Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases

In the age of growing infectious diseases, there is a great demand for new inhibitors which can exhibit minimum side effects. Owing to the importance of proteases in life cycle and invasion, they have been projected as attractive targets for structure based drug designing against microbes including viruses. Here we report the inhibitory activity of a well known natural compound succinic acid against both serine and cysteine proteases. The ligand is found co-crystallized with Bovine pancreatic trypsin in one of our crystallization trials and the diffraction data up to1.9 Å reveal its interactions with the catalytic triad residues Histidine 57 and Serine 195. Binding of the ligand with these proteases have been validated using caseinolysis inhibition. With trypsin, ITC analysis showed tight binding of the ligand, resulting in change in Gibb's free energy (ΔG) by -20.31 kJ/mol. To understand the existence of succinic acid at the active site, molecular docking was performed and it revealed binding of it with trypsin and papain at corresponding active sites. This dual inhibitory activity of natural ligand, succinic acid can be accounted for the recent reports on anti-viral property of plant extracts where dicarboxilic fatty acids are normally abundant.

Binding of glutathione and melatonin to pepsin occurs via different binding mechanisms

Glutathione is a hydrophilic antioxidant and melatonin is a hydrophobic antioxidant, thus, the binding mechanism of the two antioxidants interacting with protease may be different. In this study, binding of glutathione and melatonin to pepsin has been studied using isothermal titration calorimetry (ITC), equilibrium microdialysis, UV-Vis absorption spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling. Thermodynamic investigations reveal that the binding of glutathione/melatonin to pepsin is driven by favorable enthalpy and unfavorable entropy, and the major driving forces are hydrogen bond and van der Waals force. ITC, equilibrium microdialysis, and molecular modeling reveal that the binding of glutathione to pepsin is characterized by a high number of binding sites. For melatonin, one molecule of melatonin combines with one molecule of pepsin. These results confirm that glutathione/melatonin interact with pepsin through two different binding mechanisms. In addition, the UV-Vis absorption and CD experiments indicate that glutathione and melatonin may induce conformational and microenvironmental changes of pepsin. The conformational changes of pepsin may affect its biological function as protease.