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PMC:7219429 / 20790-22690 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T121 237-244 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T122 275-287 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T123 405-417 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T124 453-460 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T125 550-562 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T126 575-590 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T127 837-844 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T128 857-868 Body_part denotes Ganglioside http://purl.org/sig/ont/fma/fma82816
T129 980-985 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T130 1030-1037 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T131 1069-1081 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T132 1130-1141 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T133 1174-1181 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T134 1212-1224 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T135 1339-1350 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T136 1521-1528 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T137 1565-1576 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T138 1672-1679 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T79 97-105 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 108-117 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T81 197-206 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T82 820-828 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 1013-1021 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 1157-1165 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 1504-1512 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 1655-1663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T204 148-153 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T205 522-527 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T206 575-581 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T207 582-590 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T208 663-664 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 800-801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T210 854-855 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T211 920-921 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T212 1305-1310 http://purl.obolibrary.org/obo/CLO_0050605 denotes (d) 4
T213 1337-1338 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T386 79-82 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T387 237-244 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T388 275-287 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T389 397-400 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T390 405-417 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T391 453-460 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T392 513-516 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T393 550-562 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T394 712-721 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T395 732-735 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T396 751-754 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T397 803-806 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T398 837-844 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T399 857-868 Chemical denotes Ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T400 903-906 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T403 907-916 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T404 980-985 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T405 1030-1037 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T406 1061-1064 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T407 1069-1081 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T408 1117-1120 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T409 1130-1141 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T410 1174-1181 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T411 1212-1224 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T412 1318-1327 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T413 1339-1350 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T414 1363-1366 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T417 1367-1375 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T418 1401-1410 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T419 1461-1471 Chemical denotes saccharide http://purl.obolibrary.org/obo/CHEBI_16646
T420 1521-1528 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T421 1546-1549 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T424 1565-1576 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T425 1672-1679 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T426 1697-1700 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T427 1823-1826 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T428 1831-1834 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T24 903-906 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T25 1363-1366 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T26 1546-1549 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T27 1831-1834 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T155 0-288 Sentence denotes Overall, these molecular modelling studies are consistent with the notion that ATM might inhibit SARS-CoV-2 infection through direct binding to the virus spike and subsequent neutralization of the infection process, which requires spike protein recognition and attachment to gangliosides.
T156 289-340 Sentence denotes This mechanism of action is illustrated in Fig. 8 .
T157 341-370 Sentence denotes Comparing the models in Figs.
T158 371-487 Sentence denotes 8a and 8b shows that both ATM and gangliosides bind to the same site of the spike protein, centred on the QFN triad.
T159 488-601 Sentence denotes Thus, in the presence of ATM, the virus spike would not reach gangliosides on the host plasma membrane (Fig. 8c).
T160 602-736 Sentence denotes To the best of our knowledge, it is the first time that such a mechanism of action is proposed to explain the antiviral effect of ATM.
T161 737-1045 Sentence denotes Fig. 8 CLQ-OH/ATM combination therapy at the molecular level. (a) ATM bound to the SARS-CoV-2 spike protein trimer. (b) Ganglioside dimer (two symmetrically arranged GM1 molecules in a typical chalice-like shape, just like the one observed in lipid raft simulations) bound to SARS-CoV-2 spike protein trimer.
T162 1046-1189 Sentence denotes Note that both ATM and gangliosides share the same binding region. (c) ATM prevents ganglioside binding to the SARS-CoV-2 spike protein trimer.
T163 1190-1357 Sentence denotes CLQ-OH, once bound to gangliosides (blue and orange surfaces), also prevents any interaction with the viral spike. (d) 4 CLQ-OH molecules bound to a ganglioside dimer.
T164 1358-1550 Sentence denotes Each GM1 molecule is blocked by two CLQ-OH molecules (blue and orange surfaces), which wrap around the saccharide part. (e) Detail of the 134-138 SARS-CoV-2 spike protein stretch bound to GM1.
T165 1551-1701 Sentence denotes Note that the ganglioside interacts with Q-134 and F-135, but not with D-138. (f) Detail of the 134-138 SARS-CoV-2 spike protein stretch bound to ATM.
T166 1702-1779 Sentence denotes In this case, the binding site includes D-138 in addition to Q-134 and F-135.
T167 1780-1900 Sentence denotes Note that N-137, which interacts with both ATM and GM1, is not visible in these representations as it is located behind.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
567 1666-1671 Gene denotes spike Gene:43740568
568 1515-1520 Gene denotes spike Gene:43740568
569 1298-1303 Gene denotes spike Gene:43740568
570 1168-1173 Gene denotes spike Gene:43740568
571 1024-1029 Gene denotes spike Gene:43740568
572 831-836 Gene denotes spike Gene:43740568
573 820-830 Species denotes SARS-CoV-2 Tax:2697049
574 1013-1023 Species denotes SARS-CoV-2 Tax:2697049
575 1157-1167 Species denotes SARS-CoV-2 Tax:2697049
576 1504-1514 Species denotes SARS-CoV-2 Tax:2697049
577 1655-1665 Species denotes SARS-CoV-2 Tax:2697049
578 744-750 Chemical denotes CLQ-OH
579 857-868 Chemical denotes Ganglioside MESH:D005732
580 903-906 Chemical denotes GM1 MESH:D005677
581 980-985 Chemical denotes lipid MESH:D008055
582 1069-1081 Chemical denotes gangliosides MESH:D005732
583 1130-1141 Chemical denotes ganglioside MESH:D005732
584 1190-1196 Chemical denotes CLQ-OH
585 1212-1224 Chemical denotes gangliosides MESH:D005732
586 1311-1317 Chemical denotes CLQ-OH
587 1339-1350 Chemical denotes ganglioside MESH:D005732
588 1363-1366 Chemical denotes GM1 MESH:D005677
589 1394-1400 Chemical denotes CLQ-OH
590 1546-1549 Chemical denotes GM1 MESH:D005677
591 1565-1576 Chemical denotes ganglioside MESH:D005732
592 1742-1747 Chemical denotes D-138
593 1763-1768 Chemical denotes Q-134
594 1790-1795 Chemical denotes N-137 MESH:C022084
595 1831-1834 Chemical denotes GM1 MESH:D005677
605 447-452 Gene denotes spike Gene:43740568
606 528-533 Gene denotes spike Gene:43740568
607 154-159 Gene denotes spike Gene:43740568
608 231-236 Gene denotes spike Gene:43740568
609 275-287 Chemical denotes gangliosides MESH:D005732
610 405-417 Chemical denotes gangliosides MESH:D005732
611 550-562 Chemical denotes gangliosides MESH:D005732
612 97-117 Disease denotes SARS-CoV-2 infection MESH:C000657245
613 197-206 Disease denotes infection MESH:D007239