual Review of Pharmacology and Toxicology, 2019; 59: 379-403 DOI: https://doi.org/10.1146/annurev-pharmtox-010818-021637

-Pricia Ouyang

Jan 27th, 2020

Embarassed of Asian Glow? Don’t Worry, The Future is Promising

Ever find yourself beet red after having a small drink? You’re not alone. Over one-third of East Asians and eight percent of the world population experience this awkward phenomenon; however, a solution is in the works. Just last month, researchers from Weill Cornell Medical College have solved this problem in mice, using targeted gene therapy.

What does asian glow look like? A before and after comparison. (Credits: Wikimedia Commons)

The Dangers of Asian Glow

Despite the variety of memes and jokes poking lighthearted fun at this phenomenon, asian glow comes with much dire consequences than just flushing red. The red glow is related to a deficiency in the ALDH2 enzyme, a key component in detoxifying alcohol. When you drink alcohol, the body converts this substance into acetaldehyde. Normally, acetaldehyde is then converted to the safer acetate via ALDH2; however in individuals with asian glow, this enzyme does not function normally and acetaldehyde builds up to toxic quantities. Since acetaldehyde is a cancer-causing agent, its accumulation drastically increases the risk of developing esophageal cancer by six to ten folds.

Conversion of alcohol to acetate is stopped in people with asian glow. This leads to toxic buildup of acetaldehyde. (Created with Notability)

A Glowing Solution…

Matsumura’s team reasoned if a lack of ALDH2 enzyme was the problem, maybe they could simply add it back in.

“We hypothesized that a one-time administration of a […] virus […] expressing the human ALDH2 coding sequence […] would correct the deficiency”

They tested their idea on three strains of mice: mice expressing functional ALDH2, mice lacking any ALDH2, and mice expressing a non-functional version of ALDH2. The latter two simulated the asian flush syndrome seen in humans. After introducing the mice with the ALDH2 gene and feeding them alcohol, the researchers monitored acetaldehyde levels in the blood.

Their hard-work paid off! In the two strains initially deficient for ALDH2 function, acetaldehyde levels and abnormal behavior associated with alcohol consumption lowered to near-normal levels. Furthermore, they found that one dose was enough to confer persistent and long-term protection.

From Mice to Humans: A Complicated Decision

Matsumura’s team emphasize that apart from nutritional supplements, ALDH2 deficiency has no current therapies. Although making the jump from mice to humans will be challenging, they assure the concept of virus-mediated gene therapy presents as an effective therapy. The million-dollar question is whether the risks of the glow outweigh the benefits of reduced alcohol consumption seen in affected individuals. To this Matsumura’s team maintains:

“the overall burden […] on human health, particularly […] cancer, supports […] gene therapy.”

What do you think?

 

-Kenny Lin