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LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T43","span":{"begin":503,"end":507},"obj":"Body_part"},{"id":"T44","span":{"begin":811,"end":816},"obj":"Body_part"},{"id":"T45","span":{"begin":817,"end":829},"obj":"Body_part"},{"id":"T46","span":{"begin":822,"end":829},"obj":"Body_part"},{"id":"T47","span":{"begin":831,"end":837},"obj":"Body_part"},{"id":"T48","span":{"begin":3925,"end":3929},"obj":"Body_part"},{"id":"T49","span":{"begin":4903,"end":4907},"obj":"Body_part"},{"id":"T50","span":{"begin":6478,"end":6483},"obj":"Body_part"},{"id":"T51","span":{"begin":6488,"end":6494},"obj":"Body_part"}],"attributes":[{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A44","pred":"uberon_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"A45","pred":"uberon_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/UBERON_0002110"},{"id":"A46","pred":"uberon_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/UBERON_0001255"},{"id":"A47","pred":"uberon_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"A48","pred":"uberon_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A49","pred":"uberon_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A50","pred":"uberon_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"A51","pred":"uberon_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/UBERON_0002106"}],"text":"Discussion\nIn order to come up with the medications to manage SARS-CoV-2 infections, it is important to understand the virus-receptor recognition mechanisms. WHO has declared COVID-19 as a global pandemic and no drug or antiviral treatment has yet been formulated to combat the disease. Hence, repurposing drugs available for other diseases could be a potential treatment strategy against SARS-CoV-2 and can be processed further for COVID-19 trials (Rosa \u0026 Santos, 2020) . SARS-CoV-2 is known to affect lung alveolar epithelial cells via the angiotensin-converting enzyme II (ACE2) as an entry receptor, using receptor-mediated endocytosis. ACE2 (Angiotensin converting enzyme 2) is an important player in mediating the viral entry into the host cell. ACE2 is expressed in GI tract, endocrine tissues, kidneys, liver/gall bladder, testis and to smaller extents in lungs and is known to regulate cardiovascular functions, renal functions, and fertility. The newly conferred function for ACE2 is, it being a receptor for the S-protein i.e. spikes glycoprotein of all the human coronavirus such as SARS-CoV, HCoV-NL63 and SARS-CoV-2 (COVID-19 virus). The Receptor Binding Domain (RBD) of spike proteins and ACE2 receptors come in direct contact and initiate fusion with cell membrane (Kim, 2020; Robson, 2020). Since this interaction is essential for SARS-CoV-2 entry into the host cell and infection, this S-RBD–ACE2 interface can be the main target for vaccine developers (Shang et al., 2020). Also, most importantly the next proteins in the signaling pathway after attachment of S-RBD-ACE2 will decide the fate of the infection and severity in body. The information about disturbed signaling pathways in COVID-19 is of utmost importance as this can guide the route and treatment plans. It is well known that attachment of virus to the receptor protein releases signals which help the virus to replicate and spread in body. Therefore, a protein interaction network was sketched around ACE2 to decipher the pathways which will be impacted instantly when virus will attach to ACE2.\nIn the present study cytoscape was used to visualise and analyse the main interacting partners of ACE2. A PPI master network was created around ACE2 and they key first line and second line receptors were identified. In addition, BiNGO analysis of the hub nodes was performed to determine the Gene Ontology categories which are statistically overrepresented in a set of obtained proteins to decipher the major molecular processes affected when ACE2 binds to the human receptors and when all the genes obtained in our network map interact with each-other. The top ten obtained hub nodes were ACE2, INS, AKT1, VEGFA, IL6, ALB, ACE, AGT, Renin and KNG1. IL-6 is a pro-inflammatory cytokine and is suggested to be associated with SARS severity (Zhang et al., 2004). IL-6 is being used as a potential biomarker whose measurements seem as a reliable measure to diagnose COVID-19. IL6 is also involved in host defence against bacteria related inflammation diseases (Narazaki \u0026 Kishimoto, 2018). In diseases, the IL-6 inhibitory strategy begins with the development of the anti-IL-6 receptor antibody, tocilizumab (TCZ). Clinical trials for Intravenous Tocilizumab for