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Cell Paper - 20mer peptide inhibitor of HIV

Hi there,

I hope this is the right place to post such an idea. Half an hour ago I was reading the news on the Nature homepage when I stumbled over an article about a paper in the Cell issue of April 20th 2007:

Münch J., et al. Cell, 129. 263 - 275 (2007)

I'm a geneticist not knowing much about protein/peptide structure calculations. But I was wondering whether it would be possible using the computing power within the WCG to optimize such a 20mer oligopeptide into an effective inhibtor of HI virus.

The "target" of this inhibitor agent is not the protease but an envelope protein of the virus. So I guess it would be some work to set up new algorithms?

Any responses would be appreciated.
Micha
[Apr 20, 2007 7:24:23 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Cell Paper - 20mer peptide inhibitor of HIV

Hi gene-lab2,

I'm not sure if this is the same thing you're referring to, but Rosetta@home (which currently has peptide/protein-designing algorithms in place) is designing HIV proteins for HIV vaccines (is the peptide envelope you're referring to the same thing as "binding to a critical region on is surface required for binding to and entering our cells"?):

http://boinc.bakerlab.org/rosetta/forum_threa...177&nowrap=true#37154

One of the key advances that underlies our HIV vaccine design efforts has recently been published in the scientific journal Nature by the research group of Dr. Peter Kwong, with whom we are collaborating closely. Dr. Kwong's group has determined how an antibody can neutralize the virus by binding to a critical region on its surface required for binding to and entering our cells. We have been using the newly published structure, which Dr. Kwong made available to us many months ago, to design small protein mimics of the virus that we hope will elicit similar antibodies when people are vaccinated with them. You can read about Dr. Kwong's discoveries by picking up Nature at a newstand (his work was featured on the cover!) or from the press releases; I'm pasting the first part of one of these below:

Scientists Unveil Piece of HIV Protein that May Be Key to AIDS Vaccine Development
In a finding that could have profound implications for AIDS vaccine design, researchers led by a team at the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), have generated an atomic-level picture of a key portion of an HIV surface protein as it looks when bound to an infection-fighting antibody. Unlike much of the constantly mutating virus, this protein component is stable and — more importantly, say the researchers — appears vulnerable to attack from this specific antibody, known as b12, that can broadly neutralize HIV.

“Creating an HIV vaccine is one of the great scientific challenges of our time,” says NIH Director Elias A. Zerhouni, M.D. “NIH researchers and their colleagues have revealed a gap in HIV’s armor and have thereby opened a new avenue to meeting that challenge.”

The research team was led by Peter Kwong, Ph.D., of NIAID’s Vaccine Research Center (VRC). His collaborators included other scientists from NIAID and the National Cancer Institute, NIH, as well as investigators from the Dana-Farber Cancer Institute, Boston, and The Scripps Research Institute in La Jolla, CA. Their paper appears in the February 15 issue of Nature and is now available online.

“This elegant work by Dr. Kwong and his colleagues provides us with a long-sought picture of the precise interaction between the HIV gp120 surface protein and this neutralizing antibody,” says NIAID Director Anthony S. Fauci, M.D. “This finding could help in the development of an HIV vaccine capable of eliciting a robust antibody response.”

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[Edit 2 times, last edit by Former Member at Apr 20, 2007 8:17:58 PM]
[Apr 20, 2007 8:09:06 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Cell Paper - 20mer peptide inhibitor of HIV

I believe the paper you're referring to, esoteric17, is
Zhou, T. et. al. (2007) Structural definition of a conserved neutralization epitope on HIV-1 gp120, Nature, 445 , pp. 732-737
(P.D. Kwong is listed as the corresponding author)

Münch et. al.'s paper was titled 'Discovery and Optimization of a Natural HIV-1 Entry Inhibitor Targeting the gp41 Fusion Peptide'.

This is good. There are at least 2 proteins that can be targeted.
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Re: Cell Paper - 20mer peptide inhibitor of HIV

http://www.sun-sentinel.com/features/health/s...ry?coll=sfla-news-science

Peptide that thwarts HIV found

By Thomas H. Maugh II
Los Angeles Times Staff Writer
Posted April 22 2007, 1:59 PM EDT

German researchers have found a peptide in human blood that blocks HIV and have identified a synthetic variant that is 100 times more potent, they reported Friday in the journal Cell.

The synthetic version has been shown to be safe in animals and the team hopes to begin trials in humans this year, they said.

The peptide could be a major improvement over existing HIV drugs because it works equally well against drug-resistant viruses, said virologist Frank Kirchhoff of the University of Ulm, who led the team. "That's a big advantage," he said.

Several other compounds isolated from human blood have been shown to block HIV replication, but none has yet proved useful as a therapeutic or preventive agent. The team does not yet know if the newly discovered compound, called virus inhibitory peptide, or virip, plays a role in the natural resistance some people display against HIV infection.

Kirchhoff and his colleagues discovered virip by screening the hundreds of thousands of proteins filtered from the blood of patients undergoing kidney dialysis.

The peptide they ultimately identified contains 20 amino acids and appears to be a fragment from the end of an enzyme called alpha-1-antitrypsin. They have so far found no natural function for the peptide, but the extremely small quantity present in humans makes such studies difficult.

In laboratory dishes, virip blocked all the strains of HIV the researchers tested, and none of those strains appeared to develop resistance to its activity. The peptide targets a viral protein called gp41 fusion peptide, which plays a crucial role in entry of the virus into cells. That viral peptide appears to be stable to mutation, which may explain the lack of resistance to virip.

The team found that changing three amino acids in virip produced a peptide that was 100 times more potent than the naturally occurring product. Tests conducted with researchers at IPF Pharmaceuticals in Hannover show that the synthetic peptide is safe in animals at even high concentrations.
[Apr 23, 2007 8:39:11 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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