|Year : 2021 | Volume
| Issue : 5 | Page : 528-546
Quinazoline analogues as cytotoxic agents; QSAR, docking, and in silico studies
Leila Emami1, Razieh Sabet2, Soghra Khabnadideh1, Zeinab Faghih3, Parvin Thayori2
1 Department of Medicinal Chemistry, Faculty of Pharmacy; Department of Medicinal Chemistry, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
2 Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
3 Department of Medicinal Chemistry, Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, I.R. Iran
|Date of Submission||05-Dec-2020|
|Date of Decision||13-Feb-2021|
|Date of Acceptance||25-Jul-2021|
|Date of Web Publication||18-Aug-2021|
Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz
Source of Support: None, Conflict of Interest: None
Background and purpose: Synthesis and investigation of pharmacological activity of novel compounds are time and money-consuming. However, computational techniques, docking, and in silico studies have facilitated drug discovery research to design pharmacologically effective compounds.
Experimental approach: In this study, a series of quinazoline derivatives were applied to quantitative structure-activity relationship (QSAR) analysis. A collection of chemometric methods were conducted to provide relations between structural features and cytotoxic activity of a variety of quinazoline derivatives against breast cancer cell line. An in silico-screening was accomplished and new impressive lead compounds were designed to target the epidermal growth factor receptor (EGFR)-active site based on a new structural pattern. Molecular docking was performed to delve into the interactions, free binding energy, and molecular binding mode of the compounds against the EGFR target.
Findings/Results: A comparison between different methods significantly indicated that genetic algorithm-partial least-squares were selected as the best model for quinazoline derivatives. In the current study, constitutional, functional, chemical, resource description framework, 2D autocorrelation, and charge descriptors were considered as significant parameters for the prediction of anticancer activity of quinazoline derivatives. In silico screening was employed to discover new compounds with good potential as anticancer agents and suggested to be synthesized. Also, the binding energy of docking simulation showed desired correlation with QSAR and experimental data.
Conclusion and implications: The results showed good accordance between binding energy and QSAR results. Compounds Q1-Q30 are desired to be synthesized and applied to in vitro evaluation.
Keywords: Cytotoxic; Molecular docking; QSAR; Quinazoline.
|How to cite this article:|
Emami L, Sabet R, Khabnadideh S, Faghih Z, Thayori P. Quinazoline analogues as cytotoxic agents; QSAR, docking, and in silico studies. Res Pharma Sci 2021;16:528-46
|How to cite this URL:|
Emami L, Sabet R, Khabnadideh S, Faghih Z, Thayori P. Quinazoline analogues as cytotoxic agents; QSAR, docking, and in silico studies. Res Pharma Sci [serial online] 2021 [cited 2022 Aug 14];16:528-46. Available from: https://www.rpsjournal.net/text.asp?2021/16/5/528/323919
| Introduction|| |
Among the nitrogen-containing compounds, the quinazoline ring was a very privileged and effective scaffold in pharmaceutical and medicinal chemistry; they have a broad spectrum of biological activities such as anticancer, diuretic, anti-inflammatory, anticonvulsant, antimicrobial, antiviral, antiplasmodial, and antihypertensive effects. Also, among the different quinazoline scaffolds, 2-substituted-4(3H)-quinazolinone has been used as an attractive pharmacophore for drug design purposes,. Quinazoline which is substituted at C4, C6, and C7 has been applied as one of the most significant classes of quinazoline-based epidermal growth factor receptor (EGFR) inhibitors. The quinazoline skeleton is also a substructure of natural purine bases, plant alkaloids, and several FDA-approved drugs such as prazosin, alfuzosin, erlotinib, gefitinib [Figure 1],.
|Figure 1: Previously reported epidermal growth factor receptor inhibitors bearing quinazoline scaffold.|
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Synthesis and investigation of pharmacological activity of novel compounds, usually take large amounts of expenditures and time. The use of computational techniques, docking, and in silico studies for designing pharmacologically effective compounds has opened a new approach to drug discovery research. Quantitative structure-activity relationships (QSAR) studies, as one of the important subjects in chemometrics, provide the ability to biological activities prediction for the novel or even non-synthesized compounds by medicinal chemists,,,,.
