BackgroundAndrographis paniculata is a well-known medicinal plant that contains various classes of bioactive secondary metabolites. It is widely used by the traditional medicinal healers for treatment of malaria and other diseases. There is an urgent need for screening of potent novel compounds from the methanol extract of A. paniculata. Earlier, we obtained appreciable in vitro anti-malarial activity (IC50-10.75 μg/ml) in the same plant. In current study, we developed novel analytical methods for rapid identification and characterization of diterpenes and flavones using chromatographic and spectroscopic techniques and identified major compounds that might possess anti-malarial activities.ResultsBased on the chromatographic and mass spectrometric features, we have identified a total of 74 compounds (25 compounds from positive ion mode; 49 compounds from negative ion mode). The mass spectrum data predicted andrographolide (15%) presence in the highest amount in both positive and negative ion modes. Based on the percentage purity, Andrographolide and skullcapflavone I was selected as representative class of diterpenes and flavones for fragmentation studies.ConclusionsThe result led to identification of Neoandrographolide, andrographolactone, 14-dehydroxy-11,12-didehydroandrographolide, skullcapflavone I, and 5-Hydroxy-2′,7,8-tri methoxy flavone from the methanolic extract of A. paniculata that is used in traditional medicine by tribal healers of Amarkantak region for treating malaria. These could be lead compounds for the development of novel anti-malarial drugs.