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PMC:7352545 / 138-3437 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 280-291 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T2 293-295 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T3 707-709 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T4 829-831 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T5 900-902 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T6 1037-1039 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T7 1244-1246 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T8 1431-1433 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T9 1530-1532 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T10 1611-1613 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T11 2162-2164 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T12 2199-2201 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T13 2327-2329 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T14 2346-2348 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T15 2434-2436 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 418-430 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T2 506-511 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T3 1061-1068 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T4 1069-1081 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T5 1110-1122 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T6 1149-1153 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T7 1216-1220 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T8 1852-1856 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T9 2236-2243 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10 2368-2375 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 2590-2602 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T12 2622-2630 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T13 2892-2900 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
51 524-546 Gene denotes hemagglutinin-esterase Gene:17603139
52 21-31 Species denotes SARS-CoV-2 Tax:2697049
53 229-232 Species denotes CoV Tax:11118
54 251-268 Species denotes influenza viruses Tax:11308
55 324-334 Species denotes SARS-CoV-2 Tax:2697049
56 434-444 Species denotes SARS CoV-2 Tax:2697049
57 513-523 Species denotes SARS-CoV-2 Tax:2697049
58 634-638 Species denotes CoVs Tax:11118
59 735-739 Species denotes CoVs Tax:11118
60 1175-1180 Species denotes β-CoV Tax:694002
61 1267-1282 Species denotes influenza virus Tax:11308
62 1465-1468 Species denotes CoV Tax:11118
63 1964-1980 Species denotes bovine torovirus Tax:74501
64 2046-2052 Species denotes murine Tax:10090
65 2053-2057 Species denotes CoVs Tax:11118
66 2083-2088 Species denotes β-CoV Tax:694002
67 2904-2914 Species denotes SARS-CoV-2 Tax:2697049
68 3036-3046 Species denotes SARS-CoV-2 Tax:2697049
69 3093-3101 Species denotes patients Tax:9606
70 3153-3163 Species denotes SARS-CoV-2 Tax:2697049
71 412-417 Gene denotes spike Gene:43740568
72 280-291 Chemical denotes sialic acid MESH:D019158
73 574-580 Chemical denotes glycan MESH:D011134
74 649-663 Chemical denotes 9-O-acetyl-SAs
75 696-709 Chemical denotes 4-O-acetyl-SA
76 1002-1012 Chemical denotes 4-O-acetyl
77 1026-1039 Chemical denotes 9-O-acetyl SA MESH:C025676
78 1069-1081 Chemical denotes carbohydrate MESH:D002241
79 1110-1122 Chemical denotes carbohydrate MESH:D002241
80 1237-1246 Chemical denotes 9-O-Ac-SA
81 1445-1452 Chemical denotes glycans MESH:D011134
82 1530-1539 Chemical denotes SA-glycan
83 1905-1920 Chemical denotes 7,9-di-O-Ac-SAs
84 2155-2164 Chemical denotes 9-O-Ac-SA
85 2192-2201 Chemical denotes 4-O-Ac-SA
86 2320-2329 Chemical denotes acetyl SA
87 2339-2348 Chemical denotes acetyl SA
88 2376-2382 Chemical denotes glycan MESH:D011134
89 2590-2602 Chemical denotes carbohydrate MESH:D002241
90 2603-2609 Chemical denotes glycan MESH:D011134
91 3232-3238 Chemical denotes glycan MESH:D011134
92 80-104 Disease denotes coronavirus disease 2019 MESH:C000657245
93 106-114 Disease denotes COVID-19 MESH:C000657245
94 159-172 Disease denotes CoV infection MESH:D018352
95 189-205 Disease denotes zoonotic disease MESH:D015047
96 863-880 Disease denotes quasi-synchronous MESH:D009378
97 3084-3092 Disease denotes infected MESH:D007239

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 21-29 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 80-104 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T4 106-114 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 163-172 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T6 189-205 Disease denotes zoonotic disease http://purl.obolibrary.org/obo/MONDO_0025481
T7 251-260 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T8 324-332 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 434-438 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 513-521 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 1267-1276 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T12 2904-2912 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 3036-3044 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 3153-3161 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 261-268 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T3 378-381 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T4 475-482 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T5 506-511 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T6 660-663 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T7 778-781 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T8 820-823 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T9 1149-1153 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T10 1173-1174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1189-1190 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T12 1216-1220 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T13 1235-1238 http://purl.obolibrary.org/obo/CLO_0001618 denotes a 9
T14 1235-1238 http://purl.obolibrary.org/obo/CLO_0001619 denotes a 9
T15 1235-1238 http://purl.obolibrary.org/obo/CLO_0001620 denotes a 9
