PMC:7441777 / 31988-32893 JSON TXT

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LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T199","span":{"begin":209,"end":212},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T200","span":{"begin":279,"end":281},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T201","span":{"begin":279,"end":281},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information). This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG. The potency of the five inhibitors decreases in the following order: TF3 \u003e TF2a \u003e EGCG \u003e TF2b \u003e remdesivir. TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors. Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol)."}

LitCovid-PD-CHEBI

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"777","span":{"begin":69,"end":73},"obj":"Gene"},{"id":"778","span":{"begin":374,"end":378},"obj":"Gene"},{"id":"779","span":{"begin":496,"end":500},"obj":"Gene"},{"id":"780","span":{"begin":542,"end":546},"obj":"Gene"},{"id":"781","span":{"begin":684,"end":688},"obj":"Gene"},{"id":"782","span":{"begin":709,"end":713},"obj":"Gene"},{"id":"783","span":{"begin":869,"end":873},"obj":"Gene"},{"id":"784","span":{"begin":46,"end":56},"obj":"Chemical"},{"id":"785","span":{"begin":58,"end":62},"obj":"Chemical"},{"id":"786","span":{"begin":168,"end":177},"obj":"Chemical"},{"id":"787","span":{"begin":179,"end":192},"obj":"Chemical"},{"id":"788","span":{"begin":194,"end":204},"obj":"Chemical"},{"id":"789","span":{"begin":261,"end":271},"obj":"Chemical"},{"id":"790","span":{"begin":336,"end":346},"obj":"Chemical"},{"id":"791","span":{"begin":401,"end":405},"obj":"Chemical"},{"id":"792","span":{"begin":489,"end":493},"obj":"Chemical"},{"id":"793","span":{"begin":503,"end":513},"obj":"Chemical"},{"id":"794","span":{"begin":701,"end":705},"obj":"Chemical"},{"id":"795","span":{"begin":829,"end":833},"obj":"Chemical"}],"attributes":[{"id":"A777","pred":"tao:has_database_id","subj":"777","obj":"Gene:2959"},{"id":"A778","pred":"tao:has_database_id","subj":"778","obj":"Gene:43740578"},{"id":"A779","pred":"tao:has_database_id","subj":"779","obj":"Gene:2959"},{"id":"A780","pred":"tao:has_database_id","subj":"780","obj":"Gene:43740578"},{"id":"A781","pred":"tao:has_database_id","subj":"781","obj":"Gene:43740578"},{"id":"A782","pred":"tao:has_database_id","subj":"782","obj":"Gene:2959"},{"id":"A783","pred":"tao:has_database_id","subj":"783","obj":"Gene:2959"},{"id":"A784","pred":"tao:has_database_id","subj":"784","obj":"MESH:C000606551"},{"id":"A785","pred":"tao:has_database_id","subj":"785","obj":"MESH:C045651"},{"id":"A786","pred":"tao:has_database_id","subj":"786","obj":"MESH:C040015"},{"id":"A787","pred":"tao:has_database_id","subj":"787","obj":"MESH:C079163"},{"id":"A788","pred":"tao:has_database_id","subj":"788","obj":"MESH:D006569"},{"id":"A789","pred":"tao:has_database_id","subj":"789","obj":"MESH:C000606551"},{"id":"A790","pred":"tao:has_database_id","subj":"790","obj":"MESH:D059808"},{"id":"A791","pred":"tao:has_database_id","subj":"791","obj":"MESH:C045651"},{"id":"A792","pred":"tao:has_database_id","subj":"792","obj":"MESH:C045651"},{"id":"A793","pred":"tao:has_database_id","subj":"793","obj":"MESH:C000606551"},{"id":"A794","pred":"tao:has_database_id","subj":"794","obj":"MESH:C045651"},{"id":"A795","pred":"tao:has_database_id","subj":"795","obj":"MESH:C045651"}],"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":"The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information). This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG. The potency of the five inhibitors decreases in the following order: TF3 \u003e TF2a \u003e EGCG \u003e TF2b \u003e remdesivir. TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors. Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol)."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T15","span":{"begin":209,"end":212},"obj":"GlycoEpitope"}],"attributes":[{"id":"A15","pred":"glyco_epitope_db_id","subj":"T15","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information). This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG. The potency of the five inhibitors decreases in the following order: TF3 \u003e TF2a \u003e EGCG \u003e TF2b \u003e remdesivir. TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors. Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T302","span":{"begin":0,"end":316},"obj":"Sentence"},{"id":"T303","span":{"begin":317,"end":406},"obj":"Sentence"},{"id":"T304","span":{"begin":407,"end":514},"obj":"Sentence"},{"id":"T305","span":{"begin":515,"end":644},"obj":"Sentence"},{"id":"T306","span":{"begin":645,"end":905},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information). This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG. The potency of the five inhibitors decreases in the following order: TF3 \u003e TF2a \u003e EGCG \u003e TF2b \u003e remdesivir. TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors. Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol)."}