In silico studies on potential MCF-7 inhibitors: a combination of pharmacophore and 3D-QSAR modeling, virtual screening, molecular docking, and pharmacokinetic analysis

Abstract

Gallic acid and its derivatives exhibit a diverse range of biological applications, including anti-cancer activity. In this work, a data-set of forty-six molecules containing the galloyl moiety, and known to show anticarcinogenic activity against the MCF-7 human cancer cell line, have been chosen for pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies. A tree-based partitioning algorithm has been used to find common pharmacophore hypotheses. The QSAR model was generated for three, four, and five featured hypotheses with increasing PLS factors and analyzed. Results for five featured hypotheses with three acceptors and two aromatic rings were the best out of all the possible combinations. On analyzing the results, the most robust (R²= .8990) hypothesis with a good predictive power (Q²= .7049) was found to be AAARR.35. A good external validation (R² = .6109) was also obtained. In order to design new MCF-7 inhibitors, the QSAR model was further utilized in pharmacophore-based virtual screening of a large database. The predicted IC₅₀ values of the identified potential MCF-7 inhibitors were found to lie in the micromolar range. Molecular docking into the colchicine domain of tubulin was performed in order to examine one of the probable mechanisms. This revealed various interactions between the ligand and the active site protein residues. The present study is expected to provide an effective guide for methodical development of potent MCF-7 inhibitors.

Keywords:

• gallic acid
• MCF-7
• anti-cancer
• tubulin
• colchicine
• pharmacophore
• QSAR
• virtual screening
• molecular docking

Acknowledgements

One of the authors (B.B.) thanks the Council of Scientific and Industrial Research (CSIR), New Delhi, for a Senior Research Fellowship. The authors thank University of Delhi’s ‘Scheme to Strengthen R&D by Providing Funds to Faculty’ for a research grant.

Notes

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