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PMC:7291971 / 25171-28031
Annnotations
LitCovid-PMC-OGER-BB
{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T543","span":{"begin":34,"end":42},"obj":"SP_10"},{"id":"T544","span":{"begin":43,"end":48},"obj":"PR:000000125"},{"id":"T545","span":{"begin":49,"end":57},"obj":"SP_10"},{"id":"T546","span":{"begin":58,"end":63},"obj":"PR:000000125"},{"id":"T547","span":{"begin":64,"end":73},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T548","span":{"begin":285,"end":293},"obj":"SP_10"},{"id":"T549","span":{"begin":352,"end":360},"obj":"CHEBI:23357;CHEBI:23357"},{"id":"T550","span":{"begin":422,"end":431},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T551","span":{"begin":476,"end":484},"obj":"SP_10"},{"id":"T552","span":{"begin":514,"end":521},"obj":"GO:0032508"},{"id":"T553","span":{"begin":649,"end":654},"obj":"CHEBI:24433;CHEBI:24433"},{"id":"T554","span":{"begin":718,"end":728},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T555","span":{"begin":745,"end":758},"obj":"CHEBI:23447;CHEBI:23447"},{"id":"T556","span":{"begin":774,"end":782},"obj":"SP_10"},{"id":"T557","span":{"begin":783,"end":788},"obj":"PR:000000125"},{"id":"T558","span":{"begin":913,"end":922},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T559","span":{"begin":950,"end":958},"obj":"SP_10"},{"id":"T560","span":{"begin":959,"end":964},"obj":"PR:000000125"},{"id":"T561","span":{"begin":1002,"end":1011},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T562","span":{"begin":1059,"end":1067},"obj":"SP_10"},{"id":"T563","span":{"begin":1110,"end":1119},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T564","span":{"begin":1203,"end":1212},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T565","span":{"begin":1292,"end":1301},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T566","span":{"begin":1341,"end":1349},"obj":"SP_10"},{"id":"T567","span":{"begin":1536,"end":1544},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T568","span":{"begin":1610,"end":1619},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T569","span":{"begin":1633,"end":1641},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T570","span":{"begin":1668,"end":1677},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T571","span":{"begin":1724,"end":1732},"obj":"SP_10"},{"id":"T572","span":{"begin":1733,"end":1738},"obj":"PR:000000125"},{"id":"T573","span":{"begin":1781,"end":1788},"obj":"CHEBI:33543;CHEBI:33543"},{"id":"T574","span":{"begin":1789,"end":1794},"obj":"CHEBI:24433;CHEBI:24433"},{"id":"T575","span":{"begin":1800,"end":1802},"obj":"CHEBI:17996;CHEBI:17996"},{"id":"T576","span":{"begin":1807,"end":1810},"obj":"CHEBI:17997;CHEBI:17997"},{"id":"T577","span":{"begin":1861,"end":1870},"obj":"CHEBI:62946;CHEBI:62946"},{"id":"T578","span":{"begin":1870,"end":1871},"obj":"CHEBI:86228;CHEBI:86228"},{"id":"T579","span":{"begin":1871,"end":1875},"obj":"CHEBI:62946;CHEBI:62946"},{"id":"T580","span":{"begin":1875,"end":1892},"obj":"CHEBI:8102;CHEBI:8102"},{"id":"T581","span":{"begin":1934,"end":1942},"obj":"SP_10"},{"id":"T582","span":{"begin":1943,"end":1948},"obj":"PR:000000125"},{"id":"T583","span":{"begin":2016,"end":2024},"obj":"SP_10"},{"id":"T584","span":{"begin":2132,"end":2135},"obj":"CHEBI:17997;CHEBI:17997"},{"id":"T585","span":{"begin":2156,"end":2162},"obj":"CHEBI:30396;CHEBI:30396"},{"id":"T586","span":{"begin":2206,"end":2214},"obj":"SP_10"},{"id":"T587","span":{"begin":2215,"end":2220},"obj":"PR:000000125"},{"id":"T588","span":{"begin":2327,"end":2335},"obj":"SP_10"},{"id":"T589","span":{"begin":2336,"end":2341},"obj":"PR:000000125"},{"id":"T590","span":{"begin":2394,"end