|Year : 2019 | Volume
| Issue : 4 | Page : 269-276
Computer-aided docking studies of phytochemicals from plants Salix subserrata and Onion as inhibitors of glycoprotein G of rabies virus
Tehseen M Dhorajiwala1, Sumit T Halder1, Lalit R Samant2
1 Department of Bioinformatics, Patkar College of Arts and Science, Mumbai, Maharashtra, India
2 Molecular Genetics Research Laboratory, Bai Jerbai Wadia Hospital for Children, Mumbai, Maharashtra, India
|Date of Submission||22-Aug-2019|
|Date of Acceptance||28-Sep-2019|
|Date of Web Publication||03-Dec-2019|
Mr. Lalit R Samant
Molecular Genetics Research Laboratory, Bai Jerbai Wadia Hospital for Children, Parel, Mumbai - 400 012, Maharashtra
Source of Support: None, Conflict of Interest: None
Objective: Rabies is a viral disease caused by the bite of an infected animal commonly a dog majorly affecting people in Africa and Asia and is extremely fatal if the infected person is not vaccinated. The glycoprotein G of the rabies virus is an important viral protein involved in the virus entry through endocytosis and its replication in the host cell; this protein was chosen as the target protein for modeling and docking analysis. Methods: Phytochemicals from plants Salix subserrata and onion have been reported to showing anti-rabies activity and were screened for in silico toxicity using SwissADME and Protox-II servers, and the two phytochemicals passing the filters (+)-catechin and kaempferol were docked with the receptor protein. The phytochemicals were docked using the software AutoDock Vina and SwissDock server by keeping the grid dimensions the same to validate the docking results. Results: (+)-Catechin gave better binding affinity, full fitness, and estimated ΔG values by AutoDock Vina and SwissADME than kaempferol and also formed conventional hydrogen bonds with the target protein; thus, the important active binding residues were also obtained from the results. Conclusion: Hence, ligand (+)-catechin is a potential natural inhibitor against rabies, and the study thus established the importance of natural product-based drug discovery against one of the most neglected and fatal diseases that is rabies.
Keywords: (+)-Catechin, docking analysis, glycoprotein G, kaempferol, protein modeling
|How to cite this article:|
Dhorajiwala TM, Halder ST, Samant LR. Computer-aided docking studies of phytochemicals from plants Salix subserrata and Onion as inhibitors of glycoprotein G of rabies virus. Biomed Biotechnol Res J 2019;3:269-76
|How to cite this URL:|
Dhorajiwala TM, Halder ST, Samant LR. Computer-aided docking studies of phytochemicals from plants Salix subserrata and Onion as inhibitors of glycoprotein G of rabies virus. Biomed Biotechnol Res J [serial online] 2019 [cited 2019 Dec 9];3:269-76. Available from: http://www.bmbtrj.org/text.asp?2019/3/4/269/272185
Tehseen M. Dhorajiwala and Sumit T. Halder, these authors contributed equally
| Introduction|| |
Rabies is a zoonotic disease caused due to the rabies virus of the Rhabdoviridaefamily belonging to the genus causing 59,000 annually in over 150 countries and is endemic on all continents except Antarctica., The disease is fatal in humans, transmitted through the bites of an infected animal such as dog, bat, and raccoons. Nonbite exposure to the virus can also be a mode of transmission in rare cases. Rabies is manifested in five stages which include incubation, prodrome, acute neurologic period, coma, and death. Symptoms observed include malaise, fever, nausea, vomiting, and abdominal pain which will progress to headache, irritability, agitation, and photophobia leading to encephalitis. There is no medication available for the treatment of rabies, and vaccination is the only way to prevent getting infected. The disease has always been a cause of public health concern in Asia and Africa where the most numbers of rabies cases are reported every year.
The virus is a negative sense, single-stranded RNA weighing 12 kb in size. The virus encodes for five proteins which include nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and RNA-dependent RNA polymerase (L).,
Glycoprotein G (495 amino acid residues) of rabies virus is exposed on the virus surface weighing 65–67 kDa encoded by the G gene (1674 bases) located in the lipid bilayer of the virus protruding as spikes. It participates in many important processes for virus replication and mediates the entry of the virus inside the host cell through endocytosis as well as entry into the central nervous system. It binds to many host cellular receptors such as myocytes, neurons, and acini, which helps in the attachment to the viral envelope to the host endosomal membrane. Other processes it carries out are apoptosis, protecting the virus from the host's immune response, and axonal transport of the virus after invasion into the host cell making it a very important target in structure-based drug designing. Being an important protein responsible for the virus entry and replication, it is also an antigen activator protein eliciting an immune response and is used to produce commercial rabies vaccine. Thus, by inhibiting this protein using anti-rabies phytochemical compounds, we can stop the viral entry and further replication of the virus inside the host., Considering the importance of glycoprotein G for the virus entry and replication, the protein was chosen for the study and modeled as no proper structure for this protein exists in the protein structure database (PDB).
Available treatment and vaccines
Only seven people have survived rabies to date as there is no medication available postexposure to the virus also known as postexposure prophylaxis. In the case of postexposure prophylaxis, to prevent a person's chance of developing clinical symptoms, the only treatment that can be done is cleaning the wound, administration of rabies vaccine, and human rabies immunoglobulin to the patient. The survival depends on how quickly the vaccine is administered after exposure. Vaccines Imovax Rabies and RabAvert are the only two vaccines manufactured for use and are available in the United States. Administration of these vaccines also has side effects which include itching, swelling, and redness at the site of injection.,
Being labeled as a neglected tropical disease by the WHO, rabies is rampant in developing nations and mostly affects people in the rural region. There is a severe lack of awareness and contribution of government and health-care bodies to invest time and money for the management of rabies as well as for researching newer medications against the disease mainly because it affects people of lower socioeconomic class.
Phytochemical-based treatment against rabies
Natural treatment which includes phytochemicals is being studied and used since ancient times for the treatment of many ailments by people specifically in Asia. It is reported that about 25% of all drugs have plant-based origins. Phytochemicals derived from plants are studied to have antiviral potential and can inhibit virus replication. The major advantage of using plant-based drugs is that they have very few to no side effects when used while treating the patient in contrast to conventional drugs which are observed to have toxicity and severe side effects. The other advantage is the abundance of medicinal plant species reported worldwide around 2500 species exist. Considering these factors, naturally derived products that are phytochemicals were investigated for studying if they have any affinity against the glycoprotein G of the rabies virus.
Phytochemicals isolated from plant Salix subserrata were proven throughin vitro studies to have anti-rabies activity. These phytochemicals included flavonoids such as (+)-catechin, 1,2-benzenedicarboxylic acid, bis (2-ethylhexyl) ester, saligenin, methyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, catechol, propyl acetate, β-sitosterol, and β-sitosterol glucopyranoside. Similarly, In another study, flavonoids, kaempferol, and quercetin from onion were reported to have anti-rabies activity. The aim of the study was to model glycoprotein G and dock it using two different algorithms that are software AutoDock Vina (Molecular Graphics Laboratory, The Scripps Research Institute, La Jolla, California, United States) and server SwissDock to analyze the binding site and binding affinity using ten phytochemicals from the literature showing anti-rabies activity; they were used in the in silico docking study to find a potential natural drug against the rabies virus after they pass the toxicity filters of SwissADME and Protox-II servers. Currently, there is an urgent need to develop safer alternatives for rabies, as this disease is extremely fatal and postinfection with the virus always results in the death of the patient.
| Methods|| |
Modeling of the target protein
The target protein for rabies, that is, glycoprotein G, has no proper structure in the PDB database; its sequence was retrieved from Swiss-Prot, having UniProt id-P03524, and submitted on Robetta server to build the protein structure. Robetta is a fully automated method that builds the model protein using comparative modeling in which structure is parsed into domains, and models are built by searching homologous structure using Blast, Psi-Blast, and 3D-Jury which will be used as a template. The server accepts the target protein sequence as the input, and the result generated is mailed to the user. The structure was downloaded and visualized in the Discovery Studio Visualizer.
