The “AlphaGo” in Chemistry: Organic Retrosynthesis Using Artificial Intelligence

Since the AlphaGo defeated the world Go champion in 2016, artificial intelligence (AI) has revolutionized many fields in our life. It has also become a new star in science and opened up new possibilities to solve the most complicated problems by computers.

Not long ago, a group of chemists and computer scientists built the “AlphaGo” in chemistry. Published in Nature, they designed an AI tool that can plan organic retrosynthesis faster than any similar programs. In a double-blind AB test, chemists on average considered the AI-generated routes to be equivalent to reported literature routes. This achievement may shorten the process for drug designs and accelerate pharmaceutical research in the future.

Retrosynthetic analysis is the canonical technique used to plan the synthesis of organic molecules. In the past, scientists have also tried to design retrosynthetic routes by computers. Although this method can improve the synthesis efficiency, the traditional algorisms are slow and have many errors.

However, the AI developed by Segler’s group speeds up this process significantly. Described by Segler, the synthesis of molecules is very similar to playing Go: Each molecule can be constructed by synthons which are the “playing pieces”. Computers then design routes for the synthons and combine them together.

Figure 1. Translation of the traditional chemists’ retrosynthetic route representation to the search tree representation. Source: Nature

In the research, the AI tool learned more than 12 million single-step chemical reactions by the deep neural network. This can help AI predict any chemical reactions in the synthetic sequence. AI can also apply the neutral network repeatedly to plan routes and construct synthons until ending up with accessible starting reagents.

So far, much research focuses on combing deep neural networks with Monte Carlo tree search (MCTS). Monte Carlo tree search is a method widely used in video games to evaluate the movement of an object. After the player moving one step in the game, the computer will simulate infinite possibilities that may occur and choose the best step. Similarly, computers can also use this network to find the optimal method in organic synthesis.

In a trial test, Waller’s group used this algorism to propose a six-step synthesis for a precursor used in Alzheimer’s treatment. It turns out the AI designed the same route as the literature in less than 5.4 seconds

Figure 2. Comparison between the MCTS and two traditional algorisms: Neural and Heuristic Best First Search (BFS). (A) Performance characteristics of the different search algorithms by finding synthesis routes. (B) Amount of time per molecule to find the optimal route. Adapted from: Nature

More surprisingly, the AI can perform as good as organic chemists in predicting synthetic routes for novel drugs. Segler and his team invited 45 world-leading organic chemists from Germany and China to examine two potential synthetic routes for nine molecules. One route was designed by AI and the other by humans. Results show that chemists cannot distinguish between the two methods. 

Figure 3. Double-blind AB testing of AI route (MCTS) against literature and traditional (BFS) routes. AI route is as preferable as literature routes and much better than traditional methods. (Original)

What we have seen here is that this kind of artificial intelligence can capture this expert knowledge,” says Pablo Carbonell, a famous computational chemist at the University of Manchester. He describes the effort as “a landmark paper”. Maybe in the near future, AI will make a revolutionary change in chemical research and industry.

Revised: 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. With the outbreak of this novel coronavirus, it is crucial to know how this virus spread and evolved, more importantly, how we can take precautions against it.

The spread of the novel Coronavirus

Sources: National Health Commission of the People’s Republic of China; local governments. Note: Data as of 9 p.m E.T., Jan. 27

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.

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. Therefore, Wuhan coronavirus and SARS or SARS-like coronavirus may share common ancestor. 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

Reacting with Extremely Short-Lived Radioisotopes

A study led by the University of British Columbia reveals the potential of applying short-lived radioactive species in ordinary chemical reactions.

Stable isotopes–––atoms of lifetime longer than the age of the universe (t1/2> ~10^20 years)–––predominate the every-day chemistry labs. Introducing radioactive isotopes in chemical reactions can greatly improve the diversity of available reaction mechanisms. But most of these isotopes have an extremely short lifetime, decaying into the void before any reaction will occur. 

An Imaginary Muon Source: Scorge (Deviantart)

The team led by Fleming and Macfarlane successfully introduced a highly unstable hydrogen isotope, muonium, in reactions with gold nanoparticles (AuNPs) and benzene molecules. Theoretical calculations on relevant reaction rates and quantum mechanical variables are now realized in real-life experiments.

