How exactly do coronavirus hijack and reprogram human cells to cause disease and kill?
This issue has troubled Nevan Krogan since February, when the UCSF virus expert and his colleagues realized that before many people, the situation in the United States would soon become very bad.
Since then, this problem has become more urgent. In the past four months, Krogan and the expanding team of scientific partners in San Francisco and around the world have reversed their laboratories and opened up the possibility. Point out the cure.
They have built an innovative system that can quickly generate clues about viral weaknesses, and use these clues to search the huge drug database for existing drugs that may prevent their development. First, they assembled the first picture of the internal workings of the virus, using the picture to identify 10 compounds that killed the virus in laboratory tests and could eventually become a drug for COVID-19.
Now, the team led by UCSF has used similar techniques to explore the biological characteristics of the virus at a deeper level, thereby marking new drug candidates that work through different and powerful mechanisms.
This time, scientists took photos of the virus infected host cells, providing the first clear visual images of deadly pathogens at work-and exposed the weird cell structures created by the virus, which have never been seen before. May help explain why it is so contagious.
Krogan, a research fellow at the Gladstone Institute, a molecular biologist at the University of California, San Francisco, who leads a large research team, said: “The more you know about this organism, the more you can fight it.” “So, We are trying to understand as much as possible about how the virus infects us.”
Krogan leads the Institute of Quantitative Biological Sciences at the University of California, San Francisco School of Pharmacy, which consists of 100 research laboratories that often collaborate on projects to generate large amounts of biological data and screen these data Set to find clues to fight the disease.
The new discovery is expected to be published in the famous “Cell” magazine on Saturday, which was developed by 22 QBI laboratories working together to focus on the virus. The research organization called QBI COVID-19 Research Group (QCRG for short) attracted 80 scientists from four countries to participate in the project, and the UCSF and Icahn School of Medicine at Mount Sinai in New York, the Pasteur Institute in Paris, Germany The University of Freiburg and the European Molecular Biology Laboratory in Cambridge, UK.
These findings were a sensation following the innovative research that began in March, and QCRG began to publish a surprising set of results published in Nature in late April.
The core of the project is the “protein-protein” map: by combining human own proteins with human proteins, we can fully understand how viruses occupy human cells. The virus cannot survive on its own. They need host cells to reproduce. The figure reveals 332 different protein-protein interactions-a lot of information about virus vulnerabilities.
Scientists at the University of California, San Francisco said that the new study highlighted in the “Cell” magazine carried out more in-depth research on the map, while expanding the knowledge of the virus.
This time, they explored the virus’ ability to manipulate a powerful biological process called phosphorylation.
During the phosphorylation process—viral or virus-free has always occurred inside the cell—some chemicals are added to or removed from the protein, thereby slightly changing their structure. Because proteins are the microscopic forces of cells, they build tissues and trigger chemical reactions that control various body functions. Therefore, these seemingly small changes will have a major impact on the way proteins work, giving them new functions. Therefore, phosphorylation is like a shortcut to reconnect biology. You don’t need to make brand-new protein to get the job done; you only need to add or shred a small piece of existing protein.
The tools for adhesion and shredding are a class of about 500 kinds of proteins called kinases, which have a powerful impact on human growth, stem cell renewal, the immune system, and memory and learning.
“They are unbelievable in signal processing,” said Kevan Shokat, a chemist at the University of California, San Francisco who has studied kinases for 25 years. He described them as a control system, such as a silicon gate on a computer chip or a traffic signal in a city: kinases appear throughout the cell, regulating the flow of structure and information.
Kinase is also “prone to drugs”, Krogan said. “Many anti-cancer drugs target kinases.”
Scientists do not yet understand how kinases work. But they know a lot. Decades ago, the University of California, San Francisco made significant progress, allowing researchers Michael Bishop and Harold Varmus to win the 1989 Nobel Prize in Medicine. This discovery opened up a new world of drugs, namely kinase inhibitors that block kinases, and such kinases are called kinase inhibitors. Since then, the US Food and Drug Administration has approved about 50 such drugs for combating a variety of diseases, mainly cancer, and thousands of others are in the experimental stage.
“It’s amazing that a discovery can catalyze.” “Shockart said.” “We want this virus to be the same.”
Beginning in March, scientists at the University of California, San Francisco speculated that coronaviruses are using kinases to cause damage in the human body-to seize human proteins and reconnect them for viral bidding.
The researchers believe that if they can learn more about how the virus “talks” to kinases, then they can find drugs that silence the virus.
A few months ago, when the UCSF group created a protein map, they used only one viral fragment at a time instead of the entire virus to analyze one viral protein.
