Citation: ZHANG Qing-Qing, YAO Qi-Zheng, ZHANG Sheng-Ping, BI Le-Ming, ZHOU Zhi-Guang, ZHANG Ji. Homology Modeling, Molecular Docking, and 3D-QSAR of Indirubin Analogues as CDK1 Inhibitors[J]. Acta Physico-Chimica Sinica, ;2014, 30(2): 371-381. doi: 10.3866/PKU.WHXB201312192 shu

Homology Modeling, Molecular Docking, and 3D-QSAR of Indirubin Analogues as CDK1 Inhibitors

1.
1 School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China;
2 Department of Physical Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China

Received Date: 29 October 2013
Available Online: 19 December 2013
Fund Project: 科技重大专项(2009ZX09103-149)资助 (2009ZX09103-149)

The abnormal expression of cyclin-dependent kinase 1 (CDK1) leads to stagnation of the G2 phase and a variety of tumors. Therefore, CDK1 has been reported recently as an ideal cell cycle target for cancer drug discovery. In this paper, we use the cell division control protein 2 homolog as a template to homologically model the protein of CDK1 that is subsequently docked with the inhibitors of indirubin analogues. Three molecular alignment methods were used, and the corresponding three- dimensional quantitative structure-activity relationship (3D-QSAR) models were built using the comparative molecular field analysis (CoMFA) protocol in Sybyl 7.1 and the 3D-QSAR protocol (abbreviated for DS) in Discovery Studio 3.0. It was found that the molecular alignment method combining molecular docking with public template is most suitable for building the 3D-QSARmodels, and shows the best calculated results (CoMFA: q²=0.681, r²=0.909, and r_pred.²=0.836; DS: q²= 0.579, r²=0.971, and r_pred.²=0.795, where q² denotes the cross-validated correlation coefficient and r² denotes the non- cross- validated correlation coefficient). This paper may provide significant theoretical foundation for designing novel CDK1 inhibitors by carrying out structural modifications of indirubin analogues.
- Cyclin-dependent kinase 1,
- Indirubin,
- 3D-QSAR,
- CoMFA,
- Homology modeling
1. [1]
  
