Monday, March 4, 2013


We'll start things off with our lab's recent synthesis of ouabagenin. We'll skip the biological relevance of the molecule for the purpose of this blog and go straight to the actual synthesis. 

We knew that the C19-OH and the butenolide installations would be trouble when we first walked into this project, and this suspicion was proven to be true as these 2 transformations took the longest time to achieve. As alluded in the paper, we initially tried to effect a porphyrin-catalyzed direct C19 hydroxylation, but this unfortunately didn't work in our hands. Thus, after months of experiments, we eventually settled on a Norrish type II photochemistry/oxidative fragmentation route to install this alcohol. The next few steps that followed proved to be rather straightforward.

We did not, however, expect the diepoxide fragmentation to be as difficult as it turned out to be. Shown here is a small sampling of conditions that we tried:
As you can see, the only reagent that could consistently give our desired product was aluminum amalgam, and even then we had to play around extensively with the condition to get satisfactory yield. 

The last thing that I would like to highlight is the butenolide installation as this took more than 6 months to achieve (including going back and forth between our estrone model system and the real system and endless procrastination on Facebook :)). We started with our estrone model system and did a Stille coupling to arrive at the corresponding dienoate. Initial reduction screening, however, gave only the undesired epimeric product at C17, which led us to consider a different strategy. We decided to try Barluenga's hydrazone/boronic acid cross-coupling (Nature Chem. 2009, 1, 494), and while we could get it to go on the estrone model system, it just wouldn't work on the actual substrate. In the end, desperation kicked in, as I really need to graduate. To reinvent my exit, we decided to go back to the Stille coupling route (directly on the model system this time). As was observed in the model system, the penultimate reduction of the dienoate proved to be difficult, but we were fortunate to  find the right condition—specifically by heating with Barton's base—that eventually delivered synthetic ouabagenin.


  1. Thanks for posting this, but it really makes me wonder what is the point of organic synthesis research. Your long hours working on just the right conditions for this will not result in more of the natural product being made available for medical research, because the conditions use heavy metals, and besides you use a hash tag that admits this is not a prep scale. So what was the benefit to the public that funded this research?

  2. Champollion: You can also ask the same question about mathematics, particles physics, philosophy or astronomy. Much of the research in these fields also does not have immediate practical benefits and yet it has propelled our understanding of science forward by leaps and bounds. This is curiosity-driven research without immediate practical benefits. The beauty of it is that a lot of times this kind of research does lead to practical, mostly unintended benefits.

    If we only decided to do research that was of benefit to the public, then not only would we not have relativity, quantum mechanics, evolution and crystallography but we also would not have lasers, computers, satellites and drugs. It is exactly work like this that carefully investigates different reaction conditions, catalyst concentrations, temperatures and reagent modifications which has led to all the practical synthetic organic products which we take for granted.

  3. Champollion asks a great question - one that has been asked continually since I was a graduate student. It is raised everywhere - from referees to NIH review panels to Derek Lowe's blog. What is the point of this kind of research? This could be the subject of an hour long lecture so let me just focus on the present work. Over the course of this blog there will be plenty of time to address this completely valid question.

    First, this work was funded almost entirely by a private company, LEO Pharma because they specifically needed a scalable route (hundreds of mg to grams) of these types of compounds. So I can assure you that in the present case it is leading to direct benefits (at least to this company that is trying to make medicines). Second, the route is quite scalable to the final key intermediate (ouabageninone, see the paper) which is the truly important compound since we don't need to make large amounts of the natural material. Finally, I should note that the key reactions in this paper were enabling to this company for the invention of some new steroidal compounds that might one day be therapeutics – I can't say more because of IP concerns.

    So rest easy, your taxes didn't pay for this work, regardless if it ends up leading to a medicine or not :)

  4. Thanks to both Phil and Wavefunction for your insights.

    Champollion, if you're referring to the diepoxide fragmentation step, I should add that we could get the desired fragmentation to work sometimes with high pressure hydrogenation, but we found this hydrogenation to be finicky and very sensitive to pressure changes, and we eventually opted not to use it as the aluminum amalgam condition proved to be more consistent and reproducible. This to me seems to illustrate a more general point that if we have access to better analytical tools and equipments to monitor the variables in our reactions, we could possibly further optimize some of our steps to make it even more scalable.

