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Generative AI used to develop potential new drugs for antibiotic-resistant bacteria

Acinetobacter is a group of bacteria commonly found in the environment. The most common cause of infections is Acinetobacter baumannii. (credit: CDC) 

Researchers at Stanford Medicine and McMaster University have devised a new AI model, SyntheMol (“synthesizing molecules”), which creates recipes for chemists to synthesize drugs in the lab. With nearly 5 million deaths linked to antibiotic resistance globally every year, new ways to combat resistant bacterial strains are urgently needed, according to the researchers.

Using SyntheMol, the researchers have so far developed six novel drugs aimed at killing resistant strains of Acinetobacter baumannii, one of the leading pathogens responsible for antibacterial resistance-related deaths, as noted in a study published March 22 in the journal Nature Machine Intelligence.

25,000 possible antibiotics and the recipes to make them in less than nine hours

The model was trained to construct potential drugs using a library of more than 130,000 molecular building blocks and a set of validated chemical reactions. It generated the final compound and the steps it took with those building blocks, giving the researchers a set of recipes to produce the drugs.

The researchers also trained the model on existing data of different chemicals’ antibacterial activity against A. baumannii. With these guidelines and its building block starting set, SyntheMol generated around 25,000 possible antibiotics and the recipes to make them in less than nine hours.

To prevent the bacteria from quickly developing resistance to the new compounds, researchers then filtered the generated compounds to only those that were dissimilar from existing compounds.

“Now we have not just entirely new molecules but also explicit instructions for how to make those molecules,” said James Zou, PhD, an associate professor of biomedical data science and co-senior author on the study.

A new chemical space

The researchers chose the 70 compounds with the highest potential to kill the Acinetobacter baumannii bacterium. The company was able to efficiently generate 58 of these compounds, six of which killed a resistant strain of A. baumannii when researchers tested them in the lab. These new compounds also showed antibacterial activity against other kinds of infectious bacteria prone to antibiotic resistance, including E. coli, Klebsiella pneumoniae and MRSA.

The scientists were able to further safety-test two of the six compounds for toxicity in mice. The next step is to test the drugs in mice infected with A. baumannii to see if they work in a living body,” Zou said. “This AI is really designing and teaching us about this entirely new part of the chemical space that humans just haven’t explored before.”

The study was funded by the Weston Family Foundation, the David Braley Centre for Antibiotic Discovery, the Canadian Institutes of Health Research, M. and M. Heersink, the Chan-Zuckerberg Biohub, and the Knight-Hennessy scholarship.

Citation: Swanson, K., Liu, G., Catacutan, D.B. et al. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nat Mach Intell 6, 338–353 (2024). https://www.nature.com/articles/s42256-024-00809-7

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Implantable batteries could one day run on your body’s own oxygen

Implantable and biocompatible Na-O2 battery (credit: Chem/Lv et al.)

Implantable medical devices rely on batteries (such as pacemakers, which keep the heart on beat). But batteries eventually run low and require invasive surgeries to replace.

So researchers at Tianjin University of Technology, China devised an implantable battery that runs on oxygen in the body. Their study with rats, published in the journal Chem, shows that the proof-of-concept design can deliver stable power and is compatible with the body’s biological system.

Biocompatible electrodes

To build a safe and efficient battery, the researchers made its electrodes out of a sodium-based alloy and nanoporous gold, a material with pores thousands of times smaller than a hair’s width. Gold is compatible with living systems and sodium is an essential and ubiquitous element in the human body.

The electrodes undergo chemical reactions with oxygen in the body to produce electricity. To protect the battery, the researchers encased it within a porous polymer film that is soft and flexible.

The researchers implanted the battery under the skin on the backs of rats and measured its electricity output. Two weeks later, they found that the battery can produce stable voltages between 1.3 V and 1.4 V. Although the output is insufficient to power medical devices, the design shows that harnessing oxygen in the body for energy is possible.

No inflammatory reactions

The team also evaluated inflammatory reactions, metabolic changes, and tissue regeneration around the battery. The rats showed no apparent inflammation.

Byproducts from the battery’s chemical reactions, including sodium ions, hydroxide ions, and low levels of hydrogen peroxide, were easily metabolized by the body and did not affect the kidneys and liver. The rats healed well after implantation, with the hair on their back completely regrown after four weeks. Blood vessels also regenerated around the battery.

