Molecular dynamic investigate the affection of EGFR by Tubemoside

• Published in: Journal of molecular graphics & modelling 2019-05, Vol.88, p.203-208
• Main Authors: Du, Xia, Chen, Zhi-yong, Guo, Dong, Zhang, Hong, Liu, Yang, Wang, Chun-liu, Sun, Ting-ting, Shi, Long-fei, Li, Ye, Liu, Feng
• Format: Article
• Language: English
• Subjects: Drugs, Chinese Herbal - chemistry; Electrostatic interaction; Epidermal growth factor receptor (EGFR); ErbB Receptors - chemistry; ErbB Receptors - genetics; Humans; Hydrogen bond network analysis; Hydrogen Bonding; Molecular dynamic (MD) simulation; Molecular Dynamics Simulation; Principal component analysis; Protein Binding; Protein Conformation; Saponins - chemistry; Static Electricity; Structure-Activity Relationship; Tubemoside
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2019.01.017

Tubemoside as a common traditional Chinese medicine is playing an important role in the field of prevention and treatment of lung cancer without any side effects. However, the reason and its mechanism remain unclear. In our study, the molecular dynamic simulation was used to investigate the mechanism at the molecular level. We found that the hydrogen bond network of proteins (three states of EGFR) was affected by Tubemoside. The movement and opening/closing state of protein was changed when combine with Tubemoside. The results of principal component analysis were used to prove the transform of proteins and the change of its movement. Electrostatic interactions of proteins also were studied. The numbers of active interaction sites will decrease while Tubemoside emerged in the protein, which will cause the activity change of EGFR for forming asymmetric dimers required for activation. [Display omitted] •The molecular dynamic simulation was used to investigate the mechanism.•The opening/closing state of proteins was changed according to the hydrogen bond.•The PCA were used to prove the transform of proteins and the change of its movement.•The active interaction sites will decrease while Tubemoside emerged in the protein.