ModRefiner is an energy minimization server which was used to perform energy minimization of the protein structure. The server performs the energy minimization process through a lower resolution refinement of protein followed by the building of side-chain rotamers. The server requires a protein structure submitted in PDB format.
Protein validation using Rampage
The energy-minimized structure was downloaded and validated by submitting it on the Rampage server. The protein structure both before and after energy minimization was submitted simultaneously on Rampage to validate and check how energy minimization improved the overall quality of the structure. The Ramachandran plot includes information about the number of amino acid residues present in the allowed region and favored regions. The server also predicts outlier residues present in the protein structure, if any.
Active site prediction
The target protein against rabies, that is, glycoprotein G, was submitted on 3DLigandSite, MetaPocket 2.0 server, and RaptorX-Binding Site. 3DLigandSite predicts the active site of the submitted structure by comparing with ligands bound to the homologous structure to the query structure; MetaPocket 2.0 uses eight prediction methods that are LIGSITEcs, PASS, Q-SiteFinder, SURFNET, Fpocket, GHECOM, ConCavity, and POCASA to identify the active sites on the protein structure; and Raptor-X accepts protein sequence as input, builds a structure, and predicts active site based on similar pockets occurring in homologous structure in PDB database.,,
Ligand preparation and drug-likeness prediction
Ten anti-rabies phytochemicals from plants Salix subserrata and onion were selected based on literature studies. MarvinSketch software was used to draw the structure of selected phytochemicals. Then explicit hydrogens were added to the structures from the add hydrogen option. The structures were cleaned in 2D and 3D using the 'Clean 2D' and 'Clean 3D' option in MarviSketch, and the structures were saved in SMILES and PDB formats.
The ligands were submitted in SMILES format on SwissADME and Protox-II servers. SwissADME is a server which predicts whether a compound has potential to be drug-like by checking various properties and filters of the submitted compound which includes physicochemical properties such as molar mass, hydrogen donor, acceptor, log P value, pharmacokinetic properties (gastrointestinal [GI] absorption), water solubility, and topological polar surface area (TPSA).
Protox-II server is a free in silico toxicity predictor which predicts the lethal dose 50 (LD50) value in mg/kg body weight, according to which the server has classified the six classes into which the drug can fall depending on its predicted LD50 value. Class 6 is nontoxic and safe for consumption. LD50 is the dose at which 50% or half of the test population will die upon exposure to a compound. The server accepts input in SMILES format and also by drawing through its embedded structure drawing plugin on the site. After submission, the results are returned as the predicted LD50 value in mg/kg weight, the prediction accuracy in percentage, and the similarity of the input compound with other similar toxic compounds from the dataset with known rodent oral toxicity values.
AutoDock Vina and SwissDock were used to carry out the in silico docking analysis, whereas AutoDock Tools were used to generate the input files for docking using AutoDock Vina.,,
For AutoDock Vina, the input required was generated using AutoDock Tools that were the pdbqt files of the ligands, protein target, and the configuration file containing dimensions of the grid box that is x, y, and z coordinates. The target protein in PDB format was loaded in MGLTools, the water molecules were deleted, and nonpolar hydrogen was added; it was then saved in pdbqt format. Active site residues predicted by the three servers were selected of the protein, and the grid box around these active sites was made in order to direct the algorithm about the position of the active site residues, using spacing of 1 angstrom, the grid box was made, and the coordinate values were: center_x = −7.106, center_y = 32.915, center_z = 13.673, size_x = 60, size_y = 50, and size_z = 56 were typed and saved in a configuration file, along with protein and ligand filename. The ligand molecule in PDB format was then loaded, and all its nonrotatable bonds were made rotatable using the choose torsion option in the ligand menu of AutoDock Tools; the Gasteiger charges were added, and the file was saved in pdbqt format. On completion of docking, AutoDock Vina generated the outfile which gives the nine different poses by which the ligand binds to the target protein and the log file which has the binding energy and root-mean-square deviation values of the ligand binding to the target protein.
