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PMC:7216760 / 16284-20132 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T105 32-40 Body_part denotes cysteine http://purl.org/sig/ont/fma/fma82751
T106 118-126 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T107 175-180 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T108 1791-1800 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T109 2116-2122 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T110 2180-2186 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T111 2601-2611 Body_part denotes microsomes http://purl.org/sig/ont/fma/fma67438
T112 2735-2739 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T113 3164-3166 Body_part denotes AG http://purl.org/sig/ont/fma/fma61898

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T26 2735-2739 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T100 1187-1195 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 1956-1964 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 2310-2318 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 2327-2335 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 2502-2510 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 3108-3116 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 3612-3620 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T107 3693-3701 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T170 131-136 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T171 175-180 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T172 286-291 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T173 424-427 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T174 521-522 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T175 667-675 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T176 714-715 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 734-735 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T178 848-850 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T179 943-945 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T180 966-971 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T181 987-988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 1227-1228 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 1392-1394 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T184 1392-1394 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T185 1689-1690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 1733-1734 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 1764-1765 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 1779-1781 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T189 2036-2038 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T190 2055-2056 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 2116-2122 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T192 2180-2186 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T193 2210-2211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 2258-2259 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 2410-2412 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T196 2585-2590 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T197 2595-2600 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T198 2735-2739 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T199 2735-2739 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T200 3058-3068 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T201 3181-3183 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T202 3181-3183 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T203 3382-3384 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T204 3382-3384 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T205 3386-3388 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T206 3389-3390 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T131 32-40 Chemical denotes cysteine http://purl.obolibrary.org/obo/CHEBI_15356
T132 89-101 Chemical denotes polypeptides http://purl.obolibrary.org/obo/CHEBI_15841
T133 118-126 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T134 231-235 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T135 354-362 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T136 523-526 Chemical denotes Cys http://purl.obolibrary.org/obo/CHEBI_15356|http://purl.obolibrary.org/obo/CHEBI_17561|http://purl.obolibrary.org/obo/CHEBI_29950
T139 746-749 Chemical denotes Cys http://purl.obolibrary.org/obo/CHEBI_15356|http://purl.obolibrary.org/obo/CHEBI_17561|http://purl.obolibrary.org/obo/CHEBI_29950
T142 758-761 Chemical denotes Glu http://purl.obolibrary.org/obo/CHEBI_16015|http://purl.obolibrary.org/obo/CHEBI_18237|http://purl.obolibrary.org/obo/CHEBI_29972
T145 762-765 Chemical denotes Asp http://purl.obolibrary.org/obo/CHEBI_17053|http://purl.obolibrary.org/obo/CHEBI_22660|http://purl.obolibrary.org/obo/CHEBI_29958
T148 837-840 Chemical denotes Gln http://purl.obolibrary.org/obo/CHEBI_30011
T149 848-850 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T150 919-922 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T151 924-927 Chemical denotes Ala http://purl.obolibrary.org/obo/CHEBI_16977|http://purl.obolibrary.org/obo/CHEBI_46217
T153 932-935 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T155 943-945 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T156 1088-1098 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T157 1229-1243 Chemical denotes peptidomimetic http://purl.obolibrary.org/obo/CHEBI_63175
T158 1256-1265 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T159 1392-1394 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T160 1469-1477 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T161 1551-1560 Chemical denotes aldehydes http://purl.obolibrary.org/obo/CHEBI_17478
T162 1619-1624 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T163 1642-1645 Chemical denotes Cys http://purl.obolibrary.org/obo/CHEBI_15356|http://purl.obolibrary.org/obo/CHEBI_17561|http://purl.obolibrary.org/obo/CHEBI_29950
