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Structural investigations of T854A mutation in EGFR and identification of novel inhibitors using structure activity relationships
© Goyal et al.; licensee BioMed Central Ltd. 2015
Published: 26 May 2015
The epidermal growth factor receptor (EGFR) is a member of the ErbB family that is involved in a number of processes responsible for cancer development and progression such as angiogenesis, apoptosis, cell proliferation and metastatic spread. Malfunction in activation of protein tyrosine kinases has been shown to result in uncontrolled cell growth. The EGFR TK domain has been identified as suitable target in cancer therapy and tyrosine kinase inhibitors such as erlotinib have been used for treatment of cancer. Mutations in the region of the EGFR gene encoding the tyrosine kinase (TK) domain causes altered responses to EGFR TK inhibitors (TKI). In this paper we perform molecular dynamics simulations and PCA analysis on wild-type and mutant (T854A) structures to gain insight into the structural changes observed in the target protein upon mutation. We also report two novel inhibitors identified by combined approach of QSAR model development.
The wild-type and mutant structure was observed to be stable for 26 ns and 24 ns respectively. In PCA analysis, the mutant structure proved to be more flexible than wild-type. We developed a 3D-QSAR model using 38 thiazolyl-pyrazoline compounds which was later used for prediction of inhibitory activity of natural compounds of ZINC library. The 3D-QSAR model was proved to be robust by the statistical parameters such as r2 (0.9751), q2(0.9491) and pred_r2(0.9525).
Analysis of molecular dynamics simulations results indicate stability loss and increased flexibility in the mutant structure. This flexibility results in structural changes which render the mutant protein drug resistant against erlotinib. We report two novel compounds having high predicted inhibitory activity to EGFR TK domain with both wild-type and mutant structure.
The epidermal growth factor receptor (EGFR) is a member of the ErbB family that is involved in a number of processes responsible for cancer development and progression such as angiogenesis, apoptosis, cell proliferation and metastatic spread . The EGFR family comprises of four receptors namely, EGFR (ErbB1/HER1), ErbB2 (HER2/neu), ErbB3 (HER3) and ErbB4 (HER4). Various mechanisms including gene amplification and mutations result in a disturbed regulatory mechanism of EGFR signalling . Malfunction in activation of such kinases has been shown to result in uncontrolled cell growth. The EGFR TK domain has been identified as suitable target in cancer therapy and drugs such as erlotinib have been used for treatment of cancer. However, mutations in the region of the EGFR gene encoding the tyrosine kinase (TK) domain causes altered responses to EGFR TK inhibitors (TKI) . In 2004, these mutations were first identified in patients with non-small cell lung cancer (NSCLC). NSCLC of Caucasian origin account for 15% while NSCLC of Asian ethnicity for 30% of EGFR mutations. These mutations are known to be associated with non-smoking status, adenocarcinoma histology and female gender [3, 4].
The most common mutations involve point mutations in exon 18 and exon 21, insertions or deletions in exon 19, insertions/duplications and point mutations in exon 20 . Destabilization of equilibrium between the active and inactive state of EGFR kinase activity toward promoting enzyme activation is a result of these mutations which in turn causes EGFR to translate into tumor growth and gives a survival advantage [1, 6]. Mutations T790M (gatekeeper), M766T (C helix), L718A (solvent chanel) and T854A (activation loop) are most common in erlotinib resistance . For this study we will be studying a drug-sensitive second-site EGFR mutation, T854A, which occurs due to change of Guanine in place of Adenine at nucleotide 2560 (exon 21). This non-synonymous single nucleotide polymorphism (SNP) results in substitution of Alanine for Threonine at position 854. The T854A residue is located at the bottom of the ATP binding site on C-lobe and its side chain is in contact distance of erlotinib or gefitinib. Thus, T854A substitution results in loss of contacts and binding affinity to these inhibitors.
In silico methodology for drug development is a viable and good option when compared to conventional drug development methods. One such in silico method involves development of quantitative structure activity relationship (QSAR) which establishes a correlation between the structure and inhibitory activity of molecular fragments of interests. 3D-QSAR is a robust technique in drug design process used to predict the inhibitory activities of the prospective lead compounds by applying the knowledge of three-dimensional properties of the lead compounds through a chemometric approach [9, 10]. It develops models which indicate the synthesis of novel inhibitors assuming that the receptor binding ability is related to its inhibitory activity [11, 12]. For development of QSAR model, the binding site of receptor is considered to be rigid and that the ligand molecules belong to a set of congeneric series . Molecular fields including hydrophobic, steric and electrostatic interaction energies are calculated for the set of compounds. A molecular field analysis model is generated and evaluated for its robustness by calculation of statistical parameters.
In this study we performed molecular dynamics simulations on both wild-type (WT) and mutant (T854A) structures and analysed the structural changes [13–16]. A 3D-QSAR model was developed using 38 thiazolyl-pyrazoline derivatives reported by Lv et al (2011) against WT EGFR . This model was then used to screen ZINC libraries for compounds with high predicted activity values which can be considered as lead drug candidates against both WT and mutant (T854A). This paper gives insights to the structural changes brought about by single nucleotide polymorphism in tyrosine kinase domain of EGFR. The compounds reported in this study can be considered for further experimental validation as potent lead compounds.