Linear QSAR models are mathematical equations that deliver good information for better explaining the mechanisms of action of the compounds, and proving the relationship between chemical structures and pharmacological activities.
The most important phase in constructing QSAR models is the suitable description of the structural and physicochemical properties of chemical structures,,,. These properties called molecular descriptors have a high impact on the pharmacological properties of a compound,,,. Molecular descriptors have been classified into different groups including physiochemical, constitutional, geometrical, topological, and quantum chemical descriptors. Dragon and Hyperchem as two famous computational packages are able to calculate more than 7000 of these parameters,.
An important approach for the researchers is establishing a complete SAR of quinazoline derivatives of cytotoxic agents to modify the quinazoline moiety,. In this paper, we investigated QSAR studies of some quinazoline derivatives which have been recently reported to exhibit cytotoxic activity against the MCF-7 cell line. Different QSAR models including multiple linear regressions were used to establish the relationship between descriptors and anti-breast cancer activity of compounds,,,. Our QSAR models would be established mathematical equations between pharmacological activities and calculable parameters such as topological, quantum, physicochemical, stereochemical, or electronic parameters. In addition, molecular docking simulation was also done to reach the most favorable conformation and binding modes of all compounds as well as newly designed compounds towards EGFR as possible targets for their anticancer effect.
The molecular docking simulation help us to understand the possible interactions between the ligands and enzyme’s active sites in detail and also helps to design novel potent inhibitors. In 2017, Tu et al. reported docking studies of new synthesized quinazoline bearing aryl semi carbazole ([Figure 1], structure I) and showed that tetrahydrofuran substituent was necessary for the anti-cancer activity of these compounds. The in vitro cytotoxic activities of new quinazoline compounds were determined against three human cancer cell lines (A549, MCF-7, and PC-3), and showing that the introduction of quinazoline derivatives bearing 2,3 dihydro-indole or 1, 2, 3, 4-tetrahydroquinoline moiety ([Figure 1], structure II] could act appropriately to interact with the active site of the EGFR target [Figure 1].
| Material and Methods|| |
Data set and descriptor generation
In this study, the experimental biological activities of anticancer activity against MCF-7 cell line were used (in terms of -log IC50), of a set of 81 quinazoline derivatives,,,,. The structural feature and antiproliferative values of these compounds were shown in [Table 1].
|Table 1: Chemical structure of quinazoline derivatives used in this study and their docking binding energy.|
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Hyperchem 8.0 software (Hypercube Inc. version 8.0.3) was used to draw the structures and optimization by semi-empirical AM1 calculations and Polak-Ribiere algorithm until the root mean square gradient of 0.01 kcal/mol. Molecular volume, molecular surface area, hydrophobicity (Log P), hydration energy, and molecular polarizability were achieved by Hyperchem software. The other descriptors such as topological, constitutional, and functional descriptors were achieved by the Dragon package (version 5.5), developed by the Milano chemometrics and QSAR group. The calculated descriptors are briefly introduced in [Table 2]. Finally, kenardston algorithm was used for the classification of the data set into calibration and test sets. This method is not accompanied by error and randomness.
Data screening and model building
Stepwise regression SPSS (version 22.0) software was used to analyze the experimental data to achieve effective descriptors. Then, the effective descriptors were hoarded in a data matrix that the number of molecules and descriptors were collected in rows and columns, respectively. Multiple linear regressions (MLR), partial least squares (PLS), MLR with factor analysis (FA-MLR), and principal component regression analysis (PCRA) methods were utilized to derive the QSAR equations.
A cross-validation and external test set were used to evaluate the model’s stability and prediction ability. For this purpose leave-one-out, leave-group-out were used. Also, the PLS regression with NIPALS-based algorithm existed in the chemometrics toolbox of MATLAB software (version 21 Math work Inc.) was used to obtain the optimum number of factors based on the Harland and Thomas F-ratio criterion.
