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LitCovid_Glycan-Motif-Structure

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T39","span":{"begin":104,"end":120},"obj":"Body_part"},{"id":"T40","span":{"begin":285,"end":289},"obj":"Body_part"},{"id":"T41","span":{"begin":294,"end":299},"obj":"Body_part"},{"id":"T42","span":{"begin":2816,"end":2819},"obj":"Body_part"},{"id":"T43","span":{"begin":2905,"end":2909},"obj":"Body_part"}],"attributes":[{"id":"A39","pred":"uberon_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/UBERON_4200047"},{"id":"A40","pred":"uberon_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/UBERON_0002387"},{"id":"A41","pred":"uberon_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/UBERON_0000165"},{"id":"A42","pred":"uberon_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"},{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0001456"}],"text":"7.2. Interaction of Membrane Gangliosides in Lipid Rafts with CLQ and CLQ-OH\nLipid rafts are also viral attachment sites. Viruses such as IBV, dengue virus, Ebola virus, hepatitis C virus, HIV, human herpes virus 6, measles virus, Newcastle disease virus, poliovirus, West Nile virus, foot-and-mouth disease virus, simian virus 40, rotavirus, influenza virus and Marburg virus also use lipid rafts for virus entry [151,152,153,154,155,156]. In avian CoV IBV, structural proteins of the IBV virus are co-localized with PM lipid rafts embedded with the ganglioside GM1. HCoV-229E entry is prevented by cholesterol depleted conditions because HCoV-229E clusters in caveolae-associated lipid rafts [157]. Caveolae of caveolin-1, -2 and -3 are cross-linked [158] and control the molecular distribution between rafts and caveolae in a regulatory mechanism. S protein-CD13 cross-linking occurs via CD13-caveolin-1 sequestering. HCoV-229E particles similarly exhibit a longitudinal distribution property. HCoV-229E-colocalized caveolin-1 undergoes the next step of virus infection. Caveolin-1 knockdown inhibited HCoV-229E endocytosis and entry and thus caveolin-1 is essential for HCoV-229E infection. TGEV also endocytoses by a clathrin-mediated mechanism in MDCK cells [159]. Other viruses including HCoV-OC43 also use an entry receptor sequestered to cross-linked caveolae [160]. In SARS-CoV, the first entry step to host cells needs ACE2 in intact lipid rafts by the S glycoprotein [151]. ACE2 is associated with caveolin-1 and GM1 in membrane rafts depending on its cell-type specific localization [161]. Raft integrity with cholesterol and ACE2 is necessary for SARS-CoV pseudovirus entry into Vero E6 cells and for SARS-CoV-microdomain-based entry. C-type lectin, CD209 L (L-SIGN), can also form lipid rafts and acts as a SARS-CoV receptor [162]. Information of the CoV entry pathways is important for therapeutic designation of SARS-CoV-targeting drugs, for example, if agents disrupt lipid-raft localization of the ACE2 receptor.\nCLQ binds the SAs and gangliosides in lipid rafts with a high affinity. Therefore, CLQ or CLQ-OH prevents the S glycoprotein–ganglioside binding. CLQ (or CLQ-OH) binding to SA consequently prevents S glycoprotein binding to host receptors. The N-terminal region of SARS-CoV-2 S glycoprotein interacts with gangliosides. A ganglioside-binding site (GBS) or ganglioside-binding domain (GBD) is present in the NTD of the S glycoprotein of SARS-CoV-2. Using molecular modeling and simulation technology, CLQ has been suggested to recognize the SAs and gangliosides. Human type Neu5Ac binds to CLQ and CLQ-OH. Thus, SAs are binding targets of CLQ and CLQ-OH. CLQ and CLQ-OH have two specific recognition sites in the polar sugar residues of ganglioside GM1. The first site is found at the tip of the sugar residues of GM1 with an interaction energy of −47 kJ/mol. The CLQ rings face the GalNAc residue of GM1, while the second site is in a large region of the sugar-ceramide junction and the sugar residues. Several amino acid residues of the S protein NTD, which are Phe-135, Asn-137 and Arg-158, recognize the