The HADDOCK initiative supports COVID-19 research with EGI High-Throughput Compute resources

Talking about impact in the context of the novel COVID-19 research is, unfortunately, still inconceivable in terms of finding a vaccine or any other solution to eliminate the virus as such. That is not to say that there isn’t any progress being made, by tons of researchers, many of them benefiting from Open Science initiatives.

One example of these initiatives is HADDOCK (High Ambiguity Driven protein-protein DOCKing), developed at Utrecht University and operated as a thematic service under the EOSC-hub project and a core software of the BioExcel Center of Excellence. This structural biology simulation tool supports complex simulations to generate 3D models revealing how virus proteins interact with human ones, or to dock small molecules to targets such as the SARS-CoV-2 protease.

This potential drug target plays an essential role in processing the polyproteins that are translated from the viral RNA during replication. Targeting it and other viral proteins such as the RNA polymerase with small molecules could make for effective anti-coronaviral drug cocktails (as is done for example for HIV). Due to the urgency, researchers made use of a strategy that repurposes existing and already approved drugs toward new diseases. The HADDOCK WeNMR platform supported this drug repurposing effort by screening over 2000 chemical compounds against the protease structure in about only 3.5 days using EGI High-Throughput Compute resources made available via the European Open Science Cloud. The initial results have revealed interesting compounds, some of which are already under clinical trials, supporting the validity of the screening methodology. 

In order to monitor better COVID-19 related runs, the portal allows tagging of submission as COVID-19. Since this monitoring started over 3000 runs (not counting the drug repurposing screen) were processed in a month period. This tagging also allows to target the HTC jobs to sites specifically supporting this research. Another great result or impact, if you will, is to see the international mobilisation of additional resources to support HADDOCK jobs from both European, often high energy physics sites like CPPM (France), KIT (Germany) and USC-LCG2 (Spain), and worldwide sites such as the Open Science Grid (USA).

For more results visit the dedicated webpage of Bonvin Lab’s website.