> top > docs > PMC:7214327 > annotations

PMC:7214327 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 534-537 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 1785-1795 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T3 1901-1904 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 1915-1918 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 1993-1996 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 2251-2261 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T7 2279-2282 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 2402-2412 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T9 2454-2457 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 2473-2484 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T11 3253-3256 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 3324-3330 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T13 3500-3503 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 3873-3876 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 4000-4003 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 4322-4326 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 64-72 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 102-110 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 390-398 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 551-559 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 675-683 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 718-726 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 752-762 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T8 1617-1622 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T9 1742-1746 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 2099-2107 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 2112-2120 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 2761-2769 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 2774-2782 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 3721-3729 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3798-3806 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 3842-3850 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 4174-4189 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T18 4180-4189 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 697-698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 858-859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 1170-1171 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 1292-1297 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 1329-1330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1354-1355 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1425-1426 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1551-1552 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1582-1590 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T10 1604-1611 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T11 1669-1674 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T12 1696-1697 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1783-1784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1874-1875 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1954-1957 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 2010-2011 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2138-2141 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 2309-2312 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T19 2366-2367 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 2580-2583 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 2696-2703 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T22 2859-2862 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T23 2961-2962 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 3033-3034 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 3177-3178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 3281-3284 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 3455-3456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3569-3576 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T29 3665-3666 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3733-3735 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T31 3808-3814 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2. (A)
T32 3922-3923 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T33 4069-4070 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 4103-4111 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T35 4144-4145 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 4221-4226 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T37 4270-4271 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 4322-4326 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 226-236 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T2 241-255 Chemical denotes antiviral drug http://purl.obolibrary.org/obo/CHEBI_36044
T3 241-250 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T4 251-255 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T5 273-281 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T6 364-368 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T7 508-518 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T8 641-651 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T9 1021-1025 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T10 1237-1242 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T11 1346-1350 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T12 1404-1408 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T13 1512-1517 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T14 1521-1531 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T15 1785-1795 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T16 1818-1830 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T17 1854-1856 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T18 2165-2167 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T19 2191-2213 Chemical denotes Adenosine triphosphate http://purl.obolibrary.org/obo/CHEBI_15422
T20 2191-2200 Chemical denotes Adenosine http://purl.obolibrary.org/obo/CHEBI_16335
T21 2201-2213 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T22 2215-2218 Chemical denotes ATP http://purl.obolibrary.org/obo/CHEBI_15422|http://purl.obolibrary.org/obo/CHEBI_30616
T24 2220-2228 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T25 2251-2261 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T26 2335-2349 Chemical denotes hydroxyl group http://purl.obolibrary.org/obo/CHEBI_43176
T27 2335-2343 Chemical denotes hydroxyl http://purl.obolibrary.org/obo/CHEBI_29191
T28 2344-2349 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T29 2357-2359 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T30 2402-2412 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T31 2473-2484 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T32 2542-2544 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T33 3026-3028 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T34 3324-3338 Chemical denotes serine residue http://purl.obolibrary.org/obo/CHEBI_32848
T35 3324-3330 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T36 3642-3644 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 522-547 http://purl.obolibrary.org/obo/GO_1902679 denotes inhibit the RNA synthesis
T2 534-547 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T3 538-547 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T4 1993-2006 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T5 1997-2006 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T6 2279-2292 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T7 2283-2292 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T8 2435-2444 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T9 2454-2467 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T10 2458-2467 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T11 3253-3266 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T12 3257-3266 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T13 3500-3513 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T14 3504-3513 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T15 3873-3886 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T16 3877-3886 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T17 3981-3990 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T18 4174-4189 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-73 Sentence denotes Probable Molecular Mechanism of Remdesivir for the Treatment of COVID-19:
T2 74-91 Sentence denotes Need to Know More
T3 93-101 Sentence denotes Abstract
T4 102-148 Sentence denotes COVID-19 is now pandemic throughout the world.
T5 149-221 Sentence denotes Scientist, doctors are searching for effective therapy of this diseases.
T6 222-325 Sentence denotes The remdesivir, an antiviral drug, is appeared as ‘molecule of hope’ for the treatment of this disease.
T7 326-399 Sentence denotes USFDA gave emergency approval to this drug for the treatment of COVID-19.
