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PMC:7544943 / 25792-28937 JSONTXT

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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T57 25-33 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 105-113 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 248-256 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 430-438 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 512-520 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 988-996 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 1439-1447 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 1914-1922 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 2071-2079 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 2345-2349 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 2881-2889 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 3041-3049 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T121 382-385 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T122 909-910 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1576-1577 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T124 2003-2007 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4(c)
T125 2979-2980 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 2993-2994 http://purl.obolibrary.org/obo/CLO_0001021 denotes b

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
501 25-35 Species denotes SARS-CoV-2 Tax:2697049
590 2892-2896 Gene denotes Mpro Gene:8673700
591 2356-2360 Gene denotes Mpro Gene:8673700
592 2082-2086 Gene denotes Mpro Gene:8673700
593 1925-1929 Gene denotes Mpro Gene:8673700
594 1450-1454 Gene denotes Mpro Gene:8673700
595 999-1003 Gene denotes Mpro Gene:8673700
596 441-445 Gene denotes Mpro Gene:8673700
597 259-263 Gene denotes Mpro Gene:8673700
598 116-120 Gene denotes Mpro Gene:8673700
599 105-115 Species denotes SARS-CoV-2 Tax:2697049
600 248-258 Species denotes SARS-CoV-2 Tax:2697049
601 430-440 Species denotes SARS-CoV-2 Tax:2697049
602 512-522 Species denotes SARS-CoV-2 Tax:2697049
603 988-998 Species denotes SARS-CoV-2 Tax:2697049
604 1439-1449 Species denotes SARS-CoV-2 Tax:2697049
605 1914-1924 Species denotes SARS-CoV-2 Tax:2697049
606 2071-2081 Species denotes SARS-CoV-2 Tax:2697049
607 2345-2355 Species denotes SARS-Cov-2 Tax:2697049
608 2881-2891 Species denotes SARS-CoV-2 Tax:2697049
609 373-381 Chemical denotes Piperine MESH:C008922
610 788-796 Chemical denotes Piperine MESH:C008922
611 815-824 Chemical denotes Capsaicin MESH:D002211
612 843-850 Chemical denotes Carvone MESH:C006923
613 869-877 Chemical denotes Gingerol MESH:C007845
614 952-960 Chemical denotes Piperine MESH:C008922
615 1021-1029 Chemical denotes hydrogen MESH:D006859
616 1099-1105 Chemical denotes GLN299
617 1110-1116 Chemical denotes VAL303
618 1137-1145 Chemical denotes hydrogen MESH:D006859
619 1167-1173 Chemical denotes ASP295
620 1178-1184 Chemical denotes ARG298
621 1217-1221 Chemical denotes MET6
622 1226-1230 Chemical denotes PRO9
623 1281-1289 Chemical denotes Piperine MESH:C008922
624 1372-1376 Chemical denotes PHE8
625 1378-1384 Chemical denotes GLY127
626 1386-1392 Chemical denotes ILE152
627 1394-1400 Chemical denotes PHE291
628 1405-1411 Chemical denotes THR304
629 1469-1478 Chemical denotes Capsaicin MESH:D002211
630 1594-1598 Chemical denotes MET6
631 1600-1604 Chemical denotes PHE8
632 1606-1610 Chemical denotes PRO9
633 1615-1621 Chemical denotes ILE152
634 1707-1716 Chemical denotes Capsaicin MESH:D002211
635 1718-1727 Chemical denotes Capsaicin MESH:D002211
636 1757-1761 Chemical denotes ALA7
637 1763-1768 Chemical denotes GLY11
638 1770-1775 Chemical denotes LYS12
639 1777-1783 Chemical denotes GLN127
640 1785-1791 Chemical denotes TYR154
641 1793-1799 Chemical denotes PHE291
642 1801-1807 Chemical denotes ASP295
643 1809-1815 Chemical denotes ARG298
644 1817-1823 Chemical denotes GLN299
645 1825-1831 Chemical denotes VAL303
646 1836-1842 Chemical denotes THR304
647 1897-1904 Chemical denotes Carvone MESH:C006923
648 2010-2017 Chemical denotes Carvone MESH:C006923
649 2052-2056 Chemical denotes PHE8
650 2061-2067 Chemical denotes ARG298
651 2130-2134 Chemical denotes ALA7
652 2136-2140 Chemical denotes PRO9
653 2142-2148 Chemical denotes GLN127
654 2150-2156 Chemical denotes ASP295
655 2158-2164 Chemical denotes GLN299
656 2166-2172 Chemical denotes GLY302
657 2177-2183 Chemical denotes VAL303
658 2223-2230 Chemical denotes Carvone MESH:C006923
659 2232-2240 Chemical denotes Gingerol MESH:C007845
660 2258-2266 Chemical denotes hydrogen MESH:D006859
661 2376-2382 Chemical denotes VAL303
662 2406-2414 Chemical denotes hydrogen MESH:D006859
663 2437-2445 Chemical denotes Gingerol MESH:C007845
664 2460-2465 Chemical denotes LYS12
665 2470-2476 Chemical denotes THR304
666 2493-2499 Chemical denotes carbon MESH:D002244
667 2500-2508 Chemical denotes hydrogen MESH:D006859
668 2539-2543 Chemical denotes ALA7
669 2545-2549 Chemical denotes PHE8
670 2551-2557 Chemical denotes GLN127
671 2559-2565 Chemical denotes TYR154
672 2567-2573 Chemical denotes ASP295
673 2578-2584 Chemical denotes ARG298
674 2637-2645 Chemical denotes Gingerol MESH:C007845
675 2666-2674 Chemical denotes Gingerol MESH:C007845
676 2693-2697 Chemical denotes PRO9
677 2702-2708 Chemical denotes ILE152
684 3052-3056 Gene denotes Mpro Gene:8673700
685 3041-3051 Species denotes SARS-CoV-2 Tax:2697049
686 2982-2990 Chemical denotes Piperine MESH:C008922
687 2996-3005 Chemical denotes Capsaicin MESH:D002211
688 3011-3018 Chemical denotes Carvone MESH:C006923
689 3027-3035 Chemical denotes Gingerol MESH:C007845

