In Silico study of Wheatgrass constituents against Coronavirus COVID-19 Proteins.

doi:10.21203/rs.3.rs-1167417/v1

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In Silico study of Wheatgrass constituents against Coronavirus COVID-19 Proteins.

https://doi.org/10.21203/rs.3.rs-1167417/v1

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As a result of COVID-19, the coronavirus associated with SARS-CoV-2 has emerged as the most lethal and infectious pandemic in history. Vaccines alone cannot assure us of a healthy future. As a result, drug production must go hand in hand with vaccine production. The purpose of this study is to evaluate the therapeutic potential of certain chemical constituents of Wheatgrass (Triticum aestivum Linn.,) that may be useful for treatment of COVID19. Seven chemical constituents of Wheatgrass, including Ascobic acid (SWA00A), Rutin (SWA00B), Ferulic acid (SWA00C), quercetin (SWA00D), Luteolin (SWA00E), Apigenin (SWA00F), and Kaempferol (SWA00G), were used for virtual screening. Covid19 viral proteins such as 6lu7-SARS-CoV2 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain-like protease of SARS-CoV-2, and 6m71-RNA-dependent RNA polymerase were selected for study. Drugs used in the treatment of COVID-19 namely Remdesivir, Darunavir, Ralimetinib, Berzosertib, Alpha-interferon, Arabinol, Chloroquine phosphate, Indinavir, Lopinavir, Ritonavir, Plegylated alfa interferon, 2-chloro-2-deoxy-D-glucose are taken as standards. Molecular docking was performed using the PyRx Virtual Screening tool. Among all 7 chemical components, Rutin (SWA00B) had the strongest binding affinity. According to the present study, Rutin present in Wheatgrass shows the highest potential to inhibit SARS-CoV-2 proteins. Wheatgrass has promising anti-SARS-CoV-2 properties, but further research is needed to prove their efficacy in vivo.

Wheatgrass

SARS-Cov-2

Molecular Docking

Rutin

The World Health Organization (WHO) was informed on December 31, 2019 that an outbreak of pneumonia cases was reported in Wuhan, Hubei Province, China. World Health Organization declared a pandemic on 12 March 2020 due to global spread of SARS-CoV-2 and increased mortality from Coronavirus disease[1, 2]. Vaccines cannot guarantee a long-term cure, as we do not know how long the vaccines will remain effective. The best drugs come from nature. In ancient times, herbal plants were used to cure diseases such as cancer, diabetes, and atherosclerosis[3, 4]. It has played an important role as a dietary supplement in most nations around the world[5, 6]. Wheatgrass contain bioflavonoids and the flavonoids have an ability to show antimicrobial and antiviral activity[6, 7]. Based on the above properties of Wheatgrass, the present study focused on computational investigation of few chemical constituents in Wheatgrass against 6lu7-COVID-19 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain-like protease found to be essential for management of SARSCoV-2, and 6m71-RNA-dependent RNA polymerase of SARS-COVID proteins of SARSCoV-2 found to be essential for management of SARSCoV-2.

An important application of molecular docking is the prediction of the binding orientation of small molecules to their protein targets when they are bound to each other in order to produce a stable complex[8, 9]. During the drug discovery and design process, docking is an integral part of the process. Through molecular docking methods, the structure of ligand-receptor complexes can be predicted.

In our previous study we have identified rutin as PARP-1 inhibitor [11].In the present study, some chemical constituents present in Wheatgrass were investigated against SARS-COVID proteins.

Software used - PyRx is a software package for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx allows users to run Virtual Screening from any platform and assists users at every step of the way - from data preparation to job submission and analysis. PyRx is a valuable tool for Computer-Assisted Drug Design since it comes with a docking wizard with an easy-to-use user interface that makes docking wizards easy to use. Additionally, PyRx includes chemical spreadsheet functionality and a powerful visualization engine essential to rational drug design. PyRx is using a large body of established open source software including:AutoDock 4 and AutoDock Vina are used as docking software.AutoDockTools, used to generate input files. Python as a programming/scripting language. WxPython for cross-platform GUI. The Visualization ToolKit (VKT) by Kitware, Inc. Enthought Tool Suite, including Traits, for application building blocks. Open Babel for importing SDF files, removing salts and energy minimization. matplotlib for 2D plotting.

BIOVIA Discovery Studio Visualizer – it is a free, feature-rich molecular modeling application for viewing, sharing and analyzing protein and small molecule.

Preparation of Proteins:

The structures of proteins of SARS-COVID (6lu7, 6zsl, 6w9c, 6m71) have been downloaded from the PDB protein databank. Preparation of proteins for docking simulation was achieved by using BIOVIA Discovery Studio Visualizer. Receptor protein preparation for docking study was initiated by removing water molecules, hetero atoms and co-crystallized ligands from PDB crystal structures of proteins (6lu7-COVID-19 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain like protease of SARS CoV-2, 6m71-RNA-dependent RNA polymerase of SARS-COVID), polar hydrogen atoms were added subsequently to the receptor proteins and finally the receptor protein input files were saved as pdbqt file. This procedure was followed for every single protein.

Preparation of Ligands:

The 3D structures of chemical constituents present in Wheatgrass and Standard drugs were obtained from PubChem Database (https:pubchem.ncbi.nih.gov).

Table 1

standard drug used in the treatment of covid19
Standards	Pubchem CIDs
Remdesvir	121304016
Daunavir	213039
Ralimetinib	11539025
Berzosirtib	59472121
alpha-interferon	465690
Arabinol	94154
Chloroquine phosphate	2719
Indinavir	5362440
Lopinavir Ritonavir mix structure	11979606
Plegylated alfa interferon	86278337
2-chloro-2-deoxy-D- glucose	151933

Table 2

-Pubchem CIDs of all ligands
Chemical Constituents	Pubchem CIDs
Ascobic acid SWA00A	54670067
Rutin SWA00B	5280805
Ferulic acid SWA00C	445858
Quercetin SWA00D	5280343
Luteolin SWA00E	5280445
Apigenin SWA00F	5280443
kaempferol SWA00G	5280863

Open babel tool were used for ligand energy minimization by using the force field; using conjugated gradients in 1000 steps.

Compound screening using the PyRx program.

The docking was conducted using PyRx 0.8, a virtual screening tool that utilizes Autodock Vina as a docking engine. During molecular docking, the ligands were considered flexible while proteins were thought of as rigid. SARS-COVID (6lu7-COVID-19 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain like protease of SARS CoV-2, 6m71-RNA-dependent RNA polymerase of SARS-COVID) proteins were uploaded to the program and it was converted into .pdbqt format. Then all ligands (standards and chemical constituents) were converted separately into pdbqt format. The Gridbox was generated by covering active sites of the protein with coordination and box dimension. The exhaustiveness values were set to 8. Then clicked on forward. After that Autodock vina docks each ligand one by one.. Ligand showing the lowest binding affinity and ability to bind in the active site was identified and a snapshot of that ligand and protein was taken by using PyRx software. whole procedure was carried out separately for every single protein and for ligands

Table 3 to 6 below shows the results of docking analysis between the different ligands with the receptor proteins.

Table 3

Binding of ligands with 6lu7-COVID-19 main protease.
Complex (protein+ ligand)	Binding Affinity (kcal/mol)	Ligands
Standards
6lu7_59472121_mmff94_E=143.39	-8.1	Berzosertib
6lu7_11539025_mmff94_E=29.70	-8.2	Ralimetinib
6lu7_213039_mmff94_E=-16.24	-7.5	Darunavir
6lu7_121304016_mmff94_E=-55.11	-6.6	Remdesivir
6lu7_465690_uff_E=535.19	-7.2	Alpha-interferon
6lu7_94154_uff_E=122.55	-4.7	Arabinol
6lu7_2719_uff_E=262.55	-5.4	Chloroquine Phosphate
6lu7_5362440_uff_E=626.41	-7.7	Indinavir
6lu7_11979606_uff_E=2802.52	-7.5	Lopinavir Ritonavir mix structure
6lu7_86278337_uff_E=173.27	-4.3	Plegylated alfa interferon
6lu7_151933_uff_E=127.56	-4.6	2-chloro-2-deoxy-D- glucose
Chemical constituents
6lu7_54670067_uff_E=200.65	-5.1	SWA00A
6lu7_5280805_uff_E=751.59	-9	SWA00B
6lu7_445858_uff_E=177.42	-6	SWA00C
6lu7_5280343_uff_E=380.43	-7.3	SWA00D
6lu7_5280445_uff_E=242.10	-7.4	SWA00E
6lu7_5280443_uff_E=233.26	-7.8	SWA00F
6lu7_5280863_uff_E=362.50	-7.1	SWA00G

