Protease Patrol

Identifying anti-viral drug candidates for COVID 19

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Inspiration

COVID-19 is a serious problem in the world, even if the pandemic ended years ago. Finding better treatments for COVID has the potential to save thousands or even millions of lives, making this very important problem to solve in science.

What it does

SARS-CoV-2 (the virus that causes COVID 19) has a protein called main protease that acts like scissors, cutting long polyproteins (protein chains) into smaller, usable pieces. Like in the game of rock, paper, scissors, getting something stuck between the "blades" (the active site) of the protease disables is and prevents the virus from reproducing. By blocking reproducing, a potential drug can prevent the virus from making a patient sicker and sicker.

How we built it

First, we started with a pool of about 120 compounds that seemed promising. Then, we tested how well they fit in the active site, leaving us with 20 compounds that were more likely to be effective. After, we ran a second, more accurate round of testing on these 20 compounds, leaving us with 8 final candidates. Finally, we simulated the toxicity of these compounds and checked to see if they will be absorbed by patients.

Results

The following compounds were identified as candidates:

  • Ensitrelvir
  • PF00835231
  • Ibuzatrelvir
  • Imatinib
  • NZ-804
  • Olgotrelvir
  • Iscartrelvir
  • Kaempferol

All attached images show candidates in the active site (where the protein chains are cut)

Challenges we ran into

Docking was very slow and many libraries had bad documentation.

Accomplishments that we're proud of

We are proud that we were able to identify many promising drug candidates.

What we learned

We learned a lot about how the SARS-CoV-2 virus works and how drug discovery is performed.

What's next for Protease Patrol

Good next steps would be in vitro testing of the compounds and potentially some kind of clinical trial to see if they can actually help patients.

Created by Samir Rangwalla, Gary Goodson, Neil Bhatt, and Ali Sayed. Due to technical issues, Neil and Ali could not join Devpost, but they were still part of the team.

Built With

  • autodock-vina
  • google-colab
  • python
  • rdkit
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