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HPC5 for EXSCALATE4CoV: supercomputer versus Coronavirus

Effective drugs to stop the SARS-CoV-2 virus: HPC5 plays a key role in the EXSCALATE4CoV European project to treat Covid-19.

Sixty ‘Fast Track’ hours in the search for the anti-Covid-19 drug

In mid-November 2020, HPC5 enabled the most complex molecular supercomputing experiment to date to be carried out to identify new treatments for the virus. Everything took place as planned and on schedule, making it the largest study globally on the interaction of the virus with possible drugs. The data is currently being processed and the results will be made freely available to the scientific community.

The experiment, called the Fast Track phase, began on the evening of Friday, 19 November and ended on the morning of Monday, 21 November, for a total of 60 processing hours. The goal was to test the interaction of 71.6 billion molecules on 15 "active sites" of the virus. Therefore, a total of 1074 billion interactions equal to 5 million simulations per second were processed.  The experiment generated 65 TeraBytes of results, i.e. 4.33 TB for each SARS-CoV2 site analysed.

To achieve this, 1,500 HPC5 nodes worked continuously. In total, the supercomputer deployed 6,000 high-performance GPU graphics cards, that are particularly well suited to the large mass of highly parallel calculations required for these simulations. The movement of the virus and its interactions with each molecule were reproduced on the computer to identify those molecules that interact best with the virus and manage to bind to it, neutralising it and preventing it from replicating itself by destroying the host cells.

The experiment simulated "molecular docking", i.e. all possible intermolecular links between virus proteins and other already known molecules among potentially usable drugs, natural products, nutraceuticals and other substances on the market from public databases and those made available by pharmaceutical companies. By processing the results of the screening, it is possible to identify candidate molecules, i.e. those capable of attacking the virus and locking it in and preventing it from unleashing its viral load. The aim is to have more effective drugs that have already been clinically tested and are therefore immediately available. HPC5 and the Marconi supercomputer by Cineca have a total computing capacity of 81.1 Petaflop/s , equivalent to 81 million billion floating point operations per second when taking both supercomputers into account.

In the first phase of the trial, from the start of the project until June 2020, HPC5 and three other supercomputers involved in the research conducted docking tests on over 400,000 molecules, including artificial drugs and natural products, made available by Dompé. This phase of the project ended with the identification of a molecule, Raloxifene, a drug used for the treatment of osteoporosis, which has demonstrated a potential effectiveness in blocking https://www.eni.com/it-IT/ricerca-scientifica/sfida-sanitaria-modellistica-molecolare.html the replication of the virus within the cells.

Technology

Our supercomputer infrastructure HPC5 is the best-performing in use in industry anywhere in the world, with peak processing speeds of 51.7 petaflops per second. Combined with its predecessor HPC4, which is still running, the system can reach record speeds of 70 petaflops, meaning 70 million billion mathematical operations, per second. Its 3,400 computing nodes and 10,000 graphics cards allow HPC5 to process enormous quantities of data at once, while consuming very little electricity. The machine was designed and created for the energy industry, to reduce computing times and make it quicker to develop innovative ideas. One of its applications is in molecular modelling, the study of molecules using mathematical models that simulate their characteristics. Molecular modellers, who are hybrid scientists with expertise in chemistry, physics and mathematics, use complex algorithms developed by special programs to simulate molecules on the supercomputer, ridding them of the need to produce and study them physically in a laboratory. They can then study the behaviour and properties of well-known molecules and even predict how little-known ones will act. Applied to the field of energy, supercomputing and molecular modelling can select the best photoactive substances for Organic Photovoltaics (OPV) or Luminescent Solar Concentrators (LSC). In medicine and pharmaceuticals, they can be used to find new cures.

Context

The spread of the SARS-CoV2 virus, which causes COVID-19, is putting the entire planet to the test. That’s why we need to combine our forces and all help look for solutions to this global struggle. Marrying the powers of HPC5 with the skills of the molecular modellers could provide real arms in the battle against this medical emergency. EXSCALATE4CoV, acronym of EXaSCale smArt pLatform Against paThogEns, seeks to find the safest and most promising drugs for fighting coronavirus. Steering the project is the Italian biopharmaceutical company Dompé, at the helm of 18 institutions and research centres in seven European countries, including Cineca in Bologna.