severe COVID-19 pneumonia are underway. TCZ therapy is being given to prevent/treat the cytokine storms emerged as an outcome of severe COVID-9 infections due to sharp rise in IL-6 levels. In moderately and critically ill patients, repeated TCZ therapy seems beneficial (Luo et al., 2020). Cytokine-mediated signaling pathways, which also have a key role in SARS-CoV-1 infection, are the most dysregulated pathways in early SARS-CoV-2 infection (Catanzaro et al., 2020). The change in cytokines’ expression (i.e. IL6, IL8, IL17, CCL2) are indicative of pro-inflammation in early stages of SARS-CoV-2 infection. A moderate exposure to hypoxia combined with viral infection increases the lung VEGF levels. This increase is mediated by an elevation in the levels of Endothelin (ET) which further induces HIF1A mRNA expression. High VEGF expression allows the pulmonary vascular albumin extravasation which leads to the vascular permeability (Carpenter et al., 2005;Hicklin et al., 2005). HIF1A along with AKT1 are indicated to be upregulated by viral entry mediated by endocytosis, import/export and translation of viral mRNA which is fundamental for their multiplication (Cava et al., 2020). HIF1A activators may be used for relieving the symptoms of SARS-CoV-2 as it is responsible for the upregulation of glycolytic genes like phosphoglycerate kinase (PGK) and lactate dehydrogenase A (LDHA) under hypoxic conditions which help the tissues to adapt to oxygen deprived conditions and resort to anaerobic ATP formation (Hu et al., 2003; Lee et al., 2019). Oxidative stress induces AkT inactivation which eventually reduces HIF1A and VEGFA levels in the body causing lung impairment (Lee et al., 2019). Hence, compounds with Akt activating properties can be used to alleviate oxygen tension and improve the symptoms of SARS-CoV-2. BiNGO analysis of cytoscape generated protein networks helped to understand the role of major hub nodes in understanding the pathology of SARS-CoV-2 and hence could be used as druggable targets for the treatment of SARS-CoV-2.\nTo date, a lot of therapeutic benefits of N. sativa are known and it has been shown to be effective against a wide range of illnesses like neurologic disorders, Diabetes Mellitus, hypertension, dyslipidemia, inflammatory disorders, cancer, etc. (chronic non-infectious diseases) and bacterial, fungal, viral, and parasitic infections (infectious disease) (Yimer et al., 2019; Adamska et al., 2019). Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2, 5-diene-1, 4-dione) is a major bioactive constituent of N. sativa. It has anti-inflammatory effects besides providing protection against gastrointestinal problems, bronchial headache, asthma, and dysentery (Khader \u0026 Eckl, 2014). It possesses anti-inflammatory properties as it inhibits thromboxane B2 and leukotriene, the oxidative products of arachidonic acid by blocking the activity of cyclooxygenase and lipoxygenase enzymes (Majdalawieh \u0026 Fayyad, 2015; Chung et al., 2020). Therefore, controlling the overexpression of cytokines may help in managing the SARS-CoV-2 infection. In a study by Salem and Hossain (2000), N. sativa seed oil was found to suppress viral load caused by cytomegalovirus in mice to untraceable levels in the liver and spleen within a span of 10 days of intraperitoneal administration. This may be attributed to the increase in expression of CD-T cells and interferon- (INF-) gamma. Mu et al., 2015, reported that Thymoquinone acts as a potent chemosensitizer and apoptotic agent via downregulation of the PI3K/Akt/mTOR activation. A gradual decline in the downstream effector S6 ribosomal protein which is linked to the chemoresistance of human malignancies to standard anticancer drugs was also reported by them (Fruman et al., 2017). As in SARS-CoV-2 infection an over expression of PI3K/Akt/mTOR signaling is reported therefore intervention of N.sativa may prove useful against SARS-CoV-2.\nTo study the effectiveness of N.sativa against SARS-CoV-2, protein interactions studies were carried out for receptors predicted via swiss target prediction for this plant’s bioactive constituents, to understand their beneficial effect on SARS-CoV-2 in humans. Through literature search, the chemical constituents of N. sativa were retrieved and were allowed to undergo an ADME analysis. Through ADME studies false-positive compounds can easily be predicted and hence, can be excluded. It helps in determining the properties like absorption distribution, metabolism, excretion and toxicity of drug molecules, thereby, reduces the screening cost and also increases the rate of success of drug designing. In the