Molecular modeling procedure
3D X-ray crystal structures of EGFR in complex with erlotinib (PDB ID: 1M17) were selected from Protein Data Bank (http://www.rcsb.org) based on the similarity of its co-crystal ligand to studied compounds,. The structure of studied compounds was generated, minimized, and converted to pdbqt format. The pdbqt formats of the ligands were prepared by adding Gasteiger charges and setting the degree of torsions by the AutoDock tools package (1.5.6). For the preparation of pdbqt format of protein, we removed cognate ligand, water molecules, added missing hydrogen atoms, and finally merged non-polar hydrogens according to their corresponding carbons,. All preparation was performed by the AutoDock tools package (1.5.6). Docking procedure was done at the grid box with a size of 70 × 70 ×70 and the centre of x = 20.14, y = 0.3, z = 52.2 Å by AutoDock Vina (1.1.2). Using an in-house batch script (DOCKFACE). The exhaustiveness was set to 100, and other docking parameters were set as default. The binding interactions of the docked compounds and the receptor were visualized by a fully automated protein-ligand interaction profiler.
| Results|| |
The resulted QSAR models from different types of descriptors for the compounds (65 molecules as calibration and 16 molecules as prediction sets) are listed in [Table 3]. The stepwise selection was used to achieve MLR analyses.
|Table 3: The results of multiple linear regressions analysis with different types of descriptors.|
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[Table 4] includes the statistical parameters of prediction that indicate the suitability of the proposed QSAR model based on MLR analysis of molecular parameters. The correlation coefficient of prediction is 0.97, which means that the resulted QSAR model could predict 97% of variances in the anti-breast cancer activity data. It has a root mean square error (RMSE) of 0.21.
|Table 4: Statistical parameters for testing prediction ability of the MLR, GA-PLS, PCR, and FA-MLR models|
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Genetic algorithm-PLS analysis
Genetic algorithm (GA) method was used to select the variable to find more effective descriptors to improve the performance of PLS analysis. The data set (n = 81) was disported in calibration (n = 65) and prediction set (n = 16) groups. A cross-validation procedure was used to achieve the optimum number of latent variables for each PLS model. In this work, many different GA-PLS runs were conducted using the different initial set of populations (50-250), therefore, the most convenient GA-PLS model that resulted in the best fitness contained 15 descriptors including six constitutional descriptors (nI, nR10, nBnz, nArX, nO, nX), five functional descriptors (n ROR, nC=S, npyridine, nHAcc, nArNO2), one chemical (SA), one resource description framework (RDF) parameter (RDF115v), one 2D autocorrelation parameter (MATS3m), and one charge (Qneg) parameter. The majority of these descriptors are constitutional indices. All of them being those obtained by different MLR-based QSAR models. The PLS estimate of the regression coefficients is shown in [Figure 2].
|Figure 2: Partial least squares regression coefficients for the variables used in the genetic algorithm-partial least squares model.|
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In order to investigate the relative importance of the variable that appeared in the final model, the variable important in projection (VIP) was employed. VIP values reflect the importance of terms in the PLS model. According to Erikson et al. X-variables (predictor variables) could be classified according to their relevance in explaining y (predicted variable), so that VIP > 1.0 and VIP < 0.8 mean highly or less influential, respectively, and 0.8 < VIP< 1.0 means moderately influential [Figure 3].
|Figure 3: Plot of VIP for the descriptors used in genetic algorithm-partial least squares model. VIP, variables important in projection.|
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FA-MLR and PCRA
In FA-MLR analysis, Factor Analysis was used to decrease the number of variables and also to identify the effective predictor variables and to decrease collinearities between them. PCRA was tried for the dataset along with FA-MLR. In this method, factor scores, as obtained from FA, were used as the predictor variables.
Based on the process explained in the experimental part, the following five-parametric equation is shown in [Table 5].
|Table 5: The results of multiple linear regressions analysis with factor analysis with different types of descriptors|
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This equation could explain about 97% of the variance and predict 96% of the variance in pIC50 data. It has an RSME of 0.15. This equation describes the effect of functional, constitutional and so on descriptors (nI, n = CHR, nO-O, nCONR2 and nN-N) on anti-breast activity of the studied molecules. Multiple regression equation using stepwise selection method (PCRA), the following equation was gained [Table 6].
