Team:ZJU-China/model s1 2.htm

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Latest revision as of 22:12, 26 October 2012

Docking

Introduction

Docking is a method which predicts the preferred orientation and binding affinity of one molecule to a second when bound to each other to form a stable complex. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs.

In our cases, riboscaffolds are designed as targets of small ligands, so we can dock the ligand to the riboscaffold to find the binding site and evaluate the binding state.

Methods

Although most docking algorithms and tools, as well as tutorials and documents are designed for drug-protein docking, we managed to find several approaches to conduct docking on RNA aptamers[1,2], which is a heating ground in the research of RNA targeting drugs. Among the popular docking tools, AutoDock package [3] has demonstrated its ability to dock compounds to RNA molecules [1]. In our approach, we docked theophylline to our riboscaffolds (with the predicted 3D structure) to search for the binding sites and construct ligand-riboscaffold complex for dynamic analysis.

Step1: Preparation of riboscaffold

The coordinate files predicted by NAST, refined by C2A, balanced and optimized by OpenMM Zephyr were used for docking. But they can still have potential problems that need to be corrected. The preparation was done in AutoDock Tools, including merging the non-polar hydrogen atoms on RNA molecules and computing Gasteiger charges. Then, the PDB files were converted to PDBQT files used in AutoDock.

Step2: Preparation of theophylline.

The ligand theophylline was obtained from chEBI database (www.ebi.ac.uk/chebi/) as MOL file and converted to PDB coordinate file using OpenBable [4]. Preparation was performed also in AutoDock Tools, and because the molecule of theophylline is quite rigid, there is no need to specify rotatable bonds and active torsions, just used the default settings and generated PDBQT file.

Step3: Run docking with AutoDock.

Once the receptor and ligand are prepared, we can use the AutoDock 4.2 package. The grid box for site searching was created on different arms on our riboscaffolds according to their dimensions with the default 0.375 angstrom for spacing between the grid points. For each riboscaffold, 20 docking experiments were performed using the Lamarckian genetic algorithm conformational search, with the population size of 150, one million energy evaluations, and a maximum of 27 000 generations per run.

Results

Figure6. This figure shows the docking result of the three arms (theophylline aptamer, MS2 aptamer and PP7 aptamer). Ligands are in white.

There are more binding sites of theophylline on the theophylline aptamer than on the other two aptamers, which indicates the present of theophylline is highly probable to have some effects on the theophylline aptamer. And the effects caused by theophylline is mainly through its interation with theophylline aptamer, which is consistent with our experimental results.

The docking results were used to generate riboscaffold-theophylline complex for molecular dynamics analysis of the whole system.