PMC:7219429 / 629-2409
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T5 | 516-531 | Body_part | denotes | plasma membrane | http://purl.org/sig/ont/fma/fma63841 |
| T6 | 540-545 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T7 | 608-613 | Body_part | denotes | sugar | http://purl.org/sig/ont/fma/fma82737 |
| T8 | 631-636 | Body_part | denotes | lipid | http://purl.org/sig/ont/fma/fma67264 |
| T9 | 642-653 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T10 | 760-771 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T11 | 807-814 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T12 | 877-887 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T13 | 944-951 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T14 | 1018-1030 | Body_part | denotes | gangliosides | http://purl.org/sig/ont/fma/fma82816 |
| T15 | 1358-1371 | Body_part | denotes | cell membrane | http://purl.org/sig/ont/fma/fma63841 |
| T16 | 1358-1362 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T17 | 1438-1453 | Body_part | denotes | plasma membrane | http://purl.org/sig/ont/fma/fma63841 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T1 | 927-930 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T2 | 998-1014 | Body_part | denotes | attachment sites | http://purl.obolibrary.org/obo/UBERON_4200047 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T6 | 17-33 | Disease | denotes | SARS-coronavirus | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T7 | 37-45 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T8 | 125-133 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T9 | 250-258 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T10 | 790-798 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T11 | 1324-1332 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T12 | 1635-1643 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T6 | 49-52 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T7 | 60-61 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T8 | 222-228 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T9 | 397-399 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T10 | 502-507 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T11 | 516-522 | http://purl.obolibrary.org/obo/UBERON_0001969 | denotes | plasma |
| T12 | 523-531 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T13 | 540-545 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T14 | 629-630 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T15 | 664-665 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T16 | 707-714 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T17 | 865-866 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T18 | 992-997 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T19 | 1190-1195 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T20 | 1358-1362 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T21 | 1363-1371 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T22 | 1397-1398 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T23 | 1438-1444 | http://purl.obolibrary.org/obo/UBERON_0001969 | denotes | plasma |
| T24 | 1445-1453 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T25 | 1748-1749 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T11 | 164-176 | Chemical | denotes | azithromycin | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T12 | 178-181 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T13 | 397-399 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T14 | 440-445 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T15 | 596-599 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T16 | 624-627 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T19 | 631-636 | Chemical | denotes | lipid | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T20 | 642-653 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T21 | 682-690 | Chemical | denotes | cofactor | http://purl.obolibrary.org/obo/CHEBI_23357 |
| T22 | 737-740 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T23 | 760-771 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T24 | 807-814 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T25 | 844-847 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T26 | 852-855 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T29 | 877-887 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T30 | 877-882 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T31 | 883-887 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T32 | 944-951 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T33 | 960-969 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T34 | 1018-1030 | Chemical | denotes | gangliosides | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T35 | 1084-1095 | Chemical | denotes | angiotensin | http://purl.obolibrary.org/obo/CHEBI_48433 |
