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PMC:7441777 / 229-2035 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T3 381-384 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 395-398 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 438-441 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 600-603 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 53-61 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 77-124 Disease denotes Severe Acute Respiratory Syndrome Coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 126-134 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 244-252 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 371-379 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 427-435 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 810-818 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 862-870 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1762-1770 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 144-145 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 604-611 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T3 690-691 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 888-889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1099-1102 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T6 1262-1268 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T7 1292-1293 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1545-1546 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 212-216 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T6 292-296 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T7 310-314 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T8 352-360 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T9 490-504 Chemical denotes antiviral drug http://purl.obolibrary.org/obo/CHEBI_36044
T10 490-499 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T11 500-504 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T12 550-561 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T13 631-642 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T14 793-804 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T15 901-912 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T16 1081-1085 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T17 1087-1097 Chemical denotes theaflavin http://purl.obolibrary.org/obo/CHEBI_136609
T18 1105-1115 Chemical denotes theaflavin http://purl.obolibrary.org/obo/CHEBI_136609
T19 1121-1128 Chemical denotes gallate http://purl.obolibrary.org/obo/CHEBI_16918
T20 1137-1147 Chemical denotes theaflavin http://purl.obolibrary.org/obo/CHEBI_136609
T21 1151-1158 Chemical denotes gallate http://purl.obolibrary.org/obo/CHEBI_16918
T22 1167-1192 Chemical denotes theaflavin 3,3'-digallate http://purl.obolibrary.org/obo/CHEBI_136608
T23 1167-1177 Chemical denotes theaflavin http://purl.obolibrary.org/obo/CHEBI_136609
T24 1183-1192 Chemical denotes digallate http://purl.obolibrary.org/obo/CHEBI_17866
T25 1194-1197 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T26 1200-1210 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T27 1212-1225 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T28 1231-1240 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T30 1344-1348 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T31 1362-1365 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T32 1474-1476 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707
T34 1684-1688 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T35 1702-1705 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 438-453 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T2 740-751 http://purl.obolibrary.org/obo/GO_0042592 denotes homeostasis

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
44 411-415 Gene denotes RdRp Gene:43740578
45 586-590 Gene denotes RdRp Gene:43740578
46 821-825 Gene denotes RdRp Gene:43740578
47 1044-1048 Gene denotes RdRp Gene:43740578
48 1160-1164 Gene denotes TF2b Gene:2959
49 1277-1281 Gene denotes RdRp Gene:43740578
50 1356-1360 Gene denotes TF2b Gene:2959
51 1415-1419 Gene denotes RdRp Gene:43740578
52 1696-1700 Gene denotes TF2b Gene:2959
53 1718-1722 Gene denotes RdRp Gene:43740578
54 77-124 Species denotes Severe Acute Respiratory Syndrome Coronavirus 2 Tax:2697049
55 126-136 Species denotes SARS-CoV-2 Tax:2697049
56 427-437 Species denotes SARS-CoV-2 Tax:2697049
57 810-820 Species denotes SARS-CoV-2 Tax:2697049
58 550-561 Chemical denotes polyphenols MESH:D059808
59 631-642 Chemical denotes polyphenols MESH:D059808
60 793-804 Chemical denotes polyphenols MESH:D059808
61 901-912 Chemical denotes polyphenols MESH:D059808
62 1081-1085 Chemical denotes EGCG MESH:C045651
63 1087-1097 Chemical denotes theaflavin MESH:C056068
64 1105-1128 Chemical denotes theaflavin-3’-O-gallate
65 1137-1158 Chemical denotes theaflavin-3’-gallate
66 1167-1192 Chemical denotes theaflavin 3,3'-digallate MESH:C585473
67 1194-1197 Chemical denotes TF3 MESH:C585473
68 1200-1210 Chemical denotes hesperidin MESH:D006569
69 1212-1225 Chemical denotes quercetagetin MESH:C079163
70 1231-1240 Chemical denotes myricetin MESH:C040015
71 1344-1348 Chemical denotes EGCG MESH:C045651
72 1477-1481 Chemical denotes PBSA MESH:C437084
73 1568-1572 Chemical denotes ADME
74 1684-1688 Chemical denotes EGCG MESH:C045651
75 32-51 Disease denotes Coronavirus disease MESH:D018352
76 53-61 Disease denotes COVID-19 MESH:C000657245
77 244-252 Disease denotes COVID-19 MESH:C000657245
78 371-379 Disease denotes COVID-19 MESH:C000657245
79 862-870 Disease denotes COVID-19 MESH:C000657245
80 1585-1593 Disease denotes toxicity MESH:D064420
81 1762-1770 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 1099-1102 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T6 0-8 Sentence denotes Abstract
T7 9-185 Sentence denotes The sudden outburst of Coronavirus disease (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses a massive threat to global public health.
T8 186-253 Sentence denotes Currently, no therapeutic drug or vaccine exists to treat COVID-19.
T9 254-380 Sentence denotes Due to the time taking process of new drug development, drug repurposing might be the only viable solution to tackle COVID-19.
T10 381-512 Sentence denotes RNA‐dependent RNA polymerase (RdRp) catalyzes SARS-CoV-2 RNA replication and hence, is an obvious target for antiviral drug design.
T11 513-612 Sentence denotes Interestingly, several plant-derived polyphenols effectively inhibit the RdRp of other RNA viruses.
T12 613-752 Sentence denotes More importantly, polyphenols have been used as dietary supplementations for a long time and played beneficial roles in immune homeostasis.
T13 753-871 Sentence denotes We were curious to study the binding of polyphenols with SARS-CoV-2 RdRp and assess their potential to treat COVID-19.
T14 872-986 Sentence denotes Herein, we made a library of polyphenols that have shown substantial therapeutic effects against various diseases.
T15 987-1049 Sentence denotes They were successfully docked in the catalytic pocket of RdRp.
T16 1050-1282 Sentence denotes The investigation reveals that EGCG, theaflavin (TF1), theaflavin-3’-O-gallate (TF2a), theaflavin-3’-gallate (TF2b), theaflavin 3,3'-digallate (TF3), hesperidin, quercetagetin, and myricetin strongly bind to the active site of RdRp.
T17 1283-1420 Sentence denotes Further, a 150-ns molecular dynamic simulation revealed that EGCG, TF2a, TF2b, TF3 result in highly stable bound conformations with RdRp.
T18 1421-1526 Sentence denotes The binding free energy components calculated by the MM-PBSA also confirm the stability of the complexes.
T19 1527-1649 Sentence denotes We also performed a detailed analysis of ADME prediction, toxicity prediction, and target analysis for their druggability.
T20 1650-1771 Sentence denotes Overall, our results suggest that EGCG, TF2a, TF2b, TF3 can inhibit RdRp and represent an effective therapy for COVID-19.
T21 1772-1800 Sentence denotes Communicated by Ramaswamy H.
T22 1801-1806 Sentence denotes Sarma