  (1) Lees, E. Curr. Opin. Cell Biol. 1995, 7 (6), 773. doi: 10.1016/0955-0674(95)80060-3
2. [2]
  (2) Zhang, L.; Zhu, H.;Wang, Q.; Fang, H.; Xu,W.; Li, M. J. Mol. Model. 2011, 17 (2), 219. doi: 10.1007/s00894-010-0710-z
3. [3]
  (3) Quereda, V.; Malumbres, M. J. Mol. Endocrinol. 2009, 42 (2),75.
4. [4]
  (4) Santamaria, D.; Barriere, C.; Cerqueira, A.; Hunt, S.; Tardy, C.;Newton, K.; Caceres, J. F.; Dubus, P.; Malumbres, M.; Barbacid,M. Nature 2007, 448 (7155), 811. doi: 10.1038/nature06046
5. [5]
  (5) Wang, Q.; Su, L.; Niu, N.; Zhang, L.; Xu,W.; Fang, H. Curr. Med. Chem. 2011, 18 (13), 2025. doi: 10.2174/092986711795590110
6. [6]
  (6) Singh, S. K.; Dessalew, N.; Bharatam, P. V. Med. Chem. 2007, 3 (1), 75. doi: 10.2174/157340607779317517
7. [7]
  (7) McGrath, C. F.; Pattabiraman, N.; Kellogg, G. E.; Lemcke, T.;Kunick, C.; Sausville, E. A.; Zaharevitz, D.W.; Gussio, R.J. Biomol. Struct. Dyn. 2005, 22 (5), 493. doi: 10.1080/07391102.2005.10531227
8. [8]
  (8) Gussio, R.; Zaharevitz, D.W.; McGrath, C. F.; Pattabiraman,N.; Kellogg, G. E.; Schultz, C.; Link, A.; Kunick, C.; Leost, M.;Meijer, L.; Sausville, E. A. Anticancer Drug Des. 2000, 15 (1),53.
9. [9]
  (9) Li,W. Y.; Zhang, L.; Li, F. L.;Wang, Z. H.; Yao, Q. Z. World Notes Antibiot. 2009, 30 (3), 113. [李文赟, 张磊, 李福龙,王朝晖, 姚其正. 国外医药抗生分册, 2009, 30 (3), 113.]
10. [10]
  (10) Beauchard, A.; Ferandin, Y.; Frere, S.; Lozach, O.; Blairvacq,M.; Meijer, L.; Thiery, V.; Besson, T. Bioorganic & Medicinal Chemistry 2006, 14 (18), 6434. doi: 10.1016/j.bmc.2006.05.036
11. [11]
  (11) Ferandin, Y.; Bettayeb, K.; Kritsanida, M.; Lozach, O.;Polychronopoulos, P.; Magiatis, P.; Skaltsounis, A. L.; Meijer,L. J. Med. Chem. 2006, 49 (15), 4638. doi: 10.1021/jm060314i
12. [12]
  (12) Leclerc, S.; Garnier, M.; Hoessel, R.; Marko, D.; Bibb, J. A.;Snyder, G. L.; Greengard, P.; Biernat, J.;Wu, Y. Z.; Mandelkow,E. M.; Eisenbrand, G.; Meijer, L. J. Biol. Chem. 2001, 276 (1),251.
13. [13]
  (13) Meijer, L.; Skaltsounis, A. L.; Magiatis, P.; Polychronopoulos,P.; Knockaert, M.; Leost, M.; Ryan, X. P.; Vonica, C. A.;Brivanlou, A.; Dajani, R.; Crovace, C.; Tarricone, C.;Musacchio, A.; Roe, S. M.; Pearl, L.; Greengard, P. Chem. Biol.2003, 10 (12), 1255. doi: 10.1016/j.chembiol.2003.11.010
14. [14]
  (14) Hyperchem, Release 7.0 forWindows; Hypercube, Inc.:Gainesville, 2002.
15. [15]
  (15) Robbins, T. J.;Wang, Y.; Yao, Q. Z.;Wang, Z. H.; Cheng, J.; Li,Y. S. J. Mol. Struct. 2013, 1048, 51. doi: 10.1016/j.molstruc.2013.05.012
16. [16]
  (16) Tian, F. A.; Li, C. M.; ng, K. C.; Zhou, Z. H.; Mao, Z. H.;Guo, Y. H. Chin. J. Med. Chem. 1994, 4 (12), 101. [田发安, 李春敏, 龚考才, 周宗华, 毛治华, 郭韵洪. 中国药物化学杂志,1994, 4 (12), 101.]
17. [17]
  (17) Discovery Studio 3.0; Accelrys Inc.: San Die , CA.
18. [18]
  (18) Honma, T.; Hayashi, K.; Aoyama, T.; Hashimoto, N.; Machida,T.; Fukasawa, K.; Iwama, T.; Ikeura, C.; Ikuta, M.; Suzuki-Takahashi, I.; Iwasawa, Y.; Hayama, T.; Nishimura, S.;Morishima, H. J. Med. Chem. 2001, 44 (26), 4615. doi: 10.1021/jm0103256
19. [19]
