PMC:7441777 / 30994-31987 JSONTXT

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T195","span":{"begin":568,"end":571},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T196","span":{"begin":583,"end":585},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T197","span":{"begin":583,"end":585},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T198","span":{"begin":950,"end":951},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T422","span":{"begin":204,"end":214},"obj":"Chemical"},{"id":"T423","span":{"begin":221,"end":225},"obj":"Chemical"},{"id":"T424","span":{"begin":232,"end":235},"obj":"Chemical"},{"id":"T425","span":{"begin":511,"end":520},"obj":"Chemical"},{"id":"T427","span":{"begin":527,"end":540},"obj":"Chemical"},{"id":"T428","span":{"begin":547,"end":557},"obj":"Chemical"},{"id":"T429","span":{"begin":583,"end":585},"obj":"Chemical"},{"id":"T430","span":{"begin":845,"end":856},"obj":"Chemical"},{"id":"T431","span":{"begin":868,"end":878},"obj":"Chemical"}],"attributes":[{"id":"A422","pred":"chebi_id","subj":"T422","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A423","pred":"chebi_id","subj":"T423","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A424","pred":"chebi_id","subj":"T424","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A425","pred":"chebi_id","subj":"T425","obj":"http://purl.obolibrary.org/obo/CHEBI_18152"},{"id":"A426","pred":"chebi_id","subj":"T425","obj":"http://purl.obolibrary.org/obo/CHEBI_58395"},{"id":"A427","pred":"chebi_id","subj":"T427","obj":"http://purl.obolibrary.org/obo/CHEBI_8695"},{"id":"A428","pred":"chebi_id","subj":"T428","obj":"http://purl.obolibrary.org/obo/CHEBI_28775"},{"id":"A429","pred":"chebi_id","subj":"T429","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A430","pred":"chebi_id","subj":"T430","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A431","pred":"chebi_id","subj":"T431","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"}],"text":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T12","span":{"begin":776,"end":785},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}

{"project":"LitCovid-PubTator","denotations":[{"id":"744","span":{"begin":199,"end":203},"obj":"Gene"},{"id":"745","span":{"begin":216,"end":220},"obj":"Gene"},{"id":"746","span":{"begin":227,"end":231},"obj":"Gene"},{"id":"747","span":{"begin":241,"end":245},"obj":"Gene"},{"id":"748","span":{"begin":246,"end":250},"obj":"Gene"},{"id":"749","span":{"begin":506,"end":510},"obj":"Gene"},{"id":"750","span":{"begin":522,"end":526},"obj":"Gene"},{"id":"751","span":{"begin":542,"end":546},"obj":"Gene"},{"id":"752","span":{"begin":563,"end":567},"obj":"Gene"},{"id":"753","span":{"begin":645,"end":649},"obj":"Gene"},{"id":"754","span":{"begin":883,"end":887},"obj":"Gene"},{"id":"755","span":{"begin":204,"end":214},"obj":"Chemical"},{"id":"756","span":{"begin":845,"end":856},"obj":"Chemical"},{"id":"757","span":{"begin":868,"end":878},"obj":"Chemical"}],"attributes":[{"id":"A744","pred":"tao:has_database_id","subj":"744","obj":"Gene:43740578"},{"id":"A745","pred":"tao:has_database_id","subj":"745","obj":"Gene:43740578"},{"id":"A746","pred":"tao:has_database_id","subj":"746","obj":"Gene:43740578"},{"id":"A747","pred":"tao:has_database_id","subj":"747","obj":"Gene:43740578"},{"id":"A748","pred":"tao:has_database_id","subj":"748","obj":"Gene:2959"},{"id":"A749","pred":"tao:has_database_id","subj":"749","obj":"Gene:43740578"},{"id":"A750","pred":"tao:has_database_id","subj":"750","obj":"Gene:43740578"},{"id":"A751","pred":"tao:has_database_id","subj":"751","obj":"Gene:43740578"},{"id":"A752","pred":"tao:has_database_id","subj":"752","obj":"Gene:43740578"},{"id":"A753","pred":"tao:has_database_id","subj":"753","obj":"Gene:43740578"},{"id":"A754","pred":"tao:has_database_id","subj":"754","obj":"Gene:43740578"},{"id":"A755","pred":"tao:has_database_id","subj":"755","obj":"MESH:C000606551"},{"id":"A756","pred":"tao:has_database_id","subj":"756","obj":"MESH:D059808"},{"id":"A757","pred":"tao:has_database_id","subj":"757","obj":"MESH:C000606551"}],"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":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T14","span":{"begin":568,"end":571},"obj":"GlycoEpitope"}],"attributes":[{"id":"A14","pred":"glyco_epitope_db_id","subj":"T14","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}

{"project":"LitCovid-sentences","denotations":[{"id":"T297","span":{"begin":0,"end":169},"obj":"Sentence"},{"id":"T298","span":{"begin":170,"end":616},"obj":"Sentence"},{"id":"T299","span":{"begin":617,"end":735},"obj":"Sentence"},{"id":"T300","span":{"begin":736,"end":888},"obj":"Sentence"},{"id":"T301","span":{"begin":889,"end":993},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol. Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information). In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol). Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp. Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process."}