Identification of potential hits against novel coronavirus-targeting glycoprotein for multi-target approach

Coronavirus disease (COVID-19) is an infectious disease caused by a novel coronavirus impacting more than 75 million people across 220 countries. The pharma and biotech industries, along with research institutes, strive to develop an effective vaccine against the novel coronavirus. Efforts are also underway for finding drugs through drug repurposing and novel drug discovery methods. In this study, we have used a multi-target drug approach. The objective is to identify phytochemicals from plant sources effective against novel coronavirus. Natural products having good medicinal properties are known to have minimal side effects compared to synthetic drugs. Therefore, the medicinal products from natural sources are of significance in drug discovery research. In this study, compounds from three common plants were selected for analysis, namely, Tinospora cordifolia, Withania somnifera, and Punica granatum. The primary target selected for this study was glycoprotein. Glycoproteins are known to play a key role in the regulation of cell proliferation, growth, and signaling pathways. We also investigated the effect of screened compounds on other targets in order to have a multi-target therapy. The target proteins chosen for drug design are Spike glycoprotein, Main Protease, and uridylate-specific Endoribonuclease (EndoU). The spike glycoprotein (S) of coronavirus, is a trimeric transmembrane protein, which facilitates entry into cells and is the main target of antibodies. The spike glycoprotein is highly sensitive to mutation. The main protease (MPro) of SRAS-CoV-2 plays an essential role in disease propagation by processing the polyproteins necessary for its replication. Inhibiting the main protease by designing agonists/antagonists can serve in the repair mechanism—the uridylate-specific Endoribonuclease (EndoU) of SRAS-CoV-2 causes a delay in the host sensor system. The objective of this study was to identify potential natural hit compounds which could target multiple proteins of coronavirus. Compounds that can target all the three, namely, Spike glycoprotein, EndoU, and MPro will have better therapeutic index and efficacy than a single target approach. Therefore, the compounds were screened against all these three structural targets. The compounds targeting only one of the proteins were filtered and only those compounds showing activity against all the three structural proteins were retained for further analysis. Drug design methods, including Absorption, Distribution, Metabolism and Elimination (ADME) profiling and molecular docking studies, have been used in the study to identify potential hit molecules. The twenty four hits obtained targeted all the three selected proteins. This will pave the way for developing lead molecules from the screened compounds effective against all three proteins of novel coronavirus: Main protease, Spike glycoprotein, and Endoribonuclease. © 2021, Trends In Carbohydrate Research. All rights reserved.

Identification of potential hits against novel coronavirus-targeting glycoprotein for multi-target approach

Coronavirus disease (COVID-19) is an infectious disease caused by a novel coronavirus impacting more than 75 million people across 220 countries. The pharma and biotech industries, along with research institutes, strive to develop an effective vaccine against the novel coronavirus. Efforts are also underway for finding drugs through drug repurposing and novel drug discovery methods. In this study, we have used a multi-target drug approach. The objective is to identify phytochemicals from plant sources effective against novel coronavirus. Natural products having good medicinal properties are known to have minimal side effects compared to synthetic drugs. Therefore, the medicinal products from natural sources are of significance in drug discovery research. In this study, compounds from three common plants were selected for analysis, namely, Tinospora cordifolia, Withania somnifera, and Punica granatum. The primary target selected for this study was glycoprotein. Glycoproteins are known to play a key role in the regulation of cell proliferation, growth, and signaling pathways. We also investigated the effect of screened compounds on other targets in order to have a multi-target therapy. The target proteins chosen for drug design are Spike glycoprotein, Main Protease, and uridylate-specific Endoribonuclease (EndoU). The spike glycoprotein (S) of coronavirus, is a trimeric transmembrane protein, which facilitates entry into cells and is the main target of antibodies. The spike glycoprotein is highly sensitive to mutation. The main protease (MPro) of SRAS-CoV-2 plays an essential role in disease propagation by processing the polyproteins necessary for its replication. Inhibiting the main protease by designing agonists/antagonists can serve in the repair mechanism-the uridylate-specific Endoribonuclease (EndoU) of SRAS-CoV-2 causes a delay in the host sensor system. The objective of this study was to identify potential natural hit compounds which could target multiple proteins of coronavirus. Compounds that can target all the three, namely, Spike glycoprotein, EndoU, and MPro will have better therapeutic index and efficacy than a single target approach. Therefore, the compounds were screened against all these three structural targets. The compounds targeting only one of the proteins were filtered and only those compounds showing activity against all the three structural proteins were retained for further analysis. Drug design methods, including Absorption, Distribution, Metabolism and Elimination (ADME) profiling and molecular docking studies, have been used in the study to identify potential hit molecules. The twenty four hits obtained targeted all the three selected proteins. This will pave the way for developing lead molecules from the screened compounds effective against all three proteins of novel coronavirus: Main protease, Spike glycoprotein, and Endoribonuclease.

