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PMC:7544943 / 1858-41408 JSONTXT

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LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1175-1179 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T2 18112-18117 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T3 19883-19902 Body_part denotes blood–brain barrier http://purl.obolibrary.org/obo/UBERON_0000120
T4 19883-19888 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T5 19889-19894 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T6 20135-20139 Body_part denotes skin http://purl.obolibrary.org/obo/UBERON_0000014
T7 20190-20194 Body_part denotes skin http://purl.obolibrary.org/obo/UBERON_0000014
T8 23055-23059 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T3 263-267 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T4 312-325 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T5 353-365 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T6 667-674 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 858-870 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T8 986-998 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T9 1146-1153 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10 1175-1179 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T11 1374-1377 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 9084-9092 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T13 9229-9236 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 9950-9957 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T15 12929-12935 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T16 13773-13781 Body_part denotes Gprotein http://purl.org/sig/ont/fma/fma61788
T17 13807-13815 Body_part denotes Gprotein http://purl.org/sig/ont/fma/fma61788
T18 13881-13888 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T19 14030-14037 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 15155-15179 Body_part denotes biological macromolecule http://purl.org/sig/ont/fma/fma63887
T21 18112-18117 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T22 19389-19393 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T23 19883-19888 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T24 19889-19894 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T25 20135-20139 Body_part denotes skin http://purl.org/sig/ont/fma/fma7163
T26 20190-20194 Body_part denotes skin http://purl.org/sig/ont/fma/fma7163
T27 21046-21053 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 23055-23059 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T29 27210-27217 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 27622-27630 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T31 27650-27658 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T32 28034-28042 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T33 28063-28071 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T34 28551-28559 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T35 28684-28692 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T36 28738-28746 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T37 29247-29254 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T38 29618-29624 Body_part denotes Radius http://purl.org/sig/ont/fma/fma23463
T39 29734-29740 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T40 29763-29769 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T41 29821-29828 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 30371-30378 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 30427-30433 Body_part denotes Radius http://purl.org/sig/ont/fma/fma23463
T44 30744-30751 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 30827-30834 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T46 31543-31550 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 32534-32542 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T48 32899-32906 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T49 33242-33249 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T50 34863-34870 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 34882-34889 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T52 34979-34987 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T53 35001-35009 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T54 35223-35231 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T55 35362-35370 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T56 35779-35786 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 35802-35809 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 35888-35896 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T59 35949-35957 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T60 36185-36193 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T61 38675-38683 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T14 27-51 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T15 53-61 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 159-206 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T17 159-192 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T18 208-216 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 501-534 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T20 548-556 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 607-615 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1185-1193 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 1601-1609 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 2189-2197 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 2672-2680 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 3672-3680 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 3940-3948 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 4281-4289 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 4404-4412 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 4900-4908 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 4924-4928 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T32 8367-8375 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 8391-8395 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 9135-9143 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 9170-9178 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 9416-9420 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 10398-10406 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 10511-10519 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 10589-10597 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 10613-10621 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 11308-11316 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 11332-11340 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 12353-12356 Disease denotes PME http://purl.obolibrary.org/obo/MONDO_0020074
T44 13992-13994 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T46 14053-14055 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T48 15496-15504 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 20711-20719 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 20735-20743 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 21005-21013 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 21242-21250 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 22259-22267 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 22320-22328 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 22933-22937 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T56 23126-23134 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 23959-23967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 24039-24047 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 24182-24190 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 24364-24372 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 24446-24454 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 24922-24930 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 25373-25381 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 25848-25856 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 26005-26013 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 26279-26283 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 26815-26823 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 26975-26983 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 32213-32221 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 34402-34410 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 35077-35080 Disease denotes PC1 http://purl.obolibrary.org/obo/MONDO_0008173
T72 35085-35088 Disease denotes PC2 http://purl.obolibrary.org/obo/MONDO_0008174
T73 36435-36443 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 36588-36596 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 37193-37201 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 38010-38018 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 38181-38189 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 38514-38522 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 38850-38858 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 39072-39076 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T81 39327-39335 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T9 63-66 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T10 74-75 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 263-267 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T12 415-416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 441-446 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T14 621-627 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T15 697-702 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T16 752-761 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T17 778-786 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes by human
T18 1297-1298 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1413-1414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1426-1428 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T21 1556-1564 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T22 1711-1712 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2203-2204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 2410-2412 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T25 2955-2963 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T26 3091-3097 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T27 3194-3195 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3330-3333 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T29 3512-3513 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 4454-4457 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T31 4458-4459 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4968-4970 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T33 5005-5011 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T34 5089-5091 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T35 6269-6271 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T36 6830-6832 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T37 7142-7144 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T38 7559-7561 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T39 8220-8221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 8244-8250 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T41 8259-8260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 8335-8341 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T43 8493-8495 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T44 8846-8848 http://www.ebi.ac.uk/efo/EFO_0000265 denotes Da
T45 9538-9540 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T46 9701-9706 http://purl.obolibrary.org/obo/UBERON_0007688 denotes Field
T47 10120-10123 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T48 10161-10162 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 10191-10192 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 10297-10298 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 10314-10315 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T52 10321-10322 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T53 10328-10329 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T54 10415-10416 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 10437-10438 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T56 10441-10443 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T57 10444-10445 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T58 10451-10452 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T59 10858-10864 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T60 10932-10935 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC
T61 11181-11184 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC
T62 11220-11222 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T63 11366-11368 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T64 11721-11722 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T65 11920-11921 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 12127-12129 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T67 12222-12223 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 12773-12775 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T69 13274-13276 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T70 13486-13488 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T71 14111-14112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 14401-14402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 14886-14887 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 14961-14967 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T75 15063-15069 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T76 15153-15154 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 15336-15341 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T78 15638-15640 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T79 15638-15640 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T80 15768-15769 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 15905-15913 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T82 16062-16070 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T83 16339-16342 http://purl.obolibrary.org/obo/UBERON_0001013 denotes fat
T84 16359-16360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 16407-16410 http://purl.obolibrary.org/obo/UBERON_0001013 denotes fat
T86 17221-17225 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T87 17904-17905 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 17991-17992 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T89 18059-18060 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 18112-18117 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T91 18112-18117 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T92 18170-18174 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T93 19329-19330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 19460-19461 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 19598-19603 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T96 19883-19888 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T97 19883-19888 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T98 19889-19894 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T99 19889-19894 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T100 19923-19924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 20135-20139 http://purl.obolibrary.org/obo/UBERON_0000014 denotes skin
T102 20135-20139 http://purl.obolibrary.org/obo/UBERON_0001003 denotes skin
T103 20135-20139 http://purl.obolibrary.org/obo/UBERON_0002097 denotes skin
T104 20135-20139 http://purl.obolibrary.org/obo/UBERON_0002199 denotes skin
T105 20135-20139 http://www.ebi.ac.uk/efo/EFO_0000962 denotes skin
T106 20183-20184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 20190-20194 http://purl.obolibrary.org/obo/UBERON_0000014 denotes skin
T108 20190-20194 http://purl.obolibrary.org/obo/UBERON_0001003 denotes skin
T109 20190-20194 http://purl.obolibrary.org/obo/UBERON_0002097 denotes skin
T110 20190-20194 http://purl.obolibrary.org/obo/UBERON_0002199 denotes skin
T111 20190-20194 http://www.ebi.ac.uk/efo/EFO_0000962 denotes skin
T112 20359-20360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 21095-21096 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 21308-21311 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T115 21887-21888 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 22435-22436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 22632-22633 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T118 22865-22866 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 22879-22880 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T120 23337-23338 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 24316-24319 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T122 24843-24844 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 25510-25511 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T124 25937-25941 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4(c)
T125 26913-26914 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 26927-26928 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T127 27107-27109 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T128 27132-27134 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T129 27245-27246 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 27378-27379 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 27387-27389 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T132 27517-27519 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T133 27650-27676 http://purl.obolibrary.org/obo/GO_0043234 denotes proteins and their complex
T134 28216-28217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 28293-28297 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T136 28320-28324 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T137 28375-28376 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 28425-28426 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T139 28738-28764 http://purl.obolibrary.org/obo/GO_0043234 denotes proteins and their complex
T140 29056-29057 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 29088-29089 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T142 29229-29230 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 29247-29263 http://purl.obolibrary.org/obo/CHEBI_33708 denotes protein residues
T144 29392-29398 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T145 29420-29421 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T146 29517-29518 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 29567-29568 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T148 29683-29689 http://purl.obolibrary.org/obo/BFO_0000030 denotes object
T149 29785-29786 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 29880-29881 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 30177-30178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 30179-30180 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T153 30212-30213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T154 30456-30457 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 30506-30507 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T156 30647-30649 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T157 30894-30895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 30989-30990 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 31681-31683 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T160 32192-32193 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 32281-32282 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T162 33030-33031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T163 33080-33081 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T164 33167-33169 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T165 33747-33748 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T166 33874-33882 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T167 33942-33945 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T168 33946-33947 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T169 34305-34307 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T170 34305-34307 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T171 34914-34916 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T172 35115-35116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 35117-35118 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T174 35416-35417 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T175 35466-35467 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T176 36342-36343 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 36410-36416 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T178 36736-36737 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 37068-37069 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 37166-37168 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T181 37237-37238 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T182 37360-37362 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T183 37403-37411 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T184 37468-37474 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T185 37504-37510 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T186 37742-37748 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T187 37822-37824 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T188 37866-37867 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 38076-38078 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T190 38210-38211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 38338-38342 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T192 38406-38407 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 38477-38485 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T194 38956-38957 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 38995-38997 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T196 39163-39169 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T197 39289-39295 http://purl.obolibrary.org/obo/CLO_0001658 denotes active

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
79 447-478 Gene denotes angiotensin-converting enzyme 2 Gene:59272
80 480-484 Gene denotes ACE2 Gene:59272
81 703-707 Gene denotes ACE2 Gene:59272
82 852-857 Gene denotes spike Gene:43740568
83 874-878 Gene denotes ACE2 Gene:59272
84 1050-1054 Gene denotes ACE2 Gene:59272
85 1211-1215 Gene denotes Mpro Gene:8673700
86 159-206 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
87 208-218 Species denotes SARS-CoV-2 Tax:2697049
88 239-250 Species denotes coronavirus Tax:11118
89 441-446 Species denotes human Tax:9606
90 501-546 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
91 548-556 Species denotes SARS-CoV Tax:694009
92 607-617 Species denotes SARS-CoV-2 Tax:2697049
93 621-627 Species denotes humans Tax:9606
94 697-702 Species denotes human Tax:9606
95 781-786 Species denotes human Tax:9606
96 1185-1195 Species denotes SARS-CoV-2 Tax:2697049
97 1601-1611 Species denotes SARS-CoV-2 Tax:2697049
98 1140-1145 Gene denotes spike Gene:43740568
99 654-659 Gene denotes spike Gene:43740568
100 306-311 Gene denotes spike Gene:43740568
101 660-666 Chemical denotes glycol MESH:D006018
102 897-903 Chemical denotes ARG403
103 905-911 Chemical denotes TYR453
104 913-919 Chemical denotes SER494
105 921-927 Chemical denotes TYR495
106 929-935 Chemical denotes PHE497
107 937-943 Chemical denotes GLN498
108 945-951 Chemical denotes THR500
109 953-959 Chemical denotes ASN501
110 961-967 Chemical denotes TYR505
111 21-46 Disease denotes novel coronavirus disease MESH:C000657245
112 53-61 Disease denotes COVID-19 MESH:C000657245
113 1479-1487 Disease denotes toxicity MESH:D064420
128 1906-1913 Species denotes patient Tax:9606
129 2672-2682 Species denotes SARS-CoV-2 Tax:2697049
130 2810-2827 Species denotes novel coronavirus Tax:2697049
131 2223-2233 Chemical denotes remdesivir MESH:C000606551
132 2235-2253 Chemical denotes hydroxychloroquine MESH:D006886
133 2610-2620 Chemical denotes remdesivir MESH:C000606551
134 2622-2631 Chemical denotes lopinavir MESH:D061466
135 2633-2640 Chemical denotes emetine MESH:D004640
136 2645-2662 Chemical denotes homoharringtonine MESH:D000077863
137 2775-2785 Chemical denotes remdesivir MESH:C000606551
138 2790-2801 Chemical denotes chloroquine MESH:D002738
139 1897-1905 Disease denotes infected MESH:D007239
140 2081-2097 Disease denotes coronavirus-2019 MESH:C000657245
141 2189-2197 Disease denotes COVID-19 MESH:C000657245
155 4415-4419 Gene denotes Mpro Gene:8673700
156 3951-3955 Gene denotes Mpro Gene:8673700
157 4935-4939 Gene denotes Mpro Gene:8673700
158 4292-4296 Gene denotes Mpro Gene:8673700
