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PMC:7441777 / 19374-23484 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T34 554-564 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T35 1278-1288 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T36 1465-1476 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T37 3426-3439 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 3426-3439 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T52 113-121 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 204-212 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 324-332 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 499-507 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 700-708 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 849-857 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 1355-1363 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 2648-2656 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 2703-2711 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 2840-2848 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 3283-3292 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251
T63 3303-3312 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T64 3481-3490 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T65 3750-3754 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 3828-3839 Disease denotes hepatitis C http://purl.obolibrary.org/obo/MONDO_0005231
T67 3828-3837 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251
T68 4043-4051 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 4054-4063 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T115 902-905 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T116 1223-1225 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T117 1695-1698 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T118 2519-2522 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T119 2893-2901 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T120 3069-3074 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T121 3119-3123 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T122 3126-3129 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T123 3245-3253 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T124 3267-3274 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T125 3293-3298 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T126 3313-3314 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T127 3319-3320 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T128 3321-3328 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T129 3348-3352 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T130 3401-3409 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T131 3426-3439 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T132 3491-3492 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 3493-3498 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T134 3534-3535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 3564-3567 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T136 3624-3632 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T137 3700-3703 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T138 3840-3845 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T139 3869-3877 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T273 89-100 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T274 165-175 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T275 220-222 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T276 289-300 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T277 466-477 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T278 547-553 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T279 554-564 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T280 554-559 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T281 560-564 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T282 598-601 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T284 606-616 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T285 723-734 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T286 818-829 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T287 891-894 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T288 913-923 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T289 925-929 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T290 931-940 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T292 945-958 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T293 1135-1146 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T294 1278-1288 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T295 1278-1283 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T296 1284-1288 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T297 1331-1342 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T298 1465-1476 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T299 1465-1470 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T300 1471-1476 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T301 1480-1483 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T302 1886-1896 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T304 1988-1992 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T305 2059-2068 Chemical denotes Myricetin http://purl.obolibrary.org/obo/CHEBI_18152
T306 2142-2155 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T307 2329-2332 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T309 2458-2468 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T310 2506-2517 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T311 2536-2539 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T312 2541-2551 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T313 2553-2557 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T314 2559-2568 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T316 2573-2586 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T317 2630-2640 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T318 2687-2694 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T319 2781-2792 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T320 2994-3005 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T321 3138-3145 Chemical denotes gallate http://purl.obolibrary.org/obo/CHEBI_16918
