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LitCovid-PMC-OGER-BB

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T44","span":{"begin":814,"end":819},"obj":"Body_part"},{"id":"T45","span":{"begin":1370,"end":1381},"obj":"Body_part"},{"id":"T46","span":{"begin":1389,"end":1396},"obj":"Body_part"},{"id":"T47","span":{"begin":1525,"end":1532},"obj":"Body_part"},{"id":"T48","span":{"begin":1831,"end":1838},"obj":"Body_part"},{"id":"T49","span":{"begin":2047,"end":2052},"obj":"Body_part"}],"attributes":[{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma82767"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"We performed a structure-based virtual screening by targeting W43 in the hydrophobic pocket of the N-NTD dimeric interface. H37 and M38 were removed from the template to identify compounds that could replace the vector-fusion residues and, therefore, contribute to the stabilizing effect (Figures 2A and S2A,B). We chose the highest-scoring hits, listed in Table S2, based on shape complementarity, the presence of aromatic moieties, and the ability to stack onto W43 of N-NTD. Because the formation of the non-native dimers was primarily mediated by hydrophobic interactions in our structure (Figure 1C,D), we next considered the hydrophobic complementarity between the acquired ligands and N-NTD in the form of the lipophilic match surface (SL/L).31 We also took into account the ability of the drug to permeate cells by aiming for lower topological polar surface areas (TPSA). Based on the above criteria, three compounds were finally chosen for further study. Benzyl-2-(hydroxymethyl)-1-indolinecarboxylate (P1) and 5-benzyloxygramine (P3) had higher SL/L and docking scores and lower TPSA. The clinical drug etodolac (P2) had a comparable SL/L but a lower docking score. It too was selected as a candidate. However, only P3 induced a comparatively larger blue shift in the intrinsic N-NTD fluorescence spectrum, indicating that the microenvironment surrounding the tryptophans of the protein increased in rigidity and hydrophobicity in the presence of P3.32 The result also indicated that P3 bound more tightly to the N protein than P1 or P2 by interacting with the W43 pocket (Figure 2B). Fluorescent thermal stability assays disclosed that the N-NTD denaturation melting temperature had increased from 42 to 45 °C when P3 was added. The sigmoidal melting curve for MERS-CoV N-NTD changed in the presence of P3. The delay in protein denaturation suggests that P3 stabilized the MERS-CoV N-NTD dimer structure (Figure 2C). We then measured the cytotoxic concentration (CC50) and effective concentration (EC50) for each compound using Vero E6 cells infected with MERS-CoV. Table 1 shows that P3 had a favorable therapeutic index among the lead compounds tested in this study. Therefore, P3 is an excellent candidate inhibitor against MERS-CoV."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T11","span":{"begin":490,"end":499},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T12","span":{"begin":1831,"end":1851},"obj":"http://purl.obolibrary.org/obo/GO_0030164"}],"text":"We performed a structure-based virtual screening by targeting W43 in the hydrophobic pocket of the N-NTD dimeric interface. H37 and M38 were removed from the template to identify compounds that could replace the vector-fusion residues and, therefore, contribute to the stabilizing effect (Figures 2A and S2A,B). We chose the highest-scoring hits, listed in Table S2, based on shape complementarity, the presence of aromatic moieties, and the ability to stack onto W43 of N-NTD. Because the formation of the non-native dimers was primarily mediated by hydrophobic interactions in our structure (Figure 1C,D), we next considered the hydrophobic complementarity between the acquired ligands and N-NTD in the form of the lipophilic match surface (SL/L).31 We also took into account the ability of the drug to permeate cells by aiming for lower topological polar surface areas (TPSA). Based on the above criteria, three compounds were finally chosen for further study. Benzyl-2-(hydroxymethyl)-1-indolinecarboxylate (P1) and 5-benzyloxygramine (P3) had higher SL/L and docking scores and lower TPSA. The clinical drug etodolac (P2) had a comparable SL/L but a lower docking score. It too was selected as a candidate. However, only P3 induced a comparatively larger blue shift in the intrinsic N-NTD fluorescence spectrum, indicating that the microenvironment surrounding the tryptophans of the protein increased in