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Sydney Grammar School Daraprim Synthesis #374

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alintheopen opened this Issue Mar 8, 2016 · 111 comments

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alintheopen commented Mar 8, 2016

As decided in issue #311, Sydney Grammar School Students are attempting to synthesise Daraprim at School. Background below is edited from issue #311

This molecule received a lot of press back in 2015 owing to the price hiking over in the USA. Turing pharmaceuticals wanted to raise the price from $13.50 to $750 per dose. Public and media outcry led the company to reconsider the pricing options but a synthesis in the open would be great to see. Daraprim was originally synthesised as an antimalarial (by Nobel prize winner Gertrude Elion) and is now used in combination with a sulfonamide for the treatment of toxoplasmosis.

The students could synthesise pyrimethamine using the route highlighted below (nabbed from Wikipedia https://en.wikipedia.org/wiki/Pyrimethamine) and with supporting evidence found in the literature. Stronger bases are typically used for step one, and some routes use diazo compounds for step 2, but I think this method looks quite robust and uses reagents that are accessible and could be handled by the students, under your supervision of course. We could potentially test all compounds against malaria (after designing some novel analogs), TB and also against toxoplasma gondii if we can set up a collaboration.

daraprim_num_update

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alintheopen commented Mar 8, 2016

@tscmacdonald summarised his progress on the Daraprim synthesis at the end of 2015 here Tom performed the first reaction, acyl condensation and optimised conditions (potassium tert-butoxide, THF) to obtain the first product (2) in ~70% yield.
*edit: lit conditions use diazomethane to obtain 3 from 2 and we need to avoid this as the synthetic work is being done in a high school *
Tom then performed enol alkylation and used the crude material (3, uncharacterised)** in a guanadine condensation that failed to yield the desired product (4).

Originally we had hoped to run an 1st year UG project at USyd concurrently with Sydney Grammar's work but decided that this project wasn't suitable for 60 students at this stage.

@ErinSheridan and I have just chatted on the phone and agreed on the following plan of action for Sydney Grammar's project.

  1. Erin to drop off sample of SGS-10-1 for NMR analysis at USyd. I will check to see if they have successfully made 2
  2. SGS will resynthesise 2 using Tom's method and upscale their own route.
  3. I will purify a large quantity of this material so that we have grams to work with.
  4. SGS will attempt different conditions for the transformation of 2 to 3 without the use of diazomethane

Any suggestions for conditions for the transformation described in point four would be very welcome so please, post away.

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drc007 commented Mar 8, 2016

A few thoughts

It would be worth spending a little time conforming the identity and purity of intermediate 2. NMR would be very useful.

Whilst I agree I would not want school students using diazomethane, could a more experienced person use it to make an authentic sample of intermediate 3 on a small scale? Perhaps use TMSdiazomethane. This would make optimisation of the alternative procedures much easier to follow.

On 8 Mar 2016, at 05:06, alintheopen notifications@github.com wrote:

@tscmacdonald https://github.com/tscmacdonald summarised his progress on the Daraprim synthesis at the end of 2015 here http://malaria.ourexperiment.org/daraprim_synthesis/13962/Pyrimethamine_synthesis_Status_at_end_of_2015.html Tom performed the first reaction, acyl condensation and optimised conditions (potassium tert-butoxide, THF) to obtain the first product (2) in ~70% yield. Tom then performed enol alkylation and used the crude material (3, uncharacterised)** in a guanadine condensation that failed to yield the desired product (4).

Originally we had hoped to run an 1st year UG project at USyd concurrently with Sydney Grammar's work but decided that this project wasn't suitable for 60 students at this stage.

@ErinSheridan https://github.com/ErinSheridan and I have just chatted on the phone and agreed on the following plan of action for Sydney Grammar's project.

Erin to drop off sample of SGS-10-1 http://malaria.ourexperiment.org/daraprim_synthesis/13973/Synthesis_of_24chlorophenyl3oxopentanenitrile_SGS_101.html for NMR analysis at USyd. I will check to see if they have successfully made 2
SGS will resynthesise 2 using Tom's method and upscale their own route.
I will purify a large quantity of this material so that we have grams to work with.
SGS will attempt different conditions for the transformation of 2 to 3 without the use of diazomethane
Any suggestions for conditions for the transformation described in point four would be very welcome so please, post away.


