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LitCovid_Glycan-Motif-Structure

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T16","span":{"begin":434,"end":445},"obj":"https://glytoucan.org/Structures/Glycans/G81533KY"},{"id":"T17","span":{"begin":447,"end":449},"obj":"https://glytoucan.org/Structures/Glycans/G81533KY"},{"id":"T18","span":{"begin":914,"end":922},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T19","span":{"begin":914,"end":922},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T20","span":{"begin":1395,"end":1397},"obj":"https://glytoucan.org/Structures/Glycans/G81533KY"},{"id":"T21","span":{"begin":1551,"end":1553},"obj":"https://glytoucan.org/Structures/Glycans/G81533KY"},{"id":"T22","span":{"begin":2347,"end":2349},"obj":"https://glytoucan.org/Structures/Glycans/G81533KY"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

LitCovid-PD-FMA-UBERON

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T31","span":{"begin":376,"end":385},"obj":"Disease"},{"id":"T32","span":{"begin":533,"end":541},"obj":"Disease"},{"id":"T33","span":{"begin":702,"end":706},"obj":"Disease"},{"id":"T34","span":{"begin":761,"end":771},"obj":"Disease"},{"id":"T35","span":{"begin":1913,"end":1921},"obj":"Disease"}],"attributes":[{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T6","span":{"begin":778,"end":803},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T7","span":{"begin":2640,"end":2647},"obj":"http://purl.obolibrary.org/obo/GO_0009606"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T38","span":{"begin":0,"end":144},"obj":"Sentence"},{"id":"T39","span":{"begin":145,"end":190},"obj":"Sentence"},{"id":"T40","span":{"begin":191,"end":352},"obj":"Sentence"},{"id":"T41","span":{"begin":353,"end":464},"obj":"Sentence"},{"id":"T42","span":{"begin":465,"end":614},"obj":"Sentence"},{"id":"T43","span":{"begin":615,"end":760},"obj":"Sentence"},{"id":"T44","span":{"begin":761,"end":913},"obj":"Sentence"},{"id":"T45","span":{"begin":914,"end":1001},"obj":"Sentence"},{"id":"T46","span":{"begin":1002,"end":1135},"obj":"Sentence"},{"id":"T47","span":{"begin":1136,"end":1295},"obj":"Sentence"},{"id":"T48","span":{"begin":1296,"end":1412},"obj":"Sentence"},{"id":"T49","span":{"begin":1413,"end":1562},"obj":"Sentence"},{"id":"T50","span":{"begin":1563,"end":1858},"obj":"Sentence"},{"id":"T51","span":{"begin":1859,"end":1972},"obj":"Sentence"},{"id":"T52","span":{"begin":1973,"end":2097},"obj":"Sentence"},{"id":"T53","span":{"begin":2098,"end":2197},"obj":"Sentence"},{"id":"T54","span":{"begin":2198,"end":2285},"obj":"Sentence"},{"id":"T55","span":{"begin":2286,"end":2438},"obj":"Sentence"},{"id":"T56","span":{"begin":2439,"end":2648},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":914,"end":922},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0004"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

2_test

{"project":"2_test","denotations":[{"id":"32604730-24524838-51943949","span":{"begin":139,"end":140},"obj":"24524838"},{"id":"32604730-14557669-51943950","span":{"begin":141,"end":142},"obj":"14557669"},{"id":"32604730-24227863-51943951","span":{"begin":187,"end":188},"obj":"24227863"},{"id":"32604730-3380803-51943952","span":{"begin":461,"end":462},"obj":"3380803"},{"id":"32604730-3380803-51943953","span":{"begin":1407,"end":1408},"obj":"3380803"},{"id":"32604730-1984649-51943954","span":{"begin":1409,"end":1410},"obj":"1984649"},{"id":"T53109","span":{"begin":139,"end":140},"obj":"24524838"},{"id":"T96251","span":{"begin":141,"end":142},"obj":"14557669"},{"id":"T80079","span":{"begin":187,"end":188},"obj":"24227863"},{"id":"T76200","span":{"begin":461,"end":462},"obj":"3380803"},{"id":"T31655","span":{"begin":1407,"end":1408},"obj":"3380803"},{"id":"T65223","span":{"begin":1409,"end":1410},"obj":"1984649"}],"text":"The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6]. CoVs can also rarely infect neural cells [7]. There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak. This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8]. Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species. Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells. Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution. O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1). Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells. For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains. Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9]. Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding. This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI). Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs. Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10]. If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants. Previous reports suggest that carbohydrates act as receptor determinants in most cases. The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain. This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism."}

PMC:7352545 / 4959-7607 JSONTXT

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PMC:7352545 / 4959-7607 JSON TXT