Thursday, January 14, 2016

Strain-Release Amination – Your Guide to Make Super-Paxil!

HELLO AND WELCOME TO MARS!!: This post chronicles the path that we took to solve a 45 YEAR OLD PROBLEM and how this led to our exploration of privileged strained ring systems that look like they come from another planet.

It all started in late 2014 when we were approached by Pfizer to provide a kilo-scale synthesis of [1.1.1]Bicyclopentylamine – that’s right…..1KG!!

          The need for the supply of [1.1.1]Bicyclopentylamine was URGENT as medicinal chemistry programs were HALTED due to lack of a route to provide large quantities of this material for clinical trials. Yes folks, I’m talking about a true REAL WORLD problem that required an immediate response. A problem of this ilk was a first for the Baran Lab and we were definitely blown back on our heels by this seemingly insurmountable challenge. But we
were determined to solve this in order to facilitate the delivery of potential therapeutics to patients.
         After conducting an extensive literature search, it became apparent why this structure is so difficult to access in any meaningful quantity. Upon analysis of all of the previous routes, we identified an approach that we felt was the most direct route and thus, the most challenging. Due to A LOT of development in the synthesis of [1.1.1]Propellane, we figured a direct amination across the central bond would be the best approach to solve this
problem. However, we knew that this would be a daunting task as the approach was simple and surely someone has tried to develop this reaction in the past….right? In fact, several innovative attempts were made to directly aminate [1.1.1]Propellane but all of these attempts were 3 steps or more, utilized toxic/hazardous reagents, or provided non-viable intermediates that could not be converted to the desired product.
        We were inspired by a report by Ernest Della in 1990 where a halogen-metal exchange and subsequent quench with CO2 was attempted but an unusual reaction occurred whereby t-Buli essentially added across the central bond and was subsequently quenched with CO2.

          I then wondered if a metalated amine could do the same sort of reaction and it was around this time that Justin courageously joined my project and we sought out to test this hypothesis. During this time, I would often keep saying that "There is a light at the end of the tunnel." and Justin would respond "Umm..yeah...let's hope a train isn't on the other side though." I have to admit, he was right in saying that as this problem was anything but trivial. Anyhow, we pressed on into the dark unknown.


        After countless attempts to develop a direct amination reaction, we were finally successful when we generated the lithiated amide of dibenzylamine and added it to a mixture of [1.1.1]Propellane. However, we were somewhat disappointed with this result because we obtained methylated dibenzylamine as a major product of the reaction due to the MeBr that was generated from the Wurtz reaction. Then, we thought we had an “AHA” moment when we swapped out methyllithium for phenyllitium but we just ended up getting phenyl dibenzylamine as the major product presumably from an aryne intermediate (from bromobenzene).
        It was at this point where Phil asked “Can you optimize this reaction?”….which translates as “You better fix this reaction!!” So, we ran A LOT of reactions in an attempt to fix this reaction but we were unsuccessful at every attempt.
      It was during this time that I remembered that Knochel’s turbo Grignard reagents have a similar reactivity profile as non-turbo Grignard reagents but tend to display some subtle differences in reactivity. When we generated our turbo dibenzylamine and added it to an in-situ prepared [1.1.1]Propellane solution and stirred overnight at 50°C in a sealed tube, we consistently obtained yields of 50-60% . WuXi was able to successfully scale-up this reaction on 100g scale and Pfizer developed deprotection conditions using their parallel optimization technology to give us our desired product.
*You can now purchase the starting cyclopropyl-tetrahalide here and  [1.1.1]Bicyclopentylamine here
     At this point, we experienced a scientific epiphany when we realized that our new method could potentially be used to "propellerize" ANY amine. I can remember the look on everyone's faces (especially the Pfizer team) when we proposed that compounds such as Paxil could be propellerized directly. The reason for this excitement is borne out of the fact that it is EXTREMELY difficult and even IMPOSSIBLE to incorporate the bicyclopentyl
moiety onto amines; especially amines within complex structures. The reason for this is that chemists are restricted to starting with the bicyclopentylamine and building up the structure of interest around it. While this may be possible for compounds such as tetrahydroisoquinoline, it is nearly impossible for compounds such as Paxil.
            