The team plans to increase the battery’s energy delivery by exploring more efficient materials for electrodes and optimizing battery structure and design.

Beyond powering medical devices

Corresponding author Xizheng Liu, who specializes in energy materials and devices, noted that the battery is easy to scale up in production; and choosing cost-effective materials can further lower the price. The team’s battery may also find other purposes beyond powering medical devices.

“Because tumor cells are sensitive to oxygen levels, implanting this oxygen-consuming battery may help starve cancers. It’s also possible to convert the battery energy to heat and kill cancer cells,” says Liu.

This work was financially supported by the National Key Research and Development Program of China, the National Science Fund for Distinguished Young Scholars, and the National Natural Science Foundation of China.

Citation: Lv et al. Implantable and Bio-compatible Na-O2 battery. Chem (Cell Press. https://cell.com/chem/fulltext/S2451-9294(24)00074-3 (open access)

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SingularityNET to merge crypto network with FETCH.ai and Ocean protocol

In the biggest event in the history of the SingularityNET token, it was announced Wednesday that the token will merge with two other tokens.

SingularityNET launched the AGI or AGIX token in 2017 as a funding mechanism for decentralised AI. It has established itself as a top-100 cryptocurrency and provided funding for the company, its research, and its many projects (including Mindplex).

Ocean Protocol and Fetch.ai are like-minded projects. Ocean Protocol is a platform for tokenising and exchanging datasets, and Fetch.ai is a decentralised machine-learning network. The executive teams of the three companies have agreed on the terms of the merger, which now will be put to a vote of the tokenholders of the networks.

Since the merger was announced on Wednesday, the prices of all three tokens (ticker symbols FET, AGIX, and OCEAN) have risen significantly, forming a combined market capitalisation of over $6.2 billion at the time of writing: comparable to the market cap of DAI or Litecoin.

The three companies will maintain separate teams and managerial independence after the merger; the aim is not necessarily to turn their three software products into one, but rather to unify and strengthen their economic health to facilitate building Artificial Superintelligence.

The new token is to be called the ASI token, representing its goal of helping create Artificial Superintelligence, as the same way as the AGI token aimed at Artificial General Intelligence.

We will have more on this story as it unfolds.

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“Put your hips into it!” researchers tell robots

Researchers at the Shanghai Jiao Tong University have published a new technique for coordinating a robot’s whole body – arms and legs – to improve how it handles real-world objects.

It may seem more obvious to use the legs for one purpose (moving about), and the arm for another (performing the task), but the research showed that better results are achieved if the legs get involved in the manipulation.

The robot used in the research was a quadruped with a single arm, and it was tested picking up 14 different objects at various heights.

Image from the paper 'Visual Whole-Body Control for Legged Loco-Manipulation'

The robot “could operate fully autonomously using only visual input and its proprioception”, rather than using electronic rangefinders or other scanning methodologies. This is comparable to a person picking things up using mostly visual cues and proprioception. The researchers call their method ‘Visual Whole-Body Control’ (VBC), because it is controlled visually and uses the whole body as one piece.

The key to their technique is providing simple goals that govern the whole body together: “Our low-level goal-reaching policy controls the quadruped robot and the mounted arm simultaneously. For the quadruped robot, our low-level policy outputs the target joint angles for all 12 joints of the robot”.

This has an obvious similarity with human movement: you’ll find it easier to crack an egg or hammer a nail if you position your legs right. Surely it’s a good idea to teach robots the same tricks of proper technique that we teach people.

Citation: Liu, Minghuan ; Chen, Zixuan ; Cheng, Xuxin ; Ji, Yandong ; Yang, Ruihan ; Wang, Xiaolong. Visual Whole-Body Control for Legged Loco-Manipulation. eprint (2024). https://arxiv.org/abs/2403.16967 (open access)

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Key ocean current carries serious warnings on climate and extreme heat

Scientists extracted a 5.3 million-year record of the Antarctic Circumpolar Current by drilling sediment cores in the Earth’s most remote waters. Here, the drill ship JOIDES Resolution makes its way through the far southeast Pacific. (credit: Gisela Winckler)

The Antarctic Circumpolar Current carries more than 100 times as much water as all the world’s rivers combined. It reaches from the ocean’s surface to its bottom and 2,000 kilometers across, connecting the three oceans. It also plays a key role in regulating global climate.

