Research Outputs
A computational study of the antioxidant power of eugenol compared to Vitamin C
The antioxidant power of eugenol and vitamin C was examined by analyzing the ability of these ligands to bind to the NADPH oxidase protein target and evaluating their bond interactions with critical residues. The results confirm that docked ligands are more stable in the specified active region of 2CDU during a MD simulation of 100 ns and 2CDU protein-ligand interactions with docked ligands showed significant hydrogen bond, hydrophobic, and water bridge formation. Eugenol exhibits hydrogen bond interactions with critical residues in the selective pocket in comparison to vitamin C. Also, eugenol had a similar binding orientation and very considerable stability in the selective pocket of 2CDU with a high binding energy with lipophilic energy. The electrostatic potential maps indicate that for eugenol, the –OH and –OCH3 sites, while that the –OH and –CO functional groups in vitamin C are responsible of the antioxidant activities of these compounds. HAT and SET mechanisms suggest that eugenol may become a better antioxidant than vitamin C.
Synthesis, chemical identification, drug release and docking studies of the Amlodipine–Chitosan nanobiopolymer composite
A new amlodipine-chitosan nanocomposite was built using amlodipine nanoparticles as primary scaffolds by spontaneous emulsification, and its complete elucidation was performed by using several spectrometric techniques. Our results indicate that the amlodipine-chitosan nanocomposite has better solubility than amlodipine at pH 7.4 with a nearly all the drug substance dissolved (97%) by the final time-point measured. The docking study support the existence of intermolecular interactions are established between amlodipine and chitosan
Theoretical investigation of the molecular structure and molecular docking of etoricoxib
In this work, a computational chemical study of Etoricoxib was carried out at the X/6311G(d,p) (where X=B3LYP, M06 and B97XD) level of theory, at the gas, aqueous and ethanol phases. Through the chemical reactivity descriptors derived from the DFT, it was possible to find that Etoricoxib structure exhibits a major chemical activity in water and ethanol phases in comparison to the gas phase, which suggests this drug would be more active in biological solvents like in blood, tissues and places where the ciclooxigenasa 2 (COX)-2 is found. In addition, a molecular docking analysis was conducted to study the interaction of Etoricoxib with the COX-2 active site. The results suggest that Etoricoxib interacts with 19 amino acid residues inside the COX-2 active site.
Identification of natural diterpenes isolated from Azorella species targeting dispersin B using in silico approaches
A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (− 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of − 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals. Methods: Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski’s rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.