12/24/2021

‫الصيدلة‬

Computer Aided
Drug Design
(CADD)

‫ تصميم الدواء‬: ‫اسم المادة‬ ‫ صفاء داود‬.‫ د‬:‫مدرس المادة‬

Drug Design
• Is the inventive process of finding new medications
based on the knowledge of a biological target.

• It involves the design of molecules that are

complementary in shape and charge to the biomolecular
target with which they interact and therefore will bind to
it.

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Computer-aided drug design(CADD)

• CADD represents computational methods and resources
that are used to facilitate the design and discovery of new
therapeutic solutions.
• Drug design with the help of computers may be used at
any of the following stages of drug discovery:
- hit identification using virtual screening (structure- or
ligand-based design)
- hit-to-lead optimization of affinity and selectivity
(structure-based design, QSAR, etc.)
- lead optimization: optimization of other pharmaceutical
properties while maintaining affinity

Molecular Modeling:
Refers to theoretical and computational methods to model
or “mimic” the behavior of molecules.
The various operations carried out in molecular modelling
involve the use of programs or algorithms which calculate
the structure and property data for the molecule

Molecular modeling applications in the drug design

process, include:
- Molecular Graphics
- Ligand Based Drug Design
- Structure Based Drug Design

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Molecular Graphics

• Studying molecules and their properties through graphical

representation, including :
1. 2D structure of ligand
2. 3D structure of ligands
3. 3D structure of protein
4. Energy minimization
5. Molecular dimensions
6. Molecular properties e.g. partial charges, electrostatic potential.
7. Conformational analysis
8. Structure comparison and structures overlay

Molecular Graphics
- 2D structure of ligand
- 3D structure of ligands
• It is possible to automatically convert a two-dimensional (2D)
drawing into a 3D structure, and most molecular modelling packages
have this facility.
• For example, the 2D structure of adrenaline in Fig. was drawn in
ChemDraw, then copied and pasted into Chem3D, resulting in the
automatic construction of the 3D model shown.

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Molecular Graphics
- Energy minimization
• Whichever soft ware program is used to create a 3D structure, energy
minimization should be carried out once the structure is built.
• This is because the construction process may have resulted in:
unfavourable bond lengths, bond angles, or torsion angles.
Energy minimization process is
usually carried out by a molecular
mechanics program which calculates
the energy of the starting molecule,
then varies the bond lengths, bond
angles, and torsion angles to create a
new structure.
The energy of the new structure is
calculated to see whether it is
energetically more stable or not. 7

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Molecular Graphics
Viewing 3D molecules
Once a structure has been energy minimized, it can be rotated in various
axes to study its shape from different angles. It is also possible to display
the structure in different formats (i.e. cylindrical bonds, wire frame, ball
and stick, space-filling (CPK)

Molecular Graphics
- Molecular dimensions
Once a 3D model of a structure has been constructed, it is a
straightforward procedure to measure all of its bond lengths, bond
angles, and torsion (or dihedral) angles.

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Molecular Graphics
- Molecular properties
Various properties of the 3D structure can be calculated once it has
been built and minimized. For example:
• The steric energy is automatically measured as part of the
minimization process and takes into account the various strain
energies within the molecule. such as bond stretching or bond
compression, deformed bond angles
The steric energy is useful when comparing different conformations
of the same structure, but the steric energies of different molecules
should not be compared.
• Partial charges
• Electrostatic potential

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Molecular Graphics
- Conformational analysis
In “energy minimization, the structure obtained is not necessarily the
most stable conformation. This is because energy minimization stops
as soon as it reaches the first stable conformation it finds, which will
be the one closest to the starting structure.
Energy saddle
Encountered by energy minimization
algorithm and so it stops
at the local energy minimum
Local energy minimum:
At this point, variations in structure result
in low-energy changes
and so the minimization will stop.
Global energy minimum
This is attained by generating different
conformations
and comparing their steric energies to find 12
a minimum

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Molecular Graphics

Remember the most energetically stable conformer doesn’t

have to be the bioactive conformer

The best way to know the bioactive conformation is by

cocrystallization with a macromolecule and studying its x-
ray image

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Molecular Graphics
-Structure comparison and structures overlay
Molecular modelling can be used to overlay two molecules in order to assess their
similarity.
•local anaesthetic property of cocaine and procaine
•structure–activity relationships indicate that the important pharmacophore for
local anaesthesia is the presence of an amine, an ester, and an aromatic ring.
•These functional groups are present in cocaine and procaine
•but the pharmacophore also requires the functional groups to be in the same
relative positions in space with respect to each other.
•If we use a 2D overlay the distribution in space is not correct for procaine

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• With molecular modelling (3D models):

– The important atoms of the structures can be matched up, in this
case the nitrogens and the aromatic rings of both structures.
– The software then strives to find the best fit, resulting in the best
overlay
How does a software program know when a best fit has been
achieved?
This is done by calculating the root mean square distance
(RMSD) between all the atom pairs which are matched up, and
finding the relative orientation of the molecules where this value
is a minimum.