T166 1754-1760 Chemical denotes lactam http://purl.obolibrary.org/obo/CHEBI_24995
T167 1779-1781 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T168 1791-1800 Chemical denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T169 2036-2038 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T170 2039-2044 Chemical denotes amide http://purl.obolibrary.org/obo/CHEBI_29337|http://purl.obolibrary.org/obo/CHEBI_32988
T172 2057-2065 Chemical denotes pyridone http://purl.obolibrary.org/obo/CHEBI_38183
T173 2410-2412 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T174 2702-2704 Chemical denotes CD http://purl.obolibrary.org/obo/CHEBI_8673
T175 3009-3024 Chemical denotes Mpro inhibitors http://purl.obolibrary.org/obo/CHEBI_147285
T176 3014-3024 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T177 3108-3131 Chemical denotes SARS-CoV Mpro inhibitor http://purl.obolibrary.org/obo/CHEBI_147285
T178 3122-3131 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T179 3164-3166 Chemical denotes AG http://purl.obolibrary.org/obo/CHEBI_27569|http://purl.obolibrary.org/obo/CHEBI_40618|http://purl.obolibrary.org/obo/CHEBI_73757
T182 3181-3183 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T183 3259-3269 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T184 3282-3296 Chemical denotes peptidomimetic http://purl.obolibrary.org/obo/CHEBI_63175
T185 3305-3313 Chemical denotes acceptor http://purl.obolibrary.org/obo/CHEBI_15339
T186 3348-3357 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T187 3382-3384 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T188 3596-3598 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T189 3804-3814 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T190 3823-3833 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T30 1676-1685 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T31 2740-2747 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T70 0-12 Sentence denotes Novel Agents
T71 13-956 Sentence denotes Mpro and PLpro are cysteine proteases responsible for the cleavage of viral polypeptides into functional proteins for virus replication and packaging within host cells.24 These enzymes represent the best characterized drug targets among coronaviruses and are currently the focus of attention among scientists seeking novel coronavirus small molecule therapeutics.25 Mpro is shared by all coronavirus genera and has similarity to the 3Cpro of the Enterovirus genus in the picornavirus family.24 Mpro contains a Cys···His catalytic dyad with an additional α-helical domain involved in the dimerization of the protease, which is essential for its catalytic activity.25 The enteroviral 3Cpro functions as a monomer featuring a classical Cys···His···Glu/Asp catalytic triad.24 Yet, they share the almost absolute requirement for Gln in the P1 position of the substrate and space for only small residues such as Gly, Ala, or Ser in the P1′ position.
T72 957-1705 Sentence denotes Since no human proteases with a similar cleavage specificity are known, it may be possible to identify highly selective Mpro/3Cpro inhibitors, which display minimal inhibition of host proteases.26 The 3-D structures of unliganded SARS-CoV-2 Mpro and of its complex with a peptidomimetic α-ketoamide inhibitor (11r) have been solved26 and were used to support the design of an optimized derivative (13b) through docking studies (Figure S2). α-Ketoamides can interact with the catalytic center of Mpro through two hydrogen bonding interactions rather than only one as with other warheads such as aldehydes or Michael acceptors.24 Nucleophilic attack of the α-keto group by the catalytic Cys residue results in reversible formation of a thiohemiketal.
T73 1706-2081 Sentence denotes These α-ketoamides feature a 5-membered rigid γ-lactam as a mimic of the P1 residue, glutamine, required for Mpro specificity, with the advantage of reducing the loss of entropy upon binding.24 Follow up optimization efforts guided by docking to the SARS-CoV-2 Mpro co-crystal structure with 11r, included incorporation of the P3-P2 amide bond into a pyridone ring as in 13a.
T74 2082-2274 Sentence denotes The resulting half-life of 13a in plasma was enhanced by 3 fold relative to 11r, in vitro kinetic plasma solubility improved by a factor of ∼19 and thermodynamic solubility by a factor of ∼13.
T75 2275-2523 Sentence denotes 13a inhibited purified recombinant SARS-CoV-2 Mpro, SARS-CoV Mpro, and MERS-CoV Mpro in the submicromolar range.26 Modification of the P1′ and P3 moieties of 13a afforded an optimized derivative 13b which was crystallized with SARS-CoV-2 Mpro (PDB:
T76 2524-2539 Sentence denotes 6Y2G and 6Y2F).
T77 2540-2612 Sentence denotes Both 13a and 13b displayed good stability in mouse and human microsomes.
T78 2613-2712 Sentence denotes 13b (3 mg/kg) showed longer t1/2, tmax, and residence time compared to 13a (20 mg/kg) in CD-1 mice.
T79 2713-2782 Sentence denotes Both compounds showed lung tropism which is thought to be beneficial.
T80 2783-3025 Sentence denotes While the development of these ketoamides into clinical candidates requires additional safety studies, the availability of their crystal structures is of great importance in facilitating the discovery and development of other Mpro inhibitors.
T81 3026-3185 Sentence denotes One of the suggested agents for testing is the previously reported Rhinovirus and SARS-CoV Mpro inhibitor clinical candidate rupintrivir (AG-7088) (Figure S2).
T82 3186-3322 Sentence denotes In addition, other groups recently reported Mpro crystal structures with inhibitors such as the peptidomimetic Michael acceptor N3 (PDB:
T83 3323-3367 Sentence denotes 6LU7) and the reversible inhibitor X77 (PDB:
T84 3368-3586 Sentence denotes 6W63) (Figure S2).27 A large array of Mpro crystal structures with multiple covalent and noncovalent fragments were solved through an exceptionally large screen with vast opportunities for fragment growing and merging.
