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PMC:7784829 / 6045-10412 JSONTXT

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LitCovid-sentences

Id Subject Object Predicate Lexical cue
T46 0-20 Sentence denotes Experimental section
T47 22-39 Sentence denotes Sequence analysis
T48 40-152 Sentence denotes The sequences of the SARS-CoV-2 and SARS-CoV were downloaded from National Center for Biotechnology Information.
T49 153-321 Sentence denotes Multiple sequence analysis and pairwise sequence identity was determined using the Clustal Omega server at the European Bioinformatics Institute (Sievers et al., 2011).
T50 323-353 Sentence denotes Preparation of coordinate file
T51 354-435 Sentence denotes The X-ray crystal structure of spike surface glycoprotein of SARS-CoV (PDB entry:
T52 436-545 Sentence denotes 6CRV, resolution = 3.2 Å) and co-crystallized structure of SARS-CoV-2 RBD with human ACE2 Protein (PDB entry:
T53 546-636 Sentence denotes 6M0J, resolution = 2.45 Å) was retrieved from Protein Data Bank (https:/www.rscb.org/pdb).
T54 637-1001 Sentence denotes The protein structure was prepared using the Discovery Studio Visualizer (version 3.1) and AutoDock Tools (ADT; version 1.5.4) through different steps viz. removal of water molecules and co-crystallized ligand, addition of missing hydrogen atoms, addition of Gasteiger-Marsili and Kollman charges, merging of non-polar hydrogens, and assignment of rotatable bonds.
T55 1002-1068 Sentence denotes The file was then saved in pdbqt file format for further analysis.
T56 1070-1092 Sentence denotes Preparation of ligands
T57 1093-1226 Sentence denotes The chemical structures of curcumin derivatives were constructed using Chem3D 15.0 module of ChemOffice 15.0 and saved in PDB format.
T58 1227-1396 Sentence denotes The structures were optimized using “Prepare Ligands” in the AutoDock 4.2, flexible torsions were assigned and the acyclic dihedral angles were allowed to rotate freely.
T59 1397-1463 Sentence denotes The file was then saved as pdbqt file format for further analysis.
T60 1465-1482 Sentence denotes Molecular docking
T61 1483-1664 Sentence denotes Molecular docking simulations were conducted on the curcumin derivatives using the AutoDock 4.2 to get insight into their binding preferences within the active site of the receptor.
T62 1665-1786 Sentence denotes The molecular docking simulations were performed on the PC based machines running on Windows 7 (x86) as operating system.
T63 1787-1984 Sentence denotes The software included MGL tools 1.5.4 based AutoDock 4.2 (www.scripps.edu) which uses Python 2.7 language - Cygwin C:\program (www.cygwin.com) and Python 2.5 (www.python.com) (Morris et al., 2009).
T64 1986-2005 Sentence denotes Docking methodology
T65 2006-2128 Sentence denotes The flexible docking was performed using the refined spike protein of SARS-CoV (6CRV) and RBD domain of SARS-CoV-2 (6M0J).
T66 2129-2232 Sentence denotes The grid maps of the interaction energies of various atom types were pre-calculated using AutoGrid 4.2.
T67 2233-2433 Sentence denotes In each docking for spike surface glycoprotein and spike RBD, a grid box was created using a grid map of 45 × 45 × 45 points, 60 × 60 × 60 points with grid spacing of 0.375 Å and 0.420 Å respectively.
T68 2434-2531 Sentence denotes The grid maps were centred on the corresponding ligand binding site within the protein structure.
T69 2532-2654 Sentence denotes Lamarckian Genetic Algorithm (LGA) was adopted to perform docking simulations using the following default parameters, viz.
T70 2655-3012 Sentence denotes 100 independent runs with step sizes of 0.2 Å for translations and 5 Å for orientations and torsions, an initial population of random individuals with a population size of 150 individuals, a maximum of 2.5 × 106 energy evaluations, maximum number of generations of 27,000; mutation and crossover rates of 0.02 and 0.8 respectively and an elitism value of 1.
T71 3013-3178 Sentence denotes All the computations were carried out on Cygwin and was used to generate both grid parameter file (.gpf file) and docking parameter file (.dpf file) for each ligand.
T72 3179-3334 Sentence denotes The docked conformations of each ligand were ranked into clusters based on the binding energy and the top ranked conformations were used for further study.
T73 3335-3462 Sentence denotes The pose with the lowest ΔG-score was considered the best fitted one and was further analyzed for Ligand-receptor interactions.
T74 3464-3527 Sentence denotes In-silico drug-likeness and pharmacokinetic property prediction
T75 3528-3747 Sentence denotes The in-silico prediction studies were performed, using pkCSM online prediction platforms (Pires et al., 2015), to assess the theoretical pharmacokinetic parameters of the ligands to predict the drug-likeness of ligands.
T76 3748-3936 Sentence denotes The software calculated pharmaceutically relevant properties such as H-bond donor, H-bond acceptor, octanol-water partition coefficient (LogP), surface area, and number of rotatable bonds.
T77 3937-4367 Sentence denotes In addition the ADME parameters of the curcumin analogs such as water solubility, Caco2 permeability, human intestinal absorption, skin permeability, P-glycoprotein I and II inhibition, volume of distribution, fraction of unbound drug, Blood Brain Barrier and CNS permeability, cytochrome P450 (CYP3A4 and CYP2C9 inhibition) inhibition, total clearance, action as renal OCT2 (organic cation transporter 2) substrate were analysed.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
166 61-71 Species denotes SARS-CoV-2 Tax:2697049
167 76-84 Species denotes SARS-CoV Tax:694009
177 521-525 Gene denotes ACE2 Gene:59272
178 605-609 Gene denotes Bank Gene:55024
179 415-423 Species denotes SARS-CoV Tax:694009
180 495-505 Species denotes SARS-CoV-2 Tax:2697049
181 515-520 Species denotes human Tax:9606
182 804-809 Chemical denotes water MESH:D014867
183 868-876 Chemical denotes hydrogen MESH:D006859
184 956-965 Chemical denotes hydrogens MESH:D006859
185 896-913 Disease denotes Gasteiger-Marsili
187 1120-1128 Chemical denotes curcumin MESH:D003474
189 1535-1543 Chemical denotes curcumin MESH:D003474
194 2059-2064 Gene denotes spike Gene:43740568
195 2253-2279 Gene denotes spike surface glycoprotein
196 2076-2084 Species denotes SARS-CoV Tax:694009
197 2110-2120 Species denotes SARS-CoV-2 Tax:2697049
199 2993-3000 Disease denotes elitism
210 4232-4238 Gene denotes CYP3A4 Gene:1576
211 4243-4249 Gene denotes CYP2C9 Gene:1559
212 4307-4311 Gene denotes OCT2 Gene:6582
213 4313-4341 Gene denotes organic cation transporter 2 Gene:6582
214 4039-4044 Species denotes human Tax:9606
215 3848-3855 Chemical denotes octanol MESH:D000442
216 3856-3861 Chemical denotes water MESH:D014867
217 3976-3984 Chemical denotes curcumin MESH:D003474
218 4001-4006 Chemical denotes water MESH:D014867
219 4019-4024 Chemical denotes Caco2