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PMC:7441777 / 49529-51434 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T105 295-298 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T77 71-79 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 82-91 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T79 263-271 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 827-835 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 1258-1266 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 1536-1544 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 1763-1771 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 1884-1892 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 1895-1904 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T324 42-43 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T325 120-121 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T326 165-166 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T327 510-513 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T328 1187-1188 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T329 1490-1491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T46875 26-36 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T22320 194-205 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T80937 221-230 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T24344 341-352 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T98962 499-503 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T71966 552-562 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T90398 569-578 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T23792 585-598 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T42245 616-626 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T90588 728-730 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T93177 861-872 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T65194 1067-1073 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T29242 1126-1128 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T73139 1153-1157 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T70168 1230-1234 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T25385 1235-1245 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T98626 1459-1463 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T66579 1711-1722 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T46661 1744-1754 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T39 295-310 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T40 810-819 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1524 21-25 Gene denotes RdRp Gene:43740578
1525 274-278 Gene denotes RdRp Gene:43740578
1526 494-498 Gene denotes RdRp Gene:43740578
1527 505-509 Gene denotes RdRp Gene:43740578
1528 515-519 Gene denotes RdRp Gene:43740578
1529 526-530 Gene denotes RdRp Gene:43740578
1530 531-535 Gene denotes TF2b Gene:2959
1531 537-541 Gene denotes RdRp Gene:43740578
1532 547-551 Gene denotes RdRp Gene:43740578
1533 564-568 Gene denotes RdRp Gene:43740578
1534 580-584 Gene denotes RdRp Gene:43740578
1535 611-615 Gene denotes RdRp Gene:43740578
1536 1165-1169 Gene denotes TF2b Gene:2959
1537 1269-1273 Gene denotes RdRp Gene:43740578
1538 1471-1475 Gene denotes TF2b Gene:2959
1539 1524-1528 Gene denotes RdRp Gene:43740578
1540 838-842 Gene denotes RdRp Gene:43740578
1541 1774-1778 Gene denotes RdRp Gene:43740578
1542 263-273 Species denotes SARS-CoV-2 Tax:2697049
1543 827-837 Species denotes SARS-CoV-2 Tax:2697049
1544 1258-1268 Species denotes SARS-CoV-2 Tax:2697049
1545 1536-1546 Species denotes SARS-CoV-2 Tax:2697049
1546 1763-1773 Species denotes SARS-CoV-2 Tax:2697049
1547 194-205 Chemical denotes polyphenols MESH:D059808
1548 341-352 Chemical denotes polyphenols MESH:D059808
1549 616-626 Chemical denotes remdesivir MESH:C000606551
1550 861-872 Chemical denotes polyphenols MESH:D059808
1551 1129-1133 Chemical denotes PBSA MESH:C437084
1552 1153-1157 Chemical denotes EGCG MESH:C045651
1553 1235-1245 Chemical denotes remdesivir MESH:C000606551
1554 1306-1310 Chemical denotes ADME
1555 1459-1463 Chemical denotes EGCG MESH:C045651
1556 1711-1722 Chemical denotes polyphenols MESH:D059808
1557 71-91 Disease denotes SARS-CoV-2 infection MESH:C000657245
1558 1323-1331 Disease denotes toxicity MESH:D064420
1559 1884-1904 Disease denotes SARS-CoV-2 infection MESH:C000657245

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T16 510-513 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T522 0-311 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 312-431 Sentence denotes We shortlisted eight natural polyphenols having binding energy −7.0 kcal/mol or less for molecular dynamics simulation.
T524 432-773 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 774-994 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 995-1082 Sentence denotes We have also investigated the hotspot residues controlling the receptor-ligand binding.
T527 1083-1274 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 1275-1415 Sentence denotes Further, we also looked at the ADME prediction, toxicity prediction, and target analysis to assess their druggability of the five compounds.
T529 1416-1590 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 1591-1664 Sentence denotes These bioactive compounds exhibit broad ranges of therapeutic properties.
T531 1665-1779 Sentence denotes Therefore, we believe that these four natural polyphenols can act as potential inhibitors for the SARS-CoV-2 RdRp.
T532 1780-1905 Sentence denotes However, further in vitro and in vivo studies need to be carried out to validate their efficacy against SARS-CoV-2 infection.