Friday, June 25, 2010

Reaction Attempts Explorer

Two months ago I reported on the Reaction Attempts project and the availability of the summary as a physical or electronic (PDF) book. The basic idea behind the project is to collect organic chemistry reaction attempts reported in Open Notebooks. This would include not only successful experiments but also those which could be categorized as failed, ambiguous, in progress, etc.

The book was organized with reactants listed alphabetically. In this way one could browse through summaries of the types of reactions being attempted by different researchers on a reactant of interest. There might be information there (what to do or what to avoid) of some use for a planned reaction. At the very least one could contact the researcher to initiate a discussion about work that had not yet been published in the traditional system.

Andrew Lang has just created a web-based tool to explore the Reaction Attempts database in much more sophisticated ways.

Here are some scenarios of how one could use it. On the left hand side of the page is a dropdown menu containing an alphabetically sorted list of all the reactants and products in the database. Lets select furfurylamine.

This immediately informs us that there are 230 reactions involving furfurylamine and it lists the schemes for all these reactions upon scrolling down. That's still a bit hard to process so a second dropdown menu appears populated with a list of other reactants or products involved with furfurylamine.

We now select boc-glycine and that narrows our search to 145 reactions.

Selecting benzaldehyde from the third dropdown menu narrows the search further to 61 reactions.

The final dropdown menu contains a short list of only isocyanides and thus all represent attempted Ugi reactions. Selecting t-butyl isocyanide gives us 56 reactions.

That means that these same 4 components were reacted together 56 times. Looking at the various reaction summaries will show that some of these are duplicates for reproducibility and others vary concentration and solvent and the effect on yield is included. This particular reaction was in fact the subject of a paper on the optimization of a Ugi reaction using an automated liquid handler.

Now here is where the design of the Explorer comes in handy. We might want to ask if the reaction proceeds as well with the other isocyanides. All we have to do is switch the final dropdown menu to ask what happens when we go from t-butyl to n-butyl isonitrile. There is a single attempt of this reaction and it is "failed" in the sense that no precipitate was obtained from the reaction mixture. This doesn't mean that the reaction didn't take place - it might be that the Ugi product was too soluble. We can quickly inspect that the concentration and solvent are in line with conditions that allowed precipitation of the t-butyl derivative.

OK lets see what happens with n-pentyl isocyanide.

It looks like it behaves just like n-butyl isocyanide: another single non-precipitation event. What about benzyl isocyanide?

This time we do get the Ugi product from a single attempt. Note the lower yield compared to the t-butyl isocyanide under similar conditions.

What about with cyclohexyl isocyanide?

This time we hit an experiment in progress. A precipitate was obtained but it was not characterized. We can click on the link to the lab notebook page (EXP232) to learn more about how long it took for the precipitate to appear but there are not enough data to draw a definite conclusion about the successs of the reaction. However, based on the results from the other precipitates in this series it is probably encouraging enough to repeat and characterize the product.

There are other sources of information here. Clicking on the image of the Ugi product takes us to its ChemSpider entry. In this case the only associated data relates to this reaction attempt.

Lets look at another scenario: reactions involving aminoacetaldehyde dimethyl acetal.

In this case we find the intersection of two Open Notebooks. The first reaction comes from Michael Wolfle from the Todd group.

The second comes from Khalid Mirza from the Bradley group.

In order to learn more about the nature of the overlap we can use the substructure search capabilities of the Reaction Explorer. Simply click on the image of the acetal and the ChemSpider entry pops up. Now click on the copy button next to the SMILES for the compound.

Paste the SMILES into the SMARTS box of the Reaction Explorer.

We get 13 reaction attempts for this query - the two we found earlier and the rest corresponding to attempts by Michael Wolfle to synthesize praziquanamine.

We learn that one connection between these two notebooks involves different attempts at synthesizing praziquantel.

Hopefully this demonstrates the value of abstracting organic chemistry reaction attempts from Open Notebooks into a machine readable format. Contributions to the database require only the ChemSpider IDs of the reactants and product and a link to the relevant lab notebook page. Reaction schemes are automatically generated by the system. More on the Reaction Attempts project here.

Monday, June 07, 2010

IGERT NSF panel on Digital Science

On May 24, 2010 I was part of a panel in Washington for the NSF IGERT annual meeting. As I mentioned previously, it is encouraging to find that funding agencies are paying more attention to the role of new forms of scholarship and dissemination of scientific information.

My co-panelists included Janet Stemwedel, who talked about the role of blogging in an academic career, Moshe Pritzker, who made a case for using video to communicate protocols in life sciences and Chris Impey, who demonstrated applications of clickers and Second Life in the classroom.

