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1.
Struct Chem ; 33(5): 1789-1797, 2022.
Article in English | MEDLINE | ID: covidwho-2014353

ABSTRACT

The novel coronavirus that has affected the whole world is declared a pandemic by the World Health Organization. Since the emergence of this virus, researchers worldwide have searched for potential antivirals against it. Being an RNA virus, it shows a high rate of mutability and variability in its genome. In the present study, all the reported SARS-CoV-2 genomes isolated from diverse regions of the world available in the GISAID database have been considered for phylogenetic analysis. The strain identified at the root is subjected to phylogenetic analysis with genomes of other known human viruses obtained from NCBI for identifying the nearest viral neighbor. Furthermore, the phylogenetic relationship between various human viruses was used to repurpose the known antiviral drugs towards coronavirus using in silico docking approach. The phylogeny reveals the link of the COVID virus with adenovirus. The known drugs against adenovirus are considered in the present study for drug repurposing through molecular docking analysis. The reference inhibitors of the respective targets were also considered in the docking study. The protein targets, namely protease, endoribonuclease, methyltransferase, phosphatase, and spike protein, are considered for screening with the known drug of adenovirus. Ribavirin, known to treat adenoviral infection, shows the best docking score, suggesting its use as a repurposed drug to treat SARS-CoV-2. Furthermore, the potency of the ribavirin drug is analyzed using molecular dynamics studies. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02019-6.

2.
Structural Chemistry ; : 1-9, 2022.
Article in English | EuropePMC | ID: covidwho-1958212

ABSTRACT

The novel coronavirus that has affected the whole world is declared a pandemic by the World Health Organization. Since the emergence of this virus, researchers worldwide have searched for potential antivirals against it. Being an RNA virus, it shows a high rate of mutability and variability in its genome. In the present study, all the reported SARS-CoV-2 genomes isolated from diverse regions of the world available in the GISAID database have been considered for phylogenetic analysis. The strain identified at the root is subjected to phylogenetic analysis with genomes of other known human viruses obtained from NCBI for identifying the nearest viral neighbor. Furthermore, the phylogenetic relationship between various human viruses was used to repurpose the known antiviral drugs towards coronavirus using in silico docking approach. The phylogeny reveals the link of the COVID virus with adenovirus. The known drugs against adenovirus are considered in the present study for drug repurposing through molecular docking analysis. The reference inhibitors of the respective targets were also considered in the docking study. The protein targets, namely protease, endoribonuclease, methyltransferase, phosphatase, and spike protein, are considered for screening with the known drug of adenovirus. Ribavirin, known to treat adenoviral infection, shows the best docking score, suggesting its use as a repurposed drug to treat SARS-CoV-2. Furthermore, the potency of the ribavirin drug is analyzed using molecular dynamics studies. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02019-6.

3.
Virusdisease ; 32(3): 511-517, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1336149

ABSTRACT

A novel coronavirus disease (COVID-19), caused by SARS-CoV-2, has spread over more than 100 countries all over the world. The World Health Organization has recognized Coronavirus as a pandemic and finding an effective drug for this infectious disease is of high importance. In this study, we have explored the potent inhibitors of COVID-19 main protease from Tinospora cordifolia an Ayurvedic herb locally called as Amrita meaning 'immortality' and two other Ayurveda plants namely Cinnamomum zeylanicum and Myristica fragrans. Saponarin, a phytochemical present in Tinospora cordifolia showed a very promising result with the binding affinity of - 8.75 kcal/mol. Remdesivir and Favipiravir, the experimental drugs that are known to show inhibitory activity towards COVID-19 are used as a control. The Docking results were verified by the means of molecular dynamic analysis. This study suggests that Saponarin can be a potential inhibitor for the main protease of the COVID-19.

4.
Sci Rep ; 11(1): 4516, 2021 02 25.
Article in English | MEDLINE | ID: covidwho-1104540

ABSTRACT

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has turned into a pandemic with about thirty million confirmed cases worldwide as of September 2020. Being an airborne infection, it can be catastrophic to populous countries like India. This study sets to identify potential cytotoxic T lymphocyte (CTL) epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate for the majority of the Indian population. The immunogenicity and the foreignness of the epitopes towards the human body have to be studied to further confirm their candidacy. The top-scoring epitopes were subjected to molecular docking studies to study their interactions with the corresponding human leukocyte antigen (HLA) system. The CTL epitopes were observed to bind at the peptide-binding groove of the corresponding HLA system, indicating their potency as an epitope candidate. The candidacy was further analyzed using sequence conservation studies and molecular dynamics simulation. The identified epitopes can be subjected to further studies for the development of the SARS-CoV-2 vaccine.


Subject(s)
COVID-19/immunology , Epitopes, T-Lymphocyte/immunology , HLA Antigens/immunology , SARS-CoV-2/immunology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines/immunology , Humans , India/epidemiology , Molecular Docking Simulation , Viral Proteins/immunology
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