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PMC:7441777 / 19340-23484 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T34 588-598 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T35 1312-1322 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T36 1499-1510 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T37 3460-3473 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 3460-3473 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T52 147-155 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 238-246 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 358-366 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 533-541 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 734-742 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 883-891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 1389-1397 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 2682-2690 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 2737-2745 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 2874-2882 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 3317-3326 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251
T63 3337-3346 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T64 3515-3524 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T65 3784-3788 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 3862-3873 Disease denotes hepatitis C http://purl.obolibrary.org/obo/MONDO_0005231
T67 3862-3871 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251
T68 4077-4085 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 4088-4097 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T115 936-939 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T116 1257-1259 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T117 1729-1732 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T118 2553-2556 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T119 2927-2935 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T120 3103-3108 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T121 3153-3157 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T122 3160-3163 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T123 3279-3287 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T124 3301-3308 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T125 3327-3332 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T126 3347-3348 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T127 3353-3354 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T128 3355-3362 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T129 3382-3386 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T130 3435-3443 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T131 3460-3473 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T132 3525-3526 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 3527-3532 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T134 3568-3569 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 3598-3601 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T136 3658-3666 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T137 3734-3737 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T138 3874-3879 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T139 3903-3911 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T273 123-134 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T274 199-209 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T275 254-256 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T276 323-334 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T277 500-511 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T278 581-587 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T279 588-598 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T280 588-593 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T281 594-598 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T282 632-635 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T284 640-650 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T285 757-768 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T286 852-863 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T287 925-928 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T288 947-957 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T289 959-963 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T290 965-974 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T292 979-992 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T293 1169-1180 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T294 1312-1322 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T295 1312-1317 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T296 1318-1322 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T297 1365-1376 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T298 1499-1510 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T299 1499-1504 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T300 1505-1510 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T301 1514-1517 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T302 1920-1930 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T304 2022-2026 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T305 2093-2102 Chemical denotes Myricetin http://purl.obolibrary.org/obo/CHEBI_18152
T306 2176-2189 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T307 2363-2366 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T309 2492-2502 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T310 2540-2551 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T311 2570-2573 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T312 2575-2585 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T313 2587-2591 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T314 2593-2602 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T316 2607-2620 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T317 2664-2674 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T318 2721-2728 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T319 2815-2826 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T320 3028-3039 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T321 3172-3179 Chemical denotes gallate http://purl.obolibrary.org/obo/CHEBI_16918
T322 3225-3236 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T323 3269-3278 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T324 3389-3399 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T326 3425-3434 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T327 3562-3566 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T328 3586-3596 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T329 3648-3657 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T330 3724-3733 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T332 3767-3776 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T333 3829-3842 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T334 3974-3985 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T335 4046-4051 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T8 2986-3005 http://purl.obolibrary.org/obo/GO_0019083 denotes viral transcription
T9 2992-3005 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
412 147-157 Species denotes SARS-CoV-2 Tax:2697049
413 123-134 Chemical denotes polyphenols MESH:D059808
420 226-230 Gene denotes RdRp Gene:43740578
421 369-373 Gene denotes RdRp Gene:43740578
422 238-248 Species denotes SARS-CoV-2 Tax:2697049
423 358-368 Species denotes SARS-CoV-2 Tax:2697049
424 199-209 Chemical denotes polyphenol MESH:D059808
425 323-334 Chemical denotes polyphenols MESH:D059808
446 521-525 Gene denotes RdRp Gene:43740578
447 745-749 Gene denotes RdRp Gene:43740578
448 894-898 Gene denotes RdRp Gene:43740578
449 930-934 Gene denotes TF2b Gene:2959
450 1134-1138 Gene denotes RdRp Gene:43740578
451 533-543 Species denotes SARS-CoV-2 Tax:2697049
452 734-744 Species denotes SARS-CoV-2 Tax:2697049
453 883-893 Species denotes SARS-CoV-2 Tax:2697049
454 429-440 Chemical denotes Polyphenols MESH:D059808
455 500-511 Chemical denotes polyphenols MESH:D059808
456 632-635 Chemical denotes GTP MESH:D006160
457 640-650 Chemical denotes remdesivir MESH:C000606551
458 757-768 Chemical denotes polyphenols MESH:D059808
459 852-863 Chemical denotes polyphenols MESH:D059808
460 947-957 Chemical denotes hesperidin MESH:D006569
461 959-963 Chemical denotes EGCG MESH:C045651
462 965-974 Chemical denotes myricetin MESH:C040015
463 979-992 Chemical denotes quercetagetin MESH:C079163
464 993-995 Chemical denotes as MESH:D001151
465 1169-1180 Chemical denotes polyphenols MESH:D059808
472 1633-1637 Gene denotes TF2b Gene:2959
473 1406-1407 Gene denotes S Gene:43740568
474 2250-2260 Chemical denotes Remdesivir MESH:C000606551
475 1541-1545 CellLine denotes S549 CVCL:0023
476 1715-1719 CellLine denotes S549 CVCL:0023
477 1882-1886 CellLine denotes S549 CVCL:0023
481 1400-1404 Gene denotes RdRp Gene:43740578
482 1389-1399 Species denotes SARS-CoV-2 Tax:2697049
483 1365-1376 Chemical denotes polyphenols MESH:D059808
517 2564-2568 Gene denotes TF2b Gene:2959
518 2693-2697 Gene denotes RdRp Gene:43740578
519 2748-2752 Gene denotes RdRp Gene:43740578
520 2885-2889 Gene denotes RdRp Gene:43740578
521 2922-2926 Gene denotes RdRp Gene:43740578
522 2682-2692 Species denotes SARS-CoV-2 Tax:2697049
523 2737-2747 Species denotes SARS-CoV-2 Tax:2697049
524 2874-2884 Species denotes SARS-CoV-2 Tax:2697049
525 3103-3108 Species denotes human Tax:9606
526 3215-3224 Species denotes black tea Tax:4442
527 3515-3532 Species denotes influenza A virus Tax:11320
528 3784-3800 Species denotes SARS coronavirus Tax:694009
529 3862-3879 Species denotes hepatitis C virus Tax:11103
530 3337-3346 Species denotes influenza Tax:11320
531 2492-2502 Chemical denotes remdesivir MESH:C000606551
532 2540-2551 Chemical denotes polyphenols MESH:D059808
533 2575-2585 Chemical denotes hesperidin MESH:D006569
534 2587-2591 Chemical denotes EGCG MESH:C045651
535 2593-2602 Chemical denotes myricetin MESH:C040015
536 2607-2620 Chemical denotes quercetagetin MESH:C079163
537 2815-2826 Chemical denotes polyphenols MESH:D059808
538 3028-3039 Chemical denotes polyphenols MESH:D059808
539 3172-3179 Chemical denotes gallate
540 3225-3236 Chemical denotes polyphenols MESH:D059808
541 3389-3399 Chemical denotes Hesperidin MESH:D006569
542 3562-3566 Chemical denotes EGCG MESH:C045651
543 3586-3596 Chemical denotes polyphenol MESH:D059808
544 3724-3733 Chemical denotes myricetin MESH:C040015
545 3829-3842 Chemical denotes Quercetagetin MESH:C079163
546 3974-3985 Chemical denotes polyphenols MESH:D059808
547 3058-3066 Disease denotes toxicity MESH:D064420
548 3317-3332 Disease denotes hepatitis virus MESH:D006525
549 4077-4097 Disease denotes SARS-CoV-2 infection MESH:C000657245

