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PMC:7128678 / 8023-11094 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
236 50-53 Gene denotes CLQ
237 5-17 Chemical denotes Sialic acids MESH:D012794
248 1269-1280 Chemical denotes chloroquine MESH:D002738
249 1304-1316 Chemical denotes sialic acids MESH:D012794
250 1358-1369 Chemical denotes sialic acid MESH:D019158
251 1371-1377 Chemical denotes Neu5Ac
252 1518-1523 Chemical denotes water MESH:D014867
253 1538-1544 Chemical denotes Neu5Ac
254 1559-1565 Chemical denotes Neu5Ac
255 1600-1604 Chemical denotes CH-π
256 1720-1754 Chemical denotes N-acetyl-9-O-acetylneuraminic acid MESH:C025676
257 1839-1843 Chemical denotes OH-π
275 104-109 Species denotes human Tax:9606
276 683-696 Species denotes coronaviruses Tax:11118
277 57-63 Chemical denotes Neu5Ac
278 83-94 Chemical denotes sialic acid MESH:D019158
279 128-140 Chemical denotes gangliosides MESH:D005732
280 167-173 Chemical denotes Neu5Ac
281 260-265 Chemical denotes water MESH:D014867
282 363-369 Chemical denotes Neu5Ac
283 511-522 Chemical denotes carboxylate
284 532-538 Chemical denotes Neu5Ac
285 726-760 Chemical denotes 9-O-acetyl-N-acetylneuraminic acid MESH:C025676
286 893-904 Chemical denotes sialic acid MESH:D019158
287 1032-1043 Chemical denotes carboxylate
288 1057-1068 Chemical denotes sialic acid MESH:D019158
289 1111-1119 Chemical denotes nitrogen MESH:D009584
290 1202-1206 Chemical denotes OH-π
291 177-200 Disease denotes quasi-instantaneous fit MESH:D012640
301 2763-2769 Gene denotes CLQ-OH
302 2672-2690 Chemical denotes hydroxychloroquine MESH:D006886
303 2692-2698 Chemical denotes CLQ-OH
304 2717-2729 Chemical denotes sialic acids MESH:D012794
305 2779-2813 Chemical denotes N-acetyl-9-O-acetylneuraminic acid MESH:C025676
306 2815-2822 Chemical denotes 9-O-SIA
307 2913-2919 Chemical denotes CLQ-OH
308 2981-2987 Chemical denotes CLQ-OH
309 3054-3062 Chemical denotes hydrogen MESH:D006859
316 1973-1979 Chemical denotes CLQ-OH
317 2080-2086 Chemical denotes CLQ-OH
318 2277-2283 Chemical denotes CLQ-OH
319 2317-2328 Chemical denotes sialic acid MESH:D019158
320 2356-2364 Chemical denotes hydrogen MESH:D006859
321 2397-2405 Chemical denotes hydrogen MESH:D006859

