University College London researchers are to use supercomputers to support ‘urgent investigations’ into COVID-19 disease.
The aim is to be able to accelerate the development of vaccines and antiviral drugs by using the most powerful supercomputers commonly used for high intensive tasks such as quantum mechanics and climate research.
A consortium led by Professor Peter Coveney and his colleagues at the UCL Centre for Computational Science are backed by hundreds of researchers.
The study will look into detailed aspects of the disease to focus on five areas:
- Identifying new antiviral drugs by screening libraries of potential drugs, including those that have already been licensed to treat other diseases.
- Accelerating vaccine development by identifying virus proteins or parts of protein that stimulate immunity.
- Studying the spread of the virus within communities.
- Analysing the origin and structure of the SARS-CoV-2 genome.
- Studying how the SARS-CoV-2 virus interacts with human cells to turn them into virus factories.
The supercomputers being utilised are at the Argonne Leadership Computing Facility, Brookhaven, the Texas Advanced Computing Centre, Oak Ridge – where one of the world’s most powerful supercomputers is based, the San Diego Supercomputing Centre, the Gauss Centre for Supercomputing at Leibniz Rechenzentrum, and the Hartree Centre.
The supercomputers are being used to screen libraries of drug compounds for those capable of binding to the spikes on the coronavirus. The spikes on the virus are used to invade cells and so the idea is to neutralise the spikes to prevent the virus infecting human cells.
Professor Coveney (UCL Chemistry), said “We are using the immense power of supercomputers to rapidly search vast numbers of potential compounds that could inhibit the novel coronavirus, and using the same computers again, but with different algorithms, to refine that list to the compounds with the best binding affinity.”
“That way, we are identifying the most promising compounds ahead of further investigations in a traditional laboratory to find the most effective treatment or vaccination for COVID-19.”
“We are able to scan existing drug libraries, so many of the compounds we are looking at already have approval for use in humans as they are used to treat existing diseases so could be repositioned to target COVID-19.”
“We are also able to computer generate new compounds that should bind well to the virus, which gives us a fantastic head start on discovering potential new drugs.”
Compounds selected for screening include herbal medicines, chemicals, and other natural products that have already been studied in humans or are already approved drugs.
The scanning by the supercomputers takes days and not months as a regular computer would take.
“This is a much quicker way of finding suitable treatments than the typical drug development process. It normally takes pharma companies 12 years and $2 billion to take one drug from discovery to market but we are rewriting the rules by using powerful computers to find a needle in a haystack in a fraction of that time and cost,” he added.
“Supercomputers are a remarkable resource for the development of COVID-19 treatments as they can identify possible treatments through a variety of ways including machine learning, complex molecular dynamics and artificial intelligence methods.”
“Not only do we need to find molecules that bind to the spikes on the coronavirus, but we also need to model how well these bind when we know the spikes move around.”
