> top > docs > PMC:7544943 > spans > 22807-28937 > annotations

PMC:7544943 / 22807-28937 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 2106-2110 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T27 97-104 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 2106-2110 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T51 56-64 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 293-301 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 1310-1318 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 1371-1379 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 1984-1988 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T56 2177-2185 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 3010-3018 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 3090-3098 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 3233-3241 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 3415-3423 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 3497-3505 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 3973-3981 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 4424-4432 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 4899-4907 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 5056-5064 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 5330-5334 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 5866-5874 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 6026-6034 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T113 146-147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 359-362 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T115 938-939 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 1486-1487 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 1683-1684 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T118 1916-1917 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 1930-1931 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T120 2388-2389 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 3367-3370 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T122 3894-3895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 4561-4562 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T124 4988-4992 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4(c)
T125 5964-5965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 5978-5979 http://purl.obolibrary.org/obo/CLO_0001021 denotes b

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
315 56-66 Species denotes SARS-CoV-2 Tax:2697049
368 293-303 Species denotes SARS-CoV-2 Tax:2697049
369 1310-1320 Species denotes SARS-CoV-2 Tax:2697049
370 1371-1381 Species denotes SARS-CoV-2 Tax:2697049
371 350-358 Chemical denotes Piperine MESH:C008922
372 473-481 Chemical denotes Piperine MESH:C008922
373 483-492 Chemical denotes Capsaicin MESH:D002211
374 494-502 Chemical denotes Gingerol MESH:C007845
375 507-520 Chemical denotes Terpinen-4-ol MESH:C034019
376 780-788 Chemical denotes Piperine MESH:C008922
377 826-835 Chemical denotes Capsaicin MESH:D002211
378 837-844 Chemical denotes Ginerol
379 849-862 Chemical denotes Terpinen-4-ol MESH:C034019
380 962-970 Chemical denotes Piperine MESH:C008922
381 990-998 Chemical denotes hydrogen MESH:D006859
382 1021-1027 Chemical denotes GLY164
383 1032-1038 Chemical denotes GLY170
384 1040-1046 Chemical denotes TYR173
385 1048-1054 Chemical denotes TYR505
386 1060-1066 Chemical denotes SER162
387 1068-1074 Chemical denotes SER494
388 1113-1119 Chemical denotes carbon MESH:D002244
389 1120-1128 Chemical denotes hydrogen MESH:D006859
390 1247-1252 Chemical denotes ARG71
