esearchers have detailed a mechanism in the distinctive corona of Covid-19 that could help scientists to rapidly find new treatments for the virus, and quickly test whether existing treatments are likely to work with mutated versions as they develop.
The team, led by the University of Warwick as part of the EUTOPIA community of European universities, have simulated movements in nearly 300 protein structures of the Covid-19 virus spike protein by using computational modelling techniques, in an effort to help identify promising drug targets for the virus.
In a new paper published today (19 February) in the journal Scientific Reports, the team of physicists and life scientists detail the methods they used to model the flexibility and dynamics of all 287 protein structures for the Covid-19 virus, also known as SARS-CoV-2, identified so far. Just like organisms, viruses are composed of proteins, large biomolecules that perform a variety of functions. The scientists believe that one method for treating the virus could be interfering with the mobility of those proteins.
They have made their data, movies and structural information, detailing how the proteins move and how they deform, for all 287 protein structures for Covid-19 that were available at the time of the study, publicly accessible to allow others to investigate potential avenues for treatments.
The researchers focused particular efforts on a part of the virus known as the spike protein, also called the Covid-19 echo domain structure, which forms the extended corona that gives coronaviruses their name. This spike is what allows the virus to attach itself to the ACE2 enzyme in human cell membranes, through which it causes the symptoms of Covid-19.
The spike protein is in fact a homotrimer, or three of the same type of protein combined. By modelling the movements of the proteins in the spike, the researchers identified a ‘hinge’ mechanism that allows the spike to hook onto a cell, and also opens up a tunnel in the virus that is a likely means of delivering the infection to the hooked cell. The scientists suggest that by finding a suitable molecule to block the mechanism – literally, by inserting a suitably sized and shaped molecule – pharmaceutical scientists will be able to quickly identify existing drugs that could be effective against the virus.
Lead author Professor Rudolf Roemer from the Department of Physics at the University of Warwick, who conducted the work while on a sabbatical at CY Cergy-Paris Université, said: “Knowing how this mechanism works is one way in which you can stop the virus, and in our study we are the first to see the detailed movement of opening. Now that you know what the range of this movement is, you can figure out what can block it.
“All those people who are interested in checking whether the protein structures in the virus could be drug targets should be able to examine this and see if the dynamics that we compute are useful to them.
“We couldn’t look closely at all the 287 proteins though in the time available. People should use the motion that we observe as a starting point for their own development of drug targets. If you find an interesting motion for a particular protein structure in our data, you can use that as the basis for further modelling or experimental studies.”
To investigate the proteins’ movements, the scientists used a protein flexibility modelling approach…
Image Credit: University of Warwick
Post by Amanda Scott, NA CEO. Follow her on twitter @tantriclens
Thanks to Heinz V. Hoenen. Follow him on twitter: @HeinzVHoenen
News
Fake Science Is Growing Faster Than Legitimate Research, New Study Warns
New research reveals organized networks linking paper mills, intermediaries, and compromised academic journals Organized scientific fraud is becoming increasingly common, ranging from fabricated research to the buying and selling of authorship and citations, according [...]
Scientists Unlock a New Way to Hear the Brain’s Hidden Language
Scientists can finally hear the brain’s quietest messages—unlocking the hidden code behind how neurons think, decide, and remember. Scientists have created a new protein that can capture the incoming chemical signals received by brain [...]
Does being infected or vaccinated first influence COVID-19 immunity?
A new study analyzing the immune response to COVID-19 in a Catalan cohort of health workers sheds light on an important question: does it matter whether a person was first infected or first vaccinated? [...]
We May Never Know if AI Is Conscious, Says Cambridge Philosopher
As claims about conscious AI grow louder, a Cambridge philosopher argues that we lack the evidence to know whether machines can truly be conscious, let alone morally significant. A philosopher at the University of [...]
AI Helped Scientists Stop a Virus With One Tiny Change
Using AI, researchers identified one tiny molecular interaction that viruses need to infect cells. Disrupting it stopped the virus before infection could begin. Washington State University scientists have uncovered a method to interfere with a key [...]
Deadly Hospital Fungus May Finally Have a Weakness
A deadly, drug-resistant hospital fungus may finally have a weakness—and scientists think they’ve found it. Researchers have identified a genetic process that could open the door to new treatments for a dangerous fungal infection [...]
Fever-Proof Bird Flu Variant Could Fuel the Next Pandemic
Bird flu viruses present a significant risk to humans because they can continue replicating at temperatures higher than a typical fever. Fever is one of the body’s main tools for slowing or stopping viral [...]
What could the future of nanoscience look like?
Society has a lot to thank for nanoscience. From improved health monitoring to reducing the size of electronics, scientists’ ability to delve deeper and better understand chemistry at the nanoscale has opened up numerous [...]
Scientists Melt Cancer’s Hidden “Power Hubs” and Stop Tumor Growth
Researchers discovered that in a rare kidney cancer, RNA builds droplet-like hubs that act as growth control centers inside tumor cells. By engineering a molecular switch to dissolve these hubs, they were able to halt cancer [...]
Platelet-inspired nanoparticles could improve treatment of inflammatory diseases
Scientists have developed platelet-inspired nanoparticles that deliver anti-inflammatory drugs directly to brain-computer interface implants, doubling their effectiveness. Scientists have found a way to improve the performance of brain-computer interface (BCI) electrodes by delivering anti-inflammatory drugs directly [...]
After 150 years, a new chapter in cancer therapy is finally beginning
For decades, researchers have been looking for ways to destroy cancer cells in a targeted manner without further weakening the body. But for many patients whose immune system is severely impaired by chemotherapy or radiation, [...]
Older chemical libraries show promise for fighting resistant strains of COVID-19 virus
SARS‑CoV‑2, the virus that causes COVID-19, continues to mutate, with some newer strains becoming less responsive to current antiviral treatments like Paxlovid. Now, University of California San Diego scientists and an international team of [...]
Lower doses of immunotherapy for skin cancer give better results, study suggests
According to a new study, lower doses of approved immunotherapy for malignant melanoma can give better results against tumors, while reducing side effects. This is reported by researchers at Karolinska Institutet in the Journal of the National [...]
Researchers highlight five pathways through which microplastics can harm the brain
Microplastics could be fueling neurodegenerative diseases like Alzheimer's and Parkinson's, with a new study highlighting five ways microplastics can trigger inflammation and damage in the brain. More than 57 million people live with dementia, [...]
Tiny Metal Nanodots Obliterate Cancer Cells While Largely Sparing Healthy Tissue
Scientists have developed tiny metal-oxide particles that push cancer cells past their stress limits while sparing healthy tissue. An international team led by RMIT University has developed tiny particles called nanodots, crafted from a metallic compound, [...]
Gold Nanoclusters Could Supercharge Quantum Computers
Researchers found that gold “super atoms” can behave like the atoms in top-tier quantum systems—only far easier to scale. These tiny clusters can be customized at the molecular level, offering a powerful, tunable foundation [...]
