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PMC:7544943 / 36536-39879 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T50 185-192 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 204-211 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T52 301-309 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T53 323-331 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T54 545-553 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T55 684-692 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T56 1101-1108 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 1124-1131 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 1210-1218 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T59 1271-1279 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T60 1507-1515 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T71 399-402 Disease denotes PC1 http://purl.obolibrary.org/obo/MONDO_0008173
T72 407-410 Disease denotes PC2 http://purl.obolibrary.org/obo/MONDO_0008174
T73 1757-1765 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 1910-1918 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 2515-2523 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 3332-3340 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T171 236-238 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T172 437-438 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 439-440 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T174 738-739 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T175 788-789 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T176 1664-1665 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 1732-1738 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T178 2058-2059 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 2390-2391 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 2488-2490 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T181 2559-2560 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T182 2682-2684 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T183 2725-2733 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T184 2790-2796 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T185 2826-2832 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T186 3064-3070 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T187 3144-3146 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T188 3188-3189 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
846 407-410 Gene denotes PC2 Gene:3854
847 399-402 Gene denotes PC1 Gene:5167
848 490-494 Gene denotes Mpro Gene:8673700
849 472-485 Chemical denotes Spro-Piperine
856 917-921 Gene denotes Mpro Gene:8673700
857 904-908 Gene denotes Mpro Gene:8673700
858 808-812 Gene denotes Mpro Gene:8673700
859 791-795 Gene denotes Mpro Gene:8673700
860 763-776 Chemical denotes Spro-Piperine
861 882-895 Chemical denotes Spro-Piperine
865 1529-1533 Gene denotes Mpro Gene:8673700
866 1457-1461 Gene denotes Mpro Gene:8673700
867 1439-1452 Chemical denotes Spro-Piperine
896 2765-2769 Gene denotes Mpro Gene:8673700
897 2901-2905 Gene denotes ACE2 Gene:59272
898 3012-3016 Gene denotes ACE2 Gene:59272
899 3083-3087 Gene denotes Mpro Gene:8673700
900 3228-3232 Gene denotes Mpro Gene:8673700
901 2526-2530 Gene denotes Mpro Gene:8673700
902 1902-1906 Gene denotes Mpro Gene:8673700
903 1699-1703 Gene denotes Mpro Gene:8673700
904 1757-1767 Species denotes SARS-CoV-2 Tax:2697049
905 1910-1920 Species denotes SARS-CoV-2 Tax:2697049
906 2515-2525 Species denotes SARS-CoV-2 Tax:2697049
907 3332-3342 Species denotes SARS-CoV-2 Tax:2697049
908 1649-1657 Chemical denotes Piperine MESH:C008922
909 1819-1827 Chemical denotes Piperine MESH:C008922
910 1986-1994 Chemical denotes Piperine MESH:C008922
911 2087-2098 Chemical denotes chloroquine MESH:D002738
912 2100-2111 Chemical denotes favipiravir MESH:C462182
913 2113-2131 Chemical denotes hydroxychloroquine MESH:D006886
914 2133-2144 Chemical denotes oseltamivir MESH:D053139
915 2146-2156 Chemical denotes remdesivir MESH:C000606551
916 2161-2170 Chemical denotes ribavirin MESH:D012254
917 2284-2292 Chemical denotes Piperine MESH:C008922
918 2640-2648 Chemical denotes Piperine MESH:C008922
919 2716-2724 Chemical denotes Piperine MESH:C008922
920 2804-2812 Chemical denotes Piperine MESH:C008922
921 2926-2934 Chemical denotes Piperine MESH:C008922
922 3048-3056 Chemical denotes Piperine MESH:C008922
923 3173-3181 Chemical denotes Piperine MESH:C008922

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T25 3104-3121 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T26 3104-3121 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T327 0-6 Sentence denotes 3.6.8.
T328 8-42 Sentence denotes Principal component analysis (PCA)
T329 43-132 Sentence denotes The PCA is an essential technique to monitor the conformational dynamics of biomolecules.
T330 133-252 Sentence denotes It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories.
T331 253-422 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 423-599 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 600-693 Sentence denotes It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.
T334 694-703 Sentence denotes Figure 9.
T335 705-829 Sentence denotes Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue).
T336 830-931 Sentence denotes Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.
T337 932-1147 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 1148-1363 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 1364-1611 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 1612-1768 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 1769-1953 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 1954-2242 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 2243-2363 Sentence denotes From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above.
T344 2364-2558 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 2559-2677 Sentence denotes A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2.
T346 2678-2803 Sentence denotes The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites.
T347 2804-2906 Sentence denotes Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2.
T348 2907-3017 Sentence denotes So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2.
T349 3018-3122 Sentence denotes Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication.
T350 3123-3343 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.