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
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