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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T170 33-255 SO:0000855 denotes or SARS-CoV-2 infection, kinase inhibitors were mapped to the most differentially regulated kinase activities (Figure 7 A) and to specific phosphorylation sites (Table S8; STAR Methods). This resulted in a list of 87 drugs

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T364 432-436 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T365 794-802 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T366 977-981 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T367 1386-1391 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T368 1550-1558 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T369 1590-1594 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T370 1674-1679 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T371 1763-1770 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T372 2084-2089 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T373 2265-2269 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T374 2270-2286 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T375 2281-2286 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T376 2388-2391 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T377 2567-2571 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T378 2714-2719 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T16 2265-2269 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T219 36-44 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T220 47-56 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T221 205-209 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T222 690-698 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T223 1168-1176 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T224 1276-1284 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T225 1287-1296 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T226 1456-1464 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T227 1467-1476 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T228 2229-2237 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T229 2240-2249 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T230 2344-2352 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T231 2355-2364 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T232 2479-2487 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T233 2814-2822 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T234 2825-2834 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T535 132-142 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T536 153-154 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T537 237-238 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T538 311-318 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T539 432-436 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T540 452-453 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T541 563-570 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T542 742-748 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T543 791-793 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T544 977-987 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell lines
T545 989-993 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T546 989-993 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T547 1006-1010 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T548 1006-1010 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T549 1006-1010 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T550 1006-1010 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T551 1006-1010 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T552 1006-1010 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T553 1006-1010 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T554 1006-1010 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T555 1084-1086 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T556 1190-1191 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T557 1250-1258 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T558 1375-1376 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T559 1378-1391 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T560 1481-1483 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T561 1547-1549 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T562 1590-1594 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T563 1662-1663 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T564 1666-1679 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T565 1828-1829 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T566 1896-1904 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T567 1917-1926 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T568 2072-2073 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T569 2076-2089 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T570 2255-2259 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T571 2255-2259 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T572 2255-2259 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T573 2255-2259 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T574 2255-2259 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T575 2255-2259 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T576 2255-2259 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T577 2255-2259 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T578 2265-2286 http://purl.obolibrary.org/obo/CL_0000082 denotes lung epithelial cells
T579 2425-2430 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T580 2434-2438 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T581 2434-2438 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T582 2434-2438 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T583 2434-2438 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T584 2434-2438 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T585 2434-2438 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T586 2434-2438 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T587 2434-2438 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T588 2453-2454 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T589 2567-2571 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T590 2693-2697 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T591 2693-2697 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T592 2704-2708 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T593 2704-2708 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T594 2704-2708 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T595 2704-2708 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T596 2704-2708 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T597 2704-2708 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T598 2704-2708 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T599 2704-2708 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T600 2714-2719 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T300 65-75 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T301 201-203 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T302 250-255 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T303 353-358 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T304 571-580 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T305 717-722 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T306 753-762 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T307 791-793 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T310 915-920 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T311 1084-1086 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T312 1097-1099 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T313 1200-1210 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T314 1359-1363 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T315 1409-1419 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T316 1526-1530 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T317 1547-1549 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T320 1647-1649 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T321 1706-1715 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T322 1763-1770 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T323 1939-1944 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T324 2044-2056 Chemical denotes gilteritinib http://purl.obolibrary.org/obo/CHEBI_145372
T325 2107-2120 Chemical denotes AXL inhibitor http://purl.obolibrary.org/obo/CHEBI_62434
T326 2111-2120 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T327 2121-2133 Chemical denotes gilteritinib http://purl.obolibrary.org/obo/CHEBI_145372
T328 2153-2162 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T329 2194-2203 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T330 2316-2325 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T331 2746-2755 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T332 2776-2789 Chemical denotes CDK inhibitor http://purl.obolibrary.org/obo/CHEBI_82665
T333 2780-2789 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T321 58-75 http://purl.obolibrary.org/obo/GO_0033673 denotes kinase inhibitors
T322 125-142 http://purl.obolibrary.org/obo/GO_0016301 denotes kinase activities
T323 172-187 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T324 1139-1156 http://purl.obolibrary.org/obo/GO_0033673 denotes Kinase Inhibitors
T325 1193-1210 http://purl.obolibrary.org/obo/GO_0033673 denotes Kinase inhibitors
T326 1889-1904 http://purl.obolibrary.org/obo/GO_0016301 denotes kinase activity
T327 1917-1934 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathway
T328 1917-1926 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T329 2490-2507 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T330 2490-2507 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T331 2776-2789 http://purl.obolibrary.org/obo/GO_0004861 denotes CDK inhibitor

