N-benzylbenzamide derivative (SBM685) as a novel MDR1 inhibitor for overcoming 5 fluorouracil resistance in gastric cancer through computational and in vitro analysis

The overexpression of Multidrug Resistance Protein 1 (MDR1) contributes to the failure of existing chemotherapeutic agents like 5-fluorouracil (5FU). This study aims to identify and evaluate a novel small molecule inhibitor of MDR1 in 5FU-resistant gastric cancer (GC). Comprehensive in silico approach using Discovery Studio Visualizer, Protein-Ligand Interaction Profiler, GROMACS, and GMX_MMPBSA methods were employed to identify potential MDR1 inhibitors from the ZINC natural product-like compound library. MKN-45 and SNU-5 cells were utilized in cell proliferative and flow cytometry assays for in vitro validations. Virtual screening identified SBM685 as a promising MDR1 inhibitor, with a docking score of -9.4 kcal/mol. Root Mean Square Deviation (RMSD) values were around 0.2 nm. Gibbs binding free energy calculations indicated a highly favorable binding energy of -49.02 kcal/mol. SBM685 reduced the MDR1-positive (MDR1⁺) cell population in MKN-45 and SNU-5 gastric cancer cells. SBM685 also inhibited the proliferation of parental MKN-45 cells as well as MDR1⁺ MKN-45 and MDR1⁺ SNU-5 cells. In contrast, 5-fluorouracil (5-FU) showed limited efficacy in suppressing proliferation in MDR1⁺ gastric cancer cells. In addition, SBM685 induced apoptosis in both parental and MDR1⁺ gastric cancer cells, whereas 5-FU failed to promote apoptosis in MDR1⁺ cells. The combination of computational and in vitro evaluations indicates that SBM685 is a potent MDR1 inhibitor which is also effective in MDR1+ GC cells where 5FU exhibited resistance. The findings of this study highlight SBM685 as a promising candidate for further preclinical evaluations, that could pave the way for new therapeutic strategies in overcoming the MDR1-mediated chemoresistance of GC.