This time, starting in April, they began to infect host cells with live virus. Then, once the infection raged on the laboratory plate, the scientists looked up at the virus fundamentally and analyzed the host cells by analyzing the host protein (when the intruder changed it) to observe the virus infection. Host cell.
To select these proteins from the mixture and understand the viruses at work, the team relied on a machine called a mass spectrometer to determine the identity and abundance of the proteins. The fire hoses of protein data quickly flowed out of the mass spectrometer, screening all the data, and scientists began to pick out the specific kinases that the virus seems to be weaponizing. If a cell is like a city, it is as if the team is floating above the city grid at night and sees many signal lights (kinases) all flashing green or red at the same time.
On several streets, most lights are green, which means the virus may be activating these areas to perform work that may harm the host. A kinase called casein kinase II rules a seemingly particularly active street, and this kinase happens to be one of the 332 proteins marked in the team’s early protein map.
As clues from mass spectrometers continue to accumulate, UCSF researchers have collaborated with scientists in Germany and Montana to use ultra-large close-up shots of virus-operated host cells using powerful electron microscopes.
When the research team looked at the photos, they were shocked: the surface of the host cells was filled with thin, finger-like lines, called filamentous pseudopods-sharp little straws, which usually did not exist, but were made by viruses. They poked out the inside of the infected cells, cut holes in the membrane, and opened a tunnel to the outside.
Observing carefully and conducting more tests, scientists began to feel excited because the virus is doing unexpected things.
Usually, the way viruses spread is to turn infected cells into virus factories. The cells are filled with viral replicas, such as water balloons, which eventually rupture and release viral particles. However, the filamentous pseudopods seem to indicate that the virus has devised another method to promote infection: after replicating itself in the host cell (but before the cell ruptures), the virus escapes through the filamentous pseudopods from the infected cells Cells that pierce out and are uninfected nearby make the virus swim from one cell to another.
Similar silk foot disease has been found in other viruses (such as smallpox), but Crogan said that this level of virus has never been found. Tests and electron micrographs show that these filamentous pseudopods are filled with copies of coronavirus and casein kinase II. Photos taken by Elizabeth Fischer, the head of the Microscopy Department of the Rocky Mountain Laboratory and scientists at the University of Freiburg, show that the virus is “sprouting” from the filiform pseudopod and is incredible Yes, some filamentous pseudopodia can even branch. Just like trees, a single chain is allowed to make holes in two units at a time.
When talking about these photos, Krogan said: “It has a biological significance, calling them “the most fascinating and terrifying thing I have ever seen.” “
He added: “It is incredible what this virus can do.”
Now that scientists have a better understanding of which kinases the virus is manipulating, they browse the database of existing drugs and experimental compounds to discover that chemicals that may inhibit those specific kinases will one day become anti-COVID-19 drug.
They identified 87 potentially effective kinase inhibitors, including 10 kinase inhibitors that have been approved by the FDA for the treatment of other diseases, 53 inhibitors that are being tested in human trials, and 24 “preclinical” agents that have not been provided to humans “Inhibitor. Shokat happened to save thousands of kinase inhibitors in UCSF’s freezer (Krogan called it the “world’s largest freezer” for such molecules), and they selected 68 candidates from 87 lists to deal with this A virus for testing. laboratory.
The tests were conducted by virologists at Mount Sinai and the Pasteur Institute, who infected the host cells with viruses and added kinase inhibitors. Will they kill the virus? Will they turn the cellular traffic lights from green to red to stop harmful kinases?
In the end, out of 68 candidates, more than 12 looked promising. The research team narrowed the list to seven or eight particularly powerful lists, including a list that blocks casein kinase II. Five drugs have shown greater lethality in the laboratory environment than ramcivir, which is currently the only antiviral drug available for emergency use by some patients (in addition, a drug called dexamethasone has been discovered Steroids can reduce COVID-19 mortality).
Scientists still do not understand how coronaviruses infect cells. They want to understand why the virus chooses and uses certain kinases; they are also not sure if filamentous pseudopods will stop forming after casein kinase II blockade. As for the candidate drugs marked in the new paper, they must be tested in human trials to see if they are safe and effective for patients with COVID-19.
But Krogan said he is optimistic that some people will succeed. According to recent statistics from Natural Biotechnology, the research work led by the University of California, San Francisco has spawned more than a dozen clinical trials of potential COVID-19 therapies. Eventually, if the trial goes smoothly, some of these drugs can be used in combination with ramcivir to produce COVID-19 cocktail therapy.
Crogan said: “I have absolutely no doubt that there is a cocktail there that can cure this problem.” “Just: can we be smart enough and find it fast enough?”
Jason Fagone is a contributor to the San Francisco Chronicle. Email: firstname.lastname@example.org Twitter: @jfagone