Reply to this email directly or view it on GitHub #374 (comment).

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alintheopen commented Mar 8, 2016

Hi @drc007. I have a sample of SGS '2' that @ErinSheridan dropped off today. I'm going to analyse tomorrow and see if it's the right product. Then the students will scale up Tom's synthesis and we'll purify their starting material. Good idea with the authentic sample, we mentioned that in the call today and it would certainly be good to have something for the students to TLC against. There have also been a few suggestions over on Twitter.

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MedChemProf commented Mar 8, 2016

@alintheopen It may be too late in the game to modify the synthetic plan, but it might be worth considering the below route for any future modifications. Below are listed a few examples, but there are other Suzuki examples on similar pyrimidines.
suzuki1
"Structural studies on bioactive compounds. Part 37. Suzuki coupling of diaminopyrimidines: a new synthesis of the antimalarial drug pyrimethamine", Journal of Chemical Research, Synopses (2002), (10), 482-484. Publisher: (Science Reviews) CODEN:JRPSDC ISSN:0308-2342.
suzuki2
"Rational design of 6-(2,4-diaminopyrimidinyl)-1,4-benzoxazin-3-ones as small molecule renin inhibitors", Bioorganic&Medicinal Chemistry (2007), 15, (17), 5912-5949. Publisher: (Elsevier Ltd.) CODEN:BMECEP ISSN:0968-0896.
bromination
Kosogof, Christi; Liu, Bo; Liu, Gang; Liu, Mei; Nelson, Lissa T. J.; Serby, Michael D.; Sham, Hing L.; Szczepankiewicz, Bruce G.; Xin, Zhili; Zhao, Hongyu, U.S. Pat. Appl. Publ. (2005), US 20050171131 A1 Aug 04, 2005.

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alintheopen commented Aug 15, 2016

Good news! Looks like SGS 10-2 could be the right product. Awaiting HRMS data and will run a mp to compare to literature values:
http://malaria.ourexperiment.org/uri/93c

'quartet' is more complicated

sgs-10-2-3 400 mhz proton
sgs 10-2-3 carbon
mp daraprim

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mattodd commented Aug 15, 2016

Beautiful spectra! And nice pictures in Malcolm's ELN post.

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MalBinns commented Aug 15, 2016

I have noticed that the 3-D structure of Daraprim has the heterocyclic ring orthogonal to the chlorophenyl group, which could be due to electronic or steric effects. SGS 10-2-3 has similar steric interactions of the pendant keto-nitrile functionality to Daraprim. I presume that the complex CH2 quartet in the SGS 10-2-3 NMR spectra indicates the non-equivalence of the two hydrogens due to restricted rotation of the pendant keto-nitrile group.

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alintheopen commented Aug 15, 2016

👍

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MalBinns commented Aug 20, 2016

Any news on the melting point of the SGS 10-2-3? Also, the boys would love an IR to look over and interpret. Are you able to have one run and added to the NMR data?
Have you been able to identify the beautifully crystalline SGS 10-2-1? I notice that the NMR integration missed the spike at about 7.25. The spike is not due to solvent as it was recrystallized from ethanol. can you get the spike integrated too? Do you think it is an olefinic H?
The boys have been working on converting the SGS 10-2-3 to Daraprim. I think that they may be onto something, however it has been somewhat difficult as the reaction products formed appear to be highly dependent on the concentration of the reagents used. It has also taken us ages to find a suitable solvent system for the TLC analysis of the reaction products. We will know in a few days whether we have a system to make a single decomposition product of the SGS 10-2-3 or a system to make pretty pure Daraprim in a few hours. I am hoping that we will be able to post the 6 or so reaction conditions in a nice table later this week

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alintheopen commented Aug 20, 2016

Hi @MalBinns
I'll ping you when the data is ready, busy time in the lab at the moment as we try to finish #400.
mp, IR, HRMS and C13 NMR will be coming but its good that the boys have plenty to get on with for now.
The m.p will be useful to match with literature values but I would feel free to go ahead with any recrytallisation experiments in the mean time.
Peak at ~7.25 is residual CHCl3 in the deuterated chloroform - hence why it isn't integrated. Always a possibility that a proton can hide underneath this peak but unlikely - will see what C13 and HRMS say and then reassess.
Table will be absolutely great but would be really fantastic if you could post the experiments as they are being performed - this way others from the community can see the fantastic work that you are doing and make suggestions as you go.
Thanks for the update - great to be working with you! Alice

