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LitCovid-PubTator

LitCovid-PMC-OGER-BB

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T4","span":{"begin":68,"end":85},"obj":"Body_part"},{"id":"T5","span":{"begin":622,"end":625},"obj":"Body_part"},{"id":"T6","span":{"begin":2595,"end":2598},"obj":"Body_part"}],"attributes":[{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000065"},{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"}],"text":"3.3 Molecular recognition of gangliosides by CLQ and CLQ-OH\nIn the respiratory tract, sialic acids are usually part of glycoproteins and gangliosides. Molecular modelling approaches were used to assess whether CLQ and CLQ-OH can recognize sialic acid units in their natural molecular environment. In these simulations, ganglioside GM1 was chosen as a representative example of human plasma membrane gangliosides. A first series of simulations was performed with CLQ. When merged with the ganglioside, CLQ had two distinct binding sites, both located in the polar saccharide part of GM1. The first site was located at the tip of the saccharide moiety of the ganglioside Fig. 4 (a,b). The energy of interaction was estimated to be -47 kJ.mol−1. CLQ retained the typical L-shape structure of the water-soluble conformer bound to isolated sialic acids [compare Figs 2(c) and 4(a)]. From a mechanistic point of view, the carboxylate group of the sialic acid of GM1 was oriented towards the cationic groups of CLQ. The rings of CLQ faced the N-acetylgalactosamine (GalNAc) residue of GM1, establishing both OH-π interaction and hydrogen bonding Fig. 4(b). The second site was in a large area including both the ceramide–sugar junction and the saccharide moiety Fig. 4(c). The chlorine atom of CLQ was oriented towards the ceramide axis, allowing the nitrogen-containing ring of CLQ to stack on to the pyrane ring of the first sugar residue [i.e. glucose (Glc)]. The perfect geometric complementarity of the two partners Fig. 4(c,d) accounted for a particularly high energy of interaction in this case (-61 kJ.mol−1). Interestingly, there was no overlap between the two CLQ-binding sites on GM1, so the ganglioside could accommodate two CLQ molecules Fig. 4(e), reaching a global energy of interaction of -108 kJ.mol−1. A similar situation was observed with CLQ-OH, which occupies the same binding site as CLQ Fig. 4(f). In this case, the energy of interaction was further increased by stabilizing contacts established between the two CLQ-OH molecules, reaching -120 kJ.mol−1. Overall, these data showed that CLQ and CLQ-OH have a good fit for sialic acids, either isolated or bound to gangliosides.\nFig. 4 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)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GlycoEpitope

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T83","span":{"begin":0,"end":60},"obj":"Sentence"},{"id":"T84","span":{"begin":61,"end":151},"obj":"Sentence"},{"id":"T85","span":{"begin":152,"end":297},"obj":"Sentence"},{"id":"T86","span":{"begin":298,"end":413},"obj":"Sentence"},{"id":"T87","span":{"begin":414,"end":467},"obj":"Sentence"},{"id":"T88","span":{"begin":468,"end":587},"obj":"Sentence"},{"id":"T89","span":{"begin":588,"end":683},"obj":"Sentence"},{"id":"T90","span":{"begin":684,"end":743},"obj":"Sentence"},{"id":"T91","span":{"begin":744,"end":878},"obj":"Sentence"},{"id":"T92","span":{"begin":879,"end":1009},"obj":"Sentence"},{"id":"T93","span":{"begin":1010,"end":1150},"obj":"Sentence"},{"id":"T94","span":{"begin":1151,"end":1266},"obj":"Sentence"},{"id":"T95","span":{"begin":1267,"end":1456},"obj":"Sentence"},{"id":"T96","span":{"begin":1457,"end":1611},"obj":"Sentence"},{"id":"T97","span":{"begin":1612,"end":1813},"obj":"Sentence"},{"id":"T98","span":{"begin":1814,"end":1914},"obj":"Sentence"},{"id":"T99","span":{"begin":1915,"end":2070},"obj":"Sentence"},{"id":"T100","span":{"begin":2071,"end":2193},"obj":"Sentence"},{"id":"T101","span":{"begin":2194,"end":2313},"obj":"Sentence"},{"id":"T102","span":{"begin":2314,"end":2764},"obj":"Sentence"},{"id":"T103","span":{"begin":2765,"end":3280},"obj":"Sentence"},{"id":"T104","span":{"begin":3281,"end":3388},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.3 Molecular recognition of gangliosides by CLQ and CLQ-OH\nIn the respiratory tract, sialic acids are usually part of glycoproteins and gangliosides. Molecular modelling approaches were used to assess whether CLQ and CLQ-OH can recognize sialic acid units in their natural molecular environment. In these simulations, ganglioside GM1 was chosen as a representative example of human plasma membrane gangliosides. A first series of simulations was performed with CLQ. When merged with the ganglioside, CLQ had two distinct binding sites, both located in the polar saccharide part of GM1. The first site was located at the tip of the saccharide moiety of the ganglioside Fig. 4 (a,b). The energy of interaction was estimated to be -47 kJ.mol−1. CLQ retained the typical L-shape structure of the water-soluble conformer bound to isolated sialic acids [compare Figs 2(c) and 4(a)]. From a mechanistic point of view, the carboxylate group of the sialic acid of GM1 was oriented towards the cationic groups of CLQ. The rings of CLQ faced the N-acetylgalactosamine (GalNAc) residue of GM1, establishing both OH-π interaction and hydrogen bonding Fig. 4(b). The second site was in a large area including both the ceramide–sugar junction and the saccharide moiety Fig. 4(c). The chlorine atom of CLQ was oriented towards the ceramide axis, allowing the nitrogen-containing ring of CLQ to stack on to the pyrane ring of the first sugar residue [i.e. glucose (Glc)]. The perfect geometric complementarity of the two partners Fig. 4(c,d) accounted for a particularly high energy of interaction in this case (-61 kJ.mol−1). Interestingly, there was no overlap between the two CLQ-binding sites on GM1, so the ganglioside could accommodate two CLQ molecules Fig. 4(e), reaching a global energy of interaction of -108 kJ.mol−1. A similar situation was observed with CLQ-OH, which occupies the same binding site as CLQ Fig. 4(f). In this case, the energy of interaction was further increased by stabilizing contacts established between the two CLQ-OH molecules, reaching -120 kJ.mol−1. Overall, these data showed that CLQ and CLQ-OH have a good fit for sialic acids, either isolated or bound to gangliosides.\nFig. 4 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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PMC:7128678 / 11096-14484 JSON TXT