NSP15 Endoribonuclease Research Articles

Trivalent transition metal ion mediated template synthesis: In silico molecular docking, DNA binding, antimicrobial evaluation and DFT studies

In order to reduce the chances of multiple drug resistance, there is an urgent requirement for the designing of new antimicrobial agents. In this current research, series of novel hexaazamacrocyclic trivalent transition metal complexes of ChromiumIII and IronIII have been prepared by adopting the pathway of metal ion mediated template condensation. The newly synthesized macrocyclic complexes were analyzed by Infra-Red Spectroscopy, Carbon-Hydrogen-Nitrogen analyzer, UltraViolet–visible, Powder X-Ray Diffraction, Electron Paramagnetic Resonance, Magnetic Susceptibilities, Molar conductance, Electron Spray Ionisation-Mass Spectrometry and Thermogravimetric analysis techniques. The electro-lytic behaviour of the complexes was suggested by conductance (molar) values. All the complexes (T7-T12) can be formulated or represented as [MLX] X2·yH2O, where M = FeIII, CrIII and L is the macrocyclic ring resulting from 1,8-diaminonaphthalene and succinimide and X = NO3−, Cl−, CH3COO− and y = 1 or 2. All the macrocyclic complexes have been anticipated to have a penta coordinated square pyramidal shape using several physico-analytical approaches. Monomeric nature of the complexes was confirmed by CHN analysis and mass spectral data. Powder X-Ray Diffraction studies were carried out for interpreting the crystallinity of the complexes. Density Functional Theory studies were performed for energy optimization and theoretical calculations of UV & IR. The DNA interaction studies showed intercalative mode of binding is present in the newly designed complexes with the DNA. In addition to these, all the metal complexes were screened for their antibacterial and antifungal activity against pathogenic strains of bacteria and fungi, Complex T7 has effective bactericidal action against B. cereus and E. coli. Molecular docking studies were also performed on SARS Cov-2 and Mycobacterium tuberculosis. The used proteins are NSP15 Endoribonuclease from SARS CoV-2 and DNA of Mycobacterium tuberculosis H37Rv. The results revealed that complex T10 is having good binding affinity against DNA of Mycobacterium tuberculosis H37Rv.

SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused millions of deaths since its emergence in 2019. Innate immune antagonism by lethal CoVs such as SARS-CoV-2 is crucial for optimal replication and pathogenesis. The conserved nonstructural protein 15 (nsp15) endoribonuclease (EndoU) limits activation of double-stranded (ds)RNA-induced pathways, including interferon (IFN) signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L) during diverse CoV infections including murine coronavirus and Middle East respiratory syndrome (MERS)-CoV. To determine how nsp15 functions during SARS-CoV-2 infection, we constructed a recombinant SARS-CoV-2 (nsp15mut) expressing catalytically inactivated nsp15, which we show promoted increased dsRNA accumulation. Infection with SARS-CoV-2 nsp15mut led to increased activation of the IFN signaling and PKR pathways in lung-derived epithelial cell lines and primary nasal epithelial air-liquid interface (ALI) cultures as well as significant attenuation of replication in ALI cultures compared to wild-type virus. This replication defect was rescued when IFN signaling was inhibited with the Janus activated kinase (JAK) inhibitor ruxolitinib. Finally, to assess nsp15 function in the context of minimal (MERS-CoV) or moderate (SARS-CoV-2) innate immune induction, we compared infections with SARS-CoV-2 nsp15mut and previously described MERS-CoV nsp15 mutants. Inactivation of nsp15 had a more dramatic impact on MERS-CoV replication than SARS-CoV-2 in both Calu3 cells and nasal ALI cultures suggesting that SARS-CoV-2 can better tolerate innate immune responses. Taken together, SARS-CoV-2 nsp15 is a potent inhibitor of dsRNA-induced innate immune response and its antagonism of IFN signaling is necessary for optimal viral replication in primary nasal ALI cultures.

Reversible and irreversible inhibitors of coronavirus Nsp15 endoribonuclease

The emergence of severe acute respiratory syndrome coronavirus 2, the causative agent of coronavirus disease 2019, has resulted in the largest pandemic in recent history. Current therapeutic strategies to mitigate this disease have focused on the development of vaccines and on drugs that inhibit the viral 3CL protease or RNA-dependent RNA polymerase enzymes. A less-explored and potentially complementary drug target is Nsp15, a uracil-specific RNA endonuclease that shields coronaviruses and other nidoviruses from mammalian innate immune defenses. Here, we perform a high-throughput screen of over 100,000 small molecules to identify Nsp15 inhibitors. We characterize the potency, mechanism, selectivity, and predicted binding mode of five lead compounds. We show that one of these, IPA-3, is an irreversible inhibitor that might act via covalent modification of Cys residues within Nsp15. Moreover, we demonstrate that three of these inhibitors (hexachlorophene, IPA-3, and CID5675221) block severe acute respiratory syndrome coronavirus 2 replication in cells at subtoxic doses. This study provides a pipeline for the identification of Nsp15 inhibitors and pinpoints lead compounds for further development against coronavirus disease 2019 and related coronavirus infections.

Structural studies of non-structural protein 15 (Nsp15) endoribonuclease from original SARS-Cov-2 and its variant epsilon for therapeutic intervention

Structural studies of non-structural protein 15 (Nsp15) endoribonuclease from original SARS-Cov-2 and its variant epsilon for therapeutic intervention

Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.

Identification and characterization of E266Q mutation in Nsp15 endoribonuclease from SARS-CoV-2 Epsilon variant.

SARS-CoV-2 is responsible for the ongoing global pandemic of COVID-19. Nsp15, an endoribonuclease from SARS-CoV-2 plays active roles in immune evasion and hence emerged as a drug target for COVID-19. Here we report the identification and characterization of a high frequency mutation in Nsp15 from the SARS-CoV-2 variant, Epsilon. First detected in California, USA in July 2020, Epsilon exhibited increased transmissibility compared to other SARS-CoV-2 variants circulating at the time. We performed multiple sequence alignment of 126 genomes of epsilon and identified four non-synonymous amino acid changes in Nsp15 (V66L, A81V, D183N and E266Q). We created these four single mutants to study their impact on Nsp15 catalysis. We also created a catalytically inactive mutant (H234A) for comparative analysis. Initial protein expressions revealed, E266Q which had a mutation rate of 4.76% exhibited very low expression levels compared to wild type (WT) whereas the inactive H234A exhibited very higher expression levels. This observation was reiterated by large-scale protein purification as well. We hypothesize that being an endoribonuclease, Nsp15 might be cleaving its own mRNA during recombinant expression, thus the activity levels of E266Q, WT, and H234A directly correlate to their corresponding expression levels. We performed a preliminary activity assay which demonstrated catalytic efficiency of E266Q is equal to or even slightly higher than WT. Enzyme kinetics experiments are underway to confirm this phenomenon. We also designed a new mutation E266A to further explore the effect of the E266 residue in Nsp15 activity. Currently, we are pursuing comparative structural and functional studies on E266Q, E266A, WT, and H234A to understand how E266Q mutation renders increased catalytic activity to Nsp15 and influences Epsilon's disease transmissibility.

Phytochemicals Against SARS-COV-2 Infection

Natural Product Communications Special Collection “Phytochemicals against SARS-COV-2 Infection” accepted 13 manuscripts, represented by 2 reviews, 9 original articles, and 1 letter to the editor. These deal with the use of traditional medicines, the use of network pharmacology, and docking studies to identify active compounds with prominent binding to various receptors responsible for internalization and replication, such as ACE2, S-protein, Mpro, PLpro, RdRp, and NSP15 endoribonuclease, as well as the possible use of phytochemicals against virus-associated inflammation.

Exploring cleavage activity of NSP15 using single molecule PIE-FRET.

The NSP15 endoribonuclease is used by coronaviruses (CoVs) to avoid detection by host immune systems by cleaving viral RNA and therefore can be considered a possible therapeutic target for CoV diseases. Cryo-EM structures from prior studies have indicated NSP15 has a strong preference for cleaving uridine, but a more dynamic picture of enzyme kinetics would be useful for a complete understanding of enzyme activity. To explore real time cleavage dynamics of NSP15 in solution, we designed a single molecule assay using Pulsed Interleaved Excitation Fluorescence Resonance Energy Transfer (PIE-FRET) to monitor the cleavage of engineered fluorescently-labeled RNA substrates containing either A, U, or C at a specific site. We also used Fluorescence Correlation Spectroscopy (FCS) to determine diffusion times of RNA sub-populations during the cleavage process. To probe cleavage activity of individual complexes of NSP15 and RNA, we immobilized the RNA substrate and measured changes in the fluorescence intensity and lifetime over several minutes and performed FRET analysis. We found that PIE-FRET and FCS of the RNA substrates incubated with NSP15 suggest cleavage happens quickly for equimolar ratios of substrate and protein. Furthermore, analysis from both techniques indicates folding at the U base, which prior research has suggested may be a possible marker that host immune systems use for identifying viral RNA. Detailed analysis of the dynamics of the NSP15-RNA substrate interaction improves our understanding of NSP15 cleavage activity and may serve as a basis for exploring the kinetics of other enzymes implicated in human diseases.

Investigating protein-ligand interactions for crystal structure of NSP15 endoribonuclease from SARS CoV-2 against caffeine

Investigating protein-ligand interactions for crystal structure of NSP15 endoribonuclease from SARS CoV-2 against caffeine

Screening of Phytoconstituents from Traditional Plants against SARSCoV- 2 using Molecular Docking Approach

Background: The emergence of COVID-19 as a fatal viral disease encourages researchers to develop effective and efficient therapeutic agents. The intervention of in silico studies has led to revolutionary changes in the conventional method of testing the bioactivity of plant constituents. Objective: The current study deals with the investigation of some traditional immunomodulators of plant origin to combat this ailment. Materials and Methods: A total of 151 phytomolecules of 12 immunomodulatory plants were evaluated for their inhibitory action against the main protease (PDB ID: 7D1M) and NSP15 endoribonuclease (PDB ID: 6WLC) by structure-based virtual screening. In addition, the promising molecules with ligand efficiency of more than -0.3(kcal/mol)/heavy atoms were further predicted for pharmacokinetic properties and druggability using the SwissADME web server, and their toxicity was also evaluated using Protox-II. Result: Myricetin-3-O-arabinofuranoside of cranberry plant was found to be the most potential candidate against both enzymes: main protease (–14.2 kcal/mol) and NSP15 endoribonuclease (–12.2 kcal/mol). Conclusion: The promising outcomes of the current study may be implemented in future drug development against coronavirus. The findings also help in the development of lead candidates of plant origin with a better ADMET profile in the future.

Plant Metabolites as SARS-CoV-2 Inhibitors Candidates: In Silico and In Vitro Studies

Since it acquired pandemic status, SARS-CoV-2 has been causing all kinds of damage all over the world. More than 6.3 million people have died, and many cases of sequelae are in survivors. Currently, the only products available to most of the world’s population to fight the pandemic are vaccines, which still need improvement since the number of new cases, admissions into intensive care units, and deaths are again reaching worrying rates, which makes it essential to compounds that can be used during infection, reducing the impacts of the disease. Plant metabolites are recognized sources of diverse biological activities and are the safest way to research anti-SARS-CoV-2 compounds. The present study computationally evaluated 55 plant compounds in five SARS-CoV-2 targets such Main Protease (Mpro or 3CL or MainPro), RNA-dependent RNA polymerase (RdRp), Papain-Like Protease (PLpro), NSP15 Endoribonuclease, Spike Protein (Protein S or Spro) and human Angiotensin-converting enzyme 2 (ACE-2) followed by in vitro evaluation of their potential for the inhibition of the interaction of the SARS-CoV-2 Spro with human ACE-2. The in silico results indicated that, in general, amentoflavone, 7-O-galloylquercetin, kaempferitrin, and gallagic acid were the compounds with the strongest electronic interaction parameters with the selected targets. Through the data obtained, we can demonstrate that although the indication of individual interaction of plant metabolites with both Spro and ACE-2, the metabolites evaluated were not able to inhibit the interaction between these two structures in the in vitro test. Despite this, these molecules still must be considered in the research of therapeutic agents for treatment of patients affected by COVID-19 since the activity on other targets and influence on the dynamics of viral infection during the interaction Spro x ACE-2 should be investigated.

Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants

Global sequencing efforts from the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, continue to provide insight into the evolution of the viral genome. Coronaviruses encode 16 nonstructural proteins, within the first two-thirds of their genome, that facilitate viral replication and transcription as well as evasion of the host immune response. However, many of these viral proteins remain understudied. Nsp15 is a uridine-specific endoribonuclease conserved across all coronaviruses. The nuclease activity of Nsp15 helps the virus evade triggering an innate immune response. Understanding how Nsp15 has changed over the course of the pandemic, and how mutations affect its RNA processing function, will provide insight into the evolution of an oligomerization-dependent endoribonuclease and inform drug design. In combination with previous structural data, bioinformatics analyses of 1.9 + million SARS-CoV-2 sequences revealed mutations across Nsp15′s three structured domains (N-terminal, Middle, EndoU). Selected Nsp15 variants were characterized biochemically and compared to wild type Nsp15. We found that mutations to important catalytic residues decreased cleavage activity but increased the hexamer/monomer ratio of the recombinant protein. Many of the highly prevalent variants we analyzed led to decreased nuclease activity as well as an increase in the inactive, monomeric form. Overall, our work establishes how Nsp15 variants seen in patient samples affect nuclease activity and oligomerization, providing insight into the effect of these variants in vivo.

Multitargeted Molecular Dynamic Understanding of Butoxypheser Against SARS-CoV-2: An in Silico Study

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was initially reported in the Wuhan province of China, spread throughout the world, and caused massive destruction in the form of a global pandemic that started back in 2020. SARS-CoV-2 is an RNA virus with various proteins like main protease, spike protein, NSP15 endoribonuclease, RNA-dependent RNA polymerase, and papain-like protease targeted to screen and find the novel drug candidate that can potentially work against the virus. Previous studies have reported multiple drugs after screening and validation against a single target and reported multiple medications. Nevertheless, many drugs are being used to date but do not have enough potential to work against SARS-CoV-2 and curb the spread and death rate. In this study, with the hypothesis of 1 drug and multiple targets, we have taken 5 main target proteins and screened the Asinex's complete BioDesign library (1,70,269 compounds) and identified N-{2-[(2S)-2-Amino-3-methylbutoxy]-6-propylbenzoyl}-L-phenylalanyl-L-serine (Butoxypheser) as multitarget inhibitor against SARS-CoV-2. Also, Butoxypheser has shown excellent docking scores, hydrogen bonding, and other bonding configurations like van der Waals force and water bridges. The stability and interaction pattern of the compound was validated with structural interaction fingerprints (SIFts) and molecular dynamics (MD) simulation. The Butoxypheser has performed flawlessly throughout the study, and the same results were used to compare the compound's activity against multiple targets. After a thorough theoretical comparative analysis, Butoxypheser can be treated as a multitargeted inhibitor candidate against SARS-CoV-2. Further, this study needs to be validated experimentally before human use.

Conserved coronavirus proteins as targets of broad-spectrum antivirals

Coronaviruses are a class of single-stranded, positive-sense RNA viruses that have caused three major outbreaks over the past two decades: Middle East respiratory syndrome–related coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All outbreaks have been associated with significant morbidity and mortality. In this study, we have identified and explored conserved binding sites in the key coronavirus proteins for the development of broad-spectrum direct acting anti-coronaviral compounds and validated the significance of this conservation for drug discovery with existing experimental data. We have identified four coronaviral proteins with highly conserved binding site sequence and 3D structure similarity: PLpro, Mpro, nsp10-nsp16 complex(methyltransferase), and nsp15 endoribonuclease. We have compiled all available experimental data for known antiviral medications inhibiting these targets and identified compounds active against multiple coronaviruses. The identified compounds representing potential broad-spectrum antivirals include: GC376, which is active against six viral Mpro (out of six tested, as described in research literature); mycophenolic acid, which is active against four viral PLpro (out of four); and emetine, which is active against four viral RdRp (out of four). The approach described in this study for coronaviruses, which combines the assessment of sequence and structure conservation across a viral family with the analysis of accessible chemical structure – antiviral activity data, can be explored for the development of broad-spectrum drugs for multiple viral families.

Molecular docking unveils the potential of andrographolide derivatives against COVID-19: an in silico approach

BackgroundThe recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection cause high mortality and there is an emergency need to develop a specific drug to treat the novel coronavirus disease, COVID-19. However, some natural and synthetic products with action against SARS-CoV-2 have been reported in recent research, there is no specific drug available for treating COVID-19. In the present study, molecular interaction analysis was performed for 16 semisynthetic andrographolides (AGP) against 5 SARS-CoV-2 enzymes main protease (Mpro, PDB: 6LU7), papain-like protease (PLpro, PDB: 6WUU), spike glycoprotein (S, PDB: 6VXX), NSP15 endoribonuclease (NSP15, PDB: 6VWW), and RNA-dependent RNA polymerase (RdRp, PDB: 6M71). Moreover, the compounds pharmacokinetic and toxic profiles were also analyzed using computational tools. ResultsThe protein−ligand docking score (kcal/mol) revealed that all the tested AGP derivatives showed a better binding affinity towards all the tested enzymes than hydroxychloroquine (HCQ). Meanwhile, all the tested AGP derivatives showed a better binding score with RdRp and S than remdesivir (REM). Interestingly, compounds 12, 14, and 15 showed a better binding affinity towards the all the tested enzyme than AGP, REM, and HCQ. AGP-16 had shown − 8.7 kcal/mol binding/docking score for Mpro, AGP-15 showed − 8.6 kcal/mol for NSP15, and AGP-10, 13, and 15 exhibited − 8.7, − 8.9, and − 8.7 kcal/mol, respectively, for S. ConclusionOverall results of the present study concluded that AGP derivatives 14 and 15 could be the best ‘lead’ candidate for the treatment against SARS-CoV-2 infection. However, molecular dynamic studies and pharmacological screenings are essential to developing AGP derivatives 14 and 15 as a drug against COVID-19.

Molecular Docking of Cyanine and Squarylium Dyes with NSP15 Endoribonuclease of the SARS-CoV-2 Coronavirus

The ongoing spread of the COVID-19 coronavirus infection requires us to find new tools and methods for detecting and studying the infection and preventing morbidity (new analytical procedures and tests). With the aim of developing probes for the detection of SARS-CoV-2 coronavirus by modeling in silico (molecular docking), the noncovalent binding of cyanine and squarylium dyes with different molecular charges and different types of heterocyclic residues and substituents (42 compounds in total) with different variants of the NSP15 endoribonuclease of the SARS-CoV-2 coronavirus (COVID-19) of the original (wild) type and mutant types is studied. The interaction energies and spatial configurations of the dye molecules in complexes with NSP15 are determined. Some dyes with negative values of the total energy of the complex Etot are promising for further practical study as probes for coronavirus.

Exploring the therapeutic nature of limonoids and triterpenoids against SARS-CoV-2 by targeting nsp13, nsp14, and nsp15 through molecular docking and dynamics simulations

Background and aimThe ongoing global pandemic due to SARS-CoV-2 caused a medical emergency. Since December 2019, the COVID-19 disease is spread across the globe through physical contact and respiratory droplets. Coronavirus caused a severe effect on the human immune system where some of the non-structural proteins (nsp) are involved in virus-mediated immune response and pathogenesis. To suppress the viral RNA replication mechanism and immune-mediated responses, we aimed to identify limonoids and triterpenoids as antagonists by targeting helicases (nsp13), exonuclease (nsp14), and endoribonuclease (nsp15) of SARS-CoV-2 as therapeutic proteins. Experimental procedureIn silico molecular docking and drug-likeness of a library of 369 phytochemicals from limonoids and triterpenoids were performed to screen the potential hits that binds effectively at the active site of the proteins target. In addition, the molecular dynamics simulations of the proteins and their complexes with the potential hits were performed for 100 ns by using GROMACS. Results and conclusionThe potential compounds 26-deoxyactein and 25-O-anhydrocimigenol 3-O-beta-d-xylopyranoside posing strong interactions with a minimum binding energy of −10.1 and −9.5 kcal/mol, respectively and sustained close contact with nsp13 for 100 ns. The nsp14 replication fork activity was hindered by the tomentosolic acid, timosaponin A-I, and shizukaol A with the binding affinity score of −9.2, −9.2, and −9.0 kcal/mol, respectively. The nsp15 endoribonuclease catalytic residues were inhibited potentially by limonin, 25-O-anhydrocimigenol 3-O-alpha-l-arabinopyranoside, and asperagenin posing strong binding affinity scores of −9.0, −8.8, and −8.7 kcal/mol, respectively. Computationally predicted potential phytochemicals for SARS-CoV-2 are known to possess various medicinal properties.

Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis.

