The B-factor index for the binding site (BFIbs) to prioritize crystal protein structures for docking

Structural Chemistry - In cheminformatics, protein-ligand docking is a powerful tool applied for virtual screening, pose prediction, and binding affinity estimation. However, docking results depend...     

Modeling of dexmedetomidine conformers and their interactions with alpha2 adrenergic receptor subtypes

Dexmedetomidine (4-[(S)-1-(2,3-dimethyl-phenyl)-ethyl]-1H-imidazole), Dex, is potent agonist acting on α₂-adrenergic receptors (α₂-ARs). It can exist at the physiological pH in both forms: neutral and protonated. The results of receptor-independent and receptor-dependent studies applied to both forms of Dex are reported. A conformational analysis with PM3 semiempirical MO and ab initio HF/6-31G* methods was carried out for both forms of Dex. The calculated geometries of low-energy conformers of Dex were compared with X-ray geometry and those of conformers resulted from molecular docking of Dex in the binding pockets of 3D homology models of the α_2A-, α_2B-, and α_2C-adrenoceptor subtypes. A MM/QM (molecular mechanics/quantum mechanics) docking study was performed to refine and optimize receptor–ligand complex and close contacts between the ligand and amino acids lining the binding cavity. Two-dimensional potential energy surface and docking results suggest that the imidazole ring can easily adopt the best orientation for an efficient interaction with the carboxylate group of Asp3.32 from the binding cavity of alpha2 adrenergic receptor subtypes.     

Investigation of aggregation behavior using computational methods and absorption spectra for trisazo direct dyes

Direct dyes are likely to self-associate in aqueous solutions. Here, we present the aggregation characteristics of three trisazo direct dyes investigated using a procedure, which combines computational and experimental approaches. The geometric features of the molecules and their aggregates were elucidated by molecular modeling and optimization. The relative energies specific for the aggregation process yielded the optimum number of molecules forming an aggregate: two for AHDS dye and three for SDH and AIDS dyes. The results were further confirmed by using spectrometric determination and mathematical analysis. Accordingly, molecular aggregation was studied in aqueous solutions as a function of dye concentration (10^?6–10^?3 mol/l) and solution pH (4–10). As the dye concentration increased, shifts in absorption spectra were observed, suggesting the formation of aggregates. The pH variation produced a change in the spectral maximum, confirming the aggregation. The mathematical processing of the absorption spectrum data confirmed the number of chemical species of each aggregate as resulted from computational calculations.     

Synthesis,structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study

Background

Nitroaromatic and chloronitroaromatic compounds have been a subject of great interest in industry and recently in medical-pharmaceutic field. 2-Chloro-4-nitro/2-chloro-5-nitrobenzoic acids and 4-nitrobenzoic acid are promising new agents for the treatment of main infectious killing diseases in the world: immunodeficiency diseases and tuberculosis.

Results

New ethanolamine nitro/chloronitrobenzoates were synthesized and characterized by X-ray crystallography, UV–vis, FT-IR and elementary analysis techniques. The toxicity of the compounds prepared and correspondent components was evaluated using Hydractinia echinata as test system. A significant lower toxicity was observed for nitro-derivative compared with chloronitro-derivatives and individual components. Crystallographic studies, together with the chemical reactivity and stability profiles resulted from density functional theory and ab initio molecular orbital calculations, explain the particular behavior of ethanolamine 4-nitrobenzoate in biological test.

Conclusions

The experimental and theoretical data reveal the potential of these compounds to contribute to the design of new active pharmaceutical ingredients with lower toxicity.

     

Structure- and ligand- based studies to gain insight into the pharmacological implications of histamine H3 receptor

Structural Chemistry - In the context of unknowing the experimental structure for histamine H3 receptor, which is a potential therapeutical target for numerous disorders and diseases, the...