  (19) Ikuta, M.; Kamata, K.; Fukasawa, K.; Honma, T.; Machida, T.;Hirai, H.; Suzuki-Takahashi, I.; Hayama, T.; Nishimura, S.J. Biol. Chem. 2001, 276 (29), 27548. doi: 10.1074/jbc.M102060200
20. [20]
  (20) Zhang, N.; Jiang, Y. J.; Zou, J.W.; Zeng, M.; Hu, G. X.; Yu, Q.S. Acta. Chim. Sin. 2005, 63 (9), 809. [张娜, 蒋勇军, 邹建卫, 曾敏, 胡桂香, 俞庆森. 化学学报, 2005, 63 (9), 809.]
21. [21]
  (21) Davies, T. G.; Tunnah, P.; Meijer, L.; Marko, D.; Eisenbrand,G.; Endicott, J. A.; Noble, M. E. M. Structure 2001, 9 (5),389. doi: 10.1016/S0969-2126(01)00598-6
22. [22]
  (22) Polychronopoulos, P.; Magiatis, P.; Skaltsounis, A. L.;Myrianthopoulos, V.; Mikros, E.; Tarricone, A.; Musacchio, A.;Roe, S. M.; Pearl, L.; Leost, M.; Greengard, P.; Meijer, L.J. Med. Chem. 2004, 47 (4), 935. doi: 10.1021/jm031016d
23. [23]
  (23) SYBYL 7.1; Tripos Inc.: St. Louis, Missouri, 63144, U.S.A.
1. [1]
  Yifan Xie , Liyun Yao , Ruolin Yang , Yuxing Cai , Yujie Jin , Ning Li . Application of Comparative Pedagogy in Instrumental Analysis Experiment Teaching. University Chemistry, 2024, 39(3): 266-273. doi: 10.3866/PKU.DXHX202309068
2. [2]
  Jingming Li , Bowen Ding , Nan Li , Nurgul . Application of Comparative Teaching Method in Experimental Project Design of Instrumental Analysis Course: A Case Study in Chromatography Experiment Teaching. University Chemistry, 2024, 39(8): 263-269. doi: 10.3866/PKU.DXHX202312078
3. [3]
  Junjun Huang , Ran Chen , Yajian Huang , Hang Zhang , Anran Zheng , Qing Xiao , Dan Wu , Ruxia Duan , Zhi Zhou , Fei He , Wei Yi . Discovery of an enantiopure N-[2-hydroxy-3-phenyl piperazine propyl]-aromatic carboxamide derivative as highly selective α_1D/1A-adrenoceptor antagonist and homology modelling. Chinese Chemical Letters, 2024, 35(11): 109594-. doi: 10.1016/j.cclet.2024.109594
4. [4]
  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
5. [5]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
6. [6]
  Yuexi Guo , Zhaoyang Li , Jingwei Dai . Charlie and the 3D Printing Chocolate Factory. University Chemistry, 2024, 39(9): 235-242. doi: 10.3866/PKU.DXHX202309067
7. [7]
  Qianqian Liu , Xing Du , Wanfei Li , Wei-Lin Dai , Bo Liu . Synergistic Effects of Internal Electric and Dipole Fields in SnNb₂O₆/Nitrogen-Enriched C₃N₅ S-Scheme Heterojunction for Boosting Photocatalytic Performance. Acta Physico-Chimica Sinica, 2024, 40(10): 2311016-. doi: 10.3866/PKU.WHXB202311016
8. [8]
  Liyang ZHANG , Dongdong YANG , Ning LI , Yuanyu YANG , Qi MA . Crystal structures, luminescent properties and Hirshfeld surface analyses of three cadmium(Ⅱ) complexes based on 2-(3-(pyridin-2-yl)-1H-pyrazol-1-yl)benzoate. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1943-1952. doi: 10.11862/CJIC.20240079
9. [9]
  Tianlong Zhang , Rongling Zhang , Hongsheng Tang , Yan Li , Hua Li . Online Monitoring and Mechanistic Analysis of 3,5-diamino-1,2,4-triazole (DAT) Synthesis via Raman Spectroscopy: A Recommendation for a Comprehensive Instrumental Analysis Experiment. University Chemistry, 2024, 39(6): 303-311. doi: 10.3866/PKU.DXHX202312006
10. [10]