Docking analysis using the SwissDock server was carried out, by submitting the target protein in PDB format and the ligands in mol2 format. SwissDock allows the user to edit advance parameters and gives the grid space inputs which include the center x, y, z and size x, y, z values. The values used for these parameters were the same as AutoDock Vina to compare and validate the docking results. The results are generated as zip files which can be extracted to view the different docking poses of the ligand with the protein, and the server also has inbuilt JSMOL viewer to view the binding pose of the ligands.
The 2D and 3D protein–ligand interactions of the results generated by AutoDock Vina and SwissDock were visualized in Discovery Studio Visualizer; the software also gives the type of interaction with which the ligand binds to the protein.
| Results|| |
Energy minimization and protein validation using Rampage server
The target glycoprotein G of rabies virus was chosen for the study cause of its importance in viral replication for the docking analysis, as there is no 3D structure of the protein and its modeling was carried out. After submission of Swiss-Prot sequence id-P03524 on Robetta, the modeled protein obtained was downloaded and visualized in Discovery Studio Visualizer, as shown in [Figure 1].
|Figure 1: Modeled protein glycoprotein G of rabies virus predicted by Robetta server, visualized in Discovery Studio Visualizer in ribbon format|
Click here to view
After modeling, energy minimization was carried out using the ModRefiner server on the modeled protein. The energy minimized refined protein file, as well as the original modeled protein file, was validated on the Rampage server to check the Ramachandran plot. The resulting output is the number of residues in the allowed regions, favored region, and outliers summarized in [Table 1] of the modeled protein structure for before and after the energy minimization step.
|Table 1: Ramachandran results for before and after the energy minimization of the target protein glycoprotein, using the Rampage server|
Click here to view
The Ramachandran plot maps the psi versus phi backbone angles for each amino acid residue in a protein structure. This plot thus gives essential information about the conformation and folding of a protein structure. The results are shown as number of residues in the allowed region, which should be around 98%, number of residues in the favored region – expected value is around 2%, and the number of outlier residues which should be zero. Target protein followed the Rampage plot after energy minimization having residues in the desirable range of allowed and favored regions, as shown in [Table 1]. The results showed that the energy minimization process improved the overall quality and stability of the structure. The number of residues in the allowed and favored regions also increased and now after minimization was in the acceptable range of the Ramachandran plot, whereas the number of outliers before the energy minimization of the protein was four outliers which decreased to 1 outlier that is glycine in the final result.
Glycine does not follow the Ramachandran plot as it has no side chain; thus, it can adopt the psi and phi angles in any region of the plot and is frequently found in an allowed region or as an outlier where other residues should not fall. Hence, having glycine residues as an outlier is acceptable while docking and selection of active site having no impact on the final result. The modeled protein following the expected range of Ramachandran plot can thus be deemed as a stable protein structure.
Active site results
The active site of glycoprotein G of the rabies virus was submitted on servers 3DLigandSite, MetaPocket, and RaptorX-Binding Site, and the predicted sites by these servers are summarized in [Table 2].
|Table 2: Active site results predicted by 3DLigandSite, MetaPocket, and RaptorX- binding site servers for target glycoprotein|
Click here to view
All the three servers have different algorithms, and their combined results give us the increased probability of where the binding pockets are located in the protein structure.
