3D QSAR AND MOLECULAR DOCKING STUDIES OF FLAVONOIDS AS SPLEEN TYROSINE KINASE INHIBITORSHTML Full Text
3D QSAR AND MOLECULAR DOCKING STUDIES OF FLAVONOIDS AS SPLEEN TYROSINE KINASE INHIBITORS
A. Basu * 1, A. Sarkar 2 and P. Basak 3
Department of Biochemistry 1, Gurudas College, Kolkata - 700054, West Bengal, India.
Department of Computer Science and Engineering 2, School of Bioscience and Engineering 3, Jadavpur University, Kolkata 700032, West Bengal, India.
ABSTRACT: Spleen tyrosine kinase (Syk) is a member of tyrosine kinase family protein. Syk protein plays a vital role during intracellular signal transduction from high affinity IgE receptor (FcεRI) in allergic reaction. Flavonoids are well known compounds for their anti-allergic properties. In this present work, thirty-four structurally similar flavonoids are investigated as Syk inhibitors by using 3-dimensional quantitative structure-activity relationship (QSAR) models and molecular docking studies. By applying genetic algorithm (GA) method, different types of 3D-MoRSE descriptors are selected from various types of geometrical descriptors for model building. A Multiple Linear Regression is built up, considering the inhibitory effect of seventeen flavonoids on model mast cells by QSARINS software. The model is validated internally using the Q2 LOO criterion in leave-one-out method. William graph and Insubria graph are plotted to identify the application domain for that model. The same model is also externally validated for other seventeen flavonoid compounds. Docking studies of these thirty-four compounds are also performed using AutoDock to identify interacting amino acids of Syk protein. Docking analysis reveals that flavonoid chrysin depicts lowest binding energy, -2.74 with Syk protein. Methoxy substitution causes adverse effect on binding. The flavonoid chrysin is found in carrot. Pharmacokinetics study of chrysin shows that the gastrointestinal absorption of chrysin is high with bioavailability score of 0.55. The current work will help in drug design of human Syk inhibitors and provides information for molecular level of interactions between Syk and the flavonoid group of compounds.
Spleen tyrosine kinase, QSAR, Flavonoids, Allergic reaction, Molecular docking, Chrysin
INTRODUCTION: The spleen tyrosine kinase Syk is a tyrosine kinase protein, which is involved in signal transduction in hematopoietic cells, as well as non-hematopoietic cells.
In first type of cells, it plays crucial roles in normal function of B and T cells, neutrophils, macrophage, aggregation of platelets and cell signalling in mast cells of origin and plays a crucial role in signalling in most of these cells.
It is involved in B and T-cell functions, platelet aggregation, mast cell signalling, neutrophils and macrophages 1, 2. The activity of Syk protein as tumor suppressor is an example of its function in second type of cells.
From this point of view, Syk has been introduced as a target for a new type of anticancer drugs in breast cancer, overian cancer 3. Syk kinase inhibitor is also used in treatment of rheumatoid artharitis 4, lupus nephritis 5, vascular diseases 6, allergic asthma and rhinitis 7. When antigens bind to immunoglobulin E (IgE) during allergic reaction, mast cells and basophils are activated to release inflammatory mediators e.g. histamine, prostaglandin, leukotriens, serotonin etc. In both early- and late-phase allergen-induced type I hypersensitivity reactions, Syk protein inhibitor completely blocks serotonin mediator release from mast cell 8. Syk binds with FcεRI, the high affinity receptor for IgE, for degranulation in mast cells 1. Activation of tyrosine kinases plays the most important role during transmission of downstream signalling events in mast cells. This signal transduction pathway is required for the regulation of mast cell degranulation 9.
There are several compounds e.g. triazolopyridine 10, fostamatinib 11, 6- [(1R, 2S)- 2- Amino- cyclo-hexylamino]- 4- (5, 6-dimethyl-pyridin-2-ylamino)-pyridazine-3-carboxylic acid amide 12 and a series of pyrazolopyrazine- 3- amine and pyrazolo-pyrimidine-3-amine derivatives 13, which are synthesized and screened as Syk protein inhibitors in various immunological processes.
