The compounds X-12, X-19, X-29, X-32, X-35, X-39, X-40, X-44, X-45, X-48, and X-49 (Table S3) were selected as candidate compounds based on their high docking score compared to doxorubicin. of the training set. Leave one out cross-validation Leave one out cross-validation (LOOCV) is one of the most effective methods for validation of a model with a small training dataset. Here, training is done with a data size of (NC1) and tested the remaining one, where N represents the complete set of data. In the LOOCV method, the training and testing are repeated for N amount of time, so as to pass each individual data through the testing process. Virtual designing of novel xanthone derivatives The 50 compounds (Table S3) were virtually designed and then validated. The QSAR model was used to predict the biological responses to these chemical structures. Rule of five filters All the chemical structures are evaluated for good oral bioavailability in order to be an effective drug-like compound, subject to Lipinskis rule of five.18 According to this rule, a drug-like molecule should have not more than one of the following violations: no more than five hydrogen bond donors; no more than ten hydrogen bond acceptors; molecular weight no more than 500; and LogP no more than 5. Protein preparation The protein preparation protocol is used to perform tasks such as inserting missing atoms in incomplete residues, deleting alternate conformations (disorder), removing waters, standardizing the names of the Pulegone atoms, modeling missing loop regions, and protonating titratable residues by using predicted pKs (unfavorable logarithmic measure of acid dissociation constant). CHARMM (Chemistry at HARvard Macromolecular Mechanics; Cambridge, MA, USA) is used for protein preparation with an energy of ?31.1116, initial RMS gradient energy of 181.843, and grid spacing of 0.5 Nkx2-1 angstrom (?). The hydrogen atoms were added before the processing. Protein coordinates from the crystal structure of Top2A (PDB [Protein Data Lender] ID: 1ZXM) Chain A decided at a resolution of 1 1.87 ? were used (Physique 2). Open in a separate window Physique 2 (A) Structural model of human DNA Top2A (PDB ID: 1ZXM) with ATP binding site (yellow); (B) ATP binding site pocket residues. Abbreviations: ATP, adenosine triphosphate; DNA, deoxyribonucleic acid; Top2A, topoisomerase type II. ProteinCligand docking Molecular docking studies were performed to generate the bio-active binding poses of inhibitors in the active site of enzymes by using the LibDock program from Discovery Studio, version 3.5 (Accelrys, San Diego, CA, USA). LibDock uses protein site features, referred to as warm spots, consisting of two types (polar and apolar). The ligand poses are placed into the polar and apolar receptor interactions site. In the current study, the Merck Molecular Pressure Field was used for energy minimization of the ligands. The binding Pulegone sphere was primarily defined as all residues of the target within 5 ? from the first binding site. Here, the ATP binding site was used to define the active site, referred to as the warm spots (Physique 2). Conformer Algorithm based on Energy Screening And Recursive build-up (CAESAR) was used for generating conformations. Then, the wise minimizer was used for in situ ligand minimization. All other docking and consequent scoring parameters used were kept at their default settings. We also analyzed the protein ligand complexes to better understand the interactions between protein residues and bound ligands, along with the binding site residues of the defined receptor. The 2D diagrams helped to identify the binding site residue, including amino acid residues, waters, and metal atoms. The score ligand poses protocol was used for the scoring functions, such as LibDock score, Jain, LigScore 1, LigScore 2, piecewise linear potential (PLP) and potential Pulegone of mean pressure (PMF) 04, to evaluate ligand binding in a receptor cavity. Validation using AutoDock Vina AutoDock Vina19 software (Scripps Research Institute, La Jolla, CA, USA) was also used for molecular docking studies to validate the LibDock score. For this, the designed compounds were optimized and then used for docking experiments. The same binding site and receptor used in the LibDock program are used for this study. The docking program takes the PDBQT file format of ligands and receptor, a altered PDB file, which has added polar hydrogens and partial charges. Other docking parameters were set to the softwares default values. Pharmacokinetics parameters ADMET refers to the absorption, distribution, metabolism, excretion, and toxicity properties of a molecule within an organism, and were predicted.