Ethanopharmacological Approach to Control the Replication of 2019-nCov in Host- An Insilico Study.

doi:10.21203/rs.3.rs-982988/v1

2019- nCoV viral disease threatening every individual throughout the world. It is a highly challenging task to control the spread everywhere. There are certain antiviral drugs, steroids that are currently being prescribed to infected patients for faster recovery. But there is no proper cure today for this pandemic. In this present study, we have focused on controlling the replication and other possibilities of interaction of the 2019-nCoV virus inside the host cells. There are various herbs prescribed to us to improve our immunity and prepare our bodies to fight against this pathogen. In this study, herb compounds that are selected are Andrographolide (AP₁), 14-deoxy-11,12-didehydroandrographolide(AP₃), Ascorbic acid, Cinnamaldehyde, Curcumin, Diallyl sulfide, Eugenol. Gingerol, Kaempferol, Deacetylnimbin, Piperine, Quercetin, thymol, thymoquinone, Vasicine based on the literature survey. Selected ligands are most of them to treat respiratory tract infections and are also related to improving humoral immunity. Selected Ligand was allowed to dock against viral proteins which Crystal Structure of the SARS COV-2 Papain-like protease (Figure 1a) (PDB ID: 6wx4), RNA dependent RNA polymerase (Figure 1b) (PDB ID: 7c2k), Crystal structure of SARS COV-2 ORF7A encoded accessory protein (Figure 1c) (PDB ID: 6w37) Crystal structure of SARS COV-2 ADP-Ribose phosphatase NSP3 Proteins (PDB ID: 6w6y), PDB ID 6zsl Crystal structure of SARS COV-2 helicase NSP13 (PDB ID: 6ZSL), Crystal structure of NSP10-NSP16 Complex (PDB ID: 7bq7), PDB ID 6xdc Crystal structure of SARS COV-2 ORF3a Protein (PDB ID: 6xdc) to study their efficacy to control the replication and possible interactions in the human system using computational docking study. A Protein-Protein interaction study was also performed to study the efficacy of papain enzyme inhibitory efficacy of selected target proteins. Molecular dynamics studies were also performed to ensure the ligand efficacy for the selected target proteins.

Spectroscopy

Materials Chemistry

2019-nCoV

Target proteins

docking

dynamics

ligand efficacy

2019-nCoV viral strain is a new edition of the coronavirus family. Coronovirade is a family of novel corona viral strains. It belongs to RNA viruses. Nowadays many anti-viral drugs, steroids are practicing to treat them to control the disease but it works differently with patients some may get cured others may continue to suffer (Yu et al., 2020). This viral genome expresses many proteins and it happens to interact with human host cells. There are various docking studies to carried out on envelop proteins. This present study focuses on three target proteins which are as follows Crystal Structure of the SARS COV-2 Papain-like protease (Figure 1a) (PDB ID: 6wx4), RNA dependent RNA polymerase (Figure 1b) (PDB ID: 7c2k), Crystal structure of SARS COV-2 ORF7A encoded accessory protein (Figure 1c) (PDB ID: 6w37) Crystal structure of SARS COV-2 ADP-Ribose phosphatase NSP3 Proteins (PDB ID: 6w6y), PDB ID 6zsl Crystal structure of SARS COV-2 helicase NSP13 (PDB ID: 6ZSL), Crystal structure of NSP10-NSP16 Complex (PDB ID: 7bq7), PDB ID 6xdc Crystal structure of SARS COV-2 ORF3a Protein (PDB ID: 6xdc) helped the virus to replicate in the host system (Barik et al., 2020).

papain-like protease is one of the two important proteases in the viral genome. papain-like protease helps in the virus replication process and helps to destroy the viral response in the deubiquitination of host cell factors. The papain-like protease one of the targets for antiviral development processes (Rut et al., 2020).

RNA-dependent RNA polymerase is one of the important proteins in viral replication. It is a central compartment of viral replication and transcription machinery. It is one of the targets for antiviral drugs (Ishihama&Barbier 1994; Wang et al., 2020).