Materials and methods
Generation of wild-type and mutant EGFR structures
The crystal structure of WT EGFR was extracted from Protein Data Bank (PDB) [PDB ID: 4G5J]. The obtained crystal structure was first prepared using Protein preparation utility of Schrodinger [19–21]. Mutant structure was generated using Schrodinger Glide software through Maestro interface. The WT structure of EGFR was also subject to the identical in silico mutational method in which the wild-type residue (Threonine) was mutated to itself (Threonine) to ensure that mutation process is uniform for all structures. These structures were then subject to MD simulations.
Molecular dynamics simulations
The GROMACS package [22, 23] was used for carrying out MD simulations using the same conditions as mentioned in previous works of our lab [15, 24, 25]. Comparative analysis of structural deviations in WT and mutated (T854A) structures of EGFR were carried out using Gromacs utility tools such as g_rmsf, g_rms, g_gyrate, g_sas etc.
Principal component analysis
The essential dynamics (ED) method was used for the computation of eigenvectors and eigenvalues with their projection along the first two principal components with the help of a protocol present in the GROMACS software package . The principal component analysis (PCA) or ED is a protocol that simplifies the complexity of data obtained and extracts the important motion in MD that are significant for the biological function of the protein . In this evaluation, a covariance matrix was created from the obtained trajectories once the rotational and translational movements were removed. The matrix was then diagonalized to identify a set of eigenvectors and eigenvalues. The amplitude of eigenvectors and the displacement of atoms along each of these eigenvectors show the concentrated motions of protein along each direction and were represented by eigenvalues. This analysis was performed using g_covar and g_anaeig of GROMACS utility tools.
Selection and presentation of data set for QSAR model development
Computation of force field
The 38 thiazolyl-pyrazoline derivatives along with their pIC50 (negative logarithm of IC50) values (Table S1; additional file 1) were used for calculation of force field as described previously [9, 27–29].
Building the 3D-QSAR model of thiazolyl-pyrazoline derived compounds
Sphere exclusion method was applied for division of 38 compounds comprising the dataset into training and test set. Stepwise forward multiple regression method was utilized using the advanced variable selection and model building wizard for development of the 3D-QSAR model with default values. The stepwise forward variable selection algorithm has been described in previous studies [9, 27, 28, 31].
Validation of the developed 3D-QSAR model
The integrity of the developed 3D-QSAR model was confirmed with the help of different statistical parameters including squared correlation coefficient (r2), cross validated squared correlation coefficient (q2), predicted squared correlation coefficient (pred_r2), F-test and standard error. The model is said to be robust if it has the following statistical parameters r2 > 0.6, q2 > 0.6 and pred_r2 > 0.5 [32–34]. The F-test is described as the variance observed by the developed QSAR model divided by the variance due to the error in the regression. Hence, statistical significance of the developed model can be explained with high F-test. The low standard error of Pred_r2se, q2_se and r2_se showed absolute fitness quality of the model.
The developed model was first validated internally and then externally as described previously [9, 27, 28, 31]. Briefly internal validation was carried out using the leave-one-out (q2, LOO) method while external validation involved prediction of inhibitory activity of each molecule comprising the test set by means of the QSAR model generated using compounds in the training set.
Prediction of ZINC library using developed 3D-QSAR model
A natural compound ZINC database containing 0.2 million compounds was prepared and used for prediction of inhibitory activity using the developed 3D-QSAR model. Compounds with high predicted inhibitory activity were selected for docking analysis.
Docking of top scoring compounds with EGFR
Results and discussion
Structural and functional analysis of EGFR tyrosine kinase domain upon mutation
Another parameter radius of gyration (Rg) defined as the mass-weight root mean square distance of collection of atoms from their common centre of mass was helpful in giving further insight into the structural changes due to mutation and the overall dimension of the protein. Plot of radius of gyration of protein vs. time is shown in Figure 2c. It can be seen that mutant (T854A) structure exhibited higher Rg value in comparison to WT structure. Variation of SASA for both WT and mutant (T854A) proteins with respect to time can be seen in Figure S1(a). WT structure was observed to have higher value of SASA with time, while mutant (T854A) showed lower value of SASA. Greater fluctuation in Rg in mutant (T854A) structure suggested structural alteration in the mutant structure. Since, hydrogen bonds play an important role in maintaining the stable conformation of protein, analysis of WT and mutant (T854A) proteins were performed with respect to time (Figure S1(b)). The total energy (Figure S1(c)) was observed to be more or less the same throughout the simulations for both WT and mutant (T854A).
All these results indicate that mutation (T854A) rendered the protein structure more flexible affecting the structural and functional behaviour of EGFR TK protein. This result was further validated by principal component analysis (PCA) analysis.
