Molecular Docking

Presented toDr. Pramod Yadav

Presented byPiyush Pandey

Bioinformatics
13MTBINF006

Introduction
Docking attempts to find the best matching between two molecules
Docking is frequently used to predict the binding orientation of small
molecule drug to their protein targets.
The small molecule called Ligand usually interacts with proteins
binding sites.
Binding sites are areas of protein known to be active in forming of
compounds.
The results of docking can be used to find inhibitors for specific target
proteins and to design new drugs.

Different types of Interactions

Electrostatic forces - Forces with electrostatic origin are due to the
charges residing in the matter. The most common interactions are
charge-charge, charge-dipole and dipole-dipole.
Electrodynamics forces-The most widely known is probably the van
der Waals interaction. Van der Waals forces are driven by induced
electrical interactions between two or more atoms or molecules that
are very close to each other.
Steric forces - Steric forces are caused by entropy. For example,
in cases where entropy is limited, there may be forces to minimize
the free energy of the system, which are due to entropy.

Different types of Interactions

Solvent-related forces - Solvent-related forces are due to the
structural changes of the solvent. These structural changes are
generated, when ions, colloids, proteins etc. are added into the
structure of solvent. The most commonly are Hydrogen bond and
hydrophobic interactions.
conformational changes in the protein and the ligand are often
necessary for a successful docking process

Molecular docking can be divided into

two separate sections.
Search algorithm-The algorithm should create an optimum number
of configurations that include the experimentally determined binding
modes.
Molecular dynamics
Monte Carlo methods
Genetic algorithms
Fragment-based methods
Distance geometry methods

Scoring Function
scoring functions are fast approximate mathematical methods used to
predict the strength of the non-covalent interaction between two
molecules after they have been docked.
Scoring functions have also been developed to predict the strength of
other types of intermolecular interactions.

The following are majorly used method

for docking
1-Lock and Key Docking:-Here, the protein can be thought of as the
lock and the ligand can be thought of as a key. find the correct
relative orientation of the key which will open up the lock.
2-Induced fit:-An enumeration on the rotations of one of the molecules
is performed. Every rotation the surface cell occupancy and energy
is calculated; later the most optimum pose is selected.

Major steps in molecular docking:

Building the ReceptorThis step the 3D structure of the receptor should be considered which
can be downloaded from PDB; later the available structure should be
processed.
Identification of the Active Site
the active site within the receptor should be identified. The receptor
may have many active sites but the one of the interest should be
selected. Most of the water molecules and heteroatom if present
should be removed.

Major steps in molecular docking:

Ligand Preparation
Ligands can be obtained from various databases like ZINC, PubChem
or can be sketched using tools Chemsketch. While selecting the ligand,
the LIPINSKYS RULE OF 5 should be applied.
LIPINSKYS RULE: Not more than 5 H bond donors.
Molecular Weight NOT more than 500 Da.
Log P not over 5.
NOT more than 10 H bond acceptors.

Major steps in molecular docking:

Docking
This is the last step, where the ligand is docked onto the receptor
and the interactions are checked. The scoring function generates
score depending on which the best fit ligand is selected.

Application

Virtual screening
Drug discovery
Binding site identification
Protein-protein or protein-nucleotide interaction.

Software's for Molecular Docking:

SANJEEVINI.
SCHRODINGER
DOCK
AUTOLOCK TOOLS.
DISCOVERY STUDIO.
iGemDock

Thank you