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PMC:7094172 / 1322-4751 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T124 19-27 CHEBI:36357;CHEBI:36357 denotes molecule
T123 119-123 CHEBI:23888;CHEBI:23888 denotes drug
T122 171-176 NCBITaxon:10239 denotes viral
T121 220-229 CHEBI:36357;CHEBI:36357 denotes molecules
T120 309-324 GO:0051260 denotes oligomerization
T119 370-379 CHEBI:36357;CHEBI:36357 denotes molecules
T118 383-391 GO:0065007 denotes modulate
T117 427-437 CHEBI:35718;CHEBI:35718 denotes anticancer
T116 438-442 CHEBI:23888;CHEBI:23888 denotes drug
T115 443-453 CHEBI:45863;CHEBI:45863 denotes paclitaxel
T114 492-503 GO:0005874;GO:0090307 denotes microtubule
T113 504-522 GO:0090307 denotes structure assembly
T112 539-546 PR:000028799 denotes tubulin
T111 570-579 CHEBI:33893;CHEBI:33893 denotes rapamycin
T110 589-605 CHEBI:67079;CHEBI:67079 denotes anticancer agent
T109 647-653 PR:000007536 denotes FKBP12
T108 699-706 GO:0032991 denotes complex
T107 767-771 CHEBI:23888;CHEBI:23888;GO:0017144 denotes drug
T106 772-783 GO:0017144 denotes development
T105 960-964 CHEBI:23888;CHEBI:23888 denotes drug
T104 1099-1112 PG_4 denotes nucleoprotein
T103 1132-1141 NCBITaxon:7719 denotes influenza
T102 1142-1147 NCBITaxon:10239 denotes virus
T101 1175-1198 GO:0051259 denotes protein oligomerization
T100 1211-1216 NCBITaxon:10239 denotes viral
T99 1230-1241 SP_9 denotes Middle East
T98 1242-1253 SP_9;UBERON:0001004 denotes respiratory
T97 1254-1274 SP_9 denotes syndrome coronavirus
T96 1276-1284 SP_9 denotes MERS-CoV
T95 1301-1316 SP_8;NCBITaxon:694002 denotes betacoronavirus
T94 1351-1362 UBERON:0001004 denotes respiratory
T93 1402-1408 NCBITaxon:9606 denotes humans
T92 1449-1460 NCBITaxon:11118 denotes coronavirus
T91 1462-1473 NCBITaxon:11118 denotes coronavirus
T90 1488-1496 SP_7 denotes COVID-19
T89 1750-1758 SP_9 denotes MERS-CoV
T88 1772-1778 SO:0001026 denotes genome
T87 1821-1838 GO:0005840 denotes ribonucleoprotein
T86 1845-1852 GO:0032991 denotes complex
T85 1879-1884 NCBITaxon:10239 denotes viral
T84 1948-1958 GO:0065007 denotes modulation
T83 1966-1967 PG_4 denotes N
T82 1968-1975 PG_4;GO:0051259 denotes protein
T81 1976-1991 GO:0051259 denotes oligomerization
T80 2001-2010 CHEBI:36357;CHEBI:36357 denotes molecules
T79 2035-2039 CHEBI:36044;CHEBI:36044 denotes drug
T78 2071-2074 NCBITaxon:11886 denotes CoV
T77 2075-2084 PG_4 denotes N protein
T76 2118-2124 SO:0000417 denotes domain
T75 2150-2156 SO:0000417 denotes domain
T74 2174-2181 SO:0000417 denotes domains
T73 2353-2354 GO:0051260;PG_4 denotes N
T72 2355-2362 PG_4;GO:0051259 denotes protein
T71 2363-2378 GO:0051259 denotes oligomerization
T70 2459-2467 SP_9 denotes MERS-CoV
T69 2786-2790 CHEBI:23888;CHEBI:23888 denotes drug
T68 2819-2835 CHEBI:41237;CHEBI:41237 denotes benzyloxygramine
T67 2894-2903 PG_4 denotes N protein
T66 3007-3008 PG_4 denotes N
T65 3009-3016 PG_4;GO:0051259 denotes protein
T64 3017-3032 GO:0051259 denotes oligomerization
T63 3100-3108 SP_9 denotes MERS-CoV
T62 3115-3124 GO:0032991 denotes complexed
T61 3130-3148 CHEBI:41237;CHEBI:41237 denotes 5-benzyloxygramine

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T12 45-52 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T13 53-60 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 344-351 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T15 492-503 Body_part denotes microtubule http://purl.org/sig/ont/fma/fma63849
T16 539-546 Body_part denotes tubulin http://purl.org/sig/ont/fma/fma67116
T17 564-568 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T18 1175-1182 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T19 1772-1778 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T20 1801-1808 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T21 1968-1975 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T22 2077-2084 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23 2199-2202 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T24 2355-2362 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T25 2383-2390 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T26 2391-2398 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 2896-2903 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 2945-2949 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T29 3009-3016 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 3053-3057 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T31 3303-3310 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 564-568 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p35652s4 309-336 MPA denotes oligomerization equilibrium
p35652s8 344-351 Protein denotes protein
p35652s29 483-491 PosReg denotes enhances
p35652s30 492-522 MPA denotes microtubule structure assembly
p35655s32 1183-1198 MPA denotes oligomerization
p35655s34 1203-1207 NegReg denotes loss
p35655s37 1217-1226 MPA denotes viability

