Sydney Grammar School Daraprim Synthesis

[alintheopen]

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.

[alintheopen]

@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.

[drc007]

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).

[alintheopen]

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.

[MedChemProf]

@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.

"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.

"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.

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.

[MFernflower]

@alintheopen - I present to you daracube!

http://www.chemicalize.org/structure/#!mol=5-%284-chlorocubyl%29-6-ethylpyrimidine-2%2C4-diamine&source=calculate

[alintheopen]

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

[mattodd]

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

[MalBinns]

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.

[alintheopen]

👍