159 3500-3506 Species denotes garlic Tax:4682
160 3672-3682 Species denotes SARS-CoV-2 Tax:2697049
161 3940-3950 Species denotes SARS-CoV-2 Tax:2697049
162 4281-4291 Species denotes SARS-CoV-2 Tax:2697049
163 4404-4414 Species denotes SARS-CoV-2 Tax:2697049
164 4900-4910 Species denotes SARS-CoV-2 Tax:2697049
165 4924-4934 Species denotes SARS-Cov-2 Tax:2697049
166 4161-4170 Chemical denotes alkaloids MESH:D000470
167 4175-4185 Chemical denotes terpenoids MESH:D013729
194 5353-5356 Gene denotes Pgp Gene:283871
195 5430-5434 Gene denotes Mpro Gene:8673700
196 5448-5463 Chemical denotes 2-Decenoic acid MESH:C052476
197 5533-5551 Chemical denotes α-Terpinyl acetate
198 5622-5631 Chemical denotes Capsaicin MESH:D002211
199 5701-5708 Chemical denotes Carvone MESH:C006923
200 5779-5793 Chemical denotes Cinnamaldehyde MESH:C012843
201 5863-5876 Chemical denotes Cuminaldehyde MESH:C007165
202 5946-5964 Chemical denotes Dipropyl disulfide MESH:C041288
203 6034-6044 Chemical denotes Eucalyptol MESH:D000077591
204 6114-6122 Chemical denotes Linalool MESH:C018584
205 6193-6201 Chemical denotes Vanillin MESH:C100058
206 6349-6365 Chemical denotes Sabinene hydrate MESH:C534325
207 6437-6445 Chemical denotes Piperine MESH:C008922
208 6516-6523 Chemical denotes Menthol MESH:D008610
209 6594-6601 Chemical denotes Eugenol MESH:D005054
210 6673-6682 Chemical denotes Estragole MESH:C007633
211 6754-6762 Chemical denotes Gingerol MESH:C007845
212 6911-6918 Chemical denotes Paradol MESH:C421614
213 6990-6999 Chemical denotes Zingerone MESH:C013738
214 7146-7160 Chemical denotes Bornyl acetate MESH:C071528
215 7393-7405 Chemical denotes 2-Undecanone MESH:C526928
216 7477-7492 Chemical denotes Geranyl acetate MESH:C432872
217 7563-7572 Chemical denotes Nerolidol MESH:C037055
218 7643-7656 Chemical denotes Terpinen-4-ol MESH:C034019
219 7728-7737 Chemical denotes Terpineol
225 8458-8466 Gene denotes RBD Spro
226 8471-8475 Gene denotes Mpro Gene:8673700
227 8402-8406 Gene denotes Mpro Gene:8673700
228 8367-8377 Species denotes SARS-CoV-2 Tax:2697049
229 8391-8401 Species denotes SARS-Cov-2 Tax:2697049
234 8763-8771 Chemical denotes hydrogen MESH:D006859
235 8801-8809 Chemical denotes hydrogen MESH:D006859
236 8858-8865 Chemical denotes octanol MESH:D000442
237 8866-8871 Chemical denotes water MESH:D014867
244 9496-9500 Gene denotes ACE2 Gene:59272
245 9181-9185 Gene denotes Mpro Gene:8673700
246 9135-9145 Species denotes SARS-CoV-2 Tax:2697049
247 9170-9180 Species denotes SARS-CoV-2 Tax:2697049
248 9416-9426 Species denotes SARS-Cov-2 Tax:2697049
249 9289-9294 Chemical denotes water MESH:D014867
256 10600-10604 Gene denotes Mpro Gene:8673700
257 10409-10413 Gene denotes Mpro Gene:8673700
258 10398-10408 Species denotes SARS-CoV-2 Tax:2697049
259 10511-10521 Species denotes SARS-CoV-2 Tax:2697049
260 10589-10599 Species denotes SARS-CoV-2 Tax:2697049
261 10613-10623 Species denotes SARS-CoV-2 Tax:2697049
269 11457-11461 Gene denotes Mpro Gene:8673700
270 11343-11347 Gene denotes Mpro Gene:8673700
271 11308-11318 Species denotes SARS-CoV-2 Tax:2697049
272 11332-11342 Species denotes SARS-CoV-2 Tax:2697049
273 11439-11452 Chemical denotes Spro-Piperine
274 11769-11774 Chemical denotes water MESH:D014867
275 12910-12918 Chemical denotes hydrogen MESH:D006859
277 13183-13187 Chemical denotes PBSA MESH:C437084
279 14131-14132 Chemical denotes S MESH:D013455
282 15496-15506 Species denotes SARS-CoV-2 Tax:2697049
283 15520-15524 Gene denotes Mpro Gene:8673700
286 16463-16468 Chemical denotes water MESH:D014867
287 16469-16478 Chemical denotes n-octanol MESH:D020003
290 17451-17459 Chemical denotes Vanillin MESH:C100058
291 17480-17489 Chemical denotes Nerolidol MESH:C037055
293 17696-17701 Chemical denotes Water MESH:D014867
296 18548-18553 Chemical denotes water MESH:D014867
297 18824-18828 Chemical denotes ESOL
306 20474-20480 Gene denotes CYP1A2 Gene:1544
307 20482-20489 Gene denotes CYP2C19 Gene:1557
308 20491-20497 Gene denotes CYP2C9 Gene:1559
309 20499-20505 Gene denotes CYP2D6 Gene:1565
310 20510-20516 Gene denotes CYP3A4 Gene:1576
311 20746-20750 Gene denotes Mpro Gene:8673700
312 20711-20721 Species denotes SARS-CoV-2 Tax:2697049
313 20735-20745 Species denotes SARS-CoV-2 Tax:2697049
315 21005-21015 Species denotes SARS-CoV-2 Tax:2697049
368 21242-21252 Species denotes SARS-CoV-2 Tax:2697049
369 22259-22269 Species denotes SARS-CoV-2 Tax:2697049
370 22320-22330 Species denotes SARS-CoV-2 Tax:2697049
371 21299-21307 Chemical denotes Piperine MESH:C008922
372 21422-21430 Chemical denotes Piperine MESH:C008922
373 21432-21441 Chemical denotes Capsaicin MESH:D002211
374 21443-21451 Chemical denotes Gingerol MESH:C007845
375 21456-21469 Chemical denotes Terpinen-4-ol MESH:C034019
376 21729-21737 Chemical denotes Piperine MESH:C008922
377 21775-21784 Chemical denotes Capsaicin MESH:D002211
378 21786-21793 Chemical denotes Ginerol
379 21798-21811 Chemical denotes Terpinen-4-ol MESH:C034019
380 21911-21919 Chemical denotes Piperine MESH:C008922
381 21939-21947 Chemical denotes hydrogen MESH:D006859
382 21970-21976 Chemical denotes GLY164
383 21981-21987 Chemical denotes GLY170
384 21989-21995 Chemical denotes TYR173
385 21997-22003 Chemical denotes TYR505
386 22009-22015 Chemical denotes SER162
387 22017-22023 Chemical denotes SER494
388 22062-22068 Chemical denotes carbon MESH:D002244
389 22069-22077 Chemical denotes hydrogen MESH:D006859
390 22196-22201 Chemical denotes ARG71
391 22203-22209 Chemical denotes TYR121
392 22211-22217 Chemical denotes TYR453
393 22220-22226 Chemical denotes TYR163
394 22228-22234 Chemical denotes TYR495
395 22240-22246 Chemical denotes ASN169
396 22248-22254 Chemical denotes ASN501
397 22306-22314 Chemical denotes Piperine MESH:C008922
398 22366-22374 Chemical denotes hydrogen MESH:D006859
399 22458-22467 Chemical denotes Capsaicin MESH:D002211
400 22496-22502 Chemical denotes GLY164
401 22507-22513 Chemical denotes TYR173
402 22515-22521 Chemical denotes TYR505
403 22540-22548 Chemical denotes hydrogen MESH:D006859
404 22595-22602 Chemical denotes benzene MESH:D001554
405 22650-22655 Chemical denotes ARG71
406 22657-22663 Chemical denotes ARG403
407 22666-22671 Chemical denotes ASP73
408 22673-22678 Chemical denotes GLU74
409 22680-22685 Chemical denotes GLN77
410 22687-22692 Chemical denotes LYS85
411 22694-22700 Chemical denotes TYR121
412 22702-22708 Chemical denotes TYR453
413 22711-22717 Chemical denotes SER162
414 22719-22725 Chemical denotes SER494
415 22728-22734 Chemical denotes TYR163
416 22736-22742 Chemical denotes TYR495
417 22748-22754 Chemical denotes ASN169
418 22756-22762 Chemical denotes ASN501
419 22813-22822 Chemical denotes Capsaicin MESH:D002211
425 22933-22943 Species denotes SARS-Cov-2 Tax:2697049
426 22868-22876 Chemical denotes Piperine MESH:C008922
427 22882-22891 Chemical denotes Capsaicin MESH:D002211
428 22897-22905 Chemical denotes Gingerol MESH:C007845
429 22914-22927 Chemical denotes Terpinen-4-ol MESH:C034019
465 23126-23136 Species denotes SARS-CoV-2 Tax:2697049
466 23061-23069 Chemical denotes Gingerol MESH:C007845
467 23174-23180 Chemical denotes GLY164
468 23182-23188 Chemical denotes ASN169
469 23190-23196 Chemical denotes ASN501
470 23202-23208 Chemical denotes GLY170
471 23229-23237 Chemical denotes hydrogen MESH:D006859
472 23260-23268 Chemical denotes Gingerol MESH:C007845
473 23285-23293 Chemical denotes hydrogen MESH:D006859
474 23311-23317 Chemical denotes TYR173
475 23319-23325 Chemical denotes TYR505
476 23375-23382 Chemical denotes benzene MESH:D001554
477 23391-23399 Chemical denotes Gingerol MESH:C007845
478 23406-23411 Chemical denotes ARG71
479 23413-23419 Chemical denotes ARG403
480 23422-23428 Chemical denotes TYR121
481 23430-23436 Chemical denotes TYR453
482 23439-23445 Chemical denotes TYR163
483 23447-23453 Chemical denotes TYR495
484 23456-23462 Chemical denotes PHE165
485 23464-23470 Chemical denotes PHE497
486 23476-23482 Chemical denotes GLN166
487 23484-23490 Chemical denotes GLN498
488 23549-23562 Chemical denotes Terpinen-4-ol MESH:C034019
489 23622-23628 Chemical denotes ARG125
490 23630-23636 Chemical denotes LYS126
491 23638-23644 Chemical denotes TYR141
492 23649-23655 Chemical denotes PRO159
493 23675-23681 Chemical denotes ARG122
494 23683-23689 Chemical denotes PHE124
495 23691-23697 Chemical denotes ASP135
496 23699-23705 Chemical denotes SER137
497 23707-23713 Chemical denotes GLU139
498 23718-23724 Chemical denotes ILE140
499 23773-23786 Chemical denotes Terpinen-4-ol MESH:C034019
501 23959-23969 Species denotes SARS-CoV-2 Tax:2697049
590 26826-26830 Gene denotes Mpro Gene:8673700
591 26290-26294 Gene denotes Mpro Gene:8673700
592 26016-26020 Gene denotes Mpro Gene:8673700
593 25859-25863 Gene denotes Mpro Gene:8673700
594 25384-25388 Gene denotes Mpro Gene:8673700
595 24933-24937 Gene denotes Mpro Gene:8673700
596 24375-24379 Gene denotes Mpro Gene:8673700
597 24193-24197 Gene denotes Mpro Gene:8673700
598 24050-24054 Gene denotes Mpro Gene:8673700
599 24039-24049 Species denotes SARS-CoV-2 Tax:2697049
600 24182-24192 Species denotes SARS-CoV-2 Tax:2697049
601 24364-24374 Species denotes SARS-CoV-2 Tax:2697049
602 24446-24456 Species denotes SARS-CoV-2 Tax:2697049
603 24922-24932 Species denotes SARS-CoV-2 Tax:2697049
604 25373-25383 Species denotes SARS-CoV-2 Tax:2697049
605 25848-25858 Species denotes SARS-CoV-2 Tax:2697049
606 26005-26015 Species denotes SARS-CoV-2 Tax:2697049
607 26279-26289 Species denotes SARS-Cov-2 Tax:2697049
608 26815-26825 Species denotes SARS-CoV-2 Tax:2697049
609 24307-24315 Chemical denotes Piperine MESH:C008922
610 24722-24730 Chemical denotes Piperine MESH:C008922
611 24749-24758 Chemical denotes Capsaicin MESH:D002211
612 24777-24784 Chemical denotes Carvone MESH:C006923
613 24803-24811 Chemical denotes Gingerol MESH:C007845
614 24886-24894 Chemical denotes Piperine MESH:C008922
615 24955-24963 Chemical denotes hydrogen MESH:D006859
616 25033-25039 Chemical denotes GLN299
617 25044-25050 Chemical denotes VAL303
618 25071-25079 Chemical denotes hydrogen MESH:D006859
619 25101-25107 Chemical denotes ASP295
620 25112-25118 Chemical denotes ARG298
621 25151-25155 Chemical denotes MET6
622 25160-25164 Chemical denotes PRO9
623 25215-25223 Chemical denotes Piperine MESH:C008922
624 25306-25310 Chemical denotes PHE8
625 25312-25318 Chemical denotes GLY127
626 25320-25326 Chemical denotes ILE152
627 25328-25334 Chemical denotes PHE291
628 25339-25345 Chemical denotes THR304
629 25403-25412 Chemical denotes Capsaicin MESH:D002211
630 25528-25532 Chemical denotes MET6
631 25534-25538 Chemical denotes PHE8
632 25540-25544 Chemical denotes PRO9
633 25549-25555 Chemical denotes ILE152
634 25641-25650 Chemical denotes Capsaicin MESH:D002211
635 25652-25661 Chemical denotes Capsaicin MESH:D002211
636 25691-25695 Chemical denotes ALA7
637 25697-25702 Chemical denotes GLY11
638 25704-25709 Chemical denotes LYS12
639 25711-25717 Chemical denotes GLN127
640 25719-25725 Chemical denotes TYR154
641 25727-25733 Chemical denotes PHE291
642 25735-25741 Chemical denotes ASP295
643 25743-25749 Chemical denotes ARG298
644 25751-25757 Chemical denotes GLN299
645 25759-25765 Chemical denotes VAL303
646 25770-25776 Chemical denotes THR304
647 25831-25838 Chemical denotes Carvone MESH:C006923
648 25944-25951 Chemical denotes Carvone MESH:C006923
649 25986-25990 Chemical denotes PHE8
650 25995-26001 Chemical denotes ARG298
651 26064-26068 Chemical denotes ALA7
652 26070-26074 Chemical denotes PRO9
653 26076-26082 Chemical denotes GLN127
654 26084-26090 Chemical denotes ASP295
655 26092-26098 Chemical denotes GLN299
656 26100-26106 Chemical denotes GLY302
657 26111-26117 Chemical denotes VAL303
658 26157-26164 Chemical denotes Carvone MESH:C006923
659 26166-26174 Chemical denotes Gingerol MESH:C007845
660 26192-26200 Chemical denotes hydrogen MESH:D006859
661 26310-26316 Chemical denotes VAL303
662 26340-26348 Chemical denotes hydrogen MESH:D006859
663 26371-26379 Chemical denotes Gingerol MESH:C007845
664 26394-26399 Chemical denotes LYS12
665 26404-26410 Chemical denotes THR304
666 26427-26433 Chemical denotes carbon MESH:D002244
667 26434-26442 Chemical denotes hydrogen MESH:D006859
668 26473-26477 Chemical denotes ALA7
669 26479-26483 Chemical denotes PHE8
670 26485-26491 Chemical denotes GLN127
671 26493-26499 Chemical denotes TYR154
672 26501-26507 Chemical denotes ASP295
673 26512-26518 Chemical denotes ARG298
