Monday, January 14, 2019

Technique primer: Test tube columns

As many of you remember, a little over a year ago Phil did a AMA on reddit. On that AMA, a bunch of people requested that we do a post on how to build/run disposable test tube columns:

Well, writing up this blog post somehow slipped through the cracks for a year (Sorry!!), but without further delay, here's how we do the technique.

Step 1: Building the glassware. 

We use these columns on crude reaction mixtures from ~10 to ~500 mg scale. For smaller scale than this, we use prep TLC; larger, just a standard reusable column.

To build the column, for 10-50 mg, we just use a Pasteur pipette as the column. For 50-200 mg, we build it out of a 16 X 150mm tube. For 200-500 mg, we build it out of a 25 X 150 mm tube.

For the latter two, the first step is to pull a bottom spout from the test tube. Basically, you heat the tube with a Benzomatic torch, until you see the bottom glow orange and "wilt" slightly. At this point, you grab the glass with a pair of tweezers and steadily pull to make a long stem. It's hard to explain, but easy to demonstrate:

It's a bit tricky the first time, but gets simple with practice.

After letting the tube cool to rt, snapping off the bulk of the stem gets you a nice looking column:

(If you're using a Pasteur pipette, you get to skip to this stage)

Step 2: Building/running the column.

From here, it's just a matter of packing a small chunk of Kimwipe into the bottom, and tamping it down, followed by adding a bit of sand, and then silica gel. With modern silica gel, we have found that even <3" column height is still plenty to do reasonable separations. After equilibrating with a column volume or two of solvent, here's what it looks like, ready to load and use as usual:

One nice thing about the column sizes is that the 16mm tube (loosely) accommodates a 14/20 inlet adapter, while the 25mm tube (loosely) takes a 24/40 adapter. This way, you can run it with positive air pressure exactly as you would any other flash column. This is a 16mm tube, and as you can see, the small inlet adapter fits it nicely:

When the column is finished, here at Scripps, our EH&S allows us to dispose of the whole thing, tube and all, into our silica waste stream. Check with your EH&S for what to do at your institution.

Regardless, the best part of this technique is there are no dishes to wash!

Hope that this helps aspiring chromatographers,

Baran Lab

Sunday, January 13, 2019

11-Step Total Synthesis of Teleocidins B-1–B-4

Our paper describing the total synthesis of Teleocidins B-1–B-4 is now published in JACS! I started working on this project in November 2017 and completed the synthesis in June 2018. I then spent another 6 months optimizing the route to increase the yield and decrease the step count.

In the biosynthesis of these molecules the indolactam core is transformed into Teleocidin by a Friedel-Crafts type reaction with a terpene fragment. However, nature’s synthetic strategy provides a mixture of Teleocidins B-1-B-4 which is something we wanted to avoid. When I started to evaluate our own synthetic strategy, I immediately identified the introduction of the two quaternary carbons to the indolactam core in a stereocontrolled fashion as the major challenge (even one sterically hindered quaternary carbon can be difficult!). I knew we would have to establish the relative stereochemistry independently because the terpene fragment and amino acid moieties are quite distal. 

I also realized we needed to install a functional handle on the indole moiety in a highly regioselective fashion to facilitate coupling with the terpene fragment.With a bit of luck (and a lot of hard work) we were able to overcome these challenges and you can find the details in the paper/SI. I wanted to use this blog post to provide further insight into some of the key reactions which led us to success.

In the beginning, we had to fight against nature…

The first step in our synthesis is an electrochemical amination between our indole scaffold and valine. After optimization, I tried to scale up the reaction using some conventional large glassware which I bought from our local Japanese supermarket. However, almost no desired product was observed and even worse, I lost 6 grams of starting material along with the nickel, ligand and my time. I was so shocked that I couldn't even find my tongue! Phil suggested to try again but this time using the ElectraSyn carousel. The switch in setup facilitated reactivity and with a little optimization the desired product was formed in 51% yield.

I also want to highlight one of the unexpected problems we faced in this synthesis which is not described in the paper. While the desired indolactam is commercially available, it costs $274 per mg (Sigma) so it was a bit outside of our budget! We first tried to make the 9-membered ring by hydrolysis of the valine methyl ester followed by condensation using HATU, but the desired product was isolated in just 19% yield. However, after plenty of screening we found that the use of LDA was crucial for this reaction and we managed to obtain 2.1 grams of the protected indolactam! That was a really great day in the lab.

