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PMC:7605337 / 45013-49729 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T64 1751-1758 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T65 2528-2535 Body_part denotes Alanine http://purl.org/sig/ont/fma/fma82749
T66 3295-3302 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T67 3755-3762 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T307 56-65 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T308 70-74 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T309 142-151 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T310 220-224 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T311 367-376 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T312 381-385 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T313 432-441 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T314 446-450 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T315 668-677 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T316 796-805 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T317 1378-1382 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T318 1457-1466 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T319 1589-1593 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T320 1983-1992 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T321 2119-2123 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T322 2166-2170 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T323 2289-2293 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T324 2602-2611 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T325 2780-2789 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T326 2853-2857 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T327 2969-2973 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T328 3029-3038 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T329 3097-3106 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T330 3517-3521 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T331 3599-3608 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T332 3851-3860 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T333 4085-4094 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T278 112-117 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T279 176-180 http://purl.obolibrary.org/obo/CLO_0050298 denotes 10 H
T280 234-237 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T281 1055-1058 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T282 1405-1406 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T283 1840-1841 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T284 2478-2479 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T285 2636-2637 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T286 2697-2698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T287 2978-2981 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T288 3107-3110 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T289 3195-3196 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T290 3866-3869 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T291 3870-3871 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T141 15-23 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T142 33-37 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T144 189-193 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T146 250-254 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T148 1030-1033 Chemical denotes Ala http://purl.obolibrary.org/obo/CHEBI_16977|http://purl.obolibrary.org/obo/CHEBI_46217
T150 1751-1758 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T151 2323-2326 Chemical denotes Ala http://purl.obolibrary.org/obo/CHEBI_16977|http://purl.obolibrary.org/obo/CHEBI_46217
T153 2528-2535 Chemical denotes Alanine http://purl.obolibrary.org/obo/CHEBI_16449
T154 3197-3201 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T156 3295-3302 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T157 3380-3384 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T159 3755-3762 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T160 4197-4199 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T307 0-272 Sentence denotes The details of hydrogen bond and salt-bridge pattern in nCOV-2019 and SARS-COV to ACE2 (Table 1) are key to the virus attachment to the host. nCOV-2019 residues participate in 10 H-bonds/1 salt bridge with ACE2, whereas SARS-COV only has 5 H-bonds/1 salt bridge with ACE2.
T308 273-390 Sentence denotes This significantly contributes to ∼30 kcal/mol difference in the total binding free energy of nCOV-2019 and SARS-COV.
T309 391-767 Sentence denotes The binding energies calculated here for nCOV-2019 and SARS-COV (−50.22 ± 1.93 and −18.79 ± 1.53 kcal/mol, respectively) are in good agreement with the binding energies calculated using the generalized Born method by Spinello et al.30 Moreover, the patterns of H-bonds between nCOV-2019 and ACE2 were also already characterized by other groups26,30 which agrees with our work.
T310 768-855 Sentence denotes An important H-bond between nCOV-2019 and ACE2 is between G502 on RBD and K353 of ACE2.
T311 856-935 Sentence denotes G502 is in the L4 region, which is populated by 5 H-bonds between RBD and ACE2.
T312 936-1226 Sentence denotes The contribution of this residue to the total binding energy is −2.03 ± 0.04 kcal/mol and the Ala-substitution at G502 has the highest effect on the binding energy among all the residues by lowering the total binding affinity to 24.31 ± 2.98 kcal/mol, which is the lowest among all mutants.
T313 1227-1316 Sentence denotes This mutation breaks the other H-bonds in L4 such as H-bonds from residues Q498 and T500.
T314 1317-1440 Sentence denotes This residue is preserved and corresponds to residue G488 in SARS-COV, which also makes a H-bond with residue K353 on ACE2.
T315 1441-1552 Sentence denotes Residue Q493 in nCOV-2019 participates in binding ACE2 by making two H-bonds with residues E35 and K31 on ACE2.
T316 1553-1654 Sentence denotes Q493 corresponds to residue N479 in SARS-COV, which only makes one H-bond with residue Lys31 on ACE2.
T317 1655-1741 Sentence denotes This caused Q493 to have more contribution to total binding than its counterpart N479.
T318 1742-1956 Sentence denotes However, alanine substitution at Q493 did not affect the total binding energy and this mutant had a total binding energy similar to the wild-type complex as it maintains the number H-bonds in the wild-type complex.
