First open source all-atom models of COVID-19 protein developed

Agencies
June 22, 2020

A team of scientists has produced first open source all-atom models of full-length COVID-19 Spike protein that facilitates viral entry into host cells – a discovery that can facilitate a faster vaccine and antiviral drug development.

The group from Seoul National University in South Korea, University of Cambridge in the UK and Lehigh University in the US produced the first open-source all-atom models of a full-length S protein.

The researchers say this is of particular importance because the S protein plays a central role in viral entry into cells, making it a main target for vaccine and antiviral drug development.

"Our models are the first full-length SARS-CoV-2 spike (S) protein models that are available to other scientists," said Wonpil Im, a professor in Lehigh University.

"Our team spent days and nights to build these models very carefully from the known cryo-EM structure portions. Modeling was very challenging because there were many regions where simple modeling failed to provide high-quality models," he wrote in a paper published in The Journal of Physical Chemistry B.

Scientists can use the models to conduct innovative and novel simulation research for the prevention and treatment of Covid-19.

Though the coronavirus uses many different proteins to replicate and invade cells, the Spike protein is the major surface protein that it uses to bind to a receptor.

The total number of global COVID-19 cases was nearing 9 million, while the deaths have increased to over 467,000, according to the Johns Hopkins University.

With 2,279,306 cases and 119,967 deaths, the US continues with the world's highest number of COVID-19 infections and fatalities, according to the CSSE.

Brazil comes in the second place with 1,083,341 infections and 50,591 deaths.

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News Network
February 21,2020

Washington, Feb 21: The fat around arteries may play an important role in keeping the blood vessels healthy, according to a study in rats that may affect how researchers test for treatments related to plaque buildup, as seen in conditions leading to heart attack.

The study, published in the journal Scientific Reports, noted that the fat, known as perivascular adipose tissue, or PVAT, helps arteries let go of muscular tension while under constant strain.

According to the researchers, including Stephanie W. Watts from the Michigan State University in the US, this feature is similar to how the bladder expands to accommodate more liquid, while at the same time keeping it from spilling out.

"In our study, PVAT reduced the tension that blood vessels experience when stretched," Watts said.

"And that's a good thing, because the vessel then expends less energy. It's not under as much stress," she added.

According to Watts and her team, PVAT has largely been ignored by researchers believing its main job was to store lipids and do little more.

Until now, she said, scientists only divided blood vessels into three parts, the innermost layer called the tunica intima, the middle layer called the tunica media, and the outermost layer called the tunica adventitia.

Watts believes PVAT is the fourth layer, which others have called tunica adiposa.

Tunica, she said, meant a membranous sheath enveloping or lining an organ, and adiposa is a synonym for fat.

"For years, we ignored this layer -- in the lab it was thrown out. In the clinic it wasn't imaged. But now we're discovering it may be integral to our blood vessels," Watts said.

"Our finding redefines what the functional blood vessels are, and is part of what can be dysfunctional in diseases that afflict us, including hypertension. We need to pay attention to this layer of a blood vessel because it does far more than we originally thought," she added.

Earlier studies, Watts said, had shown that PVAT plays a role in the functioning of blood vessels, finding that it secretes substances that can cause blood vessels to relax as well as substances that can cause it to contract.

In the current study, the researchers decided to test whether PVAT provides a structural benefit to arteries by assisting the function of stress relaxation.

They tested the thoracic aorta in rats, and found those with intact PVAT had more stress relaxation than those without.

The study revealed that the pieces of artery with surrounding fat had measurably relaxed more than those without.

Watts and her colleagues then tested other arteries, and were able to duplicate the same response.

"It's not something you see only in this particular vessel or this particular species or this particular strain. But that maybe it's a general phenomenon," she said.

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Agencies
May 30,2020

Drinking coffee may help reduce the risk of certain digestive disorders, including gallstone disease and pancreatitis, a new study has suggested.

The study from the Institute for Scientific Information on Coffee (ISIC) also highlighted other beneficial effects that coffee consumption may have on the process of digestion, including supporting gut microflora and promoting gut motility.

"Data indicates benefits against common digestive complaints such as constipation, as well as a potential reduction in the risk of more serious conditions like chronic liver diseases," said study author Carlo La Vecchia from the University of Milan in Italy.

Gallstone disease is a common digestive disorder, caused by the accumulation of gallstones in the gallbladder or bile duct, which affects approximately 10-15 per cent of the adult population.

While the mechanism by which coffee may protect against gallstone disease is not yet known, it has been observed that the risk for the condition declines with increasing daily consumption of coffee, the researchers said.

Caffeine is thought to play a role in these associations, as the same effect is not observed with decaffeinated coffee.

A common question among consumers and focus area for research is whether coffee is associated with heartburn or gastro-oesophageal reflux disease (GORD).

While a small number of studies have suggested an association between coffee drinking and GORD, the majority of studies reviewed suggest that coffee is not a major trigger of these conditions.

The report also reviewed a growing area of health and nutrition research, namely: the effect of coffee on the gut microflora (microorganism populations).

Recent studies suggest that populations of the beneficial gut bacteria Bifidobacterium spp, increase after drinking coffee.

The findings showed the dietary fibre and polyphenols found in coffee, support the healthy growth of microflora populations.

Additional research findings highlighted that coffee consumption is thought to stimulate digestion by encouraging the release of gastric acid, bile and pancreatic secretions.

Coffee is one of the most widely researched components of the diet, and its effect on digestion remains a growing area of research, the researchers noted.

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Agencies
June 4,2020

The World Health Organisation on Wednesday said that anti-malarial drug hydroxychloroquine (HCQ) will return to the solidarity trial for the potential treatment of coronavirus disease.

At a press conference in the WHO headquarters in Geneva, Director General Tedros Adhanom Ghebreyesus said: "On the basis of the available mortality data, the members of the committee recommended that there are no reasons to modify the trial protocol. The Executive Group received this recommendation and endorsed continuation of all arms of the solidarity trial, including hydroxychloroquine."

The world health body had temporarily suspended the usage of HCQ from the solidarity trial for coronavirus treatment on May 25 soon after a study published in one of the most reliable medical journals, which had suggested that the drug could cause more fatalities among COVID-19 patients.

However, the WHO chief said that the decision was taken as a precaution while the safety data was reviewed.

Ghebreyesus also said that the Data Safety and Monitoring Committee will continue to closely monitor the safety of all therapeutics being tested in the solidarity trial.

"So far, more than 3,500 patients have been recruited in 35 countries. WHO is committed to accelerating the development of effective therapeutics, vaccines and diagnostics as part of our commitment to serving the world with science, solutions and solidarity," he said.

Soon after HCQ was suspended from the trial, the Indian government had said that the antimalarial drug has been known for its benefits for a long time and its usage will be continued on the frontline workers, including police and healthcare professionals, as prophylaxis. The government had also said that studies were being conducted and the drug would be included in the clinical trial also for the treatment of coronavirus disease.

US President Donald Trump also had strongly advocated the use of HCQ and called it a "game-changer". He went to the extent of saying that he had taken the medicine.

Launched by WHO and partners, solidarity trial is an international clinical trial to find an effective treatment for COVID-19, including drugs to slow the progression of the disease or improve survival. The trial, which enrols patients from different countries, "will compare four treatment options against standard of care to assess their relative effectiveness against COVID-19", said WHO. 

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