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MalBinns commented Aug 21, 2016

Thanks for the feedback.
We are working with 80mg of material at a time to conserve resources and conducting the reactions in tablet tubes. They don't take long to set up and almost all have all been assembled in one go, hence the reporting all in one go. I will attach a photo of the boys with their "reaction vessels" along with their report. It looks like real schoolboy chemistry!!

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MalBinns commented Aug 21, 2016

Hi @alintheopen and @mattodd ,

I think that the unknown material is no longer unknown. I had been wrongly assuming that the chloroform peak was some type of olefinic peak. Once again Alice, thanks for setting me straight on that. I think that the product is most likely 2-(4-chlorophenyl)-2-oxoethanenitrile, a.k.a. 4-chlorobenzoyl cyanide, The predicted nmr is reasonably close to actual with the downfield aromatic protons approaching 8.0. As the reaction was conducted in air rather than under nitrogen the formation 2-(4-chlorophenyl)-2-oxoethane can be envisaged as starting with the addition of the oxygen to the C-2 carbanion of the 4-chlorophenyl acetonitrile to form the alkoxide of the resulting peroxide. During the reaction or during workup the peroxide decomposes (abstraction of H on C-2 to form the carbonyl group on elimination of -OH?)

Is this a new way to make this compound? The yield should be able to increased greatly if there is nothing else present to react with the carbanion and dry air is bubbled through the mixture. Is there a separate paper in it "Production of xxx by the addition of oxygen to carbanion yyy and decomposition of the resulting peroxide"? I note that the cheapest source of 4-chlorobenzoyl cyanide that i could find was US$368 for 25g!

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MalBinns commented Aug 21, 2016

I think that the unknown material is no longer unknown. I had been wrongly assuming that the chloroform peak was some type of olefinic peak. Once again Alice, thanks for setting me straight on that. I think that the product is most likely 2-(4-chlorophenyl)-2-oxoethanenitrile, a.k.a. 4-chlorobenzoyl cyanide, The predicted nmr is reasonably close to actual with the downfield aromatic protons approaching 8.0. As the reaction was conducted in air rather than under nitrogen the formation 2-(4-chlorophenyl)-2-oxoethane can be envisaged as starting with the addition of the oxygen to the C-2 carbanion of the 4-chlorophenyl acetonitrile to form the alkoxide of the resulting peroxide. During the reaction or during workup the peroxide decomposes (abstraction of H on C-2 to form the carbonyl group on elimination of -OH?)

Is this a new way to make this compound? The yield should be able to increased greatly if there is nothing else present to react with the carbanion and dry air is bubbled through the mixture. Is there a separate paper in it "Production of xxx by the addition of oxygen to carbanion yyy and decomposition of the resulting peroxide"? I note that the cheapest source of 4-chlorobenzoyl cyanide that i could find was US$368 for 25g!

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MalBinns commented Aug 21, 2016

Hi, i am having difficulty saving comments. can you help? Which button do i press?

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MalBinns commented Aug 21, 2016

I think that the unknown material is no longer unknown. I had been wrongly assuming that the chloroform peak was some type of olefinic peak. Once again Alice, thanks for setting me straight on that. I think that the product is most likely 2-(4-chlorophenyl)-2-oxoethanenitrile, a.k.a. 4-chlorobenzoyl cyanide, The predicted nmr is reasonably close to actual with the downfield aromatic protons approaching 8.0. As the reaction was conducted in air rather than under nitrogen the formation 2-(4-chlorophenyl)-2-oxoethane can be envisaged as starting with the addition of the oxygen to the C-2 carbanion of the 4-chlorophenyl acetonitrile to form the alkoxide of the resulting peroxide. During the reaction or during workup the peroxide decomposes (abstraction of H on C-2 to form the carbonyl group on elimination of -OH?)