SwissADME and Protox-II results for phytochemicals
The anti-rabies phytochemicals from the plants Salix subserrata and onion were first drawn on Marvin Sketch, cleaned in 2D and 3D, and then, their SMILES format was submitted to the SwissADME server and Protox-II to check if they have potential properties to be a drug-like compound. After submitting ten ligands, the two ligands that passed all the SwissADME and Protox-II filters were (+)-catechin and kaempferol whose chemical figures are shown in
[Figure 2]a and [Figure 2]b.
|Figure 2: (a) Structure of ligand (+)-catechin drawn in MarvinSketch. (b) Structure of ligand kaempferol drawn in MarvinSketch|
Click here to view
The ligands were checked for their Lipinski's rule of five properties, TPSA, water solubility, and gastrointestinal absorption. The Lipinski's filter of five states that for a molecule to be considered drug-like and orally bioavailable, it should pass four different physiochemical parameters (molecular weight ≤ 500, log P ≤ 5, H-bond donors ≤ 5, H-bond acceptors ≤ 10); both the ligands (+)-catechin and kaempferol passed these four parameters predicted by SwissADME. TPSA is shown to be a very important property for drug-like molecule influencing drug absorption, intestinal absorption, bioavailability, and blood–brain barrier penetration and should be less than 140Å2., The SwissADME results are summarized in [Table 3].
|Table 3: Hydrogen donor, hydrogen acceptor, molar mass, water solubility, log P, gastrointestinal absorption, topological polar surface area, drug-likeness predicted by SwissADME for ligands (+)-catechin and kaempferol|
Click here to view
The Protox-II results are shown in [Table 4]. (+)-Catechin had an LD50 value of 10,000 mg/kg which was predicted belonging to Class 6 of Protox classification. Kaempferol had an LD50 value of 3919 mg/kg and predicted to be a Class 5 compound. Compounds belonging to Classes 5 and 6 are relatively safe for consumption and nontoxic, specifically LD50 value of above than 5000 mg/kg (Class 6) is labeled as the safest nontoxic class of compounds for oral consumption which will thus have no side effects in a patient, and LD50 value (2000 < LD50 ≤5000 mg/kg) is classified as Class 5 compound.
|Table 4: LD50 and toxicity class predicted by Protox-II for the ligands (+)-catechin and kaempferol|
Click here to view
The receptor glycoprotein G of rabies virus was docked using the two ligands: (+)-catechin and kaempferol which passed the in silico toxicity tests of the SwissADME and Protox-II parameters. The output of the docking carried out using AutoDock Vina and SwissDock was the free binding energy, full fitness (kcal/mol), and estimated ΔG (kcal/mol) with which the ligand binds to the pocket of the receptor protein. The docking results of the ligands are summarized in [Table 5].
|Table 5: Binding energy, full fitness, and estimated ΔG values predicted for ligands docked with the target protein glycoprotein by AutoDock Vina and SwissDock|
Click here to view
For docking carried out using AutoDock Vina, the best conformation of glycoprotein G with (+)-catechin complex with binding energy (−8.0 kcal/mol) was visualized in Discovery Studio; the 2D interaction of the residues of the protein–ligand complex is shown in [Figure 3]a and 3D interaction in [Figure 3]b. The ligand formed conventional hydrogen bonds with the residue proline-15.
|Figure 3: (a) Docking result of AutoDock Vina showing the two-dimensional interaction of ligand (+)-catechin with receptor glycoprotein G visualized in Discovery Studio showing the residues and type of interactions, the ligand forms a conventional hydrogen bond with residue proline-15 shown in green dotted line. (b) Docking result of AutoDock Vina showing the three-dimensional interaction of (+)-catechin represented in ball and stick format in yellow color with glycoprotein G in stick format, visualized using Discovery Studio showing the interacting residues labeled in green color|
Click here to view
Similarly, the best conformation of glycoprotein G with kaempferol complex with binding energy (−7.5 kcal/mol) was visualized in Discovery Studio; the 2D interacting residues of the protein–ligand complex are shown in [Figure 4]a and 3D interaction in [Figure 4]b. No residues formed a conventional hydrogen bond with the ligand.
