Ecology, Environment and Conservation Paper

EXPLORATION OF TARGET ASSAY AS GUIDANCE FOR POTENCIAL CYTOTOXIC COMPOUND ISOLATION FROM STREPTOMYCES SP. GMY01 BACTERIA USING IN SILICO AND IN VITRO STUDY

Rifki Febriansah, Triana Hertiani, Jaka Widada, Mustofa and Puspita Lisdiyani

Abstract

GMY01 bacteria was known to have good activity as cytotoxic agents in some cancer cells. Methanol extract from Streptomyces sp. GMY01 has potential cytotoxic activity against breast cancer cells lines MCF-7 and T47D with IC50 values of 0.8 and 127 g/ml, respectively. Methanol extract of Streptomyces sp. GMY01 also proved to be non-toxic in normal NIH-3T3 cells line with IC50 values of 3707 g/ml (Farida et al., 2007). As part of the effort to isolate the active compound, the appropriate screening methods for appropriate guidance bioassay are needed, so an in silico approach is needed using molecular docking methods. The aim of this study was to analyze the best docking score of some possibilities active compounds which maybe containing in the GMY01 bacteria by Autodock Vina method and the cytotoxic activity of GMY01 methanol extract in MCF-7 breast cancer cells line. In silico study was carried out using molecular docking method by Autodock Vina software. Some amina peptide of the active compounds contained in Streptomyces sp. which are mitomycin C, mutalomycin and scabichelin compounds were docked in several target proteins (cyclin D1, cyclin E, COX-2, BCl-2 and VEGF) with the doxorubicin as comparative compound. In vitro study was done by cytotoxic MTT Assay in MCF-7 cells line and LC-MS analysis to know the active compounds profile containing in GMY01 methanol extract. The results of the in silico study obtained the target proteins with PDB ID codes, namely Cyclin D1 (5VZU), cyclin E (1W98), COX-2 (5IKQ), BCl-2 (4IEH) and VEGF (5XV7). All active and native ligand compounds have RMSD values that meet the requirements of less than 2.0 A. Molecular docking results showed that the mutalomycin compound had the lowest docking score compared to other active compounds in some of the target proteins except for cyclin D1 protein (-8.9 in cyclin E; -8.0 in p53; -7.5 in BCl-2; -8.6 in COX-2 and -8.8 in VEGF proteins). Based on in vitro study showed that GMY01 extract has IC50 value was 4 ug/ml in MCF-7 cells line. From LC-MS result showed that the extract containing the different compounds with the predicted compounds because the differentiation of the molecular weight (MW) values profile. From the study it can be concluded that the mutalomycin has the best potential in inhibiting some target proteins and GMY01 may has different active compounds compared with the predicted compounds.