current study ADME analysis was carried out as a preliminary test to find out whether the proposed drug candidate will work satisfactorily in the clinical trials or not, based on a thorough analysis (Liu et al., 2007). To find the binding receptors of the retrieved Nigella constituents inside the human body, Swiss target prediction tool was used. To understand which N.sativa constituent has the finest binding affinity (ΔG; Gibbs free energy) with the receptors present in human system molecular docking analysis was performed and also to determine the predominant binding mode(s) of a ligand with a purposed protein (ACE2). The most suitable binding ligand to ACE2 was found to be α-hederin (-6.265 kcal/mol), Thymohydroquinone (-5.466 kcal/mol) and Thymoquinone (-5.048 kcal/mol). Since ACE2 is the entry site of virus in the human system, the N. sativa bioactive constituents were taken further for a docking study. The receptor chosen was ACE2 (PDB ID: 1R4L). LigPrep v3.1 was used to prepare all the ligands. All the possible stereoisomers of all compounds were prepared, and their energy was minimized before docking. ACE2 was found to bind to the components- α-hederin and Thymohydroquinone with good binding energies. Hence, these 2 components of Nigella can be exploited therapeutically.\nThe chemo-proteomic analysis that emerges from this study not only highlights clinically actionable human proteins in the interactome, but also provides a context for interpreting their mechanism of action. This is the first study that has interpreted the role played by several proteins like ACE2, INS, AKT1, VEGFA, IL6, ALB, ACE, AGT, Renin, KNG1 etc. in the progression of SARS-CoV-2 pathology through cytoscape and BiNGO plugin. Therapeutically targeting these proteins can reveal the wide scope for designing the treatment against the disease so that to stop its progression at an early stage. Isolation of bioactive components of N.sativa and its oil and confirmatory clinical studies of their pharmacological effects are further recommended as the results obtained through swiss target prediction and docking studies are in favour of its use in SARS-CoV-2 pathology."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T41","span":{"begin":3255,"end":3264},"obj":"Phenotype"},{"id":"T42","span":{"begin":3327,"end":3342},"obj":"Phenotype"},{"id":"T43","span":{"begin":3873,"end":3880},"obj":"Phenotype"},{"id":"T44","span":{"begin":4793,"end":4809},"obj":"Phenotype"},{"id":"T45","span":{"begin":5455,"end":5472},"obj":"Phenotype"},{"id":"T46","span":{"begin":5474,"end":5486},"obj":"Phenotype"},{"id":"T47","span":{"begin":5488,"end":5500},"obj":"Phenotype"},{"id":"T48","span":{"begin":5526,"end":5532},"obj":"Phenotype"},{"id":"T49","span":{"begin":5916,"end":5924},"obj":"Phenotype"},{"id":"T50","span":{"begin":5926,"end":5932},"obj":"Phenotype"}],"attributes":[{"id":"A41","pred":"hp_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A42","pred":"hp_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/HP_0033041"},{"id":"A43","pred":"hp_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/HP_0012418"},{"id":"A44","pred":"hp_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/HP_0025464"},{"id":"A45","pred":"hp_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/HP_0000819"},{"id":"A46","pred":"hp_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A47","pred":"hp_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/HP_0003119"},{"id":"A48","pred":"hp_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/HP_0002664"},{"id":"A49","pred":"hp_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/HP_0002315"},{"id":"A50","pred":"hp_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/HP_0002099"}],"text":"Discussion\nIn order to come up with the medications to manage SARS-CoV-2 infections, it is important to understand the virus-receptor recognition mechanisms. WHO has declared COVID-19 as a global pandemic and no drug or antiviral treatment has yet been formulated to combat the disease. Hence, repurposing drugs available for other diseases could be a potential treatment strategy against SARS-CoV-2 and can be processed further for COVID-19 trials (Rosa \u0026 Santos, 2020) . SARS-CoV-2 is known to affect lung alveolar epithelial cells via the angiotensin-converting enzyme II (ACE2) as an entry receptor, using receptor-mediated endocytosis. ACE2 (Angiotensin converting enzyme 2) is an important player in mediating the viral entry into the host cell. ACE2 is expressed in GI tract, endocrine tissues, kidneys, liver/gall bladder, testis and to smaller extents in lungs and is known to regulate