674 26571-26579 Chemical denotes Gingerol MESH:C007845
675 26600-26608 Chemical denotes Gingerol MESH:C007845
676 26627-26631 Chemical denotes PRO9
677 26636-26642 Chemical denotes ILE152
684 26986-26990 Gene denotes Mpro Gene:8673700
685 26975-26985 Species denotes SARS-CoV-2 Tax:2697049
686 26916-26924 Chemical denotes Piperine MESH:C008922
687 26930-26939 Chemical denotes Capsaicin MESH:D002211
688 26945-26952 Chemical denotes Carvone MESH:C006923
689 26961-26969 Chemical denotes Gingerol MESH:C007845
692 27345-27349 Gene denotes Mpro Gene:8673700
693 27355-27363 Chemical denotes Piperine MESH:C008922
699 27858-27862 Gene denotes Mpro Gene:8673700
700 27867-27871 Gene denotes Mpro Gene:8673700
701 27682-27690 Chemical denotes Piperine MESH:C008922
702 27843-27856 Chemical denotes Spro-Piperine
703 28019-28027 Chemical denotes Piperine MESH:C008922
707 28428-28432 Gene denotes Mpro Gene:8673700
708 28445-28449 Gene denotes Mpro Gene:8673700
709 28403-28416 Chemical denotes Spro-Piperine
721 29151-29155 Gene denotes Mpro Gene:8673700
722 29064-29068 Gene denotes Mpro Gene:8673700
723 28876-28880 Gene denotes Mpro Gene:8673700
724 28867-28871 Gene denotes Mpro Gene:8673700
725 28573-28577 Gene denotes Mpro Gene:8673700
726 28666-28674 Chemical denotes Piperine MESH:C008922
727 28770-28778 Chemical denotes Piperine MESH:C008922
728 28852-28865 Chemical denotes Spro-Piperine
729 29032-29045 Chemical denotes Spro-Piperine
730 29343-29351 Chemical denotes Piperine MESH:C008922
731 29410-29418 Chemical denotes Piperine MESH:C008922
735 29570-29574 Gene denotes Mpro Gene:8673700
736 29587-29591 Gene denotes Mpro Gene:8673700
737 29545-29558 Chemical denotes Spro-Piperine
744 30275-30279 Gene denotes Mpro Gene:8673700
745 30047-30051 Gene denotes Mpro Gene:8673700
746 30317-30321 Gene denotes Mpro Gene:8673700
747 30056-30060 Gene denotes Mpro Gene:8673700
748 30032-30045 Chemical denotes Spro-Piperine
749 30406-30414 Chemical denotes Piperine MESH:C008922
756 30509-30513 Gene denotes Mpro Gene:8673700
757 30619-30623 Gene denotes Mpro Gene:8673700
758 30526-30530 Gene denotes Mpro Gene:8673700
759 30484-30497 Chemical denotes Spro-Piperine
760 30567-30575 Chemical denotes hydrogen MESH:D006859
761 30601-30614 Chemical denotes Spro-Piperine
763 30681-30689 Chemical denotes hydrogen MESH:D006859
776 30859-30863 Gene denotes Mpro Gene:8673700
777 31209-31213 Gene denotes Mpro Gene:8673700
778 31078-31082 Gene denotes Mpro Gene:8673700
779 30710-30718 Chemical denotes hydrogen MESH:D006859
780 30880-30888 Chemical denotes Piperine MESH:C008922
781 30919-30927 Chemical denotes hydrogen MESH:D006859
782 31017-31025 Chemical denotes hydrogen MESH:D006859
783 31060-31073 Chemical denotes Spro-Piperine
784 31121-31129 Chemical denotes hydrogen MESH:D006859
785 31187-31190 Chemical denotes RBD
786 31191-31204 Chemical denotes Spro-Piperine
787 31344-31352 Chemical denotes hydrogen MESH:D006859
794 32070-32074 Gene denotes Mpro Gene:8673700
795 31891-31895 Gene denotes Mpro Gene:8673700
796 32213-32223 Species denotes SARS-CoV-2 Tax:2697049
797 31873-31886 Chemical denotes Spro-Piperine
798 32035-32043 Chemical denotes Piperine MESH:C008922
799 32180-32188 Chemical denotes Piperine MESH:C008922
804 32676-32680 Gene denotes Mpro Gene:8673700
805 32667-32671 Gene denotes Mpro Gene:8673700
806 32273-32277 Chemical denotes SASA
807 32652-32665 Chemical denotes Spro-Piperine
811 33083-33087 Gene denotes Mpro Gene:8673700
812 33100-33104 Gene denotes Mpro Gene:8673700
813 33058-33071 Chemical denotes Spro-Piperine
819 33631-33635 Gene denotes Mpro Gene:8673700
820 34256-34260 Gene denotes Mpro Gene:8673700
821 33714-33718 Gene denotes Mpro Gene:8673700
822 33571-33584 Chemical denotes Spro-Piperine
823 34238-34251 Chemical denotes Spro-Piperine
831 34503-34507 Gene denotes Mpro Gene:8673700
832 34529-34540 Chemical denotes Chloroquine MESH:D002738
833 34553-34564 Chemical denotes Favipiravir MESH:C462182
834 34577-34595 Chemical denotes Hydroxychloroquine MESH:D006886
835 34608-34619 Chemical denotes Oseltamivir MESH:D053139
836 34632-34642 Chemical denotes Remdesivir MESH:C000606551
837 34655-34664 Chemical denotes Ribavirin MESH:D012254
840 34402-34412 Species denotes SARS-CoV-2 Tax:2697049
841 34353-34361 Chemical denotes Piperine MESH:C008922
846 35085-35088 Gene denotes PC2 Gene:3854
847 35077-35080 Gene denotes PC1 Gene:5167
848 35168-35172 Gene denotes Mpro Gene:8673700
849 35150-35163 Chemical denotes Spro-Piperine
856 35595-35599 Gene denotes Mpro Gene:8673700
857 35582-35586 Gene denotes Mpro Gene:8673700
858 35486-35490 Gene denotes Mpro Gene:8673700
859 35469-35473 Gene denotes Mpro Gene:8673700
860 35441-35454 Chemical denotes Spro-Piperine
861 35560-35573 Chemical denotes Spro-Piperine
865 36207-36211 Gene denotes Mpro Gene:8673700
866 36135-36139 Gene denotes Mpro Gene:8673700
867 36117-36130 Chemical denotes Spro-Piperine
896 37443-37447 Gene denotes Mpro Gene:8673700
897 37579-37583 Gene denotes ACE2 Gene:59272
898 37690-37694 Gene denotes ACE2 Gene:59272
899 37761-37765 Gene denotes Mpro Gene:8673700
900 37906-37910 Gene denotes Mpro Gene:8673700
901 37204-37208 Gene denotes Mpro Gene:8673700
902 36580-36584 Gene denotes Mpro Gene:8673700
903 36377-36381 Gene denotes Mpro Gene:8673700
904 36435-36445 Species denotes SARS-CoV-2 Tax:2697049
905 36588-36598 Species denotes SARS-CoV-2 Tax:2697049
906 37193-37203 Species denotes SARS-CoV-2 Tax:2697049
907 38010-38020 Species denotes SARS-CoV-2 Tax:2697049
908 36327-36335 Chemical denotes Piperine MESH:C008922
909 36497-36505 Chemical denotes Piperine MESH:C008922
910 36664-36672 Chemical denotes Piperine MESH:C008922
911 36765-36776 Chemical denotes chloroquine MESH:D002738
912 36778-36789 Chemical denotes favipiravir MESH:C462182
913 36791-36809 Chemical denotes hydroxychloroquine MESH:D006886
914 36811-36822 Chemical denotes oseltamivir MESH:D053139
915 36824-36834 Chemical denotes remdesivir MESH:C000606551
916 36839-36848 Chemical denotes ribavirin MESH:D012254
917 36962-36970 Chemical denotes Piperine MESH:C008922
918 37318-37326 Chemical denotes Piperine MESH:C008922
919 37394-37402 Chemical denotes Piperine MESH:C008922
920 37482-37490 Chemical denotes Piperine MESH:C008922
921 37604-37612 Chemical denotes Piperine MESH:C008922
922 37726-37734 Chemical denotes Piperine MESH:C008922
923 37851-37859 Chemical denotes Piperine MESH:C008922
939 39242-39246 Gene denotes MPro Gene:8673700
940 38874-38878 Gene denotes Mpro Gene:8673700
941 39096-39100 Gene denotes Mpro Gene:8673700
942 38538-38542 Gene denotes Mpro Gene:8673700
943 38181-38191 Species denotes SARS-CoV-2 Tax:2697049
944 38241-38247 Species denotes people Tax:9606
945 38514-38524 Species denotes SARS-CoV-2 Tax:2697049
946 38850-38860 Species denotes SARS-CoV-2 Tax:2697049
947 39072-39082 Species denotes SARS-Cov-2 Tax:2697049
948 39327-39337 Species denotes SARS-CoV-2 Tax:2697049
949 38762-38770 Chemical denotes Piperine MESH:C008922
950 38903-38911 Chemical denotes Piperine MESH:C008922
951 39058-39066 Chemical denotes Piperine MESH:C008922
952 39187-39195 Chemical denotes Piperine MESH:C008922
953 39274-39282 Chemical denotes Piperine MESH:C008922

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T7 1353-1364 http://purl.obolibrary.org/obo/GO_0006412 denotes translation
T8 1457-1474 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T9 1457-1474 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T10 1747-1772 http://purl.obolibrary.org/obo/GO_1903901 denotes inhibit viral replication
T11 1755-1772 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T12 1755-1772 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T13 14873-14882 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T14 16168-16185 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T15 16168-16185 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T16 19507-19517 http://purl.obolibrary.org/obo/GO_0008152 denotes metabolism
T17 19519-19528 http://purl.obolibrary.org/obo/GO_0007588 denotes excretion
T18 20298-20309 http://purl.obolibrary.org/obo/GO_0045158 denotes cytochromes
T19 20298-20309 http://purl.obolibrary.org/obo/GO_0045157 denotes cytochromes
T20 20298-20309 http://purl.obolibrary.org/obo/GO_0045156 denotes cytochromes
T21 20298-20309 http://purl.obolibrary.org/obo/GO_0008121 denotes cytochromes
T22 20420-20430 http://purl.obolibrary.org/obo/GO_0008152 denotes metabolism
T23 20616-20627 http://purl.obolibrary.org/obo/GO_0009056 denotes degradation
T24 20806-20815 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T25 37782-37799 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T26 37782-37799 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T27 39214-39223 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T22 0-2 Sentence denotes 1.
T23 4-16 Sentence denotes Introduction
T24 17-132 Sentence denotes The novel coronavirus disease 2019 (COVID-19) has become a major threat worldwide due to its fast-spreading nature.
T25 133-220 Sentence denotes This disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
T26 221-347 Sentence denotes The entry of this coronavirus to the host cell is mediated through the transmembrane spike glycoproteins (Hasan et al., 2020).
T27 348-649 Sentence denotes This glycoprotein consists of two subunits and is reported to have a similar affinity to the human angiotensin-converting enzyme 2 (ACE2) as that of the severe acute respiratory syndrome coronavirus (SARS-CoV), which in turn results in efficient spreading of SARS-CoV-2 in humans (Walls et al., 2020).
T28 650-817 Sentence denotes The spike glycol protein binds to its receptor human ACE2 by its receptor-binding domain (RBD) and is activated proteolytically by human protease (Shang et al., 2020).
T29 818-1018 Sentence denotes The interaction of the RBD of the spike glycoprotein to ACE2 is carried out by ARG403, TYR453, SER494, TYR495, PHE497, GLN498, THR500, ASN501, TYR505 residues of spike glycoprotein (Lan et al., 2020).
T30 1019-1161 Sentence denotes The interaction of RBD Spro to ACE2 can be inhibited by the small molecules that interact with the above residues of RBD spike protein (Spro).
T31 1162-1378 Sentence denotes On the other hand, the SARS-CoV-2 main protease (Mpro), also known as chymotrypsin-like protease, or 3-C-like protease (3CLpro), plays a vital role in processing the polyproteins through the translation of viral RNA.
T32 1379-1509 Sentence denotes This protease is reported to have a minimum of 11 cleavage sites resulting in viral replication and toxicity (Zhang et al., 2020).
T33 1510-1612 Sentence denotes The inhibition of these two viral targets can actively block the fusion and replication of SARS-CoV-2.
T34 1613-1798 Sentence denotes Currently, researchers are working globally for finding treatment for this disease in identifying a specific drug or vaccine that can inhibit viral replication at the earliest possible.
T35 1799-2115 Sentence denotes The devastation of this disease is vividly seen from the data on the WHO website, which shows the infected patient number more than 245 lakhs and casualties more than 8 lakhs, worldwide from 216 countries, and still, it is continuing (https://www.who.int/emergencies/diseases/novel-coronavirus-2019, 29 August 2020).
T36 2116-2331 Sentence denotes Currently, there are no approved drugs and vaccines for the treatment of COVID-19, but a few drugs such as remdesivir, hydroxychloroquine, etc. are under restricted use in case of emergency (Magagnoli et al., 2020).
T37 2332-2563 Sentence denotes Meanwhile, the computational tools, molecular docking and molecular dynamics (MD) have gained attention as essential tools to investigate potential inhibitor molecules (Anurag et al., 2020; Gupta et al., 2020; Sourav et al., 2020).
T38 2564-2715 Sentence denotes Choy et al. reported in-vitro studies showing remdesivir, lopinavir, emetine and homoharringtonine inhibits SARS-CoV-2 replication (Choy et al., 2020).
T39 2716-2848 Sentence denotes Similarly, Wang et al. reported the inhibition property of remdesivir and chloroquine against novel coronavirus (Wang et al., 2020).
T40 2849-2964 Sentence denotes In addition to different drug compounds, researchers also searched for natural molecules having antiviral activity.
T41 2965-3067 Sentence denotes Natural constituents from foods, spices, herbs are also being found to have anti-infective properties.
