Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study
Mehran Alavi, M R Mozafari, Saba Ghaemi, Morahem Ashengroph, Fatemeh Hasanzadeh Davarani, Mohammadreza Mohammadabadi
Biomedicines, doi:10.3390/biomedicines10123074
Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of −9.9 and −8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
References
Ahmadi, Ahmadi, Ahmadi, A review on antifungal and antibacterial activities of some medicinal plants, Micro Nano Bio Asp
Al-Karmalawy, Dahab, Metwaly, Elhady, Elkaeed et al., Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor, Front. Chem,
doi:10.3389/fchem.2021.661230Alavi, Adulrahman, Haleem, Al-Râwanduzi, Khusro et al., Nanoformulations of curcumin and quercetin with silver nanoparticles for inactivation of bacteria, Cell. Mol. Biol,
doi:10.14715/cmb/2021.67.5.21Alavi, Asare-Addo, Nokhodchi, Lectin Protein as a Promising Component to Functionalize Micelles, Liposomes and Lipid NPs against Coronavirus, Biomedicines,
doi:10.3390/biomedicines8120580Alavi, Hamblin, Martinez, Aghaie, Khan et al., Micro and nanoformulations of insulin: New approaches, Nano Micro Bios
Alavi, Hamblin, Martinez, Kennedy, Khan, Synergistic combinations of metal, metal oxide, or metalloid nanoparticles plus antibiotics against resistant and non-resistant bacteria, Micro Nano Bio Asp
Alavi, Hamblin, Mozafari, Rose Alencar De Menezes, Douglas Melo Coutinho, Surface modification of SiO 2 nanoparticles for bacterial decontaminations of blood products, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2022.338888.1039Alavi, Kowalski, Capasso, Douglas Melo Coutinho, Rose Alencar De Menezes, Various novel strategies for functionalization of gold and silver nanoparticles to hinder drug-resistant bacteria and cancer cells, Micro Nano Bio Asp
Alavi, Martinez, Delgado, Tinjacá, Anticancer and antibacterial activities of embelin: Micro and nano aspects, Micro Nano Bio Asp
Alavi, Rai, Antisense RNA, the modified CRISPR-Cas9, and metal/metal oxide nanoparticles to inactivate pathogenic bacteria, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2021.142436.1014Alavi, Rai, Martinez, Kahrizi, Khan et al., The efficiency of metal, metal oxide, and metalloid nanoparticles against cancer cells and bacterial pathogens: Different mechanisms of action, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2022.147090.1023Alavi, Thomas, Sreedharan, Modification of silica nanoparticles for antibacterial activities: Mechanism of action, Micro Nano Bio Asp
Albuquerque, Heleno, Oliveira, Barros, Ferreira, Phenolic compounds: Current industrial applications, limitations and future challenges, Food Funct,
doi:10.1039/D0FO02324HAljelehawy, Alshaibah, Khafaji, Evaluation of virulence factors among Staphylococcus aureus strains isolated from patients with urinary tract infection in Al-Najaf Al-Ashraf teaching hospital, Cell. Mol. Biomed. Rep
Almasian-Tehrani, Alebouyeh, Armin, Soleimani, Azimi et al., Overview of typing techniques as molecular epidemiology tools for bacterial characterization, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2021.143413.1016Amraei, Ahmadi, Recent studies on antimicrobial and anticancer activities of saponins: A mini-review, Nano Micro Bios
Andijani, Wazzan, The effect of electron-donating substituents on tuning the nonlinear optical properties of pyrene-core arylamine derivatives: DFT calculations, Results Phys,
doi:10.1016/j.rinp.2018.10.002Arévalo, Pagotto, Pórfido, Daghero, Segovia et al., Ivermectin reduces in vivo coronavirus infection in a mouse experimental model, Sci. Rep,