":2406},"obj":"CHEBI:23447;CHEBI:23447"},{"id":"T591","span":{"begin":2407,"end":2417},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T592","span":{"begin":2451,"end":2459},"obj":"SP_10"},{"id":"T593","span":{"begin":2460,"end":2465},"obj":"PR:000000125"},{"id":"T594","span":{"begin":2574,"end":2581},"obj":"CHEBI:60004;CHEBI:60004"},{"id":"T595","span":{"begin":2589,"end":2594},"obj":"CHEBI:46756;CHEBI:46756"},{"id":"T596","span":{"begin":2612,"end":2616},"obj":"CHEBI:26710;CHEBI:26710"},{"id":"T597","span":{"begin":2627,"end":2633},"obj":"CHEBI:51461;CHEBI:51461"},{"id":"T598","span":{"begin":2634,"end":2637},"obj":"CHEBI:37958;CHEBI:37958"},{"id":"T599","span":{"begin":2663,"end":2671},"obj":"SP_10"},{"id":"T600","span":{"begin":2672,"end":2677},"obj":"PR:000000125"},{"id":"T601","span":{"begin":2695,"end":2703},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T602","span":{"begin":2733,"end":2737},"obj":"CHEBI:51231;CHEBI:51231"},{"id":"T83376","span":{"begin":64,"end":73},"obj":"CHEBI:35222;CHEBI:35222"},{"id":"T91238","span":{"begin":87,"end":95},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T42222","span":{"begin":122,"end":131},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T27451","span":{"begin":178,"end":186},"obj":"SP_10"},{"id":"T6980","span":{"begin":187,"end":192},"obj":"PR:000000125"},{"id":"T57622","span":{"begin":235,"end":242},"obj":"CHEBI:33543;CHEBI:33543"},{"id":"T35844","span":{"begin":243,"end":248},"obj":"CHEBI:24433;CHEBI:24433"},{"id":"T99111","span":{"begin":254,"end":256},"obj":"CHEBI:17996;CHEBI:17996"},{"id":"T33412","span":{"begin":261,"end":264},"obj":"C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Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-PD-FMA-UBERON
{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T79","span":{"begin":156,"end":163},"obj":"Body_part"},{"id":"T80","span":{"begin":789,"end":796},"obj":"Body_part"},{"id":"T81","span":{"begin":1195,"end":1202},"obj":"Body_part"},{"id":"T82","span":{"begin":1827,"end":1834},"obj":"Body_part"},{"id":"T83","span":{"begin":2678,"end":2685},"obj":"Body_part"}],"attributes":[{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-PubTator
{"project":"LitCovid-PubTator","denotations":[{"id":"439","span":{"begin":2377,"end":2387},"obj":"Chemical"},{"id":"440","span":{"begin":2589,"end":2594},"obj":"Chemical"},{"id":"441","span":{"begin":2612,"end":2616},"obj":"Chemical"},{"id":"442","span":{"begin":2621,"end":2633},"obj":"Chemical"},{"id":"443","span":{"begin":2733,"end":2737},"obj":"Chemical"},{"id":"451","span":{"begin":376,"end":386},"obj":"Chemical"},{"id":"452","span":{"begin":745,"end":758},"obj":"Chemical"},{"id":"453","span":{"begin":1012,"end":1022},"obj":"Chemical"},{"id":"454","span":{"begin":1781,"end":1788},"obj":"Chemical"},{"id":"455","span":{"begin":1807,"end":1810},"obj":"Chemical"},{"id":"456","span":{"begin":1861,"end":1892},"obj":"Chemical"},{"id":"457","span":{"begin":2279,"end":2291},"obj":"Chemical"}],"attributes":[{"id":"A439","pred":"tao:has_database_id","subj":"439","obj":"MESH:C006235"},{"id":"A440","pred":"tao:has_database_id","subj":"440","obj":"MESH:D006531"},{"id":"A441","pred":"tao:has_database_id","subj":"441","obj":"MESH:D012965"},{"id":"A443","pred":"tao:has_database_id","subj":"443","obj":"MESH:D004121"},{"id":"A451","pred":"tao:has_database_id","subj":"451","obj":"MESH:C006235"},{"id":"A453","pred":"tao:has_database_id","subj":"453","obj":"MESH:C006235"},{"id":"A454","pred":"tao:has_database_id","subj":"454","obj":"MESH:D013450"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-PD-MONDO