It’s the Antarctic Circumpolar Current—the world’s most powerful, consequential mover of water, and has been speeding up. But could it amplify Earth’s warming’s effects?

Gaining speed in warm years

In a new study, published (open-access) in the journal Nature, an international research team found evidence that the current could speed up the loss of Antarctica’s ice, increase sea levels, and possibly affect the ocean’s ability to absorb carbon from the atmosphere.

The team charted the ACC’s relationship to climate over the last 5.3 million years. Their key discovery: its current has been gaining speed in warm years, suggesting that today’s speedup will continue as human-induced warming proceeds.

“This is the mightiest and fastest current on the planet. It is arguably the most important current of the Earth climate system,” said study coauthor Gisela Winckler, a geochemist at Columbia University’s Lamont-Doherty Earth Observatory who co-led the sediment sampling expedition.

Raising global sea levels by about 190 feet

The study “implies that the retreat or collapse of Antarctic ice is mechanistically linked to enhanced ACC flow, a scenario we are observing today under global warming,” she said.

Currently much of the West Antarctic Ice Sheet is frozen to land that is below sea level, so it is highly susceptible to invasion by warm ocean waters. Were it to melt entirely, it would raise global sea levels by about 190 feet.

Holding back the vast interior glaciers

Scientists have observed that winds over the Southern Ocean have increased in strength about 40% in past 40 years. Among other things, this has speeded the ACC and energized large-scale eddies within it that move relatively warm waters from the higher latitudes toward Antarctica’s huge floating ice shelves, which hold back the even vaster interior glaciers.

Their findings provide geological evidence in support of further increasing ACC flow with continued global warming, the researchers write in their paper. “If true, a future increase in ACC flow with warming climate would mark a continuation of the pattern observed in instrumental records, with likely negative consequences.”

Citation: Lamy, F., Winckler, G., Arz, H.W. et al. Five million years of Antarctic Circumpolar Current strength variability. Nature 627, 789–796 (2024). https://doi.org/10.1038/s41586-024-07143-3 (open access)

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Scientists convert CO2 into a new green fuel

Researchers have transformed CO2 (the greatest contributor to global warming) into methanol (AKA “wood alcohol”), a discovery that paves the way for creating new green fuels, they say.

They did this by simply shining sunlight on single atoms of copper deposited on light-activated nanocrystalline carbon nitride.

“Carbon dioxide valorization [assigning value] holds the key for achieving the net-zero ambition of the UK,” said professor Andrei Khlobystov, School of Chemistry, University of Nottingham. “A big advantage of the new catalyst is that it consists of sustainable elements—carbon, nitrogen and copper—all highly abundant on our planet.”

The research was conducted by an international team of researchers from the University of Nottingham’s School of Chemistry, University of Birmingham, University of Queensland and University of Ulm. It has been published in the Sustainable Energy & Fuels journal of the Royal Society of Chemistry

Citation: Tara M LeMercier,   Madasamy Thangamuthu,   Emerson C Kohlrausch,   Yifan Chen,   Craig Stoppiello,   Michael W Fay,   Graham A. Rance,   Gazi N Aliev,   Wolfgang Theis,   Johannes Biskupek,   Ute Kaiser,   Anabel E. Lanterna,   Jesum Alves Fernandes  and  Andrei Khlobystov. Synergy of Nanocrystalline Carbon Nitride with Cu Single Atom Catalyst Leads to Selective Photocatalytic Reduction of CO2 to Methanol. Sustainable Energy & Fuels. 10.1039/D4SE00028E  (open access)

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Secure quantum communication on a global scale now closer

Researchers at the University of Waterloo’s Institute for Quantum Computing (IQC) have efficiently produced nearly perfect entangled photon pairs from quantum dot sources.

Entangled photons are particles of light that remain connected, even across large distances. By combining entanglement with quantum dots, the research team aimed to optimize the process for creating entangled photons.

“The combination … is needed for exciting applications such as quantum key distribution or quantum repeaters, which are envisioned to extend the distance of secure quantum communication to a global scale or link remote quantum computers,” said Dr. Michael Reimer, professor at IQC and Waterloo’s Department of Electrical and Computer Engineering.

“Previous experiments only measured either near-perfect entanglement or high efficiency, but we’re the first to achieve both requirements with a quantum dot.”

