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LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":86,"end":109},"obj":"http://purl.obolibrary.org/obo/GO_0019048"}],"text":"4 Discussion\nIn this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment.\nTo date, there are several structural data of the SARS-CoV-2 protein in the prefusion conformation or bound to its primary receptor ACE-2 [11, 20]. However, ACE-2 is in lipid rafts and raft disruption induces a marked decrease of virus infection [15]. Thus, it is likely that the virus interacts with the raft surface through multivalent contacts involving both ACE-2 and gangliosides. The fact that the RBD and the ganglioside-binding domain belong to distinct parts of the trimeric spike is consistent with this notion. Such a complex network of virus-host cell membrane interactions is also consistent with previously characterized virus infection strategies. Indeed, the HIV-1 fusion process driven by gp120 and gp41 envelope proteins involves a receptor (CD4), a coreceptor (chiefly CCR5) and glycosphingolipid cofactors [39]. Like SARS-CoV-2, the pentameric capsid protein of SV40, and polyoma viruses display three distinct binding sites for gangliosides, which serve as critical receptors for these non-enveloped viruses in lipid raft domains [40].\nThe MD simulations in the current study indicate that both CLQ-OH and ATM may block SARS-CoV2 binding to gangliosides via mirror competitive mechanisms. ATM, which has some molecular similarity with GM1 sugar, can thus occupy the ganglioside-binding domain of the spike protein and neutralize virus binding to lipid rafts. CLQ-OH covers the ganglioside surface, and thus also prevents virus-membrane interaction through a complementary mechanism. Each of these drugs might be efficient alone to block virus attachment, ATM through virus binding, CLQ-OH through ganglioside binding. As both drugs interfere with the same mechanism but with distinct molecular targets, they are expected to work together in synergy, as indicated by recent clinical data [3].\nThe posology of the combination therapy for COVID-19 is 600 mg CLQ-OH and 250 mg ATM per day [3,34]. This ratio corresponds to a molar ratio of five CLQ-OH for one ATM. In silico calculations indicate a binding ratio of four CLQ-OH for one ATM, which is close to the posology. Furthermore, as ATM shares structural similarity with the saccharide part of GM1, one should ask whether ATM could bind to CLQ-OH and by this way reduce the potential effectiveness of this combination therapy. However, as ATM and CLQ-OH have been reported to synergistically decrease SARS-CoV-2 load in infected patients [3], drug cross-neutralization is very unlikely. There was a consistent lack of evidence of any stable ATM-CLQ-OH complexes using the molecular modelling approaches in this study.\nThe molecular mimicry between ATM and the saccharide part of GM1 gives new perspectives on the therapeutic effect of this macrolide antibiotic and this warrants further exploration. Moreover, the fact that ganglioside GM1 is a molecular target for CLQ-OH might explain the indication of this drug in rheumatological disorders, such as lupus and rheumatoid arthritis [35,36]. Indeed, GM1 overexpression and anti-GM1 antibodies are a hallmark of these diseases [37,38]. Thus, our data incidentally indicate that the therapeutic effect of CLQ-OH in these cases could also be related to its ganglioside-binding properties."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T34","span":{"begin":2500,"end":2503},"obj":"GlycoEpitope"},{"id":"T35","span":{"begin":3411,"end":3414},"obj":"GlycoEpitope"},{"id":"T36","span":{"begin":3896,"end":3899},"obj":"GlycoEpitope"},{"id":"T37","span":{"begin":4053,"end":4056},"obj":"GlycoEpitope"},{"id":"T38","span":{"begin":4218,"end":4221},"obj":"GlycoEpitope"},{"id":"T39","span":{"begin":4241,"end":4249},"obj":"GlycoEpitope"},{"id":"T40","span":{"begin":4246,"end":4249},"obj":"GlycoEpitope"}],"attributes":[{"id":"A34","pred":"glyco_epitope_db_id","subj":"T34","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A35","pred":"glyco_epitope_db_id","subj":"T35","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A36","pred":"glyco_epitope_db_id","subj":"T36","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A37","pred":"glyco_epitope_db_id","subj":"T37","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A38","pred":"glyco_epitope_db_id","subj":"T38","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A39","pred":"glyco_epitope_db_id","subj":"T39","obj":"http://www.glycoepitope.jp/epitopes/AN0713"},{"id":"A40","pred":"glyco_epitope_db_id","subj":"T40","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"4 Discussion\nIn this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment.\nTo date, there are several structural data of the SARS-CoV-2 protein in the prefusion conformation or bound to its primary receptor ACE-2 [11, 20]. However, ACE-2 is in lipid rafts and raft disruption induces a marked decrease of virus infection [15]. Thus, it is likely that the virus interacts with the raft surface through multivalent contacts involving both ACE-2 and gangliosides. The fact that the RBD and the ganglioside-binding domain belong to distinct parts of the trimeric spike is consistent with this notion. Such a complex network of virus-host cell membrane interactions is also consistent with previously characterized virus infection strategies. Indeed, the HIV-1 fusion process driven by gp120 and gp41 envelope proteins involves a receptor (CD4), a coreceptor (chiefly CCR5) and glycosphingolipid cofactors [39]. Like SARS-CoV-2, the pentameric capsid protein of SV40, and polyoma viruses display three distinct binding sites for gangliosides, which serve as critical receptors for these non-enveloped viruses in lipid raft domains [40].