Amino-thienopyrimidine Series

This procedure, adapted from Benish, Lawless & Budde (2004, p. 19), involves transforming JRC 9-2 into an aromatic thienopyrimidine molecule. It is described below:



Conclusion: The desired product was synthesised in 29% yield, albeit in a botched procedure.

Reaction start time: 10:25 am, 01/05/2012
To thieno[3,2-d]pyrimidine-4(3H)-one (384 mg, 2.52 mmol, 1 equiv.) was added phosphoryl chloride (2.1 mL, 22.6 mmol, 9 equiv.) under a nitrogenous atmosphere. No visible reaction signs occured whilst adding the first few drops of phosphoryl chloride, so the addition was sped up. Again, no visible signs of reactions occured so the reaction was heated to reflux. The syringe needle was quenched using sodium bicarbonate, followed by the syringe itself.

At +1.5 hr, the reaction was cooled to rt and saturated aqueous sodium bicarbonate was added dropwise. The reaction mixture began boiling and fuming upon addition of sodium bicarbonate, so the reaction vessel was cooled in an ice/sodium chloride bath while sodium bicarbonate was added dropwise. Once vigorous effervescence had ceased, sodium bicarbonate was added at a greater pace until vigorous effervescence had ceased. When addition of sodium bicarbonate yielded no further effervescence the reaction mixture was extracted with diethyl ether (20 mL) and washed with water (2 x 10 mL) and brine (2 x 10 mL) before the organic layer was dried with anhydrous magnesium sulfate. The organic layer was left for three hours, at which time the solvent had evaporated through the gaps in the tap of a separating funnel.

The resultant yellow crystals were dissolved in diethyl ether and this solution was washed with water (2 x 10 mL) and brine (2 x 10 mL) before the organic layer was dried with anhydrous magnesium sulfate. The solvent was removed in vacuo and the yellow solid dried under reduced pressure to yield a yellow powder (125 mg, 0.73 mmol, 29%).

¹H-NMR:


Risk Assessment: approved via email (M. Todd)


References:
Benish, M.A.; Lawless, M.; Budde, R.J. (Fulbright & Jaworski, TX, US.). Preparation pf thienopyrimidine based inhibitors of the SRC family. United States Patent Application Publication 20040077663 A1, 2004; SciFinder Scholar AN 2007:1197581 (accessed 24/04/2012).

The last series of these experiments lead to good yield, and more of the desired product is needed. This experiment, adapted from Mitchell et al. (2005) pp.67-68, is detailed below.



Conclusion: The desired product was synthesised in 47% yield. It was recrystallised in 25% yield for a total of 12% pure yield.

Part I
Reaction start time: 9:00am, 23/04/2012
Methyl-3-aminothiophene-2-carboxylate (3.03 g, 19.3 mmol, 1 equiv.) and ammonium acetate (1.13 g, 14.65 mmol, 0.76 equiv.) were dissolved in formic acid (15.0 mL, 397 mmol, 20 equiv.) and heated to reflux. Calculations at +2 hr proved to be incorrect, and more ammonium acetate was needed. At +2 hr ammonium acetate (1.044 g, 13.54 mmol, 0.70 equiv.) dissolved in formic acid (5 mL) was added to the refluxing solution for a total of 2.17 g (28.2 mmol, 1.46 equiv.). At +6 hr the heat was removed, the solution cooled and the solid filtered and washed with water. The resultant solid was dried in vacuo to yield the desired intermediate (2.744 g, 14.81 mmol, 77%). ¹H-NMR of this compound was attempted, unsuccesfully. The NMR showed no relevant peaks besides those of DMSO and water, indicating that the sample did not make it into the NMR.

m.p. 93.1 °C - 94.3 °C

¹H-NMR:


The filtrate was recovered and the solvent removed in vacuo to yield fluffy, pale brown crystals (170 mg, 0.91 mmol, 5%). Total yield for this reaction is 82%.

Part II
Reaction start time: 4pm 24/04/2012
Methyl-3-formamidothiophene-2-carboxylate (2.744 g, 14.81 mmol, 1 equiv.) and ammonium formate (3.83 g, 60.7 mmol, 4 equiv.) were dissolved in formamide (10.0 mL, 251 mmol, 16.9 equiv.) and the resultant slurry was heated to 140 °C for 40 hr. The reaction mixture was cooled on ice, filtered, washed with water and dried in vacuo to yield a brown powder (1.3752 g, 9.037 mmol, 61%). This brown powder was recrystallised from boiling ethanol/water to yield 346 mg (2.27 mmol, 25.11%).

¹H-NMR:


The solvent was removed from the filtrate in vacuo to yield the desired product (586 mg, 3.85 mmol, 26%).

¹H-NMR:


MP: 219.9-220.4

Risk Assessment: As for JRC 9-3

References:
Mitchell, I.S.; Spencer, K.L.; Stengel, P.; Han, Y.; Kallan, N.C.; Munson, M.; Vigers, G.P.A.; Blake, J.; Piscopio, A.; Josey, J.; Miller, S.; Xiao, D.; Xu, R.; Rao, C.; Wang, B.; Bernacki, A.L (Array Biopharma, CO, US.). AKT Protein Kinase Inhibitors for use in treatment of hyperproliferative diseases. World Intellectual Property Organisation 2005051304 A2, 2005; SciFinder Scholar AN 2005:490266 (accessed 24/04/2012).