In this work, ethanopharmacological drugs are investigated as potential mast cell stabilizers. Several natural constituents, which are obtained from different herbs, like Holy Basil (Ocimum tenuiflorum) 14, Chamomile (Matricaria recutita) 15, kaempferol in Cerbera manghas 16, grapeseed extract 17, polyphenols of red wine 18 are identified as mast cell stabilizers. Different types of chemical compounds are also analysed as natural mast cell stabilizers like flavonoids, stilbenes, curcuminoids 19. Numerous flavonoids like luteolin, apigenin, quercetin, fisetin, myricetin, morin, naringenin etc. are tested as Syk protein inhibitors during mast cell degranulation reaction 20, 21. Inhibitory effects of those flavonoids along with their structural requirements for antigen - induced degranulation process is estimated 22.
The role of Syk protein in mast cell degranulation reaction will be cleared only when potent, specific inhibitors of Syk are identified and evaluated in clinical trials. To do so we perform Quantitative Structure-Activity Relationship (QSAR) analysis to study the human spleen tyrosine kinase inhibitory activity of a series of flavonoid compounds. The QSAR study is based on the important chemistry principle, which states that similar compounds have similar biological properties 23. The biological activity of the chemical compounds has correlation with their physicochemical properties, which are known as molecular descriptors 24. Recently QSAR models are developed for new drug designing in cancer therapy 25 and anti-HIV therapy 26. We use the QSARINS software 27 for building a Multiple Linear Regression (MLR) model to recognize a potential flavonoid as Syk protein inhibitor.
In new drug designing study, molecular docking analysis between various ligands and the protein of interest, is gaining huge interest nowadays. In docking study, the binding energy of docked compound helps to determine the strength of interactions between ligand and protein. As an example of ethanopharmacological study, several ligands from Cassia tora, Brassica campestris and Calotropis procera, are targeted against acetylcholinesterase using molecular modelling and docking studies for drug therapy in Alzheimer’s disease 28. In a similar approach we perform the molecular docking study with flavonoid compounds with Syk protein by utilizing AutoDock 4.2.3 molecular docking software 29.
Bioavailability of herbal medicinal product is an assessment of several features e.g. degree of absorption after administration, digestion, elucidation of metabolic pathways (yielding potentially new active compounds), and the assessment of elimination routes and their kinetics 30. Bioavailability of these natural flavonoids must be considered to determine their pharmacological efficiency as mast cell stabilisers 31. This information is very relevant for good understanding of the concentrations that will be achieved in the body after administration of those flavonoids as Syk inhibitor. Using Swiss ADME 32, 33, a web tool we evaluate pharmacokinetics, drug-likeness of flavonoids.
MATERIALS AND METHODS:
Data Set for QSAR Study of Syk Inhibitor: The first step in QSAR model construction is to collect a list of flavonoid compounds with experimentally determined inhibitory activity data. The inhibitory effects of 34 flavoniods on the release of β-hexosaminidase from model human cells are compiled from experimental data 22. Their 2D chemical structures are shown in Fig. 1. The data set of 34 experimental flavonoid compounds is divided into training set for model generation, and a prediction set (marked with * in Table 1) for model validation, both containing 17 compounds. The chemical structures of flavonoids as SMILES format are retrieved from PubChem database 34. The biological activity (IC50) of the molecules are converted to their corresponding pIC50 values, and used as dependent variables in the QSAR calculations Table 1.
FIG. 1: TWO DIMENSIONAL STRUCTURES OF THIRTY - FOUR FLAVONOID COMPOUNDS
TABLE 1: LIST OF FLAVONOIDS WITH THEIR INHIBITORY ACIVITY
|Compound no.||Name of Flavonoids||CID no||IC50||pIC50|
|27||Retusin (Quercetin-3,7,3',4'-tetramethyl ether)*||5352005||25||-1.3979|
|30||7 methoxy myricetin (Europetin; 7-O-methylmyricetin)*||44259636||19||-1.2788|
|31||3,7 dimethoxy myricetin (3,7-dimethylmyricetin)*||24721651||27||-1.4314|
|32||4',7 dimethoxy myricetin (Myricetin 7,4'-dimethyl ether)*||44259638||7.9||-0.8976|
|33||3',4',7 trimethoxy myricetin (Myricetin 7,3',4'-trimethyl ether)*||12532439||13||-1.1139|
|34||3,5,7,3',4',5' hexamethoxy myricetin (Hexa-O-methylmyricitin)*||634113||58||-1.7634|
Energy Minimization of Ligand Molecules: Energy minimized structure of 34 ligand molecules are obtained using MM2 force field 35 with minimum RMS gradient 0.01.
