Drug Design- Multi disciplinary Approach

Our understanding of cell mechanisms and pathways at a molecular level

becomes deeper and clearer every day. This is largely due to the great
efforts and hard work of genomic and proteomic research groups who add
novel targets for drug intervention on a regular basis
These targets involve several families comprised of G-protein coupled
receptors (GPCRs), ligand-gated ion channels (LGICs), cytoskeleton
proteins, phosphatases, kinases, nuclear receptors (NRs) and DNA
repair proteins.
What is a target molecule: Once the structure of a target (typically a
protein) is available, docking algorithms can be used to place each
ligand (i.e. a molecule or a molecular fragment included in a typical
library of compounds) and predict its most probable binding mode
within the binding site of the target

Biomolecule: Involved in a signaling path/metabolic path

Eg: Specific epitopic regions, Epidermal growth factor, p53 cancer targets
Works by Protein-Protein interaction, Protein Nucleic acid interactions.
G Coupled receptor:
Its is Small biomolecule with hydrophobic internal binding and
has important biological role

Druggable: It is first approximation, protein exhibiting a

hydrophobic binding with the binding site with different
proportions
Drug Discoverey /Drug development process- Steps
Identification of target disease: Establishment of multidisciplinary
research team, Selection of a promising approach, decision of
sufficient budget

Start of pharmacology that includes suitable screening methods,

choice of receptor, Binding or enzymatic assays, Confirmation of
potent utility of initial classes of compounds in animals, focusing on
Potency, selectivity and toxicity.
Analogue synthesis of the most active compound, large scale
synthesis, formulation, studies and patent protection. This lasts for
4-5 years
Phase I clinical studies: Includes safety, dosages and blood level studies
Phase II: Focuses on Efficiency and side effects
Phase III: Involve studies of range of efficacy, long term and rare side effects
Regulatory review
Marketing and Phase IV clinical studies focusing on long term safety
Very large scale synthesis
Distribution, advertisement, education, marketing and information personnel.

There are also plant products and antibiotics like penicillin,, cephalosoprins,
Tetracyclines, aminoglycosides, various glycopeptides used as drug,
Natural origin cancer drugs: Taxol, Camptothecin, Vinca alkaloids,
Doxorubicin, Belomycin
Natural Products: Morphine is a classical example Radiolabelled morphine
has high affinity to bind to the receptors of nervous system. These receptors
are called opiates. Another drug called as Strychine is shown to be an
antagonist for the neuroreceptor mediating inhibitory effect of glycine on
spinal cord.
Acetocholine is a key transmitter of central and peripheral nervous system
and it operates through multiple receptor. It has high affinity binding with
nicotine and Muscarine. Ryanodine receptor is named after insecticidal
compound Ryanodine.
One of the psychoactive constituent of canabis sativa is
lipophilic tetrahydrocannabinol THC has psycho active effects
on nervous system.

It is used to treat pain, cognition disorders, depression,

schizzophrenia,Nicotine dependence. Cystein is naturally
occuring toxin acting as a powerful antagonist against nicotine
acetacholine receptor showing optimally balanced behavior
against smoking cessation.

Hence, Potency, efficacy and selectivity are important aspects

Other aspects: Freedom from Mutagenesis, freedom from teratogenecity,
chemical stability
Synthestic or biological accessibility
Acceptable cost, ability to patent, clinical efficacy, solubility, satisfactory taste,
ability to formulate for administration
Quantitative structure activity relationship-QSAR
Quantitative structure property relationship- QSPR
Usually in which data pertaining to the 3-D structure of a target protein are not
available, drug design can instead be based on processes using the known ligands
of a target protein as the starting point. This approach is known as “ligand-based
drug design”. Molecular similarity approaches, quantitative structure-activity
relationships (QSAR) and pharmacophore models are frequently used methods in
the ligand-based drug design process.

