key: cord-301828-qux5hvcw authors: Khalifa, Ibrahim; Zhu, Wei; Mohammed, Hammad Hamed Hammad; Dutta, Kunal; Li, Chunmei title: Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date: 2020-08-11 journal: J Food Biochem DOI: 10.1111/jfbc.13432 sha: doc_id: 301828 cord_uid: qux5hvcw 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 (3CL(Pro)) 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 3CL(pro) 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 3CL(Pro) 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 3CL(pro) of SARS‐CoV‐2. Pedunculagin, tercatain, and castalin interacted with Cys145 and His41 of SARS‐CoV‐2‐3CL(pro). Pedunculagin‐SARS‐CoV‐2‐3CL(pro) 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. Freshly, the new coronavirus (SARS-CoV-2) was discovered on the late of 2019 (Xu et al., 2020) . COVID-19 suddenly appeared, leading not only the health authorities, but also the scientific community to swift actions toward it. As a result, the entire-genome series of SARS-CoV-2 was issued and subsequently it was scientifically spotlighted (Jiang et al., 2020; Stebbing et al., 2020) . The SARS-CoV-2 belongs to the β-coronavirus group, sharing ancestry with bat coronavirus HKU9-1, alike to SARS, and regardless of arrangement variety its Spike protein intensely networks with human ACE 2 -receptor (Ul Qamar, Alqahtani, Alamri, & Chen, 2020). By July 13, the global death toll exceeded 574,000, with 13,200.000 confirmed cases, and 7,600.000 thousand recovered cases in 213 countries (https://www.world omete rs.info/coron avirus). Recent studies emphasized that SARS-CoV-2 genes stake <80% nucleotide uniqueness and 89.1% nucleotide likeness with SARS-genes (Kim, Kim, & Lee, 2020; Moorthy, Restrepo, Preziosi, & Swaminathan, 2020) . Usually, β-coronaviruses yield a ~800 kDa polypeptide upon dictation of the genome. This polypeptide is proteolytically slashed to create numerous proteins, and the proteolytic diversion is facilitated by papain-like protease, and slicing the polyprotein at 16 different spots to create several nonoperational proteins that are vital for the viral reproduction (Macchiagodena, Pagliai, & Procacci, 2020) . Thus, this protease portrays a key task in the virus duplication, and distinct structural/fitment protein-encoding genes situated at the 3′ end that F I G U R E 1 2D-chemical structures of 19 selected hydrolysable tannins Grandinin Tercatain Tellimagradin Granatin A Casuarinin Geraniin exhibit extreme inconsistency (Rut et al., 2020) . Therefore, 3CL Pro enzyme may assist as a possible target for natural inhibitors against COVID-19. Structure-based effect analyses and high output findings have recognized possible inhibitors of SARS-and MERS-3CL pro (Pillaiyar, Meenakshisundaram, & Manickam, 2020) . Bioactive substances, especially hydrolysable tannins, have attracted significant attention which could be valorized to develop medications without side-effects (Liu et al., 2016) . Hydrolysable tannins are also measured to be valuable in eliminating the opposing effects of several chemotherapeutic stuffs as well as in extending permanency and achieving positive overall health with anticancer possible and can be utilized as a substitute cancer-drug supply (Buzzini et al., 2008; Lin et al., 2011; Aires, 2020; Jia et al., 2019; Zhu, Khalifa, Peng, & Lic, 2018) . Hydrolysable tannins, including punicalagin, punicalin, and geraniin, exerted antiviral effects toward B virus by averting the creation of cccDNA and indorsing cccDNA decline, which may aid as chief components for the expansion of novel agents to remedy HBV-infection (Liu et al., 2016) . Likewise, tannin-type compounds, such as epiacutissimins A and B, castalin, vescalin, chebulagic acid, and punicalagin showed anti-herpesvirus activity via targeting viral glycoprotein-glycosaminoglycan binding to inhibit access and cell-to-cell feast (Lin et al., 2011; Aires, 2020 The current study was designed to find out a potent inhibitor against COVID-19 from 19 structural different hydrolysable tannins which could target the main protease of SARS-CoV-2 using in silico approaches (molecular docking and drug-likeness scan). The findings of our study will enable the researchers to rally the status of natural therapeutics against COVID-19. Structure-based simulated inspection tactic was performed using high-performing computing work-station with the subsequent stipulations (Intel(R) Core-(TM) i7-3210M