ganglioside GM1. The S glycoprotein NTD-GM1 complex is suggested to form a trimolecular complex with two molecules of ganglioside GM1 anchored to the NTD of S protein [163]. The ACE2-binding RBD is suggested to be a potential GBS located on a differential site of the S glycoprotein NTD. The protein sequence interfacing surface of the NTD is the consensus GBDs [164]. The amino acids Gly, Pro and/or Ser residues found in GBD motifs are in the same 111–158 amino acids of the NTD as the ganglioside-attachment interface. The GBD is conserved throughout viral isolates from worldwide COVID-19 patients. The GBD potentially increases viral attachment ability to PM lipid rafts and contact between host ACE-2 and S protein [165]. The interaction between CLQ-OH and 9-O-acetyl-NeuAc is also similar to the 9-O-acetyl-NeuAc-CLQ interaction. The CLQ-OH OH group enhances the interaction of CLQ with SA via a hydrogen bond [163]. In conditions with CLQ or CLQ-OH derivative treatment, the S glycoprotein cannot bind to gangliosides in in silico studies, which are used to uncover the action mechanism. CLQ and CLQ-OH prevent the binding of S glycoprotein to gangliosides. The CLQ-SA complex is formed in a mixed surface and balls by the positioning of the negative charged COOH group of Neu5Ac and one of the two cationic charges of CLQ [163]. CoVs preferentially bind to 9-O-acetyl-NeuAc [60], differentiating with other viral properties.\nAs CLQ interacts with the GM1 sugar part, the N-terminal domain of the S protein loses viral attachment capacity to the cell receptors [166]. The S protein NTD and the CLQ/CLQ-OH maintain the same position during GM1 binding, consequently preventing GM1 binding to the S protein and the drug at the same time, because the NTD and the CLQ/CLQ-OH simultaneously recognize GM1. Asn-167 forms a hydrogen bond with the GalNAc residue, whereas an aromatic Phe-135 stacks to the Glc residue of GM1. Therefore, the antiviral activities of CLQ and CLQ-OH is to block the interaction between the SARS-CoV-2 S glycoprotein and gangliosides on host cell surfaces. The lipid composition of host cell PM can also be a potential target for preventive and therapeutic drugs against such viruses."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T145","span":{"begin":907,"end":919},"obj":"http://purl.obolibrary.org/obo/GO_0051235"},{"id":"T146","span":{"begin":1115,"end":1126},"obj":"http://purl.obolibrary.org/obo/GO_0006897"},{"id":"T147","span":{"begin":1583,"end":1595},"obj":"http://purl.obolibrary.org/obo/GO_0051179"},{"id":"T148","span":{"begin":1986,"end":2009},"obj":"http://purl.obolibrary.org/obo/GO_0051665"},{"id":"T149","span":{"begin":1997,"end":2009},"obj":"http://purl.obolibrary.org/obo/GO_0051179"}],"text":"7.2. Interaction of Membrane Gangliosides in Lipid Rafts with CLQ and CLQ-OH\nLipid rafts are also viral attachment sites. Viruses such as IBV, dengue virus, Ebola virus, hepatitis C virus, HIV, human herpes virus 6, measles virus, Newcastle disease virus, poliovirus, West Nile virus, foot-and-mouth disease virus, simian virus 40, rotavirus, influenza virus and Marburg virus also use lipid rafts for virus entry [151,152,153,154,155,156]. In avian CoV IBV, structural proteins of the IBV virus are co-localized with PM lipid rafts embedded with the ganglioside GM1. HCoV-229E entry is prevented by cholesterol depleted conditions because HCoV-229E clusters in caveolae-associated lipid rafts [157]. Caveolae of caveolin-1, -2 and -3 are cross-linked [158] and control the molecular distribution between rafts and caveolae in a regulatory mechanism. S protein-CD13 cross-linking occurs via CD13-caveolin-1 sequestering. HCoV-229E particles similarly exhibit a longitudinal distribution property. HCoV-229E-colocalized caveolin-1 undergoes the next step of virus infection. Caveolin-1 knockdown inhibited HCoV-229E endocytosis and entry and thus caveolin-1 is essential for HCoV-229E infection. TGEV also endocytoses by a clathrin-mediated mechanism in MDCK cells [159]. Other viruses including HCoV-OC43 