The non-coding regions of SARS-CoV-2 RNA play a decisive role in viral replication. Kresten Lindorff-Larsen and Sandro Bottaro of the University of Copenhagen have been using molecular dynamics simulations to predict the structure and dynamics of these regions in the hope that this will enable the development of drugs that target them.
The pandemic has caused us to re-examine many aspects of our lives this year. The CFDforCOVID project, led by Florent Duchaine of CERFACS, has been using fluid dynamics tools usually reserved for aeronautical engines to look at how the virus can spread in enclosed environments such as buildings and vehicles, with the aim of helping to turn them into safer spaces that reduce viral transmission.
Modelling how infectious diseases spread is a complex process that involves not only understanding the virus itself, but also the behaviour of the people who are transmitting it. Rafael Villanueva of the Polytechnic University of Valencia has been leading a project that aims to ramp up the capabilities of his network models to provide a deeper understanding of the COVID-19 pandemic and eventually provide advice on the best vaccination strategies for the near future.
Molecular dynamics simulations allow us to see into the hidden atomic-scale world that makes up everything we see. Understanding SARS-CoV-2 at this level is helping Vangelis Daskalakis of the Cyprus University of Technology to identify weaknesses in the virus that can be exploited and targeted through drugs and vaccines.
Catalan-based company Mitiga Solutions uses supercomputers to provide early warnings to governments and business about natural hazards. Its recent foray into providing such information about infectious diseases has come at a time when the world needs it most, and it is now using PRACE resources to refine its methods for use on a global scale.
Irish company Nuritas has carved itself a niche in the world of drug discovery with its AI platform that analyses the therapeutic potential of thousands of naturally-occurring peptide sequences. With the onset of the COVID-19 pandemic, they are now putting all of their efforts into discovering peptides that can be used to mitigate the disease’s progression.
Molecular dynamics simulations are one of the best methods for quickly understanding the mechanisms of SARS-CoV-2. A project led by Modesto Orozco of the Spanish Institute for Research in Biomedicine is investigating the evolutionary path of the virus from bats to humans, forecasting human sensitivity to infection, and looking at the impact of viral mutations on infectivity.
Glycan shields allow viruses to hide from their host’s immune system. In SARS-CoV-2, however, it seems that they may also play a critical role in gaining access to the cell, without which the virus would be rendered harmless. Elisa Fadda of Maynooth University has been using molecular dynamics simulations to examine these complex carbohydrates in more detail.
The spike protein of SARS-CoV-2 has been the focus of a huge collective effort in computational research to fight the COVID-19 pandemic. It is crucial to the virus’s function, and also represents the best target for treating the disease. Gerhard Hummer of the Max Planck Institute of Biophysics has been leading a project that aims to elucidate the structure and dynamics of this infamous protein.
Getting new drugs approved is a lengthy process and so, in the fight against COVID-19, our best hope is to use ones that have already been approved. Vittorio Limongelli and his group from the University of Lugano USI are using their world-leading computational methodologies to identify the best candidates for the job against a number of molecular targets.