Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o -NBA photo-acid interaction with BSA

Multi-Spectroscopic and Theoretical Analysis on the Interaction between Human Serum Albumin and a Capsaicin Derivative—RPF101

“…All spectra were recorded with appropriate background corrections, with number of averaging of three scans for each recorded. In order to compensate the inner filter effect (see Figure S1 in the Supplementary Material ), the steady-state fluorescence intensity values for the association HSA: RPF101 was corrected through the absorption of RPF101 at excitation and emission wavelengths, according to Equation (1) [ 17 ]: where, F cor and F obs are the corrected and observed steady-state fluorescence intensity values, respectively. A ex and A em are the experimental absorbance value at the excitation (molar extinction coefficient at 280 nm−ε = 10,364 M −1 cm −1 ) and emission wavelength (molar extinction coefficient at 340 nm−ε = 808.75 M −1 cm −1 ), respectively.…”

Molecular Docking and Semi-Empirical Study of the Binding between Allura Red, a synthetic food dye, with Bovine Serum Albumin

“…In order to identify the main binding site on the protein, a spherical domain of 10 Å radius around each tryptophan residue was defined, then docking calculations with the ligand (Allura red) inside each of those domains were carried out, considered as the two possible interaction cavities. The score of each pose identified was calculated as the negative of the sum of a series of energy terms involved in the protein-ligand interaction process, so that the more positive the score, stronger is the interaction [20]. The number of genetic operations (crossover, migration, mutation) in each docking run used in the search procedure was set to 100,000. hydrogen-bond geometries by rotating all hydroxyl and amino groups of the amino acid side chains.…”

“…First, for the highest-ranked BSA:Allura red docking complex, all residues located into a 5 Å radius sphere around the ligand were selected, using the DeepView-Swiss- The structures were subsequently optimized with the semi-empirical molecular orbital PM7 method, which is available for the MOPAC2012™ software (Molecular Orbital PACkage, Stewart Computational Chemistry, Colorado Springs, CO, USA). Considering initially that the ligand and the selected binding pocket are involved in an aqueous phase and when the BSA:Allura red complex is formed the hydrophobicity inside the binding pocket increases, as a result of the positive experimental entropy change value [2,17], the best approximation to the dielectric constant (ε) of the continuum model for Allura red and Trp-212-containing binding site is 78.4 and for BSA:Allura red complex is 4.0 [20]. After a previous geometry optimization of all hydrogen atoms of each structure, the main amino acid chain was frozen except to the side chains and to ligand structure.…”

Drug-Protein Interaction: Spectroscopic and Theoretical Analysis on the Association between HSA and 1,4- Naphthoquinone Derivatives

“…at 280 and 340 nm ( Figure 1S, supplementary material), the correction for the inner filter effect was not necessary. 28 The UV-Vis absorption spectrum for FNP and FNP4Br (2.70x10 -5 M, in PBS) was measured in the 200-450 nm range at 310 K. The steady-state fluorescence measurements were carried out in the 290-450 nm range λ exc = 280 nm) at 305 K, 310 K and 315 K using 3.0 mL of a HSA solution (1.00x10 -5 M, in PBS). The addition of FNP or FNP4Br to the HSA solution was done manually by using a microsyringe, achieving final concentrations of 0.34; 0.67; 1.01; 1.35; 1.69; 2.02; 2.36 and 2.70x10 -5 M.…”