Citation: XU Shi-Wen, LIN Dong-Qiang, YAO Shan-Jing. Molecular Simulations on Dynamic Binding of Ibuprofen onto Site II of Human Serum Albumin: One Potential Way Analysis[J]. Acta Physico-Chimica Sinica, ;2016, 32(11): 2811-2818. doi: 10.3866/PKU.WHXB201609131 shu

Molecular Simulations on Dynamic Binding of Ibuprofen onto Site II of Human Serum Albumin: One Potential Way Analysis

Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, P. R. China

Received Date: 25 May 2016
Revised Date: 13 September 2016

Fund Project: The project was supported by the National Natural Science Foundation of China (21476198, 21276228, 21576233).

Human serum albumin (HSA) has two main drug binding sites termed Site I and Site II. Most small molecules like ibuprofen (a well-known anti-inflammatory drug) bind to Site II preferentially. In this study, molecular simulation methods were used to investigate the dynamic binding process of ibuprofen to Site II. A system of 50 ibuprofen molecules distributed randomly around HSA was constructed. After a 50-ns molecular dynamics simulation, one ibuprofen molecule bound stably to Site II. Based on trajectory analysis of this ibuprofen molecule, the binding process of ibuprofen onto Site II can be divided into four phases:(i) long-range attraction; (ii) adjustment on the surface; (iii) entering to Site II pocket; and (iv) stable binding at Site II. After evaluating van der Waals' and electrostatic interaction energies during the binding process, it was found that the initial major driving force involves electrostatic attractions. Subsequently, ibuprofen locks between two polar regions on the surface near Site II and then moves to Site II. Ibuprofen then enters the pocket of Site II by combinatorial effects of polar and hydrophobic residues nearby the entrance of Site II. Electrostatic and hydrophobic interactions form the stable binding of ibuprofen in Site II. The molecular surface near Site II was observed to change significantly during binding, which indicates an induced fit mechanism. The binding mode obtained with molecular simulations is consistent with the crystal structure of the ibuprofen-HSA complex. The results show that molecular simulations would help to evaluate the dynamic binding processes of small molecules to proteins and improve our understanding of the binding mechanisms at the molecular level.
- Human serum albumin,
- Site II,
- Ibuprofen,
- Dynamic binding,
- Molecular simulation
1. [1]
2. [2]
3. [3]
4. [4]
5. [5]
6. [6]
7. [7]
8. [8]
9. [9]
10. [10]
11. [11]
12. [12]
13. [13]
14. [14]
15. [15]
16. [16]
17. [17]
18. [18]
19. [19]
20. [20]
21. [21]
22. [22]
23. [23]
24. [24]
25. [25]
1. [1]
  Feng Zheng , Ruxun Yuan , Xiaogang Wang . “Research-Oriented” Comprehensive Experimental Design in Polymer Chemistry: the Case of Polyimide Aerogels. University Chemistry, 2024, 39(10): 210-218. doi: 10.12461/PKU.DXHX202404027
2. [2]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
3. [3]
  Zeyu XU , Anlei DANG , Bihua DENG , Xiaoxin ZUO , Yu LU , Ping YANG , Wenzhu YIN . Evaluation of the efficacy of graphene oxide quantum dots as an ovalbumin delivery platform and adjuvant for immune enhancement. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1065-1078. doi: 10.11862/CJIC.20240099
4. [4]
  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
5. [5]
  .
  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): -.
6. [6]
  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
7. [7]
  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
8. [8]
  Wenliang Wang , Weina Wang , Sufan Wang , Tian Sheng , Tao Zhou , Nan Wei . “Schrödinger Equation – Approximate Models – Core Concepts – Simple Applications”: Constructing a Logical Framework and Knowledge Graph of Atom and Molecule Structures. University Chemistry, 2024, 39(8): 338-343. doi: 10.3866/PKU.DXHX202312084
9. [9]
  Zishuo Yi , Peng Liu , Yan Xu . Fluorescent “Chameleon”: A Popular Science Experiment Based on Dynamic Luminescence. University Chemistry, 2024, 39(9): 304-310. doi: 10.12461/PKU.DXHX202311079
10. [10]
  Jin Yan , Chengxia Tong , Yajie Li , Yue Gu , Xuejian Qu , Shigang Wei , Wanchun Zhu , Yupeng Guo . Construction of a “Dual Support, Triple Integration” Chemical Safety Practical Education System. University Chemistry, 2024, 39(7): 69-75. doi: 10.12461/PKU.DXHX202405008
11. [11]
  Jia Zhou , Huaying Zhong . Experimental Design of Computational Materials Science Combined with Machine Learning. University Chemistry, 2025, 40(3): 171-177. doi: 10.12461/PKU.DXHX202406004
12. [12]
  Hongyi Zhang , Zhihong Shi , Zhijun Zhang . A New Strategy for “De-formulized” Calculation of Dynamic Buffer Capacity in Analytical Chemistry Education. University Chemistry, 2024, 39(3): 390-394. doi: 10.3866/PKU.DXHX202309030
13. [13]
  Bingliang Li , Yuying Han , Dianyang Li , Dandan Liu , Wenbin Shang . One-Step Synthesis of Benorilate Guided by Green Chemistry Principles and in vivo Dynamic Evaluation. University Chemistry, 2024, 39(6): 342-349. doi: 10.3866/PKU.DXHX202311070
14. [14]
  Manman Jin , Zhiguo Lv , Qingtao Niu . Teaching Reformation and Case Study for “Chemical Process Development and Design” Based on “Just-in-Time” Dynamic and Accurate Matching Industrial Needs. University Chemistry, 2024, 39(11): 108-116. doi: 10.12461/PKU.DXHX202403030
15. [15]
  Yi Li , Zhaoxiang Cao , Peng Liu , Xia Wu , Dongju Zhang . Revealing the Coloration and Color Change Mechanisms of the Eriochrome Black T Indicator through Computational Chemistry and UV-Visible Absorption Spectroscopy. University Chemistry, 2025, 40(3): 132-139. doi: 10.12461/PKU.DXHX202405154
16. [16]
  Hui Wang , Yiwen Zhang , Dong Liu . “三全育人”理念下培养应用型创新人才——以“赛教结合”模式为例的探索与实践. University Chemistry, 2025, 40(6): 37-42. doi: 10.12461/PKU.DXHX202407091
17. [17]
  Yongjie ZHANG , Bintong HUANG , Yueming ZHAI . Research progress of formation mechanism and characterization techniques of protein corona on the surface of nanoparticles. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2318-2334. doi: 10.11862/CJIC.20240247
18. [18]
  Miaomiao He , Zhiqing Ge , Qiang Zhou , Jiaqing He , Hong Gong , Lingling Li , Pingping Zhu , Wei Shao . Exploring the Fascinating Realm of Quantum Dots. University Chemistry, 2024, 39(6): 231-237. doi: 10.3866/PKU.DXHX202310040
19. [19]
  Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
20. [20]
  Jibin Miao , Changjie Mao , Baokang Jin . Exploration and Practice of Virtual and Real Combination Practical Curriculum During the Construction of the National Demonstration Center for Experimental Education: A Case Study of the National Demonstration Center for Experimental Chemistry & Chemical Engineering Education (Anhui University). University Chemistry, 2024, 39(7): 106-109. doi: 10.12461/PKU.DXHX202405021

Get Citation

PDF

XML

Metrics

PDF Downloads(3)
Abstract views(1005)
HTML views(232)

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 Simulations on Dynamic Binding of Ibuprofen onto Site II of Human Serum Albumin: One Potential Way Analysis

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