Discovery studio visualizer

An in silico evaluation of the compounds derived from the M. vulgare decoction was done against antimitotic, antidiabetic, and antimicrobial targets. Following the identification of the targets, their respective structures were retrieved from the RCSB protein data bank using the PDB IDs 1XO2, 4W93, and 1AJ6. The preparation of the protein before molecular docking was done using BIOVIA’s Discovery Studio Visualizer (Accelrys Software Inc, 2005 ) and Autodock tools (Morris et al., 2009 (link)). Notably, the preparatory steps included the removal of heteroatoms, cognate ligands, and water molecules, and subsequent optimization of the structure. Similarly, the structure of the ligands was drawn in ChemDraw Ultra (CambridgeSoft, 2009a ), and was subjected to preparatory steps including energy minimization using Chem3D Pro (CambridgeSoft, 2009b ). Subsequently, the ligands were converted to pdbqt files (Zentgraf et al., 2007 (link)) using OpenBabel (Morris et al., 2009 (link); Ferreira et al., 2015 (link)), while the molecular docking was performed using AutoDock Vina (Yusuf et al., 2008 (link); Trott and Olson, 2010 (link); Eberhardt et al., 2021 (link)). Following the formation of the complexes after docking, the interactions between the ligands and the protein were visualized and analyzed using BIOVIA’s Discovery Studio Visualizer.

In order to determine conserved regions (domains) in osteopontin-c of human, it was aligned with rabbit, cattle, chicken, house mouse, Norway rat and water buffalo osteopontin sequences using clustalW [29 (link)] at http://www.genome.jp/tools/clustalw/. RSK and RGD domain comparison was achieved by using Discovery Studio Visualizer (Accelrys Discovery Studio Visualizer, version 1.7, 2007; Accelrys Software Inc., San Diego). Tertiary structures of thrombin cleaved fragments were also predicted by I-TASSER server. The C-terminal fragment of osteopontin-c was used for hypothetical polymer formation using ICM Molsoft tool. Six subunits were utilized for the formation of polymer formation using import option of the ICM Molsoft tool.

We performed Vina molecular docking [46 (link)] using the virtual screening tool of POAP. The grid box size was 24x24x24 angstroms, and the box was centered on the co-crystallized ligand in the pdb structure. The exhaustiveness was 8 for Vina docking. We recorded the estimated binding energy values for the best-docked poses of the ligands.
2.2.4.1. Protein-ligand interactions. From Vina docking simulations, we retrieved pdb files of the complexes with the best-docked poses (lowest estimated binding energy). Protein-ligand interactions were visualized using Discovery Studio Visualizer (BIOVIA, Dassault Systèmes, Discovery Studio Visualizer, v20.1.0.192, 2019). We compared the interactions of the co-crystallized ligand in the pdb file with that of the curcumin.
2.2.4.2. 3D-rendering of protein-ligand complexes. We used open-source Pymol [49 ] to render 3D images of ligands and the binding sites in the proteins.