We only had 10 minutes each to speak so the presentations were basically highlights of what is possible. Still, it was enough to stimulate a vigorous discussion with the audience. There was a bit of controversy about the examples I used to demonstrate the limitations of peer review in chemistry. People can misinterpret what we are trying to do with ONS - it certainly doesn't include bringing down the peer review system (not that we could anyway). But we have to face the situation that peer review does not validate all the data and statements in a paper. It operates at a much higher level of abstraction. Providing transparency to the raw data should work in a synergistic way with the existing system.

My favorite part of the conference was easily Seth Shulman's talk on the "Telephone Gambit". Ever since reading his book, I have been using the story of how carefully reading Bell's lab notebook has forced us to revise the generally accepted notion of how the telephone was invented. Seth's presentation was truly captivating because he explained not only what was done but also what motives were at work to deceive and obfuscate. This cautionary tale is still very much relevant to science and invention today - and highlights how transparency can mitigate against this type of outcome.

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Tuesday, June 01, 2010

Use of ONS to protect Open Research: the case of the Ugi approach to Praziquantel

As we were collecting reactions from The Synaptic Leap for the Reaction Attempts project, Andrew Lang noticed that there might be a quick synthetic route to praziquantel via a Ugi reaction. I researched it further and found a paper (Kim et al 1998) where Ugi product 1 was indeed converted to racemic praziquantel via the Pictet-Spegler cyclization.

Using Beilstein Crossfire the only synthesis of 1 I found involves a multi-step amidation strategy. But this compound should be accessible in one step from commercially available starting materials via a Ugi reaction (shown above). Since all the starting materials are liquids we have some flexibility with solvent choice. Khalid first tried it in methanol EXP258 a few weeks ago but did not get a precipitate. He was going to monitor it by NMR next to see if the problem was high solubility of the Ugi product or with the reaction itself.

It was therefore with great interest that I read Mat Todd's report this morning on The Synaptic Leap that a German patent had been issued on this Ugi strategy to praziquantel. (TSL didn't provide a means of leaving a comment so I edited the page - which made me the author of that post but actually Mat wrote it)

I have often mentioned during my talks that Open Notebook Science could be used not only in a defensive manner to claim academic priority - but also as an offensive tactic to block patent applications. A company attempting to prevent the commercial exploitation of rival inventions has a few options. Where applicable, it can buy up an existing patent pool with the intention of sitting on it. For new inventions, it can do research and try to file patents before their competitors. But this is a costly process and it may make more sense to simply publish the inventions to create disclosed prior art, thereby blocking patent applications of their competitors.

But - as I and many others have discussed - the current publication system is not optimally suited for the purpose of simply disclosing and communicating science. Not only is it generally slow but the traditional article format requires a narrative of some sort - rarely can single experiments be published. This means that much (if not most) of research done by an individual or group will never be disclosed.

For these reasons I think that keeping an easily discoverable Open Notebook for projects designed to block patent submission by competitors makes a lot of sense - both economically and from a workflow perspective. Since researchers already have to keep a lab notebook, making it public doesn't impose the added time that writing an article or patent will require.

In this specific example of praziquantel we were too late. But if we had recorded this experiment a few years ago it might have worked to block Domling's patent. Now, it isn't clear to me that EXP258 would have been enough to do that. The strategy to make praziquantel via a Ugi reaction was clearly stated but the experiment was not conclusive. However, since Domling reported that methanol worked I am sure that we would have had the "reduced to practice" evidence in the notebook shortly.

Above I used a company as an example of a party motivated to disclose inventions to protect their interests. In our case it would not be a company but rather the entire Open Science community. It is in our best interest to keep our scientific territory as unencumbered by patents as possible. Keeping Open Notebooks might be one of the simplest means of ensuring that.

Consider a humanitarian organization that might want to manufacture praziquantel. I haven't researched it but presumably the Domling patent was filed in a number of countries beside Germany. In order to consider using the Ugi strategy, the organization would now have to deal with the patent holder. This might be the factor that makes this route untenable. Patents have proven to be problematic for humanitarian aid - even in the simple case of providing food.

But all is not lost. In addition to offering a simple 2-step synthesis of praziqantel, the Ugi route offers an easy way to make large libraries of analogs. Optimally we would like to work with someone who has experience with docking praziquantel. It might be interesting to screen not only the praziquantel analogs but also the uncyclized Ugi products themselves. When we did this for malarial enoyl reductase inhibitors (D-EXP005) we found that we did not need to cyclize to obtain compounds predicted to bind. This ultimately led to active compounds.

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