"...in complex with a potential inhibitor:"

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"...in complex with a potential inhibitor:"

Postby JimF » Wed May 06, 2020 4:00 pm

Some of the new CPU work units from the Voelz lab are described as:
ALL of these projects are Coronavirus SARS-CoV-2 main protease in complex with a potential inhibitor:

https://stats.foldingathome.org/project?p=14727

That sounds like progress, but what does it mean?
If you have such a complex, does it mean that you can evaluate how well the "inhibitor" works?
That would be a step in the right direction.
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Re: "...in complex with a potential inhibitor:"

Postby Joe_H » Wed May 06, 2020 5:23 pm

From what I understand of the science, these are screening to see what compounds do have interactions with potential binding sites. This will identify potential candidates for further testing to see "how well" they work. Basically cutting down from many possible drugs to a smaller group that "match up" to the binding sites being investigated.
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Re: "...in complex with a potential inhibitor:"

Postby JimF » Wed May 06, 2020 6:51 pm

OK, my Ryzen 3900X and Ryzen 3950X (about a million PPD under Ubuntu 18.04.4) are being put to good use.
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Re: "...in complex with a potential inhibitor:"

Postby JimF » Fri Jun 05, 2020 5:37 pm

Joe_H wrote:From what I understand of the science, these are screening to see what compounds do have interactions with potential binding sites.

Thank you again. But I now wonder how this compares to conventional docking. I think that FAH is much more advanced and detailed than that, but I have no idea how they compare. Would docking still need to be done if the compounds show promise here, or is docking performed first before they even get to FAH?

I know a scientist would probably have to answer, and they are busy these days, but I hope to float it up so that someone can give us the big picture eventually.
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Re: "...in complex with a potential inhibitor:"

Postby bruce » Mon Jun 08, 2020 7:13 am

The studies are essentially a pre-docking survey of a large number of fragments to see their potential ability to dock at at any of the important sites on the virus. More detailed studies of interesting fragments will still be required. See https://www.weizmann-usa.org/news-media ... -antiviral

As it says there: they started with 4,500 drug designs and decided to synthesize (only) 311.
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Re: "...in complex with a potential inhibitor:"

Postby JimF » Mon Jun 08, 2020 6:31 pm

Thanks, that places it in some context, which is a bit hard to come by these days.
I expect the scientists are busy themselves working out the procedures. But I have high hopes for the detail that Folding is able to provide.
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