PMC:7128678 / 13297-14484 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"349","span":{"begin":1052,"end":1065},"obj":"Gene"},{"id":"350","span":{"begin":35,"end":46},"obj":"Chemical"},{"id":"351","span":{"begin":57,"end":75},"obj":"Chemical"},{"id":"352","span":{"begin":77,"end":83},"obj":"Chemical"},{"id":"353","span":{"begin":96,"end":107},"obj":"Chemical"},{"id":"354","span":{"begin":108,"end":111},"obj":"Chemical"},{"id":"355","span":{"begin":152,"end":155},"obj":"Chemical"},{"id":"356","span":{"begin":219,"end":227},"obj":"Chemical"},{"id":"357","span":{"begin":321,"end":332},"obj":"Chemical"},{"id":"358","span":{"begin":344,"end":354},"obj":"Chemical"},{"id":"359","span":{"begin":405,"end":417},"obj":"Chemical"},{"id":"360","span":{"begin":428,"end":431},"obj":"Chemical"},{"id":"361","span":{"begin":460,"end":475},"obj":"Chemical"},{"id":"362","span":{"begin":627,"end":635},"obj":"Chemical"},{"id":"363","span":{"begin":636,"end":641},"obj":"Chemical"},{"id":"364","span":{"begin":664,"end":672},"obj":"Chemical"},{"id":"365","span":{"begin":716,"end":727},"obj":"Chemical"},{"id":"366","span":{"begin":770,"end":773},"obj":"Chemical"},{"id":"367","span":{"begin":884,"end":887},"obj":"Chemical"},{"id":"368","span":{"begin":915,"end":918},"obj":"Chemical"},{"id":"369","span":{"begin":962,"end":968},"obj":"Chemical"},{"id":"370","span":{"begin":1100,"end":1106},"obj":"Chemical"},{"id":"371","span":{"begin":1126,"end":1129},"obj":"Chemical"}],"attributes":[{"id":"A350","pred":"tao:has_database_id","subj":"350","obj":"MESH:D002738"},{"id":"A351","pred":"tao:has_database_id","subj":"351","obj":"MESH:D006886"},{"id":"A353","pred":"tao:has_database_id","subj":"353","obj":"MESH:D005732"},{"id":"A354","pred":"tao:has_database_id","subj":"354","obj":"MESH:D005677"},{"id":"A355","pred":"tao:has_database_id","subj":"355","obj":"MESH:D005677"},{"id":"A356","pred":"tao:has_database_id","subj":"356","obj":"MESH:D002518"},{"id":"A357","pred":"tao:has_database_id","subj":"357","obj":"MESH:D019158"},{"id":"A358","pred":"tao:has_database_id","subj":"358","obj":"MESH:D002241"},{"id":"A359","pred":"tao:has_database_id","subj":"359","obj":"MESH:D002241"},{"id":"A360","pred":"tao:has_database_id","subj":"360","obj":"MESH:D005677"},{"id":"A362","pred":"tao:has_database_id","subj":"362","obj":"MESH:D002518"},{"id":"A363","pred":"tao:has_database_id","subj":"363","obj":"MESH:D000073893"},{"id":"A364","pred":"tao:has_database_id","subj":"364","obj":"MESH:D009584"},{"id":"A365","pred":"tao:has_database_id","subj":"365","obj":"MESH:D005732"},{"id":"A366","pred":"tao:has_database_id","subj":"366","obj":"MESH:D005677"},{"id":"A367","pred":"tao:has_database_id","subj":"367","obj":"MESH:D005677"},{"id":"A368","pred":"tao:has_database_id","subj":"368","obj":"MESH:D005677"},{"id":"A371","pred":"tao:has_database_id","subj":"371","obj":"MESH:D005677"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T278","span":{"begin":35,"end":46},"obj":"CHEBI:3638;DG_10;CHEBI:3638"},{"id":"T279","span":{"begin":57,"end":75},"obj":"CHEBI:5801;DG_20;CHEBI:5801"},{"id":"T280","span":{"begin":96,"end":107},"obj":"CHEBI:16856;CHEBI:16856"},{"id":"T281","span":{"begin":179,"end":187},"obj":"GO:0016020"},{"id":"T282","span":{"begin":219,"end":227},"obj":"CHEBI:17761;CHEBI:17761"},{"id":"T283","span":{"begin":250,"end":256},"obj":"CHEBI:37527;CHEBI:37527"},{"id":"T284","span":{"begin":280,"end":299},"obj":"GO:0005615"},{"id":"T285","span":{"begin":321,"end":332},"obj":"CHEBI:26667;CHEBI:26667"},{"id":"T286","span":{"begin":344,"end":354},"obj":"CHEBI:32111;CHEBI:32111"},{"id":"T287","span":{"begin":405,"end":417},"obj":"CHEBI:16646;CHEBI:16646"},{"id":"T288","span":{"begin":464,"end":475},"obj":"CHEBI:5386;CHEBI:5386"},{"id":"T289","span":{"begin":627,"end":635},"obj":"CHEBI:17761;CHEBI:17761"},{"id":"T290","span":{"begin":673,"end":678},"obj":"CHEBI:33250;CHEBI:33250"},{"id":"T291","span":{"begin":697,"end":703},"obj":"CHEBI:37527;CHEBI:37527"},{"id":"T292","span":{"begin":716,"end":727},"obj":"CHEBI:5386;CHEBI:5386"},{"id":"T293","span":{"begin":774,"end":783},"obj":"GO:0032991"},{"id":"T294","span":{"begin":812,"end":821},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T295","span":{"begin":896,"end":905},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T296","span":{"begin":919,"end":927},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T297","span":{"begin":969,"end":978},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T298","span":{"begin":1107,"end":