(1R,2S)-2-aminocyclohexan-1-ol

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: The title compound was synthesized from 4-(9-cyclohexyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[5,4-b][1,4]diazepin-2-ylamino)-3-methoxybenzoic acid as described in the General procedure for amide bond synthesis using HATU and cis-(±)-2-aminocyclohexanol. The final compound was purified by reverse phase HPLC and basified to give the free base. 1H NMR (400 MHz, DMSO-d6) δ ppm 1.13-1.93 (m, 18H) 3.31 (s, 3H) 3.73-3.91 (m, 2H) 3.95 (s, 3H) 4.06 (t, J=13.39 Hz, 2H) 4.47 (m, 1H) 4.70 (br. s., 1H) 7.47 (d, J=8.0 Hz, 1H) 7.53 (s, 1H) 7.79 (d, J=7.83 Hz, 1H) 7.90 (s, 1H) 8.21 (s, 1H) 8.27 (d, J=8.34 Hz, 1H). [M+H] calculated for C28H36F2N6O4, 559. found 559. as described in the General procedure for amide bond synthesis The final compound was purified by reverse phase HPLC to give the free base

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: 2-[3-(Ethylsulfanyl)phenoxy]-5-fluoronicotinic acid (250 mg, 0.85 mmol) was dissolved in dimethylformamide (5 ml) and triethylamine (475 μl, 3.41 mmol) was added followed by (1R,2S)-2-aminocyclohexanol hydroformate (144 mg, 0.89 mmol), 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (180 mg, 0.94 mmol) and 1-hydroxybenzotriazole (127 mg, 0.94 mmol). The reaction was stirred under nitrogen at room temperature for 18 h and the solvent was removed under reduced pressure. The residue was partitioned between water (5 ml) and ethyl acetate (10 ml) and the aqueous phase was extracted with ethyl acetate (3×10 ml). The combined organic extracts were washed with brine (5 ml), dried over MgSO4 and the solvent was removed under reduced pressure. The residue was purified by flash column chromatography using dichloromethane:methanol:0.880 ammonia (98:2:0.2) as eluant to give 2-[3-(ethylsulfanyl)phenoxy]-5-fluoro-N-[(1S,2R)-2-hydroxycyclohexyl]nicotinamide (57 mg) as a colourless oil. the solvent was removed under reduced pressure The residue was partitioned between water (5 ml) and ethyl acetate (10 ml) the aqueous phase was extracted with ethyl acetate (3×10 ml) The combined organic extracts were washed with brine (5 ml) dried over MgSO4 the solvent was removed under reduced pressure The residue was purified by flash column chromatography

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: cis-2-Amino-cyclohexane-1-ol (85 mg, 0.56 mmol) and triethylamine (225 μl, 1.61 mmol) were dissolved in dimethylformamide (225 μl) and a solution of 5-fluoro-2-(3-methylsulfanyl-phenoxy)-nicotinic acid (150 mg, 0.54 mmol), 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (113 mg, 0.59 mmol) and 1-hydroxybenzotriazole (80 mg, 0.59 mmol) in dimethylformamide (5 ml) was added. The reaction was stirred under nitrogen at room temperature for 64 h and the solvent was removed under reduced pressure. The residue was partitioned between 0.5N HCl (10 ml) and ethyl acetate (10 ml) and the aqueous phase was extracted with ethyl acetate (2×10 ml). The combined organic phases were washed with brine (10 ml), dried over MgSO4 and the solvent was removed under reduced pressure. The residue was purified by flash column chromatography on silica gel eluting with pentane:ethyl acetate (70:30, by volume). The product was triturated with pentane (3 ml) to give 5-fluoro-N-[cis-2-hydroxy-cyclohexyl]-2-(3-methylsulfanyl-phenoxy)-nicotinamide (118 mg) as a white solid. the solvent was removed under reduced pressure The residue was partitioned between 0.5N HCl (10 ml) and ethyl acetate (10 ml) the aqueous phase was extracted with ethyl acetate (2×10 ml) The combined organic phases were washed with brine (10 ml) dried over MgSO4 the solvent was removed under reduced pressure The residue was purified by flash column chromatography on silica gel eluting with pentane:ethyl acetate (70:30, by volume) The product was triturated with pentane (3 ml)

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: 1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (293 mg, 1.53 mmol) was added to a solution of 2-(3-methylsulfanyl-phenoxy)-nicotinic acid (200 mg, 0.765 mmol), (1R,2S)-2-aminocyclohexanol hydroformate [8151/195/2] (123 mg, 0.765 mmol), 1-hydroxybenzotriazole (114 mg, 0.842 mmol) and triethylamine (430□l, 3.10 mmol) in dimethylformamide (5 ml) under nitrogen at room temperature. The reaction was stirred for 18 h and partitioned between diethyl ether (25 ml) and water (25 ml). The organic phase was washed with brine (30 ml), dried over MgSO4 and the solvent was removed under reduced pressure. The residue was purified by flash column chromatography using ethyl acetate:cyclohexane (50:50 as eluant) to give N-[(1 S,2R)-2-hydroxycyclohexyl]-2-[3-(methylsulfanyl)phenoxy]nicotinamide (133 mg) as a gum. partitioned between diethyl ether (25 ml) and water (25 ml) The organic phase was washed with brine (30 ml) dried over MgSO4 the solvent was removed under reduced pressure The residue was purified by flash column chromatography