{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T68","span":{"begin":34,"end":42},"obj":"Disease"},{"id":"T69","span":{"begin":49,"end":57},"obj":"Disease"},{"id":"T70","span":{"begin":285,"end":293},"obj":"Disease"},{"id":"T71","span":{"begin":476,"end":484},"obj":"Disease"},{"id":"T72","span":{"begin":774,"end":782},"obj":"Disease"},{"id":"T73","span":{"begin":950,"end":958},"obj":"Disease"},{"id":"T74","span":{"begin":1059,"end":1067},"obj":"Disease"},{"id":"T75","span":{"begin":1341,"end":1349},"obj":"Disease"},{"id":"T76","span":{"begin":1724,"end":1732},"obj":"Disease"},{"id":"T77","span":{"begin":1934,"end":1942},"obj":"Disease"},{"id":"T78","span":{"begin":2016,"end":2024},"obj":"Disease"},{"id":"T79","span":{"begin":2206,"end":2214},"obj":"Disease"},{"id":"T80","span":{"begin":2327,"end":2335},"obj":"Disease"},{"id":"T81","span":{"begin":2451,"end":2459},"obj":"Disease"},{"id":"T82","span":{"begin":2663,"end":2671},"obj":"Disease"}],"attributes":[{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A73","pred":"mondo_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A74","pred":"mondo_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A75","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A76","pred":"mondo_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A77","pred":"mondo_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A78","pred":"mondo_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A79","pred":"mondo_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A80","pred":"mondo_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A81","pred":"mondo_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A82","pred":"mondo_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-PD-CLO
{"project":"LitCovid-PD-CLO","denotations":[{"id":"T213","span":{"begin":245,"end":247},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T214","span":{"begin":402,"end":408},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T215","span":{"begin":622,"end":623},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T216","span":{"begin":816,"end":817},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T217","span":{"begin":884,"end":886},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T218","span":{"begin":1390,"end":1391},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T219","span":{"begin":1489,"end":1492},"obj":"http://purl.obolibrary.org/obo/CLO_0009405"},{"id":"T220","span":{"begin":1567,"end":1568},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T221","span":{"begin":1699,"end":1700},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T222","span":{"begin":1800,"end":1802},"obj":"http://purl.obolibrary.org/obo/CLO_0052906"},{"id":"T223","span":{"begin":1866,"end":1870},"obj":"http://purl.obolibrary.org/obo/CLO_0002489"},{"id":"T224","span":{"begin":2083,"end":2085},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T225","span":{"begin":2169,"end":2170},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-PD-CHEBI
{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T422","span":{"begin":64,"end":73},"obj":"Chemical"},{"id":"T423","span":{"begin":156,"end":163},"obj":"Chemical"},{"id":"T424","span":{"begin":240,"end":242},"obj":"Chemical"},{"id":"T425","span":{"begin":352,"end":360},"obj":"Chemical"},{"id":"T426","span":{"begin":371,"end":374},"obj":"Chemical"},{"id":"T428","span":{"begin":376,"end":386},"obj":"Chemical"},{"id":"T429","span":{"begin":551,"end":554},"obj":"Chemical"},{"id":"T431","span":{"begin":569,"end":579},"obj":"Chemical"},{"id":"T432","span":{"begin":649,"end":654},"obj":"Chemical"},{"id":"T433","span":{"begin":658,"end":661},"obj":"Chemical"},{"id":"T435","span":{"begin":718,"end":728},"obj":"Chemical"},{"id":"T436","span":