      Next, we wondered if we could use our newly developed reaction to directly aminate compounds that would be of interest to medicinal chemists. To investigate this approach, we prepared a stock solution of [1.1.1]Propellane by running the Wurtz reaction and distilling the resultant solution via rotovap. It turns out that this methodology was very general and we were able to “propellerize” a wide range of secondary amines including drugs such as Paxil (Paroxetine) and Zoloft (Sertraline).



"Turbo Azetidination"
     Next, we wondered if we could extend this methodology to other strained ring systems. We became aware of a strained precursor to azetidines [1.1.0]Azabicyclobutane or ABB. So, we prepared ABB in-situ from the tribromide precursor and we successfully aminated it with a range of amines and trapped the resulting amide with Boc anhydride.


Cyclobutylation with "Designer" Bicyclobutanes
    Another strained ring system that we were interested in functionalizing was [1.1.0]Bicyclobutane for the synthesis of “cyclobutylated” amines. After attempts to functionalize bicyclobutane failed, we realized that we would need an anchoring group that was attached directly to bicyclobutane to make this reaction feasible. A reaxys search revealed that substituted phenylsulfonylbicyclobutanes could be aminated under high temperature in a neat mixture. Since we believed that a method to directly append cyclobutanes onto amines would be of value, we sought out to explore ways to make this reaction broadly applicable. We started by reasoning that placement of EWG’s on the phenyl ring would increase the reactivity of the central bond which could allow for milder conditions which would hopefully lead to a broad substrate scope. After synthesizing a range of substituted phenylsulfonylbicyclobutanes, we chose to move forward with the 3,5-difluoro derivative because it offered a nice balance between reactivity, scalability, substrate scope, and cost. We were able to develop a room temperature cyclobutylation sequence by stirring the phenylsulfonylbicyclobutane with an amine in the presence of LiCl using DMSO as the solvent. The substrate scope of this reaction is VERY broad and we were able to synthesized these cyclobutylated amines in a facile manner. It is also noteworthy that we were able to make cyclopentylated derivatives.

      During of our investigation of strained ring systems, we became aware that thiophenol adds readily across the central bond of [1.1.1]Propellane high yield. We then wondered if the same type of reactivity could be displayed in our arylbicyclobutanes. We tested a reaction between our arylbicyclobutane and cysteine and we detected product in a matter of minutes. We were aware of the use of acrylates in bioconjugation chemistry and drugs such as dimethylfumarate that serve as acceptors for thiols. Generally, the aforementioned Michael acceptors often interact in a myriad of “off cycle” events and tend to not be very “tunable.” Since our bicyclobutanes can be easily modified, we speculated that they would display high reactivity with thiols but we were unsure as to their specificity. We tested our bicyclobutanes against glutathione (GSH) and it not only showed to have high reactivity but it was also completely selective for the sulfur atom. To further investigate the selectivity, we prepared a peptide that had one cysteine residue and our reagents showed complete selectivity under the same reaction conditions. While traditional reagents in bioconjugation did show reactivity, they were not completely selective for cysteine residues.
With this exciting result in hand, we believe that scientists can use strained ring systems as an alternative and perhaps improved approach for bioconjugation and drug development.

I am truly grateful to ALL of my Teammates who worked with me on this project including Justin Lopchuk, Lara Malins, Jie Wang, Eddie Pan, Mike Collins, Jillian Spangler, Gary Gallego, Neil Sach and the rest of the Pfizer team. You are all CHEMICAL ASTRONAUTS!!


* We have provided a step-by-step guide for all of our methods in the Science supporting information section. However, some of the pictures are blurry due to repeated compression. We have provided a link to a supporting information file with clearer pictures.

