Computational molecular insights into ibrutinib as a potent inhibitor of HER2-L755S mutant in breast cancer: gene expression studies, virtual screening, docking, and molecular dynamics analysis.

Background: The proposed study integrates several advanced computational techniques to unravel the molecular mechanisms underlying breast cancer progression and drug resistance.

Methods: We investigated HER2-L755S mutation through a multi-step approach, including gene expression analysis, molecular docking, and molecular dynamics simulations.

Results and discussion: By conducting a network-based analysis of gene expression data from breast cancer samples, key hub genes such as MYC, EGFR, CDKN2A, ERBB2, CDK1, E2F1, TOP2A, MDM2, TGFB1, and FOXM1 were identified, all of which are critical in tumor growth and metastasis. The study mainly focuses on the ERBB2 gene, which encodes the HER2 protein, and its common mutation HER2-L755S, associated with breast cancer and resistance to the drug lapatinib. The HER2-L755S mutation contributes to both tumorigenesis and therapeutic failure. To address this, alternative therapeutic strategies were investigated using combinatorial computational approaches. The stability and flexibility of the HER2-L755S mutation were evaluated through comparative molecular dynamics simulations over 1000 ns using Gromacs in the unbound (Apo) state. Virtual screening with Schrodinger Glide identified ibrutinib as a promising alternative to lapatinib for targeting the HER2-L755S mutant. Detailed docking and molecular dynamics simulations in the bound (Holo) state demonstrated that the HER2-L755S-ibrutinib complex exhibited higher binding affinity and lower binding energy, indicating more stable interactions compared to other complexes. MM-PBSA analysis revealed that the HER2-L755S-ibrutinib complex had more negative binding energy than the HER2-L755S-afatinib, HER2-L755S-lapatinib, and HER2-L755S-neratinib complexes, suggesting that ibrutinib forms the most stable complex with favorable binding interactions.

Conclusion: These results provide in-depth atomic-level insights into the binding mechanisms of these inhibitors, highlighting ibrutinib as a potentially effective inhibitor for the clinical treatment of breast cancer.