To a solution of 4-(2-methylsulfanyl-pyrimidin-4-yloxy)-benzene-1,2-diamine (Step B, 400 mg, 1.6 mmol, 1.0 eq.) in anhydrous CH3CN (30 mL) was added dropwise a solution of 1-(2-chloro-5-isothiocyanato-benzyl)-4-methyl-piperazine (900 mg [slightly contaminated with imidazole], 1.6 mmol, 1.0 eq.) in 20 mL of anhydrous CH3CN. The reaction was stirred for 16 h at RT then EDC (0.5 g, 2.6 mmol, 1.5 eq.) was added. The resulting mixture was heated to 80° C. for 1 h. The solvent was evaporated and the residue was diluted with CH2Cl2 (25 mL). The solution was washed with H2O (25 mL), NaHCO3 (25 mL, aq.) and brine (25 mL). The aqueous layers were back extracted with CH2Cl2 and the combined organic layers were dried over MgSO4, filtered and concentrated. The crude was further purified by column chromatography (0-7.5% MeOH/CH2Cl2) to give pure [4-chloro-3-(4-methyl-piperazin-1-ylmethyl)-phenyl]-[5-(2-methylsulfanyl-pyrimidin-4-yloxy)-1H-benzimidazol-2-yl]-amine. MS m/z=496.2 (M+H)+; MW Calc'd for C24H26N7OS: 495.16.