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T178 5-17 CHEBI:26667;CHEBI:26667 denotes Sialic acids
T179 57-63 PR:000002082 denotes Neu5Ac
T180 83-89 CHEBI:30563;CHEBI:30563 denotes sialic
T181 90-94 CHEBI:24195;CHEBI:24195 denotes acid
T182 104-109 SP_6;NCBITaxon:9606 denotes human
T183 110-123 CHEBI:17089;CHEBI:17089;BV_11 denotes glycoproteins
T184 128-140 CHEBI:28892;CHEBI:28892 denotes gangliosides
T185 167-173 PR:000002082 denotes Neu5Ac
T186 226-235 CHEBI:36357;CHEBI:36357 denotes molecules
T187 260-265 CHEBI:15377;CHEBI:15377 denotes water
T188 363-369 PR:000002082 denotes Neu5Ac
T189 370-377 GO:0032991 denotes complex
T190 532-538 PR:000002082 denotes Neu5Ac
T191 558-566 CHEBI:36916;CHEBI:36916 denotes cationic
T192 638-645 GO:0032991 denotes complex
T193 683-696 NCBITaxon:11118 denotes coronaviruses
T194 726-727 CHEBI:16066;CHEBI:16066 denotes 9
T195 730-736 CHEBI:40574;CHEBI:40574 denotes acetyl
T196 737-760 CHEBI:17012;CHEBI:17012 denotes N-acetylneuraminic acid
T197 893-904 CHEBI:26667;CHEBI:26667 denotes sialic acid
T198 1044-1049 CHEBI:24433;CHEBI:24433 denotes group
T199 1057-1068 CHEBI:26667;CHEBI:26667 denotes sialic acid
T200 1089-1103 CHEBI:64766;CHEBI:64766 denotes cationic group
T201 1168-1175 GO:0032991 denotes complex
T202 1269-1280 CHEBI:3638;DG_10;CHEBI:3638 denotes chloroquine
T203 1304-1316 CHEBI:26667;CHEBI:26667 denotes sialic acids
T204 1358-1364 CHEBI:30563;CHEBI:30563 denotes sialic
T205 1365-1369 CHEBI:41865;CHEBI:41865 denotes acid
T206 1371-1377 PR:000002082 denotes Neu5Ac
T207 1379-1386 GO:0032991 denotes complex
T208 1414-1421 GO:0032991 denotes complex
T209 1518-1523 CHEBI:15377;CHEBI:15377 denotes water
T210 1538-1544 PR:000002082 denotes Neu5Ac
T211 1559-1565 PR:000002082 denotes Neu5Ac
T212 1652-1667 CHEBI:64766;CHEBI:64766 denotes cationic groups
T213 1720-1754 CHEBI:21500;CHEBI:21500 denotes N-acetyl-9-O-acetylneuraminic acid
T214 1881-1896 CHEBI:64766;CHEBI:64766 denotes cationic groups
T215 1958-1965 GO:0032991 denotes complex
T230 2058-2065 GO:0032991 denotes complex
T231 2265-2267 CHEBI:46882;CHEBI:46882 denotes OH
T232 2268-2273 CHEBI:24433;CHEBI:24433 denotes group
T233 2317-2328 CHEBI:26667;CHEBI:26667 denotes sialic acid
T234 2534-2541 GO:0032991 denotes complex
T235 2672-2690 CHEBI:5801;DG_20;CHEBI:5801 denotes hydroxychloroquine
T236 2717-2729 CHEBI:26667;CHEBI:26667 denotes sialic acids
T237 2779-2813 CHEBI:21500;CHEBI:21500 denotes N-acetyl-9-O-acetylneuraminic acid
T238 2851-2858 GO:0032991 denotes complex

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T39 110-123 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T40 128-140 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T41 737-760 Body_part denotes N-acetylneuraminic acid http://purl.org/sig/ont/fma/fma82788

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T51 104-109 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T52 175-176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 303-308 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 (a)
T54 429-430 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 431-432 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T56 793-794 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 906-907 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T58 961-964 http://purl.obolibrary.org/obo/CLO_0002755 denotes d–f
T59 1001-1003 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T60 1319-1320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 1321-1322 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T62 1583-1584 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 1812-1813 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 1984-1990 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T65 2146-2147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 2148-2149 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T67 2354-2355 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 2628-2630 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T69 2732-2733 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 2734-2735 http://purl.obolibrary.org/obo/CLO_0001021 denotes b