rigidity and hydrophobicity in the presence of P3.32 The result also indicated that P3 bound more tightly to the N protein than P1 or P2 by interacting with the W43 pocket (Figure 2B). Fluorescent thermal stability assays disclosed that the N-NTD denaturation melting temperature had increased from 42 to 45 °C when P3 was added. The sigmoidal melting curve for MERS-CoV N-NTD changed in the presence of P3. The delay in protein denaturation suggests that P3 stabilized the MERS-CoV N-NTD dimer structure (Figure 2C). We then measured the cytotoxic concentration (CC50) and effective concentration (EC50) for each compound using Vero E6 cells infected with MERS-CoV. Table 1 shows that P3 had a favorable therapeutic index among the lead compounds tested in this study. Therefore, P3 is an excellent candidate inhibitor against MERS-CoV."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T3","span":{"begin":1410,"end":1418},"obj":"Phenotype"}],"attributes":[{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0002063"}],"text":"We performed a structure-based virtual screening by targeting W43 in the hydrophobic pocket of the N-NTD dimeric interface. H37 and M38 were removed from the template to identify compounds that could replace the vector-fusion residues and, therefore, contribute to the stabilizing effect (Figures 2A and S2A,B). We chose the highest-scoring hits, listed in Table S2, based on shape complementarity, the presence of aromatic moieties, and the ability to stack onto W43 of N-NTD. Because the formation of the non-native dimers was primarily mediated by hydrophobic interactions in our structure (Figure 1C,D), we next considered the hydrophobic complementarity between the acquired ligands and N-NTD in the form of the lipophilic match surface (SL/L).31 We also took into account the ability of the drug to permeate cells by aiming for lower topological polar surface areas (TPSA). Based on the above criteria, three compounds were finally chosen for further study. Benzyl-2-(hydroxymethyl)-1-indolinecarboxylate (P1) and 5-benzyloxygramine (P3) had higher SL/L and docking scores and lower TPSA. The clinical drug etodolac (P2) had a comparable SL/L but a lower docking score. It too was selected as a candidate. However, only P3 induced a comparatively larger blue shift in the intrinsic N-NTD fluorescence spectrum, indicating that the microenvironment surrounding the tryptophans of the protein increased in rigidity and hydrophobicity in the presence of P3.32 The result also indicated that P3 bound more tightly to the N protein than P1 or P2 by interacting with the W43 pocket (Figure 2B). Fluorescent thermal stability assays disclosed that the N-NTD denaturation melting temperature had increased from 42 to 45 °C when P3 was added. The sigmoidal melting curve for MERS-CoV N-NTD changed in the presence of P3. The delay in protein denaturation suggests that P3 stabilized the MERS-CoV N-NTD dimer structure (Figure 2C). We then measured the cytotoxic concentration (CC50) and effective concentration (EC50) for each compound using Vero E6 cells infected with MERS-CoV. Table 1 shows that P3 had a favorable therapeutic index among the lead compounds tested in this study. Therefore, P3 is an excellent candidate inhibitor against MERS-CoV."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T76","span":{"begin":0,"end":123},"obj":"Sentence"},{"id":"T77","span":{"begin":124,"end":311},"obj":"Sentence"},{"id":"T78","span":{"begin":312,"end":477},"obj":"Sentence"},{"id":"T79","span":{"begin":478,"end":879},"obj":"Sentence"},{"id":"T80","span":{"begin":880,"end":963},"obj":"Sentence"},{"id":"T81","span":{"begin":964,"end":1094},"obj":"Sentence"},{"id":"T82","span":{"begin":1095,"end":1175},"obj":"Sentence"},{"id":"T83","span":{"begin":1176,"end":1211},"obj":"Sentence"},{"id":"T84","span":{"begin":1212,"end":1594},"obj":"Sentence"},{"id":"T85","span":{"begin":1595,"end":1739},"obj":"Sentence"},{"id":"T86","span":{"begin":1740,"end":1817},"obj":"Sentence"},{"id":"T87","span":{"begin":1818,"end":1927},"obj":"Sentence"},{"id":"T88","span":{"begin":1928,"end":2076},"obj":"Sentence"},{"id":"T89","span":{"begin":2077,"end":2179},"obj":"Sentence"},{"id":"T90","span":{"begin":2180,"end":2247},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We performed a structure-based virtual screening by targeting W43 in the hydrophobic pocket of the N-NTD dimeric interface. H37 and M38 were removed from the template to identify compounds that could replace the vector-fusion residues