This research was recently published in the journal Communications Physics.

Near-perfect entangled photons

By embedding semiconductor quantum dots into a nanowire, the researchers created a source that creates near-perfect entangled photons 65 times more efficiently than previous work.

This new source can be excited with lasers to generate entangled pairs on command. The researchers then used high-resolution single photon detectors to boost the degree of entanglement.

Secure communications

To showcase future communications applications, the researchers used their new quantum dot entanglement source to simulate a secure communications method known as “quantum key distribution”—proving that the quantum dot source holds significant promise in the future of secure quantum communications. 

Citation: Pennacchietti, M., Cunard, B., Nahar, S. et al. Oscillating photonic Bell state from a semiconductor quantum dot for quantum key distribution. Commun Phys 7, 62 (2024). https://doi.org/10.1038/s42005-024-01547-3 (open access)

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AI model can design billions of superbug-fighting antibiotic molecules

Researchers at McMaster University and Stanford University have invented a new generative artificial intelligence model called SyntheMol that can design billions of new antibiotic molecules that are inexpensive and easy to build in the laboratory.  

In a new study, published today in the journal Nature Machine Intelligence, researchers report that SyntheMol can design new antibiotics to stop the spread of Acinetobacter baumannii, which the World Health Organization has identified as one of the world’s most dangerous antibiotic-resistant bacteria. 

A. baumannii can cause pneumonia and meningitis, and infect wounds, all of which can lead to death. Researchers say few treatment options remain. 

Accessing tens of billions of promising molecules

Researchers developed the generative model to access tens of billions of promising molecules quickly and cheaply. They drew from a library of 132,000 molecular fragments, which fit together like Lego pieces but are all very different in nature. 

They then cross-referenced these molecular fragments with a set of 13 chemical reactions, enabling them to identify 30 billion two-way combinations of fragments to design new molecules with the most promising antibacterial properties.

Zappjng world’s most dangerous antibiotic-resistant bacteria

Each of the molecules designed by this model was in turn fed through another AI model trained to predict toxicity. The process yielded six non-toxic molecules that display potent antibacterial activity against A. baumannii.

“Synthemol not only designs novel molecules that are promising drug candidates, but it also generates the recipe for how to make each new molecule. Generating such recipes is a new approach and a game changer because chemists do not know how to make AI-designed molecules,” says James Zou, an associate professor of biomedical data science at Stanford University, who co-authored the paper.

The research is funded in part by the Weston Family Foundation, the Canadian Institutes of Health Research, and Marnix and Mary Heersink.  

Citation: Swanson, K., Liu, G., Catacutan, D.B. et al. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nat Mach Intell 6, 338–353 (2024). https://doi.org/10.1038/s42256-024-00809-7

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Tiny magnetic sensor enables wireless health monitoring

A new miniature sensor developed by Peking University researchers can wirelessly monitor a person’s health data and communicate it in real time without going through the skin.

As noted in the journal Science Advances, the new biocompatible sensor replaces invasive through-the-skin wires, integrated-circuit chips, and cumbersome readout equipment, all of which increase risks of infection and limit portability.

The millimeter-scale, chip-less, and battery-less magnetic implants are paired with a fully integrated wearable device.

According to Peking University lead researcher Han Mengdi, in experiments conducted on rat models, the system provided “continuous, wireless monitoring of a wide range of biophysical and biochemical conditions within living organisms. The conditions include critical health parameters such as cerebrospinal fluid viscosity, intracranial pressure, and glucose levels.”

The study was supported by the National Natural Science Foundation of China; the Emerging Engineering Interdisciplinary Project, Peking University; the Fundamental Research Funds for the Central Universities; and Peking Nanofab Laboratory. 

Citation: Wan, J., Nie, Z., Xu, J., Zhang, Z., Yao, S., Xiang, Z., Lin, X., Lu, Y., Xu, C., Zhao, P., Wang, Y., Zhang, J., Wang, Y., Zhang, S., Wang, J., Man, W., Zhang, M., & Han, M. (2024). Millimeter-scale magnetic implants paired with a fully integrated wearable device for wireless biophysical and biochemical sensing. Science Advances. https://www.science.org/doi/10.1126/sciadv.adm9314 (open-access)

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Climate change will fuel spread of infectious diseases, experts warn

A team of infectious diseases experts has called for more awareness and preparedness in the medical field to deal with the impact of climate change on the spread of diseases.

