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PMC:7441777 / 28837-32893 JSONTXT

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LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T187 195-196 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 481-483 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T189 481-483 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T190 822-823 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T191 1742-1743 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 1821-1822 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T193 2071-2072 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 2097-2098 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T195 2725-2728 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T196 2740-2742 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T197 2740-2742 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T198 3107-3108 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 3360-3363 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T200 3430-3432 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T201 3430-3432 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T404 113-115 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T406 138-149 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T407 158-162 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T408 164-167 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T409 235-245 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T410 320-324 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T411 326-329 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T412 390-401 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T413 451-461 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T414 481-483 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T415 645-651 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T416 965-975 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T417 985-996 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T418 1283-1294 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T419 1306-1316 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T420 1403-1407 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T421 1409-1412 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T422 2361-2371 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T423 2378-2382 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T424 2389-2392 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T425 2668-2677 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T427 2684-2697 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T428 2704-2714 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T429 2740-2742 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T430 3002-3013 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T431 3025-3035 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T432 3197-3207 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T433 3209-3213 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T434 3215-3218 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T435 3319-3328 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T437 3330-3343 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T438 3345-3355 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T439 3412-3422 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T440 3430-3432 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T441 3487-3497 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T442 3498-3501 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T443 3552-3556 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T444 3582-3592 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T445 3627-3630 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T446 3640-3644 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T447 3654-3664 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T448 3666-3669 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T449 3784-3794 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T450 3852-3856 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T451 3980-3984 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T11 729-738 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T12 2933-2942 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
707 169-173 Gene denotes TF2b Gene:2959
708 331-335 Gene denotes TF2b Gene:2959
709 116-120 Chemical denotes PBSA MESH:C437084
710 138-149 Chemical denotes polyphenols MESH:D059808
711 158-162 Chemical denotes EGCG MESH:C045651
712 235-245 Chemical denotes remdesivir MESH:C000606551
713 320-324 Chemical denotes EGCG MESH:C045651
714 390-401 Chemical denotes polyphenols MESH:D059808
715 451-461 Chemical denotes remdesivir MESH:C000606551
718 965-975 Chemical denotes remdesivir MESH:C000606551
719 985-996 Chemical denotes polyphenols MESH:D059808
722 1414-1418 Gene denotes TF2b Gene:2959
723 1391-1401 Chemical denotes Remdesivir MESH:C000606551
727 1266-1270 Gene denotes RdRp Gene:43740578
728 1283-1294 Chemical denotes polyphenols MESH:D059808
729 1306-1316 Chemical denotes remdesivir MESH:C000606551
744 2356-2360 Gene denotes RdRp Gene:43740578
745 2373-2377 Gene denotes RdRp Gene:43740578
746 2384-2388 Gene denotes RdRp Gene:43740578
747 2398-2402 Gene denotes RdRp Gene:43740578
748 2403-2407 Gene denotes TF2b Gene:2959
749 2663-2667 Gene denotes RdRp Gene:43740578
750 2679-2683 Gene denotes RdRp Gene:43740578
751 2699-2703 Gene denotes RdRp Gene:43740578
752 2720-2724 Gene denotes RdRp Gene:43740578
753 2802-2806 Gene denotes RdRp Gene:43740578
754 3040-3044 Gene denotes RdRp Gene:43740578
755 2361-2371 Chemical denotes remdesivir MESH:C000606551
756 3002-3013 Chemical denotes polyphenols MESH:D059808
757 3025-3035 Chemical denotes remdesivir MESH:C000606551
777 3220-3224 Gene denotes TF2b Gene:2959
778 3525-3529 Gene denotes RdRp Gene:43740578
779 3647-3651 Gene denotes TF2b Gene:2959
780 3693-3697 Gene denotes RdRp Gene:43740578
781 3835-3839 Gene denotes RdRp Gene:43740578
782 3860-3864 Gene denotes TF2b Gene:2959
783 4020-4024 Gene denotes TF2b Gene:2959
784 3197-3207 Chemical denotes remdesivir MESH:C000606551
785 3209-3213 Chemical denotes EGCG MESH:C045651
786 3319-3328 Chemical denotes myricetin MESH:C040015
787 3330-3343 Chemical denotes quercetagetin MESH:C079163
788 3345-3355 Chemical denotes hesperidin MESH:D006569
789 3412-3422 Chemical denotes remdesivir MESH:C000606551
790 3487-3497 Chemical denotes polyphenol MESH:D059808
791 3552-3556 Chemical denotes EGCG MESH:C045651
792 3640-3644 Chemical denotes EGCG MESH:C045651
793 3654-3664 Chemical denotes remdesivir MESH:C000606551
794 3852-3856 Chemical denotes EGCG MESH:C045651
795 3980-3984 Chemical denotes EGCG MESH:C045651

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T14 2725-2728 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T15 3360-3363 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

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).