Is this a new way to make this compound? The yield should be able to increased greatly if there is nothing else present to react with the carbanion and dry air is bubbled through the mixture. Is there a separate paper in it "Production of xxx by the addition of oxygen to carbanion yyy and decomposition of the resulting peroxide"? I note that the cheapest source of 4-chlorobenzoyl cyanide that i could find was US$368 for 25g!

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MFernflower commented Aug 21, 2016

@MalBinns @alintheopen Perhaps this reaction could work? http://www.organic-chemistry.org/abstracts/literature/690.shtm

The second idea I had was to purge the flask with argon before carrying this reaction out but that might not be the cheapest option for a high school

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MalBinns commented Aug 23, 2016

Thanks for the idea. Other than the oxygen sensitivity the reaction seems to work well and gives a reasonable yield of the keto nitrile.

Can anyone tell me anything about the enol tautomer of the ketonitrile SGS 10-3? I think it has turned up in one of our attempted reactions.

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MalBinns commented Nov 18, 2016

Hi @mattodd , Alice's templete looks good but some changes will make it even better.

  1. The pentanol and pentyl ether needs to be changed to isobutanol and an isobutyl ether (Step E)
  2. Could you make the lines for Step B, C and E solid as we have completed these (depending on tomorrows nmr)
  3. Could you put a cross through Step D as it does not work.
  4. Could you swap around Step B and Compound 3 with Step E and Compound 4
  5. Could you remove the reaction of Step F as we have not attempted it in the time given (unless you want to leave it dotted.)
  6. Step B requires methanol as well as the trimethyl orthoformate. Nothing happens with only the trimethyl orthoformate.

regards,

Malcolm.

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MalBinns commented Nov 18, 2016

I still cannot connect to the reports from my phone or computer when at home. I cannot work out what the problem is and it is very frustrating. I will need to work on the writeups from School only. Very frustrating.  Sorry for inconvenience . 

Sent from my SAMSUNG Galaxy S7 edge on the Telstra Mobile Network
-------- Original message --------From: Mat Todd notifications@github.com Date: 18/11/2016 9:56 AM (GMT+10:00) To: OpenSourceMalaria/OSM_To_Do_List OSM_To_Do_List@noreply.github.com Cc: Malcolm Binns mbinns@hotkey.net.au, Mention mention@noreply.github.com Subject: Re: [OpenSourceMalaria/OSM_To_Do_List] Sydney Grammar School Daraprim
  Synthesis (#374)
Hi @MalBinns . Thanks for the draft poster. Actually Alice already developed a good template for this which contains the Daraprim back story, the relevant logos and other things. I've posted it again here - it'd be better to use this one I think. Alice has added the synthesis scheme. Not sure this needs altering? If so can you draw something and Alice can sketch it out in Chemdraw. How about adding arrows from compound structures to the relevant spectra, along with some photos of the vials/compounds? That'd use up some of the white space. Feel free to post a revised version for us all to look at.

Daraprim Template_2016.pptx


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MalBinns commented Nov 18, 2016

I am still unable to access the experiments from home, either on my computer or from my phone. Very frustrating. I and you will need to wait until I can access the school computer on Monday. Sorry for inconvenience.

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MalBinns commented Nov 18, 2016

My phone now has access to the website, hopefully my computer will too. I think the problem may have been the Norton Security which was classifying the site as a phi shingles site and blocking it. I sent a notice to Norton last night and things seem fixed this morning.

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mattodd commented Nov 19, 2016

OK. It's up now. Generally speaking, the ELN can go down once or twice a
day, but always comes back up. There's little that can be done during the
downtimes except wait. I had assumed that you were doing the write-ups
during the school day anyway, since the boys would be the ones completing
the ELN entries and doing the picture uploads?

Incidentally, about the structure drawings. Would the boys be able to play
with free chemical drawing software to see if they can generate pictures
that can be added to the ELN entries? I believe Chemsketch is free, and
there may be something from ChemAxon called Marvin Sketch? It'd help
browseability of the ELN.

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My phone now has access to the website, hopefully my computer will too. I
think the problem may have been the Norton Security which was classifying
the site as a phi shingles site and blocking it. I sent a notice to Norton
last night and things seem fixed this morning.


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MFernflower commented Nov 19, 2016

Marvin is my go-to drawing package! There is also a lightweight chemical
drawer that can even run on the RPI called jchempaint:
https://jchempaint.github.io/

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MalBinns commented Nov 19, 2016

Hi @MFernflower

Thanks for the feedback on drawing programs.