  Jiaxun Wu , Mingde Li , Li Dang . The R eaction of Metal Selenium Complexes with Olefins as a Tutorial Case Study for Analyzing Molecular Orbital Interaction Modes. University Chemistry, 2025, 40(3): 108-115. doi: 10.12461/PKU.DXHX202405098
11. [11]
  Jie XIE , Hongnan XU , Jianfeng LIAO , Ruoyu CHEN , Lin SUN , Zhong JIN . Nitrogen-doped 3D graphene-carbon nanotube network for efficient lithium storage. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1840-1849. doi: 10.11862/CJIC.20240216
12. [12]
  Xi Xu , Chaokai Zhu , Leiqing Cao , Zhuozhao Wu , Cao Guan . Experiential Education and 3D-Printed Alloys: Innovative Exploration and Student Development. University Chemistry, 2024, 39(2): 347-357. doi: 10.3866/PKU.DXHX202308039
13. [13]
  Qiang Zhou , Pingping Zhu , Wei Shao , Wanqun Hu , Xuan Lei , Haiyang Yang . Innovative Experimental Teaching Design for 3D Printing High-Strength Hydrogel Experiments. University Chemistry, 2024, 39(6): 264-270. doi: 10.3866/PKU.DXHX202310064
14. [14]
  Changyuan Bao , Yunpeng Jiang , Haoyin Zhong , Huaizheng Ren , Junhui Wang , Binbin Liu , Qi Zhao , Fan Jin , Yan Meng Chong , Jianguo Sun , Fei Wang , Bo Wang , Ximeng Liu , Dianlong Wang , John Wang . Synergizing 3D-printed structure and sodiophilic interface enables highly efficient sodium metal anodes. Chinese Chemical Letters, 2024, 35(11): 109353-. doi: 10.1016/j.cclet.2023.109353
15. [15]
  Chengmin Hu , Pingxuan Liu , Ziyang Song , Yaokang Lv , Hui Duan , Li Xie , Ling Miao , Mingxian Liu , Lihua Gan . Tailor-made overstable 3D carbon superstructures towards efficient zinc-ion storage. Chinese Chemical Letters, 2025, 36(4): 110381-. doi: 10.1016/j.cclet.2024.110381
16. [16]
  Jiarong Feng , Yejie Duan , Chu Chu , Dezhen Xie , Qiu'e Cao , Peng Liu . Preparation and Application of a Streptomycin Molecularly Imprinted Electrochemical Sensor: A Suggested Comprehensive Analytical Chemical Experiment. University Chemistry, 2024, 39(8): 295-305. doi: 10.3866/PKU.DXHX202401016
17. [17]
  Shuhui Li , Jing Wang , Haitao Tang , Yingming Pan . A Taste Journey with Sauerkraut. University Chemistry, 2024, 39(9): 59-63. doi: 10.12461/PKU.DXHX202404061
18. [18]
  Yuan Teng , Zichun Zhou , Jinghua Chen , Siying Huang , Hongyan Chen , Daibin Kuang . Dual atom-bridge effect promoting interfacial charge transfer in 2D/2D Cs₃Bi₂Br₉/BiOBr epitaxial heterojunction for efficient photocatalysis. Chinese Chemical Letters, 2025, 36(2): 110430-. doi: 10.1016/j.cclet.2024.110430
19. [19]
  Jiayu Huang , Kuan Chang , Qi Liu , Yameng Xie , Zhijia Song , Zhiping Zheng , Qin Kuang . Fe-N-C nanostick derived from 1D Fe-ZIFs for Electrocatalytic oxygen reduction. Chinese Journal of Structural Chemistry, 2023, 42(10): 100097-100097. doi: 10.1016/j.cjsc.2023.100097
20. [20]
  Huan Hu , Ying Zhang , Shi-Shuang Huang , Zhi-Gang Li , Yungui Liu , Rui Feng , Wei Li . Temperature- and pressure-responsive photoluminescence in a 1D hybrid lead halide. Chinese Journal of Structural Chemistry, 2024, 43(10): 100395-100395. doi: 10.1016/j.cjsc.2024.100395

Get Citation

PDF

XML

Metrics

PDF Downloads(768)
Abstract views(1553)
HTML views(127)

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