PMC:7279430 / 21100-24286 JSONTXT 9 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T139 0-2 Sentence denotes 3.
T140 3-24 Sentence denotes Materials and Methods
T141 26-30 Sentence denotes 3.1.
T142 31-60 Sentence denotes Bibliographic Search Criteria
T143 61-182 Sentence denotes The bibliographic research was performed using the databases Google Scholar, Pubmed, Science Direct, Medline, and Scopus.
T144 183-347 Sentence denotes The keywords applied were “antiviral activity” and “essential oils”, “antiviral activity” and “volatile compounds”, and “essential oils” and “respiratory diseases”.
T145 349-353 Sentence denotes 3.2.
T146 354-370 Sentence denotes Ligand Selection
T147 371-521 Sentence denotes The major components (>5%) of essential oils and pure essential oil components that have been screened against human pathogenic viruses were selected.
T148 522-616 Sentence denotes In the case where enantiomers are known to be natural products, both structures were selected.
T149 617-692 Sentence denotes A total of 171 essential oil components were used in the virtual screening.
T150 694-698 Sentence denotes 3.3.
T151 699-716 Sentence denotes Molecular Docking
T152 717-772 Sentence denotes Each ligand structure was prepared using Spartan ’18 v.
T153 773-817 Sentence denotes 1.4.4 (Wavefunction, Inc., Irvine, CA, USA).
T154 818-938 Sentence denotes The lowest-energy conformations of the ligands were determined and used as starting structures in the molecular docking.
T155 939-1182 Sentence denotes This is particularly important to include all potential conformations in medium-sized rings where interconversion between conformations may be hindered (e.g., bicyclogermacrene, costunolide, curdione, germacrene D, germacrone, and α-humulene).
T156 1183-1379 Sentence denotes A total of six protein targets of SARS-CoV-2 from the Protein Data Bank (PDB), represented by a total of 17 structures, were used in the molecular docking, including SARS-CoV-2 main protease (PDB:
T157 1380-1472 Sentence denotes 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 6LU7, 6M03, and 6Y84), SARS-CoV-2 endoribonuclease (PDB:
T158 1473-1519 Sentence denotes 6VWW), SARS-CoV-2 ADP ribose phosphatase (PDB:
T159 1520-1581 Sentence denotes 6W01 and 6W02), SARS-CoV-2 RNA-dependent RNA polymerase (PDB:
T160 1582-1634 Sentence denotes 6M71), SARS-CoV-2 spike protein binding domain (PDB:
T161 1635-1713 Sentence denotes 6M0J, 6VX1, 6VW1, and 6M17), and the human angiotensin-converting enzyme (PDB:
T162 1714-1742 Sentence denotes 6M0J, 6VX1, 6VW1, and 6M17).
T163 1743-1808 Sentence denotes Molecular docking was carried out using Molegro Virtual Docker v.
T164 1809-1866 Sentence denotes 6.0.1 (Aarhus, Denmark) as previously reported [128,129].
T165 1867-1994 Sentence denotes Briefly, a 15-Å radius sphere centered on the binding sites of each protein structure in order to permit each ligand to search.
T166 1995-2127 Sentence denotes In the case of the spike protein and human ACE2, the docking sphere was located at the interface between the spike protein and ACE2.
T167 2128-2301 Sentence denotes In one case, ACE2 was removed and docking was carried out with the spike protein, and in the other case, the spike protein was removed and docking was carried out with ACE2.
T168 2302-2479 Sentence denotes Standard protonation states of each protein, based on neutral pH, were used, and charges were assigned based on standard templates as part of the Molegro Virtual Docker program.
T169 2480-2546 Sentence denotes Each protein was used as a rigid model without protein relaxation.
T170 2547-2609 Sentence denotes Flexible-ligand models were used in the docking optimizations.
T171 2610-2711 Sentence denotes Different orientations of the ligands were searched and ranked based on their “rerank” energy scores.
T172 2712-2766 Sentence denotes A minimum of 100 runs for each ligand was carried out.
T173 2767-3134 Sentence denotes In analyzing the docking scores, we accounted for the recognized bias due to molecular weight [130,131,132] using the scheme: DSnorm = 7.2 × Edock/MW⅓, where DSnorm is the normalized docking score, Edock is the MolDock re-rank score, MW is the molecular weight, and 7.2 is a scaling constant to ensure the average DSnorm values are comparable to those of Edock [128].
T174 3135-3186 Sentence denotes The best docking results are summarized in Table 1.