Hi @mattodd and @alintheopen ,

Thanks for your feedback about the site. Its Norton status has also been upgraded from potentially dodgy to secure.

You are correct that the boys are doing most of the work; they are doing all of the experimenting and one of the boys is doing all of the drawings and most of the picture uploads. As the school closes down for two months in a little over a week (due our attendance at the RACI Organic Symposium on Wed 30th November, Tuesday 29th November will be the last school day for the nine of us) all of the write-up has to be completed this coming week. As the boys do this work before or after school (the school does not provide class-time for the boys to conduct the work and their out of school time chemistry commitment competes with their compulsory, random music and sport commitments) and as they still have to optimise/scale up the Daraprim synthesis this week (once Alice confirms its existence by nmr) it is necessary for me to assist in the writeup over the weekend as our time at school will be focussed on the final step of the synthesis.

Looking forward to seeing the final spectra so that we can complete the poster and the project!

regards,

Malcolm.

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alintheopen commented Nov 19, 2016

WOULD YOU HAVE A LOOK AT THIS......
daraprim

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mattodd commented Nov 19, 2016

Oh wow!

On 19 Nov 2016 10:38 pm, "alintheopen" notifications@github.com wrote:

WOULD YOU HAVE A LOOK AT THIS......
[image: daraprim]
https://cloud.githubusercontent.com/assets/2626599/20455129/3a6eacf2-aea8-11e6-9aa8-06ea08f4c8a6.png


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MalBinns commented Nov 19, 2016

Well done. Very pure looking except for the spec of DCM at 5.76, well vacuumed! Right on literature values, and if I may say a nicer spectrum than the spectrum in the journal article that I was looking at!

I

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alintheopen commented Nov 19, 2016

the dcm doesn't matter! :)

I have submitted for HRMS and running high field proton, carbon and COSY. Can you post the reference peaks and the reference of the paper you are referring too?
I've got this:

from

"1H NMR Spectroscopy Study of the Interaction between Pyrimethamine
Hydrochloride and Bovine Serum Albumin
Sandra Cristina Gomes Oliveira and José Daniel Figueroa-Villar∗
Departamento de Química, Instituto Militar de Engenharia,
Praça General Tibúrcio 80, 22290-270 Rio de Janeiro, Brazil, d5figuer@epq.ime.eb.br. "
http://auremn.org/Annals/PDF/Article-6-1-1.pdf

I've got the other spectra too but too sleepy to analyse now, so will post in the am or as soon as I get chance.

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MalBinns commented Nov 19, 2016

I have the same paper. It has a nice printed spectrum (but not as nice as ours) and it has a table of all of the proton shifts. Our NH2 signal at 5.55 is sharper than the signal in the article nmr, however our Daraprim solution is presumably more dilute. The article has also assigned the carbon nmr shift in the Daraprim as well as both H and C shifts for the protonated species (very different!).

Sleep well Ali. I know I will, having seen the spectrum. We should all be in bed. Thank you for your commitment to running the spectra, even when you are squeezing the last minute out of the day.

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drc007 commented Nov 19, 2016

Brilliant, ideal spectra for a undergrad tutorial ;-)

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alintheopen commented Nov 20, 2016

Hi Malcolm,

I've added all data to the ELN. Will record a mp of Daraprim tomorrow am as further evidence but I think it is all looking good.

I'm also just updating the CDraw for the poster and have made all of your changes. Could you just confirm the conditions for Step C, as I can't find these on the ELN. I can then add into poster with spectra for you to tweek.

I'll be in touch this week about how we might share this story (will keep this offline for the moment, but I have a few ideas in addition to a paper draft that I'll send to you soon).

In the meantime, it would be really excellent if the boys could scale up the route. If we could make grams of Daraprim and work out exact yields starting from say 10-15 g of the starting material that would be excellent. For the write-up of any scale-up the boys could write them straight into an experimental style (I can share a template with you all).
One other thing, some of the structures in the ELN have a slight error, including here (http://malaria.ourexperiment.org/daraprim_synthesis/15043/First_successful_synthesis_of_24chlorophenyl3methoxypent2enenitrile_SGS112.html), so would be great to fix them up, especially hopefully the Sydney Grammar ELN will be receiving a few interested visitors soon! :)

This is most excellent news and I really delighted that the boys have been able to synthesise this compound - what a result!