Orf7A is one of the open reading frame proteins in nCov19. ORF7A inhibits the activity of Bone Marrow Stromal Protein-2 (BST-2) which plays an important role in viral infections. It controls the release of virions into the system. Inactivation of BST-2 leads to the down-regulation in the inflammatory response. Inhibiting ORF7A helps to retain the BST-2 activity (Taylo et al., 2015).NSP3 is one of the important Non-structural proteins it plays a major role in host immune response. By inhibiting this NSP3 protein helps to preserve humoral immune response (Fireman et al., 2008, Lie et al., 2018,). ORF3a is one of the potential targets in treating nCov19 infection. ORF3a plays important role in viral pathogenicity (Gordon et al., 2020).

NSP13 is one of the important targets in controlling nCov19 infection. Studies showed that this hydrolase protein NSP13 plays a major role in this viral replication in the host cell (Mirza&Froeyen 2020). NSP10-NSP16 Protein complex possesses 2’ –O-MTase activity which helps in host viral replication. So it may be one of the potential targets in nCov19 infection. Papain enzyme known for its medicinal value in this present study papain enzyme docked against selected target proteins and study the efficacy of papain enzyme selected target proteins (LanLonde et al., 1998).

This present study investigates the selected target proteins that will be docked against selected ligand molecules that are using traditionally to boost the immune system and also to treat the common cold and mild infections.

Selected ligands must be tested for their drug-likeness property. It is important to analyze the selected ligands should obey Lipinski’s rule of five. It helps to analyze the stability of the compound and ensures the ability to exhibit the proposed biological activity in our system. Based on Lipinski’s rule the selected compounds ensure whether the selected ligand molecules will be orally active or not (Lipinski et al., 2001; Ghose et al., 1999; Smith 2011).

So far various computational studies carried out on main protease protein, Angiotensin converter proteins, nucleocapsid proteins, based on these studies in this study differ from other studies because the viral entry into our body is inevitable (Arya et al., 2020; Sharma et al., 2020; Narkhede et al., 2020; Khaerunnisa et al., 2020; Hall et al., 2020; Wang et al.,2015; Dipti& Ramesh 2020).

This present study deals with the viral protein interactions inside the host. Viral-host interaction mediates viral replication and other processes. Blocking viral–host interacting proteins helps to control the viral infection is the strategy of this present study. Other host-viral interacting proteins are like other open reading frame proteins and other non-structural proteins with screened ligands study are underway to publish it soon.

ADME/T Property Analysis:

The drug-likeness property of selected ligand molecules was assessed using the webserver http://www.scfbio-iitd.res.in/software/drugdesign/lipinski.jsp (Jayaram et al., 2012).

Protein preparation

The 3D structure of target proteins was Crystal Structure of the SARS COV-2 Papain-like protease (Figure 1a) (PDB ID: 6wx4), RNA dependent RNA polymerase (Figure 1b) (PDB ID: 7c2k), Crystal structure of SARS COV-2 ORF7A encoded accessory protein (Figure 1c) (PDB ID: 6w37) Crystal structure of SARS COV-2 ADP-Ribose phosphatase NSP3 Proteins (PDB ID: 6w6y), PDB ID 6zsl Crystal structure of SARS COV-2 helicase NSP13 (PDB ID: 6ZSL), Crystal structure of NSP10-NSP16 Complex (PDB ID: 7bq7), PDB ID 6xdc Crystal structure of SARS COV-2 ORF3a Protein (PDB ID: 6xdc) were downloaded from Protein Data Bank (www.rcsb.org/pdb) (Rut et al., 2020; Wang et al., 2020; Nelson et al., 2020, Michelska et al., 2020, Newman et al., 2020, Yan et al., 2020, Kerm et al., 2020).