Plasma SCD14-ST, but not SCD14, is inversely associated with risk for SARSCoV2 positivity and positively associated with COVID-19-related respiratory failure in critically ill patients admitted under suspicion for COVID-19

Intro: Early innate immune responses are hypothesized to impact inflammation and therefore severity of disease and organ injury in COVID-19. Prior work in sepsis has identified CD14 as a marker of innate immune responses to bacterial infection and emerging evidence has implicated CD14 in COVID-19. CD14 exists in membrane bound and soluble (sCD14) form. A soluble N-terminal fragment of sCD14, sCD14 subtype (sCD14-ST, “Presepsin”) has been shown to have utility in diagnosis of sepsis and prognosis of associated organ failure and death. Goal: To determine the relationship between plasma sCD14 and sCD14-ST levels, COVID-19 status, and COVID-19 related outcomes in a cohort of prospectively enrolled critically ill patients admitted under suspicion for COVID-19. Methods: Critically ill patients under investigation for COVID-19 were prospectively enrolled between April 2020 and November 2020 at three hospitals affiliated with University of Washington. We ascertained COVID-19 status by SARS-CoV-2 RT-PCR upon admission. We measured plasma sCD14 and sCD14-ST levels in samples collected within 24 hours of admission. We tested for associations between biomarker levels and COVID-19 status using logistic regression adjusting for age, sex and APACHE III. In patients with COVID-19, we tested for associations between biomarker levels and disease severity and clinical outcomes using regression analyses adjusting for age, sex and APACHE III. Results: The cohort (n=222) mean age was 55 years, it was predominantly male (66%), in hospital mortality was 26%, and 50% of patients were positive by SARS-CoV-2 RT-PCR. Patients with COVID-19 had lower APACHE III scores (p: 0.013) than non-COVID-19. SCD14-ST levels were inversely associated with risk of SARS-CoV-2 positivity in multivariate regression (OR: 0.70, 95% CI: 0.57-0.84). Among patients with COVID-19, sCD14-ST levels were associated with higher APACHE III scores (beta: 7.3, 95% CI: 4.1-11), lower ventilatorfree days (beta:-1.6, 95% CI:-3.2 to-0.05) and higher risk for AKI (OR: 1.6, 95% CI: 1.0 to 2.7). SCD14-ST levels were not associated with these clinical outcomes in non-COVID-19 controls. In contrast to sCD14-ST levels, sCD14 levels did not differ between COVID-19 and non-COVID-19 patients and were not associated with COVID-19 clinical outcomes. Conclusions: In critically ill patients, sCD14-ST levels are inversely associated with risk of COVID-19 and positively associated with severity of disease and clinical outcomes among patients with COVID-19 while sCD14 levels were not associated with COVID-19 status or related outcomes. Early measurements of sCD14-ST levels could have prognostic utility in COVID-19.

Interferon-inducible mediators are associated with sars-cov-2 and related severity amongst critically ill patients suspected of covid-19