3D QSAR model data selection
A 3D-QSAR model development gives a statistical relationship between the structures and activity of chemical compounds by calculation of 3D molecular descriptors involving steric, electrostatic and hydrophobic points marked on the 3D spatial grid. The invariable columns were removed after computing the force field grid descriptors which resulted in 3163 descriptors from 3268 descriptors, thus removing 105 invariable descriptors. For development of the QSAR model, pIC50 was chosen as the dependent variable while the calculated 3D descriptors as independent variable. Division of dataset resulted in 11 compounds in test set while the rest 27 compounds in training set. The test set consisted of compounds 6, 9, 12, 28, 29, 32, 36, 37, 40, 44 and 45.
3D-QSAR model development and validation
Each descriptor is associated with a numerical coefficient and its error while the last single numerical value is the regression coefficient. Internal and external validation of the developed model was carried out using the LOO method by calculating statistical parameters and meeting critical requirements for a model to be robust. The statistical parameters obtained for this model included correlation coefficient r2 (0.9751), cross-validated correlation coefficient q2 (0.9491), predicted correlation coefficient pred_r2 (0.9525), low standard error value, r2_se (0.0966), q2_se (0.1380) andpred_r2_se (0.1282) which confirm the model to be robust. Along with this, high value of F-test (130.3822) implied that the developed QSAR model is 99% statistically valid with 1 in 10000 chance of failure. There are other important statistical parameters such as Z-scores for r2, q2 and pred_r2 which are also important for QSAR model validation. Zscore_r2 of 6.7926 implies a 100%area under the normal curve, Zscore_q2 of 4.3671 implies a 99.99% area under the normal curve and Zscore_pred_r2 of 1.6521 implies a 95.0743% area under the normal curve. These percentages indicate that the respective scores are near the mean 'μ' thus validating the model's statistical robustness. A parameter p-value for each of r2, q2 and pred_r2 was also obtained to be statistically significant with values 0.0001, 0.0001 and 0.09 respectively.
The grid points E_337, E_832, S_335 and E_424 had a positive contribution (8.087%, 17.767%, 5.291% and 13.366% respectively) in the developed 3D-QSAR model against EGFR, while the descriptors S_151 and E_463 show negative contribution of 24.048% and 31.442% respectively. The grid points can be seen in Figure 1b. Steric descriptors represent the class of bulk descriptors which describe both size and shape of the molecules and fragments. Thus, positive contribution of a steric descriptor at specific grid point indicates the importance of a bulky group at that position. The value for each descriptor and predicted inhibitory activity for the dataset is mentioned in Table S2 (additional file 1).
The second class of descriptors, electrostatic descriptors give the importance of electronegative and electropositive groups at a particular site. Electrostatic descriptors with positive contribution imply the significance of presence of electropositive groups while those with negative contribution signify the importance of presence of electronegative groups.
Activity prediction of ZINC libraries using developed 3D-QSAR model
Predicted activity value (pIC50) of top ten ZINC compounds.
Docking analysis of HCO and NOP to both WT and T854A structures
Binding affinity of HCO and NOP with WT and T854A mutant structures.
In the present study, we performed molecular dynamics simulations on both wild-type (WT) and mutant (T854A) structures of EGFR to analyse the structural changes brought about by missense SNP resulting in T854A mutation. A 3D-QSAR model was developed using 38 thiazolyl-pyrazoline derivatives against WT which was then used to screen ZINC libraries by predicting their inhibitory activity (pIC50). The top two compounds were docked against WT and T854A structures. These compounds can be considered as lead drug candidates against both WT and mutant (T854A). The results indicate stability loss observed in RMSD, RMSF, Rg and SASA analysis. Thus it can be said that WT structure becomes more flexible upon mutation (T854A) which brings about changes in the binding site of erlotinib thus reducing its binding affinity and rendering the mutated protein to become drug resistant while maintaining its functionality. This was further supported by results obtained in PCA analysis. This generates the need to develop drugs that inhibit both WT and mutant proteins. We report two novel compounds (HCO and NOP) which have high predicted inhibitory activity against WT and high binding affinity against both WT and T854A mutant structure. Since these compounds possess better predicted inhibitory activity than BIBW2992 a known second-generation EGFR inhibitor for T854A change, they can be considered for further experimental validation as potent lead compounds. We present a comprehensive view of the correlation between the structure and inhibitory activity of thiazolyl-pyrazoline derived molecules. This study advances the use of thiazolyl-pyrazoline moiety as anti-cancer. Results of this study will also prove to be useful in designing potent anti-tumorals based on EGFR TK inhibition to further develop drugs against cancer.
AG is thankful to Jawaharlal Nehru University for usage of all computational facilities. AG is grateful to University Grants Commission, India for the Faculty Recharge Position.
AG would like to acknowledge financial support from Department of Science and Technology, Government of India towards publication of this article.
This article has been published as part of BMC Genomics Volume 16 Supplement 5, 2015: Proceedings of the 10th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-Meeting 2014). The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/16/S5.
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