Pharmacophore

The term “pharmacophore” was first defined by Ehrlich as: “a molecular framework
that carries the essential features responsible for a drug’s biological activity.
A 3-D pharmacophore would reflect how key amino acids are positioned in the
active site of a target protein.
By studying the binding site, possible interactions between the active
compound and the protein can be inferred, and pharmacophore models can be
built from data on target protein structure.
Pharmacophore models are widely used to elicit specific inhibitors of disease-
related proteins, including G-protein coupled receptors, enzymes, and ion
channels
Bioisosterism: These are functional groups or molecules that
produces similar biological effect. Molecular mimicry extensively used
by medicinal chemistry.
Classical Bioisosterism
: Exploit monovalent isosteres divided into following groups
1- Flourine verses hydrogen replacements
2- amino hydroxyl interchanges
3-Thiol- hydroxyl interchanges
4- Flourine hydroxyl, amino and methyl group interchanges

Non Classical: Are those which are not defined by classical

bioisosteres They mimic spatial arrangements, electronic properties,
and some other physiochemical properties. It is more or less
considered as qualitative or intuitive
Rational drug design

Rational drug design can be broadly divided into two categories:

(A)Development of small molecules with desired properties for

targets, biomolecules (proteins or nucleic acids), whose functional
roles in cellular processes and 3D structural information are
known. This approach in drug design is well established and is
being applied extensively by the pharmaceutical industries.

(B)Development of small molecules with predefined properties for

targets, whose cellular functions and their structural information may
be known or unknown. Knowledge of unknown targets (genes and
proteins) can be obtained by analyzing global gene expression data
of samples untreated and treated with a drug using advanced
computational tools. Steps related to these two approaches and
evaluation of other properties in rational drug design are presented
in the following flow charts
-In structure guided drug design, a known 3D structure of a target bound to
its natural ligand or a drug is determined either by X-ray crystallography
or by NMR to identify its binding site, the so called active site. For a lead
discovery, this is the starting point of structure guided drug design for a
known target.

-Once the ligand bound 3D structure is known, a virtual screening of large

collections of chemical compounds, such as ZINC can be performed.

-To enhance binding and hence to improve binding affinity/specificity, a

group of molecules with similar docking scores is generally used for
potency determination; this is High-Throughput Screening (HTS).

-After the determination of biological potency, several properties such as

relationships (QSAR, QSPR, between potency and docking scores)
including statistical analysis can be performed to ascertain the potential
molecule(s) for lead drug discovery.
Side effects of currently available structure based drugs
Many drugs developed using structure based criteria have been discontinued due to
variety of reasons.

-These reasons include safety problems, adverse toxic side effects, cardiac toxicity, and
development of drug resistance . Hence, it is worth mentioning that a relatively high
docking score or binding affinity does not necessarily mean that a substance is going to
be a potent inhibitor for that target or it would be free from undesirable side effects.
However, these criteria provide valuable information for drug design.

-As mentioned earlier, gene expression profiling/protein profiling and advanced

computational tools can be used to gain insights to overcome adverse side effects of
drugs. This can be achieved within the existing classes of structure based drugs
through modification of parent drugs or by the application of combination therapy;
this in turn, is based on genes that are expressed due to drug treatment and the
expression of such genes is undesirable.
Ancient approach
Ancient Asian (China and India) herbal medicine used the concept of combination.
Medicinal preparations had a combination of herbs for the purpose of their
recommended usage and for achieving high potency for cure and well being of
people. Eg:Neem, Tulsi, Termeric
Combining gene technology, bioinformatics tools in rational drug design
This process of combined approaches of drug development would be particularly
important for a number of reasons. To list a few, benefits would range from
improvement in disease free survival, containment/ eradication of disease,
elimination/minimization of toxic side effects.

Desirable attributes
Disease free survival
Eradication of disease
Elimination or minimization of toxic side effects
Reduction of undesirable side effects/biotransformation
Improvement in biodistribution
Bioavailability
Overcoming drug resistance
Improvement of immune response
Global gene expression profiling is an invaluable technology which
reveals novel insights into the pathogenesis of diseases including cancers.

