PMC:7128678 / 4626-6517
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 144 | 939-940 | Gene | denotes | S | Gene:43740568 |
| 145 | 928-938 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 146 | 156-159 | Chemical | denotes | GM1 | MESH:D005677 |
| 147 | 498-501 | Chemical | denotes | GM1 | MESH:D005677 |
| 148 | 557-565 | Chemical | denotes | ceramide | MESH:D002518 |
| 149 | 594-605 | Chemical | denotes | ganglioside | MESH:D005732 |
| 150 | 656-661 | Chemical | denotes | water | MESH:D014867 |
| 151 | 869-880 | Chemical | denotes | ganglioside | MESH:D005732 |
| 152 | 1219-1232 | Chemical | denotes | carbohydrates | MESH:D002241 |
| 153 | 322-346 | Disease | denotes | glycosidic torsion angle | MESH:C563601 |
| 164 | 1358-1381 | Chemical | denotes | N-acetylneuraminic acid | MESH:D019158 |
| 165 | 1383-1389 | Chemical | denotes | Neu5Ac | |
| 166 | 1434-1468 | Chemical | denotes | 9-O-acetyl-N-acetylneuraminic acid | MESH:C025676 |
| 167 | 1470-1477 | Chemical | denotes | 9-O-SIA | |
| 168 | 1525-1582 | Chemical | denotes | N-(7-chloroquinolin-4-yl)-N,N-diéthyl-pentane-1,4-diamine | |
| 169 | 1657-1663 | Chemical | denotes | CLQ-OH | |
| 170 | 1667-1735 | Chemical | denotes | (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol | |
| 171 | 1737-1743 | Chemical | denotes | CLQ-OH | |
| 172 | 1811-1817 | Chemical | denotes | CLQ-OH | |
| 173 | 1856-1861 | Chemical | denotes | water | MESH:D014867 |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T109 | 190-200 | CHEBI:33563;CHEBI:33563 | denotes | Glycolipid |
| T110 | 236-239 | CHEBI:50845;CHEBI:50845 | denotes | doc |
| T111 | 246-256 | CHEBI:33563;CHEBI:33563 | denotes | glycolipid |
| T112 | 322-332 | CHEBI:24400;CHEBI:24400 | denotes | glycosidic |
| T113 | 367-378 | CHEBI:16856;CHEBI:16856 | denotes | ganglioside |
| T114 | 400-408 | GO:0016020 | denotes | membrane |
| T115 | 502-510 | CHEBI:36357;CHEBI:36357 | denotes | molecule |
| T116 | 539-547 | GO:0016020 | denotes | membrane |
| T117 | 594-605 | CHEBI:5386;CHEBI:5386 | denotes | ganglioside |
| T118 | 656-661 | CHEBI:15377;CHEBI:15377 | denotes | water |
| T119 | 662-671 | CHEBI:36357;CHEBI:36357 | denotes | molecules |
| T120 | 869-880 | CHEBI:5386;CHEBI:5386 | denotes | ganglioside |
| T121 | 918-924 | SO:0000417 | denotes | domain |
| T122 | 928-938 | SP_7 | denotes | SARS-CoV-2 |
| T123 | 939-940 | PR:000005292;PG_1 | denotes | S |
| T124 | 941-948 | PG_1 | denotes | protein |
| T125 | 1094-1103 | GO:0032991 | denotes | complexes |
| T126 | 1219-1232 | CHEBI:16646;CHEBI:16646 | denotes | carbohydrates |
| T127 | 1288-1297 | GO:0032991 | denotes | complexes |
| T128 | 1358-1381 | CHEBI:17012;CHEBI:17012 | denotes | N-acetylneuraminic acid |
| T129 | 1383-1389 | PR:000002082 | denotes | Neu5Ac |
| T130 | 1434-1435 | CHEBI:17865;CHEBI:17865 | denotes | 9 |
| T131 | 1435-1438 | CHEBI:16066;CHEBI:16066 | denotes | -O- |
| T132 | 1438-1444 | CHEBI:40574;CHEBI:40574 | denotes | acetyl |
| T133 | 1445-1468 | CHEBI:17012;CHEBI:17012 | denotes | N-acetylneuraminic acid |
| T134 | 1528-1529 | CHEBI:17759;CHEBI:17759 | denotes | 7 |
| T135 | 1530-1544 | CHEBI:52029;CHEBI:52029 | denotes | chloroquinolin |
| T136 | 1545-1546 | CHEBI:75508;CHEBI:75508 | denotes | 4 |
| T137 | 1563-1570 | CHEBI:37830;CHEBI:37830 | denotes | pentane |
| T138 | 1571-1573 | CHEBI:52029;CHEBI:52029 | denotes | 1, |
| T139 | 1573-1574 | CHEBI:53233;CHEBI:53233 | denotes | 4 |
| T140 | 1575-1582 | CHEBI:23666;CHEBI:23666 | denotes | diamine |
| T141 | 1672-1714 | CHEBI:5801;CHEBI:5801 | denotes | 2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl |
| T142 | 1716-1721 | CHEBI:5801;CHEBI:5801 | denotes | ethyl |
| T143 | 1728-1735 | CHEBI:5801;CHEBI:5801 | denotes | ethanol |
| T144 | 1856-1861 | CHEBI:15377;CHEBI:15377 | denotes | water |
