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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T50","span":{"begin":185,"end":192},"obj":"Body_part"},{"id":"T51","span":{"begin":204,"end":211},"obj":"Body_part"},{"id":"T52","span":{"begin":301,"end":309},"obj":"Body_part"},{"id":"T53","span":{"begin":323,"end":331},"obj":"Body_part"},{"id":"T54","span":{"begin":545,"end":553},"obj":"Body_part"},{"id":"T55","span":{"begin":684,"end":692},"obj":"Body_part"},{"id":"T56","span":{"begin":1101,"end":1108},"obj":"Body_part"},{"id":"T57","span":{"begin":1124,"end":1131},"obj":"Body_part"},{"id":"T58","span":{"begin":1210,"end":1218},"obj":"Body_part"},{"id":"T59","span":{"begin":1271,"end":1279},"obj":"Body_part"},{"id":"T60","span":{"begin":1507,"end":1515},"obj":"Body_part"}],"attributes":[{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A52","pred":"fma_id","subj":"T52","obj":"http://purl.org/sig/ont/fma/fma13478"},{"id":"A53","pred":"fma_id","subj":"T53","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A54","pred":"fma_id","subj":"T54","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A55","pred":"fma_id","subj":"T55","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"3.6.8. Principal component analysis (PCA)\nThe PCA is an essential technique to monitor the conformational dynamics of biomolecules. It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories. The diagonalization of the covariance matrix of backbone atoms of the proteins and ligand-bound form were considered for the principal components PC1 and PC2 (Figure 9). From Figure 9(a,b), it is observed that both the Spro-Piperine and Mpro-Piperine are less flexible as compared to unbound proteins since they covered less conformational space. It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.\nFigure 9. Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue). Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.\nThe principal components obtained were used as the reaction coordinates to find the Gibbs free energy landscape (Figure 9) to visualize the energy minima of the unbound protein as well as the protein–ligand complex. From Figure 9(c–f), it is observed that both the ligand-bound proteins have less Gibbs-free energy values than the unbound proteins indicating their stability and energetically favourable conformational transitions. The shape and size of the minimum energy area (blue colour) in case of RBD Spro-Piperine and Mpro-Piperine are more as compared to the unbound proteins RBD Spro and Mpro, which suggests the ligand-bound forms are thermodynamically more favourable.\nThe comprehensive study reveals that Piperine forms a stable complex with RBD Spro and Mpro and can be considered as an active inhibitor against SARS-CoV-2. From the docking results, it is observed that the Piperine molecule is the best candidate for the inhibition of the RBD Spro and the Mpro of SARS-CoV-2 among the selected 30 molecules. To observe the effectiveness of Piperine over currently used drugs, we carried out the docking study of a few drug molecules such as chloroquine, favipiravir, hydroxychloroquine, oseltamivir, remdesivir and ribavirin using the same docking protocol as followed for the 30 spice molecules. From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above. The lowest energy pose of a few presently used drugs with their 2D interaction diagram is provided in Supplementary Figures S5 and S6 corresponding to SARS-CoV-2 Mpro and RBD Spro, respectively. A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2. The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites. Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2. So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2. Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication. From the docking and MD results, we conclude that Piperine forms a very stable complex with RBD Spro and Mpro and shows better affinity as compared to the currently used drugs that are mentioned above against SARS-CoV-2."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T71","span":{"begin":399,"end":402},"obj":"Disease"},{"id":"T72","span":{"begin":407,"end":410},"obj":"Disease"},{"id":"T73","span":{"begin":1757,"end":1765},"obj":"Disease"},{"id":"T74","span":{"begin":1910,"end":1918},"obj":"Disease"},{"id":"T75","span":{"begin":2515,"end":2523},"obj":"Disease"},{"id":"T76","span":{"begin":3332,"end":3340},"obj":"Disease"}],"attributes":[{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0008173"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0008174"},{"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"}],"text":"3.6.8. Principal component analysis (PCA)\nThe PCA is an essential technique to monitor the conformational dynamics of biomolecules. It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories. The diagonalization of the covariance matrix of backbone atoms of the proteins and ligand-bound form were considered for the principal components PC1 and PC2 (Figure 9). From Figure 9(a,b), it is observed that both the Spro-Piperine and Mpro-Piperine are less flexible as compared to unbound proteins since they covered less conformational space. It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.