nanoHUB IGNITE 2021
COVID-19 Challenge
Description of the challenge
Simulate different drug treatment conditions for SARS-CoV-2 infection using “COVID-19 drug treatments explorer, CompuCell3D” in nanoHUB. The tool implements two types of drug, one that inhibits viral entry to the cells and one that inhibits viral replication inside the cell. Parameters and treatments can be selected/turned on-off in the “Steering Panel” subwindow.
Note: at the start of simulation sub-windows will be generated. You can rescale the tool area by dragging on the lower right (it'll show two numbers, e.g., "123x456"), and you can make CompuCell3D fit all sub-windows by going to the menu Window -> Tile. You can also make more sub-windows showing cells in Window->New Graphics Window. This is useful to see both the epithelial layer and the immune cell layer as well as plotting both the cell “field” (the cells by themselves) and the chemical concentration overlay for the viral/cytokine densities
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Research investigation and/or Innovation
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Which of the drugs is more effective overall?
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What are the effects of changing how potent the drugs are (i.e. changing their IC50 - half maximal inhibitory concentration https://en.wikipedia.org/wiki/IC50)?
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Note that, as we are using arbitrary units, another interpretation of changing the IC50 in the simulation is that the amount of drug given is changing. This is because what determines the “strength” of the drug is the relation of drug amount / IC50, higher IC50 can imply less drug concentration.
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What are the effects of changing the dosing period?
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Is it more effective to have a weak drug given more often or the other way around?
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Any interesting or unexpected results?
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Take this a step further by proposing more drug targets.
Reference Papers and Links:
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CC3D COVID-19 study: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008451
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YouTube Video: https://youtu.be/F-oAsfmhqvU
nanoHUB Tools to use
COVID-19 drug treatments explorer, CompuCell3D
- https://nanohub.org/tools/coviddrugexp/
- CC3D Documentation: https://compucell3d.org/Manuals
- GitHub host of tool: https://github.com/JulianoGianlupi/nh-cc3d-covid-drug-explorer
COVID 19 Virtual Tissue Model - Tissue Infection and Immune Response Dynamics
- https://nanohub.org/tools/cc3dcovid19
- CC3D COVID-19 study:
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008451