doi:10.1038/s41598-021-86679-0Baral, Mozafari, Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges, ACS Pharmacol. Transl. Sci,
doi:10.1021/acsptsci.0c00005Basu, Sarkar, Maulik, Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2, Sci. Rep,
doi:10.1038/s41598-020-74715-4Casas-Sanchez, Romero-Ramirez, Hargreaves, Ellis, Grajeda et al., Inhibition of Protein N-Glycosylation Blocks SARS-CoV-2 Infection, mBio
Ceccarelli, Alessandri, Oliva, Borrazzo, Dell'isola et al., The role of teicoplanin in the treatment of SARS-CoV-2 infection: A retrospective study in critically ill COVID-19 patients (Tei-COVID study), J. Med. Virol,
doi:10.1002/jmv.26925Chamkhi, Benali, Aanniz, El Menyiy, Guaouguaou et al., Plant-microbial interaction: The mechanism and the application of microbial elicitor induced secondary metabolites biosynthesis in medicinal plants, Plant Physiol. Biochem,
doi:10.1016/j.plaphy.2021.08.001Choudhary, Zehra, Mukarram, Wani, Naeem et al., Potential Uses of Bioactive Compounds of Medicinal Plants and Their Mode of Action in Several Human Diseases
De Maat, Pijl, Kluft, Princen, Consumption of black and green tea had no effect on inflammation, haemostasis and endothelial markers in smoking healthy individuals, Eur. J. Clin. Nutr,
doi:10.1038/sj.ejcn.1601084Du, Zheng, Disoma, Li, Chen et al., Epigallocatechin-3-gallate, an active ingredient of Traditional Chinese Medicines, inhibits the 3CLpro activity of SARS-CoV-2, Int. J. Biol. Macromol
Eberhardt, Santos-Martins, Tillack, Forli, AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings, J. Chem. Inf. Model,
doi:10.1021/acs.jcim.1c00203Eweas, Alhossary, Abdel-Moneim, Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2, Front. Microbiol,
doi:10.3389/fmicb.2020.592908Fischer, Müller, Scheidt, Luck, Drug-Membrane Interactions: Effects of Virus-Specific RNA-Dependent RNA Polymerase Inhibitors Remdesivir and Favipiravir on the Structure of Lipid Bilayers, Biochemistry,
doi:10.1021/acs.biochem.2c00042Gasmi, Mujawdiya, Lysiuk, Shanaida, Peana et al., Quercetin in the Prevention and Treatment of Coronavirus Infections: A Focus on SARS-CoV-2, Pharmaceuticals,
doi:10.3390/ph15091049Golonka, Wilk, Musiał, The Influence of UV Radiation on the Degradation of Pharmaceutical Formulations Containing Quercetin, Molecules,
doi:10.3390/molecules25225454Guedes, Costa, Dos Santos, Karl, Rocha et al., Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants, Sci. Rep,
doi:10.1038/s41598-021-84700-0Han, Ren, Li, Yan, Ma et al., Advances and challenges in the prevention and treatment of COVID-19, Int. J. Med. Sci,
doi:10.7150/ijms.47836Hashemzaei, Delarami Far, Yari, Heravi, Tabrizian et al., Anticancer and apoptosis-inducing effects of quercetin in vitro and in vivo, Oncol. Rep,
doi:10.3892/or.2017.5766Hong, Seo, Woo, Kwon, Song et al., Epigallocatechin Gallate Inhibits the Uridylate-Specific Endoribonuclease Nsp15 and Efficiently Neutralizes the SARS-CoV-2 Strain, J. Agric. Food Chem,
doi:10.1021/acs.jafc.1c02050Isbrucker, Edwards, Wolz, Davidovich, Bausch, Safety studies on epigallocatechin gallate (EGCG) preparations. Part 2: Dermal, acute and short-term toxicity studies, Food Chem. Toxicol,
doi:10.1016/j.fct.2005.11.003Kabarkouhi, Mehrarya, Gharehchelou, Jalilian, Jalili et al., Nanoliposome and Allied Technologies in COVID-19 Vaccines: Key Roles and Functionalities, Curr. Drug Deliv,
doi:10.2174/1567201819666220427125342Kawano, Hwang, Influence of Guanidine, Imidazole, and Some Heterocyclic Compounds on Dissolution Rates of Amorphous Silica, Clays Clay Miner,
