Citation: YANG Li-Jun, LIU Qian, YUAN Wen-Bin, YANG Sheng-Yong. Molecular Dynamics Simulations of Interactional Mechanism and Binding Energy Calculations between Kinase ABL and Small Molecules Binding at Myristoyl Pocket[J]. Acta Physico-Chimica Sinica, ;2013, 29(02): 423-430. doi: 10.3866/PKU.WHXB201211212 shu

Molecular Dynamics Simulations of Interactional Mechanism and Binding Energy Calculations between Kinase ABL and Small Molecules Binding at Myristoyl Pocket

1.
1 Chemistry Synthesis and Pollution Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637009, Sichuan Province, P. R. China;
2 State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P. R. China

Received Date: 18 September 2012
Available Online: 21 November 2012
Fund Project: 四川省教育厅自然科学重点项目(11ZA294) (11ZA294)西华师范大学科研启动项目(10B006)资助 (10B006)

We performed molecular dynamics simulations on complexes of ABL to investigate the binding of imatinib, P16 (binding at the ATP pocket), and STJ, MS7, MS9, 3YY, and MYR (binding at the myristoyl pocket). The calculated binding energies were then decomposed to determine the ligand-residue pair interactions, using the generalized Born surface area (GBSA) method. The results showed that the binding energies are almost the same for STJ, MS7, and MS9, and their absolute values are larger than those of 3YY and MYR. The decomposition of the binding energy revealed that three residues (ILE502, VAL506, and LEU510) contribute significantly to hold the αI-helix in a bent conformation in the STJ-ABL and MYR-ABL complexes. The root mean square deviation (RMSD) values for the residues forming myristoyl pocket showed that the inhibitors in this pocket decrease the flexibility of the corresponding residues.
- Molecular dynamics,
- Kinase,
- Myristoyl pocket,
- Free energy,
- Inhibitor
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