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PMC:7094172 / 24048-28114 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T406 2056-2064 SP_9 denotes MERS-CoV
T405 2250-2263 NCBITaxon:11118 denotes coronaviruses
T404 2454-2463 CHEBI:36357;CHEBI:36357 denotes compounds
T403 2537-2545 SP_7 denotes COVID-19
T402 2568-2573 NCBITaxon:10088 denotes mouse
T401 2574-2583 NCBITaxon:5690 denotes hepatitis
T400 2584-2589 NCBITaxon:10239 denotes virus
T399 2591-2594 NCBITaxon:11757 denotes MHV
T398 2624-2629 NCBITaxon:10239 denotes viral
T397 2673-2676 NCBITaxon:11757 denotes MHV
T396 2677-2688 GO:0006260 denotes replication
T395 3479-3488 CHEBI:36357;CHEBI:36357 denotes compounds
T394 3622-3633 GO:0051259 denotes oligomerize
T393 3645-3653 SP_9 denotes MERS-CoV
T392 3654-3663 PG_4 denotes N protein
T391 3749-3757 CHEBI:36357;CHEBI:36357 denotes molecule
T390 3960-3964 CHEBI:23888;CHEBI:23888 denotes drug
T389 4030-4039 CHEBI:36357;CHEBI:36357 denotes compounds
T424 44-53 CHEBI:36357;CHEBI:36357 denotes molecules
T423 167-176 CHEBI:36357;CHEBI:36357 denotes compounds
T422 330-339 CHEBI:36357;CHEBI:36357 denotes compounds
T421 582-595 PG_4 denotes nucleoprotein
T420 671-680 CHEBI:25106;CHEBI:25106 denotes macrolide
T419 712-730 GO:0015629 denotes actin cytoskeleton
T418 745-755 CHEBI:67079;CHEBI:67079 denotes anticancer
T417 816-817 GO:0000811 denotes G
T416 817-823 GO:0031941 denotes -actin
T415 1296-1314 CHEBI:36357;CHEBI:36357 denotes molecule compounds
T414 1562-1570 SP_9 denotes MERS-CoV
T413 1613-1621 SP_9 denotes MERS-CoV
T412 1628-1640 GO:0046983 denotes dimerization
T411 1658-1667 PG_4 denotes N protein
T410 1767-1770 SO:0000694 denotes RNP
T409 1997-2001 CHEBI:23888;CHEBI:23888;GO:0017144 denotes drug
T408 2002-2013 GO:0017144 denotes development
T407 2034-2047 NCBITaxon:11118 denotes coronaviruses

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T121 712-730 Body_part denotes actin cytoskeleton http://purl.org/sig/ont/fma/fma84684
T122 816-823 Body_part denotes G-actin http://purl.org/sig/ont/fma/fma67893
T123 968-975 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T124 976-983 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T125 988-995 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T126 1506-1513 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T127 1660-1667 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T128 1969-1977 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T129 2070-2081 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T130 2715-2719 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T131 3104-3111 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T132 3602-3610 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T133 3656-3663 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 2715-2719 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p35904s12 700-707 NegReg denotes disrupt
p35904s14 712-730 MPA denotes actin cytoskeleton
p35911s11 1649-1679 MPA denotes abnormal N protein aggregation
p35918s15 2611-2620 NegReg denotes reduction

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T92 452-461 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T93 1624-1627 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T95 2135-2138 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T97 2537-2545 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 2574-2583 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T181 82-85 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T182 103-104 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 299-301 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T184 512-513 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 649-653 http://purl.obolibrary.org/obo/CLO_0001627 denotes A, a
T186 682-685 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T187 775-778 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T188 827-828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 858-860 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T190 939-940 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 1196-1204 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T192 1367-1368 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 1439-1440 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 1483-1491 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T195 1878-1881 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T196 1991-1992 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 2484-2492 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T198 2501-2502 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 2555-2561 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T200 2568-2573 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T201 2584-2589 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T202 2609-2610 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 2697-2699 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T204 3319-3321 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T205 3322-3324 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T206 3938-3944 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T200 44-53 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T201 67-70 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T203 229-232 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T205 393-396 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T207 596-605 Chemical denotes oligomers http://purl.obolibrary.org/obo/CHEBI_132554
T208 671-680 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T209 745-761 Chemical denotes anticancer agent http://purl.obolibrary.org/obo/CHEBI_35610
T210 968-975 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T211 976-983 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T212 988-995 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T213 996-1002 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T214 1265-1271 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T215 1296-1304 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T216 1506-1513 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T217 1660-1667 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T218 1969-1977 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T219 1997-2001 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T220 2070-2081 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T221 2070-2075 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T222 2076-2081 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T223 2384-2386 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T224 2697-2699 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T225 2877-2880 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T227 3104-3111 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T228 3291-3299 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T229 3300-3309 Chemical denotes deuterium http://purl.obolibrary.org/obo/CHEBI_29237
T230 3319-3321 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T231 3602-3610 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T232 3656-3663 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T233 3749-3757 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T234 3960-3964 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T235 4025-4039 Chemical denotes lead compounds http://purl.obolibrary.org/obo/CHEBI_33585