doi:10.1346/CCMN.2010.0580603Komeno, Furuta, Nakajima, Tani, Morinaga, Analysis of the responsible site for favipiravir resistance in RNA-dependent RNA polymerase of influenza virus A/PR/8/34 (H1N1) using site-directed mutagenesis, Antivir. Res,
doi:10.1016/j.antiviral.2022.105387Liu, Grimm, Dai, Hou, Xiao et al., CB-Dock: A web server for cavity detection-guided protein-ligand blind docking, Acta Pharmacol. Sin,
doi:10.1038/s41401-019-0228-6Lopes, Da Costa, Genova Ribeiro, Da Silva, Lima et al., Quercetin pentaacetate inhibits in vitro human respiratory syncytial virus adhesion, Virus Res,
doi:10.1016/j.virusres.2019.197805Maiti, 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 Dev. Res,
doi:10.1002/ddr.21730Majumder, Taufiqur Rahman, Mahedi Hasan, Didarul Islam, Taylor-Robinson et al., Decoding the enigma of antiviral crisis: Does one target molecule regulate all?, Cytokine,
doi:10.1016/j.cyto.2018.12.008Mirtaleb, Mirtaleb, Nosrati, Heshmatnia, Falak et al., Potential therapeutic agents to COVID-19: An update review on antiviral therapy, immunotherapy, and cell therapy, Biomed. Pharmacother
Mozafari, Torkaman, Karamouzian, Rasti, Baral, Antimicrobial Applications of Nanoliposome Encapsulated Silver Nanoparticles: A Potential Strategy to Overcome Bacterial Resistance, Curr. Nanosci,
doi:10.2174/1573413716999200712184148Mpiana, Ngbolua, Tshibangu, Kilembe, Gbolo et al., Identification of potential inhibitors of SARS-CoV-2 main protease from Aloe vera compounds: A molecular docking study, Chem. Phys. Lett,
doi:10.1016/j.cplett.2020.137751Muhammad, Abubakar, Muhammad, Genetic resistance to human malaria, Cell. Mol. Biomed. Rep
Muhammad, Sale, Salisu, Muhammad, Abubakar et al., Molecular analysis of Bio-makers of Chloroquine resistance in Plasmodium falciparum Isolate from Gombe Local Government Area, Gombe State, Nigeria, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2022.335753.1033Murad, Alqurashi, Hussien, Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: A molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study, BMC Complement. Med. Ther,
doi:10.1186/s12906-021-03488-8Narendrakumar, Joseph, Thomas, Potential effectiveness and adverse implications of repurposing doxycycline in COVID-19 treatment, Expert Rev. Anti-Infect. Ther,
doi:10.1080/14787210.2021.1865803Nguyen, Woo, Kang, Nguyen, Kim et al., Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in Pichia pastoris, Biotechnol. Lett,
doi:10.1007/s10529-011-0845-8Ntamo, Jack, Ziqubu, Mazibuko-Mbeje, Nkambule et al., Epigallocatechin gallate as a nutraceutical to potentially target the metabolic syndrome: Novel insights into therapeutic effects beyond its antioxidant and anti-inflammatory properties, Crit. Rev. Food Sci. Nutr,
doi:10.1080/10408398.2022.2104805Pillon, Frazier, Dillard, Williams, Kocaman et al., Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15, Biorxiv Prepr. Serv. Biol,
doi:10.1101/2020.08.11.244863Puttaswamy, Gowtham, Ojha, Yadav, Choudhir et al., In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis, Sci. Rep,
doi:10.1038/s41598-020-77602-0Quinn, Patel, Koh, Haines, Norrby et al., Automated fitting of transition state force fields for biomolecular simulations, PLoS ONE,
doi:10.1371/journal.pone.0264960Rahbar-Karbasdehi, Rahbar-Karbasdehi, Clinical challenges of stress cardiomyopathy during coronavirus 2019 epidemic, Cell. Mol. Biomed. Rep,
doi:10.55705/cmbr.2021.145790.1018Rahman, Tabrez, Ali, Alqahtani, Ahmed et al., Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins, J. Tradit. Complement. Med,