also use an entry receptor sequestered to cross-linked caveolae [160]. In SARS-CoV, the first entry step to host cells needs ACE2 in intact lipid rafts by the S glycoprotein [151]. ACE2 is associated with caveolin-1 and GM1 in membrane rafts depending on its cell-type specific localization [161]. Raft integrity with cholesterol and ACE2 is necessary for SARS-CoV pseudovirus entry into Vero E6 cells and for SARS-CoV-microdomain-based entry. C-type lectin, CD209 L (L-SIGN), can also form lipid rafts and acts as a SARS-CoV receptor [162]. Information of the CoV entry pathways is important for therapeutic designation of SARS-CoV-targeting drugs, for example, if agents disrupt lipid-raft localization of the ACE2 receptor.\nCLQ binds the SAs and gangliosides in lipid rafts with a high affinity. Therefore, CLQ or CLQ-OH prevents the S glycoprotein–ganglioside binding. CLQ (or CLQ-OH) binding to SA consequently prevents S glycoprotein binding to host receptors. The N-terminal region of SARS-CoV-2 S glycoprotein interacts with gangliosides. A ganglioside-binding site (GBS) or ganglioside-binding domain (GBD) is present in the NTD of the S glycoprotein of SARS-CoV-2. Using molecular modeling and simulation technology, CLQ has been suggested to recognize the SAs and gangliosides. Human type Neu5Ac binds to CLQ and CLQ-OH. Thus, SAs are binding targets of CLQ and CLQ-OH. CLQ and CLQ-OH have two specific recognition sites in the polar sugar residues of ganglioside GM1. The first site is found at the tip of the sugar residues of GM1 with an interaction energy of −47 kJ/mol. The CLQ rings face the GalNAc residue of GM1, while the second site is in a large region of the sugar-ceramide junction and the sugar residues. Several amino acid residues of the S protein NTD, which are Phe-135, Asn-137 and Arg-158, recognize the ganglioside GM1. The S glycoprotein NTD-GM1 complex is suggested to form a trimolecular complex with two molecules of ganglioside GM1 anchored to the NTD of S protein [163]. The ACE2-binding RBD is suggested to be a potential GBS located on a differential site of the S glycoprotein NTD. The protein sequence interfacing surface of the NTD is the consensus GBDs [164]. The amino acids Gly, Pro and/or Ser residues found in GBD motifs are in the same 111–158 amino acids of the NTD as the ganglioside-attachment interface. The GBD is conserved throughout viral isolates from worldwide COVID-19 patients. The GBD potentially increases viral attachment ability to PM lipid rafts and contact between host ACE-2 and S protein [165]. The interaction between CLQ-OH and 9-O-acetyl-NeuAc is also similar to the 9-O-acetyl-NeuAc-CLQ interaction. The CLQ-OH OH group enhances the interaction of CLQ with SA via a hydrogen bond [163]. In conditions with CLQ or CLQ-OH derivative treatment, the S glycoprotein cannot bind to gangliosides in in silico studies, which are used to uncover the action mechanism. CLQ and CLQ-OH prevent the binding of S glycoprotein to gangliosides. The CLQ-SA complex is formed in a mixed surface and balls by the positioning of the negative charged COOH group of Neu5Ac and one of the two cationic charges of CLQ [163]. CoVs preferentially bind to 9-O-acetyl-NeuAc [60], differentiating with other viral properties.\nAs CLQ interacts with the GM1 sugar part, the N-terminal domain of the S protein loses viral attachment capacity to the cell receptors [166]. The S protein NTD and the CLQ/CLQ-OH maintain the same position during GM1 binding, consequently preventing GM1 binding to the S protein and the drug at the same time, because the NTD and the CLQ/CLQ-OH simultaneously recognize GM1. Asn-167 forms a hydrogen bond with the GalNAc residue, whereas an aromatic Phe-135 stacks to the Glc residue of GM1. Therefore, the antiviral activities of CLQ and CLQ-OH is to block the interaction between the SARS-CoV-2 S glycoprotein and gangliosides on host cell surfaces. The lipid composition of host cell PM can also be a potential target for preventive and therapeutic drugs against such viruses."}

