Design, synthesis, anti-tobacco mosaic viral and molecule docking simulations of urea/thiourea derivatives of 2-(piperazine-1-yl)-pyrimidine and 1-(4-Fluoro/4-Chloro phenyl)-piperazine and 1-(4-Chloro phenyl)-piperazine - A study

Abstract

The objectives of the present work are to design, syhthesize and introduce novel urea/thiourea derivatives of 2-(piperazine-1-yl)-pyrimidine and 1-(4-Fluoro/4-Chloro phenyl)-piperazine molecules as tobacco mosaic virus (TMV) inhibitors. A series of urea/thiourea derivatives containing pyrimidine and piperazine moieties were synthesized, characterized using Fourier-transform infrared (FTIR) mass spectra, nuclear magnetic resonance (NMR) spectroscopy, elemental analysis and evaluated their sustainability using biological experiments. The anti-viral bioassay of the title compounds showed an antiviral activity against TMV. The compounds synthesized, 9j, 6g and 3d, showed highly-potential curative, protective, and inhibitory activities against TMV at 500 mg/mL formulation. All these compounds were allowed to quantum-polarized-ligand (quantum mechanical and molecular mechanical (QM/MM)) docking experiments. The compounds 9j, 6g and 3d structurally exhibited identical higher affinity towards TMV-Helicase and TMV-Coat proteins. The docking interactions proposed had two stage inhibition of TMV virus by binding to coat protein and helicase for inhibition of RNA replication. The long-range molecular dynamics (150 ns) simulations has revealed more consistency by 9j, 6g and 3d. The present study outcomes good binding propensity for active-tunnel of TMV-Hel enzyme, by these thiourea, urea derivatives, 9j, 6g and 3d, to suggest that the designed and synthesized were ideal for proposing as selective novel inhibitors to target for TMV.

Keywords: Antiviral activity; Dynamic simulations; Molecular docking; TMV-Coat protein; TMV-Helicase; Thiourea; Urea.