and, therefore, contribute to the stabilizing effect (Figures 2A and S2A,B). We chose the highest-scoring hits, listed in Table S2, based on shape complementarity, the presence of aromatic moieties, and the ability to stack onto W43 of N-NTD. Because the formation of the non-native dimers was primarily mediated by hydrophobic interactions in our structure (Figure 1C,D), we next considered the hydrophobic complementarity between the acquired ligands and N-NTD in the form of the lipophilic match surface (SL/L).31 We also took into account the ability of the drug to permeate cells by aiming for lower topological polar surface areas (TPSA). Based on the above criteria, three compounds were finally chosen for further study. Benzyl-2-(hydroxymethyl)-1-indolinecarboxylate (P1) and 5-benzyloxygramine (P3) had higher SL/L and docking scores and lower TPSA. The clinical drug etodolac (P2) had a comparable SL/L but a lower docking score. It too was selected as a candidate. However, only P3 induced a comparatively larger blue shift in the intrinsic N-NTD fluorescence spectrum, indicating that the microenvironment surrounding the tryptophans of the protein increased in rigidity and hydrophobicity in the presence of P3.32 The result also indicated that P3 bound more tightly to the N protein than P1 or P2 by interacting with the W43 pocket (Figure 2B). Fluorescent thermal stability assays disclosed that the N-NTD denaturation melting temperature had increased from 42 to 45 °C when P3 was added. The sigmoidal melting curve for MERS-CoV N-NTD changed in the presence of P3. The delay in protein denaturation suggests that P3 stabilized the MERS-CoV N-NTD dimer structure (Figure 2C). We then measured the cytotoxic concentration (CC50) and effective concentration (EC50) for each compound using Vero E6 cells infected with MERS-CoV. Table 1 shows that P3 had a favorable therapeutic index among the lead compounds tested in this study. Therefore, P3 is an excellent candidate inhibitor against MERS-CoV."}

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"32105468-19244385-61929509","span":{"begin":749,"end":751},"obj":"19244385"}],"text":"We performed a structure-based virtual screening by targeting W43 in the hydrophobic pocket of the N-NTD dimeric interface. H37 and M38 were removed from the template to identify compounds that could replace the vector-fusion residues and, therefore, contribute to the stabilizing effect (Figures 2A and S2A,B). We chose the highest-scoring hits, listed in Table S2, based on shape complementarity, the presence of aromatic moieties, and the ability to stack onto W43 of N-NTD. Because the formation of the non-native dimers was primarily mediated by hydrophobic interactions in our structure (Figure 1C,D), we next considered the hydrophobic complementarity between the acquired ligands and N-NTD in the form of the lipophilic match surface (SL/L).31 We also took into account the ability of the drug to permeate cells by aiming for lower topological polar surface areas (TPSA). Based on the above criteria, three compounds were finally chosen for further study. Benzyl-2-(hydroxymethyl)-1-indolinecarboxylate (P1) and 5-benzyloxygramine (P3) had higher SL/L and docking scores and lower TPSA. The clinical drug etodolac (P2) had a comparable SL/L but a lower docking score. It too was selected as a candidate. However, only P3 induced a comparatively larger blue shift in the intrinsic N-NTD fluorescence spectrum, indicating that the microenvironment surrounding the tryptophans of the protein increased in rigidity and hydrophobicity in the presence of P3.32 The result also indicated that P3 bound more tightly to the N protein than P1 or P2 by interacting with the W43 pocket (Figure 2B). Fluorescent thermal stability assays disclosed that the N-NTD denaturation melting temperature had increased from 42 to 45 °C when P3 was added. The sigmoidal melting curve for MERS-CoV N-NTD changed in the presence of P3. The delay in protein denaturation suggests that P3 stabilized the MERS-CoV N-NTD dimer structure (Figure 2C). We then measured the cytotoxic concentration (CC50) and effective concentration (EC50) for each compound using Vero E6 cells infected with MERS-CoV. Table 1 shows that P3 had a favorable therapeutic index among the lead compounds tested in this study. Therefore, P3 is an excellent candidate inhibitor against MERS-CoV."}

PMC:7094172 / 10194-12441 JSONTXT

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PMC:7094172 / 10194-12441 JSON TXT