Thursday, December 31, 2015

We made antroquinonol A then did things with it

Hello! I worked on this rather atypical paper and am here to tell you a little about how it progressed on the ground. As always, how the paper looks when it’s finished shares little resemblance to the journey. This is our only molecule that has its own youtube video.

A long long time ago in 2012, Bristol Myers Squibb (BMS) approached our group about working on the molecule Antroquinonol A due to interest in its anti-cancer and immunological properties. This molecule is not your typical “jungle-gym”-looking behemoth terpene that the Baran group usually pursues. Nor was it reported to have the kind of picomolar activity that makes medicinal chemists wake up in the morning. But there existed a litany of publications on the biological activity of this molecule and a company had deemed it worthy of significant financial investment, starting FDA clinical trials on the isolated natural product. This kind of molecule does not usually garner serious synthetic interest because it is not scary looking enough for an academic group but also a little too complicated to garner interest from many companies. However, at Scripps we have an interesting Academia-Industry collaboration with BMS that I think seeks to fill this gap.

Well aware of the fact that antroquinonol A lacked the kind of complexity that leaves people unsure of how it could ever be made, the goal from an academic perspective was to find a way to make antroquinonol that would be inherently interesting. In this spirit, Phil handed us a bottle of the dietary supplement Conezyme Q10 and said “why can’t we just reduce this into antroquinonol A?”.

So we quite literally isolated coenzyme Q10 from those pills and started playing around with this molecule. We had little hope this reaction could be done but I was a young second year and Phil is right in saying sometimes you just need to run the reaction. We came up with rationalizations about how the 4 consecutive oxygens on the benzene ring could reduce its aromaticity and found loosely related precedents but to no one’s surprise we were never able to get this reaction to work. Figure 1 of the paper quickly summarizes some of the things we tried but I’ll share a little more detail on two of the crazier ideas in the figure below.

   Solidly convinced that I was not going to be the one to come up with a way to reduce quinones into useful cyclohexane rings, we moved towards ring buildings strategies. Working with a talented postdoc, Dr. Eran Sella and a promising undergraduate, Garrett Saul, we were able to test out a good number of ideas on new ways to build substituted hydroxycyclohexenones. All were met eventually with failure but I’ll share with you a few of the molecules we made along the way.

Funnily enough, the route that worked and is reported in the paper was one of the first things we proposed but was shelved to try more academically interesting ideas first. You can get enough details directly from the paper (or from other bloggers) so I won’t go through it again here. As you can imagine, even this less ambitious route was met with your typical disasters but after ~9 months we had a reliable way to make a lot of antroquinonol A. I will say that it was truly fun to get to work on a molecule small enough to try so many ideas and that brainstorming these wacky ideas with lab members will be one of my favorite memories of graduate school.

So as you can read in the paper (since its open access!), we sent off a vial full of this compound to BMS for testing, only to be surprised that their data did not match what was reported in the literature. I spent most of the next year trying to convince myself that I hadn’t screwed something up. The team at BMS proposed that a metabolite of antroquinonol may be the active component and did great work identifying a not previously reported structure. We synthesized enough to test and found that this molecule was also inactive. We made the opposite enantiomer just to be cautious (even though our optical rotations matched) and also found that to be inactive. It’s beyond my scope as a synthetic chemist to guess what is really going on here but from what I have read, it is not that uncommon of a problem.

In the end I think this project was a good demonstration of why synthesis can still be relevant. Access to gram quantities of a pure, synthetically derived natural product has shed new light on a drug that is currently being tested on actual people. The mixing of interests from both industry and academia allowed us to work on a molecule of genuine importance but in an academically free way that was not just about producing the molecule as quickly as possible.

Wednesday, October 21, 2015

Baran lab does steroids!!!

Our latest installment in sterol synthesis just came out in JACS, which describes a very interesting reaction in my opinion. While you can read all about the reaction development and the synthesis in the paper, I would like to share about some ‘behind-the-scene’ stories.

As chemists, I find it strange and surprising how risk adverse many of us are when we try out new reactions or plan a synthesis, I myself included. I totally understand it when you have barely any material when you are at the frontline of your synthetic war. But more often than not, I think we can afford to be more adventurous (not in the throw Na down the sink sense) in our daily chemistry. Well perhaps if I were more adventurous, I would have saved myself ~10 months and there would not have been Figure 1B in the paper. Truth be told, I was extremely skeptical of whether the Schonecker oxidation would even work; and when it did, would I be even capable of optimizing the conditions?

While there is still a lot of work to do be done on the Schonecker oxidation conditions, there were some interesting observations that initially led us to revise the mechanism of the reaction, at least under our reported conditions. Based on Schonecker’s proposal, it seemed clear that we are getting data that suggests that something else is happening other than homodimerization as the committed step in the reaction:

This, together with a bunch of experiments that were conducted (the most important ones are in the paper) eventually led to the mechanism that was proposed.

We also tried a bunch of other non-steroidal substrates, some of which gave some interesting products:

Notably, the cleavage of the cyclobutane in the second substrate gave good support for the radical nature of the reaction. Most of these eventually did not make it to the paper partially because of us running out of writing space but also because we struggled to push the imine formation to completion (but the oxidation seems to work great > 80% NMR).

There were also a whole bunch of other substrates that just ended up not reacting:

From the substrates that failed to work, it is clear that some form of steric constrain would help direct the reaction but as with everything in Chemistry, you wouldn’t know until you try. Then again, as organic chemists, why wouldn’t you want to run a reaction that starts off brown, turns green and allows you to oxidize stuff with oxygen in 3hrs?

Having made a bunch of pyridines in the process of optimization, I think this is where the next improvement would be found. Optimization of the directing group would almost certainly lead to a reaction with a broader substrate scope than we’ve shown. To top it all off, we made 3 natural products!!!

Clearly, the journey to the eventual publication was by no way direct and short and nice and rainbows and unicorns. But it was made a lot easier with all the people along the way! So a huge thanks to the LEO guys (who were always supportive and understanding) and my teammates, Yoshi and Aaron!

- Yi Yang See