Investigation of Chemical Compounds from Phomopsis Extract as Anti-Breast Cancer Using LC-MS/MS Analysis, Molecular Docking, and Molecular Dynamic Simulations

Abstract

Since 2014, we have successfully isolated endophytic fungi from the leaves of Indonesian Annona muricata, exhibiting potential anti-breast cancer properties. The analysis of Internal Transcribed Spacer (ITS) showed the identified fungi species as Phomopsis sp. The ethyl acetate extract derived from Phomopsis sp. inhibited MCF7 cells (IC50 <20 ppm) and reduced the number and volume of nodules in Sprague-Dawley rats with breast cancer. However, molecular mechanism underlying the action of this extract in breast cancer treatment remains unclear. Therefore, this study aimed to identify the active compounds in Phomopsis extract and to predict anti-breast cancer mechanism through HER2 inhibition using MD and MDS. Using LC-MS/MS, 44 compounds were successfully identified, and 16 have the potential to be anti-cancer and obey Lipinski’s rule. In silico studies were performed on the human epidermal growth factor receptor 2 (HER2). Subsequently, molecular docking results showed that the most negative affinity energy was 3-[(4-hydroxyphenyl)methyl]-octahydropyrrolo[1,2-a]pyrazine-1,4-dione (-9.4 kcal/mol), better than trastuzumab as a comparison ligand. Molecular dynamic simulations (MDS) of protein-ligand complexes showed prominent inhibition of HER2, as shown by dynamic trajectory analysis. Based on these results, 3-[(4-hydroxyphenyl)methyl]-octahydropyrrolo[1,2-a]pyrazine-1,4-dione was identified as a promising HER2 inhibitor for breast cancer.