Polymerases of Coronaviruses

Investigation of Simultaneous and Sequential Cooperative Homotropic Inhibitor Binding to the Catalytic Chamber of SARS-CoV-2 RNA-dependent RNA Polymerase (RdRp)

In our previous report, the unique architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which harbours two distinctive binding sites, was fully characterized at molecular level. The significant differences in the two binding sites BS1 and BS2 in terms of binding pockets motif, as well as the preferential affinities of eight anti-viral drugs to each of the two binding sites were described. Recent Cryogenic Electron Microscopy (Cryo-EM) studies on the RdRp revealed that two suramin molecules, a SARS-CoV-2 inhibitor, bind to RdRp in two different sites with distinctive interaction landscape. Here, we provide the first account of investigating the combined inhibitor binding to both binding sites, and whether the binding of two inhibitors molecules concurrently is "Cooperative binding" or not. It should be noted that the binding of inhibitors to different sites do not necessary constitute mutually independent events, therefore, we investigated two scenarios to better understand cooperativity: simultaneous binding and sequential binding. It has been demonstrated by binding free energy calculations (MM/PBSA) and piecewise linear potential (PLP) interaction energy analysis that the co-binding of two suramin molecules is not cooperative in nature; rather, when compared to individual binding, both molecules adversely affect one another's binding affinities. This observation appeared to be primarily due to RdRp's rigidity, which prevented both ligands from fitting comfortably within the catalytic chamber. Instead, the suramin molecules showed a tendency to change their orientation within the binding pockets in order to maintain their binding to the protein, but at the expense of the ligand internal energies. Although co-binding resulted in the loss of several important key interactions, a few interactions were conserved, and these appear to be crucial in preserving the binding of ligands in the active site. The structural and mechanistic details of this study will be useful for future research on creating and developing RdRp inhibitors against SARS-CoV-2.

Identification of promising high-affinity inhibitors of SARS-CoV-2 main protease from African Natural Products Databases by Virtual Screening

With the rapid spread of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen agent of COVID-19 pandemic created a serious threat to global public health, requiring the most urgent research for potential therapeutic agents. The availability of genomic data of SARS-CoV-2 and efforts to determine the protein structure of the virus facilitated the identification of potent inhibitors by using structure-based approach and bioinformatics tools. Many pharmaceuticals have been proposed for the treatment of COVID-19, although their effectiveness has not been assessed yet. However, it is important to find out new-targeted drugs to overcome the resistance concern. Several viral proteins such as proteases, polymerases or structural proteins have been considered as potential therapeutic targets. But the virus target must be essential for host invasion match some drugability criterion. In this Work, we selected the highly validated pharmacological target main protease Mpro and we performed high throughput virtual screening of African Natural Products Databases such as NANPDB, EANPDB, AfroDb, and SANCDB to identify the most potent inhibitors with the best pharmacological properties. In total, 8753 natural compounds were virtually screened by AutoDock vina against the main protease of SARS-CoV-2. Two hundred and five (205) compounds showed high-affinity scores (less than - 10.0 Kcal/mol), while fifty-eight (58) filtered through Lipinski's rules showed better affinity than known Mpro inhibitors (i.e., ABBV-744, Onalespib, Daunorubicin, Alpha-ketoamide, Perampanel, Carprefen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin, Ethyl biscoumacetate…). Those promising compounds could be considered for further investigations toward the developpement of SARS-CoV-2 drug development.

The Unusual Architecture of RNA-Dependent RNA Polymerase (RdRp)'s Catalytic Chamber Provides a Potential Strategy for Combination Therapy against COVID-19

The unusual and interesting architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) was recently explored using Cryogenic Electron Microscopy (Cryo-EM), which revealed the presence of two distinctive binding cavities within the catalytic chamber. In this report, first, we mapped out and fully characterized the variations between the two binding sites, BS1 and BS2, for significant differences in their amino acid architecture, size, volume, and hydrophobicity. This was followed by investigating the preferential binding of eight antiviral agents to each of the two binding sites, BS1 and BS2, to understand the fundamental factors that govern the preferential binding of each drug to each binding site. Results showed that, in general, hydrophobic drugs, such as remdesivir and sofosbuvir, bind better to both binding sites than relatively less hydrophobic drugs, such as alovudine, molnupiravir, zidovudine, favilavir, and ribavirin. However, suramin, which is a highly hydrophobic drug, unexpectedly showed overall weaker binding affinities in both binding sites when compared to other drugs. This unexpected observation may be attributed to its high binding solvation energy, which disfavors overall binding of suramin in both binding sites. On the other hand, hydrophobic drugs displayed higher binding affinities towards BS1 due to its higher hydrophobic architecture when compared to BS2, while less hydrophobic drugs did not show a significant difference in binding affinities in both binding sites. Analysis of binding energy contributions revealed that the most favorable components are the ΔE_ele, ΔE_vdw, and ΔG_gas, whereas ΔG_sol was unfavorable. The ΔE_ele and ΔG_gas for hydrophobic drugs were enough to balance the unfavorable ΔG_sol, leaving the ΔE_vdw to be the most determining factor of the total binding energy. The information presented in this report will provide guidelines for tailoring SARS-CoV-2 inhibitors with enhanced binding profiles.

Behavioral activation / inhibition systems and lifestyle as predictors of mental disorders in adolescent athletes during Covid19 pandemic

The following study investigates the correlational relationship between behavioral activation/inhibition systems, lifestyle and mental disorders in Adolescent Athletes during the Covid-19 pandemic. Methods: Research methods are descriptive and correlational; “Of the eligible participants who were available during a COVID-19 quarantine period from June through August 2020 (N = 180), the Krejcie and Morgan Sampling Method was used to simplify the process of determining the sample size for a finite population [46], resulting in a calculation of N = 130 sample participants. to respond to Carver & White’s Behavioral activation/inhibition systems Scale (BIS/BAS), Mille’s Lifestyle Questionnaire and Goldberg & Williams’s General Health Questionnaire (GHQ-12). Data was analyzed using linear regression analysis and Pearson’s correlation coefficient. Results: Findings showed a positive correlation of statistical significance between behavioral inhibition systems (BIS) and mental disorders in Adolescent Athletes at the 0.01 level and a negative correlation of statistical significance between scaling components of the behavioral activation systems (BAS), lifestyle and mental disorders in Adolescent Athletes at the 0.05 level. Conclusions: Analyzing the data, it can thus be concluded that whilst behavioral inhibition and activation systems seem to work together to significantly predict mental disorders, lifestyle cannot.

Novel antiviral effects of chloroquine, hydroxychloroquine, and green tea catechins against SARS CoV-2 main protease (Mpro) and 3C-like protease for COVID-19 treatment

OBJECTIVES

Coronaviruses are globally emerging viruses that threaten our health care systems and have become a popular pandemic around the world. This causes a sudden rise in positive coronavirus cases and related deaths to occur worldwide, representing a significant health hazard to humans and the economy.

METHODS

We examined predominantly catechins of green tea include epigallocatechin-3-gallate (EGCG), epicatechin-3-gallate (ECG), and drugs of chloroquine (CQ), and hydroxychloroquine (HCQ) appearing to reveal anti-viral activities. Data were collected from PubMed, Google Scholar, and Science Direct databases. To investigate the role of antiviral effects (CQ and HCQ), green tea catechins, beneficial use of convalescent plasma; covaxin in COVID-19 patients faced a dangerous healthiness issue. Computational docking analysis has been used for this purpose.

RESULTS

The lead compounds are EGCG and ECG act as potential inhibitors bind to the active site region of the HKU4-CoV 3CL protease and M-Pro protease enzymes of coronavirus. Conclusions: SARS-COV-2 is a pathogen of substantial vigour concern and the review unveils the role of catechins associated with many viral diseases. We suggested that the function of green tea catechins, novel drugs of CQ, and HCQ exhibit antiviral activities against positive-sense single-stranded RNA viruses (CoVs).

