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Identification of Ellagitannins As Natural Inhibitors of Spike Proteins of COVID19 Virus: an in Silico-Based Study for Drug Development Arnica, F

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Identification of Ellagitannins As Natural Inhibitors of Spike Proteins of COVID19 Virus: an in Silico-Based Study for Drug Development Arnica, F Identification of Ellagitannins as Natural Inhibitors of Spike Proteins of COVID19 Virus: An in silico-based study for drug development Arnica, F. L. 1, Sabeena, G. 1, Sonam, B. 1*, Shaminder, S.2 & Sonia, M.3 1. Department of Pharmaceutical Sciences, SHALOM Institute of Health and Allied Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Naini, Prayagraj, Uttar Pradesh, 211007, India 2. Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad- Gurugram Expressway, Faridabad - 121 001, Haryana, India 3. Lingaya’s Vidyapeeth, Faridabad & Indraprastha Apollo Hospitals, New Delhi, India. *Corresponding Author: Sonam Bhatia, Dept. of Pharmaceutical Sciences, Faculty of Health Science, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS) (State University), Naini, Prayagraj (UP)- 211007: [email protected]. Tel: 7986612056. Summary BACKGROUND Ellagitannins are the potential source of bioactives and found abundantly in consumable food items. S-protein is a type I fusion protein of COVID19 virus and used for initial attachment with human Angiotensin converting enzyme 2 (ACE2) receptor, which facilitates its entry into the host cell. MATERIALS AND METHODS S-protein is validated target and hence, we screened food borne polyphenols and FDA approved Drugs against SARS-CoV-2 spike protein by the Autodock Vina 1.1.2. and Pymol for the molecular docking and simulation studies. RESULTS The study showed that Sanguiin-H-6, Potentillin, Punicalagin, have excellent binding affinities for S-protein as compared to its natural N-acetyl glucosamine (NAG) ligand. Theaflavin-di-galllate and Theaflavin-mono-gallate also show comparably good binding affinities and similar binding conformations. DISCUSSION SH6, Casuarictin, and Potentillin compounds have shown excellent binding on the hinge of S1 and S2 subunits of spike glycoprotein. As they show hydrogen bonding interaction with S2 unit by interacting with HR region and SD2 region, and on the other side they form hydrogen bonds with amino acid residues of NTD (which is present in S1 unit). The S1 unit is responsible for the virus attachment with its host ACE2 receptor, where potential ellagitannins where found to bind with NTD, and can modulate the binding of virus with host cell. African Journal of Health Sciences Volume 33, Issue No.5, September - October, 2020 78 Similarly, in S2 subunit its binding in HR region leads to disruption of membrane fusion stage, hence, ellagitannins have capability to act as potential inhibitor of virus spike protein by inhibiting both cell surface attachment as well as membrane fusion. These three compounds also show good drug likeliness properties apart from solubility which can be overcome by drug delivery advancements. CONCLUSION Thus, from the result it is concluded that Sanguiin-H-6, Potentillin, Casuarictin which are ellagitannins may have ability to inhibit both attachment and membrane fusion of COVID19 virus to ACE2 receptor. RECOMMENDATION This study needs further in vitro and in vivo testing which will provide a clear path for the development of novel compounds of natural origin that would most likely prevent the receptor binding or internalization of the SARS-CoV-2 spike protein and therefore could be potential drugs for COVID-19 preventive therapy. Keywords: COVID-19, Virtual Screening, Phytochemicals, Ellagitannins, Flavonoids, ADMET [Afr. J. Health Sci. 2020 33(5):78 - 97] the nucleocapsid (N), and spike (S) proteins (see Introduction Figure 1- all tables and figures are presented at The corona virus outbreak has resulted the end of this article) [6]. These proteins in a socio-economic crisis all over the world as th function in different ways to keep the viral of 11 March, 2020 [1] when the Director machinery active with E and M protein General of the World Health Organization maintaining viral assembly, N protein playing (WHO) declared COVID-19 disease to be a role in RNA synthesis [7]. The critical global pandemic. This upsurge initially started in glycoprotein S is a class I fusion protein found late December 2019 as a pneumonia-associated on the surface of COVID-19 virus, which infection, reported in Wuhan, Hubei Province of majorly causes the virus’ attachment to human China [2]. Angiotensin converting enzyme 2 (ACE2) Coronavirus is of the family of β- receptor. This is followed by its fusion with the coronavirus (bat SARS-related coronavirus host cells. The attachment is facilitated by the S1 (SARSr-CoV) strain WIV1) [3], which seem to subunit of S-protein via its receptor binding have evolved from bats and possess