1116},"obj":"CHEBI:36357;CHEBI:36357"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T59","span":{"begin":96,"end":107},"obj":"Body_part"},{"id":"T60","span":{"begin":280,"end":299},"obj":"Body_part"},{"id":"T61","span":{"begin":405,"end":417},"obj":"Body_part"},{"id":"T62","span":{"begin":464,"end":475},"obj":"Body_part"},{"id":"T63","span":{"begin":636,"end":641},"obj":"Body_part"},{"id":"T64","span":{"begin":716,"end":727},"obj":"Body_part"}],"attributes":[{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma70022"},{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma82737"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma82737"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma82816"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T6","span":{"begin":394,"end":397},"obj":"Body_part"}],"attributes":[{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T89","span":{"begin":166,"end":167},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T90","span":{"begin":179,"end":187},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T91","span":{"begin":374,"end":375},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T92","span":{"begin":434,"end":435},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T93","span":{"begin":534,"end":535},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T94","span":{"begin":642,"end":650},"obj":"http://purl.obolibrary.org/obo/UBERON_0007651"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

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},{"id":"A272","pred":"chebi_id","subj":"T272","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A273","pred":"chebi_id","subj":"T273","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A274","pred":"chebi_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A275","pred":"chebi_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A276","pred":"chebi_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T8","span":{"begin":108,"end":111},"obj":"GlycoEpitope"},{"id":"T9","span":{"begin":152,"end":155},"obj":"GlycoEpitope"},{"id":"T10","span":{"begin":428,"end":431},"obj":"GlycoEpitope"},{"id":"T11","span":{"begin":770,"end":773},"obj":"GlycoEpitope"},{"id":"T12","span":{"begin":884,"end":887},"obj":"GlycoEpitope"},{"id":"T13","span":{"begin":915,"end":918},"obj":"GlycoEpitope"},{"id":"T14","span":{"begin":1126,"end":1129},"obj":"GlycoEpitope"}],"attributes":[{"id":"A8","pred":"glyco_epitope_db_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A9","pred":"glyco_epitope_db_id","subj":"T9","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A10","pred":"glyco_epitope_db_id","subj":"T10","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A11","pred":"glyco_epitope_db_id","subj":"T11","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A12","pred":"glyco_epitope_db_id","subj":"T12","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A13","pred":"glyco_epitope_db_id","subj":"T13","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A14","pred":"glyco_epitope_db_id","subj":"T14","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T102","span":{"begin":113,"end":563},"obj":"Sentence"},{"id":"T103","span":{"begin":564,"end":1079},"obj":"Sentence"},{"id":"T104","span":{"begin":1080,"end":1187},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Molecular modelling simulations of chloroquine (CLQ) and hydroxychloroquine (CLQ-OH) binding to ganglioside GM1. The surface electrostatic potential of GM1 indicates a non-polar, membrane-embedded part corresponding to ceramide (white areas), and an acidic part protruding in the extracellular space corresponding to the sialic-acid-containing saccharide part (red areas). (a) CLQ bound to the tip of the carbohydrate moiety of GM1. (b) Molecular mechanism of CLQ–ganglioside interactions. (c) Molecular dynamics simulations revealed a second site of interaction. In this case, the aromatic cycles of CLQ are positioned at the ceramide–sugar junction, whereas the nitrogen atoms interact with the acidic part of the ganglioside (not illustrated). (d,e) Surface views of GM1 complexed with one (d) or two (e) CLQ molecules (both in blue), illustrating the geometric complementarity of GM1 and CLQ molecules. (f) One GM1 molecule can also accommodate two distinct CLQ-OH molecules simultaneously, after slight rearrangement allowing increased fit due to CLQ-OH/CLQ-OH interactions. To improve clarity, CLQ-OH molecules bound to GM1 are represented in two distinct colours (blue and green)."}