-Many such platforms have been developed over the past few years. The
most widely used global gene expression platforms include SAGE (serial
analysis of gene expression) and Microarray (MA) respectively.

-SAGE produces a comprehensive gene expression profile without an a

priori gene sequence information, which results in the identification of novel
transcripts.

-Data analysis tools would allow researchers to visualize gene expression

data by various ways such as by gene grouping, by pathways, or by
protein–protein interactions by functional categories.

-Certain databases also provide researchers with repositories of global

gene expression data that are publicly available. Examples of such
databases include the Gene Expression Omnibus (GEO), SAGE data
repository (Absolute Level Lister, SAGEMap), Stanford microarray
database, and many other similar such databases.
How these target molecules Function?
-Inhibit with the function with small molecules whose competitive
binding affinity will be greater than natural ligands that bind to the
active site
-Inhibiting the biomolecular interactions by small molecules that
functionally deregulated in some diseases like cancer.
-Developing a lead molecule with desired properties
Analysis by
-XRD, NMR, solid state Chemistry crystalography, Docking tools,
computer aided mythologies
Protein data Bank-PDB holds 57,558 3D structures
-Evaluation of binding scores (Affinity/specificilty), balance
between hydrophobicity and hydrophilicity, absorption,
Distribution, metabolism and excretion, electrophilic,
nucleophilic, radical attack (biodegradation), toxicity of the
smaller molecule, products due to biotransformation in different
phases of metabolism.
 computer-aided drug design (CADD)
Computational drug design has been widely used in the pharmaceutical
industry to either identify new compounds or optimise lead compounds
that show significant inhibitory activity against a target biological receptor
Virtual screening can be divided
into two major strategies:

a. ligand-based virtual screening

(LBVS) and
b. structure based or target-based
virtual screening (SBVS)
Structure-Based Virtual Screening (SBVS) is usually based on molecular docking. In
molecular docking, a small molecule is fitted into the protein model’s active site. The
aim of docking is to predict the structure of the complex [P+L] = [PL] under equilibrium
conditions in water and to estimate the Gibbs energy of binding ΔG. ΔG can be
described by the equation ΔG=ΔH-TΔ. Enthalphic factors (ΔH) include steric and
electrostatic complementary, hydrogen-bonding, protein strain and also ligand strain, if
the ligand is flexible. Desolvation, rotational and translational entropy are important
factors in entropy (ΔS)
There are two major components in a docking program: a search algorithm that
produces relevant binding modes (poses), and a scoring function, which should be
able to predict the affinity of the docked compound to the protein i.e. estimate ΔG. Due
to the number of atoms involved in the protein-ligand interaction, the problem is extremely
complex.
There are over 60 docking programs and more than 30 scoring functions described
in the literature. Commonly used docking methods include AutoDock, DOCK,
LigandFit, FlexX, FRED, GLIDE and GOLD
Docking
Docking procedures aim to identify correct poses of ligands in the binding pocket of a
protein and to predict the affinity between the ligand and the protein. In other words,
docking describes a process by which two molecules fit together in three-dimensional
space. One main motivation in drug discovery is the identification of innovative small
molecular scaffolds exhibiting high binding affinity and selectivity for the target
together with a reasonable ADME (absorption, distribution, metabolism, excretion)
profile, lead and/or drug likeness. Such chemical entities are likely to be able to enter
higher phases in the further drug development process. Molecular docking, compared
to the fast and successful method ofthree-dimensional pharmacophore modeling is a
rather complex and computer-intensive approach to find new compounds by virtual
screening.
Docking protocols can be described as a combination of two components; a search
strategy and a scoring function. The search algorithm should generate an optimum
number of configurations that include the experimentally determined binding mode.
Types of docking
The accurate prediction of the binding modes between the ligand and protein, (the
docking problem) is of fundamental importance in modern structure-based drug
design. The task of molecular docking can be divided according to the molecules
being involved:
1. Protein-Ligand docking
2. Protein-Protein docking