28 comments:

  1. This is very impressive, and I think it will get widely used by medicinal chemist.

    My very limited foray into this area, when I was at Pfizer, was "azetidinilation" of amines with ABB, I was using an excess (3 equivs) of secondary amine in acidified ethanol at room temp (without azetidine N-capping with Boc) and my isolated overall yields based on dibromopropylamine hydrobromide were only in 30s. (I was able to use primary amines for ABB opening also, for example cyclopropylamine, but the resulting 3-(akylamino)-azetidines with two free NH were unstable as neat free base liquids and polymerized exothermically). So your in situ method is definitely better.

    https://orgprepdaily.wordpress.com/2006/10/06/4-3-azetidino-26-cis-dimethylmorpholine-and-4-3-azetidino-morpholine/

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    1. Milkshake, I agree. This is impressive work and it will be very useful to medicinal chemists.
      It concerns me that this may be a case of industry demanding "custom synthesis – rapid delivery”. These kinds of collaborations should be approached in an incredibly careful fashion.
      The graduate students and post-docs conducting the research don't have much protection from being exploited. I'm sure they worked 70+ hour weeks and made less than $25,000 a year.
      If their research ultimately provides Pfizer with something marketable, do the students benefit? In any way other than receiving a PhD, or having their salary paid by a different source?
      In a company, someone completing a project or contributing substantially could lead to bonuses or promotions. If a contract employee were to complete a project, they might see an offer of employment extended, or not, but at the very least they will have been employed and paid at an appropriate salary. If a CRO is given a problem, their employees are compensated accordingly and have legal protections as salaried employees.
      An academic lab should not act as a CRO for industry.

      This all reads like Pfizer outsourcing a project to an academic lab to save money, not a case of a total synthesis lab using its expertise to assist industry. This is an academic lab acting as a CRO, but working longer hours and at a greatly reduced price.

      I wonder if Pfizer did anything other than sign a (small) check and say "thank you" after this was all done.

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    2. Dude, it could be worse - a lot worse. I worked with people who graduated from Katritzky group... But please lets take this elsewhere. This should not the place to continue your argument (that you started in the comment section of In the Pipeline)

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  2. Thanks milkshake! We wanted to provide a method that obviated the distillation of the ABB solution and we found that capping it with Boc was very helpful during purification. It would be nice to see people use the method.

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  3. have you tried to make some 1-bicyclo[1.1.1]pentylsulfinic acid salt, for radial propelanization of pyridine-like heterocycles?

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  4. That's a very good question and a lot of people have asked me about that! During the course of our studies on the "interrupted Barton" reaction, we were investigating preparing compounds of this type. We explored a route to a 1-bicyclo[1.1.1]pentylsulfinic acid salt with a methyl ester on the other side. This compound can be made from bis-methyl ester of [1.1.1]bicyclopentane (dimethyl bicyclo[1.1.1]pentane-1,3-dicarboxylate) through a mono hydrolysis of one of the esters to the acid. We subjected this acid to our "interrupted Barton" reaction to get to the sulfone but I never carried this material forward. At this time, I halted experiments on this project to pursue strain release. However, I do think that the interrupted Barton sequence can be used to make the sulfinate salt.
    Here's our "interrupted Barton" paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201406622/full

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  5. I think one does not need to do Barton reaction to get to this sulfinic acid, the strain release method would be faster. I think propellane might react directly with 2-mercaptopyridine. Even more direct method would be a one step process of reacting propellane with sulfoxylate anion HSO2(-). That species is unstable, a potent radical reducing agent but sulfoxylates can be made from thiourea dioxide (aka formamidine sulfinic acid) or Rongalite (hydroxymethylsulfinic acid sodium salt) by alkaline hydrolysis.

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  6. That's a great point - we tried to trap the propellane with 2-mercaptopyridine. We did see a mass hit but it turned out to only be a small quantity after isolation. I tried to drive the reaction to the sulfone in one pot and was able to do that but I didn't have a chance to try the cleavage reaction on it. I never went back to try to optimize the trapping - which would definitely be a better approach than the Barton sequence. Maybe a better behave sulfide would work too. I like the Rongalite idea - there's a real chance that it could work!

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  7. the corresponding disulfide of mercaptopyridine (Pyr-SS-Pyr) is available from Aldrich, and it is quite reactive. Maybe it could be used as catalyst/initiator for reaction of propellane with mercaptopyridine. I would use only few mol%, to avoid getting bis-substituded product

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    1. Yup - another good suggestion. Perhaps, we should think about a method where we could functionalism heterocycles directly with propellane, ABB, dehydroadamantane...etc. Do you think this would be a useful method?

