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
1. [1]
  
  (1) Wang, J. Y. J. Nat. Cell Biol. 2004, 6 (1), 3. doi: 10.1038/ncb0104-3
2. [2]
  (2) Dass, J.; Jain, S.; Tyagi, S. Leuk. Lymphoma 2011, 52, 1380.doi: 10.3109/10428194.2011.566396
3. [3]
  (3) Mian, A. A.; Metodieva, A.; Najajreh, Y. Haematologica 2012,97, 251. doi: 10.3324/haematol.2011.047191
4. [4]
  (4) Nagar, B.; Hantschel, O.; Young, M. Cell 2003, 112, 859. doi: 10.1016/S0092-8674(03)00194-6.
5. [5]
  (5) An, X.; Tiwari, A. K.; Sun, Y. Leukemia Res. 2010, 34, 1255.doi: 10.1016/j.leukres.2010.04.016
6. [6]
  (6) Skorski, T. Chem. Biol. 2011, 18, 1352. doi: 10.1016/j.chembiol.2011.11.001
7. [7]
  (7) Corbin, A. S.; Buchdunger, E.; Pascal, F. J. Biol. Chem. 2002,277, 32214. doi: 10.1074/jbc.M111525200
8. [8]
  (8) Cowan-Jacob, S.W.; Guez, V.; Fendrich, G. Mini Rev. Med. Chem. 2004, 4, 285. doi: 10.2174/1389557043487321
9. [9]
  (9) Hochhaus, A.; La Rosée, P.; Müller, M. Cell Cycle. 2011, 10,250. doi: 10.4161/cc.10.2.14537
10. [10]
  (10) Lee, T.; Potts, S.; Kantarjian, H. Cancer 2008, 112, 1744. doi: 10.1002/cncr.23355
11. [11]
  (11) Tokarski, J. S.; Newitt, J. A.; Chang, C. Y. J. Cancer Res. 2006,66, 5790. doi: 10.1158/0008-5472.CAN-05-4187
12. [12]
  (12) Valent, P.; Gastl, G.; Geissler, K. Crit. Rev. Oncol./Hematol.2011, 82, 370. doi: 10.1016/j.critrevonc.2011.08.002
13. [13]
  (13) Lu, X.; Cai, Q.; Ding, K. Curr. Med. Chem. 2011, 18, 2146. doi: 10.2174/092986711795656135
14. [14]
  (14) Ramirez, P.; DiPersio, J. F. Oncologist 2008, 13, 424. doi: 10.1634/theoncologist.2007-0170
15. [15]
  (15) Flight, M. Nat. Rev. Drug Discov. 2010, 9, 194. doi: 10.1038/nrd3119
16. [16]
  (16) Schenone, S.; Bruno, O.; Radi, M. Med. Res. Rev. 2009, 31 (1),1. doi: 10.1002/med.20175
17. [17]
  (17) De Keersmaecker, K. Haematologica 2012, 97 (1), 2. doi: 10.3324/haematol.2011.06
18. [18]
  (18) Jabbour, E.; Cortes, J. E.; Giles, F. J. Cancer 2007, 109, 2171.doi: 10.1002/cncr.22661
19. [19]
  (19) Wang, D.; Zhang, Z.; Lu, X. Bioorg. Med. Chem. Lett. 2011, 21,1965. doi: 10.1016/j.bmcl.2011.02.029
20. [20]
  (20) Zhang, J. M.; Yang, P. L.; Gray, N. S. Nature 2009, 9, 28. doi: 10.1038/nrc2559
21. [21]
  (21) Liu, Y.; Gray, N. S. Nat. Chem. Biol. 2006, 2, 358. doi: 10.1038/nchembio799
22. [22]
  (22) Choi, H.; Ren, P.; Adrian, F. J. Med. Chem. 2010, 53, 5439. doi: 10.1021/jm901808w
23. [23]
  (23) Zhang, J.; Adrian, F.; Gray, N. S. Nature 2010, 463, 501. doi: 10.1038/nature08675
24. [24]
  (24) Weisberg, E.; Deng, X.; Choi, H. Leukemia 2010, 24, 1375. doi: 10.1038/leu.2010.107
25. [25]
  (25) Quintás-Cardama, A. Leukemia 2008, 22, 932. doi: 10.1038/leu.2008.47
26. [26]
  (26) Deng, X.; Okram, B.; Ding, Q. J. Med. Chem. 2010, 53, 6934.doi: 10.1021/jm100555f
27. [27]
  (27) Choi, Y.; Seeliger, M.; Panjarian, S. J. Biol. Chem. 2009, 284,29005. doi: 10.1074/jbc.M109.026633