|Figure 4: (a) Docking result of AutoDock Vina showing the two-dimensional interaction of ligand kaempferol with receptor glycoprotein G visualized in Discovery Studio showing the residues and type of interactions formed, the ligand formed pi-alkyl, pi-pi stacked, and pi-pi t-shaped bonds with residue leucine 16, tyrosine 459, and tryptophan-456 represented in pink and dark pink dotted lines. (b) Docking result of AutoDock Vina showing the three-dimensional interaction of kaempferol represented in ball and stick format in yellow color with glycoprotein G in stick format, visualized using Discovery Studio showing the interacting residues labeled in green color|
Click here to view
SwissDock results observed in Discovery Studio for glycoprotein G with ligand (+)-catechin are shown in [Figure 5]a and [Figure 5]b. The ligand formed a conventional hydrogen bond with the residue alanine-419 of the protein, while for glycoprotein G with kaempferol interaction, as shown in [Figure 6]a and [Figure 6]b, no conventional hydrogen bonds were formed.
|Figure 5: (a) Docking result of SwissDock showing the two-dimensional interaction of ligand (+)-catechin with receptor glycoprotein G visualized in Discovery Studio showing the residues and type of interactions formed, the ligands shows conventional hydrogen bond with residue alanine-419 represented in green dotted line. (b) Docking result of SwissDock showing the three-dimensional interaction of (+)-catechin represented in ball and stick format in yellow color with glycoprotein G in stick format, visualized using Discovery Studio showing the interacting residues labeled in green color|
Click here to view
|Figure 6: (a) Docking result of SwissDock showing three-dimensional interaction of kaempferol represented in ball and stick format in yellow color with glycoprotein G in stick format, visualized in Discovery Studio showing the interacting residues labeled in green color. (b) Docking result of SwissDock showing the two-dimensional interaction of ligand kaempferol with receptor glycoprotein G visualized using Discovery Studio showing the residues and type of interactions, ligand shows alkyl bond with residue proline-421 represented in pink dotted line|
Click here to view
Ligand (+)-catechin gave better binding affinity score, while docking using AutoDock Vina and better full fitness and estimated ΔG (kcal/mol) values in SwissDock than the ligand kaempferol [Table 5].
| Discussion|| |
Glycoprotein G of the rabies virus is an essential protein in the pathogenesis of the viral disease inside the host, aside from that it is the choice of the target while designing rabies vaccines. Glycoprotein G interacts with the cellular receptor, and this interaction allows the virus to gain entry inside the host where this protein mediates endocytosis of the virus along with other essential functions required for virus replication and virulence., Considering these factors, the protein was chosen for the study and modeled. The energy minimization step improved the overall quality of the modeled protein by reducing the number of outliers. The phytochemicals exhibiting in-vitro anti-rabies activity were reviewed from literature studies as discussed below.
Meresa et al. reviewed plants which have anti-rabies activity and are used for the treatment of rabies in Ethiopia. In this study, plant Salix subserrata was reviewed to be having anti-rabies activity. Important active phytochemicals isolated from the plants include (+)-catechin, 1,2-benzenedicarboxylic acid, bis (2-ethylhexyl) ester, saligenin, methyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, catechol, propyl acetate, β-sitosterol, and β-sitosterol glucopyranoside from the plant.
The antiviral activity of the plant Salix subserrata was studiedin vitro by Deressa et al. (2010). Mice inoculated with rabies virus were administered chloroform and aqueous crude leaf extract of Salix subserrata. Chloroform and aqueous extracts of Salix subserrata showed significant anti-rabies activity by significantly increasing the survival time of the mice.
Kaempferol and quercetin isolated from onion are flavonoids, which have shown antiviral activity by inhibiting the growth of several viruses including the rabies virus. Many studies have proved the potential of flavonoids in the inhibition of viruses.,
After submitting ten reviewed phytochemicals from the above studies, ligands (+)-catechin and kaempferol were predicted to be drug-like molecules by the SwissADME server. The GI absorption and water solubility filters were passed by the ligands, both showing high GI absorption and high water solubility.
Water solubility is an important parameter because when a drug is poorly soluble, the dosage required of the drug administered to the patient orally would be much higher. Hence, higher solubility is required for a drug to elicit a pharmacological response as it will reach higher solubilized levels in the plasma quickly. These predictions indicate that ligands have drug-like properties and have the potential to be an oral drug. The phytochemicals (+)-catechin and kaempferol further passed the in silico toxicity filters of the Protox-II server, which indicate that they be further used as a potential anti-rabies drug and were further subjected for the docking studies.
Docking studies were carried out using the same grid dimensions in both AutoDock Vina and SwissDock to compare the docking studies. After docking using AutoDock Vina, both the ligands showed similar binding residues which were residue no proline-15, leucine-16, glycine-19, lysine-20, phenylalanine-21, histidine-403, tryptophan-456, and tyrosine-459. Similarly, after docking using SwissDock, both the ligands showed similar binding residues which were residue leucine-414, leucine-418, alanine-419, aspartate-420, proline-421, valine-424, phenylalanine-434, valine-437, valine-442, serine-447, leucine-461, leucine-462, glycine-465, alanine-466, and alanine-469. These residues can be considered as important interacting sites of the protein structure as both the ligands interacted and formed bonds with these specific residues only.
As there are no standard drugs available for rabies in the market, there is an urgent need for a drug with fewer side effects for helping the management of the disease, and the ligand (+)-catechin can be considered as a potent natural drug against rabies, considering the results that it showed more binding affinity, full fitness, and estimated ΔG values using both AutoDock Vina and SwissDock toward the glycoprotein G while forming conventional hydrogen bond with the residues proline-15 and alanine-419 of the target protein while kaempferol did not form any hydrogen bond. Hydrogen bonds contribute to protein–ligand binding by enhancing the ligand-binding affinity through the displacement of protein-bound water molecules. They are also known to contribute to the stability of the protein–ligand complex.
Natural compound-derived drugs are known for their nontoxic and effective nature against various viruses; rabies has been affecting people all around the world and its nature of being a fatal disease requires immediate measures to develop safer drug options which can be taken to stop the viral replication inside the host which ultimately leads to death. In this study, both the ligands showed similar binding residues with the target protein, and the study thus gave insight about which active site residues of the protein are more important for binding of a ligand. Ligand (+)-catechin gave better scores than kaempferol using both docking programs AutoDock Vina and SwissDock, thus validating the docking scores making it a viable option to be used as a natural source of the anti-rabies drug. This study thus facilitated the importance of phytochemical-based drug discovery to help people affected by rabies.
| Conclusion|| |
Protein modeling and docking analysis using AutoDock Vina and SwissDock of glycoprotein G, a protein target against the fatal rabies disease, was performed using selected phytochemicals. Glycoprotein G was selected as the virus target, after studying the importance of the protein and its importance in entry and virus replication. After modeling this protein, ten phytochemicals were screened for various properties including the physiochemical properties, pharmacokinetic properties (GI absorption), water solubility, Log P values, TPSA, and LD50(lethal dose) after which only two ligands (+)-catechin and kaempferol passed all these filters they were used for the docking analysis against modeled protein. The two phytochemicals that were (+)-catechin and kaempferol which satisfied all the filters on the SwissADME and Protox-II sever were used in docking analysis. Ligand (+)-catechin gave better binding affinity than kaempferol toward the target glycoprotein G in AutoDock Vina and also gave better full fitness and estimated ΔG values using SwissDock and thus was proved here to be a potential natural inhibitor against the rabies virus.
The authors sincerely thank Molecular Genetics Research Laboratory staff members and B. J. Wadia Hospital for Children, for providing facility and necessary effort for this research article.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
| References|| |
Nigg AJ, Walker PL. Overview, prevention, and treatment of rabies. Pharmacotherapy 2009;29:1182-95.
Rupprecht CE. Medical Microbiology. 4th
ed., Ch. 61. Galveston, TX: University of Texas Medical Branch at Galveston; 1996.
Singh R, Singh KP, Cherian S, Saminathan M, Kapoor S, Manjunatha Reddy GB, et al.
