Structure program

Using fmtD ORF sequence, a homology model was built using the YASARA structure program to determine if DcFA-o-MT folds similar to models of insect SAM-MTs. Several DcFA-o-MT models were built using templates from X-ray coordinates of methyltransferase of Anabæna variabilis (Bacteria) (PDB 3CCF) (to be published by the Joint Center of Structural Genomics, DOI: 10-2210/pdb3ccf/pdb), the trans-aconitase-3-methyltransferase of yeast (PDB 3G5T), and the dimethyladenosine transferase of Plasmodium falciparum (protozoan parasite) (PDB 2H1R) [29] (link). A hybrid model was then constructed from the three previous models. PROCHECK [30] and ANOLEA [31] (link) were used to assess the geometric quality and the energy of the three-dimensional model (3D). Docking of FA, JHA III, and SAM was performed with the YASARA structure program. Molecular models were drawn with YASARA and Chimera [32] (link).

The structure of NOR, ethyl cellulose (EC), eudragits, oleic acid (OA), sodium lauryl sulphate (SLS) and stearic acid were downloaded from PubChem. Energy minimization of all generated structures were carried out using YASARA-Structure software [30 (link)]. The structures of all ethyl cellulose, eudragits, oleic acid, sodium lauryl sulfate (SLS) and stearic acid polymers were considered as alternative receptors (host) and ligands (guest) to obtain the stable complex of co-polymeric structure, while Norfloxacin was used only as a ligand (guest) structure for the molecular docking simulations. AutoDock Vina was used for molecular docking calculation in PyRx [31 (link)], in which the grid box was set to cover the entire polymer to ensure that all possible interactions with the drug were searched [32 (link)]. The best docked complex between co-polymer and drug was then subjected to molecular dynamics (MD) to divulge its stability in time and under the influence of explicit solvent molecules. MD simulations were carried out in YASARA-Structure program using the YASARA force field with knowledge-based components [30 (link)]. Chimera and Discovery Studio Visualizer were used for the visualization and graphical representations of all co-polymer and drug complex [33 (link)].