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SUPERFACTS#5- Supercomputer Vs virus

Technological challenge

As part of the EU-funded [GC3] EXSCALATE4CoV project, in collaboration with Cineca we are offering HPC5’s computing power and our experience in molecular modelling. Our shared goal was to run simulations of the molecular dynamics in the proteins on the surface of SARS-CoV-2, which play a key part in the virus’s infection mechanism. This work lays the foundations for the next step, which is Dompé’s responsibility: screening 10,000 active ingredients in known pharmaceutical compounds, to find the most efficient for blocking the virus.

This was followed by the Fast Track phase, in mid-November 2020, during which the supercomputer was used in the molecular dynamic simulation of viral proteins considered relevant to the mechanism of infection of Covid-19. The screening was aimed at selecting the molecules with the highest anti-viral efficacy. Interactions between virus proteins and over 500 billion molecules have been reproduced on the computer using sophisticated molecular dynamics calculations to identify structures capable of attacking the virus with the aim of identifying those with the most effective pharmacological activity.

If this research bears fruit, we will have a clinically tested drug on our hands, completely ready for use. Molecular modelling uses very complex calculations that require enormous capacity. Without a powerful supercomputer to hand, it would take years to do all the necessary calculations. But HPC5 will let us study all the thirty or so proteins present in SARS-CoV-2 in just a few months. With HPC4, it would have taken two months to simulate the behaviour of a single protein. HPC5 can do the same in about 10 days. And happily, the race for new supercomputers shows no signs of stopping; after all, HPC4 was the most powerful industrial [GC4] computer in the world until last year, and HPC5 quadrupled its capacity. Our latest supercomputer also has the benefit of the ideal hardware to support Gromacs, an open-source programme that simulate molecular dynamics. This software divides the models into multiple parallel calculations, which is perfect for using all 7,280 of HPC5’s GPUs to their very best.

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SUPERFAST#2 - Together in research: collaboration is strength

Industrial integration

HPC5 was built using today’s energies to develop tomorrow’s energies. Its computing power has already proved its worth, letting us select and study new oil and gas fields faster and more accurately than ever, as well as develop innovative technologies for generating energy from renewable sources. One of these is ISWEC, which produces electricity from wave power. In fact, renewable energy is where the supercomputer revealed how useful it was for molecular modelling; the machine helped modellers pick the best photoactive compounds for luminescent solar concentrators (LSCs) and organic photovoltaics (OPV). Put to use in pharmaceutical research, HPC5 will also let us tackle new challenges and develop greater and greater skills in molecular modelling. Thanks to our part in the EXSCALATE4CoV project, we are gaining a ton of experience and building a valuable network of contacts in a sector that’s increasingly strategic for the energy industry.

The human value

In order to make the best possible use of the HPC5 supercomputer's extraordinary computing power, of course, equally exceptional skills are required. Eni's theoretical chemists, as experts in molecular dynamics, are involved in numerous projects, from the modelling of photoactive molecules for photovoltaic technologies (LSC and OPV), detergents and lubricants to improved oil recovery by means of organic polymers and aqueous emulsions. It is thanks to the synergistic work of computer scientists, organic chemists and Eni characterisers that such a wealth of experience could also be applied in the simulation framework of the EXSCALATE4CoV project. Within the company, the sharing of expertise has been the basis for many successes. Eni is a dynamic environment that puts its human capital at the heart of what it does and promotes both academic training and the circulation of company know-how.

The commitment on the part of Eni and its people to the fight against Coronavirus confirms the integration of the values expressed by the SDGs outlined in the United Nations Agenda 2030 in the company's mission and, consequently, in Eni's business model. Membership of the EXSCALATE4CoV project specifically reflects the company's commitment to Goal 3: Ensure healthy lives and promote well-being for all at all ages.

Impact on community

Molecular modelling has two great benefits to offer pharmaceutical research: it’s very fast at identifying new drugs and reduces the need for tests on patients. Studying and even predicting the pharmacological properties and side effects of active ingredients while reducing the times and difficulties of clinical trials is always important, but it’s vital in an emergency like the present one. So, now more than ever, computers may really take on a human face.

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During a global emergency such as this, we must mobilise all available resources to overcome the challenge we face. We at Eni are honoured to be able to contribute to trying to find solutions for this challenge for humanity.

Claudio Descalzi, Eni CEO
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