28. [28]
  (28) Hantschel, O. Haematologica 2012, 97, 157. doi: 10.3324/haematol.2012.061812
29. [29]
  (29) Cox, K. J.; Shomin, C. D.; Ghosh, I. Future 2011, 3, 29. doi: 10.4155/fmc.10.272
30. [30]
  (30) Cheng, H.; Johnson, T.; Mills, R. Clin. Exp. Pharmacol. Physiol. 2010, 37, 93. doi: 10.1111/j.1440-1681.2009.05237.x
31. [31]
  (31) Hassan, A.; Sharma, S.;Warmuth, M. Cell Cycle (Georgetown, Tex.) 2010, 9, 3710. doi: 10.4161/cc.9.18.13232
32. [32]
  (32) Grebien, F.; Hantschel, O.;Wojcik, J. Cell 2011, 147, 306. doi: 10.1016/j.cell.2011.08.046
33. [33]
  (33) Fabbro, D.; Manley, P.; Jahnke,W. BBA-Proteins Proteomics2010, 1804, 454. doi: 10.1016/j.bbapap.2009.12.009
34. [34]
  (34) Brehme, M.; Hantschel, O.; Colinge, J. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 7414. doi: 10.1073/pnas.0900653106
35. [35]
  (35) Fabbro, D. Nat. Chem. Biol. 2012, 8, 228. doi: 10.1038/nchembio.900
36. [36]
  (36) Jahnke,W.; Grotzfeld, R.; Pelle, X. J. Am. Chem. Soc. 2010,132, 7043. doi: 10.1021/ja101837n
37. [37]
  (37) Yang, J. P.; Campobasso, N.; Biju, M. P. Chem Biol. 2011, 18,177. doi: 10.1016/j.chembiol.2010.12.013
38. [38]
  (38) Sun, H.; Jiang, Y. J.; Yu, Q. S. Acta Phys. -Chim. Sin. 2011, 27,207. [孙浩, 蒋勇军, 俞庆森. 物理化学学报, 2011, 27,207.] doi: 10.3866/PKU.WHXB20110116
39. [39]
  (39) Yang, L. J.; Zou, J.; Xie, H. Z. PloS One 2009, 4, e8470. doi: 10.1371/journal.pone.0008470
40. [40]
  (40) Liu, F. F.; Dong, X. Y.; Sun, Y. Acta Phys. -Chim. Sin. 2010, 26,1643. [刘夫锋, 董晓燕, 孙彦. 物理化学学报, 2010, 26,1643.] doi: 10.3866/PKU.WHXB20050416
41. [41]
  (41) Adcock, S. A.; McCammon, J. A. Chem. Rev. 2006, 106, 1589.doi: 10.1021/cr040426m
42. [42]
  (42) Wang, L. D.;Wang, C. X. Acta Chim . Sin. 2008, 66, 817. [王丽东, 王存新. 化学学报, 2008, 66, 817.]
43. [43]
  (43) Lu, T.; Li, X. Y. Acta Chim . Sin. 2008, 66, 433. [卢涛, 李象远. 化学学报, 2008, 66, 433.]
44. [44]
  (44) Lovera, S.; Sutto, L.; Boubeva, R. J. Am. Chem. Soc. 2012, 134,2496. doi: 10.1021/ja210751t
45. [45]
  (45) Aleksandrov, A.; Simonson, T. J. Biol. Chem. 2010, 285, 13807.doi: 10.1074/jbc.M110.109660
46. [46]
  (46) Case, D. A.; Cheatham, T. E.; Darden, T. J. Comput. Chem.2005, 26, 1668. doi: 10.1002/jcc.20290
47. [47]
  (47) Jorgensen,W. L.; Chandrasekhar, J.; Madura, J. D. J. Chem. Phys. 1983, 79, 926. doi: 10.1063/1.445869
48. [48]
  (48) Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327. doi: 10.1016/0021-9991(77)90098-5
49. [49]
  (49) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
50. [50]
  (50) Pricl, S.; Fermeglia, M.; Ferrone, M. Mol. Cancer Ther. 2005, 4,1167. doi: 10.1158/1535-7163.MCT-05-0101
51. [51]
  (51) Cowan-Jacob, S.W.; Fendrich, G.; Floersheimer, A. Acta Cryst. D 2007, 63, 80. doi: 10.1107/S0907444906047287
1. [1]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
