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PMC:7441777 / 49513-51434 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T105 311-314 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T77 87-95 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 98-107 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 279-287 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 843-851 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 1274-1282 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 1552-1560 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 1779-1787 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 1900-1908 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 1911-1920 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T324 58-59 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T325 136-137 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T326 181-182 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T327 526-529 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T328 1203-1204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T329 1506-1507 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T46875 42-52 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T22320 210-221 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T80937 237-246 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T24344 357-368 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T98962 515-519 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T71966 568-578 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T90398 585-594 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T23792 601-614 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T42245 632-642 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T90588 744-746 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T93177 877-888 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T65194 1083-1089 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T29242 1142-1144 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T73139 1169-1173 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T70168 1246-1250 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T25385 1251-1261 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T98626 1475-1479 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T66579 1727-1738 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T46661 1760-1770 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T39 311-326 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T40 826-835 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1524 37-41 Gene denotes RdRp Gene:43740578
1525 290-294 Gene denotes RdRp Gene:43740578
1526 510-514 Gene denotes RdRp Gene:43740578
1527 521-525 Gene denotes RdRp Gene:43740578
1528 531-535 Gene denotes RdRp Gene:43740578
1529 542-546 Gene denotes RdRp Gene:43740578
1530 547-551 Gene denotes TF2b Gene:2959
1531 553-557 Gene denotes RdRp Gene:43740578
1532 563-567 Gene denotes RdRp Gene:43740578
1533 580-584 Gene denotes RdRp Gene:43740578
1534 596-600 Gene denotes RdRp Gene:43740578
1535 627-631 Gene denotes RdRp Gene:43740578
1536 1181-1185 Gene denotes TF2b Gene:2959
1537 1285-1289 Gene denotes RdRp Gene:43740578
1538 1487-1491 Gene denotes TF2b Gene:2959
1539 1540-1544 Gene denotes RdRp Gene:43740578
1540 854-858 Gene denotes RdRp Gene:43740578
1541 1790-1794 Gene denotes RdRp Gene:43740578
1542 279-289 Species denotes SARS-CoV-2 Tax:2697049
1543 843-853 Species denotes SARS-CoV-2 Tax:2697049
1544 1274-1284 Species denotes SARS-CoV-2 Tax:2697049
1545 1552-1562 Species denotes SARS-CoV-2 Tax:2697049
1546 1779-1789 Species denotes SARS-CoV-2 Tax:2697049
1547 210-221 Chemical denotes polyphenols MESH:D059808
1548 357-368 Chemical denotes polyphenols MESH:D059808
1549 632-642 Chemical denotes remdesivir MESH:C000606551
1550 877-888 Chemical denotes polyphenols MESH:D059808
1551 1145-1149 Chemical denotes PBSA MESH:C437084
1552 1169-1173 Chemical denotes EGCG MESH:C045651
1553 1251-1261 Chemical denotes remdesivir MESH:C000606551
1554 1322-1326 Chemical denotes ADME
1555 1475-1479 Chemical denotes EGCG MESH:C045651
1556 1727-1738 Chemical denotes polyphenols MESH:D059808
1557 87-107 Disease denotes SARS-CoV-2 infection MESH:C000657245
1558 1339-1347 Disease denotes toxicity MESH:D064420
1559 1900-1920 Disease denotes SARS-CoV-2 infection MESH:C000657245

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T16 526-529 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T520 0-2 Sentence denotes 4.
T521 4-15 Sentence denotes Conclusions
T522 16-327 Sentence denotes Keeping in mind that RdRp inhibitors play a crucial role to combat the SARS-CoV-2 infection, in this work, we performed a comprehensive molecular docking study with a library of hundred natural polyphenols with potential antiviral properties that may inhibit the SARS-CoV-2 RdRp and prevent the RNA replication.
T523 328-447 Sentence denotes We shortlisted eight natural polyphenols having binding energy −7.0 kcal/mol or less for molecular dynamics simulation.
T524 448-789 Sentence denotes Further, we performed 150 ns molecular dynamics simulation of RdRp/EGCG, RdRp/TF1, RdRp/TF2a, RdRp/TF2b, RdRp/TF3, RdRp/hesperidin, RdRp/myricetin, RdRp/quercetagetin, along with RdRp/remdesivir complex and computed the binding energies by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) scheme from last 50 ns trajectories.
T525 790-1010 Sentence denotes Our study suggests that the complex formation of the SARS-CoV-2 RdRp and eight natural polyphenols is favoured by the intermolecular van der Waals and electrostatic interactions as well as nonpolar solvation free energy.
T526 1011-1098 Sentence denotes We have also investigated the hotspot residues controlling the receptor-ligand binding.
T527 1099-1290 Sentence denotes Finally, molecular dynamics simulation and MM-PBSA study reveals that EGCG, TF2a, TF2b, and TF3 possess a better binding affinity than the control drug remdesivir against the SARS-CoV-2 RdRp.
T528 1291-1431 Sentence denotes Further, we also looked at the ADME prediction, toxicity prediction, and target analysis to assess their druggability of the five compounds.
T529 1432-1606 Sentence denotes The obtained results strongly suggest that EGCG, TF2a, TF2b, and TF3 have a stable binding affinity towards RdRp of the SARS-CoV-2 with favourable pharmacokinetic properties.
T530 1607-1680 Sentence denotes These bioactive compounds exhibit broad ranges of therapeutic properties.
T531 1681-1795 Sentence denotes Therefore, we believe that these four natural polyphenols can act as potential inhibitors for the SARS-CoV-2 RdRp.
T532 1796-1921 Sentence denotes However, further in vitro and in vivo studies need to be carried out to validate their efficacy against SARS-CoV-2 infection.