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: The obtained 8-methyl-6-nonenoic acid (isomer ratio trans:cis=29:1, 408 mg, 2.40 mmol) was again dissolved in chloroform (10 ml), and a solution of cis-2-aminocyclohexanol (249 mg, 2.16 mmol) in chloroform (5 ml) was added dropwise at room temperature. The reaction mixture was concentrated under reduced pressure, the residue was again dissolved in chloroform (3 ml), and hexane (12 ml) was added dropwise. The reaction mixture was stirred overnight at room temperature, and the precipitated crystals were collected by filtration. Hexane (15 ml) was added to the obtained crystal, and the mixture was washed three times with 10% aqueous citric acid solution (10 ml) and once with saturated brine (10 ml), and dried over anhydrous magnesium sulfate. Magnesium sulfate was removed by filtration, and the filtrate was concentrated under reduced pressure to give trans-8-methyl-6-nonenoic acid (250 mg, 1.47 mmol, purity 98.8%, yield 35.1%). The reaction mixture was concentrated under reduced pressure the residue was again dissolved in chloroform (3 ml) hexane (12 ml) was added dropwise the precipitated crystals were collected by filtration Hexane (15 ml) was added to the obtained crystal the mixture was washed three times with 10% aqueous citric acid solution (10 ml) once with saturated brine (10 ml), and dried over anhydrous magnesium sulfate Magnesium sulfate was removed by filtration the filtrate was concentrated under reduced pressure

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: The obtained 8-methyl-6-nonenoic acid (isomer ratio trans:cis=29:1, 408 mg, 2.40 mmol) was again dissolved in chloroform (10 ml), and a solution of cis-2-aminocyclohexanol (249 mg, 2.16 mmol) in chloroform (5 ml) was added dropwise at room temperature. The reaction mixture was concentrated under reduced pressure, the residue was again dissolved in chloroform (3 ml), and hexane (12 ml) was added dropwise. The reaction mixture was stirred overnight at room temperature, and the precipitated crystals were collected by filtration. Hexane (15 ml) was added to the obtained crystal, and the mixture was washed three times with 10% aqueous citric acid solution (10 ml) and once with saturated brine (10 ml), and dried over anhydrous magnesium sulfate. Magnesium sulfate was removed by filtration, and the filtrate was concentrated under reduced pressure to give trans-8-methyl-6-nonenoic acid (250 mg, 1.47 mmol, purity 98.8%, yield 35.1%). The reaction mixture was concentrated under reduced pressure the residue was again dissolved in chloroform (3 ml) hexane (12 ml) was added dropwise the precipitated crystals were collected by filtration Hexane (15 ml) was added to the obtained crystal the mixture was washed three times with 10% aqueous citric acid solution (10 ml) once with saturated brine (10 ml), and dried over anhydrous magnesium sulfate Magnesium sulfate was removed by filtration the filtrate was concentrated under reduced pressure

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: A mixture of 24 g (11 mmol) of racemic trans-2-benzamidocyclohexanol and 12 g of 90% H2SO4 (110 mmol) was stirred at 75°-80° for 6 hours. After the addition of 22 mL of H2O, the mixture was heated under reflux for 15 hours. The mixture was cooled to room temperature and washed with 20mL of methylene chloride. The acidic aqueous phase was separated, treated with 12.6 mL of 50% NaOH solution (240 mmol) at <40° C., 30mL of H2O was added and the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C. The combined extracts were dried over anhydrous Na2SO4 and filtered. The filtrate was concentrated in vacuo to provide crude product containing cis-2-aminocyclohexanol which was isolated and purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1) to provide 792 mg of cis-2-benzamidocyclohexanol (33% of theory). Proton and C13NMR were consistent with the proposed structure. the mixture was heated under reflux for 15 hours washed with 20mL of methylene chloride The acidic aqueous phase was separated the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C The combined extracts were dried over anhydrous Na2SO4 filtered The filtrate was concentrated in vacuo to provide crude product was isolated purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1)

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: A mixture of 24 g (11 mmol) of racemic trans-2-benzamidocyclohexanol and 12 g of 90% H2SO4 (110 mmol) was stirred at 75°-80° for 6 hours. After the addition of 22 mL of H2O, the mixture was heated under reflux for 15 hours. The mixture was cooled to room temperature and washed with 20mL of methylene chloride. The acidic aqueous phase was separated, treated with 12.6 mL of 50% NaOH solution (240 mmol) at <40° C., 30mL of H2O was added and the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C. The combined extracts were dried over anhydrous Na2SO4 and filtered. The filtrate was concentrated in vacuo to provide crude product containing cis-2-aminocyclohexanol which was isolated and purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1) to provide 792 mg of cis-2-benzamidocyclohexanol (33% of theory). Proton and C13NMR were consistent with the proposed structure. the mixture was heated under reflux for 15 hours washed with 20mL of methylene chloride The acidic aqueous phase was separated the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C The combined extracts were dried over anhydrous Na2SO4 filtered The filtrate was concentrated in vacuo to provide crude product was isolated purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1)