2. [2]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
3. [3]
  Honglian Liang , Xiaozhe Kuang , Fuping Wang , Yu Chen . Exploration and Practice of Integrating Ideological and Political Education into Physical Chemistry: a Case on Surface Tension and Gibbs Free Energy. University Chemistry, 2024, 39(10): 433-440. doi: 10.12461/PKU.DXHX202405073
4. [4]
  Shanghua Li , Malin Li , Xiwen Chi , Xin Yin , Zhaodi Luo , Jihong Yu . 基于高离子迁移动力学的取向ZnQ分子筛保护层实现高稳定水系锌金属负极的构筑. Acta Physico-Chimica Sinica, 2025, 41(1): 2309003-. doi: 10.3866/PKU.WHXB202309003
5. [5]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
6. [6]
  Jiayu Gu , Siqi Wang , Jun Ling . Kinetics of Living Copolymerization: A Brief Discussion. University Chemistry, 2025, 40(4): 100-107. doi: 10.12461/PKU.DXHX202406012
7. [7]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
8. [8]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
9. [9]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
10. [10]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
11. [11]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
12. [12]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
13. [13]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
14. [14]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . 基于激发态手性铜催化的烯烃E→Z异构的动力学拆分——推荐一个本科生综合化学实验. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
15. [15]
  Hao XU , Ruopeng LI , Peixia YANG , Anmin LIU , Jie BAI . Regulation mechanism of halogen axial coordination atoms on the oxygen reduction activity of Fe-N₄ site: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 695-701. doi: 10.11862/CJIC.20240302
16. [16]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
17. [17]
  Chengyi Xiao , Xiaoli Sun , Chen Zhang , Weiwei Li . An In-Depth Analysis of the Scientific Connotations, Testing Methods, and Applications of Free Volume in Polymer Physics. University Chemistry, 2025, 40(4): 33-45. doi: 10.12461/PKU.DXHX202403069
18. [18]
  Yikai Wang , Xiaolin Jiang , Haoming Song , Nan Wei , Yifan Wang , Xinjun Xu , Cuihong Li , Hao Lu , Yahui Liu , Zhishan Bo . 氰基修饰的苝二酰亚胺衍生物作为膜厚不敏感型阴极界面材料用于高效有机太阳能电池. Acta Physico-Chimica Sinica, 2025, 41(3): 2406007-. doi: 10.3866/PKU.WHXB202406007
19. [19]
  .
  南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积
  . CCS Chemistry, 2025, 7(0): -.
20. [20]
  Hui Wang , Abdelkader Labidi , Menghan Ren , Feroz Shaik , Chuanyi Wang . 微观结构调控的g-C₃N₄在光催化NO转化中的最新进展：吸附/活化位点的关键作用. Acta Physico-Chimica Sinica, 2025, 41(5): 100039-. doi: 10.1016/j.actphy.2024.100039

Get Citation

PDF

XML

Metrics

PDF Downloads(788)
Abstract views(1303)
HTML views(49)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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

南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积

Metrics

通讯作者: 陈斌, bchen63@163.com