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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T14","span":{"begin":1279,"end":1283},"obj":"Body_part"},{"id":"T15","span":{"begin":2238,"end":2242},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0000033"},{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0000023"}],"text":"This study also looked at CLQ-OH and its interaction with GM1. We recently published a model describing a complex formed by one GM1 and two CLQ-OH molecules [10]. For comparison, the same molecular modelling approaches as for ATM (in the presence of surrounding raft lipids) were applied to this model. A stable complex formed by a ganglioside dimer, each monomer being associated with two CLQ-OH molecules, was obtained (Fig. 8d). The stability of this complex is reinforced by a rearrangement of CLQ-OH molecules that interact with each other as well as interacting with the saccharide part of GM1. Consequently, the surface of the ganglioside is almost completely masked, so that the ganglioside dimer can no longer be recognized by the viral spike (Fig. 8c). In the presence of both ATM and CLQ-OH, virus-ganglioside interactions are efficiently blocked, preventing any close contact between the virus and the plasma membrane of host cells. The molecular details of this synergistic antiviral effect are worth mentioning. As shown in Figs. 5 and 8e and Table S1, the QFN triad of the virus spike protein is predicted to interact with the central region of the ganglioside dimer. If the dimer is compared metaphorically to a butterfly, this region corresponds to the insect's head between the wings. For its part, CLQ-OH binds to the wings (Fig. 8d), whereas ATM neutralizes the QFN triad of the virus spike protein (Fig. 8f). Indeed, all attempts to obtain a stable raft-spike protein complex aborted when GM1 was covered by CLMQ-OH and when ATM was bound to the spike protein. In the case of ATM, these data confirm that the QFN triad is critical for GM1 recognition and that although other residues are involved (Fig. 5 and Table S1), the whole binding process is fully controlled by the primary interaction driven by the QFN triad. In agreement with this notion, mutating the QFN triad with alanine residues resulted in an aborted ATM binding process at the post-docking steps. Taken together, these molecular modelling studies indicate that CLQ-OH and ATM, when bound to their respective targets, totally mask the complementary surfaces provided by the lipid raft and the virus spike (Fig. 8c): CLQ-OH binds to GM1 and covers the wing, ATM binds to the virus spike and prevents any interaction with the central area of the ganglioside dimer. Hence, both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T87","span":{"begin":2401,"end":2409},"obj":"Disease"}],"attributes":[{"id":"A87","pred":"mondo_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"This study also looked at CLQ-OH and its interaction with GM1. We recently published a model describing a complex formed by one GM1 and two CLQ-OH molecules [10]. For comparison, the same molecular modelling approaches as for ATM (in the presence of surrounding raft lipids) were applied to this model. A stable complex formed by a ganglioside dimer, each monomer being associated with two CLQ-OH molecules, was obtained (Fig. 8d). The stability of this complex is reinforced by a rearrangement of CLQ-OH molecules that interact with each other as well as interacting with the saccharide part of GM1. Consequently, the surface of the ganglioside is almost completely masked, so that the ganglioside dimer can no longer be recognized by the viral spike (Fig. 8c). In the presence of both ATM and CLQ-OH, virus-ganglioside interactions are efficiently blocked, preventing any close contact between the virus and the plasma membrane of host cells. The molecular details of this synergistic antiviral effect are worth mentioning. As shown in Figs. 5 and 8e and Table S1, the QFN triad of the virus spike protein is predicted to interact with the central region of the ganglioside dimer. If the dimer is compared metaphorically to a butterfly, this region corresponds to the insect's head between the wings. For its part, CLQ-OH binds to the wings (Fig. 8d), whereas ATM neutralizes the QFN triad of the virus spike protein (Fig. 8f). Indeed, all attempts to obtain a stable raft-spike protein complex aborted when GM1 was covered by CLMQ-OH and when ATM was bound to the spike protein. In the case of ATM, these data confirm that the QFN triad is critical for GM1 recognition and that although other residues are involved (Fig. 5 and Table S1), the whole binding process is fully controlled by the primary interaction driven by the QFN triad. In agreement with this notion, mutating the QFN triad with alanine residues resulted in an aborted ATM binding process at the post-docking steps. Taken together, these molecular modelling studies indicate that CLQ-OH and ATM, when bound to their respective targets, totally mask the complementary surfaces provided by the lipid raft and the virus spike (Fig. 8c): CLQ-OH binds to GM1 and covers the wing, ATM binds to the virus spike and prevents any interaction with the central area of the ganglioside dimer. Hence, both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T28","span":{"begin":58,"end":61},"obj":"GlycoEpitope"},{"id":"T29","span":{"begin":128,"end":131},"obj":"GlycoEpitope"},{"id":"T30","span":{"begin":596,"end":599},"obj":"GlycoEpitope"},{"id":"T31","span":{"begin":1510,"end":1513},"obj":"GlycoEpitope"},{"id":"T32","span":{"begin":1656,"end":1659},"obj":"GlycoEpitope"},{"id":"T33","span":{"begin":2219,"end":2222},"obj":"GlycoEpitope"}],"attributes":[{"id":"A28","pred":"glyco_epitope_db_id","subj":"T28","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A29","pred":"glyco_epitope_db_id","subj":"T29","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A30","pred":"glyco_epitope_db_id","subj":"T30","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A31","pred":"glyco_epitope_db_id","subj":"T31","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A32","pred":"glyco_epitope_db_id","subj":"T32","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A33","pred":"glyco_epitope_db_id","subj":"T33","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"This