Introducing Small Molecule Design Puzzles

Hi everyone,

Today we are officially launching the Foldit small molecule drug discovery game mode.

To kick off the new game mode, we are releasing a new puzzle on acquired immunodeficiency syndrome (AIDS). It has been over three decades since the CDC reported on the discovery of AIDS and its cause, the human immunodeficiency virus (HIV). Currently, 17 million people globally are being treated for HIV with antiretroviral therapy (WHO Global AIDS Update 2016). A total of 2.1 million people were infected with HIV in 2015 and 1.1 million people died from AIDS, with the majority of patients being from in Africa.


(Source: UNAIDS Global AIDS Update 2016)

Current treatment therapies focus on blocking the enzymes used by HIV to reproduce. One such enzyme is HIV protease, an enzyme which the virus uses to cleave polypeptide precursors. Without a functioning HIV protease, the virus cannot make the proteins needed to produce new virus particles. Several small molecule drugs have been created to block HIV protease, such as saquinavir and amprenavir. These compounds inhibit HIV protease by binding in the enzyme active site, a large cleft running through the middle of the protein, which prevent the enzyme's substrates from binding to the enzyme. HIV protease is a good test case for small molecule design, as there's a wealth of information about what sorts of compounds bind to the enzyme.

For this puzzle, we are interested in what small molecule inhibitors you can design for HIV protease 1. As a starting point, we're giving you the base fragment for saquinavir in the binding pocket. What we'd like you to do is use the new small molecule design tools to alter the chemical structure of the inhibitor ligand to get a better binding (better scoring) ligand.

We recommend that you use the selection interface (Menu->Selection Interface) for this process, as it gives you the most control, but you can also access some of the drug design tools through the "Modes" entry of the original interface. In particular, the Ligand Design tool will be your main tool for altering the identity of the ligand.

In the selection interface, the Ligand Design tool will pop up after clicking on the ligand. (In the original interface, click Ligand Design from the modes menu before clicking on the ligand.) You can then click one or more individual atoms to change the atom's element, or to add and delete bonds, atoms and groups. Keep in mind the advanced GUI (Main/Menu->General Options->Show advanced GUI) enables additional options under View that may help in working with small molecules. (I like the "Cartoon Ligand" view, myself, as it allows you to select ligand hydrogen atoms.)

Explore the tools and different designs you can make for the small molecule! Remember, you can use the Upload for Scientists button for designs that you want us to look at, even if they are not the best-scoring solutions!

-rmoretti & freeradical


P.S. Didn't follow the development of the drug design mode? Catch up with these previous blog posts:

* Foldit drug design introduction
* Foldit Drug Design Part Two
* Foldit Drug Design Blog: Interface Update
* Drug design puzzles coming your way!
* Let's Get Ready for Drug Design Puzzles!
* Devprev Drug Design Update
* Drug Design Update: Tool Talk
* Drug Design Update: Merk Molecular Force Field
* Big Update: Experimental Client (Drug Design)

(Note that some features discussed are for older versions and have changed since.)

( Posted by  rmoretti 83 921  |  Tue, 09/19/2017 - 23:11  |  0 comments )
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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, Microsoft, Adobe, RosettaCommons