In this study, short-lived muonium nuclides were produced from a particle accelerator at TRIUMF. It had a mean lifetime of only 2.2 microseconds, and possess only one-tenth the mass of stable hydrogen. 

TRIUMF particle accelerator at the University of British Columbia

The first reaction took place inside a cell that contained porous silica-coated AuNPs. Here, Bz vapor of known pressure monitors the study of reaction rate. Interestingly, upon introducing the Bz vapor into the reaction cell, the pressure decreased dramatically to near-zero, and its constant changes were good indications of changes in the reaction rate.

The muonium is then reacted with benzene, creating a muonated benzene radical. Radicals are highly reactive species with one unpaired electron, and they are synthesized in organic labs in limited ways. The radioisotope may build onto current techniques in creating a radical.

The researchers also analyzed the catalyzing effect of AuNPs on the muonium benzene reaction. The results show considerable weaker binding energy of benzene on AuNPs than on bulk gold metal surfaces, which indicates that the presence of AuNPs increased the reaction rate.

Gold nanoparticle
Source: Equinox Graphics (Flickr)

In Chemistry, AuNPs are great heterogeneous catalysts––––reaction accelerators that differ in phase from the reactants. These solid catalysts all together account for 90% of the catalysts used worldwide. The successful catalysis in muonium reactivity demonstrates the possible use of heterogeneous catalysts in radioisotopic reactions that await to be explored.

Besides, the reaction of AuNPs with radioisotopes would inspire more detailed studies into their biomedical benefits as cancer detectors and drug deliverers.

Unique optical properties of various sized gold. Source: Sigma-Aldrich

This avant-garde reaction will inspire the development of chemical reactions into the unstable nuclides, where new reaction pathways lie.

Revised: 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. In 2011, a study 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)

How can NSAIDs help combat aneurysms?

Inflammation is a major problem for intracranial aneurysms, as it can lead to their growth and rupture – but there is a solution! NSAIDs reduce inflammation by inhibiting the enzymes that promote inflammation and enlarge intracranial aneurysms. The study tested NSAIDs in mice and found decreased formation of intracranial aneurysms in the mice. 

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 by Athena Wang)

Lifestyle changes to prevent rupture

With around 3% of the population having unruptured aneurysms, it is beneficial to know what lifestyle changes can prevent these ruptures. Eating a healthier diet, exercising regularly, and avoiding recreational drugs can all decrease risk factors that trigger ruptured aneurysms.

How is this headache different from a “normal” one?

Normal headaches such as those caused by tension or migraines is less intense than that of an aneurysm, which is described as a thunderclap headache. More importantly, this headache may be accompanied by a stiff neck, vomit, or even a loss of consciousness.

So, the next time you feel like you’re having the worst headache of your life, seek help fast – it could be an aneurysm!

-Athena Wang

Revised: Effective Means of Diagnosing Alzheimer’s Disease

Alzheimer’s disease is an incurable disorder that must be treated early and carefully. It is a fatal disease that needs more attention. Biomarker analysis can be a method to detect early signs of the disease, and carbon nanomaterials can be a tool for this method to be applied.

It is estimated that 5.5 million Americans, mainly affecting people over the age of 65, suffer from Alzheimer’s disease without a cure, and is rapidly increasing. This does not mean nothing can be done to help treat the disease.

Researchers at the University of Porto studied carbon nanomaterials and their biosensing applications to determine the biomarkers of Alzheimer’s disease. The study in 2019 urged the importance of biomarkers for indication of Alzheimer’s disease.

To enhance treatment for this disease, early diagnosis is necessary and requires a method of indication. The study focused on biomarkers of pre-clinical stages of Alzheimer’s. Stage 1 includes increased amyloid burden, stage 2 includes neuronal injury and evidence of neurodegenerative change, and stage 3 includes subtle cognitive decline. Although the biomarkers developed can provide good results, various criteria must be met.

Biomarkers of Alzheimer’s Disease (Source: Laurent Hemoye)

Another study mentions the ability to produce biosensors from nanomaterials mainly because of their electrochemical activity and biocompatibility. Carbon nanotubes display exceptional electronic properties, due to its high surface-to-volume ratio, and is most commonly used for biosensing. Graphene is also common, and can be functionalized by various functional groups to improve selectivity to biomolecules.

Structure of Nanotubes (Source: Carneiro et al.)

A demand for more research on developing credible biomarkers for Alzheimer’s disease is crucial for early diagnosis, as more studies show biosensing as a challenge. This could potentially enhance the understanding of the disease and invent a cure.

-Wilson Wong

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

Ever find yourself beet red after one 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 by experimenting with targeted gene therapy on mice.

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

The Dangers of Asian Glow

Apart from causing embarrassment, asian glow comes with more serious consequences than just flushing red. The red glow is caused by a deficiency in the ALDH2 enzyme, a key component in detoxifying alcohol. When you drink alcohol, your body converts the alcohol into acetaldehyde. Normally, acetaldehyde is further converted to a safer compound by ALDH2; however in individuals with asian glow, ALDH2 does not function, causing acetaldehyde to build up. 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. (Credits: Me – 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 with functional ALDH2, mice lacking ALDH2, and mice with a non-functional version of ALDH2. The latter two simulated the asian flush syndrome seen in humans. After introducing all the mice with the ALDH2 gene and feeding them alcohol, the researchers carefully monitored acetaldehyde levels in the blood.

Their hard-work paid off! In the two strains deficient for ALDH2 function, acetaldehyde levels and abnormal behavior associated with alcohol consumption were back 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 a long-lasting treatment for ALDH2 deficiency currently does not exist. Although making the jump from mice to humans will be challenging, they assure that virus-mediated gene therapy shows the most promise in becoming 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 say:

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

What do you think?

-Kenny Lin

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

Revised:4 Elements Newly Found – the 7th Row of Periodic Table is Completed!

Have you ever curious about the abundance of elements in this world?

Research groups in Japan, Russia, and the USA published their discovery of elements 113,115,117 and 118. On November the 28th of 2016, International Union of Pure and Applied Chemistry (IUPAC) has formally approved the name of these elements as Nihonium (Nh), Moscovium (Mc), Tennessine (Ts), and Oganesson (Og). These four elements completed the 7th row of the periodic table and acted as an important stepping stone toward “superstable-elements” which are going to be influential in the future studies. 

Element 113, Nihonium (Nh), which called “The first element found in Asia” was found by Riken Center of Accelerator-Based Science in Japan. Joint Institute of Nuclear Research discovered three other elements of Moscovium (Mc), Tennessine (Ts), and Oganesson (Og) credited to Russia and the United States. After five months of public review, IUPAC eventually added them to the 7th row of the periodic table.

These four elements were classified as “super-heavy” elements with more than 104 protons. They were synthesized by using particle accelerators to fuse one nucleus to the other. Further experiments proved the existence of these elements by reproducing the synthesis procedures. However, the life of these “man-made” elements seem to be too short for further discovery. “A particular difficulty in establishing these new elements is that they decay into unknown isotopes very fast.” Said Paul Karol, chair of the IUPAC’s joint working party. Nihonium has a half-life of 20 seconds, which was the longest among the newly found elements. Moscovium and Tennessine have an even shorter half-life, which is only 220 milliseconds and 78 milliseconds respectively. 

Example of Super-heavy element. source:Vanderbilt University

What is the purpose of discovering these elements since they disappear almost right after they are produced?

There are “islands of stabilities” which describe certain super-heavy elements that are very stable when they have a certain number of protons or electrons, even though they are huge. Scientists believe that the next island will be in the 8th row of the periodic table. “the alleged but highly probable ‘island of stability’ at or near element 120 or perhaps 126.” Said by Paul Karol. These “Island of Stabilities” can stay from minutes to years which will be meaningful to study their chemistry.  

Although the life of these newly found elements is way too short to have a practical use, they are the sign of getting closer to the “Island of Stability” of “super-stable” heavy elements. Those “super-stable” radioactive elements are worthy of studying and could have a lot of industrial applications. For example, they might be useful as a stockpile of nuclear energy to maintain national safety. The discovery of these elements gave hope to scientists and encourage them to further discover the ultimate limit of the periodic table. Hopefully, they will be able to discover some stable super-heavy elements that are influential and have significant practical uses soon. The study of new elements would eventually be the breakthrough point of modern chemistry!

–Vicky Gu

A Bright and Sunny Future – Revised

Dye-Sensitized Solar Cells (DSSCs) are efficient and with low manufacturing costs, they are an ideal solution to our need for sustainable energy. This paper published in October 2012 reviews the fundamentals of DSSCs.

A DSSC. Retrieved from: engadget

DSSCs utilize sunlight as its source of energy, which is converted into usuable energy. It contains a light sensitizer connected to a semiconductor that faciliates the excitation of electrons which are able to enter a series of redox reactions. The continuous cycle of electrons through the circuit generates energy which can be used in our daily lives, or for other practical uses within industries.

In a separate study published in October 2019, Huang et al. proposed to optimize the counter electrode (CE) from a Pt CE, to a 2D nanosheet composed of Co-Ni-Se. This turned out to be successful as the Co-Ni-Se complex catalyzes the reduction of the I3electrolyte more effectively compared to the traditional Pt CE that is typically used. This increases the rate at which energy is generated and stored for industrial or personal use.

Schematic Diagram of a DSSC. Retrieved from: Gamry

How can this be applied to us in everyday life?

DSSCs can be installed on the roof of our houses to supply electricity during the day. This decreases our dependency on fossil fuels for energy, which are harmful to both terrestrial and marine life. It can also be used to generate energy and be stored within a battery pack for portable charging of cellular devices.

DSSCs on the Roofs of Buildings. – Retrieved from RedNewsWire

Why Should we Invest in DSSCs?

The U.S Energy Information Administration (EIA) projects that energy consumption will increase by approximately 28.6% between 2020 and 2050. This increases the demand for sustainable energy along with the depletion and harmful environmental effects of fossil fuels. Solar energy is an abundant and clean source of energy which makes photovoltaics such as DSSCs a desirable product. More money should be allocated for the research and development of DSSCs as they may be the solution to our energy crisis in the long term.

– Jackson Kuan

Revised: Dayvigo, A Novel Approach to Insomnia Therapy

For the most part, sleep is an inherently simple process. You close your eyes and wake up 8 hours later feeling refreshed. However, there is still a possibility that it can become inexplicably difficult. For instance, consider insomnia, a condition where falling asleep can feel practically impossible. One study has even estimated that the prevalence of the condition can be as high as 30%. Fortunately, there is a solution.

Man sitting on bed with head in hands
Source: Getty Images

With the FDA’s recent approval of a new drug called DAYVIGOTM, which contains the active ingredient lemborexant, there is a possibility of improving the current insomnia treatment methods.

The billion-dollar question

The first thought that tends to arise is: Is the drug actually 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 inflation, that number is staggering. Furthermore, there are a number of drugs currently available to treat insomnia. Be that as it may, DAYVIGOTM  displays a number of advantages.

It has been shown that DAYVIGOTM is one of the first FDA approved substances to report safety data for 12 months. Furthermore, the drug is rapidly absorbed and has a high affinity for the binding receptors. Another advantage is its extreme selectivity. In my opinion, the drug could be the key to providing an over-the-counter pharmaceutical that is both potent and safe. But how is it capable of achieving all of these advantages?

DAYVIGOTM and the role of Lemborexant

It is important to mention that the effects produced by this drug are attributed to lemborexant, which is an orexin receptor antagonist. The official 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.

Structure of lemborexant

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

Rather interestingly, this compound contains a number of nitrogens. While this is a common theme in most substances, this particular substance has fluorine attached to a pyridine. Although, the most important nitrogen-containing structure in this drug is a pyrimidine. What is particularly interesting about pyrimidine is that it shows a range of biological activity. For instance, it is used in depressants, anti-inflammatory drugs, analgesics and more.

A number of tests conducted with this 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 the regulation of sleep.7 Essentially what the drug does is it interacts with the receptors, preventing the “wake-promoting neuropeptides orexin A and orexin B” from interacting and therein suppressing the feeling of wakefulness.

-Akash Panjabi