T42 3068-3268 Sentence denotes In this context, small active molecules present in natural products and their derivatives have gained tremendous attention as a source of therapeutic agents due to structural diversity for many years.
T43 3269-3473 Sentence denotes From 1940 to 2014, the US Food and Drug Administration (FDA) has approved about 49% of all small molecules that are natural products or derivates linked directly to those molecules (Newman & Cragg, 2016).
T44 3474-3617 Sentence denotes The compound of essential garlic oil, a spice used in food, is reported as an inhibitor using the molecular docking method (Thuy et al., 2020).
T45 3618-3784 Sentence denotes There are several recent studies on the inhibition of SARS-CoV-2 using many different natural and antiviral molecules (Al-Khafaji et al., 2020; Joshi et al., 2020; D.
T46 3785-3841 Sentence denotes Kumar, Kumari, et al., 2020; Muralidharan et al., 2020).
T47 3842-3978 Sentence denotes Recently, Das et al., using blind molecular docking, investigated for the potential inhibitors of SARS-CoV-2 Mpro (Sourav et al., 2020).
T48 3979-4125 Sentence denotes Molecules studied by Das et al. are drug molecules, antivirals, antifungals, anti-nematodals and anti-protozoals in addition to natural compounds.
T49 4126-4318 Sentence denotes Besides, natural molecules such as alkaloids and terpenoids from African medicinal plants were studied by Gyebi et al. for the inhibition property against SARS-CoV-2 Mpro (Gyebi et al., 2020).
T50 4319-4441 Sentence denotes Recently, Umesh et al. screened compounds from Indian spices as potent inhibitors of SARS-CoV-2 Mpro (Umesh et al., 2020).
T51 4442-4722 Sentence denotes Every spice has a particular aroma, colour and flavour due to the presence of specific molecules in them, and also, have antiviral properties (Aboubakr et al., 2016; Astani et al., 2010; Brochot et al., 2017; Chang et al., 2013; Choi, 2016; Mair et al., 2016; Zhang et al., 2014).
T52 4723-4990 Sentence denotes These properties of the spice molecules compel us to conduct the present study, where we investigated the inhibition property of molecules present in various spices against the SARS-CoV-2 RBD Spro and SARS-Cov-2 Mpro using molecular docking and MD simulation studies.
T53 4991-5092 Sentence denotes The compounds tested and their source of origin with PubChem ID are listed in Supplementary Table S1.
T54 5093-5101 Sentence denotes Table 1.
T55 5103-5236 Sentence denotes Predicted data of docking score, solubility, pharmacokinetics, drug-likeness and medicinal chemistry of the screened spice molecules.
T56 5237-5240 Sentence denotes Sl.
T57 5241-5244 Sentence denotes No.
T58 5246-5429 Sentence denotes Molecule Binding energy (kcal/mol) ESOL Log S Ali Log S Silicos-IT LogSw GI absorption BBB permeant Pgp substrate Log Kp (cm/s) Bioavailability score Synthetic accessibility
T59 5430-5444 Sentence denotes Mpro RBD Spro
T60 5445-5529 Sentence denotes 1 2-Decenoic acid –5.4 –4.6 –2.8 –4.23 –2.15 High Yes No –4.68 0.56 2.44
T61 5530-5618 Sentence denotes 2 α-Terpinyl acetate –5.5 –5.0 –3.35 –4.21 –2.36 High Yes No –4.69 0.55 3.13
T62 5619-5697 Sentence denotes 3 Capsaicin –6.4 –5.5 –3.53 –4.5 –4.87 High Yes No –5.62 0.55 2.32
T63 5698-5775 Sentence denotes 4 Carvone –6.2 –5.2 –2.41 –2.72 –2.16 High Yes No –5.29 0.55 3.33
T64 5776-5859 Sentence denotes 5 Cinnamaldehyde –5.7 –5.1 –2.17 –1.88 –2.4 High Yes No –5.76 0.55 1.65
T65 5860-5942 Sentence denotes 6 Cuminaldehyde –5.9 –5.1 –2.52 –2.37 –3.15 High Yes No –5.52 0.55 1.0
T66 5943-6030 Sentence denotes 7 Dipropyl disulfide –3.1 –3.0 –2.14 –3.42 –2.48 High Yes No –5.3 0.55 2.79
T67 6031-6110 Sentence denotes 8 Eucalyptol –5.2 –4.9 –2.52 –2.59 –2.45 High Yes No –5.3 0.55 3.65
T68 6111-6188 Sentence denotes 9 Linalool –5.5 –4.9 –2.4 –3.06 –1.84 High Yes No –5.13 0.55 2.74
T69 6189-6268 Sentence denotes 10 Vanillin –5.7 –4.8 –1.82 –1.78 –1.88 High Yes No –6.37 0.55 1.15
T70 6269-6344 Sentence denotes 11 Thymol –5.8 –5.3 –3.19 –3.4 –3.01 High Yes No –4.87 0.55 1.0
T71 6345-6432 Sentence denotes 12 Sabinene hydrate –5.2 –4.7 –2.07 –2.18 –1.91 High Yes No –5.74 0.55 2.82
T72 6433-6511 Sentence denotes 13 Piperine –7.3 –6.4 –3.74 –3.96 –3.0 High Yes No –5.58 0.55 2.92
T73 6512-6589 Sentence denotes 14 Menthol –5.6 –5.2 –2.88 –3.5 –1.48 High Yes No –4.84 0.55 2.63
T74 6590-6668 Sentence denotes 15 Eugenol –6.0 –5.0 –2.46 –2.53 –2.79 High Yes No –5.69 0.55 1.58
T75 6669-6749 Sentence denotes 16 Estragole –5.7 –4.8 –3.09 –3.24 –3.35 High Yes No –4.81 0.55 1.28
T76 6750-6829 Sentence denotes 17 Gingerol –6.1 –5.5 –2.96 –3.82 –4.58 High Yes No –6.14 0.55 2.81
T77 6830-6906 Sentence denotes 18 Shogaol –5.8 –5.4 –3.7 –4.67 –4.8 High Yes No –5.15 0.55 2.51
T78 6907-6985 Sentence denotes 19 Paradol –6.0 –4.6 –3.72 –4.79 –5.52 High Yes No –5.08 0.55 2.28
T79 6986-7063 Sentence denotes 20 Zingerone –6.0 –5.1 –1.8 –1.68 –3.1 High Yes No –6.7 0.55 1.52
T80 7064-7141 Sentence denotes 21 Borneol –5.7 –4.3 –2.51 –2.8 –1.91 High Yes No –5.31 0.55 3.43
T81 7142-7227 Sentence denotes 22 Bornyl acetate –5.3 –4.8 –3.63 –4.57 –2.58 High Yes No –4.44 0.55 3.64
T82 7228-7305 Sentence denotes 23 Citral –5.5 –4.7 –2.43 –3.05 –1.96 High Yes No –5.08 0.55 2.49
T83 7306-7388 Sentence denotes 24 Citronellal –4.8 –4.8 –2.88 –3.88 –2.33 High Yes No –4.52 0.55 2.57
T84 7389-7472 Sentence denotes 25 2-Undecanone –4.9 –4.3 –2.94 –4.15 –3.83 High Yes No –4.43 0.55 1.72
T85 7473-7558 Sentence denotes 26 Geranyl acetate –5.4 –4.8 –3.21 –4.3 –2.52 High Yes No –4.63 0.55 2.72
T86 7559-7638 Sentence denotes 27 Nerolidol –5.8 –5.0 –3.8 –4.99 –3.15 High Yes No –4.23 0.55 3.53
T87 7639-7723 Sentence denotes 28 Terpinen-4-ol –5.2 –5.5 –2.78 –3.36 –1.91 High Yes No –4.93 0.55 3.28
T88 7724-7804 Sentence denotes 29 Terpineol –5.7 –5.2 –2.87 –3.49 –1.69 High Yes No –4.83 0.55 3.24
T89 7805-7883 Sentence denotes 30 Decanal –4.7 –3.9 –2.67 –3.85 –3.44 High Yes No –4.56 0.55 1.62
T90 7885-7887 Sentence denotes 2.
T91 7889-7910 Sentence denotes Materials and methods
T92 7911-8032 Sentence denotes In general, molecular modelling is implemented as an essential tool for the prediction of drug–macromolecule interaction.
T93 8033-8135 Sentence denotes This technique helps to enhance the success rate of an experiment and cuts down the experimental cost.
T94 8136-8275 Sentence denotes Hence, the molecular docking study can help to analyse the possible binding pose of a small molecule on the active site of a macromolecule.
T95 8276-8407 Sentence denotes Here we used molecular docking to screen some biologically active spice molecules with the SARS-CoV-2 RBD Spro and SARS-Cov-2 Mpro.
T96 8408-8530 Sentence denotes The molecule with the highest binding affinity to RBD Spro and Mpro was subjected to MD simulation for further validation.
T97 8532-8536 Sentence denotes 2.1.
T98 8538-8585 Sentence denotes Drug-likeness properties of the small molecules
T99 8586-8704 Sentence denotes The property of the small molecules for drug-likeness was estimated using the Lipinski’s rule (Lipinski et al., 2001).
T100 8705-8926 Sentence denotes This rule works on five parameters viz. no more than five hydrogen bond donors, no more than 10 hydrogen bond acceptors, molecular mass <500 Da, and the octanol-water partition coefficient, i.e. log P should not exceed 5.
T101 8927-9047 Sentence denotes The Lipinski’s parameters were obtained by using the SwissADME server (www.swissadme.ch/index.php) (Daina et al., 2017).
T102 9049-9053 Sentence denotes 2.2.
T103 9055-9104 Sentence denotes Structure preparation of the proteins and ligands
T104 9105-9159 Sentence denotes The crystal structures of the SARS-CoV-2 Spro (PDB ID:
T105 9160-9194 Sentence denotes 6M0J) and SARS-CoV-2 Mpro (PDB ID:
T106 9195-9247 Sentence denotes 6Y84) were obtained from the RCSB protein data bank.
T107 9248-9366 Sentence denotes All the non-standard residues, including water, were removed from the PDB file using Chimera (Pettersen et al., 2004).
T108 9367-9432 Sentence denotes The RBD domain was obtained from the PDB file of SARS-Cov-2 Spro.
T109 9433-9541 Sentence denotes The RBD Spro residue sequence number before and after removing ACE2 is presented in Supplementary Figure S1.
T110 9542-9770 Sentence denotes The 3D conformers of the ligands were obtained from the PubChem and optimized using the steepest descent and conjugate gradient steps with General Amber Force Field (GAFF) (Wang et al., 2004) in Chimera (Pettersen et al., 2004).
T111 9771-9780 Sentence denotes Figure 1.
T112 9782-9887 Sentence denotes Predicted lipophilicity (Log P) values of the spice molecules obtained from different calculation models.