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T19 1710-1718 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T20 1771-1780 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T21 2794-2803 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T22 3310-3318 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T4 2574-2583 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T193 0-26 Sentence denotes Discussion and Conclusions
T194 27-161 Sentence denotes The use of small molecules to stabilize PPI interfaces has been shown to be a viable approach for the development of new therapeutics.
T195 162-1153 Sentence denotes Most compounds created by structure-based design to manipulate the PPI depend on detailed knowledge of the native interacting interfaces.35−37 In contrast, most of the compounds with therapeutic potential that stabilize non-native PPI interfaces were discovered by chance alone.38 The anti-influenza compound nucleozin was initially discovered using a chemical genetics approach, and its ability to stabilize non-native nucleoprotein oligomers was elucidated much later.39,40 Swinholide A, a cytotoxic marine macrolide, has been known to disrupt the actin cytoskeleton and act as an anticancer agent, but it took ten years to discover that it stabilized G-actin as a non-native homodimer complex.41−43 However, these examples did underscore the importance of hydrophobicity as a crucial factor stabilizing protein–protein and protein–ligand associations.44 Here, we demonstrated the possibility of using the hydrophobic interactions on non-native interfaces as targets for virtual screening.
T196 1154-1385 Sentence denotes Combined with suitable selection criteria focusing on both shape and hydrophobic complementarities between the ligand and the receptor, small-molecule compounds that stabilize non-native PPIs may be identified in a rational manner.
T197 1386-1589 Sentence denotes Using the above approach, we successfully identified a compound P3 that affected the biochemical activity of our target protein and showed efficacy against our target pathogen MERS-CoV (Figures 2 and 4).
T198 1590-1781 Sentence denotes P3-mediated non-native MERS-CoV N-NTD dimerization induced abnormal N protein aggregation by influencing the oligomeric behavior of N-CTD and eventually halting its function in RNP formation.
T199 1782-1925 Sentence denotes To the best of our knowledge, this structure-based strategy for targeting non-native interfaces has never been proposed for therapeutic design.
T200 1926-2027 Sentence denotes Thus, non-native interaction interfaces in proteins may comprise a new drug development target class.
T201 2028-2164 Sentence denotes For β-coronaviruses such as MERS-CoV, the amino acids comprising the non-native interaction interface on N-NTD are relatively conserved.
T202 2165-2388 Sentence denotes The hydrophobic pocket surrounding W43 and F135 on monomer 1 is shared among other β-coronaviruses.24,28 The interacting surface on monomer 2, which includes G104, T105, G106, and A109, is also highly conserved (Figure S4).
T203 2389-2546 Sentence denotes This conservation may provide certain advantages when developing compounds with broad-spectrum activity against a target pathogen family, including COVID-19.
T204 2547-2701 Sentence denotes When we tested P3 on mouse hepatitis virus (MHV), we observed a reduction in viral titer, indicating that P3 may also inhibit MHV replication (Figure S5).
T205 2702-2780 Sentence denotes On the other hand, targeting non-native interaction interfaces is not trivial.
T206 2781-2952 Sentence denotes As interface formation is induced by an external agent, computations aimed at predicting native PPI structures may not be able to identify potential non-native interfaces.
T207 2953-3066 Sentence denotes Nevertheless, several stratagems may assist in the identification of potential non-native interaction interfaces.
T208 3067-3189 Sentence denotes One strategy is to search for target protein structures with crystal packing contacts known to be biologically irrelevant.
T209 3190-3516 Sentence denotes Another approach is to identify weakly interacting sites through NMR chemical shift perturbation and hydrogen-deuterium exchange MS.45 Once these potential non-native interaction interfaces are identified, standard screening and then functional characterization may be conducted for small compounds that bind to the interface.
T210 3517-3634 Sentence denotes To summarize, we demonstrated that non-native interaction interfaces might form when proteins abnormally oligomerize.
T211 3635-3785 Sentence denotes Using the MERS-CoV N protein as an example, we showed that non-native interfaces might serve as targets for small-molecule, structure-based screening.
T212 3786-3898 Sentence denotes We also proposed several stratagems to rationally identify potential non-native interface targets for screening.
T213 3899-4066 Sentence denotes We believe that we have discovered and tested an alternative drug discovery paradigm that could help expand the repertoire of lead compounds against various pathogens.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
418 1767-1770 Gene denotes RNP Gene:55599
419 1562-1570 Species denotes MERS-CoV Tax:1335626
420 1613-1621 Species denotes MERS-CoV Tax:1335626
421 2032-2047 Species denotes β-coronaviruses Tax:694002
422 2056-2064 Species denotes MERS-CoV Tax:1335626
423 2248-2263 Species denotes β-coronaviruses Tax:694002
424 2568-2589 Species denotes mouse hepatitis virus Tax:11138
425 452-461 Species denotes influenza Tax:11309
426 2591-2594 Species denotes MHV Tax:11138
427 2673-2676 Species denotes MHV Tax:11138
428 471-480 Chemical denotes nucleozin
429 664-680 Chemical denotes marine macrolide
430 1722-1727 Chemical denotes N-CTD
431 2133-2138 Chemical denotes N-NTD
432 3291-3299 Chemical denotes hydrogen MESH:D006859
433 3300-3309 Chemical denotes deuterium MESH:D003903
434 1649-1679 Disease denotes abnormal N protein aggregation MESH:D001791
435 2537-2545 Disease denotes COVID-19 MESH:C000657245
437 3645-3653 Species denotes MERS-CoV Tax:1335626

2_test

Id Subject Object Predicate Lexical cue
32105468-31141413-61929515 299-301 31141413 denotes 35
32105468-28300404-61929516 302-304 28300404 denotes 37
32105468-27820802-61929517 440-442 27820802 denotes 38
32105468-20512121-61929518 635-637 20512121 denotes 40
32105468-15797212-61929519 858-860 15797212 denotes 41
32105468-7876075-61929520 861-863 7876075 denotes 43
32105468-29308120-61929521 1016-1018 29308120 denotes 44
32105468-16775348-61929522 2267-2269 16775348 denotes 28
32105468-16503614-61929523 3322-3324 16503614 denotes 45