Assessment of the Binding of Pseudallecin A to Human Serum Albumin with Multi-Spectroscopic Analysis, Molecular Docking and Molecular Dynamic Simulation

The binding of pseudallecin A (PA), a potential antibiotic with strong inhibitory activities against Gram-positive Escherichia coli and Gram-negative Staphylococcus aureus, to human serum albumin (HSA) was explored. The interaction between them was assessed by multi-spectroscopic analysis, binding site competitive analysis, molecular docking and molecular dynamic simulation, showing the results as follows: PA effectively quenched the innate fluorescence of HSA by a static quenching process, formed a complex at a molar ratio of approximately 1 : 1 and performed an effective non-radiative energy transfer; the binding of PA to HSA was a spontaneous exothermic reaction driven by enthalpy with strong affinity and had a slight effect on the conformation of HSA; PA bound at site III of HSA and hydrogen bonds were the major binding forces to maintain the stability of the PA-HSA complex. Molecular dynamic simulation was performed to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg) for this complex and effectively supported the spectroscopic outcome. These results meant that the delivery and distribution of PA as a water-insoluble molecule can be efficiently accomplished via HSA in human blood and, it has a good potential for future drug application and pharmacological development.

Studying the Mechanism of Interaction of Doxofylline with Human Lysozyme: A Biophysical and In Silico Approach

In this study, multiple spectroscopic and computational methods were utilized to investigate the binding mechanism of doxofylline with lysozyme. The in vitro methods were used to obtain the binding kinetics and thermodynamics. UV-vis spectroscopy indicated the formation of complex between doxofylline and lysozyme. The Gibb's free energy and binding constant from UV-vis data was obtained as -7.20 kcal M^-1 and 1.929 × 10⁵ M^-1, respectively. Doxofylline successfully quenched the fluorescence of lysozyme, confirming the formation of complex. The k_q and K_sv values for the quenching of lysozyme's fluorescence by doxofylline were 5.74 × 10¹¹ M^-1 s^-1 and 3.32 × 10³ M^-1, respectively. These values signified a moderate binding affinity between doxofylline and lysozyme. In synchronous spectroscopy, red shifts were observed for indicating the changes in microenvironment of lysozyme following the binding of doxofylline. The secondary structural analysis was determined using circular dichroism (CD) which revealed an increase in % α-helical as a result of doxofylline interaction. The binding affinity and flexibility of lysozyme upon complexation have been revealed via molecular docking and molecular dynamic (MD) simulations, respectively. According to the many parameters of the MD simulation, the lysozyme-doxofylline complex was stable under physiological conditions. All during the simulation time, hydrogen bonds were continuously present. The MM-PBSA binding energy for lysozyme and doxofylline binding was found to be -30.55 kcal mol^-1.

Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: a biophysical and molecular docking approaches

Nalidixic acid is a bacterial DNA gyrase inhibitor and the first member of the synthetic quinolone antibiotics. It is used in the treatment of various infectious diseases like urinary tract infections, respiratory infections, sexually transmitted diseases, acute bronchitis, and sinusitis. Interactions studies are of great significance as it will be beneficial for designing new therapeutic molecules with preferable plasma solubility and its efficacy. In this paper, we have aim to ascertain the binding mode of nalidixic acid with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) through various biophysical and in silico method. UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with ct-DNA. The binding constant is in the range of 10³ M^-1, indicating the groove binding mode between ct-DNA and nalidixic acid. Groove binding mode was also validated by competitive displacement assay, potassium iodide quenching experiment, circular dichroism, DNA melting studies. In the case of BSA, UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with BSA. The value of a binding constant in the case of BSA was found to be 1.517 × 10⁵ M^-1. The site marker displacement experiment revealed the binding location of nalidixic acid to a site I in BSA. Secondary structural and microenvironmental changes also studied through circular dichroism and three-dimensional fluorescence. Furthermore, the synchronous fluorescence spectra of BSA with nalidixic acid showed that there were changes in the microenvironment around tryptophan residues. In silico molecular docking further confirmed the binding of nalidixic acid to site I in BSA and the minor groove of DNA.Communicated by Ramaswamy H. Sarma.