T322 3191-3202 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T323 3235-3244 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T324 3355-3365 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T326 3391-3400 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T327 3528-3532 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T328 3552-3562 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T329 3614-3623 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T330 3690-3699 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T332 3733-3742 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T333 3795-3808 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T334 3940-3951 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T335 4012-4017 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T8 2952-2971 http://purl.obolibrary.org/obo/GO_0019083 denotes viral transcription
T9 2958-2971 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
412 113-123 Species denotes SARS-CoV-2 Tax:2697049
413 89-100 Chemical denotes polyphenols MESH:D059808
420 192-196 Gene denotes RdRp Gene:43740578
421 335-339 Gene denotes RdRp Gene:43740578
422 204-214 Species denotes SARS-CoV-2 Tax:2697049
423 324-334 Species denotes SARS-CoV-2 Tax:2697049
424 165-175 Chemical denotes polyphenol MESH:D059808
425 289-300 Chemical denotes polyphenols MESH:D059808
446 487-491 Gene denotes RdRp Gene:43740578
447 711-715 Gene denotes RdRp Gene:43740578
448 860-864 Gene denotes RdRp Gene:43740578
449 896-900 Gene denotes TF2b Gene:2959
450 1100-1104 Gene denotes RdRp Gene:43740578
451 499-509 Species denotes SARS-CoV-2 Tax:2697049
452 700-710 Species denotes SARS-CoV-2 Tax:2697049
453 849-859 Species denotes SARS-CoV-2 Tax:2697049
454 395-406 Chemical denotes Polyphenols MESH:D059808
455 466-477 Chemical denotes polyphenols MESH:D059808
456 598-601 Chemical denotes GTP MESH:D006160
457 606-616 Chemical denotes remdesivir MESH:C000606551
458 723-734 Chemical denotes polyphenols MESH:D059808
459 818-829 Chemical denotes polyphenols MESH:D059808
460 913-923 Chemical denotes hesperidin MESH:D006569
461 925-929 Chemical denotes EGCG MESH:C045651
462 931-940 Chemical denotes myricetin MESH:C040015
463 945-958 Chemical denotes quercetagetin MESH:C079163
464 959-961 Chemical denotes as MESH:D001151
465 1135-1146 Chemical denotes polyphenols MESH:D059808
472 1599-1603 Gene denotes TF2b Gene:2959
473 1372-1373 Gene denotes S Gene:43740568
474 2216-2226 Chemical denotes Remdesivir MESH:C000606551
475 1507-1511 CellLine denotes S549 CVCL:0023
476 1681-1685 CellLine denotes S549 CVCL:0023
477 1848-1852 CellLine denotes S549 CVCL:0023
481 1366-1370 Gene denotes RdRp Gene:43740578
482 1355-1365 Species denotes SARS-CoV-2 Tax:2697049
483 1331-1342 Chemical denotes polyphenols MESH:D059808
517 2530-2534 Gene denotes TF2b Gene:2959
518 2659-2663 Gene denotes RdRp Gene:43740578
519 2714-2718 Gene denotes RdRp Gene:43740578
520 2851-2855 Gene denotes RdRp Gene:43740578
521 2888-2892 Gene denotes RdRp Gene:43740578
522 2648-2658 Species denotes SARS-CoV-2 Tax:2697049
523 2703-2713 Species denotes SARS-CoV-2 Tax:2697049
524 2840-2850 Species denotes SARS-CoV-2 Tax:2697049
525 3069-3074 Species denotes human Tax:9606
526 3181-3190 Species denotes black tea Tax:4442
527 3481-3498 Species denotes influenza A virus Tax:11320
528 3750-3766 Species denotes SARS coronavirus Tax:694009
529 3828-3845 Species denotes hepatitis C virus Tax:11103
530 3303-3312 Species denotes influenza Tax:11320
531 2458-2468 Chemical denotes remdesivir MESH:C000606551
532 2506-2517 Chemical denotes polyphenols MESH:D059808
533 2541-2551 Chemical denotes hesperidin MESH:D006569
534 2553-2557 Chemical denotes EGCG MESH:C045651
535 2559-2568 Chemical denotes myricetin MESH:C040015
536 2573-2586 Chemical denotes quercetagetin MESH:C079163
537 2781-2792 Chemical denotes polyphenols MESH:D059808
538 2994-3005 Chemical denotes polyphenols MESH:D059808
539 3138-3145 Chemical denotes gallate
540 3191-3202 Chemical denotes polyphenols MESH:D059808
541 3355-3365 Chemical denotes Hesperidin MESH:D006569
542 3528-3532 Chemical denotes EGCG MESH:C045651
543 3552-3562 Chemical denotes polyphenol MESH:D059808
544 3690-3699 Chemical denotes myricetin MESH:C040015
545 3795-3808 Chemical denotes Quercetagetin MESH:C079163
546 3940-3951 Chemical denotes polyphenols MESH:D059808
547 3024-3032 Disease denotes toxicity MESH:D064420
548 3283-3298 Disease denotes hepatitis virus MESH:D006525
549 4043-4063 Disease denotes SARS-CoV-2 infection MESH:C000657245

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T5 902-905 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T6 1695-1698 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T7 2519-2522 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T8 3126-3129 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T196 0-6 Sentence denotes 3.1.1.
T197 8-128 Sentence denotes The binding mode analysis and predicted binding affinity calculations of natural polyphenols against the SARS-CoV-2 RdRp
T198 129-223 Sentence denotes Herein, we investigated our natural polyphenol library against RdRp of the SARS-CoV-2 (PDB ID:
T199 224-251 Sentence denotes 6M71) by molecular docking.
T200 252-394 Sentence denotes The best conformation of the natural polyphenols was docked against the SARS-CoV-2 RdRp, and resulting binding energies are listed in Table 1.
T201 395-578 Sentence denotes Polyphenols exhibiting binding energy of −7.0 kcal/mol or lower (eight polyphenols) against RdRp of the SARS-CoV-2 are listed in Table 2 along with the ligand-amino acid interactions.
