WHY THIS MATTERS IN BRIEF
Once you digitise something you can analyse it, share it, and run simulations that wouldn’t have otherwise been possible, and in this case that means finding new COVID-19 treatments faster.
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We all hate viruses – both biological and digital versions, especially during a pandemic, and now, in a world first researchers have turned a biological virus into a digital one. That said though, and in the spirit of fairness, not all viruses are bad and some of them do have their uses – such as being turned into molecular assemblers to make Lithium Ion and next generation batteries.
While a virus that makes a battery though is very useful what’s even more useful during today’s COVID-19 pandemic is being able to create a computational model of the entire virus responsible for COVID-19 because to digitise and model it is to understand it – and help develop the vaccines to kill it. Furthermore, the team behind the new model at the University of Chicago have made it publicly available so anyone can use it to aid in their research of the deadly virus.
“If you can understand how a virus works, that’s the first step towards stopping it,” said Prof. Gregory Voth, whose team created the model published in Biophysical Journal. “Each thing you know about the virus’s life cycle and composition is a vulnerability point where you can hit it.”
Voth and his team drew on their previous experience to find the most important characteristics of each individual component of the virus, and drop the “less important” information to make a computational model that is comprehensive but still feasible to run on a computer. This technique is called coarse-graining, which Voth and his students have helped to pioneer.
The simplified framework helps address a key issue in health research: Even though a virus is one of the simpler biological entities, computational modelling is still a major challenge -especially if you want to model any of a virus’s interactions with its host’s body, which would mean representing billions of atoms.
“You could try running an atom-level model of the actual entire virus, but computationally it would bog you down immediately,” Voth said. “You might be able to manage it long enough to model, say, a few hundred nanoseconds worth of movement, but that’s not really long enough to find out the most useful information.”
Thus, many researchers have focused on creating models of individual proteins of the virus. But Voth said that while this segmented process has its uses, it also misses part of the larger picture.
“The virus itself is a holistic thing,” said Voth, a computational scientist and the Haig Papazian Distinguished Service Professor of Chemistry. “In my opinion, you can’t assume you can look at individual parts in isolation. Viruses are more than just the sum of their parts.”
Voth said even though this is the first time anyone’s ever digitised an entire virus his lab has been working for years to model other viruses, such as HIV, and one of the biggest lessons they’ve learned is that multiple parts of the virus work in cooperation with one another. For example, scientists might investigate a drug that binds to the spike proteins on the virus surface to prevent them from attaching to the host’s cells.
“One of the main things you might want to know is, do you need to dose every spike protein for it to work? If not, how low a percentage can you get away with?” Voth said. “This is a key question when you’re trying to create drugs or antibodies, and it’s something you can best understand by looking at the entire virus.”
The model also provides a framework into which scientists can integrate additional information about the SARS-COV-2 virus as soon as new discoveries are made.
Voth hopes that the model will prove useful for coronavirus drug design as well as understanding mutations that may arise, such as the one recently detected in the UK.
“Making a multiscale model of the whole virus and integrating all this information rapidly is a big technological step forward,” Voth said. “I’m really proud of my lab. We did it in record time, really – just a few months. If there is any upside to this pandemic, I hope that it advances our tools to fight viruses beyond COVID-19 – like influenza, HIV and any new coronaviruses that arise in the future.”
Source: University of Chicago