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PMC:7094172 / 24075-27564 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T406 2029-2037 SP_9 denotes MERS-CoV
T405 2223-2236 NCBITaxon:11118 denotes coronaviruses
T404 2427-2436 CHEBI:36357;CHEBI:36357 denotes compounds
T403 2510-2518 SP_7 denotes COVID-19
T402 2541-2546 NCBITaxon:10088 denotes mouse
T401 2547-2556 NCBITaxon:5690 denotes hepatitis
T400 2557-2562 NCBITaxon:10239 denotes virus
T399 2564-2567 NCBITaxon:11757 denotes MHV
T398 2597-2602 NCBITaxon:10239 denotes viral
T397 2646-2649 NCBITaxon:11757 denotes MHV
T396 2650-2661 GO:0006260 denotes replication
T395 3452-3461 CHEBI:36357;CHEBI:36357 denotes compounds
T424 17-26 CHEBI:36357;CHEBI:36357 denotes molecules
T423 140-149 CHEBI:36357;CHEBI:36357 denotes compounds
T422 303-312 CHEBI:36357;CHEBI:36357 denotes compounds
T421 555-568 PG_4 denotes nucleoprotein
T420 644-653 CHEBI:25106;CHEBI:25106 denotes macrolide
T419 685-703 GO:0015629 denotes actin cytoskeleton
T418 718-728 CHEBI:67079;CHEBI:67079 denotes anticancer
T417 789-790 GO:0000811 denotes G
T416 790-796 GO:0031941 denotes -actin
T415 1269-1287 CHEBI:36357;CHEBI:36357 denotes molecule compounds
T414 1535-1543 SP_9 denotes MERS-CoV
T413 1586-1594 SP_9 denotes MERS-CoV
T412 1601-1613 GO:0046983 denotes dimerization
T411 1631-1640 PG_4 denotes N protein
T410 1740-1743 SO:0000694 denotes RNP
T409 1970-1974 CHEBI:23888;CHEBI:23888;GO:0017144 denotes drug
T408 1975-1986 GO:0017144 denotes development
T407 2007-2020 NCBITaxon:11118 denotes coronaviruses

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T121 685-703 Body_part denotes actin cytoskeleton http://purl.org/sig/ont/fma/fma84684
T122 789-796 Body_part denotes G-actin http://purl.org/sig/ont/fma/fma67893
T123 941-948 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T124 949-956 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T125 961-968 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T126 1479-1486 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T127 1633-1640 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T128 1942-1950 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T129 2043-2054 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T130 2688-2692 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T131 3077-3084 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 2688-2692 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p35904s12 673-680 NegReg denotes disrupt
p35904s14 685-703 MPA denotes actin cytoskeleton
p35911s11 1622-1652 MPA denotes abnormal N protein aggregation
p35918s15 2584-2593 NegReg denotes reduction

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T92 425-434 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T93 1597-1600 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T95 2108-2111 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T97 2510-2518 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 2547-2556 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T181 55-58 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T182 76-77 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 272-274 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T184 485-486 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 622-626 http://purl.obolibrary.org/obo/CLO_0001627 denotes A, a
T186 655-658 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T187 748-751 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T188 800-801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 831-833 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T190 912-913 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 1169-1177 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T192 1340-1341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 1412-1413 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 1456-1464 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T195 1851-1854 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T196 1964-1965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 2457-2465 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T198 2474-2475 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 2528-2534 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T200 2541-2546 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T201 2557-2562 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T202 2582-2583 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 2670-2672 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T204 3292-3294 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T205 3295-3297 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T200 17-26 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T201 40-43 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T203 202-205 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T205 366-369 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T207 569-578 Chemical denotes oligomers http://purl.obolibrary.org/obo/CHEBI_132554
T208 644-653 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T209 718-734 Chemical denotes anticancer agent http://purl.obolibrary.org/obo/CHEBI_35610
T210 941-948 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T211 949-956 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T212 961-968 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T213 969-975 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T214 1238-1244 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T215 1269-1277 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T216 1479-1486 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T217 1633-1640 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T218 1942-1950 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T219 1970-1974 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T220 2043-2054 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T221 2043-2048 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T222 2049-2054 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T223 2357-2359 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T224 2670-2672 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T225 2850-2853 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T227 3077-3084 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T228 3264-3272 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T229 3273-3282 Chemical denotes deuterium http://purl.obolibrary.org/obo/CHEBI_29237
T230 3292-3294 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T19 1683-1691 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T20 1744-1753 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T21 2767-2776 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T22 3283-3291 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T4 2547-2556 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T194 0-134 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 135-1126 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 1127-1358 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 1359-1562 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 1563-1754 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 1755-1898 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 1899-2000 Sentence denotes Thus, non-native interaction interfaces in proteins may comprise a new drug development target class.
T201 2001-2137 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 2138-2361 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 2362-2519 Sentence denotes This conservation may provide certain advantages when developing compounds with broad-spectrum activity against a target pathogen family, including COVID-19.
T204 2520-2674 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 2675-2753 Sentence denotes On the other hand, targeting non-native interaction interfaces is not trivial.
T206 2754-2925 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 2926-3039 Sentence denotes Nevertheless, several stratagems may assist in the identification of potential non-native interaction interfaces.
T208 3040-3162 Sentence denotes One strategy is to search for target protein structures with crystal packing contacts known to be biologically irrelevant.
T209 3163-3489 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.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
418 1740-1743 Gene denotes RNP Gene:55599
419 1535-1543 Species denotes MERS-CoV Tax:1335626
420 1586-1594 Species denotes MERS-CoV Tax:1335626
421 2005-2020 Species denotes β-coronaviruses Tax:694002
422 2029-2037 Species denotes MERS-CoV Tax:1335626
423 2221-2236 Species denotes β-coronaviruses Tax:694002
424 2541-2562 Species denotes mouse hepatitis virus Tax:11138
425 425-434 Species denotes influenza Tax:11309
426 2564-2567 Species denotes MHV Tax:11138
427 2646-2649 Species denotes MHV Tax:11138
428 444-453 Chemical denotes nucleozin
429 637-653 Chemical denotes marine macrolide
430 1695-1700 Chemical denotes N-CTD
431 2106-2111 Chemical denotes N-NTD
432 3264-3272 Chemical denotes hydrogen MESH:D006859
433 3273-3282 Chemical denotes deuterium MESH:D003903
434 1622-1652 Disease denotes abnormal N protein aggregation MESH:D001791
435 2510-2518 Disease denotes COVID-19 MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32105468-31141413-61929515 272-274 31141413 denotes 35
32105468-28300404-61929516 275-277 28300404 denotes 37
32105468-27820802-61929517 413-415 27820802 denotes 38
32105468-20512121-61929518 608-610 20512121 denotes 40
32105468-15797212-61929519 831-833 15797212 denotes 41
32105468-7876075-61929520 834-836 7876075 denotes 43
32105468-29308120-61929521 989-991 29308120 denotes 44
32105468-16775348-61929522 2240-2242 16775348 denotes 28
32105468-16503614-61929523 3295-3297 16503614 denotes 45