391 1254-1260 Chemical denotes TYR121
392 1262-1268 Chemical denotes TYR453
393 1271-1277 Chemical denotes TYR163
394 1279-1285 Chemical denotes TYR495
395 1291-1297 Chemical denotes ASN169
396 1299-1305 Chemical denotes ASN501
397 1357-1365 Chemical denotes Piperine MESH:C008922
398 1417-1425 Chemical denotes hydrogen MESH:D006859
399 1509-1518 Chemical denotes Capsaicin MESH:D002211
400 1547-1553 Chemical denotes GLY164
401 1558-1564 Chemical denotes TYR173
402 1566-1572 Chemical denotes TYR505
403 1591-1599 Chemical denotes hydrogen MESH:D006859
404 1646-1653 Chemical denotes benzene MESH:D001554
405 1701-1706 Chemical denotes ARG71
406 1708-1714 Chemical denotes ARG403
407 1717-1722 Chemical denotes ASP73
408 1724-1729 Chemical denotes GLU74
409 1731-1736 Chemical denotes GLN77
410 1738-1743 Chemical denotes LYS85
411 1745-1751 Chemical denotes TYR121
412 1753-1759 Chemical denotes TYR453
413 1762-1768 Chemical denotes SER162
414 1770-1776 Chemical denotes SER494
415 1779-1785 Chemical denotes TYR163
416 1787-1793 Chemical denotes TYR495
417 1799-1805 Chemical denotes ASN169
418 1807-1813 Chemical denotes ASN501
419 1864-1873 Chemical denotes Capsaicin MESH:D002211
425 1984-1994 Species denotes SARS-Cov-2 Tax:2697049
426 1919-1927 Chemical denotes Piperine MESH:C008922
427 1933-1942 Chemical denotes Capsaicin MESH:D002211
428 1948-1956 Chemical denotes Gingerol MESH:C007845
429 1965-1978 Chemical denotes Terpinen-4-ol MESH:C034019
465 2177-2187 Species denotes SARS-CoV-2 Tax:2697049
466 2112-2120 Chemical denotes Gingerol MESH:C007845
467 2225-2231 Chemical denotes GLY164
468 2233-2239 Chemical denotes ASN169
469 2241-2247 Chemical denotes ASN501
470 2253-2259 Chemical denotes GLY170
471 2280-2288 Chemical denotes hydrogen MESH:D006859
472 2311-2319 Chemical denotes Gingerol MESH:C007845
473 2336-2344 Chemical denotes hydrogen MESH:D006859
474 2362-2368 Chemical denotes TYR173
475 2370-2376 Chemical denotes TYR505
476 2426-2433 Chemical denotes benzene MESH:D001554
477 2442-2450 Chemical denotes Gingerol MESH:C007845
478 2457-2462 Chemical denotes ARG71
479 2464-2470 Chemical denotes ARG403
480 2473-2479 Chemical denotes TYR121
481 2481-2487 Chemical denotes TYR453
482 2490-2496 Chemical denotes TYR163
483 2498-2504 Chemical denotes TYR495
484 2507-2513 Chemical denotes PHE165
485 2515-2521 Chemical denotes PHE497
486 2527-2533 Chemical denotes GLN166
487 2535-2541 Chemical denotes GLN498
488 2600-2613 Chemical denotes Terpinen-4-ol MESH:C034019
489 2673-2679 Chemical denotes ARG125
490 2681-2687 Chemical denotes LYS126
491 2689-2695 Chemical denotes TYR141
492 2700-2706 Chemical denotes PRO159
493 2726-2732 Chemical denotes ARG122
494 2734-2740 Chemical denotes PHE124
495 2742-2748 Chemical denotes ASP135
496 2750-2756 Chemical denotes SER137
497 2758-2764 Chemical denotes GLU139
498 2769-2775 Chemical denotes ILE140
499 2824-2837 Chemical denotes Terpinen-4-ol MESH:C034019
501 3010-3020 Species denotes SARS-CoV-2 Tax:2697049
590 5877-5881 Gene denotes Mpro Gene:8673700
591 5341-5345 Gene denotes Mpro Gene:8673700
592 5067-5071 Gene denotes Mpro Gene:8673700
593 4910-4914 Gene denotes Mpro Gene:8673700
594 4435-4439 Gene denotes Mpro Gene:8673700
595 3984-3988 Gene denotes Mpro Gene:8673700
596 3426-3430 Gene denotes Mpro Gene:8673700
597 3244-3248 Gene denotes Mpro Gene:8673700
598 3101-3105 Gene denotes Mpro Gene:8673700
599 3090-3100 Species denotes SARS-CoV-2 Tax:2697049
600 3233-3243 Species denotes SARS-CoV-2 Tax:2697049
601 3415-3425 Species denotes SARS-CoV-2 Tax:2697049
602 3497-3507 Species denotes SARS-CoV-2 Tax:2697049
603 3973-3983 Species denotes SARS-CoV-2 Tax:2697049