Have a lovely rest of the weekend! Alice

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alintheopen commented Nov 20, 2016

also think we need to remove the 'towards' from the poster title too 👍

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MFernflower commented Nov 20, 2016

@alintheopen @MalBinns Congratulations!!! During some free time I came across a few compounds that could be used to make novel versions of daraprim:
cyano

Edit: These aren't the best things to use. See twitter post for smaller groups that might be of use!!!!!!!!!!!!

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alintheopen commented Nov 20, 2016

Hi @MFernflower thanks for this. These may be interesting in the future, but for now we are just focusing in on Daraprim as per the issue - any analogues would come later and with some rationale but will keep these in mind. Cheers Alice

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MalBinns commented Nov 20, 2016

hi @alintheopen , Thanks for the uploads.

I think that you can safely call the 3.99 shift of the SGS 15-1 isobutyl compound a doublet rather than a multiplet. The signal at 4.07 in the isobutyoxy compound is also present in the methoxy compound (at my computer's resolution anyway) and therefore should not be assigned to the methylene protons of the isobutoxy group. This will leave you with larger and smaller overlapping doublets for the E and Z isomers providing a multiplet appearance. As with the methyl compounds, the ratios of the E and Z isomers of the isobutyl compounds are most evident in the separate resonances of the quartets of the allylic Z&E CH2 groups at 2.78 and 2.38 respectively.

How have you made the Z assignation for the major isomer?

I will get the boys to fix up the incorrect picture and name. I agree that you should remove the "towards" from the poster.

We have not tried to react the methoxy compound to make Daraprim, only the butoxy as we have more of it. The butoxy reaction is on the system, basically the guanidine carbonate in DMSO at 80 deg C overnight. This is not a good reaction to scale up and we will look at the sodium methoxide/guanidine hydrochloride alternative on Monday. We tried it out on Friday and it provides Daraprim without the problems of heterogeneity in the carbonate reaction mix but left starting material -possibly a small scale reaction issue.

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MalBinns commented Nov 20, 2016

Hi @alintheopen , I will get the boys onto scaling up the last step tomorrow. We had already agreed to meet 7:30 Monday morning to review the nmr results. Could you please provide the outine that you would like us to use.

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alintheopen commented Nov 20, 2016

Hi Malcolm,

The guide for the ELN is here and I've copied an example
Experimental Template.docx
from our last paper to help you with the style of write up for each of the scale up reactions. If we try to keep the details more like an 'experimental' for each experiment and then write up a summary later, it really helps with clarity as do clear schemes.
It might even be worth writing up two parts to each entry - one with notes and observations from each experiment which are of course vital but also with the experimental style included. If one of the boys could record the experiment in real time that would be best - to save time the entry can be prepped (Scheme, planned method, strings, titles etc) ahead of time.

I've now got a mp (consistent with literature) and IR for SGS 16-2 so just waiting for HRMS and high res NMR.

I agree with your point on isobutyl. The NMR assignments that I've done so far are just to help the boys or anyone who comes to the ELN as I'll assign the high res spectra for the paper.
I haven't done the experiments to confirm Z/E geometry, I've just drawn them that way and will fix up at some point (could have drawn a squiggly bond of course). I will do this when I have some time, but probably won't be possible before the poster presentation.

If you can link me to the relevant butoxy and methoxy entries that would be most helpful as I need to link the data I've uploaded to all relevant ELN entries and make sure anyone can follow the lab book. Also important for the paper write up that I'm working on.

I'll send the scheme over for your approval and fix up the poster in the next day or two.

Such fantastic work by the boys and yourself, I hope they were really excited to hear the news this morning!

Have a great week, Alice

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mattodd commented Nov 20, 2016

Agree with the above. @MalBinns it's important, now we have this excellent result from you all at SGS, that we distill to a summary protocol for Daraprim synthesis, while not understating the importance of all the lab book entries detailing the various attempts. Scale-up can, as Alice suggests, help to firm up yields and demonstrate reproducibility.

