PMC:7441777 / 20635-21816 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T35","span":{"begin":17,"end":27},"obj":"Body_part"},{"id":"T36","span":{"begin":204,"end":215},"obj":"Body_part"}],"attributes":[{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T58","span":{"begin":94,"end":102},"obj":"Disease"}],"attributes":[{"id":"A58","pred":"mondo_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T117","span":{"begin":434,"end":437},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T294","span":{"begin":17,"end":27},"obj":"Chemical"},{"id":"T295","span":{"begin":17,"end":22},"obj":"Chemical"},{"id":"T296","span":{"begin":23,"end":27},"obj":"Chemical"},{"id":"T297","span":{"begin":70,"end":81},"obj":"Chemical"},{"id":"T298","span":{"begin":204,"end":215},"obj":"Chemical"},{"id":"T299","span":{"begin":204,"end":209},"obj":"Chemical"},{"id":"T300","span":{"begin":210,"end":215},"obj":"Chemical"},{"id":"T301","span":{"begin":219,"end":222},"obj":"Chemical"},{"id":"T302","span":{"begin":625,"end":635},"obj":"Chemical"},{"id":"T304","span":{"begin":727,"end":731},"obj":"Chemical"},{"id":"T305","span":{"begin":798,"end":807},"obj":"Chemical"},{"id":"T306","span":{"begin":881,"end":894},"obj":"Chemical"},{"id":"T307","span":{"begin":1068,"end":1071},"obj":"Chemical"}],"attributes":[{"id":"A294","pred":"chebi_id","subj":"T294","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A295","pred":"chebi_id","subj":"T295","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A296","pred":"chebi_id","subj":"T296","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A297","pred":"chebi_id","subj":"T297","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A298","pred":"chebi_id","subj":"T298","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A299","pred":"chebi_id","subj":"T299","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A300","pred":"chebi_id","subj":"T300","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A301","pred":"chebi_id","subj":"T301","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A302","pred":"chebi_id","subj":"T302","obj":"http://purl.obolibrary.org/obo/CHEBI_28775"},{"id":"A303","pred":"chebi_id","subj":"T302","obj":"http://purl.obolibrary.org/obo/CHEBI_61606"},{"id":"A304","pred":"chebi_id","subj":"T304","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A305","pred":"chebi_id","subj":"T305","obj":"http://purl.obolibrary.org/obo/CHEBI_18152"},{"id":"A306","pred":"chebi_id","subj":"T306","obj":"http://purl.obolibrary.org/obo/CHEBI_8695"},{"id":"A307","pred":"chebi_id","subj":"T307","obj":"http://purl.obolibrary.org/obo/CHEBI_15996"},{"id":"A308","pred":"chebi_id","subj":"T307","obj":"http://purl.obolibrary.org/obo/CHEBI_37565"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-PubTator","denotations":[{"id":"472","span":{"begin":338,"end":342},"obj":"Gene"},{"id":"473","span":{"begin":111,"end":112},"obj":"Gene"},{"id":"474","span":{"begin":955,"end":965},"obj":"Chemical"},{"id":"475","span":{"begin":246,"end":250},"obj":"CellLine"},{"id":"476","span":{"begin":420,"end":424},"obj":"CellLine"},{"id":"477","span":{"begin":587,"end":591},"obj":"CellLine"},{"id":"481","span":{"begin":105,"end":109},"obj":"Gene"},{"id":"482","span":{"begin":94,"end":104},"obj":"Species"},{"id":"483","span":{"begin":70,"end":81},"obj":"Chemical"}],"attributes":[{"id":"A472","pred":"tao:has_database_id","subj":"472","obj":"Gene:2959"},{"id":"A473","pred":"tao:has_database_id","subj":"473","obj":"Gene:43740568"},{"id":"A474","pred":"tao:has_database_id","subj":"474","obj":"MESH:C000606551"},{"id":"A475","pred":"tao:has_database_id","subj":"475","obj":"CVCL:0023"},{"id":"A476","pred":"tao:has_database_id","subj":"476","obj":"CVCL:0023"},{"id":"A477","pred":"tao:has_database_id","subj":"477","obj":"CVCL:0023"},{"id":"A481","pred":"tao:has_database_id","subj":"481","obj":"Gene:43740578"},{"id":"A482","pred":"tao:has_database_id","subj":"482","obj":"Tax:2697049"},{"id":"A483","pred":"tao:has_database_id","subj":"483","obj":"MESH:D059808"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T6","span":{"begin":434,"end":437},"obj":"GlycoEpitope"}],"attributes":[{"id":"A6","pred":"glyco_epitope_db_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}

{"project":"LitCovid-sentences","denotations":[{"id":"T205","span":{"begin":0,"end":8},"obj":"Sentence"},{"id":"T206","span":{"begin":10,"end":110},"obj":"Sentence"},{"id":"T207","span":{"begin":111,"end":113},"obj":"Sentence"},{"id":"T208","span":{"begin":114,"end":117},"obj":"Sentence"},{"id":"T209","span":{"begin":119,"end":215},"obj":"Sentence"},{"id":"T210","span":{"begin":216,"end":334},"obj":"Sentence"},{"id":"T211","span":{"begin":335,"end":430},"obj":"Sentence"},{"id":"T212","span":{"begin":431,"end":519},"obj":"Sentence"},{"id":"T213","span":{"begin":520,"end":621},"obj":"Sentence"},{"id":"T214","span":{"begin":622,"end":723},"obj":"Sentence"},{"id":"T215","span":{"begin":724,"end":794},"obj":"Sentence"},{"id":"T216","span":{"begin":795,"end":877},"obj":"Sentence"},{"id":"T217","span":{"begin":878,"end":951},"obj":"Sentence"},{"id":"T218","span":{"begin":952,"end":1063},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Table 2. Ligand-amino acid interactions of top eight scoring natural polyphenols against the SARS-CoV-2 RdRp.\nS. No. Compound name Binding energy (kcal/mol) No. of non-covalent interactions Involved amino acids\n1 TF3 −9.9 17 W617, K551, S549, D623, R836, S814, E811, F812, C813, D761, D618, S759, Y619, C622, R553, K621, D760\n2 TF2b −9.6 13 K551, Y619, D760, K798, W617, W800, D761, F812, C813, E811, D618, S549, A550\n3 TF1 −9.6 12 W617, D761, D760, Y619, R553, K621, P620, F793, D164, S795, K798, D618\n4 TF2a −9.3 14 C813, F812, D761, D760, D618, K798, K551, A550, S549, K621, Y619, W800, W617, E811\n5 Hesperidin −8.8 13 Y619, D618, K798, S795, M794, P793, D164, V166, P620, K621, D623, R555, Y455\n6 EGCG −7.3 9 D623, Y619, K621, S795, C622, D618, M794, P620, K798\n7 Myricetin −7.2 10 W617, W800, D760, E811, K798, D618, Y619, C622, D761, F812\n8 Quercetagetin −7.0 8 R553, K545, K621, D623, C622, D760, P620, Y619\n9 Remdesivir (Control) −7.7 13 R553, K621, C622, D760, E811, W800, K798, P620, Y455, R624, Y619, D618, D761\n10 GTP (Control) −7.9 15 R624, T556, D623, D760, Y619, C622, K621, D452, A554, R553, Y455, R555, D761, D618, P620"}