Amalia Stefaniu

By Amalia Stefaniu and Lucia Pintilie

The main goal of this chapter is to reveal the importance of molecular structure analysis with specific computational tools using quantum chemistry methods based on density functional theory (DFT) with focus on pharmaceutical compounds. A wide series of molecular properties and descriptors related with chemical reactivity is discussed and compared for small organic molecules (e.g., quinolones, oxazolidinones). Structural and physicochemical information, important for quantitative structure-property relationships (QSPR) and quantitative structure-activity relationships (QSAR) modeling analysis, obtained using Spartan 14 software Wavefunction, are reported. Thus, by a computational procedure including energy minimization and predictive calculations, values of quantum chemical parameters and molecular properties related with electronic charge distribution are reported and discussed. Frontier molecular orbitals energy diagram and their bandgap provide indications about chemical reactivity and kinetic stability of the molecules. Derived parameters (ionization potential (I), electron affinity (A), electronegativity (χ), global hardness (η), softness (σ), chemical potential (μ) and global electrophilicity index (ω)) are given. Also, graphic quantities are reported: electrostatic potential maps, local ionization potential maps and LUMO maps, as visual representation of the chemically active sites and comparative reactivity of different constitutive atoms.

Part of the book: Symmetry (Group Theory) and Mathematical Treatment in Chemistry

By Lucia Pintilie and Amalia Stefaniu

Molecular docking studies have been carried out for a better understanding of the drug-receptor 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.

Part of the book: Molecular Docking

By Amalia Stefaniu

Part of the book: Molecular Docking and Molecular Dynamics

By Lucia Pintilie and Amalia Stefaniu

Quinolones are an important class of heterocyclic compounds that possess interesting biological activities like antimicrobial, antitubercular, and antitumor. The objective of this study is to evaluate in silico the antitumoral and antimycobacterial activity of some quinolone derivatives by using CLC Drug Discovery Workbench Software. Docking studies were carried out for all ligands, and the docking scores were compared with the scores of standard drugs, topotecan and levofloxacin. The docking studies have been carried out to predict the most possible type of interaction, the binding affinities, and the orientations of the docked ligands at the active site of the target protein.

Part of the book: Molecular Docking and Molecular Dynamics

By Amalia Stefaniu

Part of the book: Cheminformatics and its Applications