LitCovid-sentences  

PMC:7441777 / 28837-32893 JSONTXT 6 Projects

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Id Subject Object Predicate Lexical cue
T272 0-6 Sentence denotes 3.2.2.
T273 8-36 Sentence denotes Binding free energy analysis
T274 37-270 Sentence denotes We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4.
T275 271-370 Sentence denotes Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4.
T276 371-513 Sentence denotes The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information.
T277 514-739 Sentence denotes It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation.
T278 740-821 Sentence denotes Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases.
T279 822-905 Sentence denotes A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020).
T280 906-915 Sentence denotes Figure 4.
T281 917-1204 Sentence denotes Energy components (kcal/mol) for the binding of remdesivir and four polyphenols to RdRp receptor. ΔEvdW, van der Waals interaction; ΔEele, electrostatic interaction in the gas phase; ΔGpol, polar solvation energy; ΔGnp, non-polar solvation energy, and ΔGbind, estimated binding affinity.
T282 1205-1213 Sentence denotes Table 4.
T283 1215-1339 Sentence denotes Energetic components of the binding free energy of RdRp and natural polyphenols along with remdesivir complexes in kcal/mol.
T284 1340-1378 Sentence denotes Data are represented as average ± SEM.
T285 1379-1424 Sentence denotes Components Remdesivir EGCG TF3 TF2b TF2a
T286 1425-1505 Sentence denotes ΔEvdW −31.85 ± 0.15 −25.11 ± 0.18 −37.82 ± 0.21 −30.66 ± 0.23 −22.55 ± 0.19
T287 1506-1588 Sentence denotes ΔEelec −98.40 ± 0.70 −69.38 ± 0.73 −123.63 ± 0.88 −47.18 ± 0.64 −95.28 ± 1.27
T288 1589-1666 Sentence denotes ΔGpol 109.97 ± 0.57 71.62 ± 0.48 124.47 ± 0.58 55.01 ± 0.49 94.94 ± 1.10
T289 1667-1741 Sentence denotes ΔGnp −4.29 ± 0.01 −4.15 ± 0.01 −5.29 ± 0.01 −3.91 ± 0.01 −4.28 ± 0.02
T290 1742-1820 Sentence denotes aΔGsolv 105.68 ± 0.57 67.47 ± 0.48 119.18 ± 0.58 51.1 ± 0.49 90.66 ± 1.10
T291 1821-1901 Sentence denotes bΔGpol + elec 11.57 ± 0.90 2.24 ± 0.87 0.84 ± 1.05 7.83 ± 0.80 −0.34 ± 1.68
T292 1902-1985 Sentence denotes cΔEMM −130.25 ± 0.71 −94.49 ± 0.75 −161.45 ± 0.90 −77.84 ± 0.68 −117.83 ± 1.28
T293 1986-2070 Sentence denotes ΔGbindSim −24.57 ± 0.91 −27.02 ± 0.89 −42.27 ± 1.07 −26.74 ± 0.83 −27.17 ± 1.69
T294 2071-2096 Sentence denotes a ΔGsolv = ΔGnp + ΔGpol,
T295 2097-2130 Sentence denotes b ΔGpol + elec = ΔEelec + ΔGpol,
T296 2131-2156 Sentence denotes c ΔEMM = ΔEvdW + ΔEelec.
T297 2157-2326 Sentence denotes It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol.
T298 2327-2773 Sentence denotes Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information).
T299 2774-2892 Sentence denotes In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol).
T300 2893-3045 Sentence denotes Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp.
T301 3046-3150 Sentence denotes Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process.
T302 3151-3467 Sentence denotes The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information).
T303 3468-3557 Sentence denotes This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG.
T304 3558-3665 Sentence denotes The potency of the five inhibitors decreases in the following order: TF3 > TF2a > EGCG > TF2b > remdesivir.
T305 3666-3795 Sentence denotes TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors.
T306 3796-4056 Sentence denotes Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol).