Structural differences in 3C-like protease (Mpro) from SARS-CoV and SARS-CoV-2: molecular insights revealed by Molecular Dynamics Simulations

Novel coronavirus SARS-CoV-2 has infected millions of people with thousands of mortalities globally. The main protease (Mpro) is vital in processing replicase polyproteins. Both the CoV’s Mpro shares 97% identity, with 12 mutations, but none are present in the active site. Although many therapeutics and vaccines are available to combat SARS-CoV-2, these treatments may not be practical due to their high mutational rate. On the other hand, Mpro has a high degree of conservation throughout variants, making Mpro a stout drug target. Here, we report a detailed comparison of both the monomeric Mpro and the biologically active dimeric Mpro using MD simulation to understand the impact of the 12 divergent residues (T35V, A46S, S65N, L86V, R88K, S94A, H134F, K180N, L202V, A267S, T285A and I286L) on the molecular microenvironment and the interaction between crucial residues. The present study concluded that the change in the microenvironment of residues at the entrance (T25, T26, M49 and Q189), near the catalytic site (F140, H163, H164, M165 and H172) and in the substrate-binding site (V35, N65, K88 and N180) is due to 12 mutations in the SARS-CoV-2 Mpro. Furthermore, the involvement of F140, E166 and H172 residues in dimerization stabilizes the Mpro dimer, which should be considered. We anticipate that networks and microenvironment changes identified here might guide repurposing attempts and optimization of new Mpro inhibitors. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02089-6.

Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches.

Millions of lives have been infected since the SARS-CoV-2 outbreak in 2019. The high human-to-human transmission rate has warranted a need for a vaccine to protect people. Although some vaccines are in use, due to the high mutation rate in the SARS-CoV-2 multiple variants, the current vaccines may not be sufficient to immunize people against new variant threats. One of the emerging concern variants is B1.1.529 (Omicron), which carries ~ 30 mutations in the Spike protein (S) of SARS-CoV-2 and is predicted to evade antibody recognition even from vaccinated people. We used a structure-based approach and an epitope prediction server to develop a Multi-Epitope based Subunit Vaccine (MESV) involving SARS-CoV-2 B1.1.529 variant spike glycoprotein. The predicted epitope with better antigenicity and non-toxicity was used for designing and predicting vaccine construct features and structure models. In addition, the MESV construct In silico cloning in the pET28a expression vector predicted the construct to be highly translational. The proposed MESV vaccine construct was also subjected to immune simulation prediction and was found to be highly antigenic and elicit a cell-mediated immune response. Therefore, the proposed MESV in the present study has the potential to be evaluated further for vaccine production against the newly identified B1.1.529 (Omicron) variant of concern. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02027-6.

Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches

Millions of lives have been infected since the SARS-CoV-2 outbreak in 2019. The high human-to-human transmission rate has warranted a need for a vaccine to protect people. Although some vaccines are in use, due to the high mutation rate in the SARS-CoV-2 multiple variants, the current vaccines may not be sufficient to immunize people against new variant threats. One of the emerging concern variants is B1.1.529 (Omicron), which carries ~ 30 mutations in the Spike protein (S) of SARS-CoV-2 and is predicted to evade antibody recognition even from vaccinated people. We used a structure-based approach and an epitope prediction server to develop a Multi-Epitope based Subunit Vaccine (MESV) involving SARS-CoV-2 B1.1.529 variant spike glycoprotein. The predicted epitope with better antigenicity and non-toxicity was used for designing and predicting vaccine construct features and structure models. In addition, the MESV construct In silico cloning in the pET28a expression vector predicted the construct to be highly translational. The proposed MESV vaccine construct was also subjected to immune simulation prediction and was found to be highly antigenic and elicit a cell-mediated immune response. Therefore, the proposed MESV in the present study has the potential to be evaluated further for vaccine production against the newly identified B1.1.529 (Omicron) variant of concern. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02027-6.

A Rare Case of COVID-19-Induced Chronic Demyelinating Polyneuropathy

Chronic autoimmune demyelinating polyneuropathy (CIDP) is a rare autoimmune disorder in which the body's immune system attacks the myelin sheaths. Myelin sheaths are the fatty insulation covering and protecting the nerves, and damage to these can lead to neurological symptoms like numbness, tingling, and weakness. CIDP is a chronic disease in the Guillain-Barré syndrome spectrum. Numerous case reports of autoimmune diseases linked to coronavirus disease 2019 (COVID-19) have been seen since the onset of COVID-19 pandemic. We present one such challenging case of COVID-19-induced CIDP.

IS UNCONTROLLED DIABETES PRIOR TO HOSPITALIZATION A RISK FACTOR FOR WORSE OUTCOMES IN COVID-19?

B Conclusions: b Poorly controlled diabetes as judged by higher HbA1c had less severe COVID infection on admission, however, it was not associated with higher severity of COVID19 during the admission. The probability of in-hospital mortality and rate of readmissions decreased with increasing levels of HbA1c. B Introduction: b Diabetes is a known risk factor for COVID19 infection. [Extracted from the article] Copyright of Critical Care Medicine is the property of Lippincott Williams & Wilkins and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Outcomes of Covid 19 patients-Are Hispanics at greater risk?

Disparities in outcomes exist in outcomes of coronavirus disease-19 (COVID-19). Little is known about other ethnic minorities in United States. We included all COVID-19 positive adult patients (≥18 years) hospitalized between March 1, 2020 and February 5th 2021. We compared in hospital mortality, use of intensive care unit services and inflammatory markers between non-Hispanic whites with non-White/Black Hispanic. Multivariable Cox proportional Hazard models were used to adjust for differences between the two groups. There were 4059 hospital admissions with COVID-19 in the study period. Of the 3288 White, 789 (24%) required intensive care unit (ICU) admission in comparison to 187 (24.3%) of the 770 Hispanics. Unadjusted mortality was higher in Whites than Hispanics (17.1% vs. 10.7%; p < 0.001). After adjusting for confounding variables, in-hospital mortality was not statistically different for Whites in comparison to Hispanics (hazard ratio [HR]: 0.96, 95% confidence interval [CI]: 0.76-1.21, p = 0.73). The adjusted rates of ICU transfers were significantly higher in Hispanics (HR: 1.34, 95% CI: 1.11-1.61, p = 0.002). Hispanics had significantly higher C-reactive protein, lactate dehydrogenase, and fibrinogen when compared to Whites. Hispanics as compared to Whites with COVID-19 require higher rates of ICU admission but have a similar mortality. Hispanics as compared to Whites with COVID-19 require higher rates of ICU admission but have a similar mortality.

Do high-dose corticosteroids improve outcomes in hospitalized COVID-19 patients?

Coronavirus disease 2019 (COVID-19) is characterized by dysregulated hyperimmune response and steroids have been shown to decrease mortality. However, whether higher dosing of steroids results in better outcomes has been debated. This was a retrospective observation of COVID-19 admissions between March 1, 2020, and March 10, 2021. Adult patients (≥18 years) who received more than 10 mg daily methylprednisolone equivalent dosing (MED) within the first 14 days were included. We excluded patients who were discharged or died within 7 days of admission. We compared the standard dose of steroids (<40 mg MED) versus the high dose of steroids (>40 mg MED). Inverse probability weighted regression adjustment (IPWRA) was used to examine whether higher dose steroids resulted in improved outcomes. The outcomes studied were in-hospital mortality, rate of acute kidney injury (AKI) requiring hemodialysis, invasive mechanical ventilation (IMV), hospital-associated infections (HAI), and readmissions. Of the 1379 patients meeting study criteria, 506 received less than 40 mg of MED (median dose 30 mg MED) and 873 received more than or equal to 40 mg of MED (median dose 78 mg MED). Unadjusted in-hospital mortality was higher in patients who received high-dose corticosteroids (40.7% vs. 18.6%, p < 0.001). On IPWRA, the use of high-dose corticosteroids was associated with higher odds of death (odds ratio [OR] 2.14; 95% confidence interval [CI] 1.45-3.14, p < 0.001) but not with the development of HAI, readmissions, or requirement of IMV. High-dose corticosteroids were associated with lower rates of AKI requiring hemodialysis (OR 0.33; 95% CI 0.18-0.63). In COVID-19, corticosteroids more than or equal to 40 mg MED were associated with higher in-hospital mortality.

Incidence of Venous Thromboembolism and Effect of Anticoagulant Dosing in Hospitalized COVID-19 Patients.