| T145 | 1862-1871 | CHEBI:36357;CHEBI:36357 | denotes | molecules |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T28 | 190-200 | Body_part | denotes | Glycolipid | http://purl.org/sig/ont/fma/fma82780 |
| T29 | 246-256 | Body_part | denotes | glycolipid | http://purl.org/sig/ont/fma/fma82780 |
| T30 | 367-378 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T31 | 594-605 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T32 | 869-880 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T33 | 941-948 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T34 | 1219-1232 | Body_part | denotes | carbohydrates | http://purl.org/sig/ont/fma/fma82737 |
| T35 | 1358-1381 | Body_part | denotes | N-acetylneuraminic acid | http://purl.org/sig/ont/fma/fma82788 |
| T36 | 1445-1468 | Body_part | denotes | N-acetylneuraminic acid | http://purl.org/sig/ont/fma/fma82788 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T23 | 914-917 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T25 | 928-936 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T26 | 1668-1670 | Disease | denotes | RS | http://purl.obolibrary.org/obo/MONDO_0010725 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T32 | 400-408 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T33 | 446-447 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T34 | 539-547 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T35 | 622-623 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T36 | 1199-1204 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T37 | 1513-1515 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T38 | 1668-1670 | http://purl.obolibrary.org/obo/CLO_0008882 | denotes | RS |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T51 | 156-159 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T54 | 190-200 | Chemical | denotes | Glycolipid | http://purl.obolibrary.org/obo/CHEBI_33563 |
| T55 | 246-256 | Chemical | denotes | glycolipid | http://purl.obolibrary.org/obo/CHEBI_33563 |
| T56 | 367-378 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T57 | 498-501 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T60 | 502-510 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T61 | 557-565 | Chemical | denotes | ceramide | http://purl.obolibrary.org/obo/CHEBI_17761|http://purl.obolibrary.org/obo/CHEBI_52639 |
| T63 | 594-605 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T64 | 656-661 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T65 | 662-671 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T66 | 869-880 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T67 | 941-948 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T68 | 1219-1232 | Chemical | denotes | carbohydrates | http://purl.obolibrary.org/obo/CHEBI_16646 |
| T69 | 1358-1381 | Chemical | denotes | N-acetylneuraminic acid | http://purl.obolibrary.org/obo/CHEBI_17012 |
| T70 | 1377-1381 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T71 | 1383-1389 | Chemical | denotes | Neu5Ac | http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133 |
| T73 | 1438-1444 | Chemical | denotes | acetyl | http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887 |
| T75 | 1445-1468 | Chemical | denotes | N-acetylneuraminic acid | http://purl.obolibrary.org/obo/CHEBI_17012 |
| T76 | 1464-1468 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T77 | 1563-1570 | Chemical | denotes | pentane | http://purl.obolibrary.org/obo/CHEBI_37830 |
| T78 | 1575-1582 | Chemical | denotes | diamine | http://purl.obolibrary.org/obo/CHEBI_15571|http://purl.obolibrary.org/obo/CHEBI_23666 |
| T80 | 1668-1670 | Chemical | denotes | RS | http://purl.obolibrary.org/obo/CHEBI_73819 |
| T81 | 1702-1707 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T82 | 1708-1714 | Chemical | denotes | pentyl | http://purl.obolibrary.org/obo/CHEBI_25902 |
| T83 | 1716-1721 | Chemical | denotes | ethyl | http://purl.obolibrary.org/obo/CHEBI_37807|http://purl.obolibrary.org/obo/CHEBI_62801 |
