The ADME and Drug-likeness properties for the remaining 26 compounds were presented in the Supplementary Table?1a and Supplementary Table?1b
The ADME and Drug-likeness properties for the remaining 26 compounds were presented in the Supplementary Table?1a and Supplementary Table?1b. residues and hydrophobic/other interactions with amino acid residues (LEU718, LEU844, MET766, VAL726, ALA743, LYS745 and MET790) in the active site of EGFR-tyrosine kinase (EGFR-TK). The drug-likeness of these selected anti-proliferative agents were predicted via the pharmacokinetics profile of the molecules utilizing SWISS ADME. The anti-proliferative agents were found to be orally safe by not having more than 1 violation of the Lipinski’s rule of five. This research proposed a way for designing potent anti-proliferative agents against their target enzyme. activity prediction on some anti-proliferative agents using QSAR technique, study the nature of interactions between the anti-proliferative agents and EGFR-tyrosine kinase (EGFR-TK) via docking and also to predict the ADME properties and drug-likeness of these anti-proliferative agents. 2.?Computational method 2.1. Dataset collection Thirty [30] 2, 9-disubstituted 8-phenylthio/phenylsulfinyl-9H-purine derivatives as anti-proliferative agents with their anti-proliferator inhibitory activities (IC50) in nM against human lung carcinoma cell line HCC827 were selected from the work of Hei et al [19]. The anti-proliferator inhibitory activities (IC50) of all the dataset were then converted to their corresponding negative logarithms (pIC50) using Eq. (1) [20]. Table?3 presents the molecular formula, pIC50, Predicted pIC50 and residuals and docking scores for all the data set and the standard drug (Gefitinib) used in this research. pIC50 = -log IC50 10?9 (1) Table?3 The Molecular formula, pIC50, Predicted pIC50, the residual values and binding energy for the studied molecules. descriptor matrix of the training set is represented by X and is the transpose matrix X used in generating the model. The thresh-hold for the value of X is the warning threshold (which is presented in the equation below: 3(x+1)/q (5) where the number of chemicals of the model building set is given by q, and the number of the descriptors in the model under evaluation is represented by x. 2.7. Molecular docking A Dell Latitude E6520 computer system, with the following specification: Intel ? Core? i7 Dual CPU, M330 @2.75 GHz 2.75GHz, 8GB of RAM was utilized to explore the nature of interactions between the active site of EGFR-tyrosine kinase (EGFR-TK) and some selected anti-proliferative agents (ligands) with the help of Pyrex virtual screening software, Chimera, PyMOL and Discovery studio. Before the docking analysis, ligands were prepared from the optimized structures in 2.2 above saved in pdb file format using Spartan14 [13]. The 3D structure of EGFR-tyrosine kinase (EGFR-TK) was downloaded from the protein data bank (with pdb ID: 4zau) [30] The enzyme was prepared with help of Discovery Studio Visualizer for the docking analysis. In the course of the preparation, hydrogen was added. Water molecule, heteroatoms and co-ligands were eliminated from the crystal structure saved in pdb file. The docking of the ligands to the active site of EGFR-tyrosine kinase (EGFR-TK) was achieved with the help of Pyrex software using Autodock vina [12]. After successful docking protocol, re-formation of the complexes (ligand-receptor) for further investigation was also achieved utilizing Chimera software. Discovery studio visualizer and PyMOL were used to investigate the Substituted piperidines-1 interactions of the complexes. 2.8. ADME properties and drug-likeness prediction ADME properties and drug-likeness prediction of some selected anti-proliferative agents among the data set was carried out using SwissADME a free web tool used in evaluating ADME properties and drug-likeness of small molecules [17]. The Substituted piperidines-1 Lipinski’s rule of five is useful at pre-clinical stage of drug discovery which state that if any chemical violate more than 2 of these criteria (Molecular weight ? 500, Number of Substituted piperidines-1 hydrogen bond donors 5, Number of hydrogen bond acceptors 10, Calculated Log p 5 and Polar surface area (PSA) ?140 ?2), the chemical is said to be impermeable or badly absorbed Guangzhe et la., (2019) [31]. 3.?Result and discussion 3.1. 3D-QSAR modeling The model reported was found to have passed the minimum requirement for the assessment of a reliable QSAR models with the following assessment parameters: R2 of 0.919035, R2adj of 0.893733, Qcv2 of 0.866475, R2test of 0.636217 and LOF of 0.215884 as reported by [32] (Table?1). pIC50 = – 12.417755021 (AATS7e) + 5.879592939 (AATS8e) – 0.433185723 (ATSC3e) – 22.018131847 (MATS7m) + 0.333566302 (VR3_D) + 46.983337086 Table?1 General minimum required value for the assessment of QSAR model. thead th rowspan=”1″ colspan=”1″ Symbol /th th rowspan=”1″ Cav2.3 colspan=”1″ Name /th th rowspan=”1″ colspan=”1″ Recommended Value /th th rowspan=”1″ colspan=”1″ Reported Model /th /thead R2Co-efficient of determination math xmlns:mml=”http://www.w3.org/1998/Math/MathML” id=”M3″ altimg=”si3.svg” mrow mo linebreak=”goodbreak” linebreakstyle=”after” /mo /mrow /math 0.60.919035Q2Cross-Validation Co-efficient math xmlns:mml=”http://www.w3.org/1998/Math/MathML” id=”M4″.