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LitCovid_Glycan-Motif-Structure

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T42","span":{"begin":784,"end":787},"obj":"Body_part"},{"id":"T43","span":{"begin":873,"end":877},"obj":"Body_part"}],"attributes":[{"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":"CLQ 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."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T746","span":{"begin":0,"end":71},"obj":"Sentence"},{"id":"T747","span":{"begin":72,"end":145},"obj":"Sentence"},{"id":"T748","span":{"begin":146,"end":239},"obj":"Sentence"},{"id":"T749","span":{"begin":240,"end":319},"obj":"Sentence"},{"id":"T750","span":{"begin":320,"end":447},"obj":"Sentence"},{"id":"T751","span":{"begin":448,"end":561},"obj":"Sentence"},{"id":"T752","span":{"begin":562,"end":604},"obj":"Sentence"},{"id":"T753","span":{"begin":605,"end":653},"obj":"Sentence"},{"id":"T754","span":{"begin":654,"end":752},"obj":"Sentence"},{"id":"T755","span":{"begin":753,"end":858},"obj":"Sentence"},{"id":"T756","span":{"begin":859,"end":1002},"obj":"Sentence"},{"id":"T757","span":{"begin":1003,"end":1123},"obj":"Sentence"},{"id":"T758","span":{"begin":1124,"end":1280},"obj":"Sentence"},{"id":"T759","span":{"begin":1281,"end":1394},"obj":"Sentence"},{"id":"T760","span":{"begin":1395,"end":1475},"obj":"Sentence"},{"id":"T761","span":{"begin":1476,"end":1628},"obj":"Sentence"},{"id":"T762","span":{"begin":1629,"end":1709},"obj":"Sentence"},{"id":"T763","span":{"begin":1710,"end":1834},"obj":"Sentence"},{"id":"T764","span":{"begin":1835,"end":1943},"obj":"Sentence"},{"id":"T765","span":{"begin":1944,"end":2030},"obj":"Sentence"},{"id":"T766","span":{"begin":2031,"end":2202},"obj":"Sentence"},{"id":"T767","span":{"begin":2203,"end":2272},"obj":"Sentence"},{"id":"T768","span":{"begin":2273,"end":2444},"obj":"Sentence"},{"id":"T769","span":{"begin":2445,"end":2540},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"CLQ 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."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T16","span":{"begin":748,"end":751},"obj":"GlycoEpitope"},{"id":"T17","span":{"begin":813,"end":816},"obj":"GlycoEpitope"},{"id":"T18","span":{"begin":900,"end":903},"obj":"GlycoEpitope"},{"id":"T19","span":{"begin":1119,"end":1122},"obj":"GlycoEpitope"},{"id":"T20","span":{"begin":1147,"end":1150},"obj":"GlycoEpitope"},{"id":"T21","span":{"begin":1237,"end":1240},"obj":"GlycoEpitope"}],"attributes":[{"id":"A16","pred":"glyco_epitope_db_id","subj":"T16","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A17","pred":"glyco_epitope_db_id","subj":"T17","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A18","pred":"glyco_epitope_db_id","subj":"T18","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A19","pred":"glyco_epitope_db_id","subj":"T19","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A20","pred":"glyco_epitope_db_id","subj":"T20","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A21","pred":"glyco_epitope_db_id","subj":"T21","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"CLQ 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."}

2_test

{"project":"2_test","denotations":[{"id":"32604730-32251731-51944127","span":{"begin":1275,"end":1278},"obj":"32251731"},{"id":"32604730-25140899-51944128","span":{"begin":1470,"end":1473},"obj":"25140899"},{"id":"32604730-32251731-51944129","span":{"begin":2025,"end":2028},"obj":"32251731"},{"id":"32604730-32251731-51944130","span":{"begin":2439,"end":2442},"obj":"32251731"},{"id":"T25798","span":{"begin":1275,"end":1278},"obj":"32251731"},{"id":"T45602","span":{"begin":1470,"end":1473},"obj":"25140899"},{"id":"T55235","span":{"begin":2025,"end":2028},"obj":"32251731"},{"id":"T50194","span":{"begin":2439,"end":2442},"obj":"32251731"}],"text":"CLQ 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."}

PMC:7352545 / 77515-80055 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7352545 / 77515-80055 JSON TXT