<i>In Silico</i> Investigation of Electronic Structure, Binding Patterns and Molecular Docking of Nevirapine: An anti-HIV Type-1 Drug
Gargi Tiwari, Abhishek Kumar, Kaushal Kumar Dwivedi, Dipendra Sharma
Abstract
Nevirapine is used in the treatment of Human Immunodeficiency Virus Type 1 (HIV-1) infection. The structure of nevirapine belongs to the dipyridodiazepinone class of chemical. In the present work, molecular geometries of nevirapine drug, AU and GC base pairs have been optimized by DFT method with B3LYP/6-31G(d,p) basis set. The MEP and HOMO-LUMO surfaces have been scanned at 0.001 electron/Bohr3 isodensity surface. Further, HOMO-LUMO energies have been used to calculate ionization potential, electron affinity, electronegativity, global hardness and softness parameters of the drug molecule as well as AU and GC base pairs. IR and Raman spectra of the drug molecule have been analyzed in the light of standard data. Results obtained from NBO analysis have been analyzed in terms of the hybridization of atoms and electronic structure of drug molecule. Binding patterns of the drug molecule with nucleic acid base pairs (AU and GC) have been examined using second order perturbation theory valid at intermediate range. Efforts have been made to elucidate the chemical and biological properties of the drug. The inhibition activity of the drug molecule against HIV-1 reverse transcriptase (Y2NG) in complex with inhibitor GSK560 has been examined with the help of molecular docking. It has been observed that nevirapine prefers to bind in the guanine-cytosine rich region of nucleic acid helices. Further, there exists gross similarity between calculated vibrational assignment and the standard data as reported in the literature.