Identification, isolation and characterization of new impurity in rabeprazole sodium

Rabeprazole sodium [1] is a proton pump inhibitor, used as an antiulcerative. During the manufacturing of rabeprazole sodium, we observed an unknown impurity at levels 0.05–0.1% in HPLC analysis along with the known potential impurities. This new unknown impurity was isolated using preparative liquid chromatography. Based on the complete spectral analysis ( 1H NMR, 13C NMR, DEPT, Mass and IR), this new impurity was designated as 2-[[(3-methyl-4-(methylthio)-2-pyridinyl)methyl]sulfinyl]-1 H-benzimidazole (methylthio impurity of rabeprazole). Impurity isolation, structure elucidation and probable formation mechanism was discussed.