T8 400-435 Sentence denotes The molecular mechanism is unknown.
T9 436-562 Sentence denotes In this paper, we tried to describe the probable molecular mechanism of remdesivir to inhibit the RNA synthesis of SARS-CoV-2.
T10 563-652 Sentence denotes However, more detail mechanism is needed to understand mechanism of action of remdesivir.
T11 654-729 Sentence denotes The current pandemic COVID-19 is caused by a novel coronavirus, SARS-CoV-2.
T12 730-892 Sentence denotes The disease is highly infectious like other coronaviral disease and causing already more than 2.3 lacs deaths worldwide, posing a serious threat to mankind (1,2).
T13 893-1076 Sentence denotes Scientists, doctors and other health professional are working very hard to combat this current situation, but still there is no drug or vaccine available to treat this morbid disease.
T14 1077-1136 Sentence denotes But researchers are trying to develop new therapeutics (3).
T15 1137-1498 Sentence denotes However this situation initiates a global effort to find out effective measures or discovery of new drugs or vaccines to stop the spreading of this deadly virus, but, since the development of a new vaccine or drug is a time-consuming process, repurposing of existing drug could be act as a brilliant alternative with potential to combat the disease effectively.
T16 1499-1768 Sentence denotes One of these drugs is remdesivir (RDV), which shows a broad spectrum of anti-viral activity against many viruses like Ebola (4,5), Nipah (6, 7, 8), respiratory syncytial virus (RSV) family (8) and a diverse category of coronaviruses including SARS CoV and MERS CoV (9).
T17 1769-2134 Sentence denotes Remdesivir is a nucleotide analogue (4), and the triphosphate form of RDV, i.e., RDV-TP is being used as a substrate for many viral RNA-dependent RNA polymerase (RdRp) complexes and it has been reported to inhibit the viral RNA synthesis by a specific mechanism of delayed chain termination for all three coronaviruses (MERS-CoV, SARS-CoV and SARS-CoV-2) RdRp (10).
T18 2135-2305 Sentence denotes It has been observed that RDV-TP resembles specifically Adenosine triphosphate (ATP) molecule and competes with the nucleotide during the viral RNA synthesis (Figure 1 ).
T19 2306-2566 Sentence denotes It has been reported that 3′ hydroxyl group of RDV-TP forms a phosphodiester bond with the next nucleotide but it terminates the formation of viral RNA synthesis at 3 nucleotides downstream, precisely at i + 3 position, whereas the RDV-TP is the i-th position.
T20 2567-2841 Sentence denotes Moreover, it has also been fascinating to note that the underlying mechanism of chain termination is more or less common in many viruses including all the recent coronaviruses, namely MERS-CoV, SARS-CoV and SARS-CoV-2, though the precise molecular mechanism remains elusive.
T21 2842-3062 Sentence denotes Additionally, it has been reported very recently that the main reason of chain termination at i + 4 position is due to a steric clash between 1′-CN substituent of the incorporated RDV-TP and a specific residue S861 (10).
T22 3063-3267 Sentence denotes It is consistent with the chain termination at i + 3 position due to the imposed inability of RdRp to translocate a single position downstream, so eventually it terminates the nascent viral RNA synthesis.
T23 3268-3373 Sentence denotes Moreover, it has also been imperative to note that this serine residue is conserved in all coronaviruses.
T24 3374-3514 Sentence denotes Though, the actual molecular mechanism is still not very clear but this could be a plausible explanation of termination viral RNA synthesis.
T25 3515-3737 Sentence denotes Recently, scientists also expressed RdRp of different viruses and measure kinetic parameters to infer its interaction with RDV-TP and also determined a score of 0.77 mmol half maximal concentration against SARS-CoV-2 (11).
T26 3738-4004 Sentence denotes Figure 1 Probable molecular mechanism of Remdisivir against SARS-CoV- 2. (A) Thematic diagram shows the SARS-CoV-2 viral entry and its RNA synthesis which can be block by Remdisivir. (B) Detail molecular mechanism of Remdisivir to inhibit the synthesis of viral RNA.