T319 1957-2074 Sentence denotes Residues Q498 and T500 in nCOV-2019 are crucial for binding by making H-bonds with ACE2 residues D38, D355, and K353.
T320 2075-2188 Sentence denotes Residue Q498 corresponds to residue Y484 in SARS-COV which does not make any H-bond in the SARS-COV/ACE2 complex.
T321 2189-2322 Sentence denotes Q498 contributes to binding by −6.72 ± 0.18 kcal/mol which is more than the contribution of Y484 in SARS-COV (−1.83 ± 0.06 kcal/mol).
T322 2323-2402 Sentence denotes Ala-substitution at Q498 did not show large impact on the total binding energy.
T323 2403-2507 Sentence denotes Residue T500 is conserved and corresponds to residue T486 which also makes a H-bond with Asp355 on ACE2.
T324 2508-2585 Sentence denotes Mutation of T500 to Alanine lowers the binding affinity by about 10 kcal/mol.
T325 2586-2723 Sentence denotes Residue N487 in nCOV-2019 locates in L3 and plays a crucial role in stabilizing the recognition loop by making a H-bond with Y83 on ACE2.
T326 2724-2939 Sentence denotes This residue contributes to the total binding energy of nCOV-2019 by −1.52 ± 0.06 kcal/mol, whereas its corresponding residue in SARS-COV does not show any contribution to the binding energy (−0.02 ± 0.05 kcal/mol).
T327 2940-3080 Sentence denotes This demonstrates that L3 in SARS-COV has evolved to be an important recognition loop in nCOV-2019, which participates in binding with ACE2.
T328 3081-3234 Sentence denotes Residue K417 in nCOV-2019 has the most contribution to the total binding energy (−12.34 ± 0.23 kcal/mol by making a salt-bridge with residue D30 on ACE2.
T329 3235-3374 Sentence denotes This residue is crucial for the binding of RBD and ACE2 and alanine substitution lowers the total binding energy to −29.56 ± 2.95 kcal/mol.
T330 3375-3569 Sentence denotes This salt-bridge is found to be important for the stability of the crystal structure of the RBD/ACE2 complex in nCOV-2019.4 K417 is Val404 in SARS-COV which does not participate in binding ACE2.
T331 3570-3671 Sentence denotes Another important residue in nCOV-2019 is L455 which contributes to binding by −1.86 ± 0.03 kcal/mol.
T332 3672-3818 Sentence denotes This residue is important for hydrophobic interaction with ACE2 and mutating it to alanine lowers the total binding affinity by about 17 kcal/mol.
T333 3819-3969 Sentence denotes The hydrophobic residue F456 in nCOV-2019 also has a favorable contribution to the binding energy and F456A lowers the binding affinity by 5 kcal/mol.
T334 3970-4333 Sentence denotes These results are in fair agreement with experimental binding measurements with deep mutational scanning of RBD in nCOV-2019 where they used flow cytometry for different ACE2 concentrations to measure the dissociation constant KD.25 It was shown that mutations at K417, N487, T500, and G502 are detrimental for binding to ACE2, which agrees with the results here.
T335 4334-4605 Sentence denotes These experiments showed that mutations at Q493 and Q498 do not impact the binding affinity of RBD to ACE2 which demonstrates the high plasticity of the network of H-bonds at the interface where upon mutation at these residues the network can reshape to form new H-bonds.
