The four complex groups of methotrexate-GALE, methotrexate-TYMS, methotrexate-GGH, and tamoxifen-NR4A1 were selected for molecular dynamics modeling in this study based on the following considerations: molecular docking results showed that the binding energy of GALE with MTX (−10.4 kcal/mol) was significantly higher than that of its traditional classical target TYMS (−7.5 kcal/mol), suggesting that GALE may be an important but not fully understood target of MTX in the treatment of AD. This evidence concerns the gene GGH and Alzheimer disease.