Research Project by Shio Zhu, first year undergraduate student, Spring 2014

My research involved simulating the binding and unbinding of naproxen to β-cyclodextrin, analyzing the interactions leading up to those events, and computing the binding affinity of cyclodextrin for naproxen through calculating kon or koff for the system.  As of this moment, koff is difficult to compute due to the fact that naproxen and cyclodextrin bind very strongly, and thus simulating such an event may take months to complete.  Kon has been calculated for 5 separate initial systems of a single naproxen molecule and cyclodextrin molecule at varying positions.  The data for these simulations are in the spreadsheet below.

Table 1: Results of 5 independent molecular dynamics simulations of naproxen binding to β-cyclodextrin.  "Time" = time of first binding event, "average volume" = average volume of solvent box during constant pressure simulation, "Concentration" = effective naproxen concentration, "Kon" = rate constant for binding. Simulations have been conducted with the Desmond program (DE Shaw Research) and analyzed with the Maestro (Schrodinger, Inc) program. 


Work Done

Molecular Simulations

YouTube Video