PMC:7219429 / 22691-25140
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T139 | 332-343 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T140 | 634-645 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T141 | 687-698 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T142 | 809-820 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T143 | 914-929 | Body_part | denotes | plasma membrane | http://purl.org/sig/ont/fma/fma63841 |
| T144 | 938-943 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T145 | 1100-1107 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T146 | 1164-1175 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T147 | 1279-1283 | Body_part | denotes | head | http://purl.org/sig/ont/fma/fma7154 |
| T148 | 1411-1418 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T149 | 1481-1496 | Body_part | denotes | protein complex | http://purl.org/sig/ont/fma/fma67906 |
| T150 | 1573-1580 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T151 | 1898-1905 | Body_part | denotes | alanine | http://purl.org/sig/ont/fma/fma82749 |
| T152 | 2161-2166 | Body_part | denotes | lipid | http://purl.org/sig/ont/fma/fma67264 |
| T153 | 2331-2342 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T154 | 2435-2448 | Body_part | denotes | cell membrane | http://purl.org/sig/ont/fma/fma63841 |
| T155 | 2435-2439 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T14 | 1279-1283 | Body_part | denotes | head | http://purl.obolibrary.org/obo/UBERON_0000033 |
| T15 | 2238-2242 | Body_part | denotes | wing | http://purl.obolibrary.org/obo/UBERON_0000023 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T87 | 2401-2409 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T214 | 85-86 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T215 | 104-105 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T216 | 303-304 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T217 | 330-331 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T218 | 479-480 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T219 | 803-808 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T220 | 900-905 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T221 | 914-920 | http://purl.obolibrary.org/obo/UBERON_0001969 | denotes | plasma |
| T222 | 921-929 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T223 | 938-943 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T224 | 1063-1065 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
| T225 | 1088-1093 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T226 | 1226-1227 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T227 | 1279-1283 | http://purl.obolibrary.org/obo/UBERON_0000033 | denotes | head |
| T228 | 1279-1283 | http://www.ebi.ac.uk/efo/EFO_0000964 | denotes | head |
| T229 | 1399-1404 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T230 | 1461-1462 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T231 | 1481-1496 | http://purl.obolibrary.org/obo/GO_0043234 | denotes | protein complex |
| T232 | 1736-1738 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
| T233 | 2180-2185 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T234 | 2261-2266 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T235 | 2435-2439 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T236 | 2440-2448 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T431 | 58-61 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T434 | 128-131 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T437 | 147-156 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T438 | 226-229 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T439 | 267-273 | Chemical | denotes | lipids | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T440 | 332-343 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T441 | 397-406 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T442 | 505-514 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T443 | 577-587 | Chemical | denotes | saccharide | http://purl.obolibrary.org/obo/CHEBI_16646 |
| T444 | 596-599 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T447 | 634-645 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T448 | 687-698 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T449 | 787-790 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T450 | 809-820 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T451 | 987-996 | Chemical | denotes | antiviral | http://purl.obolibrary.org/obo/CHEBI_22587 |
| T452 | 1100-1107 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T453 | 1164-1175 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T454 | 1362-1365 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T455 | 1411-1418 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T456 | 1481-1488 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T457 | 1510-1513 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T460 | 1546-1549 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T461 | 1573-1580 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T462 | 1597-1600 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T463 | 1656-1659 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T466 | 1898-1905 | Chemical | denotes | alanine | http://purl.obolibrary.org/obo/CHEBI_16449 |
