PMC:7571312 / 121054-122470 JSONTXT

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T99","span":{"begin":58,"end":62},"obj":"Disease"},{"id":"T100","span":{"begin":159,"end":163},"obj":"Disease"},{"id":"T101","span":{"begin":220,"end":224},"obj":"Disease"},{"id":"T102","span":{"begin":654,"end":658},"obj":"Disease"},{"id":"T103","span":{"begin":857,"end":861},"obj":"Disease"}],"attributes":[{"id":"A99","pred":"mondo_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A100","pred":"mondo_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A101","pred":"mondo_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A102","pred":"mondo_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A103","pred":"mondo_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T96","span":{"begin":16,"end":24},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T97","span":{"begin":89,"end":90},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T98","span":{"begin":196,"end":204},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T99","span":{"begin":254,"end":255},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T100","span":{"begin":288,"end":295},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T101","span":{"begin":364,"end":365},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T102","span":{"begin":376,"end":383},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T103","span":{"begin":425,"end":432},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T104","span":{"begin":487,"end":488},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T105","span":{"begin":524,"end":525},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T106","span":{"begin":556,"end":563},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T107","span":{"begin":582,"end":588},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T108","span":{"begin":632,"end":633},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T109","span":{"begin":779,"end":786},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T110","span":{"begin":947,"end":955},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T111","span":{"begin":1037,"end":1045},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T112","span":{"begin":1051,"end":1052},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T113","span":{"begin":1090,"end":1098},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T114","span":{"begin":1134,"end":1135},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T115","span":{"begin":1386,"end":1394},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"}],"text":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T70486","span":{"begin":288,"end":295},"obj":"Chemical"},{"id":"T36781","span":{"begin":376,"end":383},"obj":"Chemical"},{"id":"T53887","span":{"begin":425,"end":432},"obj":"Chemical"},{"id":"T22935","span":{"begin":619,"end":621},"obj":"Chemical"},{"id":"T29474","span":{"begin":641,"end":650},"obj":"Chemical"},{"id":"T14079","span":{"begin":692,"end":698},"obj":"Chemical"},{"id":"T17562","span":{"begin":715,"end":719},"obj":"Chemical"},{"id":"T5538","span":{"begin":720,"end":723},"obj":"Chemical"},{"id":"T32012","span":{"begin":741,"end":745},"obj":"Chemical"},{"id":"T47682","span":{"begin":752,"end":756},"obj":"Chemical"},{"id":"T12616","span":{"begin":763,"end":767},"obj":"Chemical"},{"id":"T32778","span":{"begin":779,"end":786},"obj":"Chemical"},{"id":"T46679","span":{"begin":1395,"end":1399},"obj":"Chemical"}],"attributes":[{"id":"A71226","pred":"chebi_id","subj":"T70486","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A82127","pred":"chebi_id","subj":"T36781","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A51897","pred":"chebi_id","subj":"T53887","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A89930","pred":"chebi_id","subj":"T22935","obj":"http://purl.obolibrary.org/obo/CHEBI_74795"},{"id":"A61387","pred":"chebi_id","subj":"T22935","obj":"http://purl.obolibrary.org/obo/CHEBI_90284"},{"id":"A15460","pred":"chebi_id","subj":"T29474","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A45555","pred":"chebi_id","subj":"T14079","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A20365","pred":"chebi_id","subj":"T17562","obj":"http://purl.obolibrary.org/obo/CHEBI_9754"},{"id":"A27860","pred":"chebi_id","subj":"T5538","obj":"http://purl.obolibrary.org/obo/CHEBI_17883"},{"id":"A56739","pred":"chebi_id","subj":"T32012","obj":"http://purl.obolibrary.org/obo/CHEBI_26710"},{"id":"A31507","pred":"chebi_id","subj":"T47682","obj":"http://purl.obolibrary.org/obo/CHEBI_42191"},{"id":"A73480","pred":"chebi_id","subj":"T47682","obj":"http://purl.obolibrary.org/obo/CHEBI_64755"},{"id":"A43129","pred":"chebi_id","subj":"T12616","obj":"http://purl.obolibrary.org/obo/CHEBI_63213"},{"id":"A37237","pred":"chebi_id","subj":"T32778","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A64922","pred":"chebi_id","subj":"T46679","obj":"http://purl.obolibrary.org/obo/CHEBI_18282"},{"id":"A19021","pred":"chebi_id","subj":"T46679","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"}],"text":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T652","span":{"begin":0,"end":154},"obj":"Sentence"},{"id":"T653","span":{"begin":155,"end":565},"obj":"Sentence"},{"id":"T654","span":{"begin":566,"end":672},"obj":"Sentence"},{"id":"T655","span":{"begin":673,"end":797},"obj":"Sentence"},{"id":"T656","span":{"begin":798,"end":924},"obj":"Sentence"},{"id":"T657","span":{"begin":925,"end":1100},"obj":"Sentence"},{"id":"T658","span":{"begin":1101,"end":1189},"obj":"Sentence"},{"id":"T659","span":{"begin":1190,"end":1416},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2119","span":{"begin":58,"end":68},"obj":"Species"},{"id":"2120","span":{"begin":159,"end":169},"obj":"Species"},{"id":"2121","span":{"begin":220,"end":230},"obj":"Species"},{"id":"2122","span":{"begin":654,"end":664},"obj":"Species"},{"id":"2123","span":{"begin":857,"end":867},"obj":"Species"},{"id":"2124","span":{"begin":715,"end":723},"obj":"Chemical"},{"id":"2125","span":{"begin":741,"end":745},"obj":"Chemical"},{"id":"2126","span":{"begin":752,"end":756},"obj":"Chemical"},{"id":"2127","span":{"begin":763,"end":767},"obj":"Chemical"}],"attributes":[{"id":"A2119","pred":"tao:has_database_id","subj":"2119","obj":"Tax:2697049"},{"id":"A2120","pred":"tao:has_database_id","subj":"2120","obj":"Tax:2697049"},{"id":"A2121","pred":"tao:has_database_id","subj":"2121","obj":"Tax:2697049"},{"id":"A2122","pred":"tao:has_database_id","subj":"2122","obj":"Tax:2697049"},{"id":"A2123","pred":"tao:has_database_id","subj":"2123","obj":"Tax:2697049"},{"id":"A2125","pred":"tao:has_database_id","subj":"2125","obj":"MESH:D012965"},{"id":"A2126","pred":"tao:has_database_id","subj":"2126","obj":"MESH:D004492"},{"id":"A2127","pred":"tao:has_database_id","subj":"2127","obj":"MESH:C080938"}],"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":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}

{"project":"2_test","denotations":[{"id":"33054210-17397958-61913461","span":{"begin":384,"end":386},"obj":"17397958"}],"text":"The proteolytic activity of the main protease, 3CLpro, of SARS CoV-2 was monitored using a continuous fluorescence resonance energy-transfer (FRET) assay. The SARS CoV-2 3CLpro assay measures the activity of full-length SARS CoV-2 3CL protease to cleave a synthetic fluorogenic substrate peptide with the following sequence DABCYL-KTSAVLQ-SGFRKME-EDANS modeled on a consensus peptide.50 The fluorescence of the cleaved EDANS peptide (excitation 340 nm/emission 490 nm) is measured using a fluorescence intensity protocol on a Flexstation reader (Molecular Devices). The fluorescent signal is reduced in the presence of PF-00835231, a potent inhibitor of SARS CoV-2 3CLpro. The assay reaction buffer contained 20 mM Tris–HCl (pH 7.3), 100 nM NaCl, 1 mM EDTA, 5 mM TCEP, and 25 μM peptide substrate. Enzyme reactions were initiated with the addition of 15 nM SARS CoV-2 3CL protease and allowed to proceed for 60 min at 23 °C. Percent inhibition or activity was calculated based on control wells containing no compound (0% inhibition/100% activity) and a control compound (100% inhibition/0% activity). IC50 values were generated using a four-parameter fit model using ABASE software (IDBS). Ki values were fit to the Morrison equation with the enzyme concentration parameter fixed to 15 nM, the Km parameter fixed to 14 μM, and the substrate concentration parameter fixed to 25 μM using Activity Base software (IDBS)."}