This experiment, from Mitchell et al. (2005), is an upscale of JRC 9-2. Proper yield and characterisation of the intermediate is desired for this experiment. The procedure is summarised below.



Part I
Reaction start time: 3pm, 19/04/2012
Methyl-3-aminothiophene-2-carboxylate (738 mg, 5.19 mmol, 1 equiv.) and ammonium acetate (1.036 g, 13.44 mmol, 2.58 equiv.) were dissolved in formic acid (6.0 mL, 159 mmol, 30 equiv.) and heated to reflux for 3 hr. The mixture was cooled to rt, filtered, washed with water and then dried in vacuo to yield the desired intermediate, methyl-3-formamidothiophene-2-carboxylate (610 mg, 3.29 mmol, 63%).

¹H-NMR:

¹³C-NMR:

Low Res. Mass Spec. 607 m/z

The filtrate was collected and the water removed in vacuo to yield 1.225 g of light orange/white powder.

Part II
Reaction start time: 4pm, 23/04/2012
3-formamidothiophene-2-carboxylate (589 mg, 3.18 mmol, 1 equiv.) and ammonium formate (710 mg, 11.3 mmol, 3.5 equiv.) were dissolved in formamide (1.80 mL, 45.2 mmol, 14.2 equiv.) and the resultant slurry was heated to 140 °C. At +16 hr it was discovered that the heating apparatus had failed overnight. A TLC was performed to investigate the extent of the reaction:

TLC +16hr, 10% MeOH/DCM, visualised with UV/vanillin


Reaction mixture was re-heated to 140 °C for 6 hr. The reaction was cooled to rt before being filtered and washed with water. Very little product was left after filtration, so all the product was washed through the filter paper with acetone, and most of the solvent removed in vacuo. When only a small amount of solvent was left within the vessel, it was cooled to rt for 1 hr, and radiating orange crystals formed. These crystals were filtered, washed with water and dried in vacuo to yield the desired product (202 mg, 1.32 mmol, 42%).

¹H-NMR:


References:
Mitchell, I.S.; Spencer, K.L.; Stengel, P.; Han, Y.; Kallan, N.C.; Munson, M.; Vigers, G.P.A.; Blake, J.; Piscopio, A.; Josey, J.; Miller, S.; Xiao, D.; Xu, R.; Rao, C.; Wang, B.; Bernacki, A.L (Array Biopharma, CO, US.). AKT Protein Kinase Inhibitors for use in treatment of hyperproliferative diseases. World Intellectual Property Organisation 2005051304 A2, 2005; SciFinder Scholar AN 2005:490266 (accessed 24/04/2012).

This experiment, from Mitchell et al. (2005), combines procedural elements from both JRC 9-1 and JRC 8-1. The intended reaction is summarised below:



Conclusion: The desired product was formed over two steps in 31% yield.

Part I:

Reaction start time: 12pm 18/04/2012
Methyl-3-aminothiophene-2-carboxylate (235 mg, 1.16 mmol, 1 equiv.) and ammonium acetate (173 mg, 2.24 mmol, ~1.9 equiv.) were dissolved in formic acid (1.0 mL, 26.5 mmol, ~22.8 equiv.). The mixture was refluxed for 3 hr, before being cooled to ambient temperature. The cooled mixture was filtered, washed with water and dried under reduced pressure to afford a light brown, fluffy powder. Due to problems in arriving at the intended final product in JRC 8-1, 8-2 and 9-1, this brown powder was used immediately in the following reaction.

Part II
Reaction start time: 5pm 18/04/2012
JRC 9-2 (Part I) was assumed to be methyl-3-formamidothiophene-2-carboxylate, based on both the results from JRC 9-1 and the procedure outlined by Mitchell et al (2005). Methyl-3-formamidothiophene-2-carboxylate (268 mg, 1.44 mmol, 1 equiv.) and ammonium formate (259 mg, 4.11 mmol, 2.9 equiv.) were dissolved in formamide (0.778 mL, 19.57 mmol, 13.6 equiv.) and the resultant slurry was heated to 140 %degC and refluxed for 19.5 hr. The reaction mixture was cooled and the resultant brown sludge was filtered, washed with water and dried to yield the desired product (50.6 mg, 0.37 mmol, 25%*).

*yield from intermediate weight, which is incorrect. total yield over all steps is 31%.

¹H-NMR:


¹³C-NMR

Low Res. Mass Spec.: 153 m/z+

Risk Assessment: As for:
Synthesis of Thieno[3,2-d]pyrimidine-4(3H)-one using formic acid (JRC 9-1) and;
Synthesis of Thieno[3,2-d]pyrimidine-4(3H)-one (JRC 8-1)

References:
Mitchell, I.S.; Spencer, K.L.; Stengel, P.; Han, Y.; Kallan, N.C.; Munson, M.; Vigers, G.P.A.; Blake, J.; Piscopio, A.; Josey, J.; Miller, S.; Xiao, D.; Xu, R.; Rao, C.; Wang, B.; Bernacki, A.L (Array Biopharma, CO, US.). AKT Protein Kinase Inhibitors for use in treatment of hyperproliferative diseases. World Intellectual Property Organisation 2005051304 A2, 2005; SciFinder Scholar AN 2005:490266 (accessed 24/04/2012).