An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2

Sharma, Jyoti; Bhardwaj, Vijay Kumar; Singh, Rahul; Rajendran, Vidya; Purohit, Rituraj; Kumar, Sanjay

doi:10.1016/j.foodchem.2020.128933

Cited by 152 publications

(114 citation statements)

References 43 publications

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“…These compounds are even effective against Zika, Chikungunya, and Dengue viruses (23). Recent computational and experimental investigations documented the potent antiviral activities of bioactive tea molecules against multiple vital proteins, including the main protease (Mpro), non-structural protein 15 (Nsp15), spike, and RdRp of SARS-CoV-2 (24)(25)(26)(27)(28). The main objectives of the study were to analyze the interaction pattern and binding affinity of selected bioactive molecules and FDA-approved antiviral drugs with the active pocket of SARS-CoV-2 RdRp and, furthermore, to rank and suggest topmost molecules on the basis of their potential to hinder the replication process of SARS-CoV-2.…”

Section: Graphical Abstract |mentioning

confidence: 99%

Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2

et al. 2021

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The coronavirus disease (COVID-19), a worldwide pandemic, is caused by the severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2). At this moment in time, there are no specific therapeutics available to combat COVID-19. Drug repurposing and identification of naturally available bioactive molecules to target SARS-CoV-2 are among the key strategies to tackle the notorious virus. The enzyme RNA-dependent RNA polymerase (RdRp) performs a pivotal role in replicating the virus. RdRp is a prime target for Remdesivir and other nucleotides analog-based antiviral drugs. In this study, we showed three bioactive molecules from tea (epicatechin-3,5-di-O-gallate, epigallocatechin-3,5-di-O-gallate, and epigallocatechin-3,4-di-O-gallate) that showed better interaction with critical residues present at the catalytic center and the NTP entry channel of RdRp than antiviral drugs Remdesivir and Favipiravir. Our computational approach to identify these molecules included molecular docking studies, followed by robust molecular dynamics simulations. All the three molecules are readily available in tea and could be made accessible along with other medications to treat COVID-19 patients. However, these results require validation by further in vitro and in vivo studies.

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Section: Graphical Abstract |mentioning

confidence: 99%

Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2

et al. 2021

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“…Medicines from the natural origin are deemed to exert fewer side effects than synthetic drugs. Natural and novel molecules as inhibitors of SARS-CoV-2 are also being examined by practicing in-silico approaches [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. In earlier studies, Himachalenes scaffolds were recognized for their anti-inflammatory and antiviral activities [ 24 , 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2

Singh

Bhardwaj

Das

et al. 2021

Computers in Biology and Medicine

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Background Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. Methods Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant ( Cedrus deodara ) derived α,β,γ -Himachalenes scaffolds. Results The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. Conclusion The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein.

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“…Drug repositioning research using computational docking simulations is also very meaningful. For example, bioactive components from green tea and other herbs were tested against the SARS-CoV-2 virus by docking technology 40 – 42 . However, the docking process requires a heavy computing burden.…”

Section: Discussionmentioning

confidence: 99%

Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2

Wang

Huang

et al. 2021

Sci Rep

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Research on drugs against SARS-CoV-2 (cause of COVID-19) has been one of the major world concerns at present. There have been abundant research data and findings in this field. The interference of drugs on gene expression in cell lines, drug-target, protein-virus receptor networks, and immune cell infiltration of the host may provide useful information for anti-SARS-CoV-2 drug research. To simplify the complex bioinformatics analysis and facilitate the evaluation of the latest research data, we developed OmiczViz (http://medcode.link/omicsviz), a web tool that has integrated drug-cell line interference data, virus-host protein–protein interactions, and drug-target interactions. To demonstrate the usages of OmiczViz, we analyzed the gene expression data from cell lines treated with chloroquine and ruxolitinib, the drug-target protein networks of 48 anti-coronavirus drugs and drugs bound with ACE2, and the profiles of immune cell infiltration between different COVID-19 patient groups. Our research shows that chloroquine had a regulatory role of the immune response in renal cell line but not in lung cell line. The anti-coronavirus drug-target network analysis suggested that antihistamine of promethaziney and dietary supplement of Zinc might be beneficial when used jointly with antiviral drugs. The immune infiltration analysis indicated that both the COVID-19 patients admitted to the ICU and the elderly with infection showed immune exhaustion status, yet with different molecular mechanisms. The interactive graphic interface of OmiczViz also makes it easier to analyze newly discovered and user-uploaded data, leading to an in-depth understanding of existing findings and an expansion of existing knowledge of SARS-CoV-2. Collectively, OmicsViz is web program that promotes the research on medical agents against SARS-CoV-2 and supports the evaluation of the latest research findings.

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An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2

Cited by 152 publications

References 43 publications

Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2

Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2

A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2

Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2

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