Molecular docking investigation of cytotoxic phenanthrene derivatives

Abstract

Our previous experimental work indicated that the presence of ester functionality in phenanthrene derivatives D-1 and D-2 leads to potent cytotoxicity against the Caco-2 cell line. The present work is based on th-is experimental result. First, we optimized the structures of the studied molecules using the density functional theory method. Then we performed a study about their potential biological importance by evaluating the binding mode and exploring their intermolecular interactions with appropriate proteins using molecular docking calculations. Consequently, we confirmed the results obtained from experimental studies. In particular, our study indicated that many promising proteins are able to bind and interact with the phenanthrene skeleton from the binding site. Methyl 8-methyl-9,10-phenanthrenequinone-3-carboxylate D-1 and methyl 8-methyldibenzo[a,c]phenazine-3-carboxylate D-2 displayed strong cytotoxicity. However, the best affinity is noted for B-Raf proto-oncogene serine/threonine-protein kinase (-9.8 Kcal/mol for molecule D-1 and -11.1 Kcal/mol for molecule D-2), which is higher than that of any other protein used. Especially, this protein is involved in sending signals inside cells that are involved in directing cell growth and is found to be a significant target in both types of studied cancers.

Keywords

• Phenanthrene
• Cytotoxicity
• DFT calculations
• Molecular modeling
• Docking
• Proteins