Virtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma

Abstract

HDAC protein is associated with hepatocellular carcinoma. Different medicinal plants were selected for this study to analyze the inhibitory efficacy against the target protein, HDAC. Using virtual screening, we filtered out the best compounds, and molecular docking (XP) was carried out for the top compounds which filtered out. The molecular docking results showed that the title compound (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate (MEMNC) has the highest docking score of about −7.7 kcal/mol against the targeted protein histone deacetylase (HDAC) compared with the other selected phytocompounds. From the molecular dynamics analysis, the RMSD and RMSF plots depicted the overall stability of the protein–ligand complex. Toxicity properties show the acceptable range of various kinds of toxicity that were predicted using the ProTox-II server. In addition, DFT quantum chemical and physicochemical properties of the MEMNC molecule were reported. Initially, the molecular structure of the MEMNC molecule was optimized and harmonic vibrational frequencies were calculated using DFT/B3LYP method with a cc-pVTZ basis set using Gaussian 09 program. The calculated vibrational wavenumber values were assigned based on Potential Energy Distribution calculations using the VEDA 4.0 program and correlated well with the previous literature values. The molecule has bioactivity as a result of intramolecular charge transfer interactions, as demonstrated by frontier molecular orbital analysis. Molecular electrostatic potential surface and Mulliken atomic charge distribution analyses validate the reactive sites of the molecule. Thus, the title compound can be used as a potential inhibitor of HDAC protein, which paves the way for designing novel drugs to treat Hepatocellular carcinoma.

Communicated by Ramaswamy H. Sarma

Keywords:

• (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl)carbamate
• DFT
• molecular docking
• ADMET analysis
• molecular dynamics
• hepatocellular carcinoma

Acknowledgment

Dr. T. Rajesh Kumar thankfully acknowledges the Department of Bioinformatics, Alagappa University, for providing laboratory facilities to conduct Computational Biology research investigations.

Disclosure Statement

The authors report no conflicts of interest in this work.

Additional information

Funding

Dr. T. Rajesh Kumar, thankfully acknowledges G.T.N. Arts College, Dindigul, Tamil Nadu, India for financing through seed money scheme to carry out the research work.