April 28, 2020

Hunting for the molecular Achilles heel of Sars-CoV-2

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Image: Heidelberg Institute for Theoretical Studies (HITS)

Prof. Rebecca Wade

Institution: Heidelberg Institute for Theoretical Studies (HITS)

HBP research area:  Molecular modeling and simulation

We have been working on developing tools and workflows for molecular simulation and drug design in the HBP brain simulation platform. We have applied these methods to investigate the effects of signaling molecules on molecular networks in the brain. 

Q: What are you doing at the moment to help address the challenges posed by the novel Coronavirus?

While different strategies are required to tackle different diseases, many of the  computational tools for studying proteins and for drug discovery that can be applied to fighting brain diseases can also be applied to viral diseases. Therefore, we decided to collaborate on drug discovery against SARS-Cov-2, the virus that causes Covid-19 disease. Currently, we are doing this in the framework of the COVID-19 Grand Challenge. The first step of the challenge consists in providing a consensus list of the top 10,000 lead compounds (ranked by affinity) for at least 3 Covid-19 targets that are involved in viral entry or replication, by using three independent computational methods. My group, together with Francesca Spyrakis group (University of Turin, Italy) and the Exscale4CoV team, including HBP participants Giulia Rossetti and Paolo Carloni from Forschungszentrum Jülich, are collaborating on this task. We are employing some of the methods we have developed at HITS, such as TRAPP (Transient Pockets in Proteins) for exploring the flexibility of protein binding sites and identifying druggable structures, and RASPD+ (Rapid Screening with Physicochemical Descriptors) for the identifying molecules that might bind in a given protein binding site.

Q: How has the current shutdown affected your work?

We have been in home-office for some weeks and are fortunate that we can do most of our computational research remotely. Scientific communication mostly works pretty well with videoconferencing. We keep up social interactions in our research group with a virtual coffee after lunch each week-day.