This equation could explain and predict 93% and 91% of the variances in pIC50 data, respectively. The RSME of PCRA analysis was 0.19. PCRA equation is better than those derived from FA-MLR. While the data of this analysis showed acceptable prediction, we observed that the predicted values of some molecules are near to each other.
As it is shown in [Table 5], in the case of each factor, the loading values for some descriptors are much higher than those of the others. These high values for each factor indicate that this factor delivers higher information about each index. It should be noted that all factors have information from all descriptors but the contribution of the descriptor in different factors are not equal. For example, factors 1 and 2 have higher loadings for the chemical, atom-center, constitutional, functional, BCUT (modified burden eigenvalues) information, geometrical, 2D autocorrelations, and Walk and path counts indices whereas information about the weighted holistic invariant molecular (WHIM descriptor), connectivity indices, 3D MoRSE descriptors and functional descriptors are highly combined in factors 3 and 4.
To assess the robustness and applicability domain of all gained models, leverage as standard procedures was used [Table 7]. Warning leverage (h*) is another criterion to explain results. Leverage greater than warning leverage h* means that the predicted response is the result of substantial extrapolation of the model and therefore may not be reliable.
|Table 7: Leverage (h) of the external test set molecules for different models. The last row (h*) is the warning leverage.|
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Molecular docking simulation is the computational method of ligand binding to a receptor that indicates the affinity of the binding ligand to the active site of the target. Quinazoline derivatives are well-known as EGFR inhibitors. So, the docking study was done for EGFR kinase to predict the binding modes, affinities, and orientation of ligands at the active sites of the enzyme. In the present research, molecular docking simulations were done on 81 molecules of data set as well as 30 designs of new compounds. The docking method was verified by docking of co-crystallized ligand (erlotinib) in EGFR active site and comparison of the results between docked and crystallized erlotinib conformations. RMSD of docking for erlotinib in comparison with its coordination in the crystal structure was 1.07. The free energy binding of docked compounds is summarized in [Table 1].
Docking study on EGFR
All investigated complexes showed better docking binding energies than the reference drug (erlotinib) with a binding energy value of -5.8 kcal/mol which showed a good correlation with QSAR results, it means almost that the compounds with the lowest IC50 have the highest binding energy. The docked conformation of protein crystal structure (1M17) with erlotinib and three other quinazoline derivatives (33, 55, and 79), which possess strong binding energy, are shown in [Figure 2]. As depicted in [Figure 4], the nitrogen atom of the quinazoline moiety in compound 33 binds to the Thr 766 via hydrogen bond interactions, and some hydrophobic interactions with the residues Lys 721, Ala 719, Leu 764, Met 769, and Leu 820 were observed.
|Figure 4: The main interaction between the active site of epidermal growth factor receptor (PDB ID: 1M17) with compounds 33, 55, 79, and erlotinib.|
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In compound 55, the nitrogen atom formed hydrogen bond interaction with Thr 766 and the phenyl ring formed pi-stacking interaction with Phe 699 and also there is some hydrophobic interaction with Val 702, Leu 764, and Leu 694. Compound 79 can be summarized by hydrogen bond interactions with Glu 738 and Thr 830 and the pi-cation interaction between quinazoline ring and Lys 721. Also, interaction with Leu 699, 764, 766, 820, Val702, and Ala 719. To explain the binding mode of erlotinib, in brief, it should be announced that the oxygen atom of the erlotinib chain formed a hydrogen bond via Cys 733. In addition, pi-stacking interaction between the phenyl ring and Phe 699 was observed.
