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PMC:7544943 / 25842-28729 JSONTXT

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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T58 55-63 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 198-206 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 380-388 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 462-470 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 938-946 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 1389-1397 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 1864-1872 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 2021-2029 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 2295-2299 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 2831-2839 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T121 332-335 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T122 859-860 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1526-1527 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T124 1953-1957 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4(c)

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
590 2842-2846 Gene denotes Mpro Gene:8673700
591 2306-2310 Gene denotes Mpro Gene:8673700
592 2032-2036 Gene denotes Mpro Gene:8673700
593 1875-1879 Gene denotes Mpro Gene:8673700
594 1400-1404 Gene denotes Mpro Gene:8673700
595 949-953 Gene denotes Mpro Gene:8673700
596 391-395 Gene denotes Mpro Gene:8673700
597 209-213 Gene denotes Mpro Gene:8673700
598 66-70 Gene denotes Mpro Gene:8673700
599 55-65 Species denotes SARS-CoV-2 Tax:2697049
600 198-208 Species denotes SARS-CoV-2 Tax:2697049
601 380-390 Species denotes SARS-CoV-2 Tax:2697049
602 462-472 Species denotes SARS-CoV-2 Tax:2697049
603 938-948 Species denotes SARS-CoV-2 Tax:2697049
604 1389-1399 Species denotes SARS-CoV-2 Tax:2697049
605 1864-1874 Species denotes SARS-CoV-2 Tax:2697049
606 2021-2031 Species denotes SARS-CoV-2 Tax:2697049
607 2295-2305 Species denotes SARS-Cov-2 Tax:2697049
608 2831-2841 Species denotes SARS-CoV-2 Tax:2697049
609 323-331 Chemical denotes Piperine MESH:C008922
610 738-746 Chemical denotes Piperine MESH:C008922
611 765-774 Chemical denotes Capsaicin MESH:D002211
612 793-800 Chemical denotes Carvone MESH:C006923
613 819-827 Chemical denotes Gingerol MESH:C007845
614 902-910 Chemical denotes Piperine MESH:C008922
615 971-979 Chemical denotes hydrogen MESH:D006859
616 1049-1055 Chemical denotes GLN299
617 1060-1066 Chemical denotes VAL303
618 1087-1095 Chemical denotes hydrogen MESH:D006859
619 1117-1123 Chemical denotes ASP295
620 1128-1134 Chemical denotes ARG298
621 1167-1171 Chemical denotes MET6
622 1176-1180 Chemical denotes PRO9
623 1231-1239 Chemical denotes Piperine MESH:C008922
624 1322-1326 Chemical denotes PHE8
625 1328-1334 Chemical denotes GLY127
626 1336-1342 Chemical denotes ILE152
627 1344-1350 Chemical denotes PHE291
628 1355-1361 Chemical denotes THR304
629 1419-1428 Chemical denotes Capsaicin MESH:D002211
630 1544-1548 Chemical denotes MET6
631 1550-1554 Chemical denotes PHE8
632 1556-1560 Chemical denotes PRO9
633 1565-1571 Chemical denotes ILE152
634 1657-1666 Chemical denotes Capsaicin MESH:D002211
635 1668-1677 Chemical denotes Capsaicin MESH:D002211
636 1707-1711 Chemical denotes ALA7
637 1713-1718 Chemical denotes GLY11
638 1720-1725 Chemical denotes LYS12
639 1727-1733 Chemical denotes GLN127
640 1735-1741 Chemical denotes TYR154
641 1743-1749 Chemical denotes PHE291
642 1751-1757 Chemical denotes ASP295
643 1759-1765 Chemical denotes ARG298
644 1767-1773 Chemical denotes GLN299
645 1775-1781 Chemical denotes VAL303
646 1786-1792 Chemical denotes THR304
647 1847-1854 Chemical denotes Carvone MESH:C006923
648 1960-1967 Chemical denotes Carvone MESH:C006923
649 2002-2006 Chemical denotes PHE8
650 2011-2017 Chemical denotes ARG298
651 2080-2084 Chemical denotes ALA7
652 2086-2090 Chemical denotes PRO9
653 2092-2098 Chemical denotes GLN127
654 2100-2106 Chemical denotes ASP295
655 2108-2114 Chemical denotes GLN299
656 2116-2122 Chemical denotes GLY302
657 2127-2133 Chemical denotes VAL303
658 2173-2180 Chemical denotes Carvone MESH:C006923
659 2182-2190 Chemical denotes Gingerol MESH:C007845
660 2208-2216 Chemical denotes hydrogen MESH:D006859
661 2326-2332 Chemical denotes VAL303
662 2356-2364 Chemical denotes hydrogen MESH:D006859
663 2387-2395 Chemical denotes Gingerol MESH:C007845
664 2410-2415 Chemical denotes LYS12
665 2420-2426 Chemical denotes THR304
666 2443-2449 Chemical denotes carbon MESH:D002244
667 2450-2458 Chemical denotes hydrogen MESH:D006859
668 2489-2493 Chemical denotes ALA7
669 2495-2499 Chemical denotes PHE8
670 2501-2507 Chemical denotes GLN127
671 2509-2515 Chemical denotes TYR154
672 2517-2523 Chemical denotes ASP295
673 2528-2534 Chemical denotes ARG298
674 2587-2595 Chemical denotes Gingerol MESH:C007845
675 2616-2624 Chemical denotes Gingerol MESH:C007845
676 2643-2647 Chemical denotes PRO9
677 2652-2658 Chemical denotes ILE152

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T226 0-123 Sentence denotes The above-selected molecules were also docked with the SARS-CoV-2 Mpro to observe the inhibitory effect of these molecules.
T227 124-244 Sentence denotes The docking study reveals that all the molecules are interacting with the SARS-CoV-2 Mpro with certain binding affinity.
T228 245-292 Sentence denotes The docking data are also presented in Table 1.
T229 293-482 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 483-674 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 675-844 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 845-1035 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 1036-1240 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 1241-1405 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 1406-1530 Sentence denotes The molecule Capsaicin is stabilized in the binding pocket through van der Waals and hydrophobic interactions (Figure 4(b)).
T236 1531-1667 Sentence denotes The residues MET6, PHE8, PRO9 and ILE152 are interacting through hydrophobic interactions such as alkyl and pi–alkyl with the Capsaicin.
T237 1668-1827 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 1828-1959 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 1960-2066 Sentence denotes Carvone interacts with the residues MET6, PHE8 and ARG298 of SARS-CoV-2 Mpro through hydrophobic contacts.
T240 2067-2181 Sentence denotes The residues ALA7, PRO9, GLN127, ASP295, GLN299, GLY302 and VAL303 are in van der Waals interactions with Carvone.
T241 2182-2325 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 2326-2396 Sentence denotes VAL303 is interacting through hydrogen bond interaction with Gingerol.
T243 2397-2596 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 2597-2703 Sentence denotes The interaction of Gingerol with the residues PRO9 and ILE152 is stabilized through pi–alkyl interactions.
T245 2704-2887 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.