Binding conformations and QSAR of CA-4 analogs as tubulin inhibitors

Abstract

A theoretical study on the binding conformations and the quantitative structure–activity relationship (QSAR) of combretastatin A4 (CA-4) analogs as inhibitors toward tubulin has been carried out using docking analysis and comparative molecular field analysis (CoMFA). The appropriate binding orientations and conformations of these compounds interacting with tubulin were revealed by the docking study; and a 3D-QSAR model showing significant statistical quality and satisfactory predictive ability was established, in which the correlation coefficient (R²) and cross-validation coefficient (q²) were 0.955 and 0.66, respectively. The same model was further applied to predict the pIC₅₀ values for 16 congeneric compounds as external test set, and the predictive correlation coefficient R²_pred reached 0.883. Other tests on additional validations further confirmed the satisfactory predictive power of the model. In this work, it was very interesting to find that the 3D topology structure of the active site of tubulin from the docking analysis was in good agreement with the 3D-QSAR model from CoMFA for this series of compounds. Some key structural factors of the compounds responsible for cytotoxicity were reasonably presented. These theoretical results can offer useful references for understanding the action mechanism and directing the molecular design of this kind of inhibitor with improved activity.

Keywords::

• Combretastatin A4
• tubulin
• inhibition mechanism
• docking
• QSAR

Acknowledgments

We are pleased to acknowledge financial support from the National Natural Science Foundation of China (No.20673148). We heartily thank Molecular Discovery Ltd. for giving us the DOCK 6.0 program as a freeware and the College of Life Sciences, Sun Yat-Sen University, for SYBYL 6.9 computation environment support. We are also sincerely thankful to the referees for their valuable suggestions to improve this work.

Declaration of interest: Except for the above support and funding received by the authors to carry out the study, no conflict of interest is required.