Hand washing, disinfection, self-isolation and social distancing – these are words we hear in recent weeks, probably more often than anytime in modern times.
Indeed, observing precautions, a person can protect himself and other people, such as colleagues and family from being infected with the novel coronavirus.
For the most part that seems to be the extent of our arsenal against the coronavirus – or is it?
The authors of the research project Folding @ home said that anyone can help them in creating a medicine against coronavirus.
All that is required is to install a special program on a laptop or desktop computer. It was developed by scientists from Stanford University and has been used in medical research for 20 years (for example, it is used to search for drugs for Parkinson’s disease, cancer, HIV).
It is clarified that the Folding @ home application runs in the background and is available for users of the Windows and macOS operating systems.
Computational resources are used to model the folding of protein molecules.
As experts explain, proteins are molecular machines that perform many functions. They consist of a linear chain of amino acids, which in many cases spontaneously fold (or collapse) into compact functional structures. Exactly how the components of the protein are located and move determines its function.
COVID-19 was not created in the laboratory
An international scientific team has confirmed that the new SARS-CoV-2 coronavirus responsible for the outbreak of the infectious disease COVID-19 was not created in the laboratory.
“By comparing the available genome sequence data for known strains of coronavirus, we can firmly determine that SARS-CoV-2 arose as a result of natural processes”Kristian Andersen of the Scripps Research Institute.
What are you?
The researchers started with data obtained by Chinese colleagues: shortly after the outbreak in Wuhan, and they proceeded to “decrypt” the SARS-CoV-2 gene.
Studying the molecular structure of the virus, the authors focused on several characteristic features.
On the surface of the coronavirus there are spine-shaped structures resembling the a crown. This crown feature is what gives the coronavirus its name, as corona in Latin means crown. These structures making up the corona contain receptor-binding proteins to which transmembrane cell receptors respond.
According to experts, the entry of the virus into the cell provides a receptor binding domain (RBD) and a cleavage site to bond with.
There are 2 important components in the virus binding with the host cell. The first is a kind of hook that captures the host cells, and the second is a molecular “master key” that allows the virus to break open the “door” to the cell.
By studying the genetic sequences of SARS-CoV-2, the team found that the RBD portions of its spike proteins evolved to more efficiently act on a receptor known as angiotensin converting enzyme 2 (ACE2). This receptor is the portal to the cell that breaks the virus.
Protein SARS-CoV-2 was so effective in this regard that scientists had no doubt: this is the result of natural selection, and not genetic engineering.
This conclusion is supported by an analysis of the overall molecular structure of SARS-CoV-2. As scientists explain, if someone tried to create a new coronavirus, it would be necessary to modify some other virus that causes one or another disease in a person.
However, the team found that the “skeleton” of SARS-CoV-2 is significantly different from that of the already known “human” coronaviruses. In this regard, the new pathogen is most similar to the related viruses found in bats.
“These two features of the virus – mutations in the RBD part of the protein of its spikes and its special” skeleton “- exclude that SARS-CoV-2 was the result of manipulations in the laboratory”Kristian Andersen of the Scripps Research Institute.
How to “Hack” the virus
Viruses have proteins necessary for both cloning itself and the suppression of the host immune system. If you understand how they work, you can create effective medicines.
As already established, coronavirus has specific proteins that bind to a receptor called ACE2 and “open the door” to the cell.
To prevent this penetration with hacking, you must first study the structure of the protein and find its weak point.
In fact, there are many experimental methods for determining protein structures. But the problem is that in most cases you can get only one “snapshot”. And the protein, meanwhile, has many moving parts that need to be observed in action.
Computer simulation helps to fight viruses
For this, the team uses computer simulation. Taking experimental structures as a starting point, the program simulates the movement of all atoms in a protein. By the way, such a technique has already helped to find the Achilles heel of the Ebola virus.
“The data you help us generate will be quickly and openly disseminated through open scientific collaboration across many laboratories around the world”project manager Greg Bowman, a biochemist at the University of Washington in St. Louis.
According to scientists, after installing the application, the user does not have to do anything. Unless to select the item “Any disease” in the interface. Simulations related to COVID-19 are now a priority, although it is possible that the program will start modeling in other studies.
Volunteers can, at their discretion, start and stop the application, or make it automatically pause and resume work when the computer is not in use.
“These are huge calculations, and everyone can help a bit. Each simulation you run is like buying a lottery ticket. The more tickets we buy, the more chances we have to win the jackpot.”Greg Bowman