| T467 | 1938-1941 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T468 | 2060-2063 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T469 | 2161-2166 | Chemical | denotes | lipid | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T470 | 2219-2222 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T473 | 2244-2247 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T474 | 2331-2342 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T475 | 2362-2367 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T476 | 2387-2397 | Chemical | denotes | inhibitors | http://purl.obolibrary.org/obo/CHEBI_35222 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T28 | 58-61 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T29 | 128-131 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T30 | 596-599 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T31 | 1510-1513 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T32 | 1656-1659 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T33 | 2219-2222 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T168 | 0-62 | Sentence | denotes | This study also looked at CLQ-OH and its interaction with GM1. |
| T169 | 63-162 | Sentence | denotes | We recently published a model describing a complex formed by one GM1 and two CLQ-OH molecules [10]. |
| T170 | 163-302 | Sentence | denotes | For comparison, the same molecular modelling approaches as for ATM (in the presence of surrounding raft lipids) were applied to this model. |
| T171 | 303-431 | Sentence | denotes | A stable complex formed by a ganglioside dimer, each monomer being associated with two CLQ-OH molecules, was obtained (Fig. 8d). |
| T172 | 432-600 | Sentence | denotes | The stability of this complex is reinforced by a rearrangement of CLQ-OH molecules that interact with each other as well as interacting with the saccharide part of GM1. |
| T173 | 601-762 | Sentence | denotes | Consequently, the surface of the ganglioside is almost completely masked, so that the ganglioside dimer can no longer be recognized by the viral spike (Fig. 8c). |
| T174 | 763-944 | Sentence | denotes | In the presence of both ATM and CLQ-OH, virus-ganglioside interactions are efficiently blocked, preventing any close contact between the virus and the plasma membrane of host cells. |
| T175 | 945-1025 | Sentence | denotes | The molecular details of this synergistic antiviral effect are worth mentioning. |
| T176 | 1026-1043 | Sentence | denotes | As shown in Figs. |
| T177 | 1044-1182 | Sentence | denotes | 5 and 8e and Table S1, the QFN triad of the virus spike protein is predicted to interact with the central region of the ganglioside dimer. |
| T178 | 1183-1302 | Sentence | denotes | If the dimer is compared metaphorically to a butterfly, this region corresponds to the insect's head between the wings. |
| T179 | 1303-1429 | Sentence | denotes | For its part, CLQ-OH binds to the wings (Fig. 8d), whereas ATM neutralizes the QFN triad of the virus spike protein (Fig. 8f). |
| T180 | 1430-1581 | Sentence | denotes | Indeed, all attempts to obtain a stable raft-spike protein complex aborted when GM1 was covered by CLMQ-OH and when ATM was bound to the spike protein. |
| T181 | 1582-1838 | Sentence | denotes | In the case of ATM, these data confirm that the QFN triad is critical for GM1 recognition and that although other residues are involved (Fig. 5 and Table S1), the whole binding process is fully controlled by the primary interaction driven by the QFN triad. |
| T182 | 1839-1984 | Sentence | denotes | In agreement with this notion, mutating the QFN triad with alanine residues resulted in an aborted ATM binding process at the post-docking steps. |
| T183 | 1985-2349 | Sentence | denotes | Taken together, these molecular modelling studies indicate that CLQ-OH and ATM, when bound to their respective targets, totally mask the complementary surfaces provided by the lipid raft and the virus spike (Fig. 8c): CLQ-OH binds to GM1 and covers the wing, ATM binds to the virus spike and prevents any interaction with the central area of the ganglioside dimer. |
| T184 | 2350-2449 | Sentence | denotes | Hence, both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 647 | 1094-1099 | Gene | denotes | spike | Gene:43740568 |
| 648 | 1405-1410 | Gene | denotes | spike | Gene:43740568 |
| 649 | 1567-1572 | Gene | denotes | spike | Gene:43740568 |
| 650 | 2267-2272 | Gene | denotes | spike | Gene:43740568 |
| 651 | 2186-2191 | Gene | denotes | spike | Gene:43740568 |
| 652 | 1475-1480 | Gene | denotes | spike | Gene:43740568 |
| 653 | 746-751 | Gene | denotes | spike | Gene:43740568 |
| 654 | 2401-2411 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 655 | 26-32 | Chemical | denotes | CLQ-OH | |
| 656 | 58-61 | Chemical | denotes | GM1 | MESH:D005677 |
| 657 | 128-131 | Chemical | denotes | GM1 | MESH:D005677 |
| 658 | 140-146 | Chemical | denotes | CLQ-OH | |
| 659 | 267-273 | Chemical | denotes | lipids | MESH:D008055 |
| 660 | 332-343 | Chemical | denotes | ganglioside | MESH:D005732 |
| 661 | 390-396 | Chemical | denotes | CLQ-OH | |
| 662 | 498-504 | Chemical | denotes | CLQ-OH | |
| 663 | 596-599 | Chemical | denotes | GM1 | MESH:D005677 |
| 664 | 634-645 | Chemical | denotes | ganglioside | MESH:D005732 |
| 665 | 687-698 | Chemical | denotes | ganglioside | MESH:D005732 |
| 666 | 795-801 | Chemical | denotes | CLQ-OH | |
| 667 | 809-820 | Chemical | denotes | ganglioside | MESH:D005732 |
| 668 | 1164-1175 | Chemical | denotes | ganglioside | MESH:D005732 |
| 669 | 1317-1323 | Chemical | denotes | CLQ-OH | |
| 670 | 1510-1513 | Chemical | denotes | GM1 | MESH:D005677 |
| 671 | 1529-1536 | Chemical | denotes | CLMQ-OH | |
| 672 | 1630-1633 | Chemical | denotes | QFN | |
| 673 | 1656-1659 | Chemical | denotes | GM1 | MESH:D005677 |
| 674 | 1898-1905 | Chemical | denotes | alanine | MESH:D000409 |
| 675 | 2049-2055 | Chemical | denotes | CLQ-OH | |
| 676 | 2161-2166 | Chemical | denotes | lipid | MESH:D008055 |
| 677 | 2203-2209 | Chemical | denotes | CLQ-OH | |
| 678 | 2219-2222 | Chemical | denotes | GM1 | MESH:D005677 |
| 679 | 2331-2342 | Chemical | denotes | ganglioside | MESH:D005732 |