Types of drug design

1) Ligand based drug design 2)Structure based drug design

Know ligands Know the receptor structures
Don’t know receptors Don’t know ligands

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1. Ligand-based drug design

Relies on knowledge of molecules that bind to the

biological target of interest.

Used to derive a pharmacophore model that defines the

minimum necessary structural characteristics a molecule
must possess in order to bind to the target

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Anti JAK1 IC50=0.1nM Anti JAK1 IC50=100nM

Anti JAK1 IC50=3500 nM

Ligand-based drug design

 A model of the biological target may be built based on
the knowledge of what binds to it, and this model in turn
may be used to design new molecular entities that interact
with the target.

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Ligand-based drug design

 Alternatively, a quantitative structure-activity relationship (QSAR),
in which a correlation between calculated properties of molecules and
their experimentally determined biological activity, may be derived.
These QSAR relationships in turn may be used to predict the activity of
new analogs

log 1/C = 0.92 π + 2.08 σ − 3.26

2. Structure-based drug design:

Relies on knowledge of the three dimensional structure
of the biological target obtained through :

1. X-ray crystallography
2. Nuclear Magnetic Resonance (NMR)

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X-ray crystallography
- The most powerful method to obtain a macromolecular structure
- A technique by which it is possible to determine the three
dimensional positions of each atom in a protein.
- To date, about 100,000 protein structures have been published in
the Protein Data Bank, with almost 10,000 added every year.

X-ray crystallography
- In crystallography the crystalline atoms cause a beam
of X-rays to diffract into many specific directions.
- This produce a 3D-picture of the density of electron
within the crystal.
- From this electron density, the positions of the atoms
can be determined.

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X-ray crystallography
- Crystallographic structures are limited by inadequate
resolution.
- Crystallographic structures ignore the proton ( Don’t
differentiate between ionized & unionized).

Proteins

Co-crystallized Apo-proteins
proteins

Structure-based drug design

- If an experimental structure of a target is not available, it
may be possible to create a homology model of the target
based on the experimental structure of a related protein.

- Homology modeling, also

known as comparative
modeling of protein, refers
to constructing an atomic
resolution model of the
"target" and an experimental
three-dimensional structure
of a related homologous
protein (the "template").

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Binding site identification

- It is the first step in structure based design.
- Relies on identification of concave surfaces on the protein
that can accommodate drug sized molecules that also
possess appropriate "hot spots" (hydrophobic surfaces,
hydrogen bonding sites, etc.) that drive ligand binding.
- Site of co-crystallized ligand.

Structure-based drug design is considered one of

the most important tools in drug discovery. It can
be divided into two major methodologies:
1. De novo design
2. Docking-based design

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De novo design of new ligands:

- involves the use of computer algorithms that construct
virtual ligands inside the binding pocket.
- In this method, ligand molecules are built up within the
constraints of the binding pocket by assembling small
pieces in a stepwise manner.
- These pieces can be either individual atoms or
molecular fragments.
- The key advantage of such a method is that novel
structures can be suggested.
- optimization of known ligands by evaluating proposed
analogs within the binding cavity

De novo drug design

Procedure
- Crystallise protein + ligand
- Determine crystal structure by X-ray crystallography
- Identify the binding site
- Identify binding interactions
- Identify other potential binding regions in the binding site
- Remove ligand in silico
- Design ligands to fit and bind to the binding site in silico
- Calculate strength of binding
- Synthesise and test promising structures
- Optimise by structure-based drug design

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Points to consider
- Avoid designing structures that fill the binding site
- experimental error in crystal structure
- space needed for drug optimisation