In silico screening
In silico methods can help to discover newly designed drugs before synthesized and offers a lot of benefits such as cost savings, time-consuming, and increase the speed of predict and achieve new pharmaceutical compounds. Virtual screening is a computational technique to search active compounds from very large libraries by the effect of structural modification on binding energy and biological activity at the parent molecule. A new compound designed according to the best QSAR model and binding energy from docking simulation. We used the important descriptors selected in the GA-PLS model to design new active compounds because the GA-PLS model has the greatest statistical parameters. The in silico screen was applied by substituting different groups in different places. We also analyzed the robustness and applicability domain of the model by calculation of leverage value on the whole data set. The warning leverage (h*) was found to be 0.66 and it is cleared that all of the compounds have a smaller leverage value (h) than warning leverage (h*). The results of this investigation are summarized in [Table 8]. We designed 30 compounds (Q1-Q30) and biological activities based on the GA-PLS equation were achieved. And also, docking binding energy was obtained. From the results, the Q14 has the best activity and have a good candidate for anticancer agents.
|Table 8: Structural modification of studied compounds and their predicted activities and docking binding energies for epidermal growth factor receptor inhibitory based on genetic algorithm-partial least squares equation.|
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ADME and drug-likeness properties of designed compounds
The physicochemical properties of some potent designed compounds were calculated by http://www.swissadme.ch/, and the results are shown in [Table 9]. The molecular weight of compounds (Q7, Q14, and Q17) was in the accepted range. The log P of hit compound Q14 values is lower than 5 and displayed that it has desire lipophilicity. Furthermore, the hydrogen bond properties and total polar surface area, and rotatable bond number of compound Q14 is within the acceptable limit. Generally, the data indicated that compound Q14 followed Lipinski’s rule of five and Veber rule. The drug-likeness and absorption, distribution, metabolism, and excretion (ADME) properties of some potent compounds were derived from the preADMET online server (http://preadmet.bmdrc. org/). ADME properties including human intestinal absorption, in vitro caucasian colon adenocarcinoma cell permeability (Caco-2), skin permeability, in vitro plasma protein binding, and in vivo, blood-brain barrier penetration are shown in [Table 10].
|Table 10: In silico absorbance distribution metabolism and excretion of some potent designed compounds.|
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Human intestinal absorption analysis indicated that hit compound Q14 indicated well human intestinal absorption, which causes quick absorption from the intestine to the bloodstream. The Caco-2 permeability parameters suggest that compound Q14 has moderate permeability for penetration to biological membranes. Moreover, compound Q14 binds moderately to plasma proteins, so it may be used as an oral dosage form. It has low blood-brain barrier penetration; so, it has a low neurotoxicity effect.
| Discussion|| |
In MLR analysis the equation 1 [Table 2] explained the effect of constitutional descriptors on the cytotoxicity activity of these compounds. It showed that increasing the numbers of substitution halogen atoms (nF, nCl, nI) on the compounds results in an activity enhancement, such as molecular series 6-7, 9-14. It also showed that the iodine substitution on the 6th position of quinazoline ring would have better activity. It also explains the positive effect nR10 and nR06 (number of 6-membered rings) such as phenyl ring on activity (such as molecule series 19-24, 25-30, and 33-37 have good activity). This equation also showed the effect of O numbers on the activity. The Keto group on the quinazoline ring has better activity than thio keto group on the ring (molecules number 50 has low activity). It also explains the positive effect of nDB (number of double bonds) on the activity. Quinazoline and phenyl ring have multiple double bonds.
The result of the topological group counts parameter on cytotoxicity activity of the studied molecules has been introduced by equation 2 of [Table 2]. It showed that among the topological descriptors T (O. O), PCR, and JhetV have positive effects and T (O..I), JhetZ, SEigv, piID, and T(F..I) have negative effects on cytotoxic activity of the compounds.
The equations 3-12 of [Table 3] demonstrated the positive and negative effects of BCUT, Galvz topological, 2D autocorrelations, geometrical, RDF, 3D MoRSE, WHIM, GETAWAY, functional, and atom-centered fragments on the anti-breast cancer activity of these compounds. The MLR equation of [Table 2] obtained from the pool of functional groups descriptors, E11, explained the positive impact of the nCb (presence of benzene ring, especially with halogen atoms such as F and, Cl, is good for example compounds 33-37) n = CHR, nArX (number of X on the aromatic ring for example phenyl ring), nArNO2 (number of nitro groups (aromatic)), nN-N(number of N hydrazines), nROR (number of ethers), nSO2 (number of sulfone compounds 19-21), nHAcc(number of acceptor atoms for H-bonds (N, O, F)) on the anticancer activity. The nCONR2 (number of tertiary amides compound 2), nC=S (number of thioketo compound 42), npyridine (number of pyridines compound 21) had negative compacts on the anti-breast cancer activity. The negative sign of this group proposed that a decrease in the number of these descriptors resulted in an activity enhancement. This equation, which has a high statistical quality (R2 = 0.97, Q2 = 0.96).