Ligand Structures

The ligand selection is based on herbs that are used to treat the common cold. In this present study, these ligands were selected to study the efficiency of selected target proteins. There were no studies performed before with these target proteins against selected target proteins. Ligand structures were downloaded from the PubChem database. (Table 1) (www. https://pubchem.ncbi.nlm.nih.gov/) (Waugh & King 1932; Wong et al., 2014; Ashok Pawar et al., 2017; Johnson et al., 1996; Rao et al., 2015; Widyat et al., 2015; Ghasemzadeh et al., 2015; Cid-Ortega &Monroy-rivera 2018; Pholphana et al., 2013; Gorgani et al., 2017; Domanska et al., 2017; Sharma et al., 2017; Forouzanfar et al., 2014; Keesara& Jar 2017).

Table 1

Chemical Compound and their Structures
S.No	Source	Chemical Compound	PUBCHEMID
1	Nilavembu	Andrographolide (AP₁),	5318517
2	Nilavembu	14-deoxy-11,12-didehydroandrographolide(AP₃)	17650544
3	Citrus Fruits	Ascorbic acid	54670067
4	Cinnamon	Cinnamaldehyde	637511
5	Turmeric	Curcumin	969516
6	Garlic	Diallyl sulfide	11617
7	Cloves	Eugenol	3314
8	Ginger	Gingerol	442793
9	Green leafy Vegetables	Kaempferol	5280863
10	Neem leaves	Nimbin	108058
11	Black Pepper	Piperine	638024
12	Onions	Quercetin	5280343
13	Tulsi leaves	Thymol	6989
14	Black cumin Seeds	Thymoquinone	10281
15	Adathoda Leaves	Vasicine	72610

Molecular Docking

The protein structure was downloaded and prepared using autodock software, where Kollman charges and polar hydrogen were added and converted the structure format to .pdbqt file format. The ligand was prepared by detecting the rotatable bonds and set the aromatic criterion, and the ligand structure format converted to .pdbqt format. The Grid parameter file should get prepared for further docking study. Grid generated by selecting grid size, Crystal structure of SARS COV-2 helicase NSP13 (PDB ID: 6ZSL)-90x90x90, Crystal structure of SARS COV-2 ADP-Ribose phosphatase NSP3 Proteins (PDB ID: 6w6y)-80x80x80, Crystal structure of SARS COV-2 ORF3a Protein (PDB ID: 6xdc) - 90x90x90, RNA dependent RNA Polymerase-70x70x70, Crystal structure of SARS COV-2 ORF7A encoded accessory protein (PDB ID: 6w37)-60x70x60, Crystal structure of NSP10-NSP16 Complex- 80x80x80, Crystal Structure of the SARS COV-2 Papain-like protease (PDB ID: 6wx4)80x70x80 before performing docking study. Grid size helps the ligand to identify its binding pocket. Docking parameter file should get prepared for docking calculations by choosing macromolecule, as well as ligand file and finally docking parameter file written using the Lamrickan algorithm.

Protein-Protein Interaction Studies

Target proteins which are as follow Crystal Structure of the SARS COV-2 Papain-like protease (PDB ID: 6wx4), RNA dependent RNA polymerase (PDB ID: 7c2k), Crystal structure of SARS COV-2 ORF7A encoded accessory protein (PDB ID: 6w37) Crystal structure of SARS COV-2 ADP-Ribose phosphatase NSP3 Proteins (PDB ID: 6w6y), Crystal structure of SARS COV-2 helicase NSP13 (PDB ID: 6ZSL), Crystal structure of NSP10-NSP16 Complex (PDB ID: 7bq7), Crystal structure of SARS COV-2 ORF3a Protein (PDB ID: 6xdc) were docked against Papain enzyme which is known for its therapeutic activity using protein-protein docking server PyDock (Brain et al., 2013).

Molecular Dynamics Simulations

In our study, we performed molecular dynamics simulations of protein-ligand, protein-protein complexes using DESMOND and GROMACS 4.0.6 software package. OPLSAA and charmm forcefields were used for preparing the complexes and a 300 K constant temperature was maintained for the simulations. The molecular simulation time of protein-ligand, protein-protein complexes was set at 50ns and 30ns. xmgrace software was used to plot the RMSD graphs.

ADME/T Prediction

The drug-likeness property of selected ligands was analyzed so that it ensures oral bioavailability in the human system. Based on the results all the ligands were obeying the rule of five. Results ensured that the selected ligands are exhibits the intended property in the human system [Table2].