\nThe MD simulations in the current study indicate that both CLQ-OH and ATM may block SARS-CoV2 binding to gangliosides via mirror competitive mechanisms. ATM, which has some molecular similarity with GM1 sugar, can thus occupy the ganglioside-binding domain of the spike protein and neutralize virus binding to lipid rafts. CLQ-OH covers the ganglioside surface, and thus also prevents virus-membrane interaction through a complementary mechanism. Each of these drugs might be efficient alone to block virus attachment, ATM through virus binding, CLQ-OH through ganglioside binding. As both drugs interfere with the same mechanism but with distinct molecular targets, they are expected to work together in synergy, as indicated by recent clinical data [3].\nThe posology of the combination therapy for COVID-19 is 600 mg CLQ-OH and 250 mg ATM per day [3,34]. This ratio corresponds to a molar ratio of five CLQ-OH for one ATM. In silico calculations indicate a binding ratio of four CLQ-OH for one ATM, which is close to the posology. Furthermore, as ATM shares structural similarity with the saccharide part of GM1, one should ask whether ATM could bind to CLQ-OH and by this way reduce the potential effectiveness of this combination therapy. However, as ATM and CLQ-OH have been reported to synergistically decrease SARS-CoV-2 load in infected patients [3], drug cross-neutralization is very unlikely. There was a consistent lack of evidence of any stable ATM-CLQ-OH complexes using the molecular modelling approaches in this study.\nThe molecular mimicry between ATM and the saccharide part of GM1 gives new perspectives on the therapeutic effect of this macrolide antibiotic and this warrants further exploration. Moreover, the fact that ganglioside GM1 is a molecular target for CLQ-OH might explain the indication of this drug in rheumatological disorders, such as lupus and rheumatoid arthritis [35,36]. Indeed, GM1 overexpression and anti-GM1 antibodies are a hallmark of these diseases [37,38]. Thus, our data incidentally indicate that the therapeutic effect of CLQ-OH in these cases could also be related to its ganglioside-binding properties."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":4180,"end":4200},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0001370"}],"text":"4 Discussion\nIn this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment.\nTo date, there are several structural data of the SARS-CoV-2 protein in the prefusion conformation or bound to its primary receptor ACE-2 [11, 20]. However, ACE-2 is in lipid rafts and raft disruption induces a marked decrease of virus infection [15]. Thus, it is likely that the virus interacts with the raft surface through multivalent contacts involving both ACE-2 and gangliosides. The fact that the RBD and the ganglioside-binding domain belong to distinct parts of the trimeric spike is consistent with this notion. Such a complex network of virus-host cell membrane interactions is also consistent with previously characterized virus infection strategies. Indeed, the HIV-1 fusion process driven by gp120 and gp41 envelope proteins involves a receptor (CD4), a coreceptor (chiefly CCR5) and glycosphingolipid cofactors [39]. Like SARS-CoV-2, the pentameric capsid protein of SV40, and polyoma viruses display three distinct binding sites for gangliosides, which serve as critical receptors for these non-enveloped viruses in lipid raft domains [40].\nThe MD simulations in the current study indicate that both CLQ-OH and ATM may block SARS-CoV2 binding to gangliosides via mirror competitive mechanisms. ATM, which has some molecular similarity with GM1 sugar, can thus occupy the ganglioside-binding domain of the spike protein and neutralize virus binding to lipid rafts. CLQ-OH covers the ganglioside surface, and thus also prevents virus-membrane interaction through a complementary mechanism. Each of these drugs might be efficient alone to block virus attachment, ATM through virus binding, CLQ-OH through ganglioside binding. As both drugs interfere with the same mechanism but with distinct molecular targets, they are expected to work together in synergy, as indicated by recent clinical data [3].\nThe posology of the combination therapy for COVID-19 is 600 mg CLQ-OH and 250 mg ATM per day [3,34]. This ratio corresponds to a molar ratio of five CLQ-OH for one ATM. In silico calculations indicate a binding ratio of four CLQ-OH for one ATM, which is close to the posology. Furthermore, as ATM shares structural similarity with the saccharide part of GM1, one should ask whether ATM could bind to CLQ-OH and by this way reduce the potential effectiveness of this combination therapy. However, as ATM and CLQ-OH have been reported to synergistically decrease SARS-CoV-2 load in infected patients [3], drug cross-neutralization is very unlikely. There was a consistent lack of evidence of any stable ATM-CLQ-OH complexes using the molecular modelling approaches in this study.\nThe molecular mimicry between ATM and the saccharide part of GM1 gives new perspectives on the therapeutic effect of this macrolide antibiotic and this warrants further exploration. Moreover, the fact that ganglioside GM1 is a molecular target for CLQ-OH might explain the indication of this drug in rheumatological disorders, such as lupus and rheumatoid arthritis [35,36]. Indeed, GM1 overexpression and anti-GM1 antibodies are a hallmark of these diseases [37,38]. Thus, our data incidentally indicate that the therapeutic effect of CLQ-OH in these cases could also be related to its ganglioside-binding properties."}

LitCovid-sentences

LitCovid-PubTator

2_test

PMC:7219429 / 25142-29595 JSONTXT

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PMC:7219429 / 25142-29595 JSON TXT