June 16, 2020 — The EU’s war against COVID-19 continues and PRACE awarded another ten projects with a total of 227 578,000 core hours under the Fast Track Call for Proposals to support the mitigation of the impact of the pandemic.

With the accumulation of knowledge about this novel coronavirus, scientists are discovering new possibilities and tools to exploit its weaknesses and PRACE offers the most powerful supercomputers for their breakthroughs.

The main goal of these studies is to find ways to block the coronavirus and stop its replication in human cells, how to create more intelligent therapies, drug repositioning, anti-viral drugs, and of course, vaccines. And also, how to improve tests, how to make them more accurate, how to obtain novel and better SARS-CoV-2 therapeutics and diagnostics based on antibodies.

Moreover, the scientists will use world-class computational power to create simulations to find adequate levels of oxygen and carbon dioxide for each patient according to their condition and comorbidities. Setting these levels correctly is currently one of the main problems in treatment.

One of the PRACE-awarded studies will pinpoint the weaknesses of the lysosomal-endosomal TPC2 ion channels. This system in our cells is involved in different diseases, such as cancer, Parkinson, and viral infections. Now for the first time, it will be studied in more detail and possibly achieve important breakthroughs.

Several projects make the structure and screening results of targets in the virus such as 3CLpro, Spike, nsp1, RNA-dependent RNA polymerase, etc. visible, clarify their functions, and how they can be blocked with various compounds and tools.

To find all these answers and to make new discoveries scientists need to use different libraries with tens of millions of compounds, including ZINK drug database, Molport, SPECS, a database of natural products, etc. The teams will work with viral proteins at the all-atom resolution, they will use molecular dynamics simulations, metadynamics, quantum and molecular mechanics, X-ray crystallography, cryo electron microscopy, nanoparticle detectors, as well as virtual ligand screening, virtual drug design, and other powerful instruments and techniques. The speed and efficiency of these techniques is greatly helped by the huge supercomputing power PRACE provides to the research community.

The PRACE Fast Track Call for Proposals aims to speed up the process from application to outcome. Below is a quick outline of the work each project will undertake.

• A computational study of the reactivity in the main protease of SARS-CoV-2 to guide the design of inhibitors
• Identification of inhibitors of SARS-CoV-2 S
• AccorCOVIDYNdion Title
• Epitope vaccines based on the dynamics of mutated SARS-CoV-2 proteins at all-atom resolution
• A Computational study to guide the development of new SARS-CoV-2 detection hyper-spectral platforms
• SPIKE-CAP – Blocking SARS-CoV-2 Spike protein through Computer-Aided design of Peptide inhibitors
• Targeting the Lysosome-Endosome system to avoid virus entry/exit in cells
• Biomechanic simulations for quantification of the ventilation/perfusion ratio in COVID-19 patients
• Identification and Design of drugs interfering with the host translational inhibitor nsp1 of SARS-CoV2
• A drug discovery project against the main protease of COVID-19

This article is a summary of the second ten projects that were awarded under the PRACE Fast Track Call for Proposals to mitigate the impact of the COVID-19 pandemic. The summary article of the first ten awarded projects can be found here.

For a summary  of all projects and the full announcement, visit https://prace-ri.eu/the-net-is-closing-prace-awards-ten-further-projects-in-the-hunt-for-a-cure-for-covid-19/

About PRACE 

The mission of PRACE (Partnership for Advanced Computing in Europe) is to enable high-impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society. PRACE seeks to realise this mission by offering world class computing and data management resources and services through a peer review process. PRACE also seeks to strengthen the European users of HPC in industry through various initiatives. PRACE has a strong interest in improving energy efficiency of computing systems and reducing their environmental impact.

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Source: PRACE