Molecular docking, QSAR, and simulation analyses of EGFR-targeting phytochemicals in non-small cell lung cancer

Non-small cell lung carcinoma (NSCLC) is one of the prominent categories of cancer worldwide. It is primarily linked to mutations in the EGFR kinase domain, leading to being effectively controlled by specific allosteric inhibitors. However, current allosteric inhibitors have limited efficacy and potential resistance, leading to a need for alternative treatments. Therefore, this study aimed to identify phytochemicals from medicinal plants that can potentially be used as therapeutic agents that can inhibit the growth of NSCLC cells harboring the mutant EGFR kinase. A total of 4565 phytochemicals were selected from medicinal plants and screened by molecular docking, DFT calculation, ADMET analysis, QSAR analysis, molecular dynamics (MD) simulations, post simulation MM-GBSA, PCA, and DCCM analysis to find the potential compound that can inhibit the spread of lung cancer. The drug Alimta (pemetrexed disodium, CID 135410875), which is on the market today to inhibit the spread of lung cancer, was used as a control. After molecular docking, two compounds (kaempferol, CID 5280863, and epoxybergamottin, CID 9946625) showed higher binding affinity (-8.523 and -8.459 kcal/mol, respectively) and safety, and were further evaluated by MD simulations to analyze their stability. The two compounds exhibited stable interactions with the EGFR kinase protein, showing acceptable RMSD, RMSF, ligand RMSD, rGyr, MolSA, and SASA values, suggesting their potential as effective inhibitors of EGFR kinase activity. In conclusion, kaempferol (CID 5280863) and epoxybergamottin (CID 9946625) are promising phytochemicals that may inhibit the spread of NSCLC by targeting EGFR kinase.