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T121 12-17 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T122 57-63 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T124 83-94 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T125 90-94 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T126 110-123 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T127 128-140 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T128 167-173 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T130 226-235 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T131 260-265 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T132 363-369 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T134 523-528 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T135 532-538 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T137 730-736 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T139 737-760 Chemical denotes N-acetylneuraminic acid http://purl.obolibrary.org/obo/CHEBI_17012
T140 756-760 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T141 893-904 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T142 900-904 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T143 1044-1049 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T144 1057-1068 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T145 1064-1068 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T146 1089-1103 Chemical denotes cationic group http://purl.obolibrary.org/obo/CHEBI_64766
T147 1098-1103 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T148 1111-1119 Chemical denotes nitrogen http://purl.obolibrary.org/obo/CHEBI_25555
T149 1269-1280 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T150 1304-1316 Chemical denotes sialic acids http://purl.obolibrary.org/obo/CHEBI_26667
T151 1311-1316 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T152 1358-1369 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T153 1365-1369 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T154 1371-1377 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T156 1518-1523 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T157 1538-1544 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T159 1559-1565 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T161 1652-1667 Chemical denotes cationic groups http://purl.obolibrary.org/obo/CHEBI_64766
T162 1720-1754 Chemical denotes N-acetyl-9-O-acetylneuraminic acid http://purl.obolibrary.org/obo/CHEBI_21500
T163 1722-1728 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T165 1750-1754 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T166 1881-1896 Chemical denotes cationic groups http://purl.obolibrary.org/obo/CHEBI_64766
T167 2268-2273 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T168 2317-2328 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T169 2324-2328 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T170 2356-2364 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T171 2397-2405 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T172 2672-2690 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T173 2717-2729 Chemical denotes sialic acids http://purl.obolibrary.org/obo/CHEBI_26667
T174 2724-2729 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T175 2779-2813 Chemical denotes N-acetyl-9-O-acetylneuraminic acid http://purl.obolibrary.org/obo/CHEBI_21500
T176 2781-2787 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T178 2809-2813 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T179 3054-3062 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T62 0-56 Sentence denotes 3.2 Sialic acids as molecular targets of CLQ and CLQ-OH
T63 57-141 Sentence denotes Neu5Ac is the predominant sialic acid found in human glycoproteins and gangliosides.
T64 142-309 Sentence denotes When CLQ was merged with Neu5Ac, a quasi-instantaneous fit occurred between the two molecules, whose global shapes in water are geometrically complementary Fig. 2 (a).
T65 310-434 Sentence denotes This is particularly obvious in the views of the CLQ–Neu5Ac complex in mixed surface/balls and sticks rendition Fig. 2(a,b).
T66 435-603 Sentence denotes The interaction was driven by the positioning of the negative charge of the carboxylate group of Neu5Ac and one of the two cationic charges of CLQ (pKa 10.2) Fig. 2(c).
T67 604-679 Sentence denotes The energy of interaction of this complex was estimated to be -47 kJ.mol−1.
T68 680-905 Sentence denotes As coronaviruses preferentially interact with 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) [10], this study used a similar molecular modelling approach to assess whether CLQ could also interact with this specific sialic acid.
T69 906-1013 Sentence denotes A good fit between CLQ and 9-O-SIA was obtained Fig. 2(d–f), with an energy of interaction of -45 kJ.mol−1.
T70 1014-1163 Sentence denotes In this case, the carboxylate group of the sialic acid interacted with the cationic group of the nitrogen-containing ring of CLQ (pKa 8.1) Fig. 2(d).
T71 1164-1238 Sentence denotes The complex was further stabilized by OH-π and van der Waals interactions.
T72 1239-1387 Sentence denotes Fig. 2 Molecular modelling of chloroquine (CLQ) interaction with sialic acids. (a,b) Surface representation of the CLQ–sialic acid (Neu5Ac) complex.
T73 1388-1432 Sentence denotes Two opposite views of the complex are shown.
T74 1433-1765 Sentence denotes Note the geometric complementarity between the L-shape conformer of CLQ dissolved in water (in blue) and Neu5Ac (in red). (c) Neu5Ac bound to CLQ via a combination of CH-π and electrostatic interactions with one of the cationic groups of CLQ (+). (d) Molecular modelling of CLQ bound to N-acetyl-9-O-acetylneuraminic acid (9-O-SIA).
T75 1766-1966 Sentence denotes From right to left, the dashed lines indicate a series of van der Waals, OH-π and electrostatic contacts with both cationic groups of CLQ (+). (e,f) Surface representations of the CLQ–9-O-SIA complex.
T76 1967-2053 Sentence denotes Next, CLQ-OH was tested to assess whether it could, as CLQ, bind to 9-O-SIA (Fig. 3 ).
T77 2054-2245 Sentence denotes The complex obtained with CLQ-OH was very similar to that obtained with CLQ [compare Fig. 3(a,b) with Fig. 2(e,f), although several conformational adjustments occurred during the simulations.
T78 2246-2382 Sentence denotes Interestingly, the OH group of CLQ-OH reinforced the binding of CLQ to sialic acid through establishment of a hydrogen bond Fig. 3(c,d).
T79 2383-2641 Sentence denotes Overall, this hydrogen bond compensated for the slight loss of energy caused by the conformational rearrangement, and the energy of interaction of the complex was estimated to be -46 kJ.mol−1, which is very close to the value obtained for CLQ (-45 kJ.mol−1).
T80 2642-2824 Sentence denotes Fig. 3 Molecular modelling of hydroxychloroquine (CLQ-OH) interaction with sialic acids. (a,b) Surface representation of CLQ-OH bound to N-acetyl-9-O-acetylneuraminic acid (9-O-SIA).
T81 2825-2869 Sentence denotes Two opposite views of the complex are shown.
T82 2870-3071 Sentence denotes Note the geometric complementarity between CLQ-OH (in blue) and 9-O-SIA (in red). (c,d) Molecular mechanism of CLQ-OH binding to 9-O-SIA: combination of electrostatic interactions and hydrogen bonding.

2_test

Id Subject Object Predicate Lexical cue
32251731-23873408-48149952 772-774 23873408 denotes 10
T46400 772-774 23873408 denotes 10