doi:10.1016/j.jtcme.2021.01.006Sabbagh, Kiarostami, Khatir, Rezania, Muhamad et al., Effect of zinc content on structural, functional, morphological, and thermal properties of kappa-carrageenan/NaCMC nanocomposites, Polym. Test,
doi:10.1016/j.polymertesting.2020.106922Sabbagh, Kiarostami, Mahmoudi Khatir, Rezania, Muhamad, Green Synthesis of Mg0.99 Zn0.01O Nanoparticles for the Fabrication of κ-Carrageenan/NaCMC Hydrogel in order to Deliver Catechin, Polymers,
doi:10.3390/polym12040861Salehi, Machin, Monzote, Sharifi-Rad, Ezzat et al., Therapeutic Potential of Quercetin: New Insights and Perspectives for Human Health, ACS Omega,
doi:10.1021/acsomega.0c01818Samy, Attia, Shoman, Khalil, Sugimoto et al., Phytochemical investigation of Amphilophium paniculatum; an underexplored Bignoniaceae species as a source of SARS-CoV-2 Mpro inhibitory metabolites: Isolation, identification, and molecular docking study, S. Afr. J. Bot,
doi:10.1016/j.sajb.2021.05.023Santos, Brierley, Gandhi, Cohen, Moschella et al., Repurposing Therapeutics for Potential Treatment of SARS-CoV-2: A Review, Viruses,
doi:10.3390/v12070705Santos, Grosche, Bergamini, Sabino-Silva, Jardim, Antivirals Against Coronaviruses: Candidate Drugs for SARS-CoV-2 Treatment? Front, Microbiol,
doi:10.3389/fmicb.2020.01818Schmitz, Gilberg, Löser, Bajorath, Bartz et al., Cathepsin B: Active site mapping with peptidic substrates and inhibitors, Biorg. Med. Chem,
doi:10.1016/j.bmc.2018.10.017Shehata, Attia, Rahman, Basiouni, El-Seedi et al., Diversity of Coronaviruses with Particular Attention to the Interspecies Transmission of SARS-CoV-2, Animals,
doi:10.3390/ani12030378Taguchi, Turki, A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction, PLoS ONE,
doi:10.1371/journal.pone.0238907Tripathy, Dassarma, Roy, Chabalala, Matsabisa, A review on possible modes of action of chloroquine/hydroxychloroquine: Repurposing against SAR-CoV-2 (COVID-19) pandemic, Int. J. Antimicrob. Agents
Uzunova, Filipova, Pavlova, Vekov, Insights into antiviral mechanisms of remdesivir, lopinavir/ritonavir and chloroquine/hydroxychloroquine affecting the new SARS-CoV-2, Biomed. Pharmacother,
doi:10.1016/j.biopha.2020.110668Verma, Patel, Chandra, Identification of novel inhibitors of SARS-CoV-2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation, J. Comput. Chem,
doi:10.1002/jcc.26717Yang, Atkinson, Wang, Lee, Bogoyevitch et al., The broad spectrum antiviral ivermectin targets the host nuclear transport importin α/β1 heterodimer, Antivir. Res,
doi:10.1016/j.antiviral.2020.104760Yang, Guo, Yu, Liu, Song et al., Tocilizumab mimotope alleviates kidney injury and fibrosis by inhibiting IL-6 signaling and ferroptosis in UUO model, Life Sci,
doi:10.1016/j.lfs.2020.118487Yang, Petitjean, Koehler, Zhang, Dumitru et al., Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor, Nat. Commun,
doi:10.1038/s41467-020-18319-6Yang, Wei, Fang, Gan, Wang et al., Nanochemoprevention with therapeutic benefits: An updated review focused on epigallocatechin gallate delivery, Crit. Rev. Food Sci. Nutr
Yi, Peng, Wu, Xu, Kuang et al., The Therapeutic Effects and Mechanisms of Quercetin on Metabolic Diseases: Pharmacological Data and Clinical Evidence, Oxid. Med. Cell. Longev,
doi:10.1155/2021/6678662Zhang, Bell, Yin, Zhang, EDock: Blind protein-ligand docking by replica-exchange monte carlo simulation, J. Cheminform,
doi:10.1186/s13321-020-00440-9Zhu, Guo, Geary, Zhang, Emerging Therapeutic Strategies for COVID-19 patients, Discoveries,
doi:10.15190/d.2020.2