Stereodivergent Synthesis of Biologically Active Spironucleoside Scaffolds via Catalytic Cyclopropanation of 4-exo-Methylene Furanosides

Cyclopropane fusion of the only rotatable carbon-carbon bond in furanosyl nucleosides (i.e., exocyclic 4'-5') is a powerful design strategy to arrive at conformationally constrained analogues. Herein, we report a direct stereodivergent route toward the synthesis of the four possible configurations of 4-spirocyclopropane furanoses, which have been transformed into the corresponding 4'-spirocyclic adenosine analogues. The latter showed differential inhibition of the protein methyltransferase PRMT5-MEP50 complex, with one analogue inhibiting more effectively than adenosine itself, demonstrating the utility of rationally probing 4'-5' side chain orientations.

The importance of genomic analysis in cracking the coronavirus pandemic

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has pushed the scientific community to undertake intense research efforts. Understanding SARS-CoV-2 biology is necessary to discover therapeutic or preventive strategies capable of containing the pandemic. Knowledge of the structural characteristics of the virus genome and proteins is essential to find targets for therapies and immunological interventions.Areas covered: This review covers different areas of expertise, genomic analysis of circulating strains, structural biology, viral mutations, molecular diagnostics, disease, and vaccines. In particular, the review is focused on the molecular approaches and modern clinical strategies used in these fields.Expert opinion: Molecular approaches to SARS-CoV-2 pandemic have been critical to shorten time for new diagnostic, therapeutic and prevention strategies. In this perspective, the entire scientific community is moving in the same direction. Vaccines, together with the development of new drugs to treat the disease, represent the most important strategy to protect human from viral disease and prevent further spread. In this regard, new molecular technologies have been successfully implemented. The use of a novel strategy of communication is suggested for a better diffusion to the broader public of new data and results.

Viral reverse engineering using Artificial Intelligence and big data COVID-19 infection with Long Short-term Memory (LSTM)

This research presents a reverse engineering approach to discover the patterns and evolution behavior of SARS-CoV-2 using AI and big data. Accordingly, we have studied five viral families (Orthomyxoviridae, Retroviridae, Filoviridae, Flaviviridae, and Coronaviridae) that happened in the era of the past one hundred years. To capture the similarities, common characteristics, and evolution behavior for prediction concerning SARS-CoV-2. And how reverse engineering using Artificial intelligence (AI) and big data is efficient and provides wide horizons. The results show that SARS-CoV-2 shares the same highest active amino acids (S, L, and T) with the mentioned viral families. As known, that affects the building function of the proteins. We have also devised a mathematical formula representing how we calculate the evolution difference percentage between each virus concerning its phylogenic tree. It shows that SARS-CoV-2 has fast mutation evolution concerning its time of arising. Artificial Intelligence (AI) is used to predict the next evolved instance of SARS-CoV-2 by utilizing the phylogenic tree data as a corpus using Long Short-term Memory (LSTM). This paper has shown the evolved viral instance prediction process on ORF7a protein from SARS-CoV-2 as the first stage to predict the complete mutant virus. Finally, in this research, we have focused on analyzing the virus to its primary factors by reverse engineering using AI and big data to understand the viral similarities, patterns, and evolution behavior to predict future viral mutations of the virus artificially in a systematic and logical way.

Monitoring of three-phase variations in the mortality of COVID-19 pandemic using control charts: where does Pakistan stand?

BACKGROUND

At the end of December 2019, the world in general and Wuhan, the industrial hub of China, in particular, experienced the COVID-19 pandemic. Massive increment of cases and deaths occurred in China and 209 countries in Europe, America, Australia, Asia and Pakistan. Pakistan was first hit by COVID-19 when a case was reported in Karachi on 26 February 2020. Several methods were presented to model the death rate due to the COVID-19 pandemic and to forecast the pinnacle of reported deaths. Still, these methods were not used in identifying the first day when Pakistan enters or exits the early exponential growth phase.

OBJECTIVE

The present study intends to monitor variations in deaths and identify the growth phases such as pre-growth, growth, and post-growth phases in Pakistan due to the COVID-19 pandemic.

METHODS

New approaches are needed that display the death patterns and signal an alarming situation so that corrective actions can be taken before the condition worsens. To meet this purpose, secondary data on daily reported deaths due to the COVID-19 pandemic have been considered, and the $c$ and exponentially weighted moving average (EWMA) control charts are used To meet this purpose, secondary data on daily reported deaths in Pakistan due to the COVID-19 pandemic have been considered. The $ c$ and exponentially weighted moving average (EWMA) control charts have been used for monitoring variations.

