Integrative network pharmacology and molecular simulation approach unveils the multi-pathway therapeutic mechanism of Curcumin, Withaferin A, and andrographolide against acute Myeloid Leukemia

Acute Myeloid Leukemia (AML) is a complex blood cancer caused by the abnormal growth of myeloid progenitor cells, often leading to poor treatment outcomes and high mortality rates worldwide. Natural phytochemicals are being studied as potential treatments because they can target multiple pathways and tend to have low toxicity. In this study, we explored how Curcumin, Withaferin A, and Andrographolide act against AML using network pharmacology and molecular simulation methods. We identified compound and disease targets from several bioinformatics databases, including SwissTargetPrediction, TargetNet, SEA, BATMAN-TCM, and the Comparative Toxicogenomics Database (CTD), and collected AML-related genes from GeneCards and OMIM. We found 95 overlapping targets and analyzed them using Gene Ontology (GO) and KEGG pathway enrichment with Enrichr. Protein-protein interaction networks were built with STRING and examined in Cytoscape using the CytoNCA plugin to find key genes. Expression and survival analyses with GEPIA and KM-Plotter showed that TP53, AKT1, BCL2, KRAS, NOTCH1, and MYC are the most important for prognosis. Molecular docking with the Schrodinger Glide XP module showed that the phytochemicals bind strongly to AML-related proteins. Curcumin had the strongest binding with AKT1 (-9.77 kcal/mol) and KRAS (-6.58 kcal/mol). Withaferin A formed stable interactions with AKT1 (-7.39 kcal/mol) and TP53 (-4.22 kcal/mol). Andrographolide showed good binding with AKT1 (-6.72 kcal/mol) and BCL2 (-5.01 kcal/mol). Furthermore, the stability of these complexes were confirmed with 100 nanosecond molecular dynamics simulations using Desmond module in Schrodinger, where RMSD values stayed between 1 and 3 Å, showing stable protein-ligand structures. Binding free-energy calculations with the Prime MM-GBSA method showed that the AKT1-Curcumin complex had the most favorable binding energy (-71.31 kcal/mol), followed by AKT1-Withaferin A (-69.50 kcal/mol), BCL2-Andrographolide (-46.11 kcal/mol), and AKT1-Andrographolide (-42.40 kcal/mol), supporting strong and stable interactions. In summary, our results show that Curcumin, Withaferin A, and Andrographolide work through multiple targets and pathways to fight leukemia, and highlight Andrographolide as a promising natural compound for AML treatment. More laboratory and animal studies are needed to confirm their potential.