Antibacterial, Antifungal Chalcone Derivatives as EGFR Inhibitors-Molecular Docking and ADMET Studies

Aim: In our earlier research, we have synthesized series of substituted 1-(2, 5-dimethyl thiophene3yl)-(4-substituted phenyl)-2-propene-1-one derivatives and evaluated them for their anti-bacterial and antifungal activity. In recent years, chalcone derivatives are proved for their varied pharmacological effects ranging from antimicrobial activity to anti-cancer effects. In this study, we have hypothesized the efficiency of our earlier synthesized anti-bacterial and antifungal chalcone derivatives for their potential inhibition of epidermal growth factor receptor protein (EGFR), through molecular docking studies. Methodology: Molecular docking simulation studies are performed using the Glide XP module of Schrodinger Suite and ligand binding energies are also calculated. Results: Molecular docking studies of the selected compounds against EGFR revealed docking scores ranging from -6.746 (compound 5) to -5.681 (compound 3) and also provided insight into binding conformations of the ligands in the EGFR protein environment. Additionally, molecular property and Absorption, Distribution, Metabolism, and Excretion (ADME) predictor analysis is also performed for the dataset ligands, which further provided the probable explanation for the binding potentials. Short Research Article Sattu et al.; JPRI, 33(45B): 387-396, 2021; Article no.JPRI.74657 388 Conclusion: Among all the tested dataset ligands, compound 5 has shown the highest dock score (-6.746) with better ADME profiles. Binding energies in the protein-ligand interactions explain how fit the ligand binds with the target protein. Molecular docking studies of these anti-bacterial, antifungal chalcone derivatives provided deeper insights in understanding the probable conformations of these tested ligands in the EGFR protein environment.

These chalcone derivatives exhibited anticancer activity on various drug-sensitive cell lines [11]. In silico studies on chalcones revealed that they have interaction with various cellular proteins which are responsible for causing cancer like CDK7, EGFR, etc. During these years chalcones proved to be potent against the EGFR group of proteins.
In the present investigation, we have hypothesized the inhibitory potentials of the antibacterial, anti-fungal chalcone derivatives which were earlier designed and developed in our laboratory against EGFR protein [12]. To evaluate our hypothesis we have performed molecular docking studies to the data set compounds along with calculation of ligand binding energies. Additionally, we have also performed predictor analysis of molecular properties and ADME scores of the data set ligands.

Dataset Ligands and Ligand Optimization
Anti-bacterial, anti-fungal activity possessing chalcone derivatives which were earlier developed in our laboratory was selected (Scheme 1) [2]. 2D structures of the compounds were converted to 3D using potential algorithms and application of high efficient force fields. Initial geometrical optimization and energy minimization of molecules was performed by using the Ligprep tool of Schrodinger suite [13]. Various ionization states were generated using the Ligprep module using a special program EPIK along with various possible conformers and tautomers.

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The molecular properties of the processed ligands were studied by using the Qikprop module. Qikprop module also predicts ADME profiles like blockage of Human Ether-a-go-gorelated Gene (hERG) K+ channels, apparent Caco-2 cell permeability, brain/blood partition coefficient, apparent Madin-Darby canine kidney (MDCK) cell permeability, skin permeability, binding to human serum albumin, and human oral absorption of the given set of ligands [14].

Molecular Docking Studies
The digital structure of the EGFR protein was retrieved from the Protein databank website with PDB Id: 1M17 and the structure was optimized by deleting unbound water molecules which are over 1 Å, adding hydrogen atoms to satisfy the valences, adding missing amino acids to stabilize side chains and energy of the whole structure was minimized using OPLS-2005 force field using Protein Preparation Wizard tool of Schrodinger Suite [15].
Optimized protein structure was used to examine protein-ligand interactions of the dataset ligands using the Glide Xp docking protocol. Initially, a 3D grid was established to the binding pocket (active site) of the protein, into which all the dataset ligands were docked. Binding interactions and efficiency of the binding were calculated in terms of Glide Score, which is a combination of hydrophilic, hydrophobic, metalbinding groups, Van der Waals energy, freezing rotatable bonds, and polar interactions with receptor [16,17].

Post Docking Calculations
Prime MM/GBSA (molecular mechanics-based generalized Born/surface area) module of Schrodinger suite was used to calculate the binding energies of the docked complexes, which is a combination of OPLS molecular mechanics energies (EMM), an SGB solvation model for polar solvation (GSGB), and a non-polar solvation term (GNP) containing non-polar solvent accessible surface area and Vander Waals interactions. In this, docking results were rescored through an energy function with a welldefined description of binding contributions. The total free energy of binding is then expressed in the form below mentioned Equation [16]. ΔGbind = Gcomplex -(Gprotein + Gligand) Where ΔGbind is ligand binding energy.

Predicted Molecular Properties and ADME Profile
Various molecular properties such as Molecular weight, dipole, volume, Solvent Accessible Surface Area ( Predicted ADME parameters include partition coefficient, predicted aqueous solubility (QPlogS), probability of CNS effects, blockage of HERG K+ channels (QPlogHERG), apparent Caco-2 cell permeability (QPPCaco), brain/blood partition coefficient (QPlogBB), apparent MDCK cell permeability (QPPMDCK), skin permeability (QPlogKp), binding to human serum albumin (QPlogKhsa) and human oral absorption of the given set of ligands (Table 2). All the compounds possessed higher human oral absorption levels (94%-100%). All the compounds resulted in low to inactive effects towards CNS. The partition coefficient of all the compounds was within the recommended range (-2.0-6.5), whereas, all the compounds were found to have predicted water solubility in the recommended range. All the compounds were reported to have extremely good apparent Caco-2 cell permeability (> 500) except the compounds 1 and 8 have shown little less apparent Caco-2 cell permeability (<500), and with moderate potential to cross through the blood-brain-barrier (-0.981-0.009). As the predicted ADME properties like blood brain partition coefficient, CNS, human oral absorption are within the normal range indicates these compounds are not crossing the blood brain barrier and does not have any impact on the central nervous system. All these compounds have good oral absorption that is most of the compounds have 100% oral absorption which is a good sign of the compounds.

Molecular Docking and Binding Energy Calculations
Molecular docking studies were performed to find the possible protein-ligand interactions of the dataset ligands which were earlier proved to have anti-bacterial and anti-fungal activity. Additionally, these also assisted in identifying the conformational changes of the ligand in the protein environment.100 different protein-ligand complex conformations for each docked complex were generated through the Glide XP module. Based on the EModel energy, only one was displayed in the result. Glide dock scores of the dataset ligands were shown in Table 3  Based on the good dock score the SAR of the compound 5 might be the replacement of one of the phenyl moiety with 2,5 disubstituted thiazole heterocycle might be the reason for enhanced dock score, the two substitutions might be electron donors to the ring. The substitution of chlorine/ atom at 2,4 substitution on another phenyl moiety might be the reason for enhanced dock score.

CONCLUSION
In the current investigation, we have hypothesized the probable EGFR inhibitory potentials of anti-bacterial, antifungal chalcone derivatives, and docking simulations were performed to identify binding efficiency and binding energy towards the EGFR protein.
Among all the tested dataset ligands, compound 5 has shown the highest dock score (-6.746) with better ADME profiles. Binding energies in the protein-ligand interactions explain how fit the ligand binds with the target protein. Molecular docking studies of these anti-bacterial, antifungal chalcone derivatives provided deeper insights in understanding the probable conformations of these tested ligands in the EGFR protein environment.