T336 4606-4716 Sentence denotes Mutations at hydrophobic residues L455 and F456 are shown to reduce the binding affinity in these experiments.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1187 82-86 Gene denotes ACE2 Gene:59272
1188 206-210 Gene denotes ACE2 Gene:59272
1189 267-271 Gene denotes ACE2 Gene:59272
1190 682-686 Gene denotes ACE2 Gene:59272
1191 810-814 Gene denotes ACE2 Gene:59272
1192 850-854 Gene denotes ACE2 Gene:59272
1193 930-934 Gene denotes ACE2 Gene:59272
1194 1435-1439 Gene denotes ACE2 Gene:59272
1195 1491-1495 Gene denotes ACE2 Gene:59272
1196 1547-1551 Gene denotes ACE2 Gene:59272
1197 1649-1653 Gene denotes ACE2 Gene:59272
1198 2040-2044 Gene denotes ACE2 Gene:59272
1199 2175-2179 Gene denotes ACE2 Gene:59272
1200 2502-2506 Gene denotes ACE2 Gene:59272
1201 2718-2722 Gene denotes ACE2 Gene:59272
1202 3075-3079 Gene denotes ACE2 Gene:59272
1203 3229-3233 Gene denotes ACE2 Gene:59272
1204 3286-3290 Gene denotes ACE2 Gene:59272
1205 3471-3475 Gene denotes ACE2 Gene:59272
1206 3564-3568 Gene denotes ACE2 Gene:59272
1207 3731-3735 Gene denotes ACE2 Gene:59272
1208 4140-4144 Gene denotes ACE2 Gene:59272
1209 4292-4296 Gene denotes ACE2 Gene:59272
1210 4436-4440 Gene denotes ACE2 Gene:59272
1211 1540-1543 Gene denotes K31 Gene:3881
1212 56-60 Species denotes nCOV Tax:2697049
1213 70-78 Species denotes SARS-COV Tax:694009
1214 142-146 Species denotes nCOV Tax:2697049
1215 220-228 Species denotes SARS-COV Tax:694009
1216 367-371 Species denotes nCOV Tax:2697049
1217 381-389 Species denotes SARS-COV Tax:694009
1218 432-436 Species denotes nCOV Tax:2697049
1219 446-454 Species denotes SARS-COV Tax:694009
1220 668-672 Species denotes nCOV Tax:2697049
1221 796-800 Species denotes nCOV Tax:2697049
1222 1378-1386 Species denotes SARS-COV Tax:694009
1223 1457-1461 Species denotes nCOV Tax:2697049
1224 1589-1597 Species denotes SARS-COV Tax:694009
1225 1983-1987 Species denotes nCOV Tax:2697049
1226 2119-2127 Species denotes SARS-COV Tax:694009
1227 2166-2174 Species denotes SARS-COV Tax:694009
1228 2289-2297 Species denotes SARS-COV Tax:694009
1229 2602-2606 Species denotes nCOV Tax:2697049
1230 2780-2784 Species denotes nCOV Tax:2697049
1231 2853-2861 Species denotes SARS-COV Tax:694009
1232 2969-2977 Species denotes SARS-COV Tax:694009
1233 3029-3033 Species denotes nCOV Tax:2697049
1234 3097-3101 Species denotes nCOV Tax:2697049
1235 3487-3491 Species denotes nCOV Tax:2697049
1236 3517-3525 Species denotes SARS-COV Tax:694009
1237 3599-3603 Species denotes nCOV Tax:2697049
1238 3851-3855 Species denotes nCOV Tax:2697049
1239 4085-4089 Species denotes nCOV Tax:2697049
1240 15-23 Chemical denotes hydrogen MESH:D006859
1241 826-830 Chemical denotes G502
1242 842-846 Chemical denotes K353
1243 856-860 Chemical denotes G502
1244 1030-1033 Chemical denotes Ala MESH:D000409
1245 1370-1374 Chemical denotes G488
1246 1427-1431 Chemical denotes K353
1247 1449-1453 Chemical denotes Q493
1248 1581-1585 Chemical denotes N479
1249 1640-1645 Chemical denotes Lys31
1250 1736-1740 Chemical denotes N479
1251 1751-1758 Chemical denotes alanine MESH:D000409
1252 2083-2087 Chemical denotes Q498
1253 2111-2115 Chemical denotes Y484
1254 2189-2193 Chemical denotes Q498
1255 2281-2285 Chemical denotes Y484
1256 2323-2326 Chemical denotes Ala MESH:D000409
1257 2411-2415 Chemical denotes T500
1258 2456-2460 Chemical denotes T486
1259 2492-2498 Chemical denotes Asp355
1260 2528-2535 Chemical denotes Alanine MESH:D000409
1261 2594-2598 Chemical denotes N487
1262 2711-2714 Chemical denotes Y83
1263 3089-3093 Chemical denotes K417
1264 3222-3225 Chemical denotes D30 MESH:C005496
1265 3295-3302 Chemical denotes alanine MESH:D000409
1266 3499-3503 Chemical denotes K417
1267 3507-3513 Chemical denotes Val404
1268 3612-3616 Chemical denotes L455
1269 3755-3762 Chemical denotes alanine MESH:D000409
1270 3843-3847 Chemical denotes F456
1271 3921-3926 Chemical denotes F456A