CHAPTER 35
Molecular Docking
CS Mukhopadhyay and HK Manku
School of Animal Biotechnology, GADVASU, Ludhiana
35.1 INTRODUCTION
Docking is an attempt to determine whether two molecules interact with each other, and to find the best match between these two molecules. Biocomputational “docking”, thus, predicts the preferred orientation of one molecule (e.g., protein) bound to another molecule (a ligand) in a lock‐and‐key manner. The particular orientation necessitates overall minimum free energy (ΔG). Docking is necessary because it is a key to rational and sensible drug design. In the process of docking, all intermolecular forces (i.e., H‐bonding, hydrophobicity, dipole–dipole interaction, Van der Waals forces, electrostatic interactions and intra‐molecular forces) and the bond features (i.e., bond length, bond angle, dihedral angle) are taken into account. Docking can be rigid, or there are flexible types. The docking studies are categorized broadly into protein–ligand docking; protein–protein docking; and protein–nucleic acid docking.
35.1.1 Software used for docking
Some of the useful software tools used for docking include Sanjeevani; GOLD; ICM; AUTO DOCK; GLIDE; GRAMM‐X; FlexX; and SwissDock.
35.2 OBJECTIVE
To find the best binding poses of the receptor–ligand complex, based on energy minima of the system.
35.3 PROCEDURE
35.3.1 Target or receptor selection and preparation
The first step of docking is to select a PDB file (protein file for docking with a ligand) and prepare that file for docking. A preparation step is required because PDB structures often contain water molecules, which play no essential role in coordinating to the ligand. The selected receptor should be biologically active and stable.
In this practical example, a file, 1EIO.pdb, has been downloaded from the Protein Data Bank (http://www.rcsb.org/pdb/). We will get a complex protein, “ileal lipid binding protein”, that is already docked with the ligand glycocholic acid. The docked.pdb file has been visualized in the UCSC chimera tool (tool for structure visualization) (https://www.cgl.ucsf.edu/chimera/), and ligand and all the water molecules have been removed to prepare the receptor.
35.3.2 Location of binding site
The active site within the receptor needs to be first identified. The receptor may have multiple active sites, but one site of interest is to be selected (as the most druggable site).
FIGURE 35.1 The identified active site or cavity within the receptor is marked as a star.
35.3.3 Ligand selection and preparation
A reasonable 3D structure is required as a starting point. The ligand can be obtained from databases like ZINC (http://zinc.docking.org/) or PubChem (https://pubchem.ncbi.nlm.nih.gov/), or can be sketched using a tool such as ACS/Chemsketch (downloadable from http://www.acdlabs.com/resources/freeware/chemsketch/) or ChemDraw (commercial software with free trial: http://www.cambridgesoft.com/software/overview.aspx). In this practical example, the ligand has been extracted from the complex and saved as a *.Mol2 file separately from the receptor.
35.3.4 Docking
Open the SwissDock server (www.swissdock.ch/docking) and upload the prepared receptor molecule and the ligand molecule (*.pdb and *.Mol2 files, respectively).
FIGURE 35.2 The “Submit Docking” tab at the top of the homepage of the SwissDock online tool takes you to this page. Upload the target and ligand files by clicking on the appropriate buttons.
After uploading the files, please provide a short description and the email ID where you will receive the results. Click on the “Start Docking” button. This will first identify and analyze the active site; then the ligand will be docked onto the receptor, and the interactions will be checked. The scores generated by the scoring function enable us to identify the best fit ligand.
35.4 RESULT AND INTERPRETATION
The result pages will display the binding modes of the docked complex, along with their most fitting score and free energy score. The best binding mode can be determined through the free energy score; the lower the free energy, the better the binding mode.
FIGURE 35.3 Fitness of ligand and free energy of docked complex of the first and second binding poses, shown as “A” and “B”.
FIGURE 35.4 Fitness of ligand and free energy of docked complex of the third, fourth and fifth binding poses, shown as “C”, “D” and “E”.
The free energy (ΔG) values among all the docked poses can be compared. It is evident that first two docked complexes have very similar energy, compared with the other three docked poses, so these two poses can be considered for further analysis for potential drug discovery.
35.5 QUESTIONS
- 1. How will you prepare a cleaned receptor.pdb file?
- 2. How will you prepare the ligand molecule for docking?
- 3. Which file format for the ligand molecule will accept the SwissDock server?
- 4. How will you choose the pose if the top ten poses have minute energy differences?
- 5. Carry out the docking process for your choice of receptor and ligand molecule.
- 6. Write your interpretation of the docked complex in your own words on the basis of free energy.