Molecular Descriptors Calculation: Using energy minimized structures, molecular descriptors are calculated using ChemDes 36.ChemDes is a free web-based platform for the calculation of molecular descriptors and fingerprints, which provide more than 3,679 molecular descriptors that are divided into 61 logical blocks. Among them 3D ChemoPy molecular descriptors 37 e.g. geometric descriptors (12), CPSA descriptors (30), RDF descriptors (180), WHIM descriptors (70), MoRSE descriptors (210) are calculated for each flavonoids.
QSAR Model Construction and Validation: In order to obtain the MLR model, we use the QSARINS software 27 and a genetic algorithm (GA) method is applied to select relevant set of variables from a large number of descriptors (502). Variables are specified with 10 models per size with 0.050 cut off according to QUIK rule 38. The genetic algorithm is set up with population size 200, 2000 generations per size and mutation rate is 20. For selecting the best model with two descriptors, models are arranged by QSARINS, according to R2 (the highest value correlates with the good fitness of the model, Q2 LOO (the highest value indicates the robustness of the model).
Syk Protein 3D Structure Identification: Here, the X-ray diffraction crystallographic structure of human Spleen Tyrosine Kinase with resolution 1.9Å (EC#: 18.104.22.168) is extracted from Protein Data Bank with PDB ID 4FL3 39. This protein is prepared as receptor by using the graphical interface of the AutoDock Tools, which is present in the MGL Tools 1.4.6 program 29 by using Chem Office Professional 16 suite. All 34 inhibitors are prepared for docking studies by the same programme in the pbdqt format.
Docking Studies: In docking studies, a 60 X 60 X 60 box with a grid spacing of 2 Å is used. The centroid of the grid map has been set (0, 0, 0) with the coordinates along x, y and z axis. No. of individuals in population is 50, for 1000 generations. The maximum no. of docking is set to 20 with energy evaluations 2500. Docking results are analysed with their binding energies in dlg format by Python Molecule Viewer version 1.5.6 40.
RESULT AND DISCUSSION:
Best QSAR Model Using MLR: By using user friendly QSARINS software 27, we develop different QSAR models with low multi-collinearity between molecular descriptors and good correlation with the biological response. The best MLR model for training set is built up with 3D molecular descriptors namely Molecule Representation of Structures based on Electron Diffraction (MoRSE) and Charged Partial Surface Area descriptor (CPSA). The QSAR model and its statistical parameters are shown below:
log(1/IC50) = - 0.0817 (± 1.4970) MoRSEV5 - 0.0433 (± 0.0179) PNSA3 - 3.2940 (± 0.6482)
Where, MoRSEV5 means Molecule Representation of Structures based on Electron Diffraction signal 05, weighted by atomic van der waals volumes, PNSA3 means atomic charge weighed negative surface area.
N= 17; R2= 0.8737; R2adj = 0.8557; R2-R2adj = 0.0180; LOF = 82.8709; Kxx = 0.6603; Delta K = 0.0090; RMSE tr = 6.9614; MAE tr = 5.3576; RSS tr = 823.8344; CCC tr =0.9326; s = 7.6711; F = 48.4212
Here, N is the number of compounds of the training set, R2 is the coefficient of determination, R2 adj is adjusted R2, s is standard error of estimate, F is variance ratio, LOF is Friedman lack of fit 41, 42, Kxx is the correlation among descriptors 38, Delta K is the difference of the correlation between the descriptors (Kx) and the descriptors plus the responses (Kxy), RMSEtr is Root Mean Square Error in fitting (for training set), MAEtr is Mean Absolute Error in fitting (calculated on training set), RSStr is Residual Sum of Squares in fitting (also for training set) and CCCtr is the concordance correlation coefficient calculated over the training set 43, 44, 45. The model projects an R2 value is of 0.8737, which means a proper fitness for modelling Syk protein inhibition.
In addition, an R2adj value of 0.8557, which indicates that it is convenient to add a new descriptor with the model. Similarly, along with the low value of the Kxx (0.6603), we can say that the correlation between the model descriptors is low. Not only that the Delta K parameter has 0.0090 value which is indicative of good correlation between selected descriptors and the inhibitory response, with negligible error on experimental and calculated parameters (RMSEtr = 6.9614; MAEtr = 5.3576; s = 7.6711). The scatter plot of experimental versus predicted activity by model equation is shown in Fig. 2.
