Investigation of binding properties between a schiff base based on coumarin-hydrazone and pepsin/hsa by spectroscopic and molecular docking methods

In this thesis, a new schiff base based on coumarin-hydrazon was synthesized (HZC) and its structure were characterized by spectroscopic methods. HZC and protein (pepsin and HSA) interactions were investigated by spectroscopic (absorption, fluorescence) and molecular docking methods. HZC-pepsin and HZC-HSA interactions were studied in pH 2.0 and pH 7.4 buffer environments at different temperatures, respectively. The fluorescence quenching constants (Ksv), binding constants (K), binding part numbers (n) were obtained from fluorimetric experiments and besides, according to static quenching mechanism indicated that it was concluded a complex structure was formed between HZC and proteins. Also, bonding types were explained according to the calculated thermodynamic parameters (G, H, S). The negative H and positive S parameters showed that electrostatic interactions as well as hydrophobic forces play a role in the binding of HZC with both proteins. In the fluorimetric method proposed in the thesis, limits of detection (LOD) and limits of quantification (LOQ) values were calculated for the quantitative determination of HZC under the experimental conditions containing pepsin/ HSA. Accordingly, for HZC, the LOD and LOQ values were found as 3.52x10-6 M and 1.17x10-5 M, respectively, in the presence of pepsin; at the same time LOD and LOQ values were found 3.81x10-7 M and 1.27x10-6 M, respectively, in the presence of HSA. According to Förster's theory, using the FRET method, the distance (r) between donor-acceptor molecules was calculated as 3.67 nm for HZC-pepsin and 2.19 nm for HZC HSA. These results showed that non-radiative energy transfer between derivative-protein molecule pairs is effective. The obtained experimental data were supported and validated by molecular docking results. Both spectral and computational results show that the HZC derivative can be a good model for other similar schiff compounds and can be classified as critical molecular species for drug design.