RESULTS

The chart shows that Pakistan switches from the pre-growth to the growth phase on 31 March 2020. The EWMA chart demonstrates that Pakistan remains in the growth phase from 31 March 2020 to 17 August 2020, with some indications signaling a decrease in deaths. It is found that Pakistan moved to a post-growth phase for a brief period from 27 July 2020 to 28 July 2020. Pakistan switches to re-growth phase with an alarm on 31/7/2020, right after the short-term post-growth phase. The number of deaths starts decreasing in August in that Pakistan may approach the post-growth phase shortly.

CONCLUSION

This amalgamation of control charts illustrates a systematic implementation of the charts for government leaders and forefront medical teams to facilitate the rapid detection of daily reported deaths due to COVID-19. Besides government and public health officials, it is also the public's responsibility to follow the enforced standard operating procedures as a temporary remedy of this pandemic in ensuring public safety while awaiting a suitable vaccine to be discovered.

Journey to a Receptor for Advanced Glycation End Products Connection in Severe Acute Respiratory Syndrome Coronavirus 2 Infection: With Stops Along the Way in the Lung, Heart, Blood Vessels, and Adipose Tissue

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide and the pandemic has yet to wane. Despite its associated significant morbidity and mortality, there are no definitive cures and no fully preventative measures to combat SARS-CoV-2. Hence, the urgency to identify the pathobiological mechanisms underlying increased risk for and the severity of SARS-CoV-2 infection is mounting. One contributing factor, the accumulation of damage-associated molecular pattern molecules, is a leading trigger for the activation of nuclear factor-kB and the IRF (interferon regulatory factors), such as IRF7. Activation of these pathways, particularly in the lung and other organs, such as the heart, contributes to a burst of cytokine release, which predisposes to significant tissue damage, loss of function, and mortality. The receptor for advanced glycation end products (RAGE) binds damage-associated molecular patterns is expressed in the lung and heart, and in priming organs, such as the blood vessels (in diabetes) and adipose tissue (in obesity), and transduces the pathological signals emitted by damage-associated molecular patterns. It is proposed that damage-associated molecular pattern-RAGE enrichment in these priming tissues, and in the lungs and heart during active infection, contributes to the widespread tissue damage induced by SARS-CoV-2. Accordingly, the RAGE axis might play seminal roles in and be a target for therapeutic intervention in SARS-CoV-2 infection.

SARS-CoV-2 infection: a global outbreak and its implication on public health

BACKGROUND

A novel corona virus is formally named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which results in causing coronavirus disease 2019 (COVID-19). It is the latest prevalent pandemic worldwide when compared to other infectious diseases like Avian flu, Middle East respiratory syndrome and severe acute respiratory syndrome (SARS).

MAIN BODY

Coronavirus disease 2019 (COVID-19) is currently occurring pandemic over world. It was emerged in Wuhan, China, in the end of December 2019 and spreading across worldwide. As the coronavirus is spreading easily through direct contact with infected people droplets, inhalation, and also air droplets, it hit up a huge amount of population even reported with death. Still, with small amounts of asymptomatic transmission between people it spreads throughout the globe. People need special care to protect from the transmission of disease. However, there are no drugs so far that shows efficacy; there is an immediate need for the development of vaccines. In order to decrease the COVID-19 cases, organizations rapidly involve in the preparation of vaccine and many vaccines have been developed by various countries. The governments took safety measures to control the spread of virus and also to minimize morbidity and mortality rate to least possible.

CONCLUSION

The purpose of this review article is to increase our understanding of COVID-19 and facilitate the people to take a move in facing challenges of the world.

Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase

Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication machinery, RNA-dependent RNA polymerase (RDRP), is targeted in a virtual screening assay using a set of 1,664 FDA-approved drugs, including sets of botanical and synthetic derivatives. A set of 22 drugs showed a high docking score of >-7. Notably, approximately one-third of the top hits were either from natural products or biological molecules. The FDA-approved phytochemicals were sennosides, digoxin, asiaticoside, glycyrrhizin, neohesperidin, taxifolin, quercetin and aloin. These approved natural products and phytochemicals are used as general tonics, antioxidants, cell protectives, and immune stimulants (nadid, thymopentin, asiaticoside, glycyrrhizin) and in other miscellaneous systemic or topical applications. A comprehensive analysis was conducted on standard precision and extra precision docking, two-step molecular dynamics simulations, binding energy calculations and a post dynamics analysis. The results reveal that two drugs, docetaxel and neohesperidin, showed strong binding profiles with SARS CoV-2 RdRP. These results can be used as a primer for further drug discovery studies in the treatment of COVID-19. This initiative repurposes safe FDA-approved drugs against COVID-19 RdRP, providing a rapid channel for the discovery and application of new anti-CoV therapeutics.

Favipiravir versus other antiviral or standard of care for COVID-19 treatment: a rapid systematic review and meta-analysis

BACKGROUND

The COVID-19 causing coronavirus is an enveloped RNA virus that utilizes an enzyme RNA dependent RNA polymerase for its replication. Favipiravir (FVP) triphosphate, a purine nucleoside analog, inhibits that enzyme. We have conducted this systematic review and meta-analysis on efficacy and safety of the drug FVP as a treatment for COVID-19.

METHODS

Databases like Pubmed, Pubmed Central, Scopus, Embase, Google Scholar, preprint sites, and clinicaltirals.gov were searched. The studies with the standard of care (SOC) and FVP as a treatment drug were considered as the treatment group and the SOC with other antivirals and supportive care as the control group. Quantitative synthesis was done using RevMan 5.4. Clinical improvement, negative conversion of reverse transcription-polymerase chain reaction (RT-PCR), adverse effects, and oxygen requirements were studied.

RESULTS

We identified a total of 1798 studies after searching the electronic databases. Nine in the qualitative studies and four studies in the quantitative synthesis met the criteria. There was a significant clinical improvement in the FVP group on the 14th day compared to the control group (RR 1.29, 1.08-1.54). Clinical deterioration rates were less likely in the FVP group though statistically not significant (OR 0.59, 95% CI 0.30-1.14) at the endpoint of study (7-15 days). The meta-analysis showed no significant differences between the two groups on viral clearance (day 14: RR 1.06, 95% CI 0.84-1.33), non-invasive ventilation or oxygen requirement (OR 0.76, 95% CI 0.42-1.39), and adverse effects (OR 0.69, 0.13-3.57). There are 31 randomized controlled trials (RCTs) registered in different parts of the world focusing FVP for COVID-19 treatment.

CONCLUSION

There is a significant clinical and radiological improvement following treatment with FVP in comparison to the standard of care with no significant differences on viral clearance, oxygen support requirement and side effect profiles.

Molecular biology of coronaviruses: current knowledge

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.

Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2

The efforts towards developing a potential drug against the current global pandemic, COVID-19, have increased in the past few months. Drug development strategies to target the RNA dependent RNA polymerase (RdRP) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are being tried worldwide. The gene encoding this protein, is known to be conserved amongst positive strand RNA viruses. This enables an avenue to repurpose the drugs designed against earlier reported inhibitors of RdRP. One such strong inhibitor is remdesivir which has been used against EBOLA infections. The binding of remdesivir to RdRP of SARS-CoV-2 has been studied using the classical molecular dynamics and ensemble docking approach. A comparative study of the simulations of RdRP in the apo and remdesivir-bound form revealed blocking of the template entry site in the presence of remdesivir. The conformation changes leading to this event were captured through principal component analysis. The conformational and thermodynamic parameters supported the experimental information available on the involvement of crucial arginine, serine and aspartate residues belonging to the conserved motifs in RdRP functioning. The catalytic site comprising of SER 759, ASP 760, and ASP 761 (SDD) was observed to form strong contacts with remdesivir. The significantly strong interactions of these residues with remdesivir may infer the latter's binding similar to the normal nucleotides thereby remaining unidentified by the exonuclease activity of RdRP. The ensemble docking of remdesivir too, comprehended the involvement of similar residues in interaction with the inhibitor. This information on crucial interactions between conserved residues of RdRP with remdesivir through in silico approaches may be useful in designing inhibitors.