T16 1277-1282 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 1500-1505 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T18 1631-1632 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1736-1743 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 1780-1785 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T21 1830-1831 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 1852-1856 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T23 1917-1920 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T24 1948-1949 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 1985-1986 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T26 2014-2015 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 2097-2098 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 2289-2294 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T29 2655-2660 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T30 3204-3212 http://purl.obolibrary.org/obo/CLO_0001658 denotes activate

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 280-291 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T2 287-291 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T3 293-295 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T8 418-430 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T9 653-659 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T11 700-706 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T13 707-709 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T18 775-777 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T20 791-793 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T21 817-819 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T23 829-831 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T28 900-902 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T33 1006-1012 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T35 1030-1036 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T37 1037-1039 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T42 1061-1068 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 1069-1081 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T44 1110-1122 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T45 1241-1243 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T47 1244-1246 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T52 1431-1433 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T57 1445-1452 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T58 1530-1532 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T63 1611-1613 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T68 1614-1620 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T69 1914-1916 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T71 2159-2161 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T73 2162-2164 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T78 2196-2198 Chemical denotes Ac http://purl.obolibrary.org/obo/CHEBI_33337|http://purl.obolibrary.org/obo/CHEBI_40574
T80 2199-2201 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T85 2208-2210 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T86 2236-2243 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T87 2268-2270 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T88 2320-2326 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T90 2327-2329 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T95 2339-2345 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T97 2346-2348 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T102 2368-2375 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T103 2434-2436 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T108 2437-2443 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T109 2590-2602 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T110 2622-2630 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T111 2631-2640 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T112 2739-2748 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T113 2892-2900 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T114 3074-3079 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T115 3266-3270 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 1821-1828 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism
T4 2683-2690 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-125 Sentence denotes The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic.
T4 126-297 Sentence denotes No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA).
T5 298-364 Sentence denotes Currently, information on SARS-CoV-2 and its receptors is limited.
T6 365-512 Sentence denotes O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells.
T7 513-626 Sentence denotes SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme.
T8 627-740 Sentence denotes Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs.
T9 741-824 Sentence denotes Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs.
T10 825-956 Sentence denotes The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains.
T11 957-1141 Sentence denotes The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI).
T12 1142-1287 Sentence denotes The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA–specific HEF, as in influenza virus C/D.
T13 1288-1378 Sentence denotes HE acquisition, and expansion takes place by cross-species transmission over HE evolution.
T14 1379-1453 Sentence denotes This reflects viral evolutionary adaptation to host SA-containing glycans.
T15 1454-1563 Sentence denotes Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts.
T16 1564-1696 Sentence denotes The PCI or LCI stereochemistry potentiates the SA–ligand switch by a simple conformational shift of the lectin and esterase domains.
T17 1697-1829 Sentence denotes Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism.
T18 1830-1984 Sentence denotes A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE.
T19 1985-2231 Sentence denotes A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors.
T20 2232-2349 Sentence denotes The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA.
T21 2350-2519 Sentence denotes Principles of the protein–glycan interaction and PCI stereochemistry potentiate the SA–ligand switch via simple conformational shifts of the lectin and esterase domains.
T22 2520-2691 Sentence denotes Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism.
T23 2692-2848 Sentence denotes Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents.
T24 2849-2994 Sentence denotes As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development.
T25 2995-3102 Sentence denotes However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients.
T26 3103-3299 Sentence denotes In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future.