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Epigallocatechin gallate and theaflavin gallate interaction in SARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study.
Drug Dev Res. 2021 02; 82(1):86-96.DD

Abstract

SARS-CoV-2 or COVID-19 pandemic global outbreak created the most unstable situation of human health-economy. In the past two decades different parts of the word experienced smaller or bigger outbreak related to human coronaviruses. The spike glycoproteins of the COVID-19 (similar to SARS-CoV) attach to the angiotensin-converting enzyme (ACE2) and transit over a stabilized open state for the viral internalization to the host cells and propagate with great efficacy. Higher rate of mutability makes this virus unpredictable/less sensitive to the protein/nucleic acid based drugs. In this emergent situation, drug-induced destabilization of spike binding to RBD could be a good strategy. In the current study we demonstrated by bioinformatics (CASTp: computed atlas of surface topography of protein, PyMol: molecular visualization) and molecular docking (PatchDock and Autodock) experiments that tea flavonoids catechin products mainly epigallocatechin gallate or other like theaflavin gallate demonstrated higher atomic contact energy (ACE) value, binding energy, Ki value, ligand efficiency, surface area and more amino acid interactions than hydroxychloroquine (HCQ) during binding in the central channel of the spike protein. Moreover, out of three distinct binding sites (I, II and III) of spike core when HCQ binds only with site III (farthest from the nCoV-RBD of ACE2 contact), epigallocatechin gallate and theaflavin gallate bind all three sites. As sites I and II are in closer contact with open state location and viral-host contact area, these drugs might have significant effects. Taking into account the toxicity/side effects by chloroquine/HCQ, present drugs may be important. Our laboratory is working on tea flavonoids and other phytochemicals in the protection from toxicity, DNA/mitochondrial damage, inflammation and so on. The present data might be helpful for further analysis of flavonoids in this emergent pandemic situation.

Authors+Show Affiliations

Cell and Molecular Therapeutics Laboratory, Department of Biochemistry and Biotechnology, Oriental Institute of Science and Technology, Midnapore, India. Agricure Biotech Research Society, Epidemiology and Human Health Division, Midnapore, India.Cell and Molecular Therapeutics Laboratory, Department of Biochemistry and Biotechnology, Oriental Institute of Science and Technology, Midnapore, India.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32770567

Citation

Maiti, Smarajit, and Amrita Banerjee. "Epigallocatechin Gallate and Theaflavin Gallate Interaction in SARS-CoV-2 Spike-protein Central Channel With Reference to the Hydroxychloroquine Interaction: Bioinformatics and Molecular Docking Study." Drug Development Research, vol. 82, no. 1, 2021, pp. 86-96.
Maiti S, Banerjee A. Epigallocatechin gallate and theaflavin gallate interaction in SARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study. Drug Dev Res. 2021;82(1):86-96.
Maiti, S., & Banerjee, A. (2021). Epigallocatechin gallate and theaflavin gallate interaction in SARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study. Drug Development Research, 82(1), 86-96. https://doi.org/10.1002/ddr.21730
Maiti S, Banerjee A. Epigallocatechin Gallate and Theaflavin Gallate Interaction in SARS-CoV-2 Spike-protein Central Channel With Reference to the Hydroxychloroquine Interaction: Bioinformatics and Molecular Docking Study. Drug Dev Res. 2021;82(1):86-96. PubMed PMID: 32770567.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Epigallocatechin gallate and theaflavin gallate interaction in SARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study. AU - Maiti,Smarajit, AU - Banerjee,Amrita, Y1 - 2020/08/07/ PY - 2020/04/22/received PY - 2020/07/11/revised PY - 2020/07/14/accepted PY - 2020/8/10/pubmed PY - 2021/2/20/medline PY - 2020/8/10/entrez KW - ACE2 KW - PatchDock KW - SARS-CoV-2 or COVID-19 KW - hydroxychloroquine KW - pandemic global outbreak KW - spike glycoprotein KW - tea flavonoids SP - 86 EP - 96 JF - Drug development research JO - Drug Dev Res VL - 82 IS - 1 N2 - SARS-CoV-2 or COVID-19 pandemic global outbreak created the most unstable situation of human health-economy. In the past two decades different parts of the word experienced smaller or bigger outbreak related to human coronaviruses. The spike glycoproteins of the COVID-19 (similar to SARS-CoV) attach to the angiotensin-converting enzyme (ACE2) and transit over a stabilized open state for the viral internalization to the host cells and propagate with great efficacy. Higher rate of mutability makes this virus unpredictable/less sensitive to the protein/nucleic acid based drugs. In this emergent situation, drug-induced destabilization of spike binding to RBD could be a good strategy. In the current study we demonstrated by bioinformatics (CASTp: computed atlas of surface topography of protein, PyMol: molecular visualization) and molecular docking (PatchDock and Autodock) experiments that tea flavonoids catechin products mainly epigallocatechin gallate or other like theaflavin gallate demonstrated higher atomic contact energy (ACE) value, binding energy, Ki value, ligand efficiency, surface area and more amino acid interactions than hydroxychloroquine (HCQ) during binding in the central channel of the spike protein. Moreover, out of three distinct binding sites (I, II and III) of spike core when HCQ binds only with site III (farthest from the nCoV-RBD of ACE2 contact), epigallocatechin gallate and theaflavin gallate bind all three sites. As sites I and II are in closer contact with open state location and viral-host contact area, these drugs might have significant effects. Taking into account the toxicity/side effects by chloroquine/HCQ, present drugs may be important. Our laboratory is working on tea flavonoids and other phytochemicals in the protection from toxicity, DNA/mitochondrial damage, inflammation and so on. The present data might be helpful for further analysis of flavonoids in this emergent pandemic situation. SN - 1098-2299 UR - https://www.unboundmedicine.com/medline/citation/32770567/Epigallocatechin_gallate_and_theaflavin_gallate_interaction_in_SARS_CoV_2_spike_protein_central_channel_with_reference_to_the_hydroxychloroquine_interaction:_Bioinformatics_and_molecular_docking_study_ L2 - https://doi.org/10.1002/ddr.21730 DB - PRIME DP - Unbound Medicine ER -