LitCovid-sentences

LitCovid-PD-GlycoEpitope

2_test

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T25","span":{"begin":170,"end":179},"obj":"Phenotype"}],"attributes":[{"id":"A25","pred":"hp_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/HP_0012115"}],"text":"7.2. Interaction of Membrane Gangliosides in Lipid Rafts with CLQ and CLQ-OH\nLipid rafts are also viral attachment sites. Viruses such as IBV, dengue virus, Ebola virus, hepatitis C virus, HIV, human herpes virus 6, measles virus, Newcastle disease virus, poliovirus, West Nile virus, foot-and-mouth disease virus, simian virus 40, rotavirus, influenza virus and Marburg virus also use lipid rafts for virus entry [151,152,153,154,155,156]. In avian CoV IBV, structural proteins of the IBV virus are co-localized with PM lipid rafts embedded with the ganglioside GM1. HCoV-229E entry is prevented by cholesterol depleted conditions because HCoV-229E clusters in caveolae-associated lipid rafts [157]. Caveolae of caveolin-1, -2 and -3 are cross-linked [158] and control the molecular distribution between rafts and caveolae in a regulatory mechanism. S protein-CD13 cross-linking occurs via CD13-caveolin-1 sequestering. HCoV-229E particles similarly exhibit a longitudinal distribution property. HCoV-229E-colocalized caveolin-1 undergoes the next step of virus infection. Caveolin-1 knockdown inhibited HCoV-229E endocytosis and entry and thus caveolin-1 is essential for HCoV-229E infection. TGEV also endocytoses by a clathrin-mediated mechanism in MDCK cells [159]. Other viruses including HCoV-OC43 also use an entry receptor sequestered to cross-linked caveolae [160]. In SARS-CoV, the first entry step to host cells needs ACE2 in intact lipid rafts by the S glycoprotein [151]. ACE2 is associated with caveolin-1 and GM1 in membrane rafts depending on its cell-type specific localization [161]. Raft integrity with cholesterol and ACE2 is necessary for SARS-CoV pseudovirus entry into Vero E6 cells and for SARS-CoV-microdomain-based entry. C-type lectin, CD209 L (L-SIGN), can also form lipid rafts and acts as a SARS-CoV receptor [162]. Information of the CoV entry pathways is important for therapeutic designation of SARS-CoV-targeting drugs, for example, if agents disrupt lipid-raft localization of the ACE2 receptor.\nCLQ binds the SAs and gangliosides in lipid rafts with a high affinity. Therefore, CLQ or CLQ-OH prevents the S glycoprotein–ganglioside binding. CLQ (or CLQ-OH) binding to SA consequently prevents S glycoprotein binding to host receptors. The N-terminal region of SARS-CoV-2 S glycoprotein interacts with gangliosides. A ganglioside-binding site (GBS) or ganglioside-binding domain (GBD) is present in the NTD of the S glycoprotein of SARS-CoV-2. Using molecular modeling and simulation technology, CLQ has been suggested to recognize the SAs and gangliosides. Human type Neu5Ac binds to CLQ and CLQ-OH. Thus, SAs are binding targets of CLQ and CLQ-OH. CLQ and CLQ-OH have two specific recognition sites in the polar sugar residues of ganglioside GM1. The first site is found at the tip of the sugar residues of GM1 with an interaction energy of −47 kJ/mol. The CLQ rings face the GalNAc residue of GM1, while the second site is in a large region of the sugar-ceramide junction and the sugar residues. Several amino acid residues of the S protein NTD, which are Phe-135, Asn-137 and Arg-158, recognize the ganglioside GM1. The S glycoprotein NTD-GM1 complex is suggested to form a trimolecular complex with two molecules of ganglioside GM1 anchored to the NTD of S protein [163]. The ACE2-binding RBD is suggested to be a potential GBS located on a differential site of the S glycoprotein NTD. The protein sequence interfacing surface of the NTD is the consensus GBDs [164]. The amino acids Gly, Pro and/or Ser residues found in GBD motifs are in the same 111–158 amino acids of the NTD as the ganglioside-attachment interface. The GBD is conserved throughout viral isolates from worldwide COVID-19 patients. The GBD potentially increases viral attachment ability to PM lipid rafts and contact between host ACE-2 and S protein [165]. The interaction between CLQ-OH and 9-O-acetyl-NeuAc is also similar to the 9-O-acetyl-NeuAc-CLQ interaction. The CLQ-OH OH group enhances the interaction of CLQ with SA via a hydrogen bond [163]. In conditions with CLQ or CLQ-OH derivative treatment, the S glycoprotein cannot bind to gangliosides in in silico studies, which are used to uncover the action mechanism. CLQ and CLQ-OH prevent the binding of S glycoprotein to gangliosides. The CLQ-SA complex is formed in a mixed surface and balls by the positioning of the negative charged COOH group of Neu5Ac and one of the two cationic charges of CLQ [163]. CoVs preferentially bind to 9-O-acetyl-NeuAc [60], differentiating with other viral properties.\nAs CLQ interacts with the GM1 sugar part, the N-terminal domain of the S protein loses viral attachment capacity to the cell receptors [166]. The S protein NTD and the CLQ/CLQ-OH maintain the same position during GM1 binding, consequently preventing GM1 binding to the S protein and the drug at the same time, because the NTD and the CLQ/CLQ-OH simultaneously recognize GM1. Asn-167 forms a hydrogen bond with the GalNAc residue, whereas an aromatic Phe-135 stacks to the Glc residue of GM1. Therefore, the antiviral activities of CLQ and CLQ-OH is to block the interaction between the SARS-CoV-2 S glycoprotein and gangliosides on host cell surfaces. The lipid composition of host cell PM can also be a potential target for preventive and therapeutic drugs against such viruses."}

PMC:7352545 / 75483-80835 JSONTXT

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PMC:7352545 / 75483-80835 JSON TXT