oxSWATH: an integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening

To examine the usability of the imine-linked amino acid-based dendrimeric structures in the smart drug delivery applications, molecular dynamics simulation studies were carried out. 20 dendrimeric structures were created using amino acids (AA) as the monomer. To consider the effect of the media, three different protonation states along with two different temperatures (37 and 42 °C) were used. The neutral form of the amine moieties, 50% and 100% protonation of the amines were considered. By analyzing the results, it was found that the size of the side chain and the side chain functional groups are playing important roles in the response of the dendrimeric structures. In the hydrogen bonding analysis, it was cleared that the length of the side chain is more important than the nature of the functional group of the side chain; the bulkier side chains are leading to the lesser hydrogen bonding interactions. Analyzing the electrostatic and van der Waals interactions revealed that in higher protonation state, the electrostatics have repulsive nature. Radial distribution function analysis showed that the core section of all of the dendrimers (G0 and G1) have rigid nature. The shell section of the dendrimers (G2 and G3) are in direct contact with the media and therefore this section is responsive to the media condition.