Calculation and prediction of rate and equilibrium constants for aggregation of porphyrin by molecular dynamics, Docking and QSPR methods

The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of such aggregation behavior on varying the derivatives of porphyrin was carried out using molecular dynamics simulation and Docking. Distance diagrams of simulated compounds were obtained and decrease of curves is a clear evidence of the aggregation. Aggregation rates were studied by origin software. In order to calculate interaction energies of derivatives, compounds were docked and the equilibrium constant of porphyrin-porphyrin interaction were obtained. Quantitative Structure-Property Relationship (QSPR) studies were performed for the sets of 85 Porphyrin derivatives. Multiple Linear Regression method (MLR) and Principal Component Analysis (PCA) were used and resulted in useful models with good prediction ability. This models were able to predict the kinetic and equilibrium constant for all sets of our compounds. The correlation coefficients for prediction of rate and logarithm of equilibrium constants were 0.67 and 0.97 by MLR method respectively and 0.90 for prediction of equilibrium constant by PCA analyses. In order to have a better prediction, compounds were divided into two groups, oxygenated and non-oxygenated group and correlation coefficient for prediction of rate constants of them were obtained 0.89 and 0.94 by MLR model respectively. Results of structure-property relationship showed that, larger, more hydrophobe and more planner derivatives have higher aggregation rate.