Molecular docking involves binding a small ligand molecule to a larger target molecule to form a stable complex. Docking software simulates this binding process and calculates the energy of interactions between the ligand and target in different orientations. The best fitting ligand orientation is one that provides structural and chemical stability to the complex. Molecular docking and computer-aided drug design are used to identify chemical compounds that can interact with and inhibit or activate protein targets, with the goal of developing new drug candidates.
2. Molecular docking can be defined as the
binding of small molecule called ligand,
on to a specific site in a larger molecule
3. Docking is a structure-based technique which
attempts to find the “best” match, between two
molecules.
4. In the field of molecular modeling, docking
is a method which predicts the preferred
orientation of one molecule to a second
when bound to each other to form a stable
complex.
Knowledge of the preferred orientation in
turn may be used to predict the strength
of association or binding affinity between
two molecules
5. In bioinformatics,molecular docking
analyses are done to identify chemical
that are able to interact and form
stable complexes with target proteins
To do this , the structure of both the
ligand and the target protein should be
known, so that docking can be simulated
in a computer
6. The protein targets and the ligands are
modeled using appropriate modeling
software
The docking software then simulates the
binding of the ligand to target and
calculates the energy levels of each
such interaction in different orientations
7. It then applies thermodynamic principle and
energy minimization algorithms to identify the
molecules that form the best fit
The best fitting molecule is one which gives
structural and chemical stability to the
ligand-target complex
The ligand will thus form an ideal candidate
for drug development
Molecular docking is a key tool used in
Computer Aided Drug Design
8. COMPUTER AIDED DRUG DESIGN
The drug is most commonly an organic small
molecule that activates or inhibits the
function of a biomolecule such as a protein ,
which in turn results in a therapeutic
benefit to the pateint
Drug design is the inventive process of
finding new medications based on the
knowledge of the biological target
The designing of a drug involves design of
small molecules that are complementary in
shape and charge to the biomolecular target
to which they interact and there fore will
bind to it
9. Drug designing is essentially the designing of
appropriate ligand
Computer aided drug designing is a practical
and realistic way of helping the medical
chemist and leads to pharmaceutical
Ther are two major types of drug design:
ligand based drug design
structure based drug design
11. LIGAND BASED DRUG DESIGN
This is based on the knowledge of other
molecules
Here,the new drug is designed according to
the structure of naturally occuring ligand
or form a drug or compound that is already
in use
Most often the drugs thus invented have
spatial characteristic that are
complementary to their target site that
enable them to bind to their target.
13. STRUCTURE BASED DRUG DESIGN
Based on the structure of the target,drugs
are designed in such a way that these have
a complementary structure that fits stably
in to their target
This is done by using interactive graphics
that identifies the complementary
structure that has a high affinity to the
target
As mentioned earlier, drug designing is also
useful in modifying existing drugs or drugs
that have been identified by computer
aided drug discovery to improve upon their
efficiency