Background: Coronavirus disease 2019 (COVID-19) is characterized by coagulopathy and thrombotic events. We examined factors associated with development of venous thromboembolism (VTE) in COVID-19 and to discern if higher dose of anticoagulation was beneficial in these patients. Methods: This study involves an observational study of prospectively collected data in the setting of a large community hospital in a rural setting in Northeast Georgia with COVID-19 between March 1, 2020 and February 5, 2021. Anticoagulation dose (none, standard, intermediate, and therapeutic dosages) was studied in adult patients (≥ 18 years). We constructed multivariable logistic regression model to examine the association of clinical characteristics with VTE. To examine the effect of dose of anticoagulation in preventing VTE, we used inverse probability weighted regression adjustment. Results: Of the 4,645 patients with COVID-19, 251 (5.4%) patients were found to have VTE. Of these, 91 had pulmonary embolism, 148 had deep venous thrombosis (DVT) and 12 had both. A total of 129 of VTE cases were diagnosed at admission. Of all admissions, 12.9% did not receive any DVT prophylaxis, 70.4% received prophylactic dose, 1.3% received intermediate dose and 15.5% received therapeutic dose. Male gender (odds ratio (OR): 1.55, 95% confidence interval (CI): 1.0 - 2.4, P = 0.04) and Black race (OR: 2.0, 95% CI: 1.2 - 3.4, P = 0.01), along with higher levels of lactate dehydrogenase (LDH) and D-dimer were associated with higher odds of developing VTE. Patients receiving steroids had lower rates of VTE (3.9% vs. 8.3%, P < 0.001). Use of intermediate or therapeutic anticoagulation was not associated with lower odds of developing VTE. However, patients on therapeutic anticoagulation had lower odds of in hospital mortality when compared to standard dose (OR: 0.47, 95% CI: 0.27 - 0.80, P = 0.006). Conclusions: In COVID-19, D-dimer and LDH can be useful in predicting VTE. Steroids appear to have some protective role in development of VTE. Therapeutic anticoagulation did not result in lower rates of VTE but was associated with in-hospital mortality.

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1.

Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 3.3 million lives worldwide and still counting. As per the GISAID database, the genomics of SARS-CoV-2 has been extensively studied, with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, recent research has focused mainly on the missense variants. Moreover, significantly less attention has been accorded to delineate the role of the untranslated regions (UTRs) of the SARS-CoV-2 genome in the disease progression and etiology. One of the most frequent 5' UTR variants in the SARS-CoV-2 genome is the C241T, with a global frequency of more than 95 %. In the present study, the effect of the C241T mutation has been studied with respect to the changes in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem-loops with the host transcription factor MADP1, indicating a reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.

Does ABO Blood Groups Affect Outcomes in Hospitalized COVID-19 Patients?

BACKGROUND: Blood group type A has been associated with increased susceptibility for coronavirus disease 2019 (COVID-19) infection when compared to group O. The aim of our study was to examine outcomes in hospitalized COVID-19 patients among blood groups A and O. METHODS: This is an observational study. Kruskal-Wallis and Chi-square tests were used to compare continuous and categorical variables. Multivariable logistic regression models were used to examine association of blood groups with rates of mortality and severity of disease. All adult patients (> 18 years) admitted with COVID-19 infection between March 1, 2020 and March 10, 2021 at a large community hospital in Northeast Georgia were included. We compared mortality, severity of disease (use of mechanical ventilation, vasopressor, and acute renal failure), rates of venous thromboembolism and inflammatory markers between the blood groups. We used multivariable logistic regression model to adjust for demographical and clinical characteristics, use of COVID-19 medications and severity. RESULTS: A total of 3,563 of 5,204 admitted patients had information on blood groups. Of these, 1,301 (36.5%) were group A, 377 (10.6 %) were group B, 133 (3.7%) were group AB and 1,752 (49.2%) were group O. On adjusted analysis, there were no significant differences in rates of intensive care unit (ICU) admissions, mechanical ventilation, vasopressors, acute renal failure, venous thromboembolism and readmission rate between the blood groups A and O. In-hospital mortality was also not statistically different among the blood groups A and O (17.5% vs. 20.1%; P = 0.07). On adjusted analysis, in-hospital mortality was not lower in blood groups O (odds ratio (OR): 1.06; 95% confidence interval (CI): 0.80 - 1.40, P = 0.70). CONCLUSIONS: Once hospitalized with COVID-19 infection, blood groups A and O are not associated with increased severity or in-hospital mortality.