RATIONALE: Several studies have identified host immune signatures that are associated with COVID-19. However, it is unclear whether these immune signatures are specific to COVID-19 or are merely reflective of illness severity. In vitro studies have demonstrated that human T-cell responses to SARS-CoV-2-specific antigens are mediated through interferon-gamma (IFN-γ). Methods: We prospectively enrolled a multi-site cohort of patients admitted to the ICU under suspicion for COVID-19 who were then determined to be SARS-CoV-2-positive (n = 82) or-negative (n = 97) by RT-PCR. We measured multiple molecular and cellular immune profiles from blood and endotracheal aspirates (ETAs) collected on ICU admission. Our primary analysis tested for associations between IFN-γ and interferon-inducible mediators (CXCL10 and soluble PD-L1 (sPD-L1)) in blood or ETAs and SARS-CoV-2 status. We then stratified our cohort into SARS-CoV-2-negative and-positive groups and tested for associations between interferon-inducible mediators and clinical outcomes and SARS-CoV-2-copy-number. We used cytometry time-of-flight (CyTOF) to simultaneously measure 39 cell surface and intracellular markers on peripheral blood mononuclear cells collected from a subset of patients with ARDS. We then compared immune cell signatures in subjects with vs. without SARS-CoV-2. Results: The mean APACHE III score was higher in SARS-CoV-2-negative vs.-positive subjects (80±30 vs. 69±29), but the groups were otherwise well-matched. SARS-CoV-2-positive subjects had higher plasma concentrations of IFN-γ, CXCL10, and sPD-L1 relative to SARSCoV-2-negative patients adjusting for age, sex, and severity of illness (all p ≤ 0.01). The levels of IL-6, TNF-α, IL-8, MCP-1, and IL-17A were not significantly different between the two groups. SARS-CoV-2-positive subjects also had higher CXCL10 concentrations in ETAs than SARS-CoV-2-negative subjects. Higher plasma concentrations of CXCL10 and sPD-L1 were associated with higher mortality (Table 1) and more severe respiratory disease (ventilator-free days (VFDs), ARDS) in SARS-CoV-2-positive, but not-negative, patients. In contrast, higher IL-6 was associated with a lower number of VFDs and ARDS in both groups. IFN-γ and CXCL10 (but not IL-6) were associated with SARS-CoV-2-copy-number. Using CyTOF, we found SARS-CoV-2-positive subjects had a lower proportion of CXCR3+ (CXCL10 receptor) T-cells, a higher proportion of PD-L1+ monocytes, and less T-cell and monocyte intracellular cytokine staining vs. SARS-CoV-2-negative patients. Conclusion: Our findings suggest interferon-inducible mediator responses and immune cell hypofunction are characteristic of critically ill subjects with SARS-CoV-2 compared with similar patients without SARS-CoV-2. Our identification of immune signatures that are associated with SARS-CoV-2 infection but are distinct from other forms of critical illness clarifies COVID-19 pathophysiology.

Comparison of host endothelial, epithelial and inflammatory response in ICU patients with and without COVID-19

Rationale: Analyses of blood biomarkers involved in the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection can reveal distinct biological pathways and inform development and testing of therapeutics for COVID-19. Objective: To evaluate host endothelial, epithelial and inflammatory biomarkers in COVID-19Methods: We prospectively enrolled 169 ICU patients with suspicion of COVID-19 infection, including 78 (46%) patients positive and 91 (54%) negative for SARS-CoV-2 infection from April to September, 2020. We compared 22 plasma biomarkers in blood collected within 24 hours and 3 days after ICU admission. Measurement and Main Results: ICU patients with and without COVID-19 had similar rates of severe acute kidney injury, shock, thromboembolism and in-hospital mortality. Rates of ARDS were higher in COVID-19 (aRR = 5.9, 95% CI: 3.2-11.0). While concentrations of interleukin 6 and 8 were not different between groups, markers of epithelial cell injury (soluble receptor for advanced glycation end products, sRAGE) and acute phase proteins (serum amyloid A, SAA) were significantly higher in COVID-19 compared to non-COVID-19, adjusting for demographics and APACHE III scores (Figure 1). In contrast, angiopoietin 2:1 (Ang-2:1 ratio) and soluble tumor necrosis factor receptor 1 (sTNFR-1), markers of endothelial dysfunction and inflammation, were significantly lower in COVID-19 (Bonferroni corrected p<0.002). Ang-2:1 ratio and SAA were associated with mortality only in non-COVID-19 patients.Conclusions: These studies demonstrate that, unlike other well-studied causes of critical illness, endothelial dysfunction is not characteristic of severe COVID-19 early after ICU admission. Pathways resulting in elaboration of acute phase proteins and inducing epithelial cell injury may be promising targets for therapeutics. 2 (Table Presented).