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Source: Pourquoi Docteur as of 14-06-2020

European researchers have launched a research project combining algorithms, biochemistry and molecular screening to identify new molecules to treat Covid-19.

In the search for coronavirus, all strokes are allowed and all angles are studied. European scientists have launched a research project, called Exscalate4CoV (E4C),where they combine algorithms, biochemistry and molecular screening to find a molecule capable of treating Covid-19. This is not a first for researchers, but the complexity of SARS-CoV-2 makes the project more complex than previous work. “Compared to the other viruses we have been working on — for example, the Zika virus — coronavirus is more complex,”Andrea Beccari, a computer scientist at Dompé Farmaceutici in Naples and coordinator of the E4C project, told Euronews. It contains a much larger number of various proteins that have very different biological functions.”

Three million molecules tested per second

The goal of the researchers is to identify molecules that can block the progression of the virus in the human body. To do this, they must draw from the 500 billion molecules available to discover which ones will be the most promising. To help them, researchers rely on supercomputers capable of processing up to 3 million molecules per second. “Computers are essential,”says Beccari,  “because they can work at the same time on the 25 proteins of the virus that are involved in the various mechanisms related to infection, replication and blocking of the immune response. They do all this simultaneously.”

In addition to these machines, researchers rely on supercomputers to generate and analyze experimental 3D protein models and structures inspired by pandemic pathogens. “We are able to identify molecules that could be useful in countering coronavirus: either by looking for them among those that already exist and using the process of ‘repurposing’ (or reuse) as it is called; either by using new libraries of molecules, but by applying the models we have already optimized,”says Carmine Talarico, a computer chemist at Dompé Farmaceutici.

Two days to test the molecule

Once researchers have been able to identify potentially effective molecules against coronavirus, they are analyzed by a team of researchers based at KU Leuven University in Leuven, Belgium. There, a team is studying the effect of these molecules in infected cells. Everything is also going pretty fast since the potential of a molecule can be evaluated in just 48 hours. “These robotic arms take the plates where we grow cells and the virus,”says Johan Neyts, professor of virology at KU Leuven. Then they place them in collection machines with pipettes. After a while, the virus is placed on the cells and then the robotic arms insert them into a 37-degree incubator where they stay for two days. After that, the arms pull out the plates of the incubator and put them in an automated microscope that observes them and monitors if certain compounds block the virus.”

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