T27 4005-4378 Sentence denotes It can be concluded that this chain termination method could be a general mechanism of anti-viral activity of this particular substrate to a broad spectrum of different viral infection, but still the availability of human trial and safety data is pending, and also a detailed anti-viral profiling of this compound in cell culture study is highly appreciated at this moment.
T28 4380-4400 Sentence denotes Conflict of Interest
T29 4401-4459 Sentence denotes No potential conflict of interest was declared by authors.
T30 4461-4468 Sentence denotes Funding
T31 4469-4689 Sentence denotes This research was supported by Hallym University Research Fund and by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1A2B4012944).
T32 4691-4709 Sentence denotes Supplementary data
T33 4710-4722 Sentence denotes Data Profile

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 32-42 Chemical denotes Remdesivir MESH:C000606551
3 64-72 Disease denotes COVID-19 MESH:C000657245
10 551-561 Species denotes SARS-CoV-2 Tax:2697049
11 226-236 Chemical denotes remdesivir MESH:C000606551
12 508-518 Chemical denotes remdesivir MESH:C000606551
13 641-651 Chemical denotes remdesivir MESH:C000606551
14 102-110 Disease denotes COVID-19 MESH:C000657245
15 390-398 Disease denotes COVID-19 MESH:C000657245
21 699-716 Species denotes novel coronavirus Tax:2697049
22 718-728 Species denotes SARS-CoV-2 Tax:2697049
23 774-785 Species denotes coronaviral Tax:11118
24 675-683 Disease denotes COVID-19 MESH:C000657245
25 833-839 Disease denotes deaths MESH:D003643
31 3798-3809 Species denotes SARS-CoV- 2 Tax:2697049
32 3842-3852 Species denotes SARS-CoV-2 Tax:2697049
33 3779-3789 Chemical denotes Remdisivir
34 3909-3919 Chemical denotes Remdisivir
35 3955-3965 Chemical denotes Remdisivir
69 1931-1935 Gene denotes RdRp Gene:43740578
70 2124-2128 Gene denotes RdRp Gene:43740578
71 3157-3161 Gene denotes RdRp Gene:43740578
72 3551-3555 Gene denotes RdRp Gene:43740578
73 1617-1622 Species denotes Ebola Tax:1570291
74 1647-1674 Species denotes respiratory syncytial virus Tax:12814
75 1718-1731 Species denotes coronaviruses Tax:11118
76 1742-1750 Species denotes SARS CoV Tax:694009
77 1755-1763 Species denotes MERS CoV Tax:1335626
78 2074-2087 Species denotes coronaviruses Tax:11118
79 2089-2097 Species denotes MERS-CoV Tax:1335626
80 2099-2107 Species denotes SARS-CoV Tax:694009
81 2112-2122 Species denotes SARS-CoV-2 Tax:2697049
82 2729-2742 Species denotes coronaviruses Tax:11118
83 2751-2759 Species denotes MERS-CoV Tax:1335626
84 2761-2769 Species denotes SARS-CoV Tax:694009
85 2774-2784 Species denotes SARS-CoV-2 Tax:2697049
86 3359-3372 Species denotes coronaviruses Tax:11118
87 3721-3731 Species denotes SARS-CoV-2 Tax:2697049
88 1676-1679 Species denotes RSV Tax:12814
89 1521-1531 Chemical denotes remdesivir MESH:C000606551
90 1533-1536 Chemical denotes RDV MESH:C000606551
91 1769-1779 Chemical denotes Remdesivir MESH:C000606551
92 1839-1842 Chemical denotes RDV MESH:C000606551
93 1850-1853 Chemical denotes RDV MESH:C000606551
94 2161-2164 Chemical denotes RDV MESH:C000606551
95 2191-2200 Chemical denotes Adenosine MESH:D000241
96 2215-2218 Chemical denotes ATP MESH:D000255
97 2353-2356 Chemical denotes RDV MESH:C000606551
98 2538-2541 Chemical denotes RDV MESH:C000606551
99 3022-3025 Chemical denotes RDV MESH:C000606551
100 3324-3330 Chemical denotes serine MESH:D012694
101 3638-3641 Chemical denotes RDV MESH:C000606551
104 4221-4226 Species denotes human Tax:9606
105 4174-4189 Disease denotes viral infection MESH:D001102
145 4667-4670 Gene denotes NRF Gene:55922