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T5 936-939 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T6 1729-1732 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T7 2553-2556 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T8 3160-3163 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T194 0-4 Sentence denotes 3.1.
T195 6-32 Sentence denotes Molecular docking analysis
T196 34-40 Sentence denotes 3.1.1.
T197 42-162 Sentence denotes The binding mode analysis and predicted binding affinity calculations of natural polyphenols against the SARS-CoV-2 RdRp
T198 163-257 Sentence denotes Herein, we investigated our natural polyphenol library against RdRp of the SARS-CoV-2 (PDB ID:
T199 258-285 Sentence denotes 6M71) by molecular docking.
T200 286-428 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 429-612 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 613-750 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 751-1094 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 1095-1294 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 1295-1303 Sentence denotes Table 2.
T206 1305-1405 Sentence denotes Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.
T207 1406-1408 Sentence denotes S.
T208 1409-1412 Sentence denotes No.
T209 1414-1510 Sentence denotes Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids
T210 1511-1629 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 1630-1725 Sentence denotes 2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550
T212 1726-1814 Sentence denotes 3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618
T213 1815-1916 Sentence denotes 4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811
T214 1917-2018 Sentence denotes 5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455
T215 2019-2089 Sentence denotes 6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798
T216 2090-2172 Sentence denotes 7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812
T217 2173-2246 Sentence denotes 8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619
T218 2247-2358 Sentence denotes 9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761
T219 2359-2698 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 2699-3006 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 3007-3159 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 3160-3388 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 3389-3561 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 3562-3712 Sentence denotes EGCG, a major green tea polyphenol, has several pharmacological properties, including antiviral activity (Carneiro et al., 2016; Moon & Morris, 2007).
T225 3713-3828 Sentence denotes Similarly, myricetin has also been found to act as an inhibitor of the SARS coronavirus helicase (Yu et al., 2012).
T226 3829-3951 Sentence denotes Quercetagetin also showed strong hepatitis C virus replication inhibitory activity in vitro (Ahmed-Belkacem et al., 2014).
T227 3952-4144 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 3317-3326 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115
T8 3862-3871 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115

2_test

Id Subject Object Predicate Lexical cue
32720577-30298133-56195126 3153-3157 30298133 denotes 2018
32720577-30485282-56195127 3382-3386 30485282 denotes 2018
32720577-18089727-56195128 3555-3559 18089727 denotes 2008
32720577-17970592-56195129 3706-3710 17970592 denotes 2007
32720577-22578462-56195130 3822-3826 22578462 denotes 2012
32720577-25053847-56195131 3945-3949 25053847 denotes 2014