Table 2

ADME/T analysis results
S, No	Chemical Compound	Mass <500	Hydrogen bond donor <5	Hydrogen bond acceptor <10	Logp <5	Molar refractivity 40-130
1	Andrographolide (AP₁),	350	3	5	1.962	93.560
2	14-deoxy-11,12-didehydroandrographolide(AP₃)	332.0	2	4	2.767	92.076
3	Ascorbic acid	176.00	4	6	-1.40	35.25
4	Cinnamaldehyde	132	0	1	1.898	41.539
5	Curcumin	368	2	6	3.369	102.01
6	Diallyl sulphide	114.0	0	0	2.09	37.71
7	Eugenol	164.0	1	2	2.12	48.55
8	Gingerol	294.0	2	4	3.23	82.75
9	Kaempferol	286.0	4	6	2.30	72.38
10	Nimbin	498	1	8	3.35	127.53
11	Piperine	285	0	4	2.99	81.16
12	Quercetin	302.0	5	7	2.01	74.05
13	Thymol	150.0	1	1	2.82	46.93
14	Thymoquinone	164.0	0	2	1.66	46.69
15	Vasicine	188	1	3	1.29	54.57

Protein-ligand interactions

Crystal Structure of the SARS COV-2 Papain-like protease

Papain-like protease protein is one of the target proteins in this docking study. Ligands were selected based rationale based on their previous experimental studies for different diseases. Inhibitor efficiency of the selected ligands based on the binding affinity and hydrogen bonds formed in the active site pocket. Based on the Score Nimbin>Piperine> 14-deoxy-11,12-didehydroandrographolide(AP3)>andrographolide(AP1)> Quercetin> Kaempferol> Curcumin> Vasicine>Thymoquinone>Cinnamaldehyde>Ascorbicacid>thymol> Eugenol>Gingerol>Diallaylsulfide. Based on the hydrogen bond interactions we found that selected ligands were docked in the S1/S2 binding pockets which are said to be the active site pocket of papain-like protease (Rut et al., 2020). HIS73, ARG 82, ILE123, GLU124, LEU125, PHE127, ASP156, ASP164, ARG166, GLN174, HIS175, LEU178, LYS200, VAL202, GLU203, TYR273, THR301[Table 3]. Piperine is a potential ligand structure base on its clinically proven therapeutic activity. It showed better binding affinity but it made no hydrogen bond with active site residues (Figure 2a).

RNA dependent RNA polymerase

RNA-dependent RNA polymerase was docked against a set of ligands and the results were analyses based on the binding affinity.Nimbin>andrographolide (AP1)>curucumin> 14-deoxy-11,12didehydroandrographolide(AP3)>Kaempfrpl>Piperine>Quercetin>Gingerol>Vasicine>Thymol>Thymoquinone>Cinnamaldehyde>Eugenol> Ascorbic acid>diallylsulfide. All the ligands were bound well in the binding pocket of RNA-dependent RNA polymerase (Figure2b). PHE165, TYR169, LYS545, ARG553, ARG555, THR556, TYR619, SER681, THR680, CYS622, ARG624, ASP542, ASP618, ASP760, LYS621, ASP 452, LYS200, GLU203, VAL202. Based on the scores and interactions of Nimbin(Figure 3b), the lead molecules for the inhibition of RNA dependent RNA Polymerase (Table3).

Crystal structure of SARS COV-2 ORF7A encoded accessory protein

ORF7A protein results are Piperine> ANDROGRAPHOLIDE (AP1)>Nimbin> 14-DEOXY-11,12-DIDEHYDROANDROGRAPHOLIDE(AP3) > Cinnamaldehyde > Kaempferol> Vasicine> Curcumin > Gingerol>thymoquinone>eugenol>Quercetin>thymol> Ascorbic acid>diallylsulfide ranked according to their binding affinity. Based on the score Piperine (Figure 2c) exhibits better binding affinity and based on the interactions it bound well in the active site pocket. HIS4, TYR5, GLN 6, LYS17, GLU 18, ASN 28, TYR 60, GLN 61. These amino acid residues are interacting residues found in top-scoring docked poses [Table3].

