Molecular docking and dynamics simulation revealed the anti-breast cancer potential of andaliman (Zanthoxylum acanthopodium DC.) essential oil by targeting cyclin-dependent kinase 1 protein

Cyclin-dependent kinase 1 (CDK1) is essential in cell cycle regulation and is frequently overexpressed in cancer. This study investigated phytochemicals from Zanthoxylum acanthopodium (andaliman) as potential CDK1 inhibitors via integrating multiple in silico approaches. Drug-likeness and toxicity were assessed using Lipinski’s, Egan, Ghose, and Veber rules. Protein interactions were predicted, followed by enrichment analysis to evaluate genetic alterations, gene and protein expression, and immune infiltration correlations. Structural validation was conducted to ensure the quality of the protein structure. Furthermore, molecular docking and molecular dynamics (MD) simulations were performed to evaluate binding affinity and the stability of the protein-ligand interaction over the simulation period. Among all tested compounds, geranyl acetate emerged as the lead candidate, showing low toxicity, no significant organ-specific cytotoxicity, and a high probability of anticancer activity. CDK1 was identified as a central interaction hub, with expression levels correlating with immune infiltration linked to pro-tumor prognosis. Structural validation confirmed CDK1 suitability for computational studies. However, MD simulations indicated that the CDK1-geranyl acetate complex was less stable than the CDK1-Dinaciclib complex, suggesting lower binding stability. Overall, geranyl acetate meets drug-likeness and target relevance criteria but shows weaker MD stability compared to Dinaciclib, warranting further experimental validation.