Prediction of Binding Energy affinities of Cucurbituril clip(host) with various guests as a part of SAMPL5 Challenge

Post date: Apr 6, 2016 3:15:38 AM by Divya K.Matta

By: Divya K.Matta

 Ph.D student in Chemistry

The binding energies of Cucurbituril clip with various guests have been calculated using Binding energy distribution Analysis Method(BEDAM). The method employs AGBNP2(Analytic Generalized Born Plus NonPolar2) as an implicit(continuum) solvation model. Molecular Dynamic(MD) simulations were carried out to predict the binding free energies of these host-guest systems. Cucurbituril clip is deprotonated and has a charge of -4 due to the presence of four sulfonate groups.The values of Binding energies of these host guests system depends on the number of factors such as the strength of interactions between them, for example, depending upon whether they have hydrogen bonding, electrostatic or hydrophobic interactions, the binding energies vary accordingly. Also, it depends on the charge of guests molecules whether they are neutral or ionised.With the guidance of Prof.Emilio, I learnt the BEDAM methodology and its applications on host-guest systems. 

Image :Interaction of Cucurbituril clip(host) with the guest