Citation: DENG Yu-Ling, YU Lu, HUANG Qiang. A Multi-Target Docking System of Human Kinome[J]. Acta Physico-Chimica Sinica, ;2016, 32(9): 2355-2363. doi: 10.3866/PKU.WHXB201605171 shu

A Multi-Target Docking System of Human Kinome

1.
School of Life Sciences, Fudan University, Shanghai 200438, P. R. China;
2.
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China

Received Date: 24 March 2016
Revised Date: 16 May 2016

Fund Project: The project was supported by the National Natural Science Foundation of China (30570406, 91430112), National Hi-tech Research and Development Program of China (863) (2008AA02Z311), Shanghai Natural Science Foundation, China (13ZR1402400).

Protein kinases play critical roles in many biological processes, including signal transduction, gene transcription, and protein translation, and are therefore closely associated with various disease states. The screening of kinase inhibitors has become an important aspect of anti-tumor drug development, and has been refined to allow high-throughput, multi-target screening based on the entire human kinome. To reduce the experimental costs of large-scale inhibitor screening and to increase the success rate, our group has designed a multi-target molecular docking systemcapable of predicting kinase-inhibitor interactions. In this work we initially used homology modeling to construct three-dimensional (3D) models for approximately 500 catalytic domains of human kinase variants. We subsequently performed molecular docking to calculate the binding affinities of kinase-inhibitor pairs, employing the 3D models as receptors and kinase inhibitors as ligands. The results show that our multi-target docking system accurately predicts the interactions between known inhibitors and kinase variants, and that the calculated binding affinities are highly correlated with the experimental values. Thus, this molecular docking system could be used for computational screening of multi-target kinase inhibitors, thereby providing a theoretical basis for the development of kinase inhibitors and the design of anti-tumor drugs.
- Protein kinase,
- Kinase inhibitor,
- Interaction prediction,
- Homology modeling,
- Molecular docking
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]
26. [26]
27. [27]
28. [28]
29. [29]
30. [30]
31. [31]
32. [32]
33. [33]
34. [34]
35. [35]
36. [36]
37. [37]
38. [38]
39. [39]
40. [40]
41. [41]
42. [42]
43. [43]
1. [1]
  Xinyu ZENG , Guhua TANG , Jianming OUYANG . Inhibitory effect of Desmodium styracifolium polysaccharides with different content of carboxyl groups on the growth, aggregation and cell adhesion of calcium oxalate crystals. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1563-1576. doi: 10.11862/CJIC.20230374
2. [2]
  Shuang Meng , Haixin Long , Zhou Zhou , Meizhu Rong . Inorganic Chemistry Curriculum Design and Implementation of Based on “Stepped-Task Driven + Multi-Dimensional Output” Model: A Case Study on Intermolecular Forces. University Chemistry, 2024, 39(3): 122-131. doi: 10.3866/PKU.DXHX202309008
3. [3]
  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
4. [4]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
5. [5]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
6. [6]
  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
7. [7]
  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
8. [8]
  Yujia Luo , Yunpeng Qi , Huiping Xing , Yuhu Li . The Use of Viscosity Method for Predicting the Life Expectancy of Xuan Paper-based Heritage Objects. University Chemistry, 2024, 39(8): 290-294. doi: 10.3866/PKU.DXHX202401037
9. [9]
  Laiying Zhang , Yinghuan Wu , Yazi Yu , Yecheng Xu , Haojie Zhang , Weitai Wu . Innovation and Practice of Polymer Chemistry Experiment Teaching for Non-Polymer Major Students of Chemistry: Taking the Synthesis, Solution Property, Optical Performance and Application of Thermo-Sensitive Polymers as an Example. University Chemistry, 2024, 39(4): 213-220. doi: 10.3866/PKU.DXHX202310126
10. [10]
  Yang YANG , Pengcheng LI , Zhan SHU , Nengrong TU , Zonghua WANG . Plasmon-enhanced upconversion luminescence and application of molecular detection. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 877-884. doi: 10.11862/CJIC.20230440
11. [11]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169
12. [12]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
13. [13]
  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
14. [14]
  Rui Gao , Ying Zhou , Yifan Hu , Siyuan Chen , Shouhong Xu , Qianfu Luo , Wenqing Zhang . Design, Synthesis and Performance Experiment of Novel Photoswitchable Hybrid Tetraarylethenes. University Chemistry, 2024, 39(5): 125-133. doi: 10.3866/PKU.DXHX202310050
15. [15]
  Wenbing Hu , Jin Zhu . Flipped Classroom Approach in Teaching Professional English Reading and Writing to Polymer Graduates. University Chemistry, 2024, 39(6): 128-131. doi: 10.3866/PKU.DXHX202310015
16. [16]
  Shicheng Yan . Experimental Teaching Design for the Integration of Scientific Research and Teaching: A Case Study on Organic Electrooxidation. University Chemistry, 2024, 39(11): 350-358. doi: 10.12461/PKU.DXHX202408036
17. [17]
  Linhan Tian , Changsheng Lu . Discussion on Sextuple Bonding in Diatomic Motifs of Chromium Family Elements. University Chemistry, 2024, 39(8): 395-402. doi: 10.3866/PKU.DXHX202401056
18. [18]
  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
19. [19]
  Kai Yang , Gehua Bi , Yong Zhang , Delin Jin , Ziwei Xu , Qian Wang , Lingbao Xing . Comprehensive Polymer Chemistry Experiment Design: Preparation and Characterization of Rigid Polyurethane Foam Materials. University Chemistry, 2024, 39(4): 206-212. doi: 10.3866/PKU.DXHX202308045
20. [20]
  Zheqi Wang , Yawen Lin , Shunliu Deng , Huijun Zhang , Jinmei Zhou . Antiviral Strategies: A Brief Review of the Development History of Small Molecule Antiviral Drugs. University Chemistry, 2024, 39(9): 85-93. doi: 10.12461/PKU.DXHX202403108

Get Citation

PDF

XML

Metrics

PDF Downloads(3)
Abstract views(691)
HTML views(25)

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