FIG. 2: SCATTER PLOT OF EXPERIMENTAL IC50 VERSUS PREDICTED VALUES BY QSAR MODEL
FIG. 3: THE VALUES PREDICTED BY LOO VERSUS THE EXPERIMENTAL IC50 VALUES
Model Validation: In internal validation procedure, our model is validated for fitting and stability by using the statistical parameters of cross-validation Leave-one-out (LOO). The value of Q2 LOO is 0.8096 which is comparable with the value of R2 (0.8737). The QSAR model is robust considering the values of RMSEcv = 8.5463, MAEcv = 6.5591, CCCcv = 0.8990. In Fig. 3, biological activity values predicted by LOO versus the experimental values are shown (yellow circles for training and blue circle for prediction).
External Validation: In QSAR studies, the predictions of compounds present within the applicability domain (AD) are considered as dependable 46. William graph is plotted with leverage and standardized residuals 47 in Fig. 4. From this figure, it can be concluded that plot compound 30 and 33 are present outside the limit of critical leverage (h = 0.529). In another approach for detecting the model applicability domain using Insubria plot not only compounds 33 and 30, but also compound 34 are marginally present outside the applicability domain as shown in Fig. 5.
FIG. 4: WILLIAMS PLOT WITH HAT DIAGONAL VALUES VERSUS STANDARDIZED RESIDUALS
FIG. 5: INSUBRIA PLOT WITH APPLICABILITY DOMAIN
Molecular Docking and Visual Representation of Protein - Ligand Binding: Using AutoDock 4.2.3 software, binding energies of all 34 compounds in our dataset are calculated. Analysing the docking results, the compound 3 i.e. flavonoid chrysin (compound 3) is selected with the lowest binding energy (-2.74 kcal/mol) as most suitable flavonoid in Syk inhibition. As shown in Fig. 6, the flavonoid chrysin is present within a binding pocket region, forming hydrogen bonding with Gly 190, Lys 191 and His 209. Hydroxyl (OH) group at position 7 shows stabilizing interaction with basic amino acid residues Lys and His. Other compounds containing 7 OH group e.g. 3', 4', 7 Trihydroxyflavone, Wogonin also shows strong binding interaction with Syk protein. On the contrary, flavonoids substituted with methyl group causes unfavourable effect on protein - ligand binding depicted in their binding energy.
FIG. 6: DOCKING STRUCTURE OF COMPOUND 3, CHRYSIN WITH Syk PROTEIN
Bioavailability Predication: From Swiss ADME 33, comparing pharmacokinetic data, it can be concluded that chrysin, 3', 4', 7 Trihydroxyflavone and Wogonin are highly absorbed by GI tract. Drug likeness of all these three compounds is positive with zero violation in Liponski rule.
CONCLUSION: In our earlier work, we have identified carboxamidotetrazole derivatives of furan, thiophene, naphthalene and benzothiophene can act as potent mast cell stabilisers on human basophils 48. In our present study, by using QSAR model with MLR equation and molecular docking analysis, we want to highlight the anti-allergic effect of flavonoids as human spleen tyrosine kinase) Syk protein inhibitor. Two 3D molecular descriptors e.g. MoRSEV5 and PNSA3 are selected by genetic algorithm (GA).
The first one weights the atomic van der waals volumes of flavonoid compounds. The second one is related with solvent accessible surface area and partial charge of all negatively charged atoms e.g. oxygen atom of hydroxyl groups of flavonoids. From the molecular docking studies of all 34 flavonoids, the interaction between hydroxyl groups in 7 position of flavonoids are identified. 3', 4', 7 Trihydroxyflavone is present in Broad bean pod, ladino clover, Alfalfa and rhizome part of glycyrrhizae radix. Chrysin is present in carrot, alfalfa, parsley and thyme 49. These compounds are recognized as ethano-pharmacological drugs as mast cell stabilizers in allergic treatment.
ACKNOWLEDGEMENT: The authors thank Professor Paola Gramatica for QSARINS software support.
CONFLICT OF INTEREST: The authors have no conflict of interest.
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How to cite this article:
Basu A, Sarkar A and Basak P: 3D QSAR and molecular docking studies of flavonoids as spleen tyrosine kinase inhibitors. Int J Pharm Sci Res 2018; 9(5): 1921-28.doi: 10.13040/IJPSR.0975-8232.9(5).1921-28.
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