a dreadful domain (RBD). threat to human health. The clinical symptoms The RBD is projected upward as a associated with the SARS-CoV-2 generally hairpin, and provides a structural template for involves the upper respiratory tract infections ligand to bind, followed by antiparallel β-sheets with its mean reproduction number (R0) 3.28 [4] (N-terminal domain) NTD; both contributing to and onset of pneumonia symptoms within formation of S1 domain part. The S2 domain average of 4 days (ranging from 2 to 7) [5]. consists of a linker which connects RBD to The novel coronavirus is a positive heptad repeat (HR), a central helix (CH) and single-stranded RNA that consist of majorly four connector region (CR) (Figure 2). Two domains proteins namely, envelope (E), membrane (M), African Journal of Health Sciences Volume 33, Issue No.5, September - October, 2020 79 are responsible for the inclusive behaviour of the as a entry inhibitor to cell and anti-inflammatory virus, namely N-terminal (S1 containing RBDs) agents [13]. and C-terminal (S2 for fusion). Moreover, the S1 Since, the age old times, people have further consists of two subdomains N-terminal believed that naturally occurring substances like domain (NTD) and C-terminal domain (CTD), phytochemicals have potential to fight against both functioning as RBDs. infectious pathogens. Most of the polyphenols In β-coronavirus (SARS-CoV), the are reported to have anti-viral [14] and anti- receptor and virus fusion interaction takes place bacterial properties [15]. It is more inspiring to at C Terminal [8]. The S protein also consists of know that theaflavin derivatives (Flavon-3-ols), cleavage sites, fusion protein near to HR1 and a an active constituent of black tea is found to TM (transmembrane) span depicted in (Figure have proteolytic activity against main protease 3). It is reported that membrane fusion and (3-CL-Protease) of SARS-CoV established internalization of the COVID19 virus is brought through biological assays [16]. about by the S2 domain of spike protein. A huge In a similar context, we recently dynamism is associated with this protein as it performed virtual screening of Phenol Explorer changes its conformation from pre-fusion to post database against main protease of SARS-CoV2 fusion state after binding and internalization [9]. (COVID19 virus) and strikingly similar results Belouzard et al. [10] depicted the indicating that Theaflavin-di-gallate and mechanism of coronavirus entry mediated by Theaflavin-mono-gallate have potential to bind spike protein with the two different actively in substrate binding pocket of main conformation structures, namely, the metastable protease of COVID19 virus by a characteristic pre-fusion and the stable post fusion. When the covalent bond [17, 18]. This, study motivated us spike protein S1 attaches the host membrane, its to perform another investigation to explore the trimeric pre-fusion structure gets destabilized, capability of polyphenols (majorly ellagitannins) resulting in loss of S1, and the transition of S2 against spike protein of COVID19 virus. subunit to stable post fusion conformation. The In this study, we performed in silico virus on entering into the cell releases its screening to ascertain the most potent natural genome, followed by assembly and release of food borne compound against spike glycoprotein virions [11] from the infected cell through the of COVID19 virus which can inhibit virus process called exocytosis. The spike attachment and internalization with host cell. We glycoprotein seems to exert a potential target for found that four Ellagitannins and two flavon-3- inhibition of infection and treatment. ols can bind to (NTD) of S1 and (HR) of S2 sub Facing, the massive casualties of this unit of spike protein, with a binding interaction pandemic, researchers all around the world are more stable than that of N-acetyl glucosamine actively engaged in finding various strategies (NAG) and HCQ. These natural compounds including new and repurposed drugs to treat the have unique features of binding to both S1 and SARS-CoV-2 infection. Wei et al. [12] reported S2 subunit and most probably prevent COVID19 about Digitoxin, Bisindigotin, Polygoni Tinctorii virus from binding to the ACE2 receptor or Foliu and Raltegravir having high binding internalization during fusion [10, 19]. The affinities towards spike glycoprotein. In time of ADMET analysis also suggested that these need high-throughput virtual screening is also ellagitannins have potential to function as employed, which identified KT185, KT203 effective anti-SARS-CoV-2 agents with further GSK1838705A, BMS195614, and RS504393 as testing and scientific modifications. a potential binder of spike protein, thereby preventing spread of COVID19 by acting both African Journal of Health Sciences Volume 33, Issue No.5, September - October, 2020 80 by Wrapp et al. in 2020 [31]. This protein
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