Crystal structure of SARS COV-2 ORF7A encoded accessory protein

NSP3 Protein was docked against selected ligands and it was docked well in the active site of the NSP3 protein. PHE6, GLY8, TYR9, LYS11, LYS19, GLU120, TYR152, TYR161(Figure 2d) are the interacting residues found in top-ranked docking poses. Nimbin was the top-ranked docking pose with greater binding affinity compared with other ligand structures (Table 3).

Crystal structure of SARS COV-2 helicase NSP13

NSP13 protein was docked against selected ligand structures. Based on the docking score and interacting amino acids confirmed that the ligands are bound well in the active site of the proteins. From all the results Nimbin structure binding affinity better than other ligand structures (Table 3). It may have the inhibitory effect of the NSP13 protein thereby controlling the nCoV19 infection. LYS146, VAL181, LYS192, GLN194, THR214, SER229, MET 233, SER236, ALA237, VAL340, CYS342, ASP344, THR351, LEU363, ARG390(Figure 3e).

Crystal structure of NSP10-NSP16 Complex

NSP10-NSP16 complex was docked against the selected ligand structures and top-ranked docking poses have interacted with the following amino acid residues MET42, ASN43, THR47, HIS48, THR58, PRO59, ASP75, LYS76, ARG86, GLN87, ASN101, TYR132, LYS170, ASN198, SER201, ASN198(Figure 3f). Based on the docking score piperine was found to be a higher score than other ligand structures (Table 3). It may exhibit inhibitory efficacy against the NSP10-NSP16 complex.

Crystal structure of SARS COV-2 ORF3a Protein

ORF3a protein was docked against the selected ligand structures and it bound well in the active site of the protein (ORF3a). Top-ranked docked poses have interacted with the following amino acid residues SER60, ILE63, THR64, LYS66, LYS75, HIS78, ARG122, ASP142, ARG126, ARG122, ASP142, ASN144, TYR189, SER205, TYR206(Figure 2g). Based on the binding affinity quercetin exhibits better binding affinity towards ORF3a protein compared with other ligand structures (Table 3)

Table 3

Molecular docking score and interacting residues for selected target proteins
S.No	Ligand Name	Binding Affinity KJ/mol
S.No	Ligand Name	PDBID 6wx4	PDBID 7C2K	PDBID 6w37	PDBID 6w6y	PDBID 6zsl	PDBID 7bq7	PDBID 6xdc
1	Andrographolide (AP₁),	-6.24	-8.17	-6.46	-6.99	-6.83	-5.34	-6.82
2	14-deoxy-11,12-didehydroandrographolide(AP₃)	-6.53	-7.69	-6.26	-7.02	-6.39	-6.4	-7.05
3	Ascorbic acid	-4.64	-4.27	-3.54	-5.57	-4.24	-4.82	-4.02
4	Cinnamaldehyde	-4.75	-4.73	-5.85	-4.82	-5.05	-5.19	-4.12
5	Curcumin	-5.4	-7.84	-5.17	-6.7	-7.02	-5.66	-7.09
6	Diallylsulfide	-3.5	-3.36	-3.42	-3.36	-2.8	-3.75	-3.87
7	Eugenol	-4.54	-4.57	-4.83	-5.46	-3.3	-4.71	-4.39
8	Gingerol	-3.93	-5.42	-5.05	-6.54	-4.38	-3.58	-4.74
9	Kaempferol	-5.76	-7.33	-5.74	-7.35	-7.06	-5.13	-6.75
10	Nimbin	-6.89	-8.55	-6.03	-7.95	-8.16	-5.65	-7.08
11	Piperine	-6.77	-7.26	-6.6	-7.34	-6.92	-7.1	-7.22
12	Quercetin	-5.82	-7.16	-4.49	-7.23	-6.95	-6.14	-7.36
13	Thymol	-4.62	-5.12	-4.26	-6.64	-5.28	-5.42	-5.09
14	Thymoquinone	-4.93	-4.84	-4.91	-6.5	-5.03	-5.45	-4.97
15	Vasicine	-5.25	-5.25	-5.44	-6.17	-6.22	-5.61	-5.25