\nFigure 9. Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue). Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.\nThe principal components obtained were used as the reaction coordinates to find the Gibbs free energy landscape (Figure 9) to visualize the energy minima of the unbound protein as well as the protein–ligand complex. From Figure 9(c–f), it is observed that both the ligand-bound proteins have less Gibbs-free energy values than the unbound proteins indicating their stability and energetically favourable conformational transitions. The shape and size of the minimum energy area (blue colour) in case of RBD Spro-Piperine and Mpro-Piperine are more as compared to the unbound proteins RBD Spro and Mpro, which suggests the ligand-bound forms are thermodynamically more favourable.\nThe comprehensive study reveals that Piperine forms a stable complex with RBD Spro and Mpro and can be considered as an active inhibitor against SARS-CoV-2. From the docking results, it is observed that the Piperine molecule is the best candidate for the inhibition of the RBD Spro and the Mpro of SARS-CoV-2 among the selected 30 molecules. To observe the effectiveness of Piperine over currently used drugs, we carried out the docking study of a few drug molecules such as chloroquine, favipiravir, hydroxychloroquine, oseltamivir, remdesivir and ribavirin using the same docking protocol as followed for the 30 spice molecules. From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above. The lowest energy pose of a few presently used drugs with their 2D interaction diagram is provided in Supplementary Figures S5 and S6 corresponding to SARS-CoV-2 Mpro and RBD Spro, respectively. A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2. The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites. Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2. So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2. Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication. From the docking and MD results, we conclude that Piperine forms a very stable complex with RBD Spro and Mpro and shows better affinity as compared to the currently used drugs that are mentioned above against SARS-CoV-2."}

LitCovid-PD-CLO

LitCovid-PubTator

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T25","span":{"begin":3104,"end":3121},"obj":"http://purl.obolibrary.org/obo/GO_0019079"},{"id":"T26","span":{"begin":3104,"end":3121},"obj":"http://purl.obolibrary.org/obo/GO_0019058"}],"text":"3.6.8. Principal component analysis (PCA)\nThe PCA is an essential technique to monitor the conformational dynamics of biomolecules. It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories. The diagonalization of the covariance matrix of backbone atoms of the proteins and ligand-bound form were considered for the principal components PC1 and PC2 (Figure 9). From Figure 9(a,b), it is observed that both the Spro-Piperine and Mpro-Piperine are less flexible as compared to unbound proteins since they covered less conformational space. It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.\nFigure 9. Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue). Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.\nThe principal components obtained were used as the reaction coordinates to find the Gibbs free energy landscape (Figure 9) to visualize the energy minima of the unbound protein as well as the protein–ligand complex. From Figure 9(c–f), it is observed that both the ligand-bound proteins have less Gibbs-free energy values than the unbound proteins indicating their stability and energetically favourable conformational transitions. The shape and size of the minimum energy area (blue colour) in case of RBD Spro-Piperine and Mpro-Piperine are more as compared to the unbound proteins RBD Spro and Mpro, which suggests the ligand-bound forms are thermodynamically more favourable.\nThe comprehensive study reveals that Piperine forms a stable complex with RBD Spro and Mpro and can be considered as an active inhibitor against SARS-CoV-2. From the docking results, it is observed that the Piperine molecule is the best candidate for the inhibition of the RBD Spro and the Mpro of SARS-CoV-2 among the selected 30 molecules. To observe the effectiveness of Piperine over currently used drugs, we carried out the docking study of a few drug molecules such as chloroquine, favipiravir, hydroxychloroquine, oseltamivir, remdesivir and ribavirin using the same docking protocol as followed for the 30 spice molecules. From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above. The lowest energy pose of a few presently used drugs with their 2D interaction diagram is provided in Supplementary Figures S5 and S6 corresponding to SARS-CoV-2 Mpro and RBD Spro, respectively. A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2. The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites. Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2. So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2. Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication. From the docking and MD results, we conclude that Piperine forms a very stable complex with RBD Spro and Mpro and shows better affinity as compared to the currently used drugs that are mentioned above against SARS-CoV-2."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T327","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T328","span":{"begin":8,"end":42},"obj":"Sentence"},{"id":"T329","span":{"begin":43,"end":132},"obj":"Sentence"},{"id":"T330","span":{"begin":133,"end":252},"obj":"Sentence"},{"id":"T331","span":{"begin":253,"end":422},"obj":"Sentence"},{"id":"T332","span":{"begin":423,"end":599},"obj":"Sentence"},{"id":"T333","span":{"begin":600,"end":693},"obj":"Sentence"},{"id":"T334","span":{"begin":694,"end":703},"obj":"Sentence"},{"id":"T335","span":{"begin":705,"end":829},"obj":"Sentence"},{"id":"T336","span":{"begin":830,"end":931},"obj":"Sentence"},{"id":"T337","span":{"begin":932,"end":1147},"obj":"Sentence"},{"id":"T338","span":{"begin":1148,"end":1363},"obj":"Sentence"},{"id":"T339","span":{"begin":1364,"end":1611},"obj":"Sentence"},{"id":"T340","span":{"begin":1612,"end":1768},"obj":"Sentence"},{"id":"T341","span":{"begin":1769,"end":1953},"obj":"Sentence"},{"id":"T342","span":{"begin":1954,"end":2242},"obj":"Sentence"},{"id":"T343","span":{"begin":2243,"end":2363},"obj":"Sentence"},{"id":"T344","span":{"begin":2364,"end":2558},"obj":"Sentence"},{"id":"T345","span":{"begin":2559,"end":2677},"obj":"Sentence"},{"id":"T346","span":{"begin":2678,"end":2803},"obj":"Sentence"},{"id":"T347","span":{"begin":2804,"end":2906},"obj":"Sentence"},{"id":"T348","span":{"begin":2907,"end":3017},"obj":"Sentence"},{"id":"T349","span":{"begin":3018,"end":3122},"obj":"Sentence"},{"id":"T350","span":{"begin":3123,"end":3343},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.6.8. Principal component analysis (PCA)\nThe PCA is an essential technique to monitor the conformational dynamics of biomolecules. It is useful in determining the concerted motion of protein as well as protein–ligand complex from the MD trajectories. The diagonalization of the covariance matrix of backbone atoms of the proteins and ligand-bound form were considered for the principal components PC1 and PC2 (Figure 9). From Figure 9(a,b), it is observed that both the Spro-Piperine and Mpro-Piperine are less flexible as compared to unbound proteins since they covered less conformational space. It concludes that the ligand-bound forms are more stable as compared to the unbound proteins.\nFigure 9. Principal component analysis of (a) RBD Spro (black), RBD Spro-Piperine (red) and (b) Mpro (black) and Mpro-Piperine (blue). Free energy landscape plot of (c) RBD Spro, (d) RBD Spro-Piperine and (e) Mpro and (f) Mpro-Piperine.\nThe principal components obtained were used as the reaction coordinates to find the Gibbs free energy landscape (Figure 9) to visualize the energy minima of the unbound protein as well as the protein–ligand complex. From Figure 9(c–f), it is observed that both the ligand-bound proteins have less Gibbs-free energy values than the unbound proteins indicating their stability and energetically favourable conformational transitions. The shape and size of the minimum energy area (blue colour) in case of RBD Spro-Piperine and Mpro-Piperine are more as compared to the unbound proteins RBD Spro and Mpro, which suggests the ligand-bound forms are thermodynamically more favourable.\nThe comprehensive study reveals that Piperine forms a stable complex with RBD Spro and Mpro and can be considered as an active inhibitor against SARS-CoV-2. From the docking results, it is observed that the Piperine molecule is the best candidate for the inhibition of the RBD Spro and the Mpro of SARS-CoV-2 among the selected 30 molecules. To observe the effectiveness of Piperine over currently used drugs, we carried out the docking study of a few drug molecules such as chloroquine, favipiravir, hydroxychloroquine, oseltamivir, remdesivir and ribavirin using the same docking protocol as followed for the 30 spice molecules. From the docking score, it is found that Piperine performed better as compared to the currently used drugs stated above. The lowest energy pose of a few presently used drugs with their 2D interaction diagram is provided in Supplementary Figures S5 and S6 corresponding to SARS-CoV-2 Mpro and RBD Spro, respectively. A comparison of the lowest energy dock scores of these drug molecules along with Piperine is also provided in Table 2. The MD simulation results reveal that Piperine actively inhibits both the RBD Spro and Mpro by binding to their active sites. Piperine binds on the active site of the RBD Spro with those residues by which it interacts with ACE2. So, the binding of Piperine on that site may potentially cease the interaction tendency of RBD Spro with ACE2. Similarly, the interaction of Piperine on the active site of the Mpro may inhibit its viral replication. From the docking and MD results, we conclude that Piperine forms a very stable complex with RBD Spro and Mpro and shows better affinity as compared to the currently used drugs that are mentioned above against SARS-CoV-2."}