In April 2018 I was joined by Kosuke, a very talented visiting student from Osaka (Japan), who really helped me to optimize the route to what is now shown in the paper. Yuzuru, an amazing graduate student, also helped me by optimizing a key reaction and preparing a late-stage intermediate. I want to thank the team and especially Phil who was always ready with a lot of suggestions. I can definitely say he never compromises in the quest for an ideal total synthesis. 

Hugh and Teleocidin team

Thursday, January 3, 2019

Decarboxylative carboxylation: radiolabeling carboxylic acids the easy way

Our latest paper, which arose from a collaboration with the radiochemistry team at BMS, describes a new approach to carbon-14 radiolabeling and is now published in JACS (after previous submission to the ChemRxiv). I began working on this project as a visiting student in October 2017 and it has been an amazing learning experience with some tough challenges and valuable lessons. In this blog post I want to discuss some of the interesting problems we encountered upon diving into the field of radiochemistry.

To summarize, our synthetic approach consists of the formation of a redox-active ester followed by a chemoselective nickel-catalyzed decarboxylative carboxylation to reintroduce the (now radiolabeled) carboxylic acid. That carbon-14 label is a useful tool for radiochemists to perform the absorption, distribution, metabolism, excretion and toxicity studies required for drug development. Our method has some nice advantages including the two-step degradation-reconstruction synthetic approach (starting from the unlabeled product which is usually available in plentiful supply) and the use of [14C]-CO2, the cheapest and most common carbon-14 reagent.

During the initial reaction development, we successfully performed the desired decarboxylative carboxylation sequence using 50 psi of [13C]-CO2. Although this procedure allowed us to test the scope of the reaction (scheme 2 in the paper), our collaborators let us know the pressure and use of excess labeled reagent were big problems when it came to translating to radiolabeled [14C]-CO2.  

We first considered limiting the stoichiometry of the [14C]-CO2 to about 10 equivalents while maintaining the pressure in the system. Several options were considered included pressurizing with an inert gas (discounted due to the dependency of the concentration of CO2 on its partial pressure, rather than the overall pressure), pressurizing with unlabeled CO2 (avoided because it would dilute the radiolabel too much) or using amine additives to sequester the CO2 into solution and promote reactivity (no reaction observed presumably due to coordination to/deactivation of the catalyst). Thinking further about the factors which influence the concentration of a gas in solution we realized it may be possible to accomplish our goal by simply cooling the reaction down. Gases are more soluble at colder temperatures (when most gases dissolve in solution the process is exothermic, an increased temperature causes an increase in kinetic energy which promotes gas escape from solution). Through use of Henry’s law, the concentration of CO2 in solution under the pressurized [13C]-CO2 conditions was estimated. With this figure as a target, the temperature required to obtain a similar concentration at atmospheric pressure of CO2 was calculated to be about -25 °C. 

Running the reaction at -25 °C gave, perhaps unsurprisingly, only partial conversion of the starting material to the product. Using 10 equivalents of CO2 at atmospheric pressure and maintaining the cryogenic period for just one hour then sealing the vessel, warming to room temperature and stirring overnight gave full conversion of the sm with efficient isotopic incorporation (see the SI S12-S14 for further details)! The BMS team were now satisfied with this procedure and after making a few minor adjustments, they produced a working carbon-14 setup using standard radiochemical glassware and techniques. Upon testing the method with [14C]-CO2 we observed isotope incorporations suitable for use in all preclinical and clinical ADME studies and the project could be called a success. All in all, application of the method to the strict requirements of carbon-14 setting led us to some fun and interesting challenges and provided the answer to the age-old question…


Although we think Breeder Steve may have been considering one particular decarboxylation process, we can conclusively say the answer is yes #chemistrygoals! I would like to thank everyone in the lab for all their help on this project and please check out the complementary carbon isotope exchange methods just published by the Shultz group at Merck and the Audisio group at Universit√© Paris-Saclay.

Cian Kingston
La Jolla, CA
January, 2019