Spectroscopy and molecular docking study on the interaction of daidzein and genistein with pepsin

Abstract

The interaction of pepsin with daidzein (Dai) or genistein (Gen) was investigated using spectroscopic techniques under simulated physiological conditions. Dai and Gen can quench the fluorescence of pepsin and the quenching mechanism was a static process. The binding site number n and apparent binding constant K were measured at different temperatures. The thermodynamic parameters ΔΗ, ΔG and ΔS were calculated. The results indicated that van der Waals forces and hydrogen bond formation played major roles in the interaction of Dai or Gen with pepsin. The binding distance between pepsin and Dai or Gen was calculated according to energy transfer theory. The results of synchronous fluorescence spectra showed that the microenvironment and conformation of pepsin were changed. UV absorption and 3D fluorescence spectra showed that the binding interaction disturbed the microenvironment of amino acid residues and induced conformational changes in pepsin. Molecular docking results showed that Dai and Gen entered into the hydrophobic cavity of pepsin and two hydrogen bonds formed between Dai or Gen and pepsin. The results demonstrated that the interaction behavior between Dai and Gen with pepsin was slightly different, which denoted that the 5-hydroxyl group of Gen, to a certain extent, had an effect on ligand binding to proteins. Copyright © 2016 John Wiley & Sons, Ltd.

Comparing the interactions of nitrendipine with lysozyme or human serum albumin and the effects of vitamin C and naringin on these interactions by spectroscopy and molecular docking methods

“…During the measurement of fluorescence spectra, the following equation was used to nullify the effects of any inner filters that may be encountered [25]: …”

Evaluation of the Binding Properties of A New Phenylurea Appended Carbazole Compound to Pepsin/Trypsin by Computational and Multi-Spectral Analysis

“…Pepsin is one of the important enzymes involved in the digestive system and is used as a model of proteases in interaction studies with small molecules. Due to the highly acidic residue, pepsin with an optimum pH is 1.5-2.0 is a monomeric L-protein consisting of two structurally homologous domains [20][21][22]. Trypsin is a proteolytic enzyme that breaks down peptide bonds in the carboxylic groups of arginine, lysine and ornithine and has an optimum pH of 7.5-8.5.…”