Supercomputers versus Coronavirus

Through supercomputers Cineca is simulating the behaviour of proteins that allow the virus to replicate so that it can virtually test the most effective pharmaceutical molecules to inhibit the virus, and then go on to the laboratory validation phase. The project is Exscalate4CoV, led by Dompè. Research through supercomputers can collaborate with traditional research by shortening the time for drug development.

One of the great challenges of the international scientific community is the so called "urgent computing": being able to access the most powerful supercomputers to support research when, in emergency conditions, the time is very tight, and the variables become too many to be able to count only on traditional research resources.

One of the fields of application of urgent computing, these days, is the race against time to contain the spread of COVID-19, the "coronavirus".

Cineca takes part in the project Exscalate4CoV led by Dompè Farmaceutical, that has been funded by the European Commission with 3 million euros. The aim of the project is to identify the safest and most promising drugs for the immediate treatment of the already infected population, followed by the identification of molecules capable of inhibiting the pathogenesis of COVID-19 to counter future contagions.

Supercomputers like Marconi, the most powerful scientific research resource in Italy, are computers with immense computing powers. About millions of billions of operations per second that have been working on the coronavirus sequencing data made available by international researchers since the beginning of February.

Coronavirus study activity

Through supercomputers, in the framework of the Exscalate4CoV project, Cineca is simulating the behaviour of proteins that allow the virus to replicate so to virtually test the most effective pharmaceutical molecules to inhibit the virus, and then address the validation phase in the laboratory by accelerating the production of effective drugs to reduce its replicability.

Research through supercomputers can collaborate with traditional research by shortening the time for drug development: each protein requires at least one week of continuous simulation on 16 nodes of Cineca's supercomputer: with a normal computer it would take at least 4 months for each protein. The results of the simulations are analyzed by the Exscalate platform.

The virtual platform Exscalate

Exscalate (EXaSCale smArt pLatform Against paThogEns) is a Dompè platform, developed thanks to a collaboration between Cineca, Dompè and Politecnic of Milan. The platform, that has already been used in the study of the Zika virus, has been developed in the context of the Antarex project, funded by the European Commission, aimed at developing a sustainable supercomputing system, to support pharmacological research.

Exscalate has a "chemical library" of 500 billion molecules: researchers can simulate the behaviour of the virus in combination with pharmaceutical molecules, and thanks to the supercomputing power it is possible to evaluate more than three million molecules per second, with low costs of energy consumption.

The idea to use supercomputing power to accelerate the development o pharmaceutical drugs has been conceived by Dompè and Cineca more than 15 years ago.

European collaboration

“We are working to mitigate the consequences of a potential larger spread of the Coronavirus outbreak in the EU. Thanks to emergency research funding from Horizon 2020, we will know more about the disease,” Innovation, Research, Culture, Education and Youth Commissioner Mariya Gabriel commented.

In the beginning of February, to support traditional research in finding a solution to inhibit the spread of the virus, the European Community has launched a call for research projects aimed at guaranteeing an effective and coordinated response to the emergency.

The aim of the call was to define sustainable scientific standards to give quick responses to any pandemic scenario, quickly identifying the most effective drugs.

In order to speed up the processes of diagnosis and research and development of vaccines, the Commission has suggested, in appropriate cases, collaboration with the main European supercomputing centers to use data processing resources and simulations. In this regard, the Supercomputing structures in Barcelona and Bologna (Cineca), which have specific skills in the life sciences field, have made themselves available to collaborate. It is a research area defined as "urgent computing", i.e. the possibility of accessing supercomputers in a very short time, and international research networks in the event of supranational emergencies: from epidemics to climatic emergencies.

The Exscalate4CoV project is one of the 17 projects founded by the European Commission in this framework.

Exscalate4CoV

The public-private consortium Exscalate4CoV (E4C) is Italian-based, and has been awarded € 3 million by the European Commission’s call for research projects on Coronavirus under the Horizon 2020 framework programme.

The primary objective of E4C is to exploit the supercomputing potential integrated with the best life-science scientific skills in Europe to better and quickly face pandemic situations of supranational interest.

The core of the project is Exscalate, the supercomputing system - High Performance Computing, Structure-Based Drug Design System capable of evaluating more than three million molecules per second.

The consortium, led by Dompé pharmaceuticals, brings together 18 institutions and research centers, in 7 European countries. In brief, the project aims to identify the safest and most promising drugs for the immediate treatment of the already infected population, followed by the identification of molecules capable of inhibiting the pathogenesis of the coronavirus to counter future contagions.

The public-private nature of the project has been enhanced by the contribution of Eni's HPC5 supercomputers: Eni has freely made its supercomputing infrastructure and its molecular modelling skills available for coronavirus research, offering its contribution with its tools and resources of excellence in the fight against this global emergency.

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