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> Поиск ингибиторов вируса простуды!
Apr 20 2010, 10:56
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9 Apr 2010

While the results are still preliminary, it appears that Rosetta@home has produced an extremely exciting result! As I described a few posts ago, many of you through rosetta@home contributed to the design of proteins predicted to bind very tightly to the influenza flu virus. We have now completed the first round of testing of the designed proteins, and one of them in the experiments conducted thus far clearly binds very tightly to the virus. Our data also indicate that the binding is at a site critical to the virus invasion of our cells, and so the protein may be able to neutralize the virus. I will keep you posted over the next couple of months as the picture becomes clearer--but for now--thank you all for making this possible!!

11 Apr 2010

I was asked on the discussion thread about the timescale for learning more about the influenza binding protein I described in my previous post. I'm reposting my answer here:

We are doing a series of tests and control experiments in my lab in the next 2-3 weeks to rule out various possible artifacts. If, as we expect, the design passes with flying colors, we will send it to Scripps research institute where the ability of the design to neutralize the virus in cell based tests and the extent to which the design neutralizes different strains of virus will be measured. I would expect we would know the results of this in several months. We will also work to solve the crystal structure of the design bound to the virus to confirm the design binding mode. This hopefully will not take more than a few months as well.

I will keep all of you posted here about the results from these experiments. I am very optimistic, but one should be cautious about getting to excited too early about results like these--there are very many places where things can go wrong just with the biochemistry, and after this there are very many steps to actually make a protein into a drug--this is why there are so few new drugs for curing diseases being discovered.

For those of you who would like to try your hand at improving designed binders to the influenza virus, we are now posting virus inhibitor design challenges on foldit.

19 Apr 2010

Experiments this past week have made us even more confident that the designed influenza binder is working as in the design model. we used "directed evolution" methods to identify amino acid changes that make the rosetta@home designed protein bind even more tightly to the virus. we found mutations at two positions: first, at an alanine residue in the design, the evolution process found a valine, and inspection of the design model showed some extra space around the alanine that would be filled by the slightly larger valine. the second amino acid change involved a charged aspartate residue in the design that in retrospect was too close to the virus protein--it was changed to a non charged residue which is less energetically costly to bury upon binding.

we are now combining these two substitutions, and expect that the combination should bind still more tightly to the virus than any protein we have tested so far. we should know later this week--I'll keep you posted!

Если кратко, в Розетте рассчитали довольно реалистичный ингибитор для вируса простуды, который, как доказано на экспериментах "вживую", хорошо присоединяется к вирусу простуды, и может его нейтрализовать. Через 2-3 недели в Бейкер Лаб мы закончим внутреннее тестирование, и если все пройдет успешно, отправим новый ингибитор в исследовательский институт Скриппса чтобы измерить насколько сильно новый протеин взаимодействует с вирусом. Результат оттуда будет известен через несколько месяцев.

Девид Бейкер пишет что он очень оптимистичен, и на пути исследования могут возникнуть много "подводных камней".
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