Solvent effects on the structural, spectroscopic, electronic properties, NCI-RDG analysis, molecular docking and molecular dynamics studies of 1-benzyl-indole-3-carbinol

Abstract

This investigation focuses on the 1-benzyl-indole-3-carbinol (1-benzyl-I3C) molecule and its capacity as a drug to combat breast cancer. The research employs different computational approaches including DFT simulations, molecular docking, and molecular dynamics calculations. The molecular configuration of 1-benzyl-I3C was optimized in the COSMO solvation model, using B3LYP/cc-pVTZ basis set. The modes of vibration of the compound were identified through Potential Energy Distribution (PED) simulations, and the results were found to be consistent with the available FT-IR and Raman data. The analysis of Natural Bond Orbitals (NBO) supports the idea that 1-benzyl-I3C has bioactive properties. The impact of solvents on the electronic characteristics of studied molecule is discussed. The reactive sites of 1-benzyl-I3C were confirmed by the local reactivity descriptors and the molecular electrostatic potential (MEP) surface analyses. Additionally, Non-covalent interaction (NCI) analysis confirms the existence of the Van der Waals interactions in the compound under investigation. Anti-breast cancer activities of the 1-benzyl-I3C molecule were examined based on molecular docking analysis, which reveals a good inhibitor nature of the studied molecule against the progesterone receptor (PR). The molecular dynamics analysis through the RMSD, RMSF, and Rg plots confirms the overall stability of the obtained 1-benzyl-I3C-PR complex.