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T7 171-187 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T8 1132-1141 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T9 1462-1486 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1488-1496 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1521-1530 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T12 2126-2129 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T14 2227-2230 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T16 2470-2473 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T18 3111-3114 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T20 3409-3419 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T10 87-96 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T11 885-892 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T12 922-923 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1018-1026 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T14 1142-1147 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T15 1227-1229 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T16 1377-1378 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1402-1408 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T18 1425-1426 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1782-1783 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1819-1820 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2014-2015 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2088-2097 http://purl.obolibrary.org/obo/OBI_0000245 denotes organized
T23 2256-2257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 2477-2478 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 2760-2762 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T26 2876-2886 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T27 2945-2949 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T28 3053-3057 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T29 3242-3243 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3290-3291 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T17 19-27 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T18 45-52 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T19 53-60 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T20 119-123 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T21 220-229 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T22 344-351 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23 370-379 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T24 438-442 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T25 443-453 Chemical denotes paclitaxel http://purl.obolibrary.org/obo/CHEBI_45863
T26 570-579 Chemical denotes rapamycin http://purl.obolibrary.org/obo/CHEBI_9168
T27 589-605 Chemical denotes anticancer agent http://purl.obolibrary.org/obo/CHEBI_35610
T28 767-771 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T29 960-964 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T30 1008-1017 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T31 1057-1060 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T33 1175-1182 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T34 1714-1730 Chemical denotes antiviral agents http://purl.obolibrary.org/obo/CHEBI_22587
T35 1801-1808 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T36 1968-1975 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T37 2001-2010 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T38 2025-2039 Chemical denotes antiviral drug http://purl.obolibrary.org/obo/CHEBI_36044
T39 2025-2034 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T40 2035-2039 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T41 2077-2084 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T42 2355-2362 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 2383-2390 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T44 2391-2398 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T45 2606-2616 Chemical denotes stabilizer http://purl.obolibrary.org/obo/CHEBI_77966
T46 2760-2762 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T47 2786-2790 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T48 2850-2859 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T49 2896-2903 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T50 3009-3016 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51 3303-3310 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 171-187 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T3 1175-1198 http://purl.obolibrary.org/obo/GO_0051259 denotes protein oligomerization
T4 1879-1898 http://purl.obolibrary.org/obo/GO_0019083 denotes viral transcription
T5 1885-1898 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T6 1968-1991 http://purl.obolibrary.org/obo/GO_0051259 denotes protein oligomerization
T7 2355-2378 http://purl.obolibrary.org/obo/GO_0051259 denotes protein oligomerization
T8 3009-3032 http://purl.obolibrary.org/obo/GO_0051259 denotes protein oligomerization