T113 9889-9893 Sentence denotes 2.3.
T114 9895-9918 Sentence denotes Molecular docking study
T115 9919-10056 Sentence denotes The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott & Olson, 2010).
T116 10057-10152 Sentence denotes AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy.
T117 10153-10296 Sentence denotes It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space.
T118 10297-10414 Sentence denotes A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro.
T119 10415-10531 Sentence denotes A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro.
T120 10532-10709 Sentence denotes The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results.
T121 10710-10801 Sentence denotes The docked poses were ranked as per their binding affinities at the end of the docking run.
T122 10802-10943 Sentence denotes The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017).
T123 10944-11054 Sentence denotes The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005).
T124 11055-11192 Sentence denotes The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017).
T125 11194-11198 Sentence denotes 2.4.
T126 11200-11240 Sentence denotes Molecular dynamics (MD) simulation study
T127 11241-11516 Sentence denotes To verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015).
T128 11517-11610 Sentence denotes The CHARMM36 forcefield (Huang & MacKerell, 2013) was used for the simulation of the systems.
T129 11611-11720 Sentence denotes The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe & MacKerell, 2012).
T130 11721-11817 Sentence denotes A dodecahedron simulation box filled with TIP3P water model (Price & Brooks, 2004) was prepared.
T131 11818-11894 Sentence denotes Counter ions were added to maintain the electrical neutrality of the system.
T132 11895-11953 Sentence denotes The systems were kept at a buffer concentration of 0.15 M.
T133 11954-12055 Sentence denotes Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm.
T134 12056-12196 Sentence denotes Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run.
T135 12197-12289 Sentence denotes After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble.
T136 12290-12452 Sentence denotes For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used.
T137 12453-12683 Sentence denotes Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello & Rahman, 1981) with isotropic rescaling were used, respectively.
T138 12684-12776 Sentence denotes The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps.
T139 12777-12982 Sentence denotes The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools.
T140 12983-13092 Sentence denotes The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs.
T141 13093-13172 Sentence denotes The data were exported to origin 9.0 and plotted for further analysis purposes.
T142 13174-13178 Sentence denotes 2.5.
T143 13180-13219 Sentence denotes Mm/PBSA binding free energy calculation
T144 13220-13381 Sentence denotes The method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used.
T145 13382-13573 Sentence denotes The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014).
T146 13574-13705 Sentence denotes The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy.
T147 13706-13923 Sentence denotes The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively.
T148 13924-14160 Sentence denotes The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy.
T149 14161-14514 Sentence denotes The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions.
T150 14515-14681 Sentence denotes The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively.
T151 14683-14685 Sentence denotes 3.
T152 14687-14709 Sentence denotes Results and discussion
T153 14711-14715 Sentence denotes 3.1.
T154 14717-14773 Sentence denotes Molecular electrostatic potential (MEP) surface analysis
T155 14774-14897 Sentence denotes The electrostatic potential is an essential property for the review and prediction of the reactive behaviour of a molecule.
T156 14898-15149 Sentence denotes The study of the MEP surface can provide information about the active site of the macromolecule with the indication of relative ligand orientation and nature of the active site at which an approaching electrophile is attracted (Politzer et al., 1985).
T157 15150-15297 Sentence denotes In a biological macromolecule, the electrostatic potential surface is plotted by analysing the electron-rich and deficient regions of the molecule.
T158 15298-15461 Sentence denotes The detailed insight at the molecular label helps to predict the potentiality of the ligands to take part in chemical reactions and their mechanism of interaction.
T159 15462-15641 Sentence denotes The MEP surface representation of SARS-CoV-2 RBD Spro and Mpro ligand-binding sites with the simultaneous presence of all docked molecules are provided in Supplementary Figure S2.
T160 15642-15836 Sentence denotes The electronically poor regions (blue) are referred to as positive potential, whereas the dense electron regions (red) are at a negative potential, and the white zones are considered as neutral.
T161 15837-16011 Sentence denotes From the figure, it is observed that most of the selected molecules actively bound at the red regions that are referred to as highly negative electrostatic potential regions.
T162 16012-16186 Sentence denotes This implies that the molecules are polar and can actively take part in the binding process with stable interactions, which in turn could help to block the viral replication.
T163 16187-16196 Sentence denotes Figure 2.
T164 16198-16300 Sentence denotes Predicted solubility (Log S) values of the spice molecules obtained from different calculation models.
T165 16302-16306 Sentence denotes 3.2.
T166 16308-16321 Sentence denotes Lipophilicity
T167 16322-16458 Sentence denotes Lipophilicity or fat friendliness of a molecule defines the dissolving capability in fat, oil or any non-polar solvent (Lindsley, 2010).
T168 16459-16582 Sentence denotes The water n-octanol partition coefficient (log Po/w) is used as the measure of lipophilicity (Constantinescu et al., 2019).
T169 16583-16711 Sentence denotes Various computational methods are developed for the estimation of log Po/w for diverse performance upon different chemical sets.
T170 16712-17047 Sentence denotes The SwissADME provides five different predictive models such as XLOGP3 (Cheng et al., 2007), WLOGP (Wildman & Crippen, 1999), MLOGP (Moriguchi et al., 1992), SILICOS-IT (http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/filter-it/1.0.2/filter-it.html, 2016) and iLOGP (Daina et al., 2014) for better prediction accuracy.
T171 17048-17175 Sentence denotes Predicted lipophilicity (Log P) values of the spice molecules obtained from different calculation models are shown in Figure 1.
T172 17176-17409 Sentence denotes All the molecules subjected to lipophilicity test lie in the range of +1.2 to +4.19 of consensus value that obeys the Lipinski’s limit of log p < 5, which suggests they can be used for further clinical trials (Arnott & Planey, 2012).
T173 17410-17520 Sentence denotes The lowest lipophilicity is observed for Vanillin and the highest for Nerolidol, among the screened molecules.
T174 17521-17612 Sentence denotes From Figure 1, it is found that all the ligand molecules have positive lipophilicity value.
T175 17613-17688 Sentence denotes Hence, these molecules satisfy the essential criteria to be drug molecules.
T176 17690-17694 Sentence denotes 3.3.
T177 17696-17712 Sentence denotes Water solubility
T178 17713-17815 Sentence denotes Solubility (Log S) is the measure of homogeneity of the system from the mixture of solute and solvent.
T179 17816-17962 Sentence denotes It is considered as one of the vital parameters in drug concentration determination for a desired pharmacological response (Savjani et al., 2012).
T180 17963-18039 Sentence denotes Poor solubility of drugs is a major issue in drug discovery and development.
T181 18040-18176 Sentence denotes Solubility acts as a driving force to attain high drug concentration in blood for therapeutic effectiveness (Bergström & Larsson, 2018).
T182 18177-18270 Sentence denotes The drug solubility property of the proposed small molecules was obtained from the SwissADME.
T183 18271-18590 Sentence denotes The server used three solubility models, such as Ali (Ali et al., 2012), ESOL (Delaney, 2004) and Silicos-IT (http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/filter-it/1.0.2/filter-it.html, 2016) that is comprised of different topological methods to check the water solubility of these small molecules.
T184 18591-18706 Sentence denotes The plot for solubility of the proposed small molecules based on these three different models is shown in Figure 2.
T185 18707-18908 Sentence denotes The Log S values obtained for the ligand molecules based on these three models are in the range of −1.8 to −3.94 for ESOL method, −1.68 to −4.99 for Ali method and −1.48 to −5.52 for Silicos-IT method.
T186 18909-19016 Sentence denotes The values from different models suggest to the moderately soluble to very soluble nature of the molecules.
T187 19017-19146 Sentence denotes The reference values of Log S for moderately soluble and highly soluble molecules range from −4 to −6 and −2 to −4, respectively.
T188 19147-19224 Sentence denotes The solubility values suggest for the oral administration of these molecules.
T189 19226-19230 Sentence denotes 3.4.
T190 19232-19258 Sentence denotes Pharmacokinetic properties
T191 19259-19394 Sentence denotes The pharmacokinetic property is the prime factor for the selection of a drug candidate that describes the drug disposition in the body.
T192 19395-19561 Sentence denotes The significant parameters that quantify the pharmacokinetics of a drug are its ADME (absorption, distribution, metabolism, excretion) properties (Jang et al., 2001).
T193 19562-19769 Sentence denotes All the molecules subjected to ADME tests are qualified for drug approval with their high value of gastrointestinal (GI) absorption (Daina & Zoete, 2016), which in turn implies for their use as an oral drug.
T194 19770-19852 Sentence denotes Table 1 represents the pharmacokinetic properties of the proposed drug candidates.
T195 19853-19990 Sentence denotes The passive GI absorption and blood–brain barrier (BBB) permeation is a fundamental criterion for the distribution of the drug molecules.
T196 19991-20116 Sentence denotes From Table 1, it is observed that all the ligand molecules are BBB permeant that implies their underlying distribution index.
T197 20117-20254 Sentence denotes The high negative skin permeable coefficient (Kp) values indicate a less skin permeability that is useful for their transdermal delivery.
T198 20255-20431 Sentence denotes The interaction of the drug molecules with cytochromes P450 (CYP) is an essential property as they play a crucial role in drug elimination through biotransformation metabolism.
T199 20432-20751 Sentence denotes The noninhibition of CYP isoforms such as CYP1A2, CYP2C19, CYP2C9, CYP2D6 and CYP3A4 disclose that these molecules are not the substrate for these enzymes that resembles for the lower degradation rate of these molecules, which will make it effectively available for blocking the SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro.
T200 20752-20835 Sentence denotes The synthetic accessibility values suggest the facile synthesis of these molecules.
T201 20836-20947 Sentence denotes All these parameters infer these close to drug-like molecules, which may be used as successful drug candidates.
T202 20949-20953 Sentence denotes 3.5.
T203 20955-20978 Sentence denotes Molecular docking study
T204 20980-20986 Sentence denotes 3.5.1.
T205 20988-21053 Sentence denotes Docking study of SARS-CoV-2 receptor-binding domain spike protein
T206 21054-21262 Sentence denotes In addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro.
T207 21263-21374 Sentence denotes From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds.
T208 21375-21624 Sentence denotes The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3.
T209 21625-21872 Sentence denotes From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules.
T210 21873-21988 Sentence denotes From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170.
T211 21989-22110 Sentence denotes TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively.
T212 22111-22279 Sentence denotes The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro.
T213 22280-22457 Sentence denotes Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score.
T214 22458-22636 Sentence denotes Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)).
T215 22637-22823 Sentence denotes The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.
T216 22824-22833 Sentence denotes Figure 3.
T217 22835-22986 Sentence denotes Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram.
T218 22987-23041 Sentence denotes The colour codes represent the nature of interactions.
T219 23042-23160 Sentence denotes On the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)).