{"begin":789,"end":796},"obj":"Chemical"},{"id":"T437","span":{"begin":1002,"end":1011},"obj":"Chemical"},{"id":"T438","span":{"begin":1012,"end":1022},"obj":"Chemical"},{"id":"T439","span":{"begin":1172,"end":1175},"obj":"Chemical"},{"id":"T441","span":{"begin":1195,"end":1202},"obj":"Chemical"},{"id":"T442","span":{"begin":1203,"end":1212},"obj":"Chemical"},{"id":"T443","span":{"begin":1292,"end":1301},"obj":"Chemical"},{"id":"T444","span":{"begin":1454,"end":1456},"obj":"Chemical"},{"id":"T445","span":{"begin":1489,"end":1492},"obj":"Chemical"},{"id":"T446","span":{"begin":1610,"end":1619},"obj":"Chemical"},{"id":"T447","span":{"begin":1781,"end":1788},"obj":"Chemical"},{"id":"T448","span":{"begin":1789,"end":1794},"obj":"Chemical"},{"id":"T449","span":{"begin":1800,"end":1802},"obj":"Chemical"},{"id":"T450","span":{"begin":1807,"end":1810},"obj":"Chemical"},{"id":"T452","span":{"begin":1827,"end":1834},"obj":"Chemical"},{"id":"T453","span":{"begin":1866,"end":1868},"obj":"Chemical"},{"id":"T454","span":{"begin":1871,"end":1874},"obj":"Chemical"},{"id":"T456","span":{"begin":2132,"end":2135},"obj":"Chemical"},{"id":"T458","span":{"begin":2156,"end":2162},"obj":"Chemical"},{"id":"T459","span":{"begin":2248,"end":2253},"obj":"Chemical"},{"id":"T460","span":{"begin":2320,"end":2322},"obj":"Chemical"},{"id":"T461","span":{"begin":2372,"end":2375},"obj":"Chemical"},{"id":"T463","span":{"begin":2377,"end":2387},"obj":"Chemical"},{"id":"T464","span":{"begin":2407,"end":2417},"obj":"Chemical"},{"id":"T465","span":{"begin":2471,"end":2477},"obj":"Chemical"},{"id":"T466","span":{"begin":2574,"end":2581},"obj":"Chemical"},{"id":"T467","span":{"begin":2589,"end":2594},"obj":"Chemical"},{"id":"T468","span":{"begin":2612,"end":2616},"obj":"Chemical"},{"id":"T469","span":{"begin":2634,"end":2637},"obj":"Chemical"},{"id":"T470","span":{"begin":2678,"end":2685},"obj":"Chemical"},{"id":"T471","span":{"begin":2733,"end":2737},"obj":"Chemical"}],"attributes":[{"id":"A422","pred":"chebi_id","subj":"T422","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A423","pred":"chebi_id","subj":"T423","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A424","pred":"chebi_id","subj":"T424","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"},{"id":"A425","pred":"chebi_id","subj":"T425","obj":"http://purl.obolibrary.org/obo/CHEBI_23357"},{"id":"A426","pred":"chebi_id","subj":"T426","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A427","pred":"chebi_id","subj":"T426","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A428","pred":"chebi_id","subj":"T428","obj":"http://purl.obolibrary.org/obo/CHEBI_45453"},{"id":"A429","pred":"chebi_id","subj":"T429","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A430","pred":"chebi_id","subj":"T429","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A431","pred":"chebi_id","subj":"T431","obj":"http://purl.obolibrary.org/obo/CHEBI_45453"},{"id":"A432","pred":"chebi_id","subj":"T432","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"},{"id":"A433","pred":"chebi_id","subj":"T433","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A434","pred":"chebi_id","subj":"T433","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A435","pred":"chebi_id","subj":"T435","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A436","pred":"chebi_id","subj":"T436","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A437","pred":"chebi_id","subj":"T437","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A438","pred":"chebi_id","subj":"T438","obj":"http://purl.obolibrary.org/obo/CHEBI_45453"},{"id":"A439","pred":"chebi_id","subj":"T439","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A440