T85 3587-3848 Sentence denotes The cryo EM structure of SARS-CoV-2 RdRp was recently solved, showing nearly an identical sequence to its SARS-CoV homologue.28 RdRp should be another high priority target for therapeutic intervention given that lead inhibitors such as remdesivir already exist.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
541 2513-2517 Gene denotes Mpro Gene:8673700
542 3009-3013 Gene denotes Mpro Gene:8673700
543 3230-3234 Gene denotes Mpro Gene:8673700
544 3623-3627 Gene denotes RdRp Gene:43740578
545 3715-3719 Gene denotes RdRp Gene:43740578
546 3406-3410 Gene denotes Mpro Gene:8673700
547 3117-3121 Gene denotes Mpro Gene:8673700
548 2355-2359 Gene denotes Mpro Gene:8673700
549 2336-2340 Gene denotes Mpro Gene:8673700
550 2321-2325 Gene denotes Mpro Gene:8673700
551 1967-1971 Gene denotes Mpro Gene:8673700
552 1815-1819 Gene denotes Mpro Gene:8673700
553 1452-1456 Gene denotes Mpro Gene:8673700
554 1198-1202 Gene denotes Mpro Gene:8673700
555 507-511 Gene denotes Mpro Gene:8673700
556 379-383 Gene denotes Mpro Gene:8673700
557 13-17 Gene denotes Mpro Gene:8673700
558 250-263 Species denotes coronaviruses Tax:11118
559 330-347 Species denotes novel coronavirus Tax:2697049
560 401-412 Species denotes coronavirus Tax:11118
561 966-971 Species denotes human Tax:9606
562 1187-1197 Species denotes SARS-CoV-2 Tax:2697049
563 1956-1966 Species denotes SARS-CoV-2 Tax:2697049
564 2310-2320 Species denotes SARS-CoV-2 Tax:2697049
565 2327-2335 Species denotes SARS-CoV Tax:694009
566 2346-2354 Species denotes MERS-CoV Tax:1335626
567 2502-2512 Species denotes SARS-CoV-2 Tax:2697049
568 2585-2590 Species denotes mouse Tax:10090
569 2595-2600 Species denotes human Tax:9606
570 2707-2711 Species denotes mice Tax:10090
571 3093-3103 Species denotes Rhinovirus Tax:12059
572 3108-3116 Species denotes SARS-CoV Tax:694009
573 3612-3622 Species denotes SARS-CoV-2 Tax:2697049
574 3693-3701 Species denotes SARS-CoV Tax:694009
575 1077-1081 Gene denotes Mpro Gene:8673700
576 523-526 Chemical denotes Cys MESH:D003545
577 746-749 Chemical denotes Cys MESH:D003545
578 752-755 Chemical denotes His MESH:D006639
579 758-761 Chemical denotes Glu MESH:D018698
580 762-765 Chemical denotes Asp MESH:D001224
581 837-840 Chemical denotes Gln MESH:D005973
582 919-922 Chemical denotes Gly MESH:D005998
583 924-927 Chemical denotes Ala MESH:D000409
584 932-935 Chemical denotes Ser MESH:D012694
585 1244-1255 Chemical denotes α-ketoamide
586 1397-1409 Chemical denotes α-Ketoamides
587 1469-1477 Chemical denotes hydrogen MESH:D006859
588 1551-1560 Chemical denotes aldehydes MESH:D000447
589 1642-1645 Chemical denotes Cys MESH:D003545
590 1691-1704 Chemical denotes thiohemiketal
591 1712-1724 Chemical denotes α-ketoamides
592 1752-1760 Chemical denotes γ-lactam
593 1791-1800 Chemical denotes glutamine MESH:D005973
594 1998-2001 Chemical denotes 11r
595 2033-2035 Chemical denotes P3
596 2036-2038 Chemical denotes P2 MESH:C020845
597 2039-2044 Chemical denotes amide MESH:D000577
598 2057-2065 Chemical denotes pyridone MESH:D011728
599 2109-2112 Chemical denotes 13a
600 2433-2436 Chemical denotes 13a
601 2470-2473 Chemical denotes 13b
602 2545-2548 Chemical denotes 13a
603 2553-2556 Chemical denotes 13b
604 2613-2616 Chemical denotes 13b
605 2684-2687 Chemical denotes 13a
606 2814-2824 Chemical denotes ketoamides
607 3151-3162 Chemical denotes rupintrivir MESH:C118874
608 3164-3171 Chemical denotes AG-7088 MESH:C118874
609 3823-3833 Chemical denotes remdesivir MESH:C000606551

2_test

Id Subject Object Predicate Lexical cue
32388976-25039866-144056 376-378 25039866 denotes 25
32388976-25039866-144057 676-678 25039866 denotes 25
32388976-32277040-144058 3712-3714 32277040 denotes 28