The Exscalate4CoV project. Let's take a look at SARS-CoV-2 proteins: results and insights from virtual reality.
Virtual Reality rooms
Exscalate4Cov (E4C) is a public-private consortium supported by the European Commission’s Horizon 2020 tender to counter the Coronavirus pandemic and improve the management and care of patients. E4C aims at 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 (and cost-efficient) intelligent supercomputing platform in the world for drug discovery aiming to screen chemical libraries for potential activity against SARS-CoV-2 (the coronavirus that causes COVID-19). E4C has €3 million of emergency EU funding and has already tested 9,000 drugs and bioactive, more than 100 of which have been found to be active in vitro. The platform already has a "chemical library" of 500 billion molecules and a processing capacity of more than 3 million molecules per second. E4C aims to identify molecules capable of effectively targeting SARS-CoV-2 by screening existing libraries provided by pharmaceutical companies and research institutions and by searching its own database and to develop a model for combating future pandemics. The E4C consortium is coordinated by Dompé Farmaceutici, an Italian pharmaceutical company, and consists of 18 institutions from seven European countries (including some of the most powerful supercomputer centres in Europe: CINECA, BSC, JÜLICH, and the ENI HPC5 data centre).
The current global condition does not allow the use of canonical communication channels, so our idea is to make the results obtained within the project available, making them usable in an innovative and interactive form. That is why, thanks to the support of our partner Nanome Inc. and their VR platform, we have thought of a virtual reality session that will allow, within the workshop, a wide interaction between the participants despite being located in different places in the world. Thus, the virtual rooms that we will put at disposal, will be the place where all the scientists can virtually meet and see our results. Finally, participants will be able to share their own ideas.
The consortium is already releasing the data through peer-reviewed scientific papers. In particular, two important papers [1,2] and one review  have been published. Our last work published within the Exscalate4Cov project has studied in depth the viral 3CLpro structure and function in order to effectively target this enzyme. All-atoms molecular dynamics (MD) simulations were performed to examine the different conformational behaviours of the monomeric and dimeric form of SARS-CoV-2 3CLpro apo structure, as revealed by microsecond time scale MD simulations. In another work, we provided a useful method that allows a comprehensive mapping of the druggable cavities within the SARS-CoV-2 therapeutically relevant proteins. This proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which are clearly amenable for virtual screening campaigns and drug repurposing studies.
Our idea of using virtual reality, for the show-down of the data and to allow communication among scientists, is driven by the enormous use that has been made, in recent months, of this technology. In fact, virtual reality is now extremely useful in both the scientific and social fields [4,5].
Igor V. Tetko ( Helmholtz Zentrum München ) - Organiser
Carmine Talarico ( Dompé Farmaceutici S.p.A. ) - Organiser
Silvano Coletti ( Chelonia S.A. ) - Organiser
Edgardo Leija ( Nanome Inc. ) - Organiser