The Bacillus subtilis genome is predicted to encode numerous ribonucleases, including four 3' exoribonucleases that have been characterized to some extent. A strain containing gene knockouts of all four known 3' exoribonucleases is viable, suggesting that one or more additional RNases remain to be discovered. A protein extract from the quadruple RNase mutant strain was fractionated and RNase activity was followed, resulting in the identification of an enzyme activity catalyzed by the YloC protein. YloC is an endoribonuclease and is a member of the highly conserved "YicC family" of proteins that is widespread in bacteria. YloC is a metal-dependent enzyme that catalyzes the cleavage of single-stranded RNA, preferentially at U residues, and exists in an oligomeric form, most likely a hexamer. As such, YloC shares some characteristics with the SARS-CoV Nsp15 endoribonuclease. While the in vivo function of YloC in B. subtilis is yet to be determined, YloC was found to act similarly to YicC in an Escherichia coli in vivo assay that assesses decay of the small RNA, RyhB. Thus, YloC may play a role in small RNA regulation.

In-silico Study to Identify Dietary Molecules as Potential SARS-CoV-2 Agents

Background: Recently, Coronavirus Disease-2019 (COVID-19), caused by a fatal strain of coronavirus named Severe Acute Respiratory Syndrome-2 (SARS-CoV-2), has been declared as a pandemic by the World Health Organisation (WHO) on 11 March 2020. Globally, no therapy such as vaccines and specific therapeutic agents is available so far despite some protease inhibitors and antiviral agents. Introduction: Due to no therapeutic drug or vaccine against SARS-CoV-2 so far, phytomedicine may be developed as therapeutic agents in the prevention and treatment of current COVID-19 disease. Thus, the aim of this study was to find out a suitable therapeutic agent from selected 17 dietary molecules, which could target SARS-CoV-2 encoded proteins. Materials and Methods: In this study, 3D structures of selected dietary molecules were obtained from the PubChem database, which have previously been reported for their antiviral and anti-inflammatory effects. Then, molecular docking analysis by using AutoDoc4 and AutoDockVina software was conducted to evaluate their anti-SARS-CoV-2 activity. Lipinski’s rule of five and drug-likeness properties were also discussed with the help of Molinspiration and the OSIRIS property explorer methods. Results: Our results revealed that, among all, epigallocatechin gallate (EGCG) (7) is a lead compound that could fit well into the binding sites of docked proteins of SARS-CoV-2. EGCG showed very strong molecular interactions with the free enzyme of main protease (6y2e), chimeric receptorbinding domain complexed with human ACE2 (6vw1), and NSP15 endoribonuclease (6vww) encoded proteins of SARS-CoV-2, by showing binding energies -9.30, -8.66, and -8.38, kcal/mole, respectively. Conclusion: In the present study, EGCG (7) is more active than two standard drugs that are currently being used in COVID 19, namely remdesivir and nafamostat. Therefore, EGCG (7), as per our results, might be explored as a therapeutic agent for the treatment of COVID-19.

Computational and network pharmacology studies of Phyllanthus emblica to tackle SARS-CoV-2

BackgroundSince December 2019, SARS-CoV-2 had been a significant threat globally, which has accounted for about two million deaths. Several types of research are undergoing and have reported the significant role of repurposing existing drugs and natural lead in the treatment of COVID-19. The plant Phyllanthus emblica (Synonym-Emblica officinalis) (Euphorbiaceae) is a rich source of vitamin C, and its use as an antiviral agent has been well established. PurposeThe present study was undertaken to investigate the potency of the several components of Phyllanthus emblica against three protein targets of 2019-nCoV viz. NSP15 endoribonuclease, main protease, and receptor binding domain of prefusion spike protein using molecular docking and dynamics studies. MethodsThe docking simulation studies were carried out using Schrödinger maestro 2018-1 MM share version, while dynamics studies were conducted to understand the binding mechanism and the complexes' stability studies. ResultsOut of sixty-six tested compounds, Chlorogenic acid, Quercitrin, and Myricetin were most effective in showing the highest binding energy against selected protein targets of SARS-CoV-2. The network pharmacology analysis study confirmed these compounds' role in modulating the immune response, inflammatory cascade, and cytokine storm through different signaling pathways. ConclusionCurrent pharmacoinformatic approach shows possible role of Phyllanthus emblica in the treatment and management of COVID-19.