2 replies [Last post]
Susume's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 10/02/2011

Using a new, more accurate structure of the Ebola glycoprotein, scientists have found a binding pocket on it, and two small molecules that bind to it weakly and reduce infection in mice. There is a great possibility that a new small molecule could be developed that would bind more strongly. Is this something foldit players could work on when the drug design features of the game are released?

https://cen.acs.org/articles/94/i27/Structure-Ebola-viruss-glycoprotein-reveals.html

Joined: 01/12/2015
Groups: None
Hi Susume, This is a target

Hi Susume,

This is a target that can be used with the drug design features. There are some challenges associated with this particular puzzle, though. It looks like it is a rather large protein, which might cause problems for players who do not have fast enough computers. Some of this can be fixed (I think), by restricting movement of the protein backbone, but we would have to test it out and see.

Another problem is finding a collaborator who would synthesize the compounds and one who could test them. Ebola is a very dangerous virus and only a few labs worldwide have the equipment and ability to test drug designs against them. For synthesis, we can possibly order small molecule compounds that have already been made. What this means for Foldit players is that you would not be necessarily designing compounds, but docking them into the protein. This feature is available through the Ligand Queue tool, but it (in my opinion) is not fun compared to actually designing a small molecule. You would only get to cycle through compounds and move them around in the binding pocket.

All this being said, we do have collaborations that are starting to trickle in for drug design. One is with the Tuberculosis challenge. I wish I could say more about upcoming collaborations, but we have not set anything in stone yet.

If you have a particular disease that you think would benefit from Foldit players, let us know! I am not against emailing and calling labs in order to get these problems solved. I will look more into the Ebola puzzle.

Susume's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 10/02/2011
Thank you! I agree, pushing

Thank you! I agree, pushing something around in a pocket does not sound as fun as designing something new. One of the compounds that binds weakly in the pocket is ibuprofen - even if we could just start from that and make modifications it would be fun.

Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons