HER2 are members of the epidermal growth factor receptor tyrosine kinase protein family which includes HER1/EGFR, HER2/ErbB2, HER3/ErbB3, and ErbB4. These proteins form various homo- and hetero- dimer receptors on human cell membranes. When these receptors bind with ligands, autophosphorylation will occur and activate P13k/Akt and Ras/Raf signaling pathways, stimulating signal transduction of downstream cell growth and differentiation. Clinically, abnormalities in HER2 gene regulation will cause receptor over-production, resulting in various cancers including breast cancer, ovarian cancer, gastric cancer, and prostate cancer. Therefore, inhibiting HER2 expression and function is critical in treating cancer and preventing the spread of cancerous cells. Trastuzumaband Lapatinibare two drugs used WY 14643 clinical trial clinically in breast cancer. Trastuzumab inhibits overexpression of HER2, and Lapatinib inhibits HER2 autophosphorylation by competing with ATP for the HER2 protein kinase domain, thus preventing further signal transduction. Drug resistance issues have been reported for Trastuzumab. Synergistic effects on breast cancer is observed when Lapatinib is used with Capecitabine, but side effects such as nausea, vomiting, and diarrhea have been recorded. Computer-aided drug design is widely used in developing new drugs and has been integrated in this laboratory with our selfdeveloped TCM Database@Taiwanto design and develop novel drugs from traditional Chinese medicine. Much research has proven that traditional Chinese herb compounds exhibit antioxidation and anti-inflammation effects and have therapeutic effects on cancer. A preliminary experiment conducted in this laboratory identified several natural compounds from traditional Chinese herbs as HER2 inhibitors through docking and 3D-QSAR evaluation. However, as static state docking does not necessarily equal stability in a dynamic state, further evaluation is required. This research aims to predict biological activity with different statistical models, and evaluate candidate-HER2 complex stability under a dynamic state. Based on our previous findings, natural compounds 2-Ocaffeoyl tartaric acid, 2-O-feruloyl tartaric acid, and salvianolic acid C exhibited good docking characteristics and were selected as candidates for further investigation. Lapatinib was used as the control. The HER2 docking site was constructed through sequence homology and detailed elsewhere. The spatial location and distances of NVP-BEZ235 nearby amino acids with the centroid of each candidate ligand are depicted in Figures 7 and 8. A bimodal distribution of amino acid distances was observed for Lapatinib. On the other hand, the distance of nearby amino acids from the centroid of the TCM candidates were more uniform. The distance distributionsuggests that all test ligands were tightly fitted within the binding site and can effectively block ATP from binding. Furthermore, the candidates were more closely bound to the binding site than Lapatinib, indicating another advantage of the candidates as a potential Lapatinib substitute. MD observations indicate that the candidate compounds are more stable within the HER2 binding site than Lapatinib. The stability could be explained in part by the multiple H-bonds formed with the binding site. Conformational changes induced by the MD simulation were favorable in forming additional H-bonds that contributed to overall stability of the candidates. Possibility of the natural compound candidates as alternatives to Lapatinib was supported by the ligand based analysis and MD simulation. Candidates were predicted as biologically active by the constructed MLRand SVMmodels based on their ligand characteristics.