| T36 | 1162-1165 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T37 | 1252-1261 | Chemical | denotes | cofactors | http://purl.obolibrary.org/obo/CHEBI_23357 |
| T38 | 1285-1290 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T39 | 1310-1320 | Chemical | denotes | inhibitors | http://purl.obolibrary.org/obo/CHEBI_35222 |
| T40 | 1411-1420 | Chemical | denotes | antiviral | http://purl.obolibrary.org/obo/CHEBI_22587 |
| T41 | 1594-1597 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 624-627 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T2 | 852-855 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 0-135 | Sentence | denotes | The emergence of SARS-coronavirus-2 (SARS-CoV-2) has led to a global pandemic disease referred to as coronavirus disease 19 (COVID-19). |
| T11 | 136-283 | Sentence | denotes | Hydroxychloroquine (CLQ-OH)/azithromycin (ATM) combination therapy is currently being tested for the treatment of COVID-19, with promising results. |
| T12 | 284-370 | Sentence | denotes | However, the molecular mechanism of action of this combination is not yet established. |
| T13 | 371-546 | Sentence | denotes | Using molecular dynamics (MD) simulations, this study shows that the drugs act in synergy to prevent any close contact between the virus and the plasma membrane of host cells. |
| T14 | 547-715 | Sentence | denotes | Unexpected molecular similarity is shown between ATM and the sugar moiety of GM1, a lipid raft ganglioside acting as a host attachment cofactor for respiratory viruses. |
| T15 | 716-815 | Sentence | denotes | Due to this mimicry, ATM interacts with the ganglioside-binding domain of SARS-CoV-2 spike protein. |
| T16 | 816-952 | Sentence | denotes | This binding site shared by ATM and GM1 displays a conserved amino acid triad Q-134/F-135/N-137 located at the tip of the spike protein. |
| T17 | 953-1124 | Sentence | denotes | CLQ-OH molecules are shown to saturate virus attachment sites on gangliosides in the vicinity of the primary coronavirus receptor, angiotensin-converting enzyme-2 (ACE-2). |
| T18 | 1125-1262 | Sentence | denotes | Taken together, these data show that ATM is directed against the virus, whereas CLQ-OH is directed against cellular attachment cofactors. |
| T19 | 1263-1372 | Sentence | denotes | We conclude that both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane. |
| T20 | 1373-1523 | Sentence | denotes | This is consistent with a synergistic antiviral mechanism at the plasma membrane level, where therapeutic intervention is likely to be most efficient. |
| T21 | 1524-1644 | Sentence | denotes | This molecular mechanism may explain the beneficial effects of CLQ-OH/ATM combination therapy in patients with COVID-19. |
| T22 | 1645-1780 | Sentence | denotes | Incidentally, the data also indicate that the conserved Q-134/F-135/N-137 triad could be considered as a target for vaccine strategies. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 61 | 801-806 | Gene | denotes | spike | Gene:43740568 |
| 62 | 938-943 | Gene | denotes | spike | Gene:43740568 |
| 63 | 1117-1122 | Gene | denotes | ACE-2 | Gene:59272 |
| 64 | 17-35 | Species | denotes | SARS-coronavirus-2 | Tax:2697049 |
| 65 | 37-47 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 66 | 790-800 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 67 | 1062-1073 | Species | denotes | coronavirus | Tax:11118 |
| 68 | 1324-1334 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 69 | 1621-1629 | Species | denotes | patients | Tax:9606 |
| 70 | 136-154 | Chemical | denotes | Hydroxychloroquine | MESH:D006886 |
| 71 | 156-162 | Chemical | denotes | CLQ-OH | |
| 72 | 164-176 | Chemical | denotes | azithromycin | MESH:D017963 |
| 73 | 178-181 | Chemical | denotes | ATM | MESH:D017963 |
| 74 | 608-613 | Chemical | denotes | sugar | MESH:D000073893 |
| 75 | 624-627 | Chemical | denotes | GM1 | MESH:D005677 |
| 76 | 631-636 | Chemical | denotes | lipid | MESH:D008055 |
| 77 | 642-653 | Chemical | denotes | ganglioside | MESH:D005732 |
| 78 | 760-771 | Chemical | denotes | ganglioside | MESH:D005732 |
| 79 | 953-959 | Chemical | denotes | CLQ-OH | |
| 80 | 1018-1030 | Chemical | denotes | gangliosides | MESH:D005732 |
| 81 | 1205-1211 | Chemical | denotes | CLQ-OH | |
| 82 | 1587-1593 | Chemical | denotes | CLQ-OH | |
| 83 | 1594-1597 | Chemical | denotes | ATM | MESH:D017963 |
| 84 | 101-123 | Disease | denotes | coronavirus disease 19 | MESH:C000657245 |
| 85 | 125-133 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 86 | 250-258 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 87 | 1635-1643 | Disease | denotes | COVID-19 | MESH:C000657245 |