AUTODOCK: A USEFUL COMPUTATIONAL TOOL TO MODEL SMALL MOELCULES BINDING WITH DNA
Introduction/Abstract
AutoDock is a powerful molecular modeling simulation program, especially for studying ligand-receptor interactions. It provides insightful predictions about binding mode and affinity which can be used for improving ligand design. It is also being widely used as a complementary method to validate the experimental data for ligand-receptor binding.
Purpose
In our group, we study small molecule-DNA interactions using various biophysical and biochemical methods. However, direct visualization methods of such interactions are lacking. In the present work, we establish a computational method using AutoDock to estimate ligand binding mode and affinity towards different DNA secondary structures.
Method
A series of DNA binding ligands, including Ethidium Bromide (EB), Thiazole Orange (TO) and its derivatives were docked with duplex DNA and G-quadruplex DNA using AutoDock. The models with lowest binding energies were selected and the results were compared with the experimental data from viscosity measurements and DNA thermal denaturation experiments.
Results
Our docking results are consistent with the experimental data, suggesting that AutoDock is a useful program to predict small molecule and DNA interactions. Both EB and TO bind to DNA via intercalation and TO’s derivatives bind to DNA via either intercalation or groove binding depending on their side chains.
Significance
AutoDock is less popular in predicting small molecule binding towards DNA as it is mainly used for ligand-protein interactions. Our research illustrated that it can produce valuable information to support experimental data and enlighten future molecule design. In addition, we establish a useful method for docking small molecules binding to duplex DNA via intercalation.
Location
DeRosa University Center, Stockton campus, University of the Pacific
Format
Poster Presentation
AUTODOCK: A USEFUL COMPUTATIONAL TOOL TO MODEL SMALL MOELCULES BINDING WITH DNA
DeRosa University Center, Stockton campus, University of the Pacific
AutoDock is a powerful molecular modeling simulation program, especially for studying ligand-receptor interactions. It provides insightful predictions about binding mode and affinity which can be used for improving ligand design. It is also being widely used as a complementary method to validate the experimental data for ligand-receptor binding.
