Other known drugs being studied after researchers map proteins

2,314 Views | 8 Replies | Last: 4 yr ago by Patentmike
Not a Bot
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AG
Interesting stuff. Has been submitted for publishing but has not been peer reviewed. Read the preliminary report here: https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf+html (to read the report click "Preview .pdf" after the page loads).

Quote:

...we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays.

24 of these are already FDA approved for other things. List includes Indomethacin, Valproic Acid, Haldol, chloroquine, and many others including at least one already approved anti-viral (Ribavirin). It obviously does not mean these would necessarily be effective treatment options as the study was designed to identify known compounds that could *potentially* disrupt viral interaction with host based on their structure and known mechanisms of action, but it's a good starting point.

They specifically point out there's a clear mechanism of action for both chloroquine and azithromycin.
cisgenderedAggie
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Well that's a beast of a paper...

Thanks for posting!
kyledr04
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AG
Fascinating. I'll have to read it more closely but there are a number of commercially available products that have potential activity.
Not a Bot
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Shameless bump for the biochemistry dorks who may want to read this study. One cool thing I just noticed in reading it again is that there are some very relevant biochemistry being learned that could be useful in treating future infections / pandemics, including anthrax.

Also reading about this new mycin-type antibiotic which apparently can inhibit pretty much anything including viruses due to its mechanism of action. Of course the problem is they can't seem to make it safe enough for humans to take.
Patentmike
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Moxley said:

Shameless bump for the biochemistry dorks who may want to read this study. One cool thing I just noticed in reading it again is that there are some very relevant biochemistry being learned that could be useful in treating future infections / pandemics, including anthrax.

Also reading about this new mycin-type antibiotic which apparently can inhibit pretty much anything including viruses due to its mechanism of action. Of course the problem is they can't seem to make it safe enough for humans to take.
That is a phenomenal paper. Thanks for finding/posting.
PatentMike, J.D.
BS Biochem
MS Molecular Virology


BusterAg
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This paper is sooooo cool.

You know who is working overtime right now?

Patent lawyers / agents with any sort of biology knowledge at all.

Once a good pathway to treat this gets identified, there are going to be dozens of companies with legitimate claims on helping discover the treatment / vaccine. Publishing this paper without having filed a dozen or so patent applications would be inconceivable during regular times.

Another thing that this paper emphasizes is all those years of R&D trying to cure AIDs and Hep-C have made us much, much smarter about how to fight viruses in general. We are dusting off the old playbooks that worked or showed promise, and looking at how to use those plays in this particular situation.

I would almost bet that we have a good chance of finding an effective treatment or vaccine by the end of the year.
BusterAg
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Around 100 authors. Looking at the authors of the paper, here are all the institutions represented:

1) University of California San Francisco (this is well over 75% the authors, they were obviously the leads here)
2) University of Michigan
3) EMBL-EBI (European Bioinformatics Institute)
4) UC San Diego
5) Fred Hutchinson Cancer Research Center
6) Institute Pastuer
7) Icahn School of Medicine at Mount Sinai

That is some Grade A collaboration right there.
Not a Bot
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I think that may be a lesson learned this time. When the first SARS outbreak fizzled out a lot of the academic research continued but drug development didn't. Obviously no one wants to develop a drug for a disease that no one has. The downside of course is that when very similar outbreaks occur in the future you are starting back from square one.

Many think this virus is potentially going to end up being seasonal and there could be a lot of money made.
Ranger222
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This was a Herculean effort. I have performed a similar experiment in the past Strep-tagging a protein of interest and finding interaction partners via mass spec. It took a long time to just optimize the conditions to do it for ONE protein. They did 27. It took me 6+ months. Here, two.

One criticism is that their bead-based purification and then "bait" protein digestion occurred all in one reaction. I would have liked to seen silver stain of the elutants prior to trypsin digestion. Also, they show a western blot with an anti-Strep antibody only of whole cell lysates, not what is being bead purified.

One of the most interesting things to me is what is Orf10. There have been several suggestions floating around but it appears to be impacting ubiquitination pathways, not something that has been previously suggested.
Patentmike
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Ranger222 said:

This was a Herculean effort. I have performed a similar experiment in the past Strep-tagging a protein of interest and finding interaction partners via mass spec. It took a long time to just optimize the conditions to do it for ONE protein. They did 27. It took me 6+ months. Here, two.

One criticism is that their bead-based purification and then "bait" protein digestion occurred all in one reaction. I would have liked to seen silver stain of the elutants prior to trypsin digestion. Also, they show a western blot with an anti-Strep antibody only of whole cell lysates, not what is being bead purified.

One of the most interesting things to me is what is Orf10. There have been several suggestions floating around but it appears to be impacting ubiquitination pathways, not something that has been previously suggested.
Orf8 did something similar in SARS and may be here as well. One hypothesis is that the Ub pathways are disrupted to avoid intracellular immune responses and maybe antigen presentation.
PatentMike, J.D.
BS Biochem
MS Molecular Virology


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