604 4424-4434 Species denotes SARS-CoV-2 Tax:2697049
605 4899-4909 Species denotes SARS-CoV-2 Tax:2697049
606 5056-5066 Species denotes SARS-CoV-2 Tax:2697049
607 5330-5340 Species denotes SARS-Cov-2 Tax:2697049
608 5866-5876 Species denotes SARS-CoV-2 Tax:2697049
609 3358-3366 Chemical denotes Piperine MESH:C008922
610 3773-3781 Chemical denotes Piperine MESH:C008922
611 3800-3809 Chemical denotes Capsaicin MESH:D002211
612 3828-3835 Chemical denotes Carvone MESH:C006923
613 3854-3862 Chemical denotes Gingerol MESH:C007845
614 3937-3945 Chemical denotes Piperine MESH:C008922
615 4006-4014 Chemical denotes hydrogen MESH:D006859
616 4084-4090 Chemical denotes GLN299
617 4095-4101 Chemical denotes VAL303
618 4122-4130 Chemical denotes hydrogen MESH:D006859
619 4152-4158 Chemical denotes ASP295
620 4163-4169 Chemical denotes ARG298
621 4202-4206 Chemical denotes MET6
622 4211-4215 Chemical denotes PRO9
623 4266-4274 Chemical denotes Piperine MESH:C008922
624 4357-4361 Chemical denotes PHE8
625 4363-4369 Chemical denotes GLY127
626 4371-4377 Chemical denotes ILE152
627 4379-4385 Chemical denotes PHE291
628 4390-4396 Chemical denotes THR304
629 4454-4463 Chemical denotes Capsaicin MESH:D002211
630 4579-4583 Chemical denotes MET6
631 4585-4589 Chemical denotes PHE8
632 4591-4595 Chemical denotes PRO9
633 4600-4606 Chemical denotes ILE152
634 4692-4701 Chemical denotes Capsaicin MESH:D002211
635 4703-4712 Chemical denotes Capsaicin MESH:D002211
636 4742-4746 Chemical denotes ALA7
637 4748-4753 Chemical denotes GLY11
638 4755-4760 Chemical denotes LYS12
639 4762-4768 Chemical denotes GLN127
640 4770-4776 Chemical denotes TYR154
641 4778-4784 Chemical denotes PHE291
642 4786-4792 Chemical denotes ASP295
643 4794-4800 Chemical denotes ARG298
644 4802-4808 Chemical denotes GLN299
645 4810-4816 Chemical denotes VAL303
646 4821-4827 Chemical denotes THR304
647 4882-4889 Chemical denotes Carvone MESH:C006923
648 4995-5002 Chemical denotes Carvone MESH:C006923
649 5037-5041 Chemical denotes PHE8
650 5046-5052 Chemical denotes ARG298
651 5115-5119 Chemical denotes ALA7
652 5121-5125 Chemical denotes PRO9
653 5127-5133 Chemical denotes GLN127
654 5135-5141 Chemical denotes ASP295
655 5143-5149 Chemical denotes GLN299
656 5151-5157 Chemical denotes GLY302
657 5162-5168 Chemical denotes VAL303
658 5208-5215 Chemical denotes Carvone MESH:C006923
659 5217-5225 Chemical denotes Gingerol MESH:C007845
660 5243-5251 Chemical denotes hydrogen MESH:D006859
661 5361-5367 Chemical denotes VAL303
662 5391-5399 Chemical denotes hydrogen MESH:D006859
663 5422-5430 Chemical denotes Gingerol MESH:C007845
664 5445-5450 Chemical denotes LYS12
665 5455-5461 Chemical denotes THR304
666 5478-5484 Chemical denotes carbon MESH:D002244
667 5485-5493 Chemical denotes hydrogen MESH:D006859
668 5524-5528 Chemical denotes ALA7
669 5530-5534 Chemical denotes PHE8
670 5536-5542 Chemical denotes GLN127
671 5544-5550 Chemical denotes TYR154
672 5552-5558 Chemical denotes ASP295
673 5563-5569 Chemical denotes ARG298
674 5622-5630 Chemical denotes Gingerol MESH:C007845
675 5651-5659 Chemical denotes Gingerol MESH:C007845
676 5678-5682 Chemical denotes PRO9
677 5687-5693 Chemical denotes ILE152
684 6037-6041 Gene denotes Mpro Gene:8673700
685 6026-6036 Species denotes SARS-CoV-2 Tax:2697049
686 5967-5975 Chemical denotes Piperine MESH:C008922
687 5981-5990 Chemical denotes Capsaicin MESH:D002211
688 5996-6003 Chemical denotes Carvone MESH:C006923
689 6012-6020 Chemical denotes Gingerol MESH:C007845

LitCovid-sentences

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.