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EU Funds Exscalate supercomputing platform to fight coronavirus

Today the European Commission allocated new funding to the Exscalate (E4C) consortium for projects to counter the Coronavirus pandemic and improve the management and care of patients. As part of the effort, the E4C consortium is leveraging EU’s supercomputing resources coupling them with some of the continent’s best life-science research labs to counter international pandemics faster and more efficiently.

At the core of the project is Exscalate (EXaSCale smArt pLatform Against paThogEns), at present the most powerful, cost-efficient, and intelligent supercomputing platform in the world, developed by Dompé. Exscalate leverages a “chemical library” of 500 billion molecules, thanks to a processing capacity of more than 3 million molecules per second.

The aim of E4C is twofold, identify molecules capable of targeting the coronavirus (2019-nCoV) and develop a tool effective for countering future pandemics to be consolidated over time. More specifically, E4C aims to:

  • Establish a sustainable example for a rapid scientific answer to any future pandemic scenario. The model leverages a rapid and effective High Performance Computing platform for the generation and analysis of3D models and experimental 3D structure X-ray resolution of protein targets from pandemic pathogens
  • Drive a fast virtual identification of known drugs (repurposing) or proprietary/commercial candidate molecules to be further experimentally characterized
  • Define a workflow scheme for biochemical and cellular screening test to validate the candidate molecules in previous points and assure, through phenotypic and genomic assays.
  • Prepare together with EMA a development plan for successful candidates for direct “first in human” kind of studies or for further testing in animals for bridging studies.
  • Identify 2019-nCoV genomic regions involved in host adaptation, pathogenicity and mutations.

E4C will have two highly interconnected workstreams of activities. One will be primarily computerized and will rely on bioinformatic and chemoinformatic technologies and algorithms, while the second will be focused on a genomic, biochemical and biological approach. Starting from known bioinformatic information on protein targets, 3D molecule structures needed to exploit EXSCALATE platform potential will be prepared. This activity has already started.

The supercomputing component of the project will be then exploited to model future mutations of the virus. These activities will allow to identify candidate molecules (either from repurposing libraries or from proprietary or commercial compound libraries) which will then be provided and/or synthetized to be tested. In parallel, E4C partners shall start the protein production for some of the identified sequences.

The consortium will also open the Exscalate platform to external partners willing to cooperate in the drug hunting exercise, as previously with the Zika virus. This considerable effort to test roughly more than 25,000 compounds will ensure E4C doesn’t lose any active candidate molecules and will evaluate other possible mechanisms previously underestimated. The project will also use inverse genomic screening to identify host factors associated with virus infection and connectivity mapping analysis to predict relevant host-specific compounds for testing.

The further, development of a specific Coronavirus animal model to test the outcome of the E4C will help researchers bridge from the selection of active compounds to a possible fast first dose in humans, following EMEA directives and managed by Spallanzani Hospital Partner.

Finally, researchers will work to make the Exscalate platform a sustainable resource for an emergency engine for compound identification to be deployed in all future pandemic emergencies.

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