T220 23161-23269 Sentence denotes The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol.
T221 23270-23544 Sentence denotes Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions.
T222 23545-23801 Sentence denotes The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)).
T223 23802-23932 Sentence denotes The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3.
T224 23934-23940 Sentence denotes 3.5.2.
T225 23942-23983 Sentence denotes Docking study of SARS-CoV-2 main protease
T226 23984-24107 Sentence denotes The above-selected molecules were also docked with the SARS-CoV-2 Mpro to observe the inhibitory effect of these molecules.
T227 24108-24228 Sentence denotes The docking study reveals that all the molecules are interacting with the SARS-CoV-2 Mpro with certain binding affinity.
T228 24229-24276 Sentence denotes The docking data are also presented in Table 1.
T229 24277-24466 Sentence denotes From Table 1, it is seen that Piperine has the highest affinity at the binding site of SARS-CoV-2 Mpro among all the selected molecules, which is similar to the case of SARS-CoV-2 RBD Spro.
T230 24467-24658 Sentence denotes The ΔG value, known as binding free energy, for the four molecules having the highest affinity among all the selected molecules, along with their 2D interaction diagram, is given in Figure 4.
T231 24659-24828 Sentence denotes The four molecules have followed the binding affinity trend as Piperine (−7.3 kcal/mol) > Capsaicin (−6.4 kcal/mol) > Carvone (−6.2 kcal/mol) > Gingerol (−6.1 kcal/mol).
T232 24829-25019 Sentence denotes From Figure 4(a), it is observed that the interaction of Piperine at the binding site of the SARS-CoV-2 Mpro is stabilized by hydrogen bonding, electrostatics and van der Waals interactions.
T233 25020-25224 Sentence denotes The residues GLN299 and VAL303 are associated with hydrogen bonding interaction; ASP295 and ARG298 with charged interactions while MET6 and PRO9 are associated with hydrophobic interactions with Piperine.
T234 25225-25389 Sentence denotes The molecule is also stabilized through van der Waals interactions with residues PHE8, GLY127, ILE152, PHE291 and THR304 at the binding site of the SARS-CoV-2 Mpro.
T235 25390-25514 Sentence denotes The molecule Capsaicin is stabilized in the binding pocket through van der Waals and hydrophobic interactions (Figure 4(b)).
T236 25515-25651 Sentence denotes The residues MET6, PHE8, PRO9 and ILE152 are interacting through hydrophobic interactions such as alkyl and pi–alkyl with the Capsaicin.
T237 25652-25811 Sentence denotes Capsaicin is interacting with residues ALA7, GLY11, LYS12, GLN127, TYR154, PHE291, ASP295, ARG298, GLN299, VAL303 and THR304 through van der Waals interaction.
T238 25812-25943 Sentence denotes The interaction of Carvone with the SARS-CoV-2 Mpro is stabilized through hydrophobic and van der Walls interactions (Figure 4(c)).
T239 25944-26050 Sentence denotes Carvone interacts with the residues MET6, PHE8 and ARG298 of SARS-CoV-2 Mpro through hydrophobic contacts.
T240 26051-26165 Sentence denotes The residues ALA7, PRO9, GLN127, ASP295, GLN299, GLY302 and VAL303 are in van der Waals interactions with Carvone.
T241 26166-26309 Sentence denotes Gingerol is stabilized by hydrogen bond, hydrophobic and van der Waals interactions in the binding pocket of the SARS-Cov-2 Mpro (Figure 4(d)).
T242 26310-26380 Sentence denotes VAL303 is interacting through hydrogen bond interaction with Gingerol.
T243 26381-26580 Sentence denotes The residues LYS12 and THR304 are involved in carbon-hydrogen bond interactions while MET6, ALA7, PHE8, GLN127, TYR154, ASP295 and ARG298 are associated with van der Waals interactions with Gingerol.
T244 26581-26687 Sentence denotes The interaction of Gingerol with the residues PRO9 and ILE152 is stabilized through pi–alkyl interactions.
T245 26688-26871 Sentence denotes The lowest energy binding poses of the rest 26 molecules along with the ligand interaction diagram at the binding sites of the SARS-CoV-2 Mpro are provided in Supplementary Figure S4.
T246 26872-26881 Sentence denotes Figure 4.
T247 26883-27024 Sentence denotes Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Carvone and (d) Gingerol with SARS-CoV-2 Mpro and their 2D interaction diagram.
T248 27025-27079 Sentence denotes The colour codes represent the nature of interactions.
T249 27081-27085 Sentence denotes 3.6.
T250 27087-27127 Sentence denotes Molecular dynamics (MD) simulation study
T251 27128-27306 Sentence denotes The MD simulation is one of the proven in-silico methods for the determination of protein–ligand dynamics concerning a high temporal resolution of nanosecond or picosecond order.
T252 27307-27452 Sentence denotes Here the docked poses of RBD Spro and Mpro with Piperine were used for a 100 ns MD simulation to analyse the stability of these docked compounds.
T253 27454-27460 Sentence denotes 3.6.1.
T254 27462-27495 Sentence denotes Root mean square deviation (RMSD)
T255 27496-27597 Sentence denotes The RMSD values from MD simulation provide information about structural and conformational stability.
T256 27598-27691 Sentence denotes Figure 5 represents the backbone RMSD data of viral proteins and their complex with Piperine.
T257 27692-27801 Sentence denotes From the plot, it is observed that both the simulations have less fluctuation throughout the simulation time.
T258 27802-27987 Sentence denotes The average RMSD values of RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine are calculated as 0.143 ± 0.025 nm, 0.130 ± 0.018 nm, 0.212 ± 0.041 nm and 0.203 ± 0.028 nm, respectively.
T259 27988-28140 Sentence denotes The average RMSD values of the Piperine bound proteins as compared to only proteins are found to be less representing to their conformational stability.
T260 28141-28326 Sentence denotes Both the simulations are attained equilibrium within 0.3 nm, which is also a measure of the systems’ stability during the simulation (Al-Shabib et al., 2018, 2020; Millan et al., 2018).
T261 28327-28336 Sentence denotes Figure 5.
T262 28338-28466 Sentence denotes Root mean square deviation plots of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue).
T263 28468-28474 Sentence denotes 3.6.2.
T264 28476-28511 Sentence denotes Root mean square fluctuation (RMSF)
T265 28512-28693 Sentence denotes The conformational fluctuations of the proteins RBD Spro and Mpro were analysed by observing the residual changes that resulted due to the interaction of Piperine with the proteins.
T266 28694-28801 Sentence denotes The RMSF plots of the Cα atoms of the viral proteins and their complex with Piperine are shown in Figure 6.
T267 28802-29007 Sentence denotes From the analysis, it is found that RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine have the average RMSF values 0.099 ± 0.060 nm, 0.097 ± 0.051 nm, 0.119 ± 0.077 nm and 0.120 ± 0.077 nm, respectively.
T268 29008-29207 Sentence denotes It is observed that RBD Spro-Piperine (Figure 6(a)) and Mpro-Piperine (Figure 6(b)) show similar fluctuations as compared to only RBD Spro and Mpro, which implies to the stability of these compounds.
T269 29208-29310 Sentence denotes In addition to that, a majority of the protein residues are found to be stabilized within RMSF 0.3 nm.
T270 29311-29422 Sentence denotes The decrease in fluctuations of Piperine bound to RBD Spro also suggests for the active binding of Piperine (A.
T271 29423-29454 Sentence denotes Kumar, Choudhir, et al., 2020).
T272 29455-29464 Sentence denotes Figure 6.
T273 29466-29608 Sentence denotes Root mean square fluctuation plots of Cα-atoms of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue).
T274 29610-29616 Sentence denotes 3.6.3.
T275 29618-29641 Sentence denotes Radius of gyration (Rg)
T276 29642-29758 Sentence denotes The root mean square distance between an object and the centre of gravity is defined as the radius of gyration (Rg).
T277 29759-29983 Sentence denotes The radius of gyration is a measure of the compactness of the protein structure, where higher Rg value is referred to as a less compact structure, and low Rg value is inferred as high compactness that implies more stability.
T278 29984-30162 Sentence denotes The measured average Rg values of RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine are 1.829 ± 0.008 nm, 1.833 ± 0.010 nm, 2.233 ± 0.012 nm and 2.238 ± 0.013 nm, respectively.
T279 30163-30415 Sentence denotes From Figure 7(a,b), it is observed that there is a little enhancement in the Rg values of RBD Spro-Piperin, and Mpro-Piperine as compared to RBD Spro and Mpro, which implies to the gain in compactness of the protein structures upon binding to Piperine.
T280 30416-30425 Sentence denotes Figure 7.
T281 30427-30661 Sentence denotes Radius of gyration plots of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue); (c) Intermolecular hydrogen bonds formed between RBD Spro-Piperine and Mpro-Piperine during 100 ns MD simulation.
T282 30663-30669 Sentence denotes 3.6.4.
T283 30671-30695 Sentence denotes Number of hydrogen bonds
T284 30696-30835 Sentence denotes The number of hydrogen bonds formed between the protein–ligand complex is the measure of the binding strength of the ligand to the protein.
T285 30836-30979 Sentence denotes The RBD Spro (red) and Mpro (blue) bound to Piperine have a constant number of 1–2 hydrogen bonds throughout the simulation time (Figure 7(c)).
T286 30980-31106 Sentence denotes There is a maximum number of 3 and 4 hydrogen bonds observed in the case of RBD Spro-Piperine and Mpro-Piperine, respectively.
T287 31107-31322 Sentence denotes The number of hydrogen bonds fluctuates throughout the simulation time for both RBD Spro-Piperine and Mpro-Piperine, which suggests for conformational changes in the binding site of the ligand during the simulation.
T288 31323-31441 Sentence denotes The observation from hydrogen bond analysis indicates that the complexes are stable for the performed simulation time.
T289 31443-31449 Sentence denotes 3.6.5.
T290 31451-31469 Sentence denotes Interaction energy
T291 31470-31566 Sentence denotes The interaction energy is the measure of the interaction strength of the protein–ligand complex.
T292 31567-31709 Sentence denotes In order to validate the results of molecular docking studies, the analysis of the interaction free energies from MD simulation was performed.
T293 31710-31832 Sentence denotes The average interaction energy takes the contribution from the average short-range Lennard-Jones and van der Waals energy.
T294 31833-31989 Sentence denotes The average interaction energies of RBD Spro-Piperine and Mpro-Piperine are found to be − 41.401 ± 17.843 kJ/mol and −143.162 ± 23.043 kJ/mol, respectively.
T295 31990-32224 Sentence denotes These interaction energy values suggest that Piperine binds to the RBD Spro and Mpro with good affinity and hence supports the docking results, which in turn helps for the favourable use of Piperine as a drug candidate for SARS-CoV-2.