study also looked at CLQ-OH and its interaction with GM1. We recently published a model describing a complex formed by one GM1 and two CLQ-OH molecules [10]. For comparison, the same molecular modelling approaches as for ATM (in the presence of surrounding raft lipids) were applied to this model. A stable complex formed by a ganglioside dimer, each monomer being associated with two CLQ-OH molecules, was obtained (Fig. 8d). The stability of this complex is reinforced by a rearrangement of CLQ-OH molecules that interact with each other as well as interacting with the saccharide part of GM1. Consequently, the surface of the ganglioside is almost completely masked, so that the ganglioside dimer can no longer be recognized by the viral spike (Fig. 8c). In the presence of both ATM and CLQ-OH, virus-ganglioside interactions are efficiently blocked, preventing any close contact between the virus and the plasma membrane of host cells. The molecular details of this synergistic antiviral effect are worth mentioning. As shown in Figs. 5 and 8e and Table S1, the QFN triad of the virus spike protein is predicted to interact with the central region of the ganglioside dimer. If the dimer is compared metaphorically to a butterfly, this region corresponds to the insect's head between the wings. For its part, CLQ-OH binds to the wings (Fig. 8d), whereas ATM neutralizes the QFN triad of the virus spike protein (Fig. 8f). Indeed, all attempts to obtain a stable raft-spike protein complex aborted when GM1 was covered by CLMQ-OH and when ATM was bound to the spike protein. In the case of ATM, these data confirm that the QFN triad is critical for GM1 recognition and that although other residues are involved (Fig. 5 and Table S1), the whole binding process is fully controlled by the primary interaction driven by the QFN triad. In agreement with this notion, mutating the QFN triad with alanine residues resulted in an aborted ATM binding process at the post-docking steps. Taken together, these molecular modelling studies indicate that CLQ-OH and ATM, when bound to their respective targets, totally mask the complementary surfaces provided by the lipid raft and the virus spike (Fig. 8c): CLQ-OH binds to GM1 and covers the wing, ATM binds to the virus spike and prevents any interaction with the central area of the ganglioside dimer. Hence, both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T168","span":{"begin":0,"end":62},"obj":"Sentence"},{"id":"T169","span":{"begin":63,"end":162},"obj":"Sentence"},{"id":"T170","span":{"begin":163,"end":302},"obj":"Sentence"},{"id":"T171","span":{"begin":303,"end":431},"obj":"Sentence"},{"id":"T172","span":{"begin":432,"end":600},"obj":"Sentence"},{"id":"T173","span":{"begin":601,"end":762},"obj":"Sentence"},{"id":"T174","span":{"begin":763,"end":944},"obj":"Sentence"},{"id":"T175","span":{"begin":945,"end":1025},"obj":"Sentence"},{"id":"T176","span":{"begin":1026,"end":1043},"obj":"Sentence"},{"id":"T177","span":{"begin":1044,"end":1182},"obj":"Sentence"},{"id":"T178","span":{"begin":1183,"end":1302},"obj":"Sentence"},{"id":"T179","span":{"begin":1303,"end":1429},"obj":"Sentence"},{"id":"T180","span":{"begin":1430,"end":1581},"obj":"Sentence"},{"id":"T181","span":{"begin":1582,"end":1838},"obj":"Sentence"},{"id":"T182","span":{"begin":1839,"end":1984},"obj":"Sentence"},{"id":"T183","span":{"begin":1985,"end":2349},"obj":"Sentence"},{"id":"T184","span":{"begin":2350,"end":2449},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"This study also looked at CLQ-OH and its interaction with GM1. We recently published a model describing a complex formed by one GM1 and two CLQ-OH molecules [10]. For comparison, the same molecular modelling approaches as for ATM (in the presence of surrounding raft lipids) were applied to this model. A stable complex formed by a ganglioside dimer, each monomer being associated with two CLQ-OH molecules, was obtained (Fig. 8d). The stability of this complex is reinforced by a rearrangement of CLQ-OH molecules that interact with each other as well as interacting with the saccharide part of GM1. Consequently, the surface of the ganglioside is almost completely masked, so that the ganglioside dimer can no longer be recognized by the viral spike (Fig. 8c). In the presence of both ATM and CLQ-OH, virus-ganglioside interactions are efficiently blocked, preventing any close contact between the virus and the plasma membrane of host cells. The molecular details of this synergistic antiviral effect are worth mentioning. As shown in Figs. 5 and 8e and Table S1, the QFN triad of the virus spike protein is predicted to interact with the central region of the ganglioside dimer. If the dimer is compared metaphorically to a butterfly, this region corresponds to the insect's head between the wings. For its part, CLQ-OH binds to the wings (Fig. 8d), whereas ATM neutralizes the QFN triad of the virus spike protein (Fig. 8f). Indeed, all attempts to obtain a stable raft-spike protein complex aborted when GM1 was covered by CLMQ-OH and when ATM was bound to the spike protein. In the case of ATM, these data confirm that the QFN triad is critical for GM1 recognition and that although other residues are involved (Fig. 5 and Table S1), the whole binding process is fully controlled by the primary interaction driven by the QFN triad. In agreement with this notion, mutating the QFN triad with alanine residues resulted in an aborted ATM binding process at the post-docking steps. Taken together, these molecular modelling studies indicate that CLQ-OH and ATM, when bound to their respective targets, totally mask the complementary surfaces provided by the lipid raft and the virus spike (Fig. 8c): CLQ-OH binds to GM1 and covers the wing, ATM binds to the virus spike and prevents any interaction with the central area of the ganglioside dimer. Hence, both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane."}

LitCovid-PubTator

PMC:7219429 / 22691-25140 JSONTXT

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PMC:7219429 / 22691-25140 JSON TXT