CPU @ 2.50 GHz, 5 Core(s) CPU of 4.00 GB RAM and 64-bit Windows-10 Functioning System). Operating Environment (MOE 09). The structures of 19 hydrolysable tannins including, castalin (CID- Likewise, three-dimensional structure of 3CL pro of SARS-CoV-2 (PDB: 6y84) was regained from Protein-Data-Bank (http://www. rcsb.org) with 2.16 Å resolution. To enhance the 3CL pro -structure, previously interacted ligands and H 2 O substances were detached from 3CL pro -structure, 3D-protonation, and energy minimalization were dedicated in MOE-09. The minimalized structure was utilized for further docking operation in the following steps. It creates 2D-images signifying the forces steadying ligands within binding pouches of receptors (Khan et al., 2017) . To investigate the medication likeliness of 19 tannins, all were further clarified based on behavior suitable molecular characters to be candidate inhibitor against COVID-19. Molecular dynamics simulations (MD) were done to refine our docking results and to analyze the assembling performance and con- Furthermore, it was found that SARS-CoV-2 is much comparable to SARS than MERS, and imparts a mutual forebear with bat-based coronaviruses (Ji, Wang, Zhao, Zai, & Li, 2020; Xu et al., 2020) . The findings also discovered that SARS-CoV-2 had a Cys-His catalytic dyad (Cys145 and His41), reliable with SARS-3CL pro (Cys145 and His41), TGEV-3CL pro (Cys144 and His41), and HCoV-3CL pro (Cys144 and His41) (Yang et al., 2003) . It was disclosed that SARS-CoV-2-3CL pro receptor-binding concise configuration and be similar with that of SARS-3CL pro binding compact and increases the opportunity that inhibitors projected for SARS-3CL pro may also mitigate the motion of SARS-CoV-2-3CL pro . To manage with the continuous essential of new and operative small molecule as natural therapeutics against COVID-19 with negligible side-effects, studies are now directing more on computational drug finding (Desai et al., 2008) . Several reports testified the antiviral possible of tannins via computer-assisted medication strategy (Buzzini et al., 2008; Lin et al., 2011) . To speed the drug agreement process and to realize more effectual inhibitors with novel frameworks that can progress the antiviral-based therapeutics status, computational drug discovery methods are extremely steadfast. Note: Mol: An output pose, S: The final score, which is the score of the last stage that was not set to None, E-conf: The energy of the conformer, E-place: Score from the placement stage, E-score: Score from the rescoring stage. tannins, simulated selection was ended to realize new allosteric compounds as inhibitors against COVID-19. Allosteric directive has been described as an operative tactic to conquer irretrievable inhibition. Spatial alignment and dock score of present stated four topranked chiefs discloses effectual interacting of functional residues with greatest binding affinity. These tannins fit with the drug prospect norms tabulated in Table. 1 and S1 and may attest exceptional perceptive to use as a preparatory point. Interacting affinity analysis of 19 tannins through LigX revealed in Figure 3 . It was revealed that 19 tannins differentially interacted SARS-CoV-2-3CL pro . Among these hydrolysable tannins, pedunculagin, strongly interacted with the catalytic dyad residues (Cys-145 and His-41) of SARS-CoV-2-3CL pro , with sense binding affinity, docking score, and ADMET properties. As supplemented in Table S2 , pedunculagin is an excellent compound regarding solubility, and having high intestinal absorption, and does not shows any mutation. This molecule is not inhibitor of HERG l and HERG ll that means it is not harmful to cardiac muscles (heart muscles). Previously, pedunculagin, tercatain, and castalin which could be biological activities (Chang et al., 1995; Silva et al., 2016; Zuo, LI, Chen, & Xu, 2005) . In a related study, Park et al. (2017) acids are also the monomer types of hydrolyzed tannins (Serrano, Puupponen-Pimiä, Dauer, Aura, & Saura-Calixto, 2009; Smeriglio, Barreca, Bellocco, & Trombetta, 2017) . It was informed that ellagitannins release ellagic acid upon hydrolysis in rat's intestine. Gallic acid is infused via a paracellular route in Caco-2 cells, with t max of absorption around 1.27 hr in humans. Regarding ellagic acid absorption, some authors have detected ellagic acid in human plasma between 0.5 and 3 hr after oral administration