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    2. Sorry, I meant functionalize heterocycles directly with strained systems.

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    3. This would be impressive, if you can figure out how to do it. I have not thought of this; it would be more direct. (But sulfinate salts are rather nice and convenient - stable solids, using them requires only rudimentary techniques; just like Suzuki:). You would probably need some initiator that adds to propellane to form a reactive species without quenching it, or polymerizing propellane. I can't think of anything.

      A crazy unrelated thought: please did anyone look into activation of [1.1.1]propellane with transition metals, i.e. copper(I) and Rh(II)?

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    4. Thanks for your opinion and input! We tried a few shots with transition metals - we have a large optimization table in our SI. It would be interesting to explore reactivity with transition metals in the future though - maybe that could open the doors to more unique reactivity?

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  8. on second though, I think direct functionalization with [1.1.1]propellane would be well worth trying with the Fe(acac)3+PhSiH3 system: With nitroarenes as substrates, if this works, you would be able to access N-propellized anilines, so this would be a complementary system to your turboGrignard method

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    1. We did try the reaction you suggested a few times but never could detect any product. Maybe this is something that can be re-explored now that we have a better handle on the behavior and how to manipulate propellane well.

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  9. regarding direct radical functionalyzation of pyridine-like heterocycles with [1.1.1]propellane - please have you looked into triethylborane/O2 initiation? (I think ethyl group from BEt3 would likely end up as 1-ethyl-bicyclo[1.1.1]pentyl radical, but even that could be valuable)

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    1. We did not try triethylborane/O2 radical initiation conditions but these types of reactions are definitely something that should be explored. One thing that we've learned is that [1.1.1]propellane is very compatible with reactions that proceed via radical mechanisms and there is a lot of literature about this type of reactivity - Wiberg really pioneered this work. It is my hope that people will start doing all types of reactions on these systems as there is great potential for novel and interesting chemistry to be discovered.

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  10. Couldnt you publish it in Nature that has free acces? We dont have subscription to science for some reason :-D (jk) I dont know how you do that but it from my point of view, every new publication is blowing my mind more than the previous one, Im just wondering where you will end :-D

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    1. Hi Mike, The info. on this blog gives a very accurate summary of what is contained in the manuscript. Thanks for the kind words - we really wanted to "leave it all on the field" for this project.

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    2. Oh cool, so I can only read the 400 pages of supporting info, because I dont have any other papers to read :D
      Seriously, its like reading organic syntheses but better because there are pictures

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    3. Thanks Mike! I can't wait until we get to the point where we can make videos for supporting information!

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  11. Excellent paper! It's an inspiration.

    I like the behind-the-scenes blog post as well, I hope it becomes more common in our field.

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    1. Thanks Andre! I'm glad you enjoyed the post and I hope other labs do the same too. It would be great to learn how other scientists think and solve problems.

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  12. Why was the turbo amide not needed for strain release cyclobutylation?

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    1. Great question! When we tried the turbo amide on the arylsulfonyl bicyclobutanes, we observed messy TLC's along with masses on LC/MS that correspond to dimers, trimers and other polymeric forms. Thus, we believe that the turbo amide was too strong of a nucleophile for these activated bicyclobutane systems. That's when we decided to develop "designer" bicyclobutanes by altering the electronics on the aryl ring so that we could run the reaction with amines at room temperature. Also, the ability to run the reaction at room temperature with these bicyclobutanes (such as the difluoro derivative) was essential for our peptide examples.

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  13. Please have you tried your strain release systems on quadricyclane? It is commercially available (and not too expensive) and all that could find in Scifinder were reactions where quadricyclane behaved as a pseudodiene or cyclopropane. If you could make some nice mild aminations of it, I think it could be also useful to a medicinal chemist...

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    1. Hi Milkshake! We haven't tried to aminate quadricyclane but that did come up in one of our periodic meetings. I agree with you that it could potentially be a very useful reaction. There is so much chemistry to explore in this space - it will be interesting to see what comes next! Thanks for all of your suggestions!

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  14. very nice chemistry developed on strain molecular giving me happiness and inspiration

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