PMC:7544943 / 22838-25790 JSONTXT

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T8","span":{"begin":2075,"end":2079},"obj":"Body_part"}],"attributes":[{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"}],"text":"3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T27","span":{"begin":66,"end":73},"obj":"Body_part"},{"id":"T28","span":{"begin":2075,"end":2079},"obj":"Body_part"}],"attributes":[{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma9712"}],"text":"3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T51","span":{"begin":25,"end":33},"obj":"Disease"},{"id":"T52","span":{"begin":262,"end":270},"obj":"Disease"},{"id":"T53","span":{"begin":1279,"end":1287},"obj":"Disease"},{"id":"T54","span":{"begin":1340,"end":1348},"obj":"Disease"},{"id":"T55","span":{"begin":1953,"end":1957},"obj":"Disease"},{"id":"T56","span":{"begin":2146,"end":2154},"obj":"Disease"}],"attributes":[{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T113","span":{"begin":115,"end":116},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T114","span":{"begin":328,"end":331},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T115","span":{"begin":907,"end":908},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T116","span":{"begin":1455,"end":1456},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T117","span":{"begin":1652,"end":1653},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T118","span":{"begin":1885,"end":1886},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T119","span":{"begin":1899,"end":1900},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T120","span":{"begin":2357,"end":2358},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}

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Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}

{"project":"LitCovid-sentences","denotations":[{"id":"T204","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T205","span":{"begin":8,"end":73},"obj":"Sentence"},{"id":"T206","span":{"begin":74,"end":282},"obj":"Sentence"},{"id":"T207","span":{"begin":283,"end":394},"obj":"Sentence"},{"id":"T208","span":{"begin":395,"end":644},"obj":"Sentence"},{"id":"T209","span":{"begin":645,"end":892},"obj":"Sentence"},{"id":"T210","span":{"begin":893,"end":1008},"obj":"Sentence"},{"id":"T211","span":{"begin":1009,"end":1130},"obj":"Sentence"},{"id":"T212","span":{"begin":1131,"end":1299},"obj":"Sentence"},{"id":"T213","span":{"begin":1300,"end":1477},"obj":"Sentence"},{"id":"T214","span":{"begin":1478,"end":1656},"obj":"Sentence"},{"id":"T215","span":{"begin":1657,"end":1843},"obj":"Sentence"},{"id":"T216","span":{"begin":1844,"end":1853},"obj":"Sentence"},{"id":"T217","span":{"begin":1855,"end":2006},"obj":"Sentence"},{"id":"T218","span":{"begin":2007,"end":2061},"obj":"Sentence"},{"id":"T219","span":{"begin":2062,"end":2180},"obj":"Sentence"},{"id":"T220","span":{"begin":2181,"end":2289},"obj":"Sentence"},{"id":"T221","span":{"begin":2290,"end":2564},"obj":"Sentence"},{"id":"T222","span":{"begin":2565,"end":2821},"obj":"Sentence"},{"id":"T223","span":{"begin":2822,"end":2952},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3."}