","pred":"chebi_id","subj":"T439","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A441","pred":"chebi_id","subj":"T441","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A442","pred":"chebi_id","subj":"T442","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A443","pred":"chebi_id","subj":"T443","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A444","pred":"chebi_id","subj":"T444","obj":"http://purl.obolibrary.org/obo/CHEBI_73601"},{"id":"A445","pred":"chebi_id","subj":"T445","obj":"http://purl.obolibrary.org/obo/CHEBI_46024"},{"id":"A446","pred":"chebi_id","subj":"T446","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A447","pred":"chebi_id","subj":"T447","obj":"http://purl.obolibrary.org/obo/CHEBI_35850"},{"id":"A448","pred":"chebi_id","subj":"T448","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"},{"id":"A449","pred":"chebi_id","subj":"T449","obj":"http://purl.obolibrary.org/obo/CHEBI_23116"},{"id":"A450","pred":"chebi_id","subj":"T450","obj":"http://purl.obolibrary.org/obo/CHEBI_16301"},{"id":"A451","pred":"chebi_id","subj":"T450","obj":"http://purl.obolibrary.org/obo/CHEBI_33101"},{"id":"A452","pred":"chebi_id","subj":"T452","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A453","pred":"chebi_id","subj":"T453","obj":"http://purl.obolibrary.org/obo/CHEBI_23116"},{"id":"A454","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_16301"},{"id":"A455","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_33101"},{"id":"A456","pred":"chebi_id","subj":"T456","obj":"http://purl.obolibrary.org/obo/CHEBI_16301"},{"id":"A457","pred":"chebi_id","subj":"T456","obj":"http://purl.obolibrary.org/obo/CHEBI_33101"},{"id":"A458","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_30396"},{"id":"A459","pred":"chebi_id","subj":"T459","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"},{"id":"A460","pred":"chebi_id","subj":"T460","obj":"http://purl.obolibrary.org/obo/CHEBI_33380"},{"id":"A461","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A462","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A463","pred":"chebi_id","subj":"T463","obj":"http://purl.obolibrary.org/obo/CHEBI_45453"},{"id":"A464","pred":"chebi_id","subj":"T464","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A465","pred":"chebi_id","subj":"T465","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A466","pred":"chebi_id","subj":"T466","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A467","pred":"chebi_id","subj":"T467","obj":"http://purl.obolibrary.org/obo/CHEBI_46756"},{"id":"A468","pred":"chebi_id","subj":"T468","obj":"http://purl.obolibrary.org/obo/CHEBI_26710"},{"id":"A469","pred":"chebi_id","subj":"T469","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A470","pred":"chebi_id","subj":"T470","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A471","pred":"chebi_id","subj":"T471","obj":"http://purl.obolibrary.org/obo/CHEBI_28262"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
2_test
{"project":"2_test","denotations":[{"id":"32563813-17853878-29105589","span":{"begin":245,"end":247},"obj":"17853878"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
LitCovid-sentences