Emerging diagnostic tools for detection of COVID-19 and perspective.

The COVID-19 caused by a novel coronavirus, named Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken a great toll of life affecting lakhs of people around the globe. It was detected initially in Wuhan, China and has spread rapidly to more than 208 countries to date. A range of molecular and immunoassay-based techniques ranging from central laboratory testing to point-of-care tests is urgently needed for the diagnosis and management of COVID-19 patients. Intensive research is going on for the rapid and highly sensitive detection of COVID 19 using varied approach. Hence, this review will focus on the structure of SARS-CoV-2 and recent progress of different detection tool for the detection of COVID-19. This review will also stimulate academics and researcher to update their current technology. Additionally, we also state about the future revolving around the detection of the novel coronavirus. Lately, the way ahead for better management are also put forward.

Computational investigation of binding of chloroquinone and hydroxychloroquinone against PLPro of SARS-CoV-2.

Novel coronavirus SARS-CoV-2 has infected 18 million people with 700,000+ mortalities worldwide and this deadly numeric figure is rapidly rising. With very few success stories, the therapeutic targeting of this epidemic has been mainly attributed to main protease (Mpro), whilst Papain-like proteases (PLpro) also plays a vital role in the processing of replicase polyprotein. Multifunctional roles of PLpro such as viral polypeptide cleavage, de-ISGlyation and immune suppression have made it a promising drug target for therapeutic interventions. Whilst there have been a number of studies and others are on-going on repurposing and new-small molecule screening, albeit previously FDA approved drugs viz. Chloroquine (CQ) and Hydroxychloroquine (HCQ) have only been found effective against this pandemic. Inspired by this fact, we have carried out molecular docking and dynamics simulation studies of FDA approved CQ and HCQ against SARS-CoV-2 PLpro. The end aim is to characterise the binding mode of CQ and HCQ and identify the key amino acid residues involved in the mechanism of action. Further, molecular dynamics simulations (MDS) were carried out with the docked complex to search for the conformational space and for understanding the integrity of binding mode. We showed that the CQ and HCQ can bind with better binding affinity with PLpro as compared to reference known PLpro inhibitor. Based on the presented findings, it can be anticipated that the SARS-CoV-2 PLpro may act as molecular target of CQ and HCQ, and can be projected for further exploration to design potent inhibitors of SARS-CoV-2 PLpro in the near future.

Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches.

The recently emerged COVID-19 has been declared a pandemic by the World Health Organization as to date; no therapeutic drug/vaccine is available for the treatment. Due to the lack of time and the urgency to contain the pandemic, computational screening appears to be the best tool to find a therapeutic solution. Accumulated evidence suggests that many phyto-compounds possess anti-viral activity. Therefore, we identified possible phyto-compounds that could be developed and used for COVID-19 treatment. In particular, molecular docking was used to prioritize the possible active phyto-compounds against two key targets namely RNA dependent RNA polymerase (RdRp) and main protease (Mpro) of SARS-CoV-2. In this study, an antiviral drug- Remdesivir (RdRp inhibitor) and Darunavir (Mpro inhibitor) are used as reference drugs. This study revealed that phyto-molecules- Mulberroside-A/C/E/F, Emblicanin A, Nimbolide, and Punigluconin showed high binding affinity against RdRp while Andrographolides, Mulberrosides, Anolignans, Chebulic acid, Mimusopic acid, and Punigluconin showed better binding affinity against Mpro as compared with the reference drug. Furthermore, ADME profiles validated the drug-likeness properties of prioritized phyto-compounds. Besides, to assess the stability, MD simulations studies were performed along with reference inhibitors for Mpro (Darunavir) and RdRp (Remdesivir). Binding free energy calculations (MM-PBSA) revealed the estimated value (ΔG) of Mpro_Darunavir; Mpro_Mulberroside E; RdRp_Remdesivir and RdRp_Emblicanin A were -111.62 ± 6.788, -141.443 ± 9.313, 30.782 ± 5.85 and -89.424 ± 3.130 kJmol-1, respectively. Taken together, the study revealed the potential of these phyto-compounds as inhibitors of RdRp and Mpro inhibitor that could be further validated against SARS-CoV-2 for clinical benefits.Communicated by Ramaswamy H. Sarma.