Their article, published today in medical journal JAMA, raises the alarm about the emergence and spread of harmful pathogens. The authors also urge the medical community to update their education and training and take steps to combat global warming.

“Clinicians need to be ready to deal with the changes in the infectious disease landscape,” said lead author George R. Thompson, a professor at the UC Davis School of Medicine in the Department of Internal Medicine, Division of Infectious Diseases, and the Department of Medical Microbiology and Immunology.

“Learning about the connection between climate change and disease behavior can help guide diagnoses, treatment and prevention of infectious diseases.”

Changing infectious diseases landscape

One type of infectious disease is vector-borne disease, caused by pathogens carried by vectors like mosquitoes, fleas and ticks. Some diseases caused by vectors are dengue, malaria and Zika.

Changing rain patterns are expanding vectors’ range and their active periods. Shorter, warmer winters and longer summers are also linked to more vector-borne diseases. For example, diseases caused by ticks (like babesiosis and Lyme disease) are now occurring in the winter too. They’re also being found in regions farther west and north than in the past.

“We’re seeing cases of tick-borne diseases in January and February,” said first author of the study Matthew Phillips, an infectious diseases fellow at Massachusetts General Hospital and Harvard Medical School. “The tick season is starting earlier and with more active ticks in a wider range. This means that the number of tick bites is going up and with it, the tick-borne diseases.”

Another concern is malaria. The mosquitos that transmit the disease are expanding northward, a climate-induced change. Changing rain patterns have led to more mosquitos and a higher disease transmission rate.

Zoonotic diseases, such as plague and hantavirus (carried by rodents), are also showing changes in incidence  and location. The experts noted changes in animal migration patterns and natural ranges. Due to their habitat loss, wild animals are coming closer to humans. With that comes a higher risk of animal diseases spilling over to humans and for new pathogens to develop.

Fungal infections, storm surges

The study also pointed to the emergence of new fungal infections, such as Candida auris (C. auris), and changes in the location of some fungal pathogens. For example, the fungal infection Coccidioides (also known as Valley fever) was endemic to hot, dry areas in California and Arizona. But Valley fever was recently diagnosed as far north as Washington State.

Changes in rain patterns and coastal water temperature can also affect the spread of waterborne diseases, such as E. coli and Vibrio. According to the team, the sea level is rising, and storm surges and coastal flooding that used to be rare or extreme events are happening more frequently.

Call for medical community to take steps

The team called for stronger measures for infectious disease surveillance and urged medical clinicians to anticipate the changes in infectious disease patterns.

“Clinicians need to be ready to deal with the changes in the infectious disease landscape,” said Thompson. “Learning about the connection between climate change and disease behavior can help guide diagnoses, treatment and prevention of infectious diseases.”

Another concern is malaria. The mosquitos that transmit the disease are expanding northward, a climate-induced change. Changing rain patterns have led to more mosquitos and a higher disease transmission rate.

Zoonotic diseases, such as plague and hantavirus (carried by rodents), are also showing changes in incidence  and location. The experts noted changes in animal migration patterns and natural ranges. Due to their habitat loss, wild animals are coming closer to humans. With that comes a higher risk of animal diseases spilling over to humans and for new pathogens to develop.

The study also pointed to the emergence of new fungal infections, such as Candida auris (C. auris), and changes in the location of some fungal pathogens. For example, the fungal infection Coccidioides (also known as Valley fever) was endemic to hot, dry areas in California and Arizona. But Valley fever was recently diagnosed as far north as Washington State.

Changes in rain patterns and coastal water temperature can also affect the spread of waterborne diseases, such as E. coli and Vibrio. According to the team, the sea level is rising, and storm surges and coastal flooding that used to be rare or extreme events are happening more frequently.

The team called for stronger measures for infectious disease surveillance and urged medical educators to train clinicians to anticipate the changes in infectious disease patterns.

This study was partially supported by National Institutes of Health grants T32AI007061 and 5U19AI166798.

Citation: Matthew C. Phillips, MD, PhD1,2; Regina C. LaRocque, MD, MPH1,2; George R. Thompson III, MD3,4. JAMA. Published online March 20, 2024. Infectious Diseases in a Changing Climate10.1001/jama.2023.27724

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