- Flexible molecules better than rigid

- allows alternative binding modes

- Synthetic practicality

- Stable conformations

- Energy of desolvation

Example of de novo docking program

LUDI
- Automated program

- One of the best known de novo soft ware programs

-Identifies possible interaction sites for binding regions within the

binding site

- Fits molecular fragments to different regions of the binding site

- Links fragments

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- Stage 1: identifi cation of interaction sites: These are positions in the

binding site that define where a ligand atom could be placed to interact
with any of the above atoms.
- Suppose the binding site contains a methyl group.
This is a non-directional interaction, so a sphere is constructed around
the carbon atom with a radius corresponding to the ideal distance for
such an interaction (4 Å).
A number of points (normally 14) are then placed evenly over the
surface of the sphere to define interaction sites. Regions of the sphere
which overlap or come too close to the atoms making up the binding site
(i.e. less than 3 Å separation) are rejected, Th e remaining points are
then used as the aliphatic interaction sites.

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- Interaction sites for hydrogen bonds.

-Hydrogen bonds are directional, it is important to define not
only the distance but also the relevant orientation of the atoms.
-This can be done by defining the hydrogen bond interaction site
as a vector involving two atoms.
- The position of these atoms is determined by the ideal bond
lengths and bond angles for a hydrogen bond.

Stage 2: fitting molecular fragments

Once interaction sites

have been
determined, the LUDI
program accesses a
library of several
hundred molecular
fragments, such as
those shown in Fig.
17.51 .
Th e molecules
chosen are typically
5–30 atoms in size.

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Stage 3: fragment bridging

- Once fragments have been identified and fitted to the binding site,
the final stage is to link them up.
- The program first identifies the molecular fragments that are closest
to each other in the binding site, then identifies the closest hydrogen
atoms. These now define the link sites for the bridge.
- The program now
tries out various
molecular bridges
from a stored library
to find out which
one fits best.
- Once a suitable
bridge has been
found, a final
molecule is created.

Docking-based design
- Docking=Simulated binding
- Docking involves fitting virtual ligands, into the binding
site employing algorithms that rely on force fields to
calculate attractive and repulsive interactions between
complementary groups within virtual ligand-protein
complexes.

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Docking=Simulated binding
steps
- Identify the binding site
- flood filling
Generation of different conformers of the ligand and dock them to the
receptor.
The fitting of a drug (ligand) into a binding site
Considerations - the size, shape
- The aim is to find optimum conditions for ligands regarding
•Conformation of ligand
•Position of ligand
•Orientation of ligand
- Scoring and ranking of best poses of ligand.
Scoring is an estimation of ligand-receptor interactions energies (best
enthalpy)
- Build pharmacophore according to the best docked and scored
ligands. 39

The general methods employed in docking:

According to software used, methods assume:

- Rigid target and rigid ligand

Simplest and quickest method

- Rigid target and flexible ligand

More complex but possible

- Flexible target and flexible ligand

Very complex and expensive on computer time
Not practical

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Docking Programs
After an analysis of the active site, programs such as
•DOCK,
•AutoDock,
• FlexX,
•Glide,
•GOLD,
• Surflex,
• MolDock

are capable of docking ligands into the receptor (inserting, on the

computer, an unbound ligand into the binding site of the target)

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Docking
Validation of docking solutions:
- Self-docking: in this technique the operator removes a co-
crystallized ligand from certain ligand-protein complex and re-docks
the ligand into the binding site using the scoring-docking combination
under assessment.
The docking configuration is considered valid if it reproduces close
conformer-pose to that of the experimental (co-crystallized) pose.

- Validation through 3-D QSAR methods: In this case, a particular

docking configuration is considered valid if it succeeds in aligning a
set of known ligands (i.e., into the binding pocket) in a 3-D alignment
capable of explaining bioactivity variation, e.g., via CoMFA

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CADD used in pharmacophore identification

and Pharmacophore Modeling

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Pharmacophore Model
A 3D representation of the regions of ligands believed to be
responsible for interactions with the biological target (the
pharmacophore)
Figure 2.7

H3 C N O
N
O

H3C
CH3

When the model is derived from known ligands for the target, it is
called a ligand-based pharmacophore model (in contrast to a
structure-based pharmacophore model, which is based on knowledge
of the receptor structure )

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Pharmacophore validation:
Receiver operating
characteristic (ROC) curves:
which measure the ability of the
pharmacophore model to
discriminate between active and
inactive compounds in
structural databases.

Virtual screening for hits

- Pharmacophores are used for virtual screening databases
to capture hits ( molecules that fit the features)
-Captured hits and /or synthesized molecules are then
screened experimentally HTS. 45

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