And yes, @MFernflower I don't see a reason to pursue analogs. We'd need an assessment of i) limitations of the existing drug, ii) which analogs have been synthesised and evaluated previously and iii) a case to be made for analogs of Daraprim vs. some other compound that might be available. This constitutes a literature exercise that is not to be undertaken lightly.

IIRC the fundamental issue around Turing's monopoly was that they have the rights to be the provider of "official" daraprim samples (a so-called "closed distribution" model) against which others must judge equivalence if they wish to pursue generic versions. Rather like the international prototype kilogram, against which one must measure all mass. I think that if Turing refuses to allow people access to such samples then it's impossible to demonstrate equivalence (please someone correct me if I'm wrong). Looking at the beautiful purity of the SGS sample one can't help but wonder about the reasonableness of such a right. If we were to go further here (eventually) then we could start with that, but it's a non-chemical project (requiring advocacy) and one that does not fit well being discussed further on this Issue.

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MFernflower commented Nov 20, 2016

@mattodd I was wondering if the monopoly only applied to Daraprim and Daraprim only and not the class of chemicals as a whole? If so it could be easy to break Turning's nonsense by thinking up a modification of daraprim?

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MalBinns commented Nov 21, 2016

@alintheopen and @mattodd , I met with the boys this morning and they are very excited to have the Daraprim confirmed. We have begun working through the larger scale synthesis with a remake of the keto nitrile. We have wrapped it in foil this time to keep it warmer for longer (the temperature instantly rose to 40 deg C on addition) and it may be ready for workup this afternoon rather than after a 17 hour wait. We will see how we go with the required writeup format, though I don't think any of us are familiar with the referencing of starting materials etc.

By the way, some rather large crystals have appeared in the methyl enol ether mix. Let me know if you would like them to undertake some electron crystallography to confirm E/Z configuration.

[Butyoxy] synthesis has the incorrect diagrams still, I will get the boys to fix it. The diaigram of the methoxy [compound]http://malaria.ourexperiment.org/daraprim_synthesis/15043/First_successful_synthesis_of_24chlorophenyl3methoxypent2enenitrile_SGS112.html has been fixed()

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mattodd commented Nov 21, 2016

@MalBinns Definitely keep the crystals (no need to dry them, just seal them in a vial, wet) and we can X-ray them.

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MalBinns commented Nov 28, 2016

Hi @alintheopen @mattodd ,
I am sending through the yields of the three reactions as I know you need them and the reports wont be up on the system until tomorrow.

  1. The reaction of the phenylacetonitrile to with the ethyl propionate under basic conditions was a very clean reaction and was worked up to yield the keto-nitrile as a reddish oil (90% yield) that was used without purification in the next step.

  2. The reaction of the keto-nitile with isobutyl alcohol under acidic refluxing conditions also proceeded very cleanly, but did not go to completion. The resulting isobutyl enol ether was obtained as a pure red oil with 58% yield, however a mixture of starting keto-nitrile and isobutyl enol ether was also collected and the raw yield was 75%. The complete reaction writeup will include improvements to the large scale procedure that should improve the yield even further as the reaction was very clean and the desired isobutyl enol ether was by far the major product of the reaction.

  3. The reaction of the isobutyl enol ether with the guanidine hydrochloride and sodium methoxide in DMSO at room temperature to produce the Daraprim was a very clean reaction. The Daraprim crystallized out of the reaction mix as the reaction proceeded. The yield was only 28%, however this was because there was a lot of unreacted starting material still present at the time of work-up and we could not easily filter the viscous reaction mixture. We ended up conducting a messy aqueous workup. I have no doubt that running the reaction at a higher temperature and having better filtering facilities could improve the isolated yield to well over 60%.

Overall, the reaction yield was 90% x 58% x 28% = 15%, however I expect that refining the process should take the yield to at least 90% x 75% x 75% = 50%.

Please let me know if you have any queries. By the way, we isolated 3.7 grams of Daraprim from the last reaction.

regards,

Malcolm.

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MFernflower commented Nov 30, 2016

@MalBinns Just saw the video you guys made for the news!!! Great work everyone!!!! I'm glad I was able to help you reach your goal!!!!!

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alintheopen commented Apr 3, 2017

@MalBinns has posted a great summary of the project here. Thanks Malcolm! :)

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