Docking Studies on Novel Analogues of 8-Chloro-Quinolones against Staphylococcus aureus

Abstract

Molecular docking studies have been carried out for a better understanding of the drugreceptor interactions. All the synthesized compounds have been subjected to molecular docking against targets that have been chosen based on the specific mechanism of action of the quinolones used in the antibacterial activity screening. A study of the characteristics and molecular properties of the small molecule known as ligand has been realized. In the first stage of the study, the 2D and 3D structures have been generated. The most stable conformer for each structure was obtained by geometry optimization and energy minimization. A series of topological, conformational characteristics and QSAR properties, important to assess the flexibility and the ability of the studied conformer to bind to the protein receptor, were determined and analyzed. These properties were discussed in order to assess the flexibility and the binding ability of studied conformers to bind to the receptor protein. The docking studies have been carried out. The score and hydrogen bonds formed with the amino acids from group interaction atoms are used to predict the binding modes, the binding affinities and the orientation of the docked quinolones in the active site of the protein receptor.

Molecular Modeling and Docking Studies of Some Benzodiazole Derivatives on the Protein of Staphylococcus aureus

“…Polar hydrogens were added using Autodock tools [8]. The Lamarckian Genetic Algorithm (LGA) [9] was used for conformational search. Each docking experiment was derived from 10 different runs that were set to terminate after a maximum of 250000 energy evaluations.…”

A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study

“…In silico docking studies have been proven to be extremely useful in facilitating the structural diversity of natural metabolites, including oligopeptides, to be exploited in a controlled manner ( Pintilie and Stefaniu, 2018 ). DS ZDOCK program has been used for docking, an initial-stage docking program for protein-protein complexes but can also be used for protein-peptide docking.…”

In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound

“…To achieve the docking studies, the quinolone derivatives (ligands) must be prepared to be imported in the molecular docking project. The ligands (Table 1) [20] E: À1341.39572 au have been prepared using SPARTAN'14 software package [21] according to the protocol described in our previous work [22]. The DFT/B3LYP/6-31 G * level of basis set has been used for the computation of molecular structure, vibrational frequencies, and energies of optimized structures.…”

“…The docking protocol was performed according to the CLC Drug Discovery Workbench Software and was described in a previous paper [22]. The docking scores and hydrogen bonds formed with the amino acids from group interaction atoms were used to predict the binding modes, the binding affinities, and the orientation of the docked quinolone derivatives in the active site of the target proteins.…”

“…Important molecular properties of the investigated compounds, e.g., molecular weight, flexible bonds, the number of hydrogen bond donors, the number of hydrogen bond acceptors, and log P, have been calculated. These parameters can be used to evaluate whether a molecule has properties that would make it a likely orally active drug, according to the Lipinski's rule of five [22]. The number of violations of the Lipinski rules allows to evaluate drug likeness for a molecule ( Table 5).…”