Home

Citation: CUI Wei, ZHANG Huai, JI Ming-Juan. Molecular Dynamics Simulations and Free Energy Calculations of a Novel Series of Protein Tyrosine Phosphatase 1B Difluoromethylenephosphonic Acid Inhibitors[J]. Acta Physico-Chimica Sinica, ;2009, 25(04): 668-676. doi: 10.3866/PKU.WHXB200904271 shu

Molecular Dynamics Simulations and Free Energy Calculations of a Novel Series of Protein Tyrosine Phosphatase 1B Difluoromethylenephosphonic Acid Inhibitors

1.
College of Chemistry and Chemical Engineering, Graduate University of the Chinese Academy of Sciences, Beijing 100049, P. R. China; Laboratory of ComputationalGeodynamics, Graduate University of the Chinese Academy of Sciences, Beijing 100049, P. R. China

Corresponding author: ZHANG Huai, JI Ming-Juan, jmj@gucas.ac.cn
Received Date: 10 October 2008
Available Online: 15 January 2009

Binding models for a series of difluoromethylenephosphonic (DFMP) and difluoromethylenesulfonic (DFMS) acids to protein tyrosine phosphatase 1B (PTP1B) were studied by molecular docking, molecular dynamics (MD) simulations, and free energy calculations. Binding free energies were computed using the molecular mechanics/generalized Born surface area (MM/GBSA) methodology based on 1 ns MD simulations. The order of affinities for the studied inhibitors can be accurately predicted using previously predicted binding free energies. Inhibitor/residue interaction profiles for all inhibitors were systematically generated using MM/GBSA free energy decomposition analysis. Inhibitor/residue interaction profiles demonstrated that electrostatic interactions between the negative charge center of DFMP/DFMS groups and Arg221 of PTP1B are a crucial part of the studied molecule affinities. Furthermore, the fluorine atom or other hydrogen bonding donor atoms with appropriate radii will improve inhibitor binding to the primary binding site of PTP1B.
- Protein tyrosine phosphatase 1B,
- Molecular dynamics simulation,
- Free energy calculation,
- Free energy decomposition,
- MM/GBSA
1. [1]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
2. [2]
  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
3. [3]
  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
4. [4]
  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
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]
  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
7. [7]
  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
8. [8]
  Lei Shi . Nucleophilicity and Electrophilicity of Radicals. University Chemistry, 2024, 39(11): 131-135. doi: 10.3866/PKU.DXHX202402018
9. [9]
  Danqing Wu , Jiajun Liu , Tianyu Li , Dazhen Xu , Zhiwei Miao . Research Progress on the Simultaneous Construction of C—O and C—X Bonds via 1,2-Difunctionalization of Olefins through Radical Pathways. University Chemistry, 2024, 39(11): 146-157. doi: 10.12461/PKU.DXHX202403087
10. [10]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
11. [11]
  Yunxin Xu , Wenbo Zhang , Jing Yan , Wangchang Geng , Yi Yan . A Fascinating Saga of “Energetic Materials”. University Chemistry, 2024, 39(9): 266-272. doi: 10.3866/PKU.DXHX202307008
12. [12]
  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
13. [13]
  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
14. [14]
  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
15. [15]
  Xiao Liu , Guangzhong Cao , Mingli Gao , Hong Wu , Hongyan Feng , Chenxiao Jiang , Tongwen Xu . Seawater Salinity Gradient Energy’s Job Application in the Field of Membranes. University Chemistry, 2024, 39(9): 279-282. doi: 10.3866/PKU.DXHX202306043
16. [16]
  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
17. [17]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . Kinetic Resolution Enabled by Photoexcited Chiral Copper Complex-Mediated Alkene E→Z Isomerization: A Comprehensive Chemistry Experiment for Undergraduate Students. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
18. [18]
  Jiajia Li , Xiangyu Zhang , Zhihan Yuan , Zhengyang Qian , Jian Zhu . 3D Printing Based on Photo-Induced Reversible Addition-Fragmentation Chain Transfer Polymerization. University Chemistry, 2024, 39(5): 11-19. doi: 10.3866/PKU.DXHX202309073
19. [19]
  Zijian Zhao , Yanxin Shi , Shicheng Li , Wenhong Ruan , Fang Zhu , Jijun Jiang . A New Exploration of the Preparation of Polyacrylic Acid by Free Radical Polymerization Based on the Concept of Green Chemistry. University Chemistry, 2024, 39(5): 315-324. doi: 10.3866/PKU.DXHX202311094
20. [20]
  Xinxin JING , Weiduo WANG , Hesu MO , Peng TAN , Zhigang CHEN , Zhengying WU , Linbing SUN . Research progress on photothermal materials and their application in solar desalination. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1033-1064. doi: 10.11862/CJIC.20230371

Get Citation

PDF

XML

Metrics

PDF Downloads(1627)
Abstract views(3164)
HTML views(0)

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

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return