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T224 0-6 Sentence denotes 3.5.2.
T225 8-49 Sentence denotes Docking study of SARS-CoV-2 main protease
T226 50-173 Sentence denotes The above-selected molecules were also docked with the SARS-CoV-2 Mpro to observe the inhibitory effect of these molecules.
T227 174-294 Sentence denotes The docking study reveals that all the molecules are interacting with the SARS-CoV-2 Mpro with certain binding affinity.
T228 295-342 Sentence denotes The docking data are also presented in Table 1.
T229 343-532 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 533-724 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 725-894 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 895-1085 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 1086-1290 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 1291-1455 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 1456-1580 Sentence denotes The molecule Capsaicin is stabilized in the binding pocket through van der Waals and hydrophobic interactions (Figure 4(b)).
T236 1581-1717 Sentence denotes The residues MET6, PHE8, PRO9 and ILE152 are interacting through hydrophobic interactions such as alkyl and pi–alkyl with the Capsaicin.
T237 1718-1877 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 1878-2009 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 2010-2116 Sentence denotes Carvone interacts with the residues MET6, PHE8 and ARG298 of SARS-CoV-2 Mpro through hydrophobic contacts.
T240 2117-2231 Sentence denotes The residues ALA7, PRO9, GLN127, ASP295, GLN299, GLY302 and VAL303 are in van der Waals interactions with Carvone.
T241 2232-2375 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 2376-2446 Sentence denotes VAL303 is interacting through hydrogen bond interaction with Gingerol.
T243 2447-2646 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 2647-2753 Sentence denotes The interaction of Gingerol with the residues PRO9 and ILE152 is stabilized through pi–alkyl interactions.
T245 2754-2937 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 2938-2947 Sentence denotes Figure 4.
T247 2949-3090 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 3091-3145 Sentence denotes The colour codes represent the nature of interactions.