cardiovascular functions, renal functions, and fertility. The newly conferred function for ACE2 is, it being a receptor for the S-protein i.e. spikes glycoprotein of all the human coronavirus such as SARS-CoV, HCoV-NL63 and SARS-CoV-2 (COVID-19 virus). The Receptor Binding Domain (RBD) of spike proteins and ACE2 receptors come in direct contact and initiate fusion with cell membrane (Kim, 2020; Robson, 2020). Since this interaction is essential for SARS-CoV-2 entry into the host cell and infection, this S-RBD–ACE2 interface can be the main target for vaccine developers (Shang et al., 2020). Also, most importantly the next proteins in the signaling pathway after attachment of S-RBD-ACE2 will decide the fate of the infection and severity in body. The information about disturbed signaling pathways in COVID-19 is of utmost importance as this can guide the route and treatment plans. It is well known that attachment of virus to the receptor protein releases signals which help the virus to replicate and spread in body. Therefore, a protein interaction network was sketched around ACE2 to decipher the pathways which will be impacted instantly when virus will attach to ACE2.\nIn the present study cytoscape was used to visualise and analyse the main interacting partners of ACE2. A PPI master network was created around ACE2 and they key first line and second line receptors were identified. In addition, BiNGO analysis of the hub nodes was performed to determine the Gene Ontology categories which are statistically overrepresented in a set of obtained proteins to decipher the major molecular processes affected when ACE2 binds to the human receptors and when all the genes obtained in our network map interact with each-other. The top ten obtained hub nodes were ACE2, INS, AKT1, VEGFA, IL6, ALB, ACE, AGT, Renin and KNG1. IL-6 is a pro-inflammatory cytokine and is suggested to be associated with SARS severity (Zhang et al., 2004). IL-6 is being used as a potential biomarker whose measurements seem as a reliable measure to diagnose COVID-19. IL6 is also involved in host defence against bacteria related inflammation diseases (Narazaki \u0026 Kishimoto, 2018). In diseases, the IL-6 inhibitory strategy begins with the development of the anti-IL-6 receptor antibody, tocilizumab (TCZ). Clinical trials for Intravenous Tocilizumab for severe COVID-19 pneumonia are underway. TCZ therapy is being given to prevent/treat the cytokine storms emerged as an outcome of severe COVID-9 infections due to sharp rise in IL-6 levels. In moderately and critically ill patients, repeated TCZ therapy seems beneficial (Luo et al., 2020). Cytokine-mediated signaling pathways, which also have a key role in SARS-CoV-1 infection, are the most dysregulated pathways in early SARS-CoV-2 infection (Catanzaro et al., 2020). The change in cytokines’ expression (i.e. IL6, IL8, IL17, CCL2) are indicative of pro-inflammation in early stages of SARS-CoV-2 infection. A moderate exposure to hypoxia combined with viral infection increases the lung VEGF levels. This increase is mediated by an elevation in the levels of Endothelin (ET) which further induces HIF1A mRNA expression. High VEGF expression allows the pulmonary vascular albumin extravasation which leads to the vascular permeability (Carpenter et al., 2005;Hicklin et al., 2005). HIF1A along with AKT1 are indicated to be upregulated by viral entry mediated by endocytosis, import/export and translation of viral mRNA which is fundamental for their multiplication (Cava et al., 2020). HIF1A activators may be used for relieving the symptoms of SARS-CoV-2 as it is responsible for the upregulation of glycolytic genes like phosphoglycerate kinase (PGK) and lactate dehydrogenase A (LDHA) under hypoxic conditions which help the tissues to adapt to oxygen deprived conditions and resort to anaerobic ATP formation (Hu et al., 2003; Lee et al., 2019). Oxidative stress induces AkT inactivation which eventually reduces HIF1A and VEGFA levels in the body causing lung impairment (Lee et al., 2019). Hence, compounds with Akt activating properties can be used to alleviate oxygen tension and improve the symptoms of SARS-CoV-2. BiNGO analysis of cytoscape generated protein networks helped to understand the role of major hub nodes in understanding the pathology of SARS-CoV-2 and hence could be used as druggable targets for the treatment of SARS-CoV-2.\nTo date, a lot of therapeutic benefits of N. sativa are known and it has been shown to be effective against a wide range of illnesses like neurologic disorders, Diabetes Mellitus, hypertension, dyslipidemia, inflammatory disorders, cancer, etc. (chronic non-infectious diseases) and bacterial, fungal, viral, and parasitic infections (infectious disease) (Yimer et al., 2019; Adamska et al., 2019). Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2, 5-diene-1, 4-dione) is a major bioactive constituent of N. sativa. It has anti-inflammatory effects besides providing protection against gastrointestinal problems, bronchial headache, asthma, and dysentery (Khader \u0026 Eckl, 2014). It possesses anti-inflammatory properties as it inhibits thromboxane B2 and leukotriene, the oxidative products of arachidonic acid by blocking the activity of cyclooxygenase and lipoxygenase enzymes (Majdalawieh \u0026 Fayyad, 2015; Chung et al., 2020). Therefore, controlling the overexpression of cytokines may help in managing the SARS-CoV-2 infection. In a study by Salem and Hossain (2000), N. sativa seed oil was found to suppress viral load caused by cytomegalovirus in mice to untraceable levels in the liver and spleen within a span of 10 days of intraperitoneal administration. This may be attributed to the increase in expression of CD-T cells and interferon- (INF-) gamma. Mu et al., 2015, reported that Thymoquinone acts as a potent chemosensitizer and apoptotic agent via downregulation of the PI3K/Akt/mTOR activation. A gradual decline in the downstream effector S6 ribosomal protein which is linked to the chemoresistance of human malignancies to standard anticancer drugs was also reported by them (Fruman et al., 2017). As in SARS-CoV-2 infection an over expression of PI3K/Akt/mTOR signaling is reported therefore intervention of N.sativa may prove useful against SARS-CoV-2.\nTo study the effectiveness of N.sativa against SARS-CoV-2, protein interactions studies were carried out for receptors predicted via swiss target prediction for this plant’s bioactive constituents, to understand their beneficial effect on SARS-CoV-2 in humans. Through literature search, the chemical constituents of N. sativa were retrieved and were allowed to undergo an ADME analysis. Through ADME studies false-positive compounds can easily be predicted and hence, can be excluded. It helps in determining the properties like absorption distribution, metabolism, excretion and toxicity of drug molecules, thereby, reduces the screening cost and also increases the rate of success of drug designing. In the current study ADME analysis was carried out as a preliminary test to find out whether the proposed drug candidate will work satisfactorily in the clinical trials or not, based on a thorough analysis (Liu et al., 2007). To find the binding receptors of the retrieved Nigella constituents inside the human body, Swiss target prediction tool was used. To understand which N.sativa constituent has the finest binding affinity (ΔG; Gibbs free energy) with the receptors present in human system molecular docking analysis was performed and also to determine the predominant binding mode(s) of a ligand with a purposed protein (ACE2). The most suitable binding ligand to ACE2 was found to be α-hederin (-6.265 kcal/mol), Thymohydroquinone (-5.466 kcal/mol) and Thymoquinone (-5.048 kcal/mol). Since ACE2 is the entry site of virus in the human system, the N. sativa bioactive constituents were taken further for a docking study. The receptor chosen was ACE2 (PDB ID: 1R4L). LigPrep v3.1 was used to prepare all the ligands. All the possible stereoisomers of all compounds were prepared, and their energy was minimized before docking. ACE2 was found to bind to the components- α-hederin and Thymohydroquinone with good binding energies. Hence, these 2 components of Nigella can be exploited therapeutically.\nThe chemo-proteomic analysis that emerges from this study not only highlights clinically actionable human proteins in the interactome, but also provides a context for interpreting their mechanism of action. This is the first study that has interpreted the role played by several proteins like ACE2, INS, AKT1, VEGFA, IL6, ALB, ACE, AGT, Renin, KNG1 etc. in the progression of SARS-CoV-2 pathology through cytoscape and BiNGO plugin. Therapeutically targeting these proteins can reveal the wide scope for designing the treatment against the disease so that to stop its progression at an early stage. Isolation of bioactive components of N.sativa and its oil and confirmatory clinical studies of their pharmacological effects are further recommended as the results obtained through swiss target prediction and docking studies are in favour of its use in SARS-CoV-2 pathology."}

LitCovid-PubTator

PMC:7605643 / 33350-43396 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7605643 / 33350-43396 JSON TXT