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
929 1168-1178 Species denotes SARS-CoV-2 Tax:2697049
931 1276-1296 Disease denotes SARS-CoV-2 infection MESH:C000657245
935 1409-1419 Chemical denotes remdesivir MESH:C000606551
936 1456-1476 Disease denotes SARS-CoV-2 infection MESH:C000657245
937 1383-1385 CellLine denotes E6 CVCL:4582
942 1779-1786 Gene denotes CSNK2A2 Gene:1459
943 1761-1762 Gene denotes N Gene:43740575
944 1716-1729 Chemical denotes silmitasertib
945 1671-1673 CellLine denotes E6 CVCL:4582
950 1913-1916 Gene denotes p38 Gene:5594
951 1995-2001 Gene denotes MAPK13 Gene:5603
952 1982-1993 Chemical denotes ralimetinib
953 2044-2056 Chemical denotes gilteritinib MESH:C000609080
962 2107-2110 Gene denotes AXL Gene:103234725
963 2143-2152 Gene denotes MAPK11/14 Gene:103223551
964 2187-2193 Gene denotes MAPK13 Gene:103221595
965 2204-2210 Gene denotes MAPK13 Gene:103221595
966 2121-2133 Chemical denotes gilteritinib MESH:C000609080
967 2163-2174 Chemical denotes ralimetinib
968 2229-2249 Disease denotes SARS-CoV-2 infection MESH:C000657245
969 2081-2083 CellLine denotes E6 CVCL:4582
975 2260-2264 Gene denotes ACE2 Gene:59272
976 2309-2315 Gene denotes MAPK14 Gene:1432
977 2326-2334 Chemical denotes ARRY-797 MESH:C000592910
978 2344-2364 Disease denotes SARS-CoV-2 infection MESH:C000657245
979 2255-2259 CellLine denotes A549 CVCL:0023
985 2413-2416 Gene denotes p38 Gene:5594
986 2439-2443 Gene denotes ACE2 Gene:59272
987 2591-2595 Gene denotes ACE2 Gene:59272
988 2479-2489 Species denotes SARS-CoV-2 Tax:2697049
989 2434-2438 CellLine denotes A549 CVCL:0023
994 2790-2800 Chemical denotes dinaciclib MESH:C553669
995 2814-2834 Disease denotes SARS-CoV-2 infection MESH:C000657245
996 2698-2700 CellLine denotes E6 CVCL:4582
997 2704-2713 CellLine denotes A549-ACE2 CVCL:0023
999 2852-2854 Gene denotes S6
1006 1011-1015 Gene denotes ACE2 Gene:59272
1007 690-700 Species denotes SARS-CoV-2 Tax:2697049
1008 36-56 Disease denotes SARS-CoV-2 infection MESH:C000657245
1009 846-854 Disease denotes toxicity MESH:D064420
1010 994-996 CellLine denotes E6 CVCL:4582
1011 1006-1010 CellLine denotes A549 CVCL:0023

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T293 0-219 Sentence denotes To identify effective therapies for SARS-CoV-2 infection, kinase inhibitors were mapped to the most differentially regulated kinase activities (Figure 7 A) and to specific phosphorylation sites (Table S8; STAR Methods).
T294 220-270 Sentence denotes This resulted in a list of 87 drugs and compounds:
T295 271-340 Sentence denotes 10 FDA-approved, 53 undergoing clinical testing, and 24 pre-clinical.
T296 341-545 Sentence denotes Many of the drugs and compounds identified were reported to target several host kinases in cell-free assays at a minimum, but many have been observed to hit targets in cellular assays as well (Figure 7A).
T297 546-701 Sentence denotes We reasoned that testing molecules with both overlapping and unique targets would help specify the molecular targets of greatest importance for SARS-CoV-2.
T298 702-1022 Sentence denotes Here, 68 total drugs and compounds were tested for antiviral efficacy (via qRT-PCR, anti-NP antibody, plaque assay, and/or TCID50) and cellular toxicity at two different institutions (in New York [Mount Sinai, 25 drugs/compounds] and Paris [Institut Pasteur, 62]) and in two cell lines (Vero E6 [68] and A549-ACE2 [61]).
T299 1023-1100 Sentence denotes All pharmacological profiling results can be found in Figure S5 and Table S8.
T300 1101-1188 Sentence denotes Figure 7 Mapping Regulated Kinases to Kinase Inhibitors Identifies SARS-CoV-2 Therapies
T301 1189-1297 Sentence denotes (A) Kinase inhibitors (left) mapped to kinases (right) whose activity was regulated by SARS-CoV-2 infection.
T302 1298-1373 Sentence denotes Lines connecting them indicate known kinase targets for each drug/compound.
T303 1374-1486 Sentence denotes (B) Vero E6 cells pre-treated with remdesivir at the indicated doses, followed by SARS-CoV-2 infection for 48 h.
T304 1487-1625 Sentence denotes Percent viral titer compared with mock drug treatment (anti-NP antibody; red line, dots, and text) and cell viability (black) is depicted.
T305 1626-1650 Sentence denotes Error bars represent SD.
T306 1651-1665 Sentence denotes (C) As in (B).
T307 1666-1730 Sentence denotes Vero E6 cells were treated with the CK2 inhibitor silmitasertib.
T308 1731-1864 Sentence denotes Physical interactions between N protein and the CSNK2A2 and CSNK2B CK2 subunits were observed in a prior study (Gordon et al., 2020).
T309 1865-2058 Sentence denotes (D) Predicted increased kinase activity for the p38 signaling pathway and drugs/compounds targeting pathway members (ralimetinib, MAPK13-IN-1, and ARRY-797) and upstream drivers (gilteritinib).
T310 2059-2075 Sentence denotes (E–G) As in (B).
T311 2076-2250 Sentence denotes Vero E6 cells treated with the AXL inhibitor gilteritinib (E), the MAPK11/14 inhibitor ralimetinib (F), or the MAPK13 inhibitor MAPK13-IN-1 (G) prior to SARS-CoV-2 infection.
T312 2251-2365 Sentence denotes (H) A549-ACE2 lung epithelial cells were treated with the MAPK14 inhibitor ARRY-797 prior to SARS-CoV-2 infection.
T313 2366-2590 Sentence denotes (I) Small interfering RNA (siRNA) knockdown of p38 pathway genes in A549-ACE2 leads to a significant decrease in SARS-CoV-2 viral replication (red), as assessed by qRT-PCR in the absence of effects on cell viability (black).
T314 2591-2682 Sentence denotes ACE2 and non-targeting siRNAs are included as positive and negative controls, respectively.
T315 2683-2835 Sentence denotes (J and K) Vero E6 or A549-ACE2 cells were treated with PIKFYVE inhibitor apilimod (J) or the CDK inhibitor dinaciclib (K) prior to SARS-CoV-2 infection.
T316 2836-2855 Sentence denotes See also Figure S6.