of pomegranate juice. Following absorption, ellagic acid undergoes conjugation, and conjugated forms with methyl, glucuronyl, and sulfate groups have been found in plasma and excreted in urine. Gallotannins are easily degraded by bacteria, fungi, and yeast. Tannase produced by a group of microorganisms is active in galloyl residues of galloyls esters, as well as on hexahydroydi-phenoyl. Unlike proanthocyanidins, colonic bacteria are capable of metabolizing hydrolysable tannins. The presence of lactobacilli with distinct tannase activity proposes that gallic acid from gallotannins may be available during colonic fermentation. For example, casuarictin incubated with caecal content increase the release of ellagic acid. In rats fed with punicalagin, ellagic acid is transformed by rat microflora to 3,8-dihydroxy-6H-dibenzo (b,d)-pyran-6-one (urolithin B)derivatives, the total urinary excretion accounting for 0.7%-52.7% of the ingested punilagin in rats. When a single dose of ellagitannin-containing foodstuff was taken by each group of human volunteers, the metabolite excretion ranged from 2.8% to 16.6% of the ingested ellagitannins. Therefore, the health effects of tannins intake are probably a consequence of the biological activity of their metabolites. Looking at the antiviral drug possible of aforenoted tannins, current study was an endeavor to feat the chemical nature of three hydrolysable tannins as natural inhibitors against COVID-19. Present molecular docking study has publicized the significant interactions of medicinal tannins with the main protease of COVID-19, which were successfully block both His41 and Cys145. To authenticate the drug capacity of selected tannins, ligand characters were considered with LigX tool of MOE. All chosen tannins disclosed constructive results and accomplish the standards of the Lipinski's regulation of five (Khan et al., 2017) . The regulation defines that possible drug-like components should have about 5 H-bond donors, maximum 10 H-bond acceptors, and an octanol water panel coefficient log P not > 5. These results suggest that natural components identified in our study, specially pedunculagin, tercatain, and castalin, may demonstrate more valuable contenders for COVID-19 drug rehabilitation. To further examine the molecular docking results, pedunculagin was subjected to MD simulation; and RMSD, radius of gyration (RoG), and H-bond characters were expressed. Pedunculagin-SARS-CoV-2-3CL procomplex did not show any obvious fluctuations, referring to the stability of tannin-protein complexes with a typical RMSD value of 1.4 ± 0.01 Å ( Figure S1a ). It was also suggested normal behavior for pedunculagin-SARS-CoV-2-3CL pro complex; where it was persisted dense and steady during the 80 ns simulations ( Figure S1b) . Likewise, H-bonds which are the key stabilizing forces in proteins, proposed that the pedunculagin-SARS-CoV-2-3CL pro complex remain stable throughout the simulation, with no noticeable fluctuations ( Figure S1c ). It can be concluded from this study that each Secondary metabolite components are regularly found in medicinal plants. We therefore predicted the pharmacophore of pedunculagin based on its active groups. Hydroxy groups (−OH), ketone groups (=O), and phenolic rings in pedunculagin are projected to play parts amino acid residue binding at the energetic spot of SARS-CoV-2-3CL pro (Figure 4) . These groups were found to directly interact with the 3CL pro of SARS-CoV-2 through H-bonding and other forces. In conclusion, our study exposed that some medicinal plant rich in hydrolysable tannins, especially pedunculagin, tercatain, and castalin, could be theoretically used to treat the outbreak of COVID-19. Herein, we screened the structural relationship activity of 19 hydrolysable tannins as potential antiviral components and we chose the top three hits that may inhibit the main protease of SARS-CoV-2 and hence virus copying. Further in vitro and in vivo studies are needed to transmute these probable hydrolysable tannins inhibitors into clinical drugs. We predicted that the understandings gained in the current study may evidence valued for discovering and unindustrialized novel natural inhibitors against COVID-19 in the near future. This work was self-supported by the authors. We also acknowledge all laboratories and databases websites mentioned in this study. 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