By, Pillai Aswathy Viswanath

1. Molecular Docking And Computer
Aided Drug Design
PILLAI ASWATHY VISWANATH
BOTANY

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