The model extracted from PLS model has a high cross-validation statistic, and it also represents a high ability for modelling external test samples. It could explain and predict about 93% of variances in the cytotoxic activity of the studied molecules. There is a close agreement between the experimental and predicted values of anticancer activity data to evaluate the significance of the 15 selected PLS descriptors in the protein tyrosine kinase inhibitory activity. The VIP analysis of PLS equation is shown in [Figure 2]. As it is observed, nArX, nI, Qneg, nROR, and nArNO2 indices represent the most significant contribution in the resulted QSAR model. In addition, functional group parameters such as nO, n BnZ, and MATS3m are moderately influential parameters. The calculated leverage values of the prediction set samples for all models and the warning leverage, as the threshold value for accepted prediction, are shown in [Table 6]. As seen, the leverages of all test samples were lower than h* for all models. This means that all the predicted values were acceptable.
Finally, the FA-MLR and PCRA results shown in [Table 11], demonstrate the four-factor loadings of the variables (after VARIMAX rotation) for the compounds tested for cytotoxic activity. As it is observed, about 62% of variances in the original data matrix could be explained by the selected four factors.
|Table 11: Numerical values of factor loading numbers 1–4 for descriptors after varimax rotation|
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The results of the docking studies indicated that the important amino acid in the active site of EGFR enzyme is Thr 766, Val 719 and 702. The majority interaction of studied compounds are hydrogen bond between substituent at quinazoline moiety with Thr 766 and the pi-hydrogen bond between receptor and phenyl group of ligands. Molecular docking simulations were also applied to the newly designed compounds to obtain binding mode and energy with EGFR target. The physicochemical and ADME properties of the designed compounds were also predicted. It was indicated that these compounds were compatible with the Lipinski and Veber rules and have desired pharmacokinetic characteristics. In future studies, 30 newly designed quinazoline compounds will be synthesized and subjected to cytotoxic laboratory evaluation.
| Conclusion|| |
The quantitative relationship between molecular descriptor and cytotoxic activity of different quinazoline derivatives was discovered by different chemometrics methods, such as MLR, FA-MLR, PCR, and GA-PLS. The reliability, accuracy, and predictability of the proposed models were evaluated by RSME of cross-validation, cross-validation, and the RMSE of prediction. A static comparison between different QSAR methods indicated that GA-PLS represented a good relationship between the chemical structure of quinazoline and anticancer activity for MCF-7 cell line. This study suggested that constitutional descriptors, functional descriptors, chemical, RDF parameter, 2D autocorrelation parameter, and charge parameter descriptors of molecules were important for the prediction of anticancer activity of quinazoline derivatives. In silico screening was employed to discover new compounds such as Q14, with good potential inhibitory as anticancer agents and suggested to be synthesized, furthermore, ADME and drug-likeness properties of designed compounds indicated that compound Q14 is compatible with Lipinski and Veber rules and has desired pharmacokinetic properties. Also, the binding energy of docking simulation showed a desire correlation with QSAR and experimental data.
This work was financially supported by Shiraz University of Medical Sciences, Shiraz, I.R. Iran, under Grant No. 97-01-36-16805.
Conflict of interest statement
The authors declared no conflict of interest in this study.
L. Emami and S. Khabnadideh analyzed the data and co-wrote the paper. R. Sabet designed the experiment, analyzed the data, and co-wrote the paper. Z. Faghih and P. Thayori analyzed the data
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[Figure 1], [Figure 2], [Figure 3], [Figure 4]
[Table 1], [Table 2], [Table 3], [Table 4], [Table 5], [Table 6], [Table 7], [Table 8], [Table 9], [Table 10], [Table 11]
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