PMC:5056895 / 7396-10969 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056895","sourcedb":"PMC","sourceid":"5056895","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056895","text":"Methods\n\nHardware and software\nThe study was carried out on Dell Workstation with 2.26 GHz processor, 6 GB RAM and 500 GB hard drive running in Windows operating system. Bioinformatics software, such as PyRx 0.8 [24], Phyre2 [25], AutoDock Vina [26] and online resources like NCBI [27], ProCheck at RCSB validation server [28], ProSA-web [29], ZINC database (https://zinc.docking.org), ProQ [30], ERRAT server [31], etc. were used in this study.\n\nProtein structure prediction and validation of drug target\nThe sequence of NS3 protein (accession No. YP_009227202) of ZIKV was retrieved from NCBI database [27]. Phyre2 servers predict the three-dimensional (3D) structure of a protein sequence using the principles and techniques of homology modeling. Because the structure of a protein is more conserved in evolution than its amino acid sequence, a protein sequence of interest (the target) can be modeled with reasonable accuracy on a very distantly related sequence of known structure (the template), provided that the relationship between target and template can be discerned through sequence alignment. Phyre2 was used for modelling the 3D structure of NS3 protein, it is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools [29]. The refined model reliability was assessed through, ProSA-web, the ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures [29], and ProQ is a neural network based predictor that based on a number of structural features predicts the quality of a protein model [30]. Further the refined model was verified by ERRAT server, ERRAT is a program for verifying protein structures determined by crystallography. Error values are plotted as a function of the position of a sliding 9-residue window. The error function is based on the statistics of non-bonded atom-atom interactions in the reported structure [31].\n\nLigand preparation and molecular docking\nChemical structures of ligands (amodiaquine, prochlorperazine, quinacrine, and berberine) used in this study were retrieved from the PubChem database [32]. PDBQT files of ligands and receptor molecules (NS3) was prepared. Then the protein-ligand docking studies were performed using the AutoDock Vina program [26]. It is one of the widely use method for protein-ligand docking. AutoDock Vina significantly improves the average accuracy of the binding mode predictions. For the input and output, Vina uses the PDBQT molecular structure file format. Here PDBQT file of four drugs were taken as ligand and PDBQT file of NS3 was taken as protein. These drug compounds were docked with NS3 protein of ZIKV and NS3 protein of DENV around its important binding site residues such as His51, Asp75, and Ser135.\n\nVirtual screening\nVirtual screening is now well-known as an efficient prototype for filtering compounds for drug discovery. It was carried out using PyRx 0.8 (Virtual Screening Tools). All the drug-like compounds retrieved from ZINC database in SDF format in a single file. The SDF file was imported in open babel of PyRx and further energy minimization of all the ligands were performed followed by conversion of all the ligands into AutoDock PDBQT format. Further, these ligands were subjected to docking against NS3 protein of ZIKV using AutoDock Vina in PyRx 0.8 [26].","divisions":[{"label":"Title","span":{"begin":0,"end":7}},{"label":"Section","span":{"begin":9,"end":445}},{"label":"Title","span":{"begin":9,"end":30}},{"label":"Section","span":{"begin":447,"end":2155}},{"label":"Title","span":{"begin":447,"end":505}},{"label":"Section","span":{"begin":2157,"end":2999}},{"label":"Title","span":{"begin":2157,"end":2197}},{"label":"Title","span":{"begin":3001,"end":3018}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729840-25618350-44841854","span":{"begin":213,"end":215},"obj":"25618350"},{"id":"27729840-19247286-44841855","span":{"begin":226,"end":228},"obj":"19247286"},{"id":"27729840-19499576-44841856","span":{"begin":246,"end":248},"obj":"19499576"},{"id":"27729840-17517781-44841857","span":{"begin":339,"end":341},"obj":"17517781"},{"id":"27729840-12717029-44841858","span":{"begin":392,"end":394},"obj":"12717029"},{"id":"27729840-8401235-44841859","span":{"begin":411,"end":413},"obj":"8401235"},{"id":"27729840-17517781-44841860","span":{"begin":1412,"end":1414},"obj":"17517781"},{"id":"27729840-17517781-44841861","span":{"begin":1674,"end":1676},"obj":"17517781"},{"id":"27729840-12717029-44841862","span":{"begin":1811,"end":1813},"obj":"12717029"},{"id":"27729840-8401235-44841863","span":{"begin":2151,"end":2153},"obj":"8401235"},{"id":"27729840-19933261-44841864","span":{"begin":2349,"end":2351},"obj":"19933261"},{"id":"27729840-19499576-44841865","span":{"begin":2508,"end":2510},"obj":"19499576"},{"id":"27729840-19499576-44841866","span":{"begin":3569,"end":3571},"obj":"19499576"}],"attributes":[{"subj":"27729840-25618350-44841854","pred":"source","obj":"2_test"},{"subj":"27729840-19247286-44841855","pred":"source","obj":"2_test"},{"subj":"27729840-19499576-44841856","pred":"source","obj":"2_test"},{"subj":"27729840-17517781-44841857","pred":"source","obj":"2_test"},{"subj":"27729840-12717029-44841858","pred":"source","obj":"2_test"},{"subj":"27729840-8401235-44841859","pred":"source","obj":"2_test"},{"subj":"27729840-17517781-44841860","pred":"source","obj":"2_test"},{"subj":"27729840-17517781-44841861","pred":"source","obj":"2_test"},{"subj":"27729840-12717029-44841862","pred":"source","obj":"2_test"},{"subj":"27729840-8401235-44841863","pred":"source","obj":"2_test"},{"subj":"27729840-19933261-44841864","pred":"source","obj":"2_test"},{"subj":"27729840-19499576-44841865","pred":"source","obj":"2_test"},{"subj":"27729840-19499576-44841866","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93b0","default":true}]}]}}