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PMC:7204663 / 2796-5410 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
53 2474-2481 Chemical denotes dibasic
56 68-77 Chemical denotes nitrogens MESH:D009584
57 1429-1431 Chemical denotes H2 MESH:D003903

2_test

Id Subject Object Predicate Lexical cue
32389720-23378628-48149094 897-898 23378628 denotes 7
32389720-3067757-48149095 899-900 3067757 denotes 8
32389720-3067757-48149096 1292-1293 3067757 denotes 8
T71350 897-898 23378628 denotes 7
T29944 899-900 3067757 denotes 8
T50414 1292-1293 3067757 denotes 8

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T9 267-274 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836
T10 307-316 Body_part denotes lysosomal http://purl.org/sig/ont/fma/fma63836
T11 621-629 Body_part denotes lysosome http://purl.org/sig/ont/fma/fma63836
T12 674-682 Body_part denotes lysosome http://purl.org/sig/ont/fma/fma63836
T13 732-736 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T14 746-753 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836
T15 822-831 Body_part denotes lysosomes http://purl.org/sig/ont/fma/fma63836
T16 1092-1099 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836
T17 1113-1121 Body_part denotes lysosome http://purl.org/sig/ont/fma/fma63836
T18 1731-1740 Body_part denotes lysosomes http://purl.org/sig/ont/fma/fma63836
T19 1804-1813 Body_part denotes lysosomal http://purl.org/sig/ont/fma/fma63836
T20 2061-2069 Body_part denotes lysosome http://purl.org/sig/ont/fma/fma63836
T21 2114-2122 Body_part denotes lysosome http://purl.org/sig/ont/fma/fma63836
T22 2172-2176 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T23 2186-2193 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836
T24 2266-2275 Body_part denotes lysosomes http://purl.org/sig/ont/fma/fma63836
T25 2297-2306 Body_part denotes lysosomal http://purl.org/sig/ont/fma/fma63836
T26 2585-2594 Body_part denotes lysosomes http://purl.org/sig/ont/fma/fma63836
T27 2605-2612 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 521-523 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873
T4 706-708 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873
T5 1963-1965 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873
T6 2146-2148 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T20 155-164 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T21 307-316 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomal
T22 427-428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 456-457 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T24 481-490 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T25 496-497 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 551-560 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T27 621-629 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosome
T28 674-682 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosome
T29 758-759 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 822-831 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomes
T31 864-867 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T32 1113-1121 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosome
T33 1324-1327 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T34 1575-1576 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35 1630-1631 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 1731-1740 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomes
T37 1804-1813 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomal
T38 1869-1870 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 1898-1899 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T40 1923-1932 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T41 1938-1939 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 1993-2002 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T43 2059-2060 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 2061-2069 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosome
T45 2114-2122 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosome
T46 2198-2199 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 2266-2275 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomes
T48 2297-2306 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomal
T49 2374-2375 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 2396-2397 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 2472-2473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 2492-2493 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T53 2563-2564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 2585-2594 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomes

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T31 240-245 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T32 579-583 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T33 850-853 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T34 1343-1348 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T35 1429-1431 Chemical denotes H2 http://purl.obolibrary.org/obo/CHEBI_18276
T36 1451-1457 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T37 1814-1817 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T38 2021-2025 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T39 2307-2310 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T24 0-165 Sentence denotes If the pH of the molecular environment is lower (more acidic), more nitrogens are protonated, which in turn hinders the now-charged moieties from crossing membranes.
T25 166-286 Sentence denotes This is particularly relevant for the intracellular distribution of basic drugs crossing between the cytosol (pH approx.
T26 287-334 Sentence denotes 7.4) and the acidic lysosomal space (pH approx.
T27 335-340 Sentence denotes 5.0).
T28 341-385 Sentence denotes Fig. 2 shows this distribution conceptually.
T29 386-561 Sentence denotes Basic compounds are in an equilibrium of a less polar unionized form (B) that can easily cross membranes, and a polar protonated form (BH+) that cannot easily cross membranes.
T30 562-754 Sentence denotes As the unionized drug enters the acidic environment of the lysosome, it will be protonated and ‘trapped’ in the lysosome as the protonated form BH+ cannot easily diffuse back into the cytosol.
T31 755-832 Sentence denotes As a result, high concentrations of the compound can accumulate in lysosomes.
T32 833-902 Sentence denotes This concept of “ion-trapping” has been described and reviewed [7,8].
T33 903-1132 Sentence denotes The magnitude of this accumulation depends on the mathematical relationship of the pKa of the compound of interest, its permeability, and the pH gradient between the two environments (e.g. cytosol [pH 7.4] and lysosome [pH 5.0]).
T34 1133-1295 Sentence denotes If there is no permeability limitation, the expected ratio or concentration gradient can be calculated based on the well-known Henderson-Hasselbalch equation [8].
T35 1296-1567 Sentence denotes If the compound of interest has only one basic group, the ratio between the concentrations will be:(1) R=C1C2=H1+KaH2+Kawhere H1 and H2 are the respective proton concentrations (=10−pH) of the two environments (pH 5 and 7.4) and Ka is the dissociation constant (=10−pKa).
T36 1568-1674 Sentence denotes Fig. 3 A shows the magnitude of the resulting accumulation as a function of the pKa value of the compound.
T37 1675-1785 Sentence denotes Accumulation of up to 250-fold higher concentrations in lysosomes can be explained by the described mechanism.
T38 1786-1827 Sentence denotes Fig. 2 Concept of lysosomal ion-trapping.
T39 1828-2003 Sentence denotes Basic compounds are in an equilibrium of a less polar unionized form (B) that can easily cross membranes, and a polar protonated form (BH+) that cannot easily cross membranes.
T40 2004-2194 Sentence denotes As the unionized drug enters the acidic environment of a lysosome, it will be protonated and ‘trapped’ in the lysosome as the protonated form BH+ cannot easily diffuse back into the cytosol.
T41 2195-2276 Sentence denotes As a result, high concentrations of the compound can accumulate in the lysosomes.
T42 2277-2369 Sentence denotes Fig. 3 Magnitude of lysosomal ion-trapping depending on the pKa of the compound of interest.
T43 2370-2467 Sentence denotes For a monobasic compound (A), up to 250-fold higher concentrations are possible depending on pKa.
T44 2468-2537 Sentence denotes For a dibasic compound (B), the accumulation can be over 60 000-fold.
T45 2538-2614 Sentence denotes These simulations assume a pH gradient of 5.0 (lysosomes) and 7.4 (cytosol).