    Echoing Wavefunction's comment, I think that often times this type of curiosity-driven research could result in discovery of fundamental science. As a case in point in our work, I think that solid-state photoreaction could offer some advantages over conventional solution photolysis (some of these are outlined in Garcia-Garibay's work), and yet this method is still underutilized in our field. And I can only hope that there would be a more widespread use of it in the future.

    Lastly, organic synthesis research also could be viewed as a form of training/apprenticeship that would be highly beneficial for a career in the pharma industry. Over the past few years, I've learnt a lot in terms of problem-solving skills and how to troubleshoot a reaction when it's not working in your favor and I'm very grateful for that experience.

  5. Sure, here are 2 relevant papers for the reduction:
    Seminal report:
    Mechanistic study:
    It was proposed that the Co2B generated would act as a heterogeneous catalyst for the decomposition of NaBH4 to H2, and quite possibly as a heterogeneous catalyst for the actual reduction of the alkene. Of course, it's rather strange to have H2 do a 1,6-reduction followed by trapping at the alpha position (unless it's actually doing olefin isomerization after the initial reduction), so I'm inclined to believe that the excess NaBH4 is the actual reducing agent in our case. We do need the cobalt species as in its absence, we get only the C17-epimeric product. As you can see from the above 2 papers, this condition can reduce nitriles and isolated olefins as well.

    To be honest, we don't really understand the origin of selectivity. We went to Larock's Comprehensive Organic Transformation book and then went through the list of reagents for conjugate reduction one by one :)

    1. I can't believe you tried the tellurium reagent--by all accounts pretty unpleasant stuff, no?

    2. When you're desperate, you'll try anything :)

      We were only doing it on less than 5 mg scale, so it wasn't too bad. Making the reagent was actually pretty convenient, it was just mixing solid tellurium with NaBH4, and the substrate was then added to the mixture.

  6. Wow, thanks for the comments! I do appreciate pure research in chemistry, even synthesis, but it just seemed to be quite extreme to spend so much time on one reaction. That time, it seems to me (I don't have access to the paper) was not really driven by a deeper understanding of the chemistry but rather by a "throw everything we can at it and see what works". And therefore the results, i.e. knowing which reagent worked in this case, is not applicable to any other case and does not help the broader synthetic community. Was there some correlation between yield/products and conditions that could be extracted from these results? Of course, Prof. Baran's answer reveals the motivation for doing this, and makes it all much clearer. Thanks for the dialog. (The #notgramscale hash tag was perhaps misleading, then?)

    1. Re: hashtag- Just as medicinal chemists have a love-hate relationship with aryl ethers, our lab too has a love-hate relationship with hashtags :P

    2. Champollion you are dead-on in your general frustration with total synthesis by the general population. In fact a few years ago our grant on palau'amine was rejected largely on the basis of your statement "... is not applicable to any other case and does not help the broader synthetic community."

      We really took this criticism to heart and have tried, wherever possible, to generalize the findings made during the course of a synthesis. In the case of ouabain, although a strange observation like doing an epoxide reduction "on-water" might not be broadly interesting, it was essential for us to make large quantities of the advanced precursor to the natural product.

      Some findings are esoteric and may never lead to anything that will cure a cancer patient. Some can be more useful. Great examples abound in the literature where a strange observation made during the course of a synthesis led to methods of broad utility. Blog Syn's recent entries are based on chemistry discovered in the Nicolaou lab during a total synthesis. Another example close to my heart is the silver-mediated oxidation in the synthesis of palau'amine that led us down the road of exploring silver mediated processes and radical chemistry that some at pharma companies have found to be useful.

  7. As long as the resolution to solve a problem is adamantine, no money and time spent on finding the solution will be in vain. Even if the answer is not found before the money is exhausted, all the facts discovered during the process become the building blocks of the final solution. Knowing what doesn't work paves the way to what works eventually. And the discoveries along the way may help solve other problems that might have or haven't emerged (hope I'm not being too optimistic here). Isn't this what research is about?