{"project":"LitCovid-sentences","denotations":[{"id":"T184","span":{"begin":0,"end":48},"obj":"Sentence"},{"id":"T185","span":{"begin":49,"end":249},"obj":"Sentence"},{"id":"T186","span":{"begin":250,"end":462},"obj":"Sentence"},{"id":"T187","span":{"begin":463,"end":672},"obj":"Sentence"},{"id":"T188","span":{"begin":673,"end":888},"obj":"Sentence"},{"id":"T189","span":{"begin":889,"end":1023},"obj":"Sentence"},{"id":"T190","span":{"begin":1024,"end":1226},"obj":"Sentence"},{"id":"T191","span":{"begin":1227,"end":1548},"obj":"Sentence"},{"id":"T192","span":{"begin":1549,"end":1645},"obj":"Sentence"},{"id":"T193","span":{"begin":1646,"end":1851},"obj":"Sentence"},{"id":"T194","span":{"begin":1852,"end":1962},"obj":"Sentence"},{"id":"T195","span":{"begin":1963,"end":2168},"obj":"Sentence"},{"id":"T196","span":{"begin":2169,"end":2295},"obj":"Sentence"},{"id":"T197","span":{"begin":2296,"end":2429},"obj":"Sentence"},{"id":"T198","span":{"begin":2430,"end":2537},"obj":"Sentence"},{"id":"T199","span":{"begin":2538,"end":2738},"obj":"Sentence"},{"id":"T200","span":{"begin":2739,"end":2860},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}
MyTest
{"project":"MyTest","denotations":[{"id":"32563813-17853878-29105589","span":{"begin":245,"end":247},"obj":"17853878"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"2.5 Thermal shift DSF assays for SARS-CoV nsp14\nSARS-CoV nsp14-inhibitor interactions were further investigated by monitoring the thermal stability of the protein using differential scanning fluorimetry (DSF) (Supporting Information, Fig. S3) [34]. The change in thermal stability of SARS-CoV nsp14 was monitored in response to binding of the natural cofactor substrate SAM, sinefungin and the 9 most active and specific compounds 6 and 9–16 with IC50 \u003c 100 μM. As expected, SARS-CoV nsp14 displayed an increased melting temperature (T m) value with SAM (+6.5 °C) and sinefungin (+4.4 °C) whose structure only differs by a C–NH2 in place of S+-CH3 group in SAM (Fig. 2 ). The binding experiments with the bisubstrate inhibitors showed that all dinucleosides stabilized the SARS-CoV nsp14 protein (T m \u003e 40 °C) with a T m shift from +4.6 °C to +10.8 °C (Supporting Information, Table S1). Eight of the 9 examined compounds increased the stability of SARS-CoV nsp14 more efficiently than the well-known inhibitor sinefungin. More interestingly, T m values for SARS-CoV nsp14 were larger in the presence of five compounds 10 and 12–15 than with the natural enzyme substrate SAM, suggesting strong protein-inhibitor interactions. Remarkably, the highest T m was observed with the most efficient inhibitor 13 (IC50 0.6 ± 0.1 μM) that stabilizes SARS-CoV nsp14 against thermal denaturation with a ΔT m +10.8 °C and exhibits notable binding affinity (apparent KD 1.3 ± 0.87 μM), as deduced from TSA performed with increasing concentration of compound 13. This demonstrates a favorable interaction and highlights the inhibitor potential of compound 13. The T m comparison of compounds 16, 15 and 13 showed a respective increase in SARS-CoV nsp14 stability, settling the importance of the sulfone group, the Cl and NO2 substituents in protein binding with 13. Thus the N-(4-Cl-3-NO2-phenylsulfonamide) moiety is notably preferred for optimal SARS-CoV nsp14 interactions. Another highlight is the thermal shift (+5.4 °C) for SARS-CoV nsp14 observed in the presence of compound 10 compared to 11, both only differ by the position of OCH3 and NO2 substituents in the phenyl ring. A higher stability and inhibition of SARS-CoV nsp14 was observed when the OCH3 group is in “para” position in dinucleoside 10.\nFig. 2 Thermal shifts (ΔTm) of SARS-CoV nsp14 in the absence or presence of SAM, sinefungin and 9 dinucleoside inhibitors 6 and 9–16. Thermal stability of SARS-CoV nsp14 upon ligand binding was monitored by differential scanning fluorimetry. Assays were carried out in reaction mixture [20 mM HEPES (pH 7.5), 150 mM NaCl, 1x SYPRO orange dye] in the presence of 5 μM SARS-CoV nsp14 protein and 1 mM compound previously dissolved in 100% DMSO. The bars and error bars correspond to the mean values from three independent measurements and their s.d.’s, respectively."}