Rabies – Epidemiology, pathogenesis, public health concerns and advances in diagnosis and control: A comprehensive review. Vet Q 2017;37:212-51.
Yousaf MZ, Qasim M, Zia S, Khan MU, Ashfaq UA, Khan S, et al.
Rabies molecular virology, diagnosis, prevention and treatment. Virol J 2012;9:50.
Ross BA, Favi CM, Vásquez VA. Rabies virus glycoprotein: Structure, immunogenicity and pathogenic role Rev Chilena Infectol 2008;25:S14-8.
Kapoor R, Sharma B, Kanwar SS. Antiviral phytochemicals: An overview. Biochem Physiol Open Access 2017;6:1-7. [Doi: 10.4172/2168-9652.1000220].
Meresa A, Degu S, Tadele A, Geleta B, Moges H, Teka F, et al
. Medicinal plants used for the management of rabies in Ethiopia – A review. Med Chem (Los Angeles) 2017;7:795-806. [Doi: 10.4172/2161-0444.1000431].
Yahia EM. Fruit and Vegetable Phytochemicals: Chemistry and Human Health. Vol. 2. Chichester, UK: Wiley Blackwell; 2018. p. 1151-2.
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, et al
. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins Struct Funct Bioinform 2009;77:89-99. [Doi: 10.1002/prot.22540].
Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the robetta server. Nucleic Acids Res 2004;32:W526-31.
Biovia, Discovery Studio Visualizer, Version 18.104.22.16887 Software; 2019. Avaliable from: http://www. 3dsbiovia.com/
. [Last accessed on 2019 Jul 20].
Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 2011;101:2525-34.
Lovell SC, Davis IW, Arendall WB 3rd
, de Bakker PI, Word JM, Prisant MG, et al.
Structure validation by calpha geometry: Phi, psi and cbeta deviation. Proteins 2003;50:437-50.
Wass MN, Kelley LA, Sternberg MJ 3DLigandSite: Predicting ligand-binding sites using similar structures. Nucleic Acids Res 2010;38:W469-73.
Daina A, Michielin O, Zoete V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017;7:42717.
Banerjee P, Eckert AO, Schrey AK, Preissner R. ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Res 2018;46:W257-63.
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al.
AutoDock4 and autoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 2009;30:2785-91.
Trott O, Olson AJ. AutoDock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455-61.
Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res 2011;39:W270-7.
Gooch JW. Ramachandran plot. In: Encyclopedic Dictionary of Polymers. New York: Springer; 2011. p. 919.
Lipinski CA. Lead-and drug-like compounds: The rule-of-five revolution. Drug Discov Today 2004;1:337-41. [Doi: 10.1016/j.ddtec. 2004.11.007].
Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD. Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 2002;45:2615-23. [Doi: 10.1021/jm020017n].
Pulmanausahakul R, Li J, Schnell MJ, Dietzschold B. The glycoprotein and the matrix protein of rabies virus affect pathogenicity by regulating viral replication and facilitating cell-to-cell spread. J Virol 2008;82:2330-8.
Deressa A, Hussen K, Abebe D, Gera D. Evaluation of the efficacy of crude extracts of salix subserrata and silene macroselen for the treatment of rabies in Ethiopia. Ethiop Vet J 2010;14:1-16. [Doi: 10.4314/evj.v14i2.63880].
Ozçelik B, Kartal M, Orhan I. Cytotoxicity, antiviral and antimicrobial activities of alkaloids, flavonoids, and phenolic acids. Pharm Biol 2011;49:396-402.
Savjani KT, Gajjar AK, Savjani JK. Drug solubility: Importance and enhancement techniques. ISRN Pharm 2012;2012:195727.
Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC, et al.
Regulation of protein-ligand binding affinity by hydrogen bond pairing. Sci Adv 2016;2:e1501240.
[Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5], [Figure 6]
[Table 1], [Table 2], [Table 3], [Table 4], [Table 5]