Table 4

Binding of ligands with 6zsl-SARS-CoV-2 helicase.
Complex (protein+ ligand)	Binding Affinity(kcal/mol)	Ligands
Standards
6zsl...HELICASE_PROTEIN_...CHAIN_A_59472121_mmff94_E=143.39	-8.6	Berzosertib
6zsl...HELICASE_PROTEIN_...CHAIN_A_11539025_mmff94_E=29.70	-8.7	Ralimetinib
6zsl...HELICASE_PROTEIN_...CHAIN_A_213039_mmff94_E=-16.24	-7.1	Darunavir
6zsl...HELICASE_PROTEIN_...CHAIN_A_121304016_mmff94_E=-55.11	-8	Remdesivir
6zsl...HELICASE_PROTEIN_...CHAIN_A_465690_uff_E=535.19	-8.2	Alpha-interferon
6zsl...HELICASE_PROTEIN_...CHAIN_A_94154_uff_E=122.55	-4.6	Arabinol
6zsl...HELICASE_PROTEIN_...CHAIN_A_2719_uff_E=262.55	-5.8	Chloroquine Phosphate
6zsl...HELICASE_PROTEIN_...CHAIN_A_5362440_uff_E=626.41	-8.2	Indinavir
6zsl...HELICASE_PROTEIN_...CHAIN_A_11979606_uff_E=2868.68	-7.9	Lopinavir Ritonavir mix structure
6zsl...HELICASE_PROTEIN_...CHAIN_A_86278337_uff_E=173.27	-4.6	Plegylated alfa interferon
6zsl...HELICASE_PROTEIN_...CHAIN_A_151933_uff_E=127.56	-5.3	2-chloro-2-deoxy-D- glucose
Chemical constituents
6zsl...HELICASE_PROTEIN_...CHAIN_A_54670067_uff_E=200.65	-5.5	SWA00A
6zsl...HELICASE_PROTEIN_...CHAIN_A_5280805_uff_E=751.59	-9.3	SWA00B
6zsl...HELICASE_PROTEIN_...CHAIN_A_445858_uff_E=177.42	-6.4	SWA00C
6zsl...HELICASE_PROTEIN_...CHAIN_A_5280343_uff_E=380.43	-8	SWA00D
6zsl...HELICASE_PROTEIN_...CHAIN_A_5280445_uff_E=242.10	-7.8	SWA00E
6zsl...HELICASE_PROTEIN_...CHAIN_A_5280443_uff_E=233.26	-7.8	SWA00F
6zsl...HELICASE_PROTEIN_...CHAIN_A_5280863_uff_E=362.50	-7.7	SWA00G

Table 5

Binding of ligands with 6w9c-papain like protease of SARS CoV-2.
Complex (protein+ ligand)	Binding Affinity(kcal/mol)	Ligands
Standards
6w9c...Papain_like_protease_chain_A_59472121_mmff94_E=143.39	-8	Berzosertib
6w9c...Papain_like_protease_chain_A_11539025_mmff94_E=29.70	-7.1	Ralimetinib
6w9c...Papain_like_protease_chain_A_213039_mmff94_E=-16.24	-6.5	Darunavir
6w9c...Papain_like_protease_chain_A_121304016_mmff94_E=-55.11	-6.9	Remdesivir
6w9c...Papain_like_protease_chain_A_465690_uff_E=535.19	-7.6	Alpha-interferon
6w9c...Papain_like_protease_chain_A_94154_uff_E=122.55	-4.8	Arabinol
6w9c...Papain_like_protease_chain_A_2719_uff_E=262.55	-4.6	Chloroquine Phosphate
6w9c...Papain_like_protease_chain_A_5362440_uff_E=626.41	-7.2	Indinavir
6w9c...Papain_like_protease_chain_A_11979606_uff_E=2922.38	-6.3	Lopinavir Ritonavir mix structure
6w9c...Papain_like_protease_chain_A_86278337_uff_E=173.27	-3.8	Plegylated alfa interferon
6w9c...Papain_like_protease_chain_A_151933_uff_E=127.56	-5	2-chloro-2-deoxy-D- glucose
Chemical constituents
6w9c...Papain_like_protease_chain_A_54670067_uff_E=200.65	-5.2	SWA00A
6w9c...Papain_like_protease_chain_A_5280805_uff_E=751.59	-8.4	SWA00B
6w9c...Papain_like_protease_chain_A_445858_uff_E=177.42	-5.3	SWA00C
6w9c...Papain_like_protease_chain_A_5280343_uff_E=380.43	-7	SWA00D
6w9c...Papain_like_protease_chain_A_5280445_uff_E=242.10	-7.3	SWA00E
6w9c...Papain_like_protease_chain_A_5280443_uff_E=233.26	-7.3	SWA00F
6w9c...Papain_like_protease_chain_A_5280863_uff_E=362.50	-6.7	SWA00G

