LitCovid-sentences  

PMC:7544943 / 22807-28937 JSONTXT 7 Projects

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Id Subject Object Predicate Lexical cue
T202 0-4 Sentence denotes 3.5.
T203 6-29 Sentence denotes Molecular docking study
T204 31-37 Sentence denotes 3.5.1.
T205 39-104 Sentence denotes Docking study of SARS-CoV-2 receptor-binding domain spike protein
T206 105-313 Sentence denotes In 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.
T207 314-425 Sentence denotes From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds.
T208 426-675 Sentence denotes 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.
T209 676-923 Sentence denotes 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.
T210 924-1039 Sentence denotes From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170.
T211 1040-1161 Sentence denotes TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively.
T212 1162-1330 Sentence denotes 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.
T213 1331-1508 Sentence denotes 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.
T214 1509-1687 Sentence denotes 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)).
T215 1688-1874 Sentence denotes 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.
T216 1875-1884 Sentence denotes Figure 3.
T217 1886-2037 Sentence denotes 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.
T218 2038-2092 Sentence denotes The colour codes represent the nature of interactions.
T219 2093-2211 Sentence denotes On the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)).
T220 2212-2320 Sentence denotes The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol.
T221 2321-2595 Sentence denotes 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.
T222 2596-2852 Sentence denotes 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)).
T223 2853-2983 Sentence denotes The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3.
T224 2985-2991 Sentence denotes 3.5.2.
T225 2993-3034 Sentence denotes Docking study of SARS-CoV-2 main protease
T226 3035-3158 Sentence denotes The above-selected molecules were also docked with the SARS-CoV-2 Mpro to observe the inhibitory effect of these molecules.
T227 3159-3279 Sentence denotes The docking study reveals that all the molecules are interacting with the SARS-CoV-2 Mpro with certain binding affinity.
T228 3280-3327 Sentence denotes The docking data are also presented in Table 1.
T229 3328-3517 Sentence denotes From Table 1, it is seen that Piperine has the highest affinity at the binding site of SARS-CoV-2 Mpro among all the selected molecules, which is similar to the case of SARS-CoV-2 RBD Spro.
T230 3518-3709 Sentence denotes The ΔG value, known as binding free energy, for the four molecules having the highest affinity among all the selected molecules, along with their 2D interaction diagram, is given in Figure 4.
T231 3710-3879 Sentence denotes The four molecules have followed the binding affinity trend as Piperine (−7.3 kcal/mol) > Capsaicin (−6.4 kcal/mol) > Carvone (−6.2 kcal/mol) > Gingerol (−6.1 kcal/mol).
T232 3880-4070 Sentence denotes From Figure 4(a), it is observed that the interaction of Piperine at the binding site of the SARS-CoV-2 Mpro is stabilized by hydrogen bonding, electrostatics and van der Waals interactions.
T233 4071-4275 Sentence denotes The residues GLN299 and VAL303 are associated with hydrogen bonding interaction; ASP295 and ARG298 with charged interactions while MET6 and PRO9 are associated with hydrophobic interactions with Piperine.
T234 4276-4440 Sentence denotes The molecule is also stabilized through van der Waals interactions with residues PHE8, GLY127, ILE152, PHE291 and THR304 at the binding site of the SARS-CoV-2 Mpro.
T235 4441-4565 Sentence denotes The molecule Capsaicin is stabilized in the binding pocket through van der Waals and hydrophobic interactions (Figure 4(b)).
T236 4566-4702 Sentence denotes The residues MET6, PHE8, PRO9 and ILE152 are interacting through hydrophobic interactions such as alkyl and pi–alkyl with the Capsaicin.
T237 4703-4862 Sentence denotes Capsaicin is interacting with residues ALA7, GLY11, LYS12, GLN127, TYR154, PHE291, ASP295, ARG298, GLN299, VAL303 and THR304 through van der Waals interaction.
T238 4863-4994 Sentence denotes The interaction of Carvone with the SARS-CoV-2 Mpro is stabilized through hydrophobic and van der Walls interactions (Figure 4(c)).
T239 4995-5101 Sentence denotes Carvone interacts with the residues MET6, PHE8 and ARG298 of SARS-CoV-2 Mpro through hydrophobic contacts.
T240 5102-5216 Sentence denotes The residues ALA7, PRO9, GLN127, ASP295, GLN299, GLY302 and VAL303 are in van der Waals interactions with Carvone.
T241 5217-5360 Sentence denotes Gingerol is stabilized by hydrogen bond, hydrophobic and van der Waals interactions in the binding pocket of the SARS-Cov-2 Mpro (Figure 4(d)).
T242 5361-5431 Sentence denotes VAL303 is interacting through hydrogen bond interaction with Gingerol.
T243 5432-5631 Sentence denotes The residues LYS12 and THR304 are involved in carbon-hydrogen bond interactions while MET6, ALA7, PHE8, GLN127, TYR154, ASP295 and ARG298 are associated with van der Waals interactions with Gingerol.
T244 5632-5738 Sentence denotes The interaction of Gingerol with the residues PRO9 and ILE152 is stabilized through pi–alkyl interactions.
T245 5739-5922 Sentence denotes The lowest energy binding poses of the rest 26 molecules along with the ligand interaction diagram at the binding sites of the SARS-CoV-2 Mpro are provided in Supplementary Figure S4.
T246 5923-5932 Sentence denotes Figure 4.
T247 5934-6075 Sentence denotes Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Carvone and (d) Gingerol with SARS-CoV-2 Mpro and their 2D interaction diagram.
T248 6076-6130 Sentence denotes The colour codes represent the nature of interactions.