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MPCevat
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Compute the best molecule to fight AIDS

Hi!

Running the risk of asking stupid questions that may have been answered before, here's one that has been keeping me busy for some days now.
My understanding of the WCG is that we run our PC's to see if a molecule could serve as a drug to fight the AIDS virus. By now the community has gathered millions of results on molecules, i.e. there is quite some data on what happens with the virus when we introduce that specific molecule in it.
Wouldn't it be possible to reverse that process by now, i.e. somehow go from analyses to synthesis? I mean, isn't it possible to find the common denominator in combinations that have proven to be very successful, that is, with the largest effect from the molecule on the AIDS virus? When we have found the rules that make a molecule successful, can we then start designing a molecule that would do better?

Looking forward to your reply!
Marco Cevat
[Sep 17, 2006 4:16:12 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Compute the best molecule to fight AIDS

Hello MPCevat,
The Baker Lab (Rosetta@home - http://boinc.bakerlab.org/rosetta/ ) is working on designing proteins. Instead of a protease inhibitor, they are trying to elicit antibody responses as part of a HIV vaccine ( http://seattlepi.nwsource.com/local/278100_aidsvaccine19ww.html ). Looking over the current projects ( http://distributedcomputing.info/projects.html ) I do not see anybody trying to design a protease or integrase inhibitor. Apparently this is believed to still be beyond the state of the art. I am not a computational chemist, so I have no real idea what is practical and what is not.

Lawrence
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Re: Compute the best molecule to fight AIDS

There are certain limitations on what makes a compound suitable for use in a drug. Other scientists have already approached the problem from that end, creating designer molecules (billions of them) and filtering out the ones that don't have "drug-like" properties. This process rapidly gets too technical for me to understand, so I'll not confuse you with details.

Most of these massive libraries are also constructed in a way that means all the compounds can actually be synthesized using existing techniques, so can be used for further testing immediately.

So, MPCevat, while there are other strategies for finding drugs, other research labs around the world are already exploring these possibilities.

As for a common denominator - it is my understanding that the complexity of the bond and the number of different ways a drug can bond to a protein means that backtracking is considerably tougher than it sounds - and currently simply isn't practical (and due to these factors, there is no obvious common factor in the drugs that are already known). Besides, one of the goals of FAAH is to find drugs that are effective against many mutated forms of HIV.
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MPCevat
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Re: Compute the best molecule to fight AIDS

Thank you, Lawrencehardin and Didactylos, for your interesting answers. You both seem to say that we're just not there yet. Maybe I'm just impatient and try to look behind the limits of the state-of-the-art (or I'm that infamous fool that can ask more questions than the greatest scientists can answer). After reading some of the articles on the sites you refer to, I think that we best just keep up the good work and see where we end up.
[Sep 19, 2006 6:19:47 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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