T296 32226-32232 Sentence denotes 3.6.6.
T297 32234-32272 Sentence denotes Solvent accessible surface area (SASA)
T298 32273-32365 Sentence denotes SASA is a measure of the receptor exposure to the solvent environment during the simulation.
T299 32366-32504 Sentence denotes The hydrophobic residues that got exposed to the solvent environment upon binding with the ligand molecules contribute to the SASA values.
T300 32505-32596 Sentence denotes The plot of the SASA for the proteins and their ligand-bound form is presented in Figure 8.
T301 32597-32794 Sentence denotes The analysed average SASA values for the RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine are 106.976 ± 1.602 nm2, 107.235 ± 1.667 nm2, 150.698 ± 2.565 nm2 and 151.022 ± 2.207 nm2, respectively.
T302 32795-32969 Sentence denotes There is no significant change observed for the averaged SASA values of the complex as compared to only protein suggesting their stability after binding to the drug molecule.
T303 32970-32979 Sentence denotes Figure 8.
T304 32981-33121 Sentence denotes Solvent accessible surface area (SASA) plots of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue).
T305 33123-33129 Sentence denotes 3.6.7.
T306 33131-33166 Sentence denotes MMPBSA binding free energy analysis
T307 33167-33265 Sentence denotes MD simulation can also be used to calculate the binding free energy of the protein–ligand complex.
T308 33266-33412 Sentence denotes The binding free energy is the measure of the stability of the system in turns of consistency of nonbonded interactions throughout the simulation.
T309 33413-33520 Sentence denotes The binding free energy was calculated by using MMPBSA method by taking 2000 snapshots from the trajectory.
T310 33521-33671 Sentence denotes The computed value of binding free energy for RBD Spro-Piperine is found to be −5.533 ± 0.839 kJ/mol, and for Mpro-Piperine is −37.971 ± 0.271 kJ/mol.
T311 33672-33789 Sentence denotes It is observed that for both RBD Spro and Mpro, van der Waals energy plays a crucial role in the interaction process.
T312 33790-33915 Sentence denotes The van der Waals energy, electrostatic energy and non-polar energy are contributed actively to the total interaction energy.
T313 33916-34003 Sentence denotes In contrast, polar energy has a positive contribution to the whole interaction process.
T314 34004-34157 Sentence denotes The observed data indicate that the van der Waals, electrostatic and non-polar interactions combinedly contribute to the stability of both the compounds.
T315 34158-34308 Sentence denotes The contribution from different interactions to the binding free energy for RBD Spro-Piperine and Mpro-Piperine is provided in Supplementary Table S2.
T316 34309-34317 Sentence denotes Table 2.
T317 34319-34454 Sentence denotes Lowest energy binding affinity of Piperine and few of the currently used drugs for SARS-CoV-2 as obtained from molecular docking study.
T318 34455-34492 Sentence denotes Molecule Binding affinity (kcal/mol)
T319 34493-34507 Sentence denotes RBD Spro Mpro
T320 34508-34528 Sentence denotes Piperine –6.4 –7.3
T321 34529-34552 Sentence denotes Chloroquine –5.0 –4.9
T322 34553-34576 Sentence denotes Favipiravir –5.3 –5.6
T323 34577-34607 Sentence denotes Hydroxychloroquine –4.8 –6.0
T324 34608-34631 Sentence denotes Oseltamivir –5.1 –5.5
T325 34632-34654 Sentence denotes Remdesivir –6.1 –7.2
T326 34655-34676 Sentence denotes Ribavirin –5.6 –6.1
T327 34678-34684 Sentence denotes 3.6.8.
T328 34686-34720 Sentence denotes Principal component analysis (PCA)
T329 34721-34810 Sentence denotes The PCA is an essential technique to monitor the conformational dynamics of biomolecules.
T330 34811-34930 Sentence denotes It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories.
T331 34931-35100 Sentence denotes The diagonalization of the covariance matrix of backbone atoms of the proteins and ligand-bound form were considered for the principal components PC1 and PC2 (Figure 9).
T332 35101-35277 Sentence denotes From Figure 9(a,b), it is observed that both the Spro-Piperine and Mpro-Piperine are less flexible as compared to unbound proteins since they covered less conformational space.
T333 35278-35371 Sentence denotes It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.
T334 35372-35381 Sentence denotes Figure 9.
T335 35383-35507 Sentence denotes Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue).
T336 35508-35609 Sentence denotes Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.
T337 35610-35825 Sentence denotes The principal components obtained were used as the reaction coordinates to find the Gibbs free energy landscape (Figure 9) to visualize the energy minima of the unbound protein as well as the protein–ligand complex.
T338 35826-36041 Sentence denotes From Figure 9(c–f), it is observed that both the ligand-bound proteins have less Gibbs-free energy values than the unbound proteins indicating their stability and energetically favourable conformational transitions.
T339 36042-36289 Sentence denotes The shape and size of the minimum energy area (blue colour) in case of RBD Spro-Piperine and Mpro-Piperine are more as compared to the unbound proteins RBD Spro and Mpro, which suggests the ligand-bound forms are thermodynamically more favourable.
T340 36290-36446 Sentence denotes The comprehensive study reveals that Piperine forms a stable complex with RBD Spro and Mpro and can be considered as an active inhibitor against SARS-CoV-2.
T341 36447-36631 Sentence denotes From the docking results, it is observed that the Piperine molecule is the best candidate for the inhibition of the RBD Spro and the Mpro of SARS-CoV-2 among the selected 30 molecules.
T342 36632-36920 Sentence denotes To observe the effectiveness of Piperine over currently used drugs, we carried out the docking study of a few drug molecules such as chloroquine, favipiravir, hydroxychloroquine, oseltamivir, remdesivir and ribavirin using the same docking protocol as followed for the 30 spice molecules.
T343 36921-37041 Sentence denotes From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above.
T344 37042-37236 Sentence denotes The lowest energy pose of a few presently used drugs with their 2D interaction diagram is provided in Supplementary Figures S5 and S6 corresponding to SARS-CoV-2 Mpro and RBD Spro, respectively.
T345 37237-37355 Sentence denotes A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2.
T346 37356-37481 Sentence denotes The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites.
T347 37482-37584 Sentence denotes Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2.
T348 37585-37695 Sentence denotes So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2.
T349 37696-37800 Sentence denotes Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication.
T350 37801-38021 Sentence denotes From the docking and MD results, we conclude that Piperine forms a very stable complex with RBD Spro and Mpro and shows better affinity as compared to the currently used drugs that are mentioned above against SARS-CoV-2.
T351 38023-38025 Sentence denotes 4.
T352 38027-38037 Sentence denotes Conclusion
T353 38038-38265 Sentence denotes This study used molecular docking and MD simulation as potential tools to monitor the inhibitory efficiency of natural spice molecules against SARS-CoV-2, which emerged as a global threat to millions of people across the globe.
T354 38266-38423 Sentence denotes It is observed that all the proposed spice molecules qualified the ADME test with their suitable pharmacokinetic properties to be useful as a drug candidate.
T355 38424-38592 Sentence denotes The docking study is revealed that all the molecules actively take part in binding to the SARS-CoV-2 RBD Spro and Mpro with their low or high value of binding affinity.
T356 38593-38733 Sentence denotes This binding of these molecules will help to inhibit the replication of the viral proteins with specific hindrances upon their mutarotation.
T357 38734-38893 Sentence denotes For both the viral targets, Piperine performed well with its highest binding affinity of −6.4 and −7.3 kcal/mol for SARS-CoV-2 RBD Spro and Mpro, respectively.
T358 38894-38990 Sentence denotes Besides, Piperine is also found more effective as compared to a few of the currently used drugs.
T359 38991-39101 Sentence denotes The MD simulation study is supported for the stable interaction of Piperine with SARS-Cov-2 RBD Spro and Mpro.
T360 39102-39247 Sentence denotes The PCA and binding free energy results also suggest for the active participation of Piperine in stable complex formation with RBD Spro and MPro.
T361 39248-39338 Sentence denotes Hence, the study proposes Piperine as an active molecule for the inhibition of SARS-CoV-2.
T362 39339-39467 Sentence denotes Since this study is performed computationally, it requires wet-lab experiments in-vitroas well as in-vivofor further validation.
T363 39469-39491 Sentence denotes Supplementary Material
T364 39492-39513 Sentence denotes Supplemental Material
T365 39514-39550 Sentence denotes Click here for additional data file.

2_test

Id Subject Object Predicate Lexical cue
32938313-32155444-56197365 643-647 32155444 denotes 2020
32938313-32376634-56197366 811-815 32376634 denotes 2020
32938313-32198291-56197367 1503-1507 32198291 denotes 2020
32938313-32251767-56197368 2709-2713 32251767 denotes 2020
32938313-32020029-56197369 2842-2846 32020029 denotes 2020
32938313-26852623-56197370 3467-3471 26852623 denotes 2016
32938313-32363255-56197371 3611-3615 32363255 denotes 2020
32938313-27296605-56197372 4602-4606 27296605 denotes 2016
32938313-19653195-56197373 4623-4627 19653195 denotes 2010
32938313-23123794-56197374 4665-4669 23123794 denotes 2013
32938313-28053847-56197375 4677-4681 28053847 denotes 2016
32938313-28256516-56197376 9041-9045 28256516 denotes 2017
32938313-15264254-56197377 9360-9364 15264254 denotes 2004
32938313-15116359-56197378 9728-9732 15116359 denotes 2004
32938313-15264254-56197379 9764-9768 15264254 denotes 2004
32938313-19499576-56197380 10050-10054 19499576 denotes 2010
32938313-23832629-56197381 11561-11565 23832629 denotes 2013
32938313-23146088-56197382 11714-11718 23146088 denotes 2012
32938313-15549884-56197383 11798-11802 15549884 denotes 2004
32938313-11517324-56197384 13546-13550 11517324 denotes 2001
32938313-24850022-56197385 13567-13571 24850022 denotes 2014
32938313-2866089-56197386 15143-15147 2866089 denotes 1985
32938313-17985865-56197387 16798-16802 17985865 denotes 2007
32938313-25382374-56197388 17010-17014 25382374 denotes 2014
32938313-22992175-56197389 17403-17407 22992175 denotes 2012
32938313-22830056-56197390 17956-17960 22830056 denotes 2012
32938313-29421301-56197391 18170-18174 29421301 denotes 2018
32938313-22196228-56197392 18337-18341 22196228 denotes 2012
32938313-15154768-56197393 18359-18363 15154768 denotes 2004
32938313-11579439-56197394 19555-19559 11579439 denotes 2001
32938313-27218427-56197395 19710-19714 27218427 denotes 2016
32938313-32194324-56197396 28299-28303 32194324 denotes 2020