Investigation of binding between fluoroquinolones and pepsin by fluorescence spectroscopy and molecular simulation

Abstract

In this paper, the interactions of pepsin with fluoroquinolones, including norfloxacin (NFX) or ofloxacin (OFX), were investigated using fluorescence spectroscopy. The effects of NFX or OFX on pepsin showed that the molecular conformation of pepsin and the microenvironment of tryptophan residues were changed under mimicked physiological conditions. Static quenching was suggested as a factor. Quenching constants and binding constants were determined and thermodynamic parameters were calculated at three temperatures (25°C, 31°C and 37°C). Molecular interaction distances (binding distance r) were obtained. Binding was enthalpy driven and the process was spontaneous. Synchronous fluorescence, three-dimensional fluorescence spectroscopy and molecular simulation were used for analysis. Interactions were further tested using molecular modelling. Quenching and binding constants of NFX with pepsin were the highest when testing NFX/OFX/fleroxacin/gatifloxacin with pepsin combinations. NFX was the strongest quencher, and affinity of NFX for pepsin was higher than that of OFX/fleroxacin/gatifloxacin.

Spectroscopic studies and molecular docking on the interaction of delphinidin‐3‐O‐galactoside with tyrosinase

“…The docking programs AutoDock (4.0) and AutoDockTools 1.5.6 from (Scripps Institute, USA) were used to explore the probable interaction between DG and TY, and the docking results were visualized by the Lamarckian genetic algorithm 40 . The X‐ray crystal structure of TY from A. bisporus mushroom (AbTyr) (PDB ID: 2Y9X) was retrieved from the protein data bank (PDB) (http://www.rcsb.org/).…”