Table 6

Binding of ligands with 6m71-RNA-dependent RNA polymerase.
Complex (protein+ ligand)		Ligands
Standards
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_59472121_mmff94_E=143.39	-8.1	Berzosertib
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_11539025_mmff94_E=29.70	-8.5	Ralimetinib
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_213039_mmff94_E=-16.24	-8.3	Darunavir
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_121304016_mmff94_E=-55.11	-8.3	Remdesvir
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_465690_uff_E=535.19	-7.6	Alpha-interferon
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_94154_uff_E=122.55	-4.9	Arabinol
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_2719_uff_E=262.55	-5.3	Chloroquine Phosphate
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5362440_uff_E=626.41	-8.5	Indinavir
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_11979606_uff_E=2314.51	-7.8	Lopinavir Ritonavir mix structure
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_86278337_uff_E=173.27	-4.3	Plegylated alfa interferon
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_151933_uff_E=127.56	-4.9	2-chloro-2-deoxy-D- glucose
Chemical constituents
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_54670067_uff_E=200.65	-5.6	SWA00A
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5280805_uff_E=751.59	-9.5	SWA00B
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_445858_uff_E=177.42	-5.5	SWA00C
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5280343_uff_E=380.43	-7.4	SWA00D
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5280445_uff_E=242.10	-7.6	SWA00E
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5280443_uff_E=233.26	-7.4	SWA00F
6m71..RNA_dependant_RNA_POLYMERASE..CHAIN_A_5280863_uff_E=362.50	-7.1	SWA00G

From the above result we can infer that SWA00B exhibited high binding affinity than that of standard drugs with SARS-COVID (6lu7-COVID-19 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain like protease of SARS CoV-2, 6m71-RNA-dependent RNA polymerase of SARS-COVID) proteins Binding energies of are as follows:

9 kcal/mol against 6lu7 which is higher than the binding affinity of standard (Ralimetinib)
9.3 kcal/mol against 6zsl which is higher than the binding affinity of standard (Ralimetinib)
8.4kcal/mol against 6w9c which is higher than the binding affinity of standard (Berzosertib)
9.5kcal/mol against 6m71 which is higher than the binding affinity of standard (Ralimetnib)

Following are the images which shows binding of ligands with Proteins.

The virus has gained entry to over 210 countries and territories. Though experts assumed that the virus is transmitted from animals to humans, there are mixed reports on the origin of the virus. There are treatment options available for the virus but they, limited to the use of antivirals such as Remdesivir and Galidesivir[12].

In view of this we selected Wheatgrass for its antiviral activity against SARS CoV-2 virus, several drug candidates have been evaluated. Based on the literature, we selected to evaluate the antiviral potential of seven chemical constituents (ascorbic acid, Quercetin, Ferulic acid, Luteolin, Rutin, Kaempferol,apeginin) present in the Wheatgrass against COVID-19 infection. Among all ligands, PyRx tool identified the best fitting ligand Rutin towards 6lu7, 6zsl, 6w9c, 6m71 proteins of SARS COVID.

Vitamin P is another name of rutin in the food processing industry it has been widely used as an antioxidant most of the supplementary complex vitamins contains rutin[13].

Rutin (3,3’,4’5,7-pentahydroxyflavone-3-rhamnoglucoside) is a flavonoid of the flavonol type which is present in most of the plants and shows number of pharmacological properties that have been exploited in human medicine and nutrition[14]. Further studies need to be performed on rutin.

In the meantime taking wheatgrass products (juice, powder, tablets) will be beneficial to protect against SARS-COVID.

The molecular docking analyses helped to evaluate the binding of some chemical constituents present in Wheatgrass. Among the tested compounds SWA00B (rutin) found to be potential constituent of Wheatgrass which Posses highest binding affinity to 6lu7-COVID-19 main protease, 6zsl-SARS-CoV-2 helicase, 6w9c-papain like protease of SARS CoV-2, 6m71-RNA-dependent RNA polymerase of SARS-COVID than all other ligands. Therefore, SWA00B rich fraction of Wheatgrass will help the people to protect against SARS-COVID. Moreover, in vivo studies of rutin should be carried out to validate the results and for developing more potent drugs for control of SARS-COVID.

Competing interests: The authors declare no competing interests.

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In Silico study of Wheatgrass constituents against Coronavirus COVID-19 Proteins.

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Abstract

Figures

Introduction

Material And Methods

Preparation of Proteins:

Preparation of Ligands:

Result

Discussion

Conclusion

Declarations

References

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