| T85 | 1722-1727 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T86 | 1728-1735 | Chemical | denotes | ethanol | http://purl.obolibrary.org/obo/CHEBI_16236 |
| T87 | 1856-1861 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T88 | 1862-1871 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 156-159 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T2 | 498-501 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T33 | 0-24 | Sentence | denotes | 2 Materials and methods |
| T34 | 25-128 | Sentence | denotes | In-silico analyses were performed using Hyperchem and Molegro Molecular viewer as described [11,13,14]. |
| T35 | 129-571 | Sentence | denotes | The initial coordinates of GM1 were obtained from CHARMM-GUI Glycolipid Modeler (http://www.charmmgui.org/?doc=input/glycolipid; [15]), which uses the internal coordinate information of common glycosidic torsion angle values, orients the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, especially the membrane-embedded ceramide part. |
| T36 | 572-672 | Sentence | denotes | In the next step, the ganglioside was included in a periodic box solvated with 1128 water molecules. |
| T37 | 673-864 | Sentence | denotes | The system was energy-minimized six times, switching between runs using the steepest descent gradients and runs using Polak–Ribière conjugate gradients until convergence to machine precision. |
| T38 | 865-987 | Sentence | denotes | The ganglioside was subsequently merged with the NTD domain of SARS-CoV-2 S protein as obtained from pdb file # 6VSB [16]. |
| T39 | 988-1086 | Sentence | denotes | Initial conditions corresponded to minimized structures obtained with the Polak–Ribière algorithm. |
| T40 | 1087-1238 | Sentence | denotes | Docked complexes were subsequently submitted to iterative cycles of molecular dynamics using the CHARMM36 force field optimized for carbohydrates [17]. |
| T41 | 1239-1357 | Sentence | denotes | Interaction energies were calculated from stable complexes using the Ligand Energy Inspector function of Molegro [13]. |
| T42 | 1358-1433 | Sentence | denotes | N-acetylneuraminic acid (Neu5Ac) was generated with the Hyperchem database. |
| T43 | 1434-1517 | Sentence | denotes | 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) was retrieved from pdb file 6Q06 [18]. |
| T44 | 1518-1583 | Sentence | denotes | CLQ is N-(7-chloroquinolin-4-yl)-N,N-diéthyl-pentane-1,4-diamine. |
| T45 | 1584-1656 | Sentence | denotes | Its three-dimensioanl structure was retrieved from pdb file # 4V2O [19]. |
| T46 | 1657-1736 | Sentence | denotes | CLQ-OH is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. |
| T47 | 1737-1797 | Sentence | denotes | CLQ-OH was generated by hydroxylation of CLQ with Hyperchem. |
| T48 | 1798-1891 | Sentence | denotes | Both CLQ and CLQ-OH were energy-minimized and merged with water molecules as described below. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32251731-28205163-48149944 | 118-120 | 28205163 | denotes | 11 |
| 32251731-31431523-48149945 | 121-123 | 31431523 | denotes | 13 |
| 32251731-30525595-48149946 | 259-261 | 30525595 | denotes | 15 |
| 32251731-32075877-48149947 | 983-985 | 32075877 | denotes | 16 |
| 32251731-18470966-48149948 | 1234-1236 | 18470966 | denotes | 17 |
| 32251731-31431523-48149949 | 1353-1355 | 31431523 | denotes | 13 |
| 32251731-31792450-48149950 | 1513-1515 | 31792450 | denotes | 18 |
| 32251731-26616259-48149951 | 1652-1654 | 26616259 | denotes | 19 |
| T2815 | 118-120 | 28205163 | denotes | 11 |
| T62925 | 121-123 | 31431523 | denotes | 13 |
| T49162 | 259-261 | 30525595 | denotes | 15 |
| T59670 | 983-985 | 32075877 | denotes | 16 |
| T52855 | 1234-1236 | 18470966 | denotes | 17 |
| T31878 | 1353-1355 | 31431523 | denotes | 13 |
| T55524 | 1513-1515 | 31792450 | denotes | 18 |
| T86226 | 1652-1654 | 26616259 | denotes | 19 |