Dataset Information

Tannins inhibit SARS-CoV-2 through binding with catalytic dyad residues of 3CLpro : An in silico approach with 19 structural different hydrolysable tannins.

ABSTRACT: Coronavirus epidemic 2019 (COVID-19), instigated by SARS-CoV-2 virus, is recently raising worldwide and inspiring global health worries. The main 3-chymotrypsin-like cysteine protease (3CLPro ) enzyme of SARS-CoV-2, which operates its replication, could be used as a medication discovery point. We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS-CoV-2 by assembling with the catalytic dyad residues of its 3CLpro using molecular operating environment (MOE 09). Results discovered that pedunculagin, tercatain, and castalin intensely interacted with the receptor binding site and catalytic dyad (Cys145 and His41) of SARS-CoV-2. Our analyses estimated that the top three hits might serve as potential inhibitor of SARS-CoV-2 leading molecules for additional optimization and drug development process to combat COVID-19. This study unleashed that tannins with specific structure could be utilized as natural inhibitors against COVID-19. PRACTICAL APPLICATIONS: The 3CLPro controls SARS-CoV-2 copying and manages its life series, which was targeted in case of SARS-CoV and MERS-CoV coronavirus. About 19 hydrolysable tannins were computed against 3CLpro of SARS-CoV-2. Pedunculagin, tercatain, and castalin interacted with Cys145 and His41 of SARS-CoV-2-3CLpro . Pedunculagin-SARS-CoV-2-3CLpro remain stable, with no obvious fluctuations. We predicted that the understandings gained in the current research may evidence valued for discovering and unindustrialized innovative natural inhibitors for COVID-19 in the nearby future.

SUBMITTER: Khalifa I

PROVIDER: S-EPMC7435556 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Tannins inhibit SARS-CoV-2 through binding with catalytic dyad residues of 3CLpro: An in silico approach with 19 structural different hydrolysable tannins.

Khalifa Ibrahim I Zhu Wei W Mohammed Hammad Hamed Hammad HHH Dutta Kunal K Li Chunmei C

Journal of food biochemistry 20200811 10

Coronavirus epidemic 2019 (COVID-19), instigated by SARS-CoV-2 virus, is recently raising worldwide and inspiring global health worries. The main 3-chymotrypsin-like cysteine protease (3CLPro) enzyme of SARS-CoV-2, which operates its replication, could be used as a medication discovery point. We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS-CoV-2 by assembling with the catalytic dyad residues of its 3CLpro using molecular operatin ...[more]

PMID: 32783247

Similar Datasets

Project description:BackgroundSevere acute respiratory syndrome (SARS) has been initiating pandemics since the beginning of the century. In December 2019, the world was hit again by a devastating SARS episode that has so far infected almost four million individuals worldwide, with over 200,000 fatalities having already occurred by mid-April 2020, and the infection rate continues to grow exponentially. SARS coronavirus 2 (SARS-CoV-2) is a single stranded RNA pathogen which is characterised by a high mutation rate. It is vital to explore the mutagenic capability of the viral genome that enables SARS-CoV-2 to rapidly jump from one host immunity to another and adapt to the genetic pool of local populations.MethodsFor this study, we analysed 2301 complete viral sequences reported from SARS-CoV-2 infected patients. SARS-CoV-2 host genomes were collected from The Global Initiative on Sharing All Influenza Data (GISAID) database containing 9 genomes from pangolin-CoV origin and 3 genomes from bat-CoV origin, Wuhan SARS-CoV2 reference genome was collected from GeneBank database. The Multiple sequence alignment tool, Clustal Omega was used for genomic sequence alignment. The viral replicating enzyme, 3-chymotrypsin-like cysteine protease (3CLpro) that plays a key role in its pathogenicity was used to assess its affinity with pharmacological inhibitors and repurposed drugs such as anti-viral flavones, biflavanoids, anti-malarial drugs and vitamin supplements.ResultsOur results demonstrate that bat-CoV shares > 96% similar identity, while pangolin-CoV shares 85.98% identity with Wuhan SARS-CoV-2 genome. This in-depth analysis has identified 12 novel recurrent mutations in South American and African viral genomes out of which 3 were unique in South America, 4 unique in Africa and 5 were present in-patient isolates from both populations. Using state of the art in silico approaches, this study further investigates the interaction of repurposed drugs with the SARS-CoV-2 3CLpro enzyme, which regulates viral replication machinery.ConclusionsOverall, this study provides insights into the evolving mutations, with implications to understand viral pathogenicity and possible new strategies for repurposing compounds to combat the nCovid-19 pandemic.

Dataset Information

Tannins inhibit SARS-CoV-2 through binding with catalytic dyad residues of 3CLpro : An in silico approach with 19 structural different hydrolysable tannins.

Publications

Tannins inhibit SARS-CoV-2 through binding with catalytic dyad residues of 3CL<sup>pro</sup>: An in silico approach with 19 structural different hydrolysable tannins.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets