PMC:7441777 / 28874-29742 JSONTXT

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T187","span":{"begin":158,"end":159},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T188","span":{"begin":444,"end":446},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T189","span":{"begin":444,"end":446},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T190","span":{"begin":785,"end":786},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4. Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4. The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information. It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation. Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases. A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T404","span":{"begin":76,"end":78},"obj":"Chemical"},{"id":"T406","span":{"begin":101,"end":112},"obj":"Chemical"},{"id":"T407","span":{"begin":121,"end":125},"obj":"Chemical"},{"id":"T408","span":{"begin":127,"end":130},"obj":"Chemical"},{"id":"T409","span":{"begin":198,"end":208},"obj":"Chemical"},{"id":"T410","span":{"begin":283,"end":287},"obj":"Chemical"},{"id":"T411","span":{"begin":289,"end":292},"obj":"Chemical"},{"id":"T412","span":{"begin":353,"end":364},"obj":"Chemical"},{"id":"T413","span":{"begin":414,"end":424},"obj":"Chemical"},{"id":"T414","span":{"begin":444,"end":446},"obj":"Chemical"},{"id":"T415","span":{"begin":608,"end":614},"obj":"Chemical"}],"attributes":[{"id":"A404","pred":"chebi_id","subj":"T404","obj":"http://purl.obolibrary.org/obo/CHEBI_53458"},{"id":"A405","pred":"chebi_id","subj":"T404","obj":"http://purl.obolibrary.org/obo/CHEBI_74707"},{"id":"A406","pred":"chebi_id","subj":"T406","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A407","pred":"chebi_id","subj":"T407","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A408","pred":"chebi_id","subj":"T408","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A409","pred":"chebi_id","subj":"T409","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A410","pred":"chebi_id","subj":"T410","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A411","pred":"chebi_id","subj":"T411","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A412","pred":"chebi_id","subj":"T412","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A413","pred":"chebi_id","subj":"T413","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A414","pred":"chebi_id","subj":"T414","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A415","pred":"chebi_id","subj":"T415","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"}],"text":"We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4. Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4. The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information. It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation. Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases. A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T11","span":{"begin":692,"end":701},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4. Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4. The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information. It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation. Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases. A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"707","span":{"begin":132,"end":136},"obj":"Gene"},{"id":"708","span":{"begin":294,"end":298},"obj":"Gene"},{"id":"709","span":{"begin":79,"end":83},"obj":"Chemical"},{"id":"710","span":{"begin":101,"end":112},"obj":"Chemical"},{"id":"711","span":{"begin":121,"end":125},"obj":"Chemical"},{"id":"712","span":{"begin":198,"end":208},"obj":"Chemical"},{"id":"713","span":{"begin":283,"end":287},"obj":"Chemical"},{"id":"714","span":{"begin":353,"end":364},"obj":"Chemical"},{"id":"715","span":{"begin":414,"end":424},"obj":"Chemical"}],"attributes":[{"id":"A707","pred":"tao:has_database_id","subj":"707","obj":"Gene:2959"},{"id":"A708","pred":"tao:has_database_id","subj":"708","obj":"Gene:2959"},{"id":"A709","pred":"tao:has_database_id","subj":"709","obj":"MESH:C437084"},{"id":"A710","pred":"tao:has_database_id","subj":"710","obj":"MESH:D059808"},{"id":"A711","pred":"tao:has_database_id","subj":"711","obj":"MESH:C045651"},{"id":"A712","pred":"tao:has_database_id","subj":"712","obj":"MESH:C000606551"},{"id":"A713","pred":"tao:has_database_id","subj":"713","obj":"MESH:C045651"},{"id":"A714","pred":"tao:has_database_id","subj":"714","obj":"MESH:D059808"},{"id":"A715","pred":"tao:has_database_id","subj":"715","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":"We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4. Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4. The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information. It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation. Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases. A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T274","span":{"begin":0,"end":233},"obj":"Sentence"},{"id":"T275","span":{"begin":234,"end":333},"obj":"Sentence"},{"id":"T276","span":{"begin":334,"end":476},"obj":"Sentence"},{"id":"T277","span":{"begin":477,"end":702},"obj":"Sentence"},{"id":"T278","span":{"begin":703,"end":784},"obj":"Sentence"},{"id":"T279","span":{"begin":785,"end":868},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4. Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4. The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information. It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation. Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases. A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020)."}