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: A mixture of 24 g (11 mmol) of racemic trans-2-benzamidocyclohexanol and 12 g of 90% H2SO4 (110 mmol) was stirred at 75°-80° for 6 hours. After the addition of 22 mL of H2O, the mixture was heated under reflux for 15 hours. The mixture was cooled to room temperature and washed with 20mL of methylene chloride. The acidic aqueous phase was separated, treated with 12.6 mL of 50% NaOH solution (240 mmol) at <40° C., 30mL of H2O was added and the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C. The combined extracts were dried over anhydrous Na2SO4 and filtered. The filtrate was concentrated in vacuo to provide crude product containing cis-2-aminocyclohexanol which was isolated and purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1) to provide 792 mg of cis-2-benzamidocyclohexanol (33% of theory). Proton and C13NMR were consistent with the proposed structure. the mixture was heated under reflux for 15 hours washed with 20mL of methylene chloride The acidic aqueous phase was separated the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C The combined extracts were dried over anhydrous Na2SO4 filtered The filtrate was concentrated in vacuo to provide crude product was isolated purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1)

Conditions: temp:150.01; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: A mixture of tert-butyl 3-iodoazetidine-1-carboxylate (1 g, 3.53 mmol), 4-aminophenylboronic acid (630 mg, 4.59 mmol), NiI2 (66 mg, 0.212 mmol), NaHMDS (1.94 g, 10.6 mmol), (1R,2S)-2-aminocyclohexanol (24 mg, 0.212 mmol) in isopropanol (8 mL) was stirred at 150° C. in microwave for 2 h. It was then evaporated and the residue was dissolved with water and ethyl acetate. The water phase was separated and extracted with ethyl acetate. The combined extracts were dried over sodium sulfate and concentrated under reduced pressure. The residue was purified with column chromatography to give 298a (360 mg, 40%). MS: [M+H]+ 249. It was then evaporated the residue was dissolved with water and ethyl acetate The water phase was separated extracted with ethyl acetate The combined extracts were dried over sodium sulfate concentrated under reduced pressure The residue was purified with column chromatography

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: The title compound was synthesized from 4-(9-cyclohexyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[5,4-b][1,4]diazepin-2-ylamino)-3-methoxybenzoic acid as described in the General procedure for amide bond synthesis using HATU and cis-(±)-2-aminocyclohexanol. The final compound was purified by reverse phase HPLC and basified to give the free base. 1H NMR (400 MHz, DMSO-d6) δ ppm 1.13-1.93 (m, 18 H) 3.31 (s, 3 H) 3.73-3.91 (m, 2 H) 3.95 (s, 3 H) 4.06 (t, J=13.39 Hz, 2 H) 4.47 (m, 1 H) 4.70 (br. s., 1 H) 7.47 (d, J=8.0 Hz, 1 H) 7.53 (s, 1 H) 7.79 (d, J=7.83 Hz, 1 H) 7.90 (s, 1 H) 8.21 (s, 1 H) 8.27 (d, J=8.34 Hz, 1 H). [M+H] calculated for C28H36F2N6O4, 559; found 559. as described in the General procedure for amide bond synthesis The final compound was purified by reverse phase HPLC to give the free base

Conditions: temp:0.00; pressure:0.00; stir:; See reaction.notes.procedure_details.

Procedure: A mixture of 24 g (11 mmol) of racemic trans-2-benzamidocyclohexanol and 12 g of 90% H2SO4 (110 mmol) was stirred at 75°-80° for 6 hours. After the addition of 22 mL of H2O, the mixture was heated under reflux for 15 hours. The mixture was cooled to room temperature and washed with 20 mL of methylene chloride. The acidic aqueous phase was separated, treated with 12.6 mL of 50% NaOH solution (240 mmol) at <40° C., 30mL of H2O was added and the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C. The combined extracts were dried over anhydrous Na2SO4 and filtered. The filtrate was concentrated in vacuo to provide crude product containing cis-2-aminocyclohexanol which was isolated and purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1) to provide 792 mg of cis-2-benzamidocyclohexanol (33% of theory). Proton and C13NMR were consistent with the proposed structure. the mixture was heated under reflux for 15 hours washed with 20 mL of methylene chloride The acidic aqueous phase was separated the mixture extracted with a total of 60 mL of methylene chloride at 30°-35° C The combined extracts were dried over anhydrous Na2SO4 filtered The filtrate was concentrated in vacuo to provide crude product was isolated purified by flash chromatography on silica gel with ethyl acetate-hexane (1:1)