T202 579-716 Sentence denotes Control compounds, GTP and remdesivir, exhibited the binding energy of −7.9 and −7.7 kcal/mol, respectively, against the SARS-CoV-2 RdRp.
T203 717-1060 Sentence denotes Eight polyphenols displayed significantly higher binding affinity among the selected hundred natural polyphenols docked against the SARS-CoV-2 RdRp, with binding energies of TF3, TF2b, TF1, TF2a, hesperidin, EGCG, myricetin and quercetagetin as −9.9, −9.6, −9.6, −9.3, −8.8, −7.3, −7.2 and −7.0 kcal/mol, respectively (highlighted in Table 1).
T204 1061-1260 Sentence denotes Further, 2D LigPlot+ representation of RdRp and the above-mentioned eight polyphenols reveal the stable network of molecular interactions (see Table 2 and Figure S1 in the Supplementary Information).
T205 1261-1269 Sentence denotes Table 2.
T206 1271-1371 Sentence denotes Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.
T207 1372-1374 Sentence denotes S.
T208 1375-1378 Sentence denotes No.
T209 1380-1476 Sentence denotes Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids
T210 1477-1595 Sentence denotes 1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760
T211 1596-1691 Sentence denotes 2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550
T212 1692-1780 Sentence denotes 3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618
T213 1781-1882 Sentence denotes 4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811
T214 1883-1984 Sentence denotes 5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455
T215 1985-2055 Sentence denotes 6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798
T216 2056-2138 Sentence denotes 7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812
T217 2139-2212 Sentence denotes 8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619
T218 2213-2324 Sentence denotes 9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761
T219 2325-2664 Sentence denotes 10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620 In addition to remdesivir, here we observed that eight dietary polyphenols (TF1, TF2a, TF2b, TF3, hesperidin, EGCG, myricetin and quercetagetin) have significant potential to function as inhibitors of the SARS-CoV-2 RdRp.
T220 2665-2972 Sentence denotes The top-eight scoring ligands for the SARS-CoV-2 RdRp (as highlighted in Table 1) suggest that these set of natural polyphenols can strongly bind to the catalytic site of the SARS-CoV-2 RdRp and are expected to inhibit the RdRp activity, and thus blocking the replication and preventing viral transcription.
T221 2973-3125 Sentence denotes Many reports suggest polyphenols have low systemic toxicity, and they are highly beneficial for human health (Bhardwaj et al., 2020; Cory et al., 2018).
T222 3126-3354 Sentence denotes TF1 and its gallate derivatives, collectively known as black tea polyphenols, previously have shown to exert antiviral activity against many viruses such as hepatitis virus and influenza A and B viruses (Chowdhury et al., 2018).
T223 3355-3527 Sentence denotes Hesperidin is also known to possess antiviral activity by altering the immune system mainly via regulating interferons in the influenza A virus (Randall & Goodbourn, 2008).
T224 3528-3678 Sentence denotes EGCG, a major green tea polyphenol, has several pharmacological properties, including antiviral activity (Carneiro et al., 2016; Moon & Morris, 2007).
T225 3679-3794 Sentence denotes Similarly, myricetin has also been found to act as an inhibitor of the SARS coronavirus helicase (Yu et al., 2012).
T226 3795-3917 Sentence denotes Quercetagetin also showed strong hepatitis C virus replication inhibitory activity in vitro (Ahmed-Belkacem et al., 2014).
T227 3918-4110 Sentence denotes Thus, the set dietary polyphenols identified in the present study could be used as repurposed drugs for the treatment of the SARS-CoV-2 infection with further in-vitro and in-vivo validations.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T7 3283-3292 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115
T8 3828-3837 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115

2_test

Id Subject Object Predicate Lexical cue
32720577-30298133-56195126 3119-3123 30298133 denotes 2018
32720577-30485282-56195127 3348-3352 30485282 denotes 2018
32720577-18089727-56195128 3521-3525 18089727 denotes 2008
32720577-17970592-56195129 3672-3676 17970592 denotes 2007
32720577-22578462-56195130 3788-3792 22578462 denotes 2012
32720577-25053847-56195131 3911-3915 25053847 denotes 2014