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1351-1371 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T2 1521-1530 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T10 0-12 Sentence denotes Introduction
T11 13-134 Sentence denotes Small-molecule stabilization of protein–protein interactions (PPIs) is an extremely promising strategy in drug discovery.
T12 135-284 Sentence denotes It can be used to treat cancers and viral infections.1−3 Stabilizing PPIs with small molecules may be allosteric or direct (also called orthosteric).
T13 285-829 Sentence denotes This process alters the oligomerization equilibrium of the protein and enables small molecules to modulate its physiological function.4−7 The anticancer drug paclitaxel, for example, allosterically enhances microtubule structure assembly by binding to β-tubulin.8,9 On the other hand, rapamycin, another anticancer agent, binds directly to the interface between FKBP12 and mTOR and stabilizes the structure of the complex.10 The most well-characterized PPIs suitable as targets for drug development form natively under physiological conditions.
T14 830-973 Sentence denotes However, non-native interactions, which may form under extreme circumstances such as inside a crystal lattice, are also potential drug targets.
T15 974-1229 Sentence denotes For example, nucleozin exerts its antiviral activity by stabilizing the non-native PPI interface between the two neighboring nucleoprotein trimers within the influenza virus, which results in abnormal protein oligomerization and loss of viral viability.11
T16 1230-1333 Sentence denotes Middle East respiratory syndrome coronavirus (MERS-CoV) belongs to the betacoronavirus (β-CoVs) family.
T17 1334-1668 Sentence denotes It causes severe respiratory distress with a high mortality rate in humans.12−14 Recently, a closely related novel coronavirus, coronavirus disease 2019 (COVID-19), caused an outbreak of pneumonia in Wuhan, which further underscored the risk of CoVs to the global public health.15,16 However, there is no effective treatment for CoVs.
T18 1669-1853 Sentence denotes Thus, there is an urgent need to develop new antiviral agents against CoVs.14,17 MERS-CoV packages its genome in a nucleocapsid (N) protein and forms a ribonucleoprotein (RNP) complex.
T19 1854-1912 Sentence denotes The RNP is essential for viral transcription and assembly.
T20 1913-2281 Sentence denotes Several studies suggested that the modulation of CoV N protein oligomerization by small molecules is a feasible antiviral drug development strategy.18,19 The CoV N protein is organized into the N-terminal domain (NTD) and the C-terminal domain (CTD), with both domains participating in RNA binding.20,21 All CoV N-NTD structures are folded in a monomeric conformation.
T21 2282-2417 Sentence denotes In contrast, the CoV N-CTDs are always dimeric and are responsible for N protein oligomerization via protein–protein interactions.22,23
T22 2418-2512 Sentence denotes Here, we report the crystal structure of MERS-CoV N-NTD in a non-native dimeric configuration.
T23 2513-2617 Sentence denotes We used the non-native dimer interface as the target in virtual screening for an orthosteric stabilizer.
T24 2618-2801 Sentence denotes To this end, we considered the binding scores and hydrophobic complementarity of the acquired poses, and further selected the potential leads P1–P3 from Acros and ZINC drug databases.
T25 2802-2904 Sentence denotes Of these, only 5-benzyloxygramine (P3) had both antiviral and stabilizing activities on the N protein.
T26 2905-3064 Sentence denotes Small-angle X-ray scattering (SAXS) and cell-based assays showed that P3 induces abnormal full-length N protein oligomerization in vitro and at the cell level.
T27 3065-3188 Sentence denotes We also described the structure of MERS-CoV N-NTD complexed with 5-benzyloxygramine and revealed its stabilizing mechanism.
T28 3189-3333 Sentence denotes Our findings provide insight into the development of a new therapeutic approach based on stabilizing a non-native protein interaction interface.
T29 3334-3429 Sentence denotes It may lead to the discovery and development of new treatments for various infectious diseases.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
22 647-653 Gene denotes FKBP12 Gene:2285
23 658-662 Gene denotes mTOR Gene:2475
24 1132-1147 Species denotes influenza virus Tax:11309
25 443-453 Chemical denotes paclitaxel MESH:D017239
26 570-579 Chemical denotes rapamycin MESH:D020123
27 987-996 Chemical denotes nucleozin
28 159-166 Disease denotes cancers MESH:D009369
29 171-187 Disease denotes viral infections MESH:D001102
49 1840-1843 Gene denotes RNP Gene:55599
50 1858-1861 Gene denotes RNP Gene:55599
51 1230-1285 Species denotes Middle East respiratory syndrome coronavirus (MERS-CoV) Tax:1335626
52 1301-1316 Species denotes betacoronavirus Tax:694002
53 1402-1408 Species denotes humans Tax:9606
54 1443-1460 Species denotes novel coronavirus Tax:2697049
55 1579-1583 Species denotes CoVs Tax:11118
56 1663-1667 Species denotes CoVs Tax:11118
57 1739-1743 Species denotes CoVs Tax:11118
58 1750-1758 Species denotes MERS-CoV Tax:1335626
59 1962-1965 Species denotes CoV Tax:11118
60 2071-2074 Species denotes CoV Tax:11118
61 2221-2224 Species denotes CoV Tax:11118
62 1318-1324 Species denotes β-CoVs Tax:694002
63 1351-1371 Disease denotes respiratory distress MESH:D012128
64 1462-1486 Disease denotes coronavirus disease 2019 MESH:C000657245
65 1488-1496 Disease denotes COVID-19 MESH:C000657245
66 1521-1530 Disease denotes pneumonia MESH:D011014
67 2299-2309 Disease denotes CoV N-CTDs MESH:C000657245
77 2459-2467 Species denotes MERS-CoV Tax:1335626
78 3100-3108 Species denotes MERS-CoV Tax:1335626
79 2760-2765 Chemical denotes P1–P3
80 2817-2835 Chemical denotes 5-benzyloxygramine MESH:C006736
81 2837-2839 Chemical denotes P3
82 2975-2977 Chemical denotes P3
83 3109-3114 Chemical denotes N-NTD
84 3130-3148 Chemical denotes 5-benzyloxygramine MESH:C006736
85 3409-3428 Disease denotes infectious diseases MESH:D003141

2_test

Id Subject Object Predicate Lexical cue
32105468-28968506-61929489 190-191 28968506 denotes 3
32105468-30957264-61929490 419-420 30957264 denotes 4
32105468-30913483-61929491 421-422 30913483 denotes 7
32105468-28283069-61929492 707-709 28283069 denotes 10
32105468-29268608-61929493 1227-1229 29268608 denotes 11
32105468-23075143-61929494 1409-1411 23075143 denotes 12
32105468-32402160-61929495 1612-1614 32402160 denotes 15
32105468-31953166-61929496 1615-1617 31953166 denotes 16
32105468-31099550-61929497 1747-1749 31099550 denotes 17
32105468-26691874-61929498 2061-2063 26691874 denotes 18
32105468-26868298-61929499 2064-2066 26868298 denotes 19
32105468-25105276-61929500 2211-2213 25105276 denotes 20
32105468-27344959-61929501 2214-2216 27344959 denotes 21
32105468-24564608-61929502 2412-2414 24564608 denotes 22
32105468-30644840-61929503 2415-2417 30644840 denotes 23