Protein-Protein Interaction Study

Papain Enzyme has interacted with target proteins. Papain enzyme ASN64, TYR61, ARG59, TYR67, GLN112, SER205 interacted with amino acid residues of nCov19papin like protease enzyme TYR137, ARG138, TYR71, LEU16, ASN15. Interacting residues were found in the active site of papain-like protease protein (Figure 3a). In Papain enzyme and RNA dependent, RNA polymerase docking following papain enzyme amino acid residues which are as follows GLN112 and TYR116 have interacted with GLN444 and ALA 443 of RNA dependent RNA polymerase enzyme (Figure 3b).

Papain enzyme ASN117, ARG191, ILE1 made hydrogen bonds with the following amino acid residues from the nCov19 ORF7A which are as follows TYR5, GLU1, PRO9, and HIS58. Interacting residues were in the active sites of the ORF7A protein (Figure 3c).

Papain enzyme SER216, THR223, SER58, GLN116 made hydrogen bonds with the following amino acid residues from the nCoV ORF3A which are as follows THR223, SER216, GLN116, SER58. Interacting residues were in the active sites of ORF3A protein (Figure 3d)

Papain enzyme TYR116, ASN155, TYR59 made hydrogen bonds with the following amino acid residues from the nCoV NSP3 protein which are as follows PHE475, TYR476, GLU591 were in the active sites of NSP3 protein (Figure 3e).

Papain enzyme GLY94, ALA71, TYR96, LEU45, LYS93 made hydrogen bonds with the following amino acid residues from the nCoV NSP10-NSP16 protein which are as follows ASP106, ARG86, ALA83, GLN87, ALA107, LYS38 were in the active sites of NSP10-NSP16 protein. (Figure 3f).

Papain enzyme TYR61, ARG59 made hydrogen bonds with amino acid residues from the nCoV NSP3 protein which are as follows VAL49, GLY 48. Interacting residues were found in the active site of the target protein (Figure 3g).

Table 4

Protein-Protein interactions scores
S.No	Protein-Protein Name	Electrostatics	Desolvation	VdW
1	Papain Enzyme with Papain like protease	-19.817	-16.732	41.674
2	Papain enzyme-RNA polymerase	-4.021	-33.997	25.399
3	Papain enzyme-ORF7A	-7.718	-8.886	51.944
4	Papain enzyme-NSP3	-19.996	-5.998	6.178
5	Papain enzyme-NSP13	-4.811	-33.826	81.689
6	Papin enzyme- NSP10-NSP16 complex	-5.852	-32.194	23.797
7	Papain enzyme – ORF3a	-2.594	-58.224	20.159

Molecular dynamics simulations interpretation of docked complexes

In the molecular dynamics simulations, we used the RMSD of the backbone to examine whether the system reaches its stability and equilibrium. The prepared complexes were immersed in a periodic water box, ions added to the box and the equilibration was performed at 200 k constantly. The final molecular dynamics was performed for 30ns for all the protein-protein and 50ns for protein-ligand complexes. Figure 4 shows that the RMSD plot for 6w37-9pap complexes (red- protein, black –protein with ligand), its shows the stability of the protein-protein complex.

The RMSD of the 6w37-piperine complex shows the stable conformation after 25ns from starting point of the stimulation and it represents the steady-state up to 50ns (Figure 5 (a)). The RMSF of the protein and ligand plot shows the local characteristic changes and positions (Figure 5(b),(c)). Protein secondary structures like alpha-helix and beta-strands were interpreting throughout the simulations, alpha helices highlighted with red color and blue color indicates the beta-strands, and SSE plots show the residue index throughout the simulation (Figure 5 (d)). From the SSE plots, the residue index shows beta-strands completely. The protein-ligand contacts (Figure 5 (e)) show the bond interaction with the residues, hydrophobic interactions found with HIS4, VAL14, LEU15, LEU16, PHE48, TYR60, LEU62 residues. The hydrogen bond interactions were found with GLN6, LYS17, GLN61 residues, and only one water bridge was found with LYS17 and no ionic interactions were found between the protein-ligand.

The RMSD of the nsp16-piperine complex shows the stable conformation after 30ns from starting point of the stimulation and it represents the steady-state up to 50ns (Figure 6 (a)). The RMSF of the protein and ligand plot shows characteristic changes and positions (Figure 6(b),(c)). Protein secondary structures like alpha-helix and beta-strands were interpreting throughout the simulations, alpha helices highlighted with red color and blue color indicates the beta-strands, and SSE plots show the residue index throughout the simulation (Figure 6 (d)). From the SSE plots, the residue index shows beta-strands and alpha helices equally found. The protein-ligand contacts (Figure 6 (e)) show the bond interaction with the residues, hydrophobic interactions found with PRO80, LEU100, MET131, PHE149 residues. The hydrogen bond interactions found with ASN43, GLY71, ALA72, GLY73, GY81, ASP99, LEU100, ASN101, ASP114, CYS115, ASP30, TYR132 residues, water bridges found with ASN43, LYS46, HIS69, PHE70, ALA72, GLY73, SER74, ASP75, LYS76, THR82, ASP98, ASN101, ASP114, ASP115, ASP130, MET131, ASP133, LYS135, LYS170, ASN297, and ionic interactions found with LYS46, ASP130, ASP133 residues.

This present study deals with the computational docking study using small molecules and an enzyme to control the replication of the virus in the host cell. Selected small molecules were studied for their drug-likeness property because they are herbal-based compounds. Based on this study Nimbin, Piperine and Quercetin are the lead molecules that were bound well in the active site of target proteins (Papain-like protease, RNA dependent RNA Polymerase, ORF7A protein, NSP3, NSP13, NSP10-NSP16, ORF3A). Based on the Scores and interactions ensure the binding affinity and protein-ligand stability. It ensures that the lead molecules were strong enough to inhibit the target proteins. Papain enzyme was also docked against the selected target proteins using the Protein-Protein interaction server. Molecular dynamics studies were performed for the proteins NSP13, 6w37 with piperine ligand results were ensured that the ligand can inhibit the target proteins. In the same way, protein-protein dynamics studies were also performed and ensured that the papain enzyme structure also can control the target protein ORF7A. This present study was performed to choose multiple targets to control the infection with studied ligand structures.

Acknowledgement

I express sincere gratitude to SASTRA Deemed to be University for Schrodinger software (https://www.schrodinger.com/) support Maestro and desmond versions used maestrov12.3, desmond-v5.6.

Funding: Not Applicable

Conflicts of interest/Competing interests: Not applicable

Availability of data and material: Not Applicable

Code availability: Not Applicable

Authors' contributions: Work Planned, Docking, Material collection were performed by M.Thenmozhi, Protein-Protein dynamics & Image editing were performed by M.Sathishkumar, Protein- ligand dynamics was performed by Suma mohan, Proof reading and literature support were performed by S.T.Kumaravel. All the authors contributed to the study conception and design and approved the final manuscript.

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Ethanopharmacological Approach to Control the Replication of 2019-nCov in Host- An Insilico Study.

Status:

Version 1

Abstract

Figures

Introduction

Materials And Methods

ADME/T Property Analysis:

Protein preparation

Ligand Structures

Molecular Docking

Protein-Protein Interaction Studies

Molecular Dynamics Simulations

Results And Discussion

ADME/T Prediction

Protein-ligand interactions

Crystal Structure of the SARS COV-2 Papain-like protease

RNA dependent RNA polymerase

Crystal structure of SARS COV-2 ORF7A encoded accessory protein

Crystal structure of SARS COV-2 ORF7A encoded accessory protein

Crystal structure of SARS COV-2 helicase NSP13

Crystal structure of NSP10-NSP16 Complex

Crystal